AC GenProp0001 DE Chorismate biosynthesis via shikimate TP PATHWAY AU Haft DH TH 2 RN [1] RM 12636087 RT The biosynthesis of shikimate metabolites. RA Knaggs AR; RL Nat Prod Rep. 2003;20:119-136. DC Shikimate and Chorismate Biosynthesis DR IUBMB; misc; shikim; DC Phenylalanine, Tyrosine and Tryptophan Biosynthesis DR KEGG; map00400; DC Chorismate biosynthesis DR MetaCyc; ARO-PWY; CC Chorismate is the final common intermediate in the biosynthesis of CC phenylalanine, tyrosine and tryptophan (the aromatic amino acids) as CC well as menaquinone, ubiquinone, salicylate and phenazine. Chorismate CC is synthesized via a seven-step pathway starting from the precursors CC D-erythrose 4-phosphate and phosphoenolpyruvate. This pathway is CC widely distributed among microorganisms[1]. Certain methanogenic CC euarchaeota appear to be missing the first two steps of the pathway - CC these may be catalyzed by as of yet uncharacterized enzymes. -- SN 1 ID Phospho-2-dehydro-3-deoxyheptonate aldolase DN Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) RQ 1 EV IPR006219; TIGR00034; sufficient; TG GO:0009423; EV IPR002480; TIGR01358; sufficient; TG GO:0009423; EV IPR006268; TIGR01361; sufficient; TG GO:0009423; EV IPR010210; TIGR01949; sufficient; TG GO:0009423; -- SN 2 ID 3-dehydroquinate synthase DN 3-dehydroquinate synthase (EC 4.2.3.4) RQ 1 EV IPR016037; TIGR01357; sufficient; TG GO:0009423; EV IPR002812; PF01959; sufficient; TG GO:0009423; -- SN 3 ID 3-dehydroquinate dehydratase DN 3-dehydroquinate dehydratase (EC 4.2.1.10) RQ 1 EV IPR001874; TIGR01088; sufficient; TG GO:0009423; EV IPR001381; TIGR01093; sufficient; TG GO:0009423; -- SN 4 ID Shikimate 5-dehydrogenase DN Shikimate 5-dehydrogenase (EC 1.1.1.25) RQ 1 EV IPR011342; TIGR00507; sufficient; TG GO:0009423; EV IPR010110; TIGR01809; sufficient; TG GO:0009423; -- SN 5 ID Shikimate kinase DN Shikimate kinase (EC 2.7.1.71) RQ 1 EV IPR031322; PF01202; sufficient; TG GO:0009423; EV IPR010189; TIGR01920; sufficient; TG GO:0009423; -- SN 6 ID 3-phosphoshikimate 1-carboxyvinyltransferase DN 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) RQ 1 EV IPR006264; TIGR01356; sufficient; TG GO:0009423; -- SN 7 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; TIGR00033; sufficient; TG GO:0009423; // AC GenProp0002 DE Coenzyme F420 utilization TP GUILD AU Haft DH TH 0 RN [1] RM 11726492 RT Structures of F420H2:NADP+ oxidoreductase with and without its RT substrates bound. RA Warkentin E, Mamat B, Sordel-Klippert M, Wicke M, Thauer RK, Iwata M, RA Iwata S, Ermler U, Shima S; RL EMBO J. 2001;20:6561-6569. DC Methane Biosynthesis DR IUBMB; misc; methane; DC Coenzyme F420 hydrogenase DR IUBMB; single; 112981; CC Coenzyme F420 (a 7,8-didemethyl-8-hydroxy 5-deazaflavin) is found in CC methanogenic archaea, the Mycobacteria, and some other species[1]. Forms CC differ in the number of glutamyl residues attached. The chromophore by CC itself, FO, often can replace intact F420, so the literature will CC occasionally describe an enzyme dependent on FO. This does not CC necessarily mean the FO is not typically part of coenzyme F420 in vivo. CC However, it appears that only FO, and not F420, occurs in the CC Cyanobacteria. This property describes the presence of enzymes that use CC F420 as an electron donor or receptor, as opposed to enzymes of its CC biosynthesis. -- SN 1 ID LLM-family F420-associated subfamilies RQ 0 EV IPR019910; TIGR03564; sufficient; EV IPR019919; TIGR03617; sufficient; EV IPR019921; TIGR03619; sufficient; EV IPR019922; TIGR03620; sufficient; EV IPR019923; TIGR03621; sufficient; EV IPR022526; TIGR03841; sufficient; EV IPR022315; TIGR03842; sufficient; EV IPR022480; TIGR03856; sufficient; EV IPR022402; TIGR03854; sufficient; EV IPR022378; TIGR03857; sufficient; EV IPR023909; TIGR04024; sufficient; -- SN 2 ID Methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase RQ 0 EV IPR002844; PF01993; sufficient; -- SN 3 ID PPOX-class probable F420-dependent enzyme RQ 0 EV IPR019920; TIGR03618; sufficient; EV IPR019965; TIGR03666; sufficient; EV IPR019966; TIGR03667; sufficient; EV IPR019967; TIGR03668; sufficient; EV IPR024031; TIGR04023; sufficient; -- SN 4 ID F420H(2)-dependent quinone reductase RQ 0 EV IPR004378; TIGR00026; sufficient; -- SN 5 ID Hypothetical F420-biosynthesis associated RQ 0 EV IPR022454; TIGR03883; sufficient; -- SN 6 ID Biosynthesis of F420 RQ 1 EV GenProp0791; -- SN 7 ID 5,10-methylenetetrahydromethanopterin reductase RQ 0 EV IPR019946; TIGR03555; sufficient; -- SN 8 ID Hydrogenase, nickel and F420-dependent RQ 0 EV GenProp0723; -- SN 9 ID NADPH-dependent F420 reductase RQ 0 EV IPR010185; TIGR01915; sufficient; -- SN 10 ID F420-dependent oxidoreductase families RQ 0 EV IPR019944; TIGR03554; sufficient; EV IPR019946; TIGR03555; sufficient; EV IPR019945; TIGR03557; sufficient; EV IPR019951; TIGR03559; sufficient; EV IPR019952; TIGR03560; sufficient; EV IPR031017; TIGR04465; sufficient; // AC GenProp0007 DE Flagella TP CATEGORY AU Haft DH TH 0 CC This category refers to genome properties relating to the assembly and CC function of bacterial and archaeal flagella. -- SN 1 ID Flagellar motor stator complex RQ 0 EV GenProp0877; -- SN 2 ID Flagellar export apparatus RQ 0 EV GenProp0879; -- SN 3 ID Flagellar basal body complex RQ 0 EV GenProp0880; -- SN 4 ID Flagellar assembly apparatus RQ 0 EV GenProp0881; -- SN 5 ID Flagellar filament and hook complex RQ 0 EV GenProp0882; -- SN 6 ID Flagellar motor switch (rotor) complex RQ 0 EV GenProp0883; -- SN 7 ID Flagellar post-translational modification components RQ 0 EV GenProp0885; -- SN 8 ID Flagellar components of unknown function RQ 0 EV GenProp0886; // AC GenProp0010 DE Inteins TP SYSTEM AU Haft DH TH 0 RN [1] RM 11092822 RT Evolution and Application of Inteins in Candida species: A Review. RA Liu XQ; RL Annu Rev Genet. 2000;34:61-76. CC Inteins are protein insertion sequences that are embedded in host CC protein sequences. They are post-translationally excised from the CC host protein by a self-catalytic protein splicing process, in which CC the intein sequence is precisely excised, and the flanking host CC protein sequences (N- and C-exteins) are re-ligated to create a CC functional protein. The region between the N- and C-terminal splicing CC regions may show endonuclease homology[1]. -- SN 1 ID Intein C-terminal splicing region RQ 1 EV IPR030934; TIGR01443; sufficient; -- SN 2 ID Intein N-terminal splicing region RQ 1 EV IPR006141; TIGR01445; sufficient; // AC GenProp0011 DE Methanogenesis TP CATEGORY AU Haft DH TH 0 CC Known methanogenic species so far all belong to the Archaea and are CC most closely related to the non-methanogenic genus Pyrococcus. CC Methanogenesis requires the presence of a number of distinctive CC cofactors. Methanogens tend to be anaerobic. -- SN 1 ID Tetrahydromethanopterin S-methyltransferase complex RQ 0 EV GenProp0288; -- SN 2 ID Methyl-coenzyme M reductase RQ 0 EV GenProp0719; -- SN 3 ID Methanogenesis marker set RQ 0 EV GenProp0722; // AC GenProp0017 DE Metabolism TP CATEGORY AU Haft DH TH 0 CC The properties contained within this category describe the various CC metabolic pathways by which organisms transform chemicals in the CC processes of life. -- SN 1 ID Biosynthesis RQ 0 EV GenProp0063; -- SN 2 ID Energy metabolism RQ 0 EV GenProp0070; -- SN 3 ID Central intermediary metabolism RQ 0 EV GenProp0072; -- SN 4 ID Nucleic acid metabolism RQ 0 EV GenProp0133; -- SN 5 ID Catabolism RQ 0 EV GenProp0142; -- SN 6 ID Storage polymer systems RQ 0 EV GenProp0157; -- SN 7 ID Protein metabolism RQ 0 EV GenProp0247; -- SN 8 ID Detoxification RQ 0 EV GenProp0303; -- SN 9 ID Amino acid metabolism RQ 0 EV GenProp0731; -- SN 10 ID Iron metabolism RQ 0 EV GenProp0820; -- SN 11 ID Carbon metabolism RQ 0 EV GenProp0866; -- SN 12 ID Gibberellin inactivation II (methylation) RQ 0 EV GenProp1420; -- SN 13 ID Indole-3-acetate inactivation VIII RQ 0 EV GenProp1490; -- SN 14 ID Violaxanthin, antheraxanthin and zeaxanthin interconversion RQ 0 EV GenProp1508; -- SN 15 ID Abscisic acid degradation by glucosylation RQ 0 EV GenProp1600; -- SN 16 ID Homocysteine and cysteine interconversion RQ 0 EV GenProp1654; -- SN 17 ID Inorganic nutrients metabolism RQ 0 EV GenProp1774; // AC GenProp0021 DE CRISPR region TP GUILD AU Haft DH TH 1 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. RN [3] RM 21552286 RT Evolution and classification of the CRISPR-Cas systems. RA Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, RA Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV; RL Nat Rev Microbiol. 2011;9:467-477. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats. CRISPR loci are described as having direct repeats, CC varying in size from 21 to 37 bp, interspaced by similarly sized CC non-repetitive sequences. Certain proteins, including Cas1 to Cas4, CC are found only in genomes with CRISPR repeats, and always near these CC repeats [1]. Haft, et al. described subtypes in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed Cas genes [2]. A further review of CRISPR CC families by Makarova, et al. describes broader categories of CRISPR CC systems, using a polythetic classification system [3]. -- SN 1 ID Aferr subtype specific proteins RQ 0 EV IPR017545; TIGR03114; TG GO:0043571; EV IPR017546; TIGR03115; TG GO:0043571; EV IPR017547; TIGR03116; TG GO:0043571; EV IPR017548; TIGR03117; TG GO:0043571; -- SN 2 ID Apern subtype specific proteins RQ 0 EV IPR010153; TIGR01874; sufficient; TG GO:0043571; EV IPR010157; TIGR01878; sufficient; TG GO:0043571; EV IPR010163; TIGR01884; sufficient; TG GO:0043571; EV IPR009260; TIGR01896; sufficient; TG GO:0043571; EV IPR010184; TIGR01914; sufficient; TG GO:0043571; EV IPR002764; TIGR02583; sufficient; TG GO:0043571; EV IPR013488; TIGR02671; sufficient; TG GO:0043571; EV IPR022297; TIGR03876; TG GO:0043571; -- SN 3 ID Cas1 DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; sufficient; TG GO:0043571; -- SN 4 ID Cas2 DN CRISPR-associated protein Cas2 RQ 0 EV IPR021127; TIGR01573; sufficient; TG GO:0043571; EV IPR010152; TIGR01873; sufficient; TG GO:0043571; -- SN 5 ID Cas3 (core, HD domain, Ypest-specific) DN CRISPR-associated helicase Cas3 RQ 0 EV IPR006474; TIGR01587; sufficient; TG GO:0043571; EV IPR006483; TIGR01596; sufficient; TG GO:0043571; EV IPR013395; TIGR02562; sufficient; TG GO:0043571; EV IPR013444; TIGR02621; sufficient; TG GO:0043571; -- SN 6 ID Cas4 DN CRISPR-associated protein Cas4 RQ 0 EV IPR013343; TIGR00372; sufficient; TG GO:0043571; -- SN 7 ID Cas5 DN CRISPR-associated protein, TM1801 family RQ 0 EV IPR013422; TIGR02593; sufficient; TG GO:0043571; -- SN 8 ID Cas6 DN CRISPR-associated protein, CT1133 family RQ 0 EV IPR010156; TIGR01877; sufficient; TG GO:0043571; -- SN 9 ID Dpsyc subtype specific proteins RQ 0 EV IPR019089; TIGR02165; sufficient; TG GO:0043571; EV IPR013403; TIGR02570; sufficient; TG GO:0043571; EV IPR026391; TIGR04106; TG GO:0043571; EV IPR026483; TIGR04113; TG GO:0043571; -- SN 10 ID Dvulg subtype specific proteins RQ 0 EV IPR010144; TIGR01863; sufficient; TG GO:0043571; EV IPR010155; TIGR01876; sufficient; TG GO:0043571; EV IPR013418; TIGR02589; sufficient; TG GO:0043571; -- SN 11 ID Ecoli subtype specific proteins RQ 0 EV IPR010147; TIGR01868; sufficient; TG GO:0043571; EV IPR010148; TIGR01869; sufficient; TG GO:0043571; EV IPR010179; TIGR01907; sufficient; TG GO:0043571; EV IPR013381; TIGR02547; sufficient; TG GO:0043571; EV IPR013382; TIGR02548; sufficient; TG GO:0043571; -- SN 12 ID Hmari subtype specific proteins RQ 0 EV IPR013420; TIGR02591; sufficient; TG GO:0043571; EV IPR013419; TIGR02590; sufficient; TG GO:0043571; EV IPR013421; TIGR02592; sufficient; TG GO:0043571; -- SN 13 ID Mtube subtype specific proteins RQ 0 EV IPR010149; TIGR01870; sufficient; TG GO:0043571; EV IPR013408; TIGR02578; sufficient; TG GO:0043571; EV IPR013412; TIGR02582; sufficient; TG GO:0043571; EV IPR005510; TIGR01903; sufficient; TG GO:0043571; EV IPR010173; TIGR01899; sufficient; TG GO:0043571; EV IPR013489; TIGR02672; sufficient; TG GO:0043571; -- SN 14 ID Myxan subtype specific proteins RQ 0 EV IPR019989; TIGR03485; TG GO:0043571; EV IPR027811; TIGR03486; TG GO:0043571; EV IPR013415; TIGR02586; TG GO:0043571; -- SN 15 ID Nmeni subtype specific proteins RQ 0 EV IPR028629; TIGR01865; sufficient; TG GO:0043571; EV IPR010146; TIGR01866; sufficient; TG GO:0043571; -- SN 16 ID Pging subtype specific proteins RQ 0 EV IPR020032; TIGR03489; TG GO:0043571; EV IPR020029; TIGR03487; TG GO:0043571; -- SN 17 ID PreFran subtype specific proteins RQ 0 EV IPR027620; TIGR04330; TG GO:0043571; -- SN 18 ID RAMP module proteins RQ 0 EV IPR010160; TIGR01881; sufficient; TG GO:0043571; EV IPR013407; TIGR02577; sufficient; TG GO:0043571; EV IPR007522; TIGR01894; sufficient; TG GO:0043571; EV IPR010165; TIGR01888; sufficient; TG GO:0043571; EV IPR013410; TIGR02580; sufficient; TG GO:0043571; EV IPR010172; TIGR01898; sufficient; TG GO:0043571; -- SN 19 ID RAMPs not otherwise accounted for RQ 0 EV IPR013411; TIGR02581; sufficient; TG GO:0043571; EV IPR013490; TIGR02674; sufficient; TG GO:0043571; -- SN 20 ID Tneap subtype specific proteins RQ 0 EV IPR010180; TIGR01908; sufficient; TG GO:0043571; EV IPR013337; TIGR01895; sufficient; TG GO:0043571; EV IPR013414; TIGR02585; sufficient; TG GO:0043571; -- SN 21 ID Ypest subtype specific proteins RQ 0 EV IPR013396; TIGR02563; sufficient; TG GO:0043571; EV IPR013399; TIGR02566; sufficient; TG GO:0043571; EV IPR013398; TIGR02565; sufficient; TG GO:0043571; EV IPR013397; TIGR02564; sufficient; TG GO:0043571; -- SN 22 ID Other CRISPR-associated families RQ 0 EV IPR010171; TIGR01897; sufficient; TG GO:0043571; EV IPR011742; TIGR02221; sufficient; TG GO:0043571; EV IPR013409; TIGR02579; sufficient; TG GO:0043571; EV IPR013413; TIGR02584; sufficient; TG GO:0043571; EV IPR013443; TIGR02620; sufficient; TG GO:0043571; EV IPR013487; TIGR02670; sufficient; TG GO:0043571; EV IPR013492; TIGR03031; sufficient; TG GO:0043571; EV IPR013442; TIGR02619; TG GO:0043571; EV IPR014055; TIGR02682; TG GO:0043571; EV IPR023815; TIGR03984; TG GO:0043571; EV IPR023816; TIGR03985; TG GO:0043571; EV IPR023825; TIGR03986; TG GO:0043571; EV IPR014082; TIGR02710; TG GO:0043571; EV IPR019848; TIGR03642; TG GO:0043571; EV IPR013389; TIGR02556; TG GO:0043571; // AC GenProp0023 DE Glyoxylate shunt TP PATHWAY AU Haft DH TH 0 RN [1] RM 27036942 RT Role of Glyoxylate Shunt in Oxidative Stress Response. RA Ahn S, Jung J, Jang IA, Madsen EL, Park W; RL J Biol Chem. 2016;291:11928-11938. DC Glyoxylate Cycle DR IUBMB; misc; glyox; DC Glyoxylate and Dicarboxylate Metabolism DR KEGG; map00630; CC The glyxoylate shunt consists of two enzymes, isocitrate lyase and CC malate synthase. Its function is generally anaplerotic, meaning that it CC replenishes TCA cycle intermediates. Isocitrate (one intermediate) CC becomes succinate (one intermediate) plus glyoxylate. Glyoxylate plus CC an acetyl group from acetyl-CoA becomes malate, a second intermediate, CC for a gain of one. Acetyl groups, such as from fatty acid metabolism, CC by means of this pathway, can provide TCA cycle intermediates for use CC in amino acid biosynthesis and other biosynthetic pathways[1]. -- SN 1 ID Isocitrate lyase DN Isocitrate lyase (EC 4.1.3.1) RQ 1 EV IPR006254; TIGR01346; sufficient; TG GO:0006097; -- SN 2 ID Malate synthase DN Malate synthase (EC 2.3.3.9) RQ 1 EV IPR006252; TIGR01344; sufficient; TG GO:0006097; EV IPR006253; TIGR01345; sufficient; TG GO:0006097; // AC GenProp0027 DE Photosynthesis TP CATEGORY AU Haft DH TH 0 CC Photosynthesis is defined here as the ability to harness light energy CC to create new organic compounds from water and CO2. Note that some CC bacteria perform anoxygenic photosynthesis (either aerobic or CC anaerobic), an exception to the broadly held view that photosynthesis CC must convert water and CO2 into oxygen and carbohydrate; this can be CC achieved by using a H2S rather than H20 as a source of hydrogen, and CC releasing sulfur or sulfates rather than 02 as waste products. CC Halobacterium is currently regarded as a photoheterotroph that can CC harness light for energy for ion pumps but cannnot synthesize new CC organic compounds from this energy, nor release 02. -- SN 1 ID Photosystem II RQ 0 EV GenProp0661; -- SN 2 ID Photosynthetic reaction center, alphaproteobacterial type RQ 0 EV GenProp0662; -- SN 3 ID Photosystem I RQ 0 EV GenProp0660; // AC GenProp0029 DE Nitrogen fixation TP METAPATH AU Haft DH TH 0 RN [1] RM 15629911 RT Maturation of nitrogenase: a biochemical puzzle. RA Rubio LM, Ludden PW; RL J Bacteriol. 2005;187:405-414. DC Nitrogen Metabolism DR KEGG; map00910; CC Nitrogen fixation is the conversion of atmospheric nitrogen, N2 (with CC its difficult-to-cleave triple bond) into usable forms such as NH3. CC Conditions should be anaerobic or microaerophilic. The characteristic CC enzyme is nitrogenase, but many other proteins are involved. CC Nitrogenase is a complex composed of dinitrogenase (MoFe protein), CC which is a homodimer, and dinitrogenase reductase (Fe protein) that is CC a heterotetramer. Expected along with nitrogenase are several accessory CC proteins, the transcriptional regulator NifA, a ferredoxin or CC flavodoxin, downstream genes for nitrogen assimilation (NtrC, GlnA), CC and genes for protection from oxygen (e.g. leghemoglobin in root CC nodule bacteria). -- SN 1 ID NifX neighbor TIGR02935/DUF269 RQ 0 EV IPR004952; TIGR02935; sufficient; TG GO:0009399; -- SN 2 ID Nitrogenase component I (dinitrogenase) RQ 1 EV GenProp0633; TG GO:0009399; EV GenProp0631; TG GO:0009399; EV GenProp0632; TG GO:0009399; -- SN 3 ID Nitrogenase component II (dinitrogenase reductase) DN Nitrogenase iron protein RQ 1 EV IPR005977; TIGR01287; sufficient; TG GO:0009399; -- SN 4 ID ADP-ribosyl-[dinitrogen reductase] hydrolase RQ 0 EV IPR013479; TIGR02662; sufficient; TG GO:0009399; -- SN 5 ID NAD(+)--dinitrogen-reductase ADP-D-ribosyltransferase RQ 0 EV IPR009953; PF07357; sufficient; TG GO:0009399; -- SN 6 ID Transcriptional regulator RQ 0 EV IPR010113; TIGR01817; sufficient; TG GO:0006808; -- SN 7 ID Nitrogenase iron-molybdenum cofactor biosynthesis protein DN Nitrogenase cofactor biosynthesis protein NifB RQ 1 EV IPR005980; TIGR01290; sufficient; TG GO:0009108; -- SN 8 ID Nitrogenase iron-molybdenum cofactor biosynthesis protein DN Nitrogenase MoFe cofactor biosynthesis protein NifE RQ 1 EV IPR005973; TIGR01283; sufficient; TG GO:0009108; -- SN 9 ID Nitrogen fixation positive activator protein RQ 0 -- SN 10 ID Nitrogen fixation protein NifM RQ 0 EV IPR014282; TIGR02933; sufficient; TG GO:0009399; -- SN 11 ID Nitrogenase molybdenum-iron protein, NifN subunit DN Nitrogenase molybdenum-iron cofactor biosynthesis protein NifN RQ 1 EV IPR005975; TIGR01285; sufficient; TG GO:0016612; -- SN 12 ID Nitrogen fixation protein NifQ DN Nitrogen fixation protein NifQ RQ 0 EV IPR006975; PF04891; sufficient; -- SN 13 ID Probable nitrogen fixation protein NifT RQ 0 EV IPR009727; TIGR02934; sufficient; TG GO:0009399; -- SN 14 ID Homocitrate synthase DN Homocitrate synthase RQ 0 EV IPR013477; TIGR02660; sufficient; TG GO:0009399; -- SN 15 ID Nitrogen fixation protein DN Nitrogen fixation protein NifW RQ 0 EV IPR004893; PF03206; sufficient; -- SN 16 ID Nitrogenase molybdenum-iron cofactor biosynthesis protein RQ 0 EV IPR013480; TIGR02663; sufficient; TG GO:0009399; -- SN 17 ID Iron-sulfur cofactor synthesis protein RQ 0 EV IPR007415; PF04319; sufficient; -- SN 18 ID Nif-specific ferredoxin RQ 0 EV IPR014283; TIGR02936; sufficient; TG GO:0009399; // AC GenProp0030 DE Glutathione biosynthesis TP PATHWAY AU Haft DH TH 0 DC Glutathione Metabolism DR KEGG; map00480; CC Glutathione (GSH) is gamma-Glu-Cys-Gly, a thiol whose -SH group is an CC important reductant in many systems. Some species use thiols other than CC glutathione: mycothione in Mycobacterium tuberculosis, CC gamma-glutamylcysteine in Halobacterium, and trypanothione in CC trypanosomes. Cysteine and CoA may also serve. Glutathione biosynthesis CC is accomplished by two enzymes. First, glutamate--cysteine ligase links CC the gamma-COOH of Glu to the NH2 of Cys. Next, glutathione synthase CC creates a peptide bond from the COOH of Cys to the NH2 of Gly. Species CC that synthesize glutathione are likely to have a reductase for oxidized CC glutathione and a number of glutathione-dependent enzymes. -- SN 1 ID Glutamate--cysteine ligase DN Glutamate--cysteine ligase (EC 6.3.2.2) RQ 1 EV IPR006334; TIGR01434; sufficient; TG GO:0006750; EV IPR011556; TIGR01436; sufficient; TG GO:0006750; EV IPR004308; PF03074; sufficient; TG GO:0006750; EV IPR011718; TIGR02049; sufficient; TG GO:0006750; EV IPR011792; TIGR02048; sufficient; TG GO:0006750; EV IPR006335; TIGR01435; TG GO:0006750; -- SN 2 ID Glutathione synthetase DN Glutathione synthase (EC 6.3.2.3) RQ 1 EV IPR006284; TIGR01380; sufficient; TG GO:0006750; EV IPR005615; TIGR01986; sufficient; TG GO:0006750; EV IPR006335; TIGR01435; TG GO:0006750; // AC GenProp0033 DE TCA cycle TP METAPATH AU Haft DH TH 5 DC Citric acid cycle DR IUBMB; misc; CAcycle; DC Citrate Cycle (TCA cycle) DR KEGG; map00020; CC The TCA cycle (also known as the Krebs cycle, citrate acid cycle, and CC tricarboxylic acid cycle) is performed in eukaryotic mitochondria and CC in many prokaryotes. This property refers to the forward direction: CC from oxaloacetate and acetate to citrate, to isocitrate, to CC 2-oxoglutarate, to succinate, to fumarate, to malate, to oxaloacetate, CC with the release of two molecules of CO2. It runs only under aerobic CC conditions. The state YES means the cycle is complete. A complete TCA CC cycle may correlate with use of TCA intermediates as biosynthetic CC precursors and with anaplerotic (TCA cycle intermediate-replenishing) CC reactions such as the glyoxylate shunt. The state PARTIAL indicates CC the pathway does not form a full cycle but may contain several CC consecutive steps. The direction of flux through this arc is not CC specified when the PARTIAL state is set, and so it may be in the CC reductive (reverse) direction. The full reverse TCA cycle, an CC alternative to the Calvin cycle for carbon dioxide fixation, is CC covered by a separate property. -- SN 1 ID Citrate synthase DN Citrate (Si)-synthase (EC 2.3.3.1) RQ 1 EV IPR010953; TIGR01798; sufficient; TG GO:0006099; EV IPR011278; TIGR01800; sufficient; TG GO:0006099; EV IPR010109; TIGR01793; sufficient; TG GO:0006099; -- SN 2 ID Aconitate hydratase DN Aconitate hydratase (EC 4.2.1.3) RQ 1 EV IPR006249; TIGR01341; sufficient; TG GO:0006099; EV IPR004406; TIGR00117; sufficient; TG GO:0006099; EV IPR006248; TIGR01340; sufficient; TG GO:0006099; -- SN 3 ID Isocitrate dehydrogenase DN Isocitrate dehydrogenase (EC 1.1.1.42 1.1.1.41) RQ 1 EV IPR004434; TIGR00175; sufficient; TG GO:0006099; EV IPR004790; TIGR00127; sufficient; TG GO:0006099; EV IPR004436; TIGR00178; sufficient; TG GO:0006099; EV IPR004439; TIGR00183; sufficient; TG GO:0006099; EV IPR014273; TIGR02924; sufficient; TG GO:0006099; -- SN 4 ID 2-oxoglutarate dehydrogenase system DN Oxoglutarate dehydrogenase (succinyl-transferring) (EC 1.2.4.2) RQ 1 EV GenProp0630; TG GO:0006099; -- SN 5 ID Succinyl-CoA synthetase, alpha subunit DN Succinate--CoA ligase, alpha subunit (EC 6.2.1.-) RQ 1 EV IPR005810; TIGR01019; sufficient; TG GO:0006099; -- SN 6 ID Succinyl-CoA synthetase, beta subunit DN Succinate--CoA ligase, beta subunit (EC 6.2.1.-) RQ 1 EV IPR005809; TIGR01016; sufficient; TG GO:0006099; -- SN 7 ID Succinate dehydrogenase, flavoprotein subunit DN Succinate dehydrogenase, flavoprotein subunit (EC 1.3.5.1) RQ 1 EV IPR011281; TIGR01816; sufficient; TG GO:0006099; EV IPR011280; TIGR01811; sufficient; TG GO:0006099; -- SN 8 ID Succinate dehydrogenase, iron-sulfur protein DN Succinate dehydrogenase, iron-sulfur subunit (EC 1.3.5.1) RQ 1 EV IPR004489; TIGR00384; sufficient; TG GO:0006099; -- SN 9 ID Succinate dehydrogenase, cytochrome b subunit DN Succinate dehydrogenase, cytochrome b subunit (EC 1.3.5.1) RQ 1 EV IPR014314; TIGR02970; sufficient; TG GO:0006099; EV IPR011138; TIGR02046; sufficient; -- SN 10 ID Succinate dehydrogenase, hydrophobic membrane anchor DN Succinate dehydrogenase, hydrophobic membrane anchor protein (EC 1.3.5.1) RQ 0 EV IPR014312; TIGR02968; sufficient; TG GO:0006099; -- SN 11 ID Fumarate hydratase, class I C-term or class II DN Fumarate hydratase (EC 4.2.1.2) RQ 1 EV IPR005677; TIGR00979; sufficient; TG GO:0006099; EV IPR004647; PF05683; sufficient; TG GO:0006099; -- SN 12 ID Fumarate hydratase, class I N-term or class II DN Fumarate hydratase (EC 4.2.1.2) RQ 1 EV IPR005677; TIGR00979; sufficient; TG GO:0006099; EV IPR004646; PF05681; sufficient; -- SN 13 ID Malate dehydrogenase DN Malate dehydrogenase (EC 1.1.1.37) RQ 1 EV IPR010945; TIGR01759; sufficient; EV IPR011274; TIGR01758; sufficient; TG GO:0006099; EV IPR011275; TIGR01763; sufficient; TG GO:0006099; EV IPR010097; TIGR01772; sufficient; TG GO:0006099; EV IPR006231; TIGR01320; sufficient; TG GO:0006099; // AC GenProp0036 DE Biotin biosynthesis TP PATHWAY AU Haft DH TH 1 RN [1] RM 21437340 RT Closing in on complete pathways of biotin biosynthesis. RA Lin S, Cronan JE; RL Mol Biosyst. 2011;7(6):1811-1821. DC Biotin Metabolism DR KEGG; map00780; CC Biotin is an essential cofactor for many carboxylation (addition of CC CO2) reactions. This property reflects biosynthesis of biotin from CC pimeloyl-CoA, although the source of pimeloyl-CoA may vary. CC 8-amino-7-oxononanoate synthase (also called 7-keto-8-aminopelargonic CC acid synthetase, AONS, gene BioF) converts pimeloyl-CoA to CC 8-amino-7-oxononanoate (AON). Adenosylmethionine-8-amino-7-oxononanoate CC aminotransferase (gene BioA) converts the product to CC 7,8-diaminononanoate, from which dethiobiotin synthase (gene BioD) CC makes dethiobiotin. Biotin synthase (gene BioB) then makes biotin CC itself[1]. Enzymes such as carboxylesterase (gene BioH), which are CC involved in pimeloyl-CoA biosynthesis typically receive biotin-related CC annotations, but may also appear in genomes in which biotin is not CC synthesized and pimeloyl-CoA is used for something else. -- SN 1 ID 8-amino-7-oxononanoate synthase DN 8-amino-7-oxononanoate synthase (EC 2.3.1.47) RQ 1 EV IPR004723; TIGR00858; sufficient; TG GO:0009102; -- SN 2 ID Adenosylmethionine-8-amino-7-oxononanoate aminotransferase DN Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) RQ 1 EV IPR005815; TIGR00508; sufficient; TG GO:0009102; -- SN 3 ID Dethiobiotin synthase DN Dethiobiotin synthase (EC 6.3.3.3) RQ 1 EV IPR004472; TIGR00347; sufficient; TG GO:0009102; -- SN 4 ID Biotin synthase DN Biotin synthase (EC 2.8.1.6) RQ 1 EV IPR002684; TIGR00433; sufficient; TG GO:0009102; -- SN 5 ID BioC DN Biotin biosynthesis protein BioC RQ 0 EV IPR011814; TIGR02072; sufficient; TG GO:0009102; -- SN 6 ID BioH protein DN Carboxylesterase BioH protein (EC 3.1.1.1) RQ 0 EV IPR010076; TIGR01738; sufficient; TG GO:0009102; -- SN 7 ID BioY family protein DN BioY family protein RQ 0 EV IPR003784; PF02632; sufficient; TG GO:0009102; -- SN 8 ID Biotin ligase domain protein DN Biotin-[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15) RQ 0 EV IPR004408; TIGR00121; sufficient; TG GO:0018065; -- SN 9 ID Biotin repressor DN Biotin operon repressor RQ 0 EV IPR004409; TIGR00122; sufficient; TG GO:0009102; // AC GenProp0037 DE Tryptophan biosynthesis from ribose-5-phosphate TP PATHWAY AU Haft DH TH 2 RN [1] RM 12966138 RT Ancient origin of the tryptophan operon and the dynamics of RT evolutionary change. RA Xie G, Keyhani NO, Bonner CA, Jensen RA; RL Microbiol Mol Biol Rev. 2003;67:303-42. DC Tryptophan Biosynthesis DR IUBMB; AminoAcid; Trp; DC Tryptophan metabolism DR KEGG; map00380; CC The essential amino acid tryptophan is synthesized in prokaryotes, CC plants, and fungi via a conserved six step pathway from the branchpoint CC compound chrosimate, a common precursor in the biosynthesis of aromatic CC amino acids. Seven catalytic domains and two alpha/beta subunit CC complexes comprise this pathway. Individually expressed in some CC organisms, gene fusions encoding single proteins possessing two or more CC of these catalytic domains have been observed for every trp gene. CC Although the occurance of gene fusions have been shown to be CC phylogenetically unrelated, a conserved gene order can be discerned CC within the domain Bacteria. Occasionally gene(s) dissociations disrupt CC gene order as in Campylobacter jejuni and Deinococcus radiodurans, or CC the pathway is found split between two separate chromosomes as in CC Rhodobacter sphaeroides. In cyanobacteria, such as Nostoc and Anabaena, CC it is not uncommon to observe paralogous trp genes as part of a larger CC "supraoperon" including other aromatic amino acid synthesizing genes as CC well as their trp counterparts [1]. -- SN 1 ID Ribose-phosphate pyrophosphokinase DN Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) RQ 1 EV IPR005946; TIGR01251; sufficient; TG GO:0000162; -- SN 2 ID Anthranilate synthase component I DN Anthranilate synthase component I (EC 4.1.3.27) RQ 1 EV IPR005256; TIGR00564; sufficient; TG GO:0000162; EV IPR005257; TIGR00565; sufficient; TG GO:0000162; EV IPR010112; TIGR01815; sufficient; TG GO:0000162; EV IPR010116; TIGR01820; sufficient; TG GO:0000162; -- SN 3 ID Anthranilate synthase component II DN Anthranilate synthase component II (EC 4.1.3.27) RQ 1 EV IPR006221; TIGR00566; sufficient; TG GO:0000162; -- SN 4 ID Anthranilate phosphoribosyltransferase DN Anthranilate phosphoribosyltransferase (EC 2.4.2.18) RQ 1 EV IPR005940; TIGR01245; sufficient; TG GO:0000162; -- SN 5 ID N-(5'phosphoribosyl)anthranilate isomerase DN N-(5'phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) RQ 1 EV IPR001240; PF00697; sufficient; TG GO:0000162; EV IPR010188; TIGR01919; sufficient; TG GO:0000162; -- SN 6 ID Indole-3-glycerol phosphate synthase DN Indole-3-glycerol phosphate synthase (EC 4.1.1.48) RQ 1 EV IPR013798; PF00218; sufficient; TG GO:0000162; -- SN 7 ID Tryptophan synthase, alpha subunit DN Tryptophan synthase, alpha subunit (EC 4.2.1.20) RQ 1 EV IPR002028; TIGR00262; sufficient; TG GO:0000162; -- SN 8 ID Tryptophan synthase, beta subunit DN Tryptophan synthase, beta subunit (EC 4.2.1.20) RQ 1 EV IPR006654; TIGR00263; sufficient; TG GO:0000162; EV IPR006316; TIGR01415; sufficient; -- SN 9 ID Trp operon repressor DN Trp operon repressor RQ 0 EV IPR013335; TIGR01321; sufficient; TG GO:0006355; // AC GenProp0038 DE Tetrahydrofolate biosynthesis from GTP and PABA TP PATHWAY AU Haft DH TH 2 RN [1] RM 14982635 RT Transfection studies to explore essential folate metabolism and RT antifolate drug synergy in the human malaria parasite Plasmodium RT falciparum. RA Wang P, Wang Q, Aspinall TV, Sims PF, Hyde JE; RL Mol Microbiol. 2004;51:1425-1438. DC Folate Biosynthesis (early stages) DR IUBMB; misc; folate1; DC Folate Biosynthesis (late stages) DR IUBMB; misc; folate2; DC Folate Biosynthesis DR KEGG; map00790; CC Polyglutamylated tetrahydrofolate is the central cofactor of one-carbon CC metabolism, and is biosynthesized from GTP, para-aminobenzoate (from CC chorismate), and glutamate in a six step reaction [1]. The first enzyme CC (GTP cyclohydrolase I) catalizes dihydroneopterin triphosphate from GTP CC in the biosynthesis of tetrahydrofolate in prokaryotes, of CC tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments CC in insects. This pathway is carried out by 6 enzymes, the complete CC pathway being absent in animals. -- SN 1 ID GTP cyclohydrolase I DN GTP cyclohydrolase I (EC 3.5.4.16) RQ 0 EV IPR001474; TIGR00063; sufficient; TG GO:0046654; -- SN 2 ID Dihydroneopterin aldolase DN Dihydroneopterin aldolase (EC 4.1.2.25) RQ 1 EV IPR006156; TIGR00525; sufficient; TG GO:0046654; -- SN 3 ID 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase DN 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase (EC 2.7.6.3) RQ 1 EV IPR000550; TIGR01498; sufficient; TG GO:0046654; -- SN 4 ID Dihydropteroate synthase DN Dihydropteroate synthase (EC 2.5.1.15) RQ 1 EV IPR006390; TIGR01496; sufficient; TG GO:0046654; -- SN 5 ID Dihydrofolate synthase DN Dihydrofolate synthase/folylpolyglutamate synthase (EC 6.3.2.12 6.3.2.17) RQ 1 EV IPR001645; TIGR01499; sufficient; TG GO:0046654; -- SN 6 ID Dihydrofolate reductase DN Dihydrofolate reductase (EC 1.5.1.3) RQ 1 EV IPR001796; PF00186; sufficient; TG GO:0046654; // AC GenProp0046 DE IPP biosynthesis TP METAPATH AU Haft DH TH 0 DC Non-Mevalonate Terpenoid biosynthesis DR IUBMB; terp; nonMVA; DC Terpenoid biosynthesis DR IUBMB; terp; terp; DC Mevalonate Biosynthesis DR IUBMB; terp; MVA; CC Isopentenyl pyrophosphate (IPP) is the common intermediate of CC isoprenoid metabolism which includes the biosynthesis of terpenoid CC natural products, sterols, bile acids, carotenoids, vitamins K and E, CC isoprene and other prenylated compounds. IPP may be synthesized via one CC of two separate pathways, the mevalonate pathway is typical of CC eukaryotes while the deoxyxylulose pathway is typical of prokaryotes. CC This property summarizes the states of the two child properties, IPP CC biosynthesis via mevalonate and IPP biosynthesis from deoxyxylulose. -- SN 1 ID IPP biosynthesis RQ 1 EV GenProp0047; TG GO:0009240; EV GenProp0048; TG GO:0009240; // AC GenProp0047 DE IPP biosynthesis via mevalonate TP PATHWAY AU Haft DH TH 2 RN [1] RM 10894743 RT Identification, evolution, and essentiality of the mevalonate pathway RT for isopentenyl diphosphate biosynthesis in gram-positive cocci. RA Wilding EI, Brown JR, Bryant AP, Chalker AF, Holmes DJ, Ingraham KA, RA Iordanescu S, So CY, Rosenberg M, Gwynn MN; RL J Bacteriol. 2000;182(15):4319-4327. RN [2] RM 11042147 RT Biosynthesis of isoprenoids via mevalonate in Archaea: the lost RT pathway. RA Smit A, Mushegian A; RL Genome Res. 2000;10(10):1468-1484. DC Mevalonate Biosynthesis DR IUBMB; terp; MVA; DC Terpenoid biosynthesis DR IUBMB; terp; terp; DC Steroid biosynthesis DR KEGG; map00100; CC Isoprenyl pyrophosphate (IPP) is synthesized in eukaryotes, archaea and CC certain bacteria by the mevalonate pathway (which is in contrast to the CC non-mevalonate pathway found more generally in prokaryotes). The CC bacteria containing this pathway are believed to have acquired it by CC lateral transfer, possibly in more than one independent event [1]. CC Archaea are believed to possess a mevalonate pathway for production of CC IPP, but several of the steps are divergent from the known enzymes in CC eukaryotes and have not yet been conclusively identified [2]. In CC eukaryotes this pathway is highly regulated to control the production of CC steroids which require IPP as a precursor. IPP is also required for the CC synthesis of menaquinone, ubiquinone, terpenoids, isoprene and CC prenylated proteins. The pathway begins with synthesis of CC (S)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) from acetyl-CoA and CC acetoacetyl-CoA by HMG-CoA synthase. The pathway contains 5 steps all of CC which are included as required elements in this property. Some organisms CC contain a pathway-specific acetoacetyl-CoA synthase which is described CC in this property, but is not a required step. It is likely that other CC species obtain acetoacetyl-CoA from beta-oxidation of fatty acids or CC related processes. -- SN 1 ID Acetoacetyl-CoA synthase DN Acetoacetate—CoA ligase (EC 6.2.1.16) RQ 0 EV IPR005914; TIGR01217; sufficient; -- SN 2 ID Hydroxymethylglutaryl-CoA synthase DN Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) RQ 1 EV IPR010122; TIGR01833; sufficient; TG GO:0019287; EV IPR011554; TIGR01835; sufficient; TG GO:0019287; EV IPR004656; TIGR00748; sufficient; TG GO:0019287; -- SN 3 ID Hydroxymethylglutaryl-CoA reductase DN Hydroxymethylglutaryl-CoA reductase (EC 1.1.1.34) RQ 1 EV IPR004554; TIGR00533; sufficient; TG GO:0019287; EV IPR004553; TIGR00532; sufficient; TG GO:0019287; -- SN 4 ID Mevalonate kinase DN Mevalonate kinase (EC 2.7.1.36) RQ 1 EV IPR006205; TIGR00549; sufficient; TG GO:0019287; -- SN 5 ID Phosphomevalonate kinase DN Phosphomevalonate kinase (EC 2.7.4.2) RQ 1 EV IPR016005; TIGR01219; sufficient; TG GO:0019287; EV IPR005917; TIGR01220; sufficient; TG GO:0019287; EV IPR005919; TIGR01223; sufficient; TG GO:0019287; -- SN 6 ID Diphosphomevalonate decarboxylase DN Diphosphomevalonate decarboxylase (EC 4.1.1.33) RQ 1 EV IPR029765; TIGR01240; sufficient; TG GO:0019287; // AC GenProp0048 DE IPP biosynthesis via deoxyxylulose TP PATHWAY AU Haft DH TH 2 RN [1] RM 22216001 RT Five questions about non-mevalonate isoprenoid biosynthesis. RA Odom AR; RL PLoS Pathogens. 2011; 7(12):e1002323. DC Non-Mevalonate Terpenoid biosynthesis DR IUBMB; terp; nonMVA; DC Sterol biosynthesis DR KEGG; map00900; CC Isoprenyl pyrophosphate (IPP) is synthesised in most bacteria by CC the non-mevalonate pathway (also known as the MEP pathway, the CC glyceraldehyde-3-phosphate(GAP)-pyruvate pathway and the deoxyxylulose CC pathway). This is in contrast to the mevalonate pathway found in CC eukaryotes. This non-mevalonate pathway contains six characterized CC enzymes and may involve additional proteins as well. IPP is a basic CC building block of isoprenoids, also known as terpenoids [1]. -- SN 1 ID Deoxyxylulose-5-phosphate synthase DN 1-deoxy-D-xylulose-5-phosphate synthase (EC 2.2.1.7) RQ 1 EV IPR005477; TIGR00204; sufficient; TG GO:0019288; -- SN 2 ID 1-deoxy-D-xylulose 5-phosphate reductoisomerase DN 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) RQ 1 EV IPR003821; TIGR00243; sufficient; TG GO:0019288; -- SN 3 ID 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase DN 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) RQ 1 EV IPR001228; TIGR00453; sufficient; TG GO:0019288; -- SN 4 ID 4-diphosphocytidyl-2C-methyl-D-erythritol kinase DN 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) RQ 1 EV IPR004424; TIGR00154; sufficient; TG GO:0019288; -- SN 5 ID 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase DN 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) RQ 1 EV IPR003526; TIGR00151; sufficient; TG GO:0019288; -- SN 6 ID 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase DN 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) RQ 1 EV IPR004588; TIGR00612; TG GO:0019288; -- SN 7 ID 4-hydroxy-3-methylbut-2-enyl diphosphate reductase DN 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.7.4) RQ 1 EV IPR003451; TIGR00216; TG GO:0019288; // AC GenProp0049 DE Spore formation TP CATEGORY AU Haft DH TH 0 CC A spore is tough, durable, metabolically inert differentiated form of CC an organism, capable of returning to active growth (germination) under CC the right conditions. -- SN 1 ID Endospore formation marker gene set RQ 0 EV GenProp0610; // AC GenProp0051 DE Urease TP SYSTEM AU Haft DH TH 0 RN [1] RM 2651866 RT Microbial ureases: significance, regulation, and molecular RT characterization. RA Mobley HL, Hausinger RP; RL Microbiol Rev. 1989;53:85-108. RN [2] RM 11373617 RT Supramolecular assembly and acid resistance of Helicobacter pylori RT urease. RA Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH; RL Nat Struct Biol. 2001;8:505-509. RN [3] RM 9209019 RT Characterization of UreG, identification of a UreD-UreF-UreG complex, RT and evidence suggesting that a nucleotide-binding site in UreG is RT required for in vivo metallocenter assembly of Klebsiella aerogenes RT urease. RA Moncrief MB, Hausinger RP; RL J Bacteriol. 1997;179:4081-4086. CC Urease is a multi-subunit, nickel-containing enzyme required for the CC hydrolysis of urea to carbon dioxide and ammonia [1]. Its three CC structural genes are located in an unidirectionally transcribed gene CC cluster consisting either as separate alpha, beta, and gamma subunits, CC or as in Helicobacter pylori, a fusion of beta and gamma subunits [2]. CC Associated with these structural subunits are accessory factors CC functioning to assemble and incorporate its nickel-containing CC metallocenter [3]. This property predicts a urease system to be present CC if both its three structural subunits and four accessory proteins are CC all found. In Bacillus subtilis, the accessory proteins are not found CC by homology but urease function has been shown experimentally. This CC finding raises the question of what alternative mechanism can enable CC the assembly of functional urease. -- SN 1 ID Nickel transporter (UreH) RQ 0 EV IPR004688; TIGR00802; sufficient; -- SN 2 ID Urease, gamma subunit DN Urease, gamma subunit RQ 1 EV IPR002026; TIGR00193; sufficient; TG GO:0019627; -- SN 3 ID Urease, beta subunit DN Urease, beta subunit RQ 1 EV IPR002019; TIGR00192; sufficient; TG GO:0019627; -- SN 4 ID Urease, alpha subunit DN Urease, alpha subunit RQ 1 EV IPR005848; TIGR01792; sufficient; -- SN 5 ID Alpha-subunit, N-terminal domain DN Urease alpha-subunit, N-terminal domain RQ 1 EV IPR011612; PF00449; sufficient; TG GO:0019627; -- SN 6 ID Urease accessory protein UreD DN Urease accessory protein UreD RQ 1 EV IPR002669; PF01774; sufficient; TG GO:0019627; -- SN 7 ID Urease accessory protein UreE DN Urease accessory protein UreE RQ 1 EV IPR004029; PF02814; sufficient; TG GO:0019627; -- SN 8 ID Urease accessory protein UreF DN Urease accessory protein UreF RQ 1 EV IPR002639; PF01730; sufficient; TG GO:0019627; -- SN 9 ID Urease accessory protein UreG DN Urease accessory protein UreG RQ 1 EV IPR004400; TIGR00101; sufficient; TG GO:0019627; // AC GenProp0052 DE Type III secretion TP SYSTEM AU Haft DH TH 0 RN [1] RM 11018143 RT Assembly and function of type III secretory systems. RA Cornelis GR, Van Gijsegem F; RL Annu Rev Microbiol. 2000;54:735-774. RN [2] RM 15629935 RT The Erwinia chrysanthemi type III secretion system is required for RT multicellular behavior. RA Yap MN, Yang CH, Barak JD, Jahn CE, Charkowski AO; RL J Bacteriol. 2005;187:639-648. RN [3] RM 15808742 RT Bioinformatics, genomics and evolution of non-flagellar type-III RT secretion systems: a Darwinian perspective. RA Pallen MJ, Beatson SA, Bailey CM; RL FEMS Microbiol Rev. 2005;29:201-229. DC Type III secretion system DR KEGG; map03070; CC Type III secretion systems are found in a number of pathogenenic CC gram-negative bacteria. These systems consist of approximately CC twenty-five translocation proteins, as well as those proteins that are CC transported either across the bacterial inner and outer membrane, into CC the medium, or further across a eukaryotic target cell membrane. CC Substrates for type III secretion are not cleaved during transport, CC although the signal for transport appears to lie near the N-terminus CC (or in the RNA); chaperones act as well for some substrates and may be CC a second signal. Proteins delivered to the target cell cytosol and CC active in pathogenesis are termed effectors. Type III secretion systems CC resemble some of the flagellar export apparatus. In some cases, a type CC III pilus is observed and required for effector delivery. Gene CC nomeclature transposes across genomes: ysc in Yersinia, bsc in CC Bordetella, esc in enteropathogenic E. coli, hrc in plant pathogens, CC etc., so that YscD, EscD, HrcD, etc. are homologous and functionally CC analogous [1,2,3]. -- SN 1 ID HpaP DN Type III secretion protein HpaP RQ 0 EV IPR013390; TIGR02557; sufficient; TG GO:0030254; -- SN 2 ID HrpB1/HrpK DN Type III secretion system, HrpB1/HrpK RQ 0 EV IPR013394; TIGR02561; sufficient; TG GO:0030254; -- SN 3 ID HrpB2 DN Type III secretion protein HrpB2 RQ 0 EV IPR013391; TIGR02558; sufficient; TG GO:0030254; -- SN 4 ID HrpB4 DN Type III secretion protein HrpB4 RQ 0 EV IPR013393; TIGR02560; sufficient; TG GO:0030254; -- SN 5 ID HrpB7 DN Type III secretion protein HrpB7 RQ 0 EV IPR013392; TIGR02559; sufficient; TG GO:0030254; -- SN 6 ID LcrE/YopN/InvE/MxiC DN Type III secretion regulator, YopN/LcrE/InvE/MxiC RQ 0 EV IPR013401; TIGR02568; sufficient; TG GO:0030254; -- SN 7 ID LcrG/PcrG DN Type III secretion protein, LcrG RQ 0 EV IPR009863; TIGR02573; sufficient; TG GO:0030254; -- SN 8 ID LcrH/SycD/SpaT DN Type III secretion system, low calcium response, chaperone LcrH/SycD RQ 0 EV IPR005415; TIGR02552; sufficient; TG GO:0030254; -- SN 9 ID Regulatory component LcrR DN Type III secretion system regulator, LcrR RQ 0 EV IPR013405; TIGR02572; sufficient; TG GO:0030254; -- SN 10 ID OrgA/MxiK DN Type III secretion apparatus protein OrgA/MxiK RQ 0 EV IPR013388; TIGR02555; sufficient; TG GO:0030254; -- SN 11 ID PrgH DN Type III secretion system, PrgH/EprH RQ 0 EV IPR013387; TIGR02554; sufficient; TG GO:0030254; -- SN 12 ID SpaK/InvB/YsaK DN Surface presentation of antigens protein SpaK RQ 0 EV IPR003065; PF03519; sufficient; TG GO:0030254; -- SN 13 ID SseC/YopB/EspD DN Secretion system effector C, SseC-like RQ 0 EV IPR006972; PF04888; sufficient; TG GO:0030254; -- SN 14 ID Type III secretion chaperone SycH DN Tir chaperone protein (CesT) family RQ 0 EV IPR010261; PF05932; sufficient; TG GO:0030254; -- SN 15 ID Type III secretion chaperone SycN DN Type III secretion system chaperone SycN RQ 0 EV IPR012673; TIGR02503; sufficient; TG GO:0030254; -- SN 16 ID Type III secretion effector delivery regulator, TyeA family DN Type III secretion system effector delivery regulator TyeA-related RQ 1 EV IPR013351; TIGR02511; sufficient; TG GO:0030254; -- SN 17 ID YopD DN YopD-like RQ 0 EV IPR008898; PF05844; sufficient; TG GO:0030254; -- SN 18 ID Needle length determinant DN Type III secretion system needle length determinant RQ 0 EV IPR013354; TIGR02514; sufficient; TG GO:0030254; -- SN 19 ID Type III secretion system needle protein DN Type III secretion system, needle protein RQ 1 EV IPR011841; TIGR02105; sufficient; TG GO:0030254; -- SN 21 ID Proximal regulatory components RQ 0 EV IPR018060; PF00165; EV IPR001801; PF00816; -- SN 22 ID Secretin, type III associated DN NolW-like RQ 0 EV IPR005644; PF03958; TG GO:0030254; -- SN 24 ID Secreted proteins, effectors DN Secreted proteins, effectors RQ 0 EV IPR006972; PF04888; sufficient; EV IPR005427; TIGR02101; sufficient; EV IPR009483; TIGR02553; sufficient; -- SN 25 ID Type III secretion system chaperone, YscB family DN Type III secretion system chaperone YscB RQ 0 EV IPR013353; TIGR02513; sufficient; TG GO:0030254; -- SN 26 ID Type III secretion outer membrane pore, YscC/HrcC family DN Type III secretion system outer membrane pore YscC/HrcC RQ 1 EV IPR003522; TIGR02516; sufficient; TG GO:0030254; -- SN 27 ID Type III secretion apparatus protein, YscD/HrpQ family DN Type III secretion system YscD/HrpQ RQ 1 EV IPR012843; TIGR02500; sufficient; TG GO:0030254; -- SN 28 ID Type III secretion system protein, YseE family DN Type III secretion system, secretion protein E RQ 0 EV IPR012671; TIGR02501; sufficient; TG GO:0030254; -- SN 29 ID Type III secretion protein, YscG family DN Type III secretion system YscG RQ 0 EV IPR013348; TIGR02508; sufficient; TG GO:0030254; -- SN 30 ID Type III secretion protein YopR(YscH) DN DN Type III secretion system effector YopR RQ 0 EV IPR013349; TIGR02509; sufficient; TG GO:0030254; -- SN 31 ID Type III secretion apparatus protein, YscI/HrpB DN Type III secretion system, YscI/HrpB RQ 1 EV IPR012670; TIGR02497; sufficient; TG GO:0030254; -- SN 32 ID Type III apparatus lipoprotein, DN Type III secretion system lipoprotein HrcJ/YscJ RQ 1 EV IPR003282; TIGR02544; sufficient; TG GO:0030254; -- SN 33 ID YOP proteins translocation protein K DN Type III secretion system, secretion protein K RQ 0 EV IPR009510; PF06578; sufficient; TG GO:0030254; -- SN 34 ID Type III secretion apparatus protein, HrpE/YscL family DN Type III secretion system HrpE/YscL RQ 1 EV IPR012842; TIGR02499; sufficient; TG GO:0030254; -- SN 35 ID Type III secretion ATPase DN ATPase, type III secretion system, H+-transporting RQ 1 EV IPR013380; TIGR02546; sufficient; TG GO:0030254; -- SN 36 ID Type III secretion protein YscO DN Type III secretion sytem,YscO RQ 0 EV IPR009929; PF07321; sufficient; TG GO:0030254; -- SN 37 ID YscQ/HrcQ/SpaO DN Type III secretion system apparatus protein YscQ/HrcQ/SpaO RQ 1 EV IPR013385; TIGR02551; sufficient; TG GO:0030254; -- SN 38 ID Type III secretion apparatus protein, YscR/HrcR family DN Yop virulence translocation protein R RQ 1 EV IPR005773; TIGR01102; sufficient; TG GO:0030254; -- SN 39 ID YscS/HrcS/SctS/EscS DN Type III secretion protein HrpO RQ 1 EV IPR006306; TIGR01403; sufficient; TG GO:0030254; -- SN 40 ID Type III secretion protein, YscT/HrpX family DN Type III secretion protein SpaR/YscT RQ 1 EV IPR006304; TIGR01401; sufficient; TG GO:0030254; -- SN 41 ID Type III secretion protein, YscU/HrpY family DN Type III exporter system, secretion apparatus protein BsaZ RQ 1 EV IPR006307; TIGR01404; sufficient; TG GO:0030254; -- SN 42 ID Type III secretion protein, HrcV DN Type III secretion protein HrcV RQ 1 EV IPR006302; TIGR01399; sufficient; TG GO:0030254; -- SN 43 ID Type III secretion chaperone YscW DN Type III secretion system chaperone, YscW RQ 0 EV IPR013400; TIGR02567; sufficient; TG GO:0030254; -- SN 44 ID Type III secretion protein, YscX family DN Type III secretion system YscX RQ 0 EV IPR012672; TIGR02502; sufficient; TG GO:0030254; // AC GenProp0053 DE Type II secretion TP SYSTEM AU Haft DH TH 1 RN [1] RM 11309111 RT Biology of type II secretion. RA Sandkvist M; RL Mol Microbiol. 2001;40:271-283. RN [2] RM 11726509 RT Involvement of the twin-arginine translocation system in protein RT secretion via the type II pathway. RA Voulhoux R, Ball G, Ize B, Vasil ML, Lazdunski A, Wu LF, Filloux A; RL EMBO J. 2001;20(23):6735-6741. DC Type II secretion system DR KEGG; map03070; CC Type II secretion is also known as the main terminal branch of the CC general secretion pathway. Type II secretion systems transport folded CC proteins across the outer membrane. These proteins have previously come CC unfolded across the inner membrane by the general secretory pathway CC (Sec) and are then fully folded in the periplasm [1]. It has been CC reported that some proteins may cross the inner membrane by Tat CC (Sec-independent) protein export rather than by Sec prior to type II CC secretion [2]. -- SN 1 ID Type II secretion system protein C DN Type II secretion system protein C RQ 0 EV IPR001639; TIGR01713; sufficient; TG GO:0015628; -- SN 2 ID Type II secretion system protein D DN Type II secretion system protein D RQ 1 EV IPR013356; TIGR02517; sufficient; TG GO:0015628; -- SN 3 ID Type II secretion system protein E DN Type II secretion system protein E RQ 1 EV IPR013369; TIGR02533; sufficient; TG GO:0015628; -- SN 4 ID Type II secretion system protein F DN Type II secretion system protein F RQ 1 EV IPR011850; TIGR02120; sufficient; TG GO:0015628; -- SN 5 ID Type II secretion system protein G DN Type II secretion system protein G RQ 1 EV IPR010054; TIGR01710; sufficient; TG GO:0015628; -- SN 6 ID Type II secretion system protein H DN Type II secretion system protein H RQ 1 EV IPR002416; TIGR01708; sufficient; TG GO:0015628; -- SN 7 ID Type II secretion system protein I DN Type II secretion system protein I RQ 1 EV IPR010052; TIGR01707; sufficient; TG GO:0015628; -- SN 8 ID Type II secretion system protein J DN Type II secretion system protein J RQ 1 EV IPR010055; TIGR01711; sufficient; TG GO:0015628; EV IPR010055; PF11612; TG GO:0015628; -- SN 9 ID Type II secretion system protein K DN Type II secretion system protein K RQ 1 EV IPR005628; PF03934; sufficient; TG GO:0015628; -- SN 10 ID Type II secretion system protein L DN Type II secretion system protein L RQ 1 EV IPR007812; TIGR01709; sufficient; TG GO:0015628; -- SN 11 ID Type II secretion system protein M DN Type II secretion system protein M RQ 0 EV IPR007690; PF04612; sufficient; TG GO:0015628; EV IPR030927; TIGR04412; sufficient; TG GO:0015628; EV IPR034756; PF10741; TG GO:0015628; -- SN 12 ID Type II secretion system protein N DN Type II secretion system protein N RQ 0 EV IPR022792; PF01203; sufficient; TG GO:0015628; EV IPR030925; TIGR04411; TG GO:0015628; // AC GenProp0055 DE Polyhydroxyalkanoic acids TP SYSTEM AU Haft DH TH 0 RN [1] RM 23702844 RT The role of short-chain conjugated poly-(R)-3-hydroxybutyrate (cPHB) RT in protein folding. RA Reusch RN; RL Int J Mol Sci. 2013;14(6):10727-10748. CC Polyhydroxyalkanoic acids (PHAs) are high molecular weight carbon and CC energy storage molecules. They exist as linear polymers in which the CC monomeric units have the form -[O-CHR(CH2)xCO]-. The aliphatic CC polyesters occur in inclusion bodies in various bacteria and archaea. CC The most common form is polyhydroxybutyric acid, -[0-CHCH3-CH2-CO]-. CC Typical biosynthetic enzymes include ketothiolases, reductases, and CC PHA synthases. Additional proteins may include small PHA inclusion CC body-associated proteins. Typical gene symbols include pha (phb for CC polyhydroxybutyrate) A (ketothiolase), B (reductase), C (synthase), Z CC (depolymerase), E (second subunit of heterodimeric-type PHA synthase), CC R, and Q. It has been reported that all prokaryotes and eukaryotes CC synthesize PHB of medium-chain length (~100–200 residues) thats is CC found in lipid bilayers and vesicles, and PHB of short-chain length CC (<12 residues) which is conjugated to proteins in membranes and CC organelles [1]. However, this property refers to very high molecular CC weight (10,000 to >1,000,000 residues) PHAs in granular deposits. -- SN 1 ID Acetoacetyl-CoA reductase DN Acetoacetyl-CoA reductase (EC 1.1.1.36) RQ 1 EV IPR011283; TIGR01829; sufficient; -- SN 2 ID 3-hydroxybutyrate dehydrogenase DN D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) RQ 0 EV IPR011294; TIGR01963; sufficient; -- SN 3 ID Poly(R)-hydroxyalkanoic acid synthase DN Poly(R)-hydroxyalkanoic acid synthase RQ 1 EV IPR010963; TIGR01838; sufficient; EV IPR011287; TIGR01839; sufficient; EV IPR010125; TIGR01836; sufficient; EV IPR010123; TIGR01834; sufficient; -- SN 4 ID Esterase, PHB depolymerase family, or polyhydroxyalkanoate depolymerase, intracellular RQ 1 EV IPR010126; TIGR01840; sufficient; EV IPR010915; TIGR01849; sufficient; EV IPR011942; TIGR02240; sufficient; TG GO:0006112; -- SN 5 ID Phasin family protein or poly(hydroxyalcanoate) granule-associated protein RQ 1 EV IPR010127; TIGR01841; sufficient; EV IPR008769; TIGR01837; sufficient; EV IPR010234; TIGR01985; sufficient; TG GO:0006112; EV IPR014176; TIGR02809; sufficient; TG GO:0006112; -- SN 6 ID Predicted granule component DN Putative polyhydroxyalkanoic acid system protein RQ 0 EV IPR013433; TIGR02610; sufficient; TG GO:0006112; -- SN 7 ID PHA inclusion probable storage protein PhaP DN Polyhydroxyalkanoic acid inclusion protein PhaP RQ 0 EV IPR011728; TIGR02131; sufficient; TG GO:0006112; -- SN 8 ID Regulatory subunit of PHA synthase DN Polyhydroxyalkanoic acid synthase, PhaR subunit RQ 0 EV IPR011729; TIGR02132; sufficient; TG GO:0006112; -- SN 9 ID Polyhydroxyalkanoate synthesis repressor PhaR DN Polyhydroxyalkanoate synthesis repressor PhaR RQ 1 EV IPR010134; TIGR01848; sufficient; -- SN 10 ID Thiolase, N-terminal domain DN Thiolase, N-terminal domain RQ 0 EV IPR020616; PF00108; // AC GenProp0057 DE NAD(P) biosynthesis from L-aspartate and DHAP TP PATHWAY AU Haft DH TH 0 RN [1] RM 12496312 RT Aspartate dehydrogenase, a novel enzyme identified from structural and RT functional studies of TM1643. RA Yang Z, Savchenko A, Yakunin A, Zhang R, Edwards A, Arrowsmith C, Tong RA L; RL J Biol Chem. 2003;278:8804-8808. DC Nicotinate and nicotinamide metabolism DR KEGG; map00760; CC Nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine CC dinucleotide phosphate (NADP+) also known as pyridine nucleotides, are CC cofactors involved in numerous redox reactions through reversible CC reactions to their reduced forms NADH and NADPH. In bacteria, NAD+ is CC synthesized in a 5 step reaction (NadABCDE) from L-aspartate, and NADP+ CC is made from NAD+ by the action of NAD kinase [1]. In mammals, an CC altenative pathway exists in which the intermediate quinolinate is made CC from L-tryptophan. NAD+ may also be recycled from nicotinamide after CC nucleosidease cleavage, or synthesized from imported nicotinate CC (niacin). -- SN 1 ID L-aspartate oxidase (or dehydrogenase) DN L-aspartate oxidase/L-aspartate dehydrogenase RQ 0 EV IPR005288; TIGR00551; sufficient; TG GO:0009435; EV IPR022487; TIGR03855; TG GO:0009435; -- SN 2 ID Quinolinate synthetase complex, A subunit DN Quinolinate synthetase A RQ 1 EV IPR003473; TIGR00550; sufficient; TG GO:0009435; -- SN 3 ID Nicotinate-nucleotide pyrophosphorylase DN Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) RQ 1 EV IPR004393; TIGR00078; sufficient; TG GO:0009435; -- SN 4 ID Nicotinate nucleotide adenylyltransferase DN Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) RQ 1 EV IPR005248; TIGR00482; sufficient; TG GO:0009435; EV IPR006418; TIGR01527; sufficient; TG GO:0009435; -- SN 5 ID NAD+ synthetase DN NAD+ synthase (EC 6.3.1.5) RQ 1 EV IPR003694; TIGR00552; sufficient; TG GO:0009435; -- SN 6 ID NAD kinase DN NAD+ kinase (EC 2.7.1.23) RQ 0 EV IPR002504; PF01513; sufficient; TG GO:0009435; // AC GenProp0058 DE Menaquinone biosynthesis via SEPHCHC TP PATHWAY AU Haft DH TH 3 RN [1] RM 18284213 RT Identification and characterization of RT (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase RT in the menaquinone biosynthesis of Escherichia coli. RA Jiang M, Chen X, Guo ZF, Cao Y, Chen M, Guo Z; RL Biochemistry. 2008;47:3426-3434. RN [2] RM 17760421 RT Menaquinone biosynthesis in Escherichia coli: identification of RT 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a RT novel intermediate and re-evaluation of MenD activity. RA Jiang M, Cao Y, Guo ZF, Chen M, Chen X, Guo Z; RL Biochemistry. 2007;46:10979-10989. RN [3] RM 18801996 RT An alternative menaquinone biosynthetic pathway operating in RT microorganisms. RA Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, RA Dairi T; RL Science. 2008;321(5896):1670-1673. DC Ubiquinone and other terpenoid-quinone biosynthesis DR KEGG; map00130; CC Menaquinone (also known as Vitamin K2) is one of the quinone cofactors CC which play an essential role in hydrogen transfer reactions, CC particularly during anaerobic respiration. Menaquinone in E. coli and CC various other bacteria is synthesized from chorismate, 2-oxoglutarate, CC polyprenyl-pyrophosphate and S-adenosylmethionine via SEPHCHC and CC SHCHC intermediates [1,2]. A very similar molecule (phylloquinone, CC vitamin K1) is found in cyanobacteria and plants which contains a CC shorter isoprenoid (phytyl) chain in which three of the four double CC bonds are reduced. In animals, both vitamins K1 and K2 act as CC cofactors for gamma-carboxylation of glutamate (Glu -> Gla) which is CC critical for coagulation factors. Note that an alternative pathway for CC menaquinone biosynthesis (not described by this property) operates in CC Helicobacter pylori, Campylobacter jejuni, Streptomyces, and other CC species [3]. -- SN 1 ID Isochorismate synthase DN Isochorismate synthase (EC 5.4.4.2) RQ 1 EV IPR004561; TIGR00543; sufficient; -- SN 2 ID SEPHCHC synthase DN 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase RQ 1 EV IPR004433; TIGR00173; sufficient; TG GO:0009234; -- SN 3 ID Demethylmenaquinone methyltransferase DN Demethylmenaquinone methyltransferase (EC 2.1.1.163) RQ 0 EV IPR004033; TIGR01934; sufficient; TG GO:0009234; -- SN 4 ID 1,4-dihydroxy-2-naphthoate prenyl-transferase DN 1,4-dihydroxy-2-naphthoate octaprenyltransferase (EC 2.5.1.74) RQ 1 EV IPR004657; MF_01937; sufficient; TG GO:0009234; -- SN 5 ID Naphthoate synthase DN Naphthoate synthase (EC 4.1.3.36) RQ 1 EV IPR010198; TIGR01929; sufficient; TG GO:0009234; -- SN 6 ID O-succinylbenzoate synthase DN O-succinylbenzoate synthase (EC 4.2.1.113) RQ 1 EV IPR010196; MF_00470; sufficient; TG GO:0009234; EV IPR010197; TIGR01928; sufficient; TG GO:0009234; -- SN 7 ID O-succinylbenzoate--CoA ligase DN O-succinylbenzoate--CoA ligase (EC:6.2.1.26) RQ 1 EV IPR010192; TIGR01923; sufficient; TG GO:0009234; -- SN 8 ID SHCHC synthase DN SHCHC synthase (EC 4.2.99.20) RQ 0 EV IPR022485; TIGR03695; TG GO:0009234; // AC GenProp0059 DE Type I secretion TP SYSTEM AU Haft DH TH 1 RN [1] RM 11157948 RT Subset of hybrid eukaryotic proteins is exported by the type I RT secretion system of Erwinia chrysanthemi. RA Palacios JL, Zaror I, Martínez P, Uribe F, Opazo P, Socías T, Gidekel RA M, Venegas A. RL J Bacteriol. 2001;183(4):1346-1358. CC A type I protein secretion system is an ABC (ATP-binding cassette) CC transporter. The system is Sec-independent. ATP drives the transport of CC target proteins across both inner and outer membranes and into the CC extracellular medium. There is no cleaved N-terminal signal sequence. CC Instead, the type I system recognizes C-terminal information, localized CC to the last 50 amino acids or less. Characteristic sequence found CC nearby, such as repeats of the motif GGXGXDXXX in Erwinia, may play a CC supporting role, possibly for chaperoning the rest of the protein rather CC than for recognition of the export signal [1]. This property does NOT CC cover ABC transporter-mediated processing and secretion of class II CC bacteriocins of certain Gram-positive bacteria. -- SN 1 ID Type I secretion ATPase RQ 1 EV IPR010128; TIGR01842; sufficient; TG GO:0030253; EV IPR010132; TIGR01846; sufficient; TG GO:0030253; EV IPR017750; TIGR03375; TG GO:0030253; -- SN 2 ID Type I secretion membrane fusion protein DN Type I secretion membrane fusion protein RQ 1 EV IPR010129; TIGR01843; sufficient; TG GO:0030253; -- SN 3 ID Type I secretion outer membrane protein RQ 1 EV IPR010130; TIGR01844; sufficient; TG GO:0030253; -- SN 4 ID Type I secreted proteins GGXGXDXXX repeats DN Haemolysin-type calcium-binding repeat RQ 1 EV IPR001343; PF00353; sufficient; // AC GenProp0061 DE Lipoprotein system lgt/lsp/lnt TP SYSTEM AU Haft DH TH 0 RN [1] RM 8051048 RT Lipid modification of bacterial prolipoprotein. Transfer of RT diacylglyceryl moiety from phosphatidylglycerol. RA Sankaran K, Wu HC; RL J Biol Chem. 1994;269(31):19701-6. CC Some membrane proteins are anchored to the membrane by a lipid moiety CC attached to a modified N-terminus rather than by a transmembrane CC helix. This property describes such a system. The system starts with CC the modification of the Cys sulfhydryl of the conserved lipobox motif CC L-X-G/A-C by prolipoprotein diacylglyceryl transferase (Lgt). CC Prolipoprotein signal peptidase (Lsp) then cleaves the lipoprotein CC signal sequence leaving Cys as the new N-terminal residue. Finally CC the Cys NH2 is acylated by apolipoprotein N-acyltransferase (Lnt) [1]. -- SN 1 ID Prolipoprotein diacylglyceryl transferase DN Prolipoprotein diacylglyceryl transferase (EC:2.4.99.-) RQ 1 EV IPR001640; TIGR00544; sufficient; TG GO:0042158; -- SN 2 ID Prolipoprotein signal peptidase DN Signal peptidase II (EC:3.4.23.36) RQ 1 EV IPR001872; TIGR00077; sufficient; TG GO:0042158; -- SN 3 ID Apolipoprotein N-acyltransferase DN Apolipoprotein N-acyltransferase (EC:2.3.1.-) RQ 0 EV IPR004563; TIGR00546; sufficient; TG GO:0042158; // AC GenProp0063 DE Biosynthesis TP CATEGORY AU Haft DH TH 0 CC The process of creating complex biomolecules from simpler starting CC materials. -- SN 1 ID Natural products biosynthesis RQ 0 EV GenProp0077; -- SN 2 ID Amino acid biosynthesis RQ 0 EV GenProp0126; -- SN 3 ID Cofactor biosynthesis RQ 0 EV GenProp0184; -- SN 4 ID Nucleotide biosynthesis RQ 0 EV GenProp0185; -- SN 5 ID Storage and structural polymer biosynthesis RQ 0 EV GenProp0186; -- SN 6 ID Protein biosynthesis RQ 0 EV GenProp0197; -- SN 7 ID Osmolyte biosynthesis RQ 0 EV GenProp0267; -- SN 8 ID Carbohydrate biosynthesis RQ 0 EV GenProp0795; -- SN 9 ID Lipid biosynthesis RQ 0 EV GenProp0838; -- SN 10 ID Spermidine biosynthesis from arginine (via agmatine) RQ 0 EV GenProp0219; -- SN 11 ID Spermidine biosynthesis from putrescine and S-adenosylmethionine RQ 0 EV GenProp0641; -- SN 12 ID Putrescine biosynthesis from arginine utilizing agmatinase RQ 0 EV GenProp0642; -- SN 13 ID Putrescine biosynthesis from arginine via ornithine RQ 0 EV GenProp0643; -- SN 14 ID Putrescine biosynthesis from glutamate via ornithine RQ 0 EV GenProp0644; -- SN 15 ID Putrescine biosynthesis RQ 0 EV GenProp0645; -- SN 16 ID Phosphonoacetaldehyde biosynthesis from phosphoenolpyruvate RQ 0 EV GenProp0724; -- SN 17 ID Agmatine to putrescine via N-carbamoylputrescine RQ 0 EV GenProp0738; -- SN 18 ID Capreomycidine biosynthesis RQ 0 EV GenProp0909; -- SN 19 ID Alkane biosynthesis, cyanobacterial RQ 0 EV GenProp0942; -- SN 20 ID RSAM/selenodomain system RQ 0 EV GenProp1053; -- SN 21 ID Radical SAM/SPASM system GeoRSP RQ 0 EV GenProp1057; -- SN 22 ID Aminopropylcadaverine biosynthesis RQ 0 EV GenProp1433; -- SN 23 ID Spermine biosynthesis RQ 0 EV GenProp1571; -- SN 24 ID Octopamine biosynthesis RQ 0 EV GenProp1606; -- SN 25 ID Glutaminyl-tRNAgln biosynthesis via transamidation RQ 0 EV GenProp1383; -- SN 26 ID Vitamin Biosynthesis RQ 0 EV GenProp1765; -- SN 27 ID Glutathione biosynthesis RQ 0 EV GenProp1359; -- SN 28 ID Bacillithiol biosynthesis RQ 0 EV GenProp1505; -- SN 29 ID Gamma-glutamyl cycle RQ 0 EV GenProp1664; -- SN 30 ID Glutathione-peroxide redox reactions RQ 0 EV GenProp1721; -- SN 31 ID Hormone biosynthesis RQ 0 EV GenProp1766; -- SN 32 ID Fructose 2,6-bisphosphate biosynthesis RQ 0 EV GenProp1248; -- SN 33 ID PpGpp biosynthesis RQ 0 EV GenProp1755; -- SN 34 ID Secondary metabolites biosynthesis RQ 0 EV GenProp1767; -- SN 35 ID Yersiniabactin biosynthesis RQ 0 EV GenProp1462; -- SN 36 ID Staphyloferrin A biosynthesis RQ 0 EV GenProp1593; -- SN 37 ID Dha Kinase RQ 0 EV GenProp1146; -- SN 38 ID Superpathway of arginine and polyamine biosynthesis RQ 0 EV GenProp1253; -- SN 39 ID Superpathway of S-adenosyl-L-methionine biosynthesis RQ 0 EV GenProp1258; -- SN 40 ID Nitric oxide biosynthesis II (mammals) RQ 0 EV GenProp1320; -- SN 41 ID Superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) RQ 0 EV GenProp1322; -- SN 42 ID Superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) RQ 0 EV GenProp1541; -- SN 43 ID Superpathway of polyamine biosynthesis I RQ 0 EV GenProp1596; // AC GenProp0064 DE Biological niche TP CATEGORY AU Haft DH TH 0 CC Properties which describe the typical or optimal environment for the CC growth of the organism. This excludes places or contexts where CC biologically inert forms (such as spores) of an organism may be found. -- SN 2 ID Lifestyle RQ 0 EV GenProp0603; // AC GenProp0065 DE Genome properties TP CATEGORY AU Haft DH TH 0 -- SN 1 ID Metabolism RQ 0 EV GenProp0017; -- SN 2 ID Biological niche RQ 0 EV GenProp0064; -- SN 3 ID Selfish genetic elements RQ 0 EV GenProp0066; -- SN 6 ID Cell surface component RQ 0 EV GenProp0069; -- SN 7 ID Transport RQ 0 EV GenProp0071; -- SN 8 ID Cell motility RQ 0 EV GenProp0073; -- SN 9 ID Virulence RQ 0 EV GenProp0074; -- SN 10 ID DNA handling RQ 0 EV GenProp0076; -- SN 11 ID Cellular growth, organization and division RQ 0 EV GenProp0167; -- SN 12 ID Unknown biological process RQ 0 EV GenProp0475; -- SN 13 ID Regulatory systems RQ 0 EV GenProp1211; -- SN 14 ID Response to stimulus RQ 0 EV GenProp1213; -- SN 15 ID Quorum-sensing, biofilm formation, and developmental systems RQ 0 EV GenProp1048; -- SN 16 ID Defense systems RQ 0 EV GenProp1067; -- SN 17 ID Hormone systems RQ 0 EV GenProp1778; // AC GenProp0066 DE Selfish genetic elements TP CATEGORY AU Haft DH TH 0 CC Elements that enhance their own transmission relative to the rest of CC an individual’s genome, but are neutral or harmful to the individual CC as a whole. -- SN 1 ID Inteins RQ 0 EV GenProp0010; -- SN 2 ID Phage: major features RQ 0 EV GenProp0208; -- SN 3 ID Integron RQ 0 EV GenProp0226; -- SN 4 ID Toxin-antitoxin system, type II RQ 0 EV GenProp0321; -- SN 5 ID Protein-coding palindromic elements RQ 0 EV GenProp0476; -- SN 6 ID Toxin-antitoxin system, type I RQ 0 EV GenProp1091; -- SN 7 ID Toxin-antitoxin system, type III RQ 0 EV GenProp1092; -- SN 8 ID Addiction module, Hig class RQ 0 EV GenProp0322; -- SN 9 ID Addiction module, RelE-RelB class RQ 0 EV GenProp0324; -- SN 10 ID Viral protein sets RQ 0 EV GenProp1107; -- SN 11 ID Addiction module, ParE class RQ 0 EV GenProp0323; -- SN 12 ID HipBA toxin-antitoxin complex RQ 0 EV GenProp1120; -- SN 13 ID YoeB-YefM toxin-antitoxin complex RQ 0 EV GenProp1133; -- SN 14 ID MqsRA toxin-antitoxin complex RQ 0 EV GenProp1189; -- SN 15 ID RelBE toxin-antitoxin complex RQ 0 EV GenProp1193; // AC GenProp0069 DE Cell surface component TP CATEGORY AU Haft DH TH 0 CC Structures or systems which are localized at the surface of the cell CC and in contact with the external environment. -- SN 1 ID Lipopolysaccharide biosynthesis RQ 0 EV GenProp0297; -- SN 2 ID Protein sorting system, PEP-CTERM/exosortase (generic) RQ 0 EV GenProp0326; -- SN 3 ID Protein sorting system, sortase type, LPXTG/SrtA class RQ 0 EV GenProp0626; -- SN 4 ID Protein sorting system, sortase type, SrtB class RQ 0 EV GenProp0664; -- SN 5 ID Outer membrane protein assembly complex RQ 0 EV GenProp0725; -- SN 6 ID S-layer homology domain-mediated cell wall binding RQ 0 EV GenProp0811; -- SN 7 ID Exosporium RQ 0 EV GenProp0847; -- SN 8 ID Anchored repeat-class ABC transporter, P. acnes type RQ 0 EV GenProp0857; -- SN 9 ID Protein sorting system, proteobacterial dedicated sortase type RQ 0 EV GenProp0859; -- SN 10 ID Cohesin/dockerin (cellulosome-like) system RQ 0 EV GenProp0944; -- SN 11 ID Bam complex RQ 0 EV GenProp1116; // AC GenProp0070 DE Energy metabolism TP CATEGORY AU Haft DH TH 0 CC Processes by which chemical or photonic energy is converted into a CC common currency which is used to power the processes of life. -- SN 1 ID Glyoxylate shunt RQ 0 EV GenProp0023; -- SN 2 ID TCA cycle RQ 0 EV GenProp0033; -- SN 3 ID Pentose phosphate cycle RQ 0 EV GenProp0120; -- SN 4 ID Electron transport RQ 0 EV GenProp0131; -- SN 5 ID ATP synthases RQ 0 EV GenProp0243; -- SN 6 ID Fermentation RQ 0 EV GenProp0298; -- SN 7 ID Entner-Doudoroff pathway RQ 0 EV GenProp0468; -- SN 8 ID Arsenite oxidase RQ 0 EV GenProp0473; -- SN 9 ID Aerobic respiration RQ 0 EV GenProp0611; -- SN 10 ID Respiratory nitrate reductase RQ 0 EV GenProp0636; -- SN 11 ID Formate-dependent nitrite reductase, seven-gene type RQ 0 EV GenProp0682; -- SN 12 ID Cytochrome c nitrite reductase NrfHA RQ 0 EV GenProp0683; -- SN 13 ID Glycolysis RQ 0 EV GenProp0691; -- SN 14 ID Cytochrome b558/566 RQ 0 EV GenProp0695; -- SN 15 ID Hydrogenase, nickel and F420-dependent RQ 0 EV GenProp0723; -- SN 16 ID Anaerobic glycerol-3-phosphate dehydrogenase complex RQ 0 EV GenProp0737; -- SN 17 ID Fumarate reductase complex RQ 0 EV GenProp0756; -- SN 18 ID DMSO reductase family type II enzyme RQ 0 EV GenProp0764; -- SN 19 ID 2-oxoacid:ferredoxin oxidoreductase RQ 0 EV GenProp0841; -- SN 20 ID Hydrogenase, [FeFe]-dependent RQ 0 EV GenProp0914; -- SN 21 ID Hydrogenase, mono-iron type RQ 0 EV GenProp0915; -- SN 22 ID B12-dependent trimeric diol/glycerol dehydratase RQ 0 EV GenProp1089; -- SN 23 ID Quinoprotein cytochrome relay system RQ 0 EV GenProp1101; -- SN 24 ID 2-oxoacid:ferredoxin oxidoreductase, multisubunit form RQ 0 EV GenProp0839; -- SN 25 ID 2-oxoacid:acceptor oxidoreductase, 2 subunit form RQ 0 EV GenProp0842; -- SN 26 ID Photosynthesis RQ 0 EV GenProp0027; -- SN 27 ID Methanogenesis RQ 0 EV GenProp0011; -- SN 28 ID Anaerobic dimethyl sulfoxide reductase RQ 0 EV GenProp0637; -- SN 29 ID Glycolysis I (from glucose 6-phosphate) RQ 0 EV GenProp1306; -- SN 30 ID Glycolysis II (from fructose 6-phosphate) RQ 0 EV GenProp1407; -- SN 31 ID Glycolysis III (from glucose) RQ 0 EV GenProp1599; -- SN 32 ID Hydrogen production V RQ 0 EV GenProp1496; -- SN 33 ID Ketolysis RQ 0 EV GenProp1240; -- SN 34 ID Glycerol-3-phosphate shuttle RQ 0 EV GenProp1750; -- SN 35 ID Pentose phosphate pathway (non-oxidative branch) RQ 0 EV GenProp1294; -- SN 36 ID Pentose phosphate pathway RQ 0 EV GenProp1438; -- SN 37 ID Pentose phosphate pathway (oxidative branch) I RQ 0 EV GenProp1520; -- SN 38 ID Pentose phosphate pathway (oxidative branch) II RQ 0 EV GenProp1732; -- SN 39 ID Photorespiration RQ 0 EV GenProp1747; -- SN 40 ID 2-Oxoglutarate decarboxylation to succinyl-CoA RQ 0 EV GenProp1348; -- SN 41 ID 2-Oxoisovalerate decarboxylation to isobutanoyl-CoA RQ 0 EV GenProp1408; -- SN 42 ID TCA cycle III (animals) RQ 0 EV GenProp1693; -- SN 43 ID Glyoxylate cycle RQ 0 EV GenProp1265; -- SN 44 ID All-trans-farnesol biosynthesis RQ 0 EV GenProp1411; -- SN 45 ID Sedoheptulose bisphosphate bypass RQ 0 EV GenProp1705; -- SN 46 ID Chitin degradation to ethanol RQ 0 EV GenProp1722; -- SN 47 ID NADH repair RQ 0 EV GenProp1736; -- SN 48 ID Succinyl-CoA synthetase RQ 0 EV GenProp1201; -- SN 49 ID Superpathway of photosynthetic hydrogen production RQ 0 EV GenProp1353; -- SN 50 ID Superpathway of glycolysis and the Entner-Doudoroff pathway RQ 0 EV GenProp1691; -- SN 51 ID Superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass RQ 0 EV GenProp1710; // AC GenProp0071 DE Transport TP CATEGORY AU Haft DH TH 0 CC Process by which molecules are moved across biological membranes. -- SN 1 ID Protein transport RQ 0 EV GenProp0179; -- SN 2 ID Small molecule transport RQ 0 EV GenProp0180; -- SN 3 ID F-type conjugation system RQ 0 EV GenProp0489; -- SN 4 ID Heterocyst-related ABC exporter DevBCA RQ 0 EV GenProp0649; -- SN 5 ID Putative Na:solute symporter two-gene cassette RQ 0 EV GenProp0821; -- SN 6 ID Anchored repeat-class ABC transporter, P. acnes type RQ 0 EV GenProp0857; -- SN 7 ID Alcohol ABC transporter, PedABC-type RQ 0 EV GenProp0895; -- SN 8 ID TonB-dependent nutrient uptake pairs, RagAB/SusCD type RQ 0 EV GenProp0941; -- SN 9 ID Energy-coupling factor transporters RQ 0 EV GenProp1094; -- SN 10 ID Proposed F420-0 transporter RQ 0 EV GenProp0896; -- SN 11 ID Ferrous iron transport Feo system RQ 0 EV GenProp1075; -- SN 12 ID Lpt lipopolysaccharide export transenvelope protein complex RQ 0 EV GenProp1079; -- SN 13 ID LptDE outer membrane translocon complex RQ 0 EV GenProp1115; -- SN 14 ID UgpAEC-UgpB complex RQ 0 EV GenProp1124; -- SN 15 ID Holo-translocon SecYEG-SecDF-YajC-YidC complex RQ 0 EV GenProp1132; -- SN 16 ID TusBCDE complex RQ 0 EV GenProp1134; -- SN 17 ID Twin-arginine translocation complex RQ 0 EV GenProp1136; -- SN 18 ID Cobalamin transport complex RQ 0 EV GenProp1150; -- SN 19 ID MacAB-TolC complex RQ 0 EV GenProp1151; -- SN 20 ID Vitamin B12 outer membrane transporter complex RQ 0 EV GenProp1157; -- SN 21 ID TusE-MnmA complex RQ 0 EV GenProp1161; -- SN 22 ID IscS-IscU complex RQ 0 EV GenProp1163; -- SN 23 ID PhnGHIJKL complex RQ 0 EV GenProp1165; -- SN 24 ID CdsA-CdsE complex RQ 0 EV GenProp1174; -- SN 25 ID Protein-conducting channel SecYEG complex RQ 0 EV GenProp1176; -- SN 26 ID IscS-TusA complex RQ 0 EV GenProp1197; -- SN 27 ID MdtBC complex RQ 0 EV GenProp1199; -- SN 28 ID Maltose transport complex RQ 0 EV GenProp1204; -- SN 29 ID Nuclear pore complex, vertebrate RQ 0 EV GenProp2036; -- SN 30 ID Nuclear pore subcomplex Nup107-160 RQ 0 EV GenProp2037; -- SN 31 ID Nuclear pore complex 107-120, Schizosaccharomyces RQ 0 EV GenProp2043; // AC GenProp0072 DE Central intermediary metabolism TP CATEGORY AU Haft DH TH 0 -- SN 1 ID Ornithine biosynthesis from glutamate, acetylated branch RQ 0 EV GenProp0118; -- SN 2 ID Pentose phosphate cycle RQ 0 EV GenProp0120; -- SN 3 ID Leloir pathway (galactose/glucose interconversion) RQ 0 EV GenProp0143; -- SN 4 ID Sulfur metabolism RQ 0 EV GenProp0196; -- SN 5 ID Nitrogen metabolism RQ 0 EV GenProp0202; -- SN 6 ID Phosphorus metabolism RQ 0 EV GenProp0242; -- SN 8 ID Acetyl-CoA -- acetate interconversion via acetyl phosphate RQ 0 EV GenProp0478; -- SN 9 ID Acetate -- acetyl-CoA interconversions RQ 0 EV GenProp0479; -- SN 10 ID Glyoxalate conversion to phosphoglycerate RQ 0 EV GenProp0689; // AC GenProp0073 DE Cell motility TP CATEGORY AU Haft DH TH 0 CC The processes by which cells move from place to place. -- SN 1 ID Gliding motility, Bacteroidetes type RQ 0 EV GenProp0781; -- SN 2 ID Flagella RQ 0 EV GenProp0007; -- SN 3 ID Chemotaxis phosphorelay complex CheA-CheY RQ 0 EV GenProp1147; -- SN 4 ID Flagellar Motor Switch Complex, CCW variant RQ 0 EV GenProp1183; -- SN 5 ID Flagellar Motor Switch Complex, CW variant RQ 0 EV GenProp1194; // AC GenProp0074 DE Virulence TP CATEGORY AU Haft DH TH 0 CC Properties related to the ability of organisms to cause illness or CC damage to host species. -- SN 1 ID Type III secretion RQ 0 EV GenProp0052; -- SN 2 ID Phage shock protein regulon RQ 0 EV GenProp0648; -- SN 3 ID Botulinum toxin system RQ 0 EV GenProp0707; // AC GenProp0075 DE Protein modification, prosthetic groups and cofactors TP CATEGORY AU Haft DH TH 0 CC Properties related to those chemical species which become covalently CC bound to, or otherwise interact with proteins in ways that alter CC their biological function. -- SN 1 ID Coenzyme F420 utilization RQ 0 EV GenProp0002; -- SN 2 ID Lipoprotein system lgt/lsp/lnt RQ 0 EV GenProp0061; -- SN 3 ID Tat (Sec-independent) protein export RQ 0 EV GenProp0127; -- SN 4 ID Gamma secretase RQ 0 EV GenProp2017; -- SN 5 ID Apoptosome RQ 0 EV GenProp2021; -- SN 6 ID Prokaryotic N-terminal cleavage/methylation, type IV pilin-like RQ 0 EV GenProp0295; -- SN 7 ID Selenium-dependent molybdenum hydroxylase system RQ 0 EV GenProp0726; -- SN 8 ID Lipoyl-protein attachment RQ 0 EV GenProp0745; -- SN 9 ID Tryptophan tryptophylquinone modification of methylamine dehydrogenase RQ 0 EV GenProp0860; -- SN 10 ID Anaerobic sulfatase/maturase system RQ 0 EV GenProp0918; -- SN 11 ID Mycothiol system RQ 0 EV GenProp0923; -- SN 12 ID Bacillithiol utilization RQ 0 EV GenProp0933; -- SN 13 ID Glycine radical enzyme system, YjjI/YjjW pair RQ 0 EV GenProp0938; -- SN 14 ID Pyruvate formate-lyase system RQ 0 EV GenProp0943; -- SN 15 ID Elongation factor P beta-lysylation RQ 0 EV GenProp0988; -- SN 16 ID Chlorophyll a biosynthesis II RQ 0 EV GenProp1355; -- SN 17 ID Chlorophyll a biosynthesis I RQ 0 EV GenProp1724; -- SN 18 ID Heme b biosynthesis I (aerobic) RQ 0 EV GenProp1421; -- SN 19 ID Heme b biosynthesis IV (Gram-positive bacteria) RQ 0 EV GenProp1663; -- SN 20 ID Heme b biosynthesis II (anaerobic) RQ 0 EV GenProp1686; -- SN 21 ID Siroheme biosynthesis RQ 0 EV GenProp1215; -- SN 22 ID 2-Carboxy-1,4-naphthoquinol biosynthesis RQ 0 EV GenProp1560; -- SN 23 ID Ubiquinol-8 biosynthesis (prokaryotic) RQ 0 EV GenProp1744; -- SN 24 ID Vitamin E biosynthesis (tocopherols) RQ 0 EV GenProp1337; -- SN 25 ID Protein NEDDylation RQ 0 EV GenProp1311; -- SN 26 ID Protein Pupylation and dePupylation RQ 0 EV GenProp1317; -- SN 27 ID Lipoprotein posttranslational modification RQ 0 EV GenProp1327; -- SN 28 ID Ac/N-end rule pathway RQ 0 EV GenProp1491; -- SN 29 ID N-end rule pathway I (prokaryotic) RQ 0 EV GenProp1495; -- SN 30 ID Protein ubiquitination RQ 0 EV GenProp1754; -- SN 31 ID Superpathway of heme b biosynthesis from uroporphyrinogen-III RQ 0 EV GenProp1470; -- SN 32 ID Superpathway of menaquinol-8 biosynthesis I RQ 0 EV GenProp1498; -- SN 33 ID Superpathway of ubiquinol-8 biosynthesis (prokaryotic) RQ 0 EV GenProp1585; -- SN 34 ID Superpathway of demethylmenaquinol-8 biosynthesis I RQ 0 EV GenProp1694; -- SN 35 ID Superpathay of heme b biosynthesis from glutamate RQ 0 EV GenProp1716; -- SN 36 ID Superpathway of b heme biosynthesis from glycine RQ 0 EV GenProp1720; -- SN 37 ID Mitochondrial protein processing RQ 0 EV GenProp2039; -- SN 38 ID Mitochondrial inner membrane peptidase complex RQ 0 EV GenProp2040; -- SN 39 ID COP9 Signalosome, eukaryote RQ 0 EV GenProp2047; -- SN 40 ID BAF53 complex RQ 0 EV GenProp2080; // AC GenProp0076 DE DNA handling TP CATEGORY AU Haft DH TH 0 CC Properties related to the utilization, maintenance, duplication and CC exchange of DNA. -- SN 1 ID DNA repair RQ 0 EV GenProp0115; -- SN 2 ID RuvABC Holliday junction complex RQ 0 EV GenProp0198; -- SN 3 ID F-type conjugation system RQ 0 EV GenProp0489; -- SN 4 ID Ti-type conjugation system RQ 0 EV GenProp0490; -- SN 5 ID DNA gyrase RQ 0 EV GenProp0699; -- SN 6 ID Integrating conjugative element, PFGI-1 class RQ 0 EV GenProp0855; -- SN 7 ID Conjugative transposon, Bacteroides type RQ 0 EV GenProp0858; -- SN 8 ID Competence-related genes RQ 0 EV GenProp0311; -- SN 9 ID Transcription RQ 0 EV GenProp1214; -- SN 10 ID DNA polymerase III clamp loader chi-psi subcomplex RQ 0 EV GenProp1117; -- SN 11 ID Topoisomerase IV RQ 0 EV GenProp1149; -- SN 12 ID DnaA-DnaB complex RQ 0 EV GenProp1152; -- SN 13 ID DNA polymerase III proofreading complex RQ 0 EV GenProp1155; -- SN 14 ID GyrA-GyrB complex RQ 0 EV GenProp1178; -- SN 15 ID SAGA-like (SLIK) complex RQ 0 EV GenProp2052; -- SN 16 ID TFIID complex RQ 0 EV GenProp2054; -- SN 17 ID ADA complex RQ 0 EV GenProp2055; -- SN 18 ID TFTC-HAT complex RQ 0 EV GenProp2057; -- SN 19 ID Set1B histone H3-Lys4 methyltransferase complex RQ 0 EV GenProp2059; -- SN 20 ID COMPASS methyltransferase complex RQ 0 EV GenProp2060; -- SN 21 ID NSL complex RQ 0 EV GenProp2063; -- SN 22 ID MSL complex RQ 0 EV GenProp2064; -- SN 23 ID RuvB-like helicase RQ 0 EV GenProp2066; -- SN 24 ID MLL-HCF complex RQ 0 EV GenProp2067; -- SN 25 ID THAP1/THAP3-HCFC1-OGT complex RQ 0 EV GenProp2069; -- SN 26 ID npBAF complex RQ 0 EV GenProp2081; -- SN 27 ID SWI/SNF complex RQ 0 EV GenProp2084; // AC GenProp0077 DE Natural products biosynthesis TP CATEGORY AU Haft DH TH 0 CC The biosynthesis of complex biomolecules generally as polyketides, CC non-ribosomal peptides or polyisoprenoids (terpenoids). Often these CC molecules are extensively modified by methylation, oxidation/reduction, CC cyclization, epimerization and rearrangement reactions. Common CC functions for such compounds are as siderophores and toxins CC (antibiotics). Most often these compounds are exported from the cell. -- SN 2 ID Phosphonoacetaldehyde biosynthesis from phosphoenolpyruvate RQ 0 EV GenProp0724; -- SN 3 ID Quorum-sensing, autoinducer-2 system RQ 0 EV GenProp0757; -- SN 4 ID Bacteriocin system, lactococcin 972 group RQ 0 EV GenProp0809; -- SN 5 ID Lantibiotic system, gallidermin/epidermin family RQ 0 EV GenProp0853; -- SN 6 ID Bacteriocin system, NHLP (nif11/nitrile hydratase leader peptide) transport group RQ 0 EV GenProp0861; -- SN 7 ID Post-ribosomal natural product synthesis system, Burkholderia TOMM-type RQ 0 EV GenProp0901; -- SN 8 ID SCIFF/radical SAM Clostridial gene pair RQ 0 EV GenProp0919; -- SN 9 ID Radical SAM Y_X(10)_GDL system RQ 0 EV GenProp0920; -- SN 10 ID Radical SAM pair and His-Xaa-Ser repeats peptide RQ 0 EV GenProp0921; -- SN 11 ID Bacteriocin system, sporulation delay protein group RQ 0 EV GenProp0936; -- SN 12 ID Radical SAM maturase bacteriocin system, CLI_3235 type RQ 0 EV GenProp0945; -- SN 13 ID Radical SAM-cylized peptide, Pep1357C family RQ 0 EV GenProp0954; -- SN 14 ID Modified peptide/radical SAM maturase system, YydFG family RQ 0 EV GenProp0955; -- SN 15 ID Radical SAM maturase/selenobacteriocin system RQ 0 EV GenProp0956; -- SN 16 ID Methanobactin biosynthesis, Mb-OB3b family RQ 0 EV GenProp0962; -- SN 17 ID Radical SAM maturase system, CXXX repeats type RQ 0 EV GenProp0967; -- SN 18 ID Radical SAM maturase system, FibroRumin system RQ 0 EV GenProp0982; -- SN 19 ID Radical SAM maturase system, GG-Bacteroidales group RQ 0 EV GenProp0984; -- SN 20 ID ATP-grasp maturase system, microviridin/marinostatin class RQ 0 EV GenProp0991; -- SN 21 ID ATP-grasp maturase system, uncharacterized RQ 0 EV GenProp1000; -- SN 22 ID Grasp-with-spasm peptide maturase system RQ 0 EV GenProp1002; -- SN 23 ID Cysteine S-glycopeptide biosynthesis, sublancin family RQ 0 EV GenProp1003; -- SN 24 ID Radical SAM/SPASM system GRRM RQ 0 EV GenProp1037; -- SN 25 ID Geopeptide radical SAM/SPASM maturase system RQ 0 EV GenProp1052; -- SN 26 ID Radical SAM/SPASM system Clo7bot RQ 0 EV GenProp1062; -- SN 27 ID Radical SAM/SPASM TIGR04347/TIGR04031 system RQ 0 EV GenProp1065; -- SN 28 ID Sporulation killing factor system RQ 0 EV GenProp1078; -- SN 29 ID Cyanobactin-like ribosomal natural product biosynthesis RQ 0 EV GenProp1083; -- SN 30 ID Enduracididine biosynthesis RQ 0 EV GenProp1084; -- SN 31 ID Radical SAM/SPASM maturase system XYE RQ 0 EV GenProp1090; -- SN 32 ID 3-methylarginine biosynthesis RQ 0 EV GenProp1098; -- SN 33 ID D-alanyl-lipoteichoic acid biosynthesis RQ 0 EV GenProp0958; -- SN 34 ID Biosynthesis of UDP-N-acetyl-D-mannosaminuronic acid (UDP-ManNAcA) RQ 0 EV GenProp0969; -- SN 35 ID Biosynthesis of Und-PP-GlcNAc RQ 0 EV GenProp0970; -- SN 36 ID Radical SAM maturase system, methanogen RQ 0 EV GenProp0992; -- SN 37 ID Nodulation factor production RQ 0 EV GenProp1026; -- SN 38 ID 2,3-dihydroxybenzoate biosynthesis RQ 0 EV GenProp1058; -- SN 39 ID FxLD lantipeptide system RQ 0 EV GenProp1069; -- SN 40 ID Protein O-heptosyltransferase with autotransporter target RQ 0 EV GenProp1080; -- SN 41 ID Pyranoside core peptidyl nucleoside antibiotic biosynthesis RQ 0 EV GenProp1085; -- SN 42 ID 2,3-diaminopropionic acid biosynthesis RQ 0 EV GenProp0908; -- SN 43 ID Acetate production from acetylphosphate RQ 0 EV GenProp0754; -- SN 44 ID Lycopene biosynthesis from IPP RQ 0 EV GenProp0758; -- SN 45 ID ThiF-ThiS complex RQ 0 EV GenProp1175; // AC GenProp0109 DE Histidine biosynthesis from ribose-5-phosphate TP PATHWAY AU Haft DH TH 1 RN [1] RM 8852895 RT Histidine biosynthetic pathway and genes: structure, regulation, and RT evolution. RA Alifano P, Fani R, Liò P, Lazcano A, Bazzicalupo M, Carlomagno MS, RA Bruni CB; RL Microbiol Rev. 1996;60:44-69. RN [2] RM 11842181 RT Mechanism of action and NAD+-binding mode revealed by the crystal RT structure of L-histidinol dehydrogenase. RA Barbosa JA, Sivaraman J, Li Y, Larocque R, Matte A, Schrag JD, Cygler RA M; RL Proc Natl Acad Sci U S A. 2002;99:1859-1864. DC Histidine Biosynthesis (early stages) DR IUBMB; AminoAcid; His1; DC Histidine Biosynthesis (late stages) DR IUBMB; AminoAcid; His2; DC Histidine Metabolism DR KEGG; map00340; CC Histidine is synthesized from phosphoribosyl-pyrophosphate in a ten step CC pathway found in bacteria, archaebacteria, fungi, and plants. The early CC stage of this pathway takes a ribose and transforms it into CC imadiazoleglycerol phosphate. Once the imadiazole ring is formed, CC glutamate donates the a-amino group and the newly formed amine is CC oxidized to histidine [1]. In Salmonella typhimurium and Escherichia CC coli, this pathway is carried out by the eight genes in the 'his' CC operon. hisI, hisB, and hisD are bifunctional enzymes, hisF and CC hisH form a monofunctional dimer, and the rest are monofunctional CC enzymes [2]. -- SN 1 ID Ribose-phosphate pyrophosphokinase DN Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) RQ 1 EV IPR005946; TIGR01251; sufficient; TG GO:0000105; -- SN 2 ID His operon leader peptide DN HisL RQ 0 EV IPR012565; PF08047; -- SN 3 ID ATP phosphoribosyltransferase DN ATP phosphoribosyltransferase/HisG (EC 2.4.2.17) RQ 1 EV IPR013820; TIGR00070; sufficient; TG GO:0000105; EV IPR013820; PF01634; sufficient; TG GO:0000105; -- SN 4 ID Phosphoribosyl-ATP pyrophosphohydrolase DN Phosphoribosyl-ATP pyrophosphohydrolase/HisE (EC 3.6.1.31) RQ 1 EV IPR021130; PF01503; sufficient; TG GO:0000105; EV IPR008179; TIGR03188; TG GO:0000105; -- SN 5 ID Phosphoribosyl-AMP cyclohydrolase DN Phosphoribosyl-AMP cyclohydrolase/HisI (EC 3.5.4.19) RQ 1 EV IPR002496; PF01502; sufficient; TG GO:0000105; -- SN 6 ID Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase DN Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase/HisA (EC 5.3.1.16) RQ 1 EV IPR006063; TIGR00007; sufficient; TG GO:0000105; EV IPR011858; TIGR02129; sufficient; TG GO:0000105; EV IPR010188; TIGR01919; sufficient; TG GO:0000105; -- SN 7 ID Imidazoleglycerol phosphate synthase, glutamine amidotransferase subunit DN Imidazoleglycerol phosphate synthase, glutamine amidotransferase subunit/HisH (EC 2.4.2.-) RQ 1 EV IPR010139; TIGR01855; sufficient; TG GO:0000105; -- SN 8 ID Imidazoleglycerol phosphate synthase, cyclase subunit DN Imidazoleglycerol phosphate synthase, cyclase subunit/HisF (EC 4.1.3.-) RQ 1 EV IPR004651; TIGR00735; sufficient; TG GO:0000105; -- SN 9 ID Imidazoleglycerol-phosphate dehydratase DN Imidazoleglycerol-phosphate dehydratase/HisB (EC 4.2.1.19) RQ 1 EV IPR000807; PF00475; sufficient; TG GO:0000105; -- SN 10 ID Histidinol-phosphate aminotransferase DN Histidinol-phosphate aminotransferase/HisC (EC 2.6.1.9) RQ 1 EV IPR005861; TIGR01141; sufficient; TG GO:0000105; -- SN 11 ID Histidinol-phosphate phosphatase DN Histidinol-phosphate phosphatase/HisJ (EC 3.1.3.15) RQ 0 EV IPR005954; TIGR01261; sufficient; TG GO:0000105; EV IPR010140; TIGR01856; sufficient; EV IPR011809; TIGR02067; sufficient; -- SN 12 ID Histidinol dehydrogenase DN Histidinol dehydrogenase/HisD (EC 1.1.1.23) RQ 1 EV IPR012131; TIGR00069; sufficient; TG GO:0000105; EV IPR012131; PF00815; sufficient; TG GO:0000105; -- SN 13 ID HisG, C-terminal domain DN HisG_C RQ 0 EV IPR013115; PF08029; TG GO:0000105; EV IPR013115; TIGR03455; TG GO:0000105; -- SN 14 ID ATP phosphoribosyltransferase regulatory subunit DN ATP phosphoribosyltransferase regulatory subunit/HisZ RQ 0 EV IPR004517; TIGR00443; TG GO:0000105; // AC GenProp0110 DE Purine (inosine-5'-phosphate) biosynthesis from ribose-5-phosphate TP PATHWAY AU Haft DH TH 4 DC Purine Biosynthesis (early stages) DR IUBMB; misc; purine1; DC Purine Biosynthesis (late stages) DR IUBMB; misc; purine2; DC Purine metabolism DR KEGG; map00230; CC Inosine-5-phosphate (IMP) is synthesized in a ten step pathway from CC phosphoribosyl- pyrophosphate (PRPP) and is the precursor of all purine CC nucleosides (adenosine, guanosine, inosine and xanthosine). The CC purine ring is built from glutamine (2 nitrogens), glycine (2 carbons CC and a nitrogen), 10-formyl-THF (2 carbons), carbon dioxide (1 carbon) CC and aspartate (1 nitrogen). An intermediate, AICAR-P, is formed CC during the process of histidine biosynthesis in a 1:1 ratio with CC histidine, but this route is generally insufficient for fulfilling the CC purine needs of a dividing cell and is not considered 'de novo' purine CC biosynthesis. -- SN 1 ID Ribose-phosphate pyrophosphokinase DN Ribose-phosphate diphosphokinase (EC 2.7.6.1) RQ 1 EV IPR005946; TIGR01251; sufficient; TG GO:0006189; -- SN 2 ID Amidophosphoribosyltransferase DN Amidophosphoribosyltransferase (EC 2.4.2.14) RQ 1 EV IPR005854; TIGR01134; sufficient; TG GO:0006189; -- SN 3 ID Phosphoribosylamine--glycine ligase DN Phosphoribosylamine--glycine ligase (EC 6.3.4.13) RQ 1 EV IPR000115; TIGR00877; sufficient; TG GO:0006189; -- SN 4 ID Phosphoribosylglycinamide formyltransferase DN Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) RQ 1 EV IPR005862; TIGR01142; sufficient; TG GO:0006189; EV IPR004607; TIGR00639; sufficient; TG GO:0006189; -- SN 5 ID Phosphoribosylformylglycinamidine synthase I DN Phosphoribosylformylglycinamidine synthase I (EC 6.3.5.3) RQ 1 EV IPR010073; TIGR01735; sufficient; TG GO:0006189; EV IPR010075; TIGR01737; sufficient; TG GO:0006189; EV IPR010141; TIGR01857; sufficient; TG GO:0006189; -- SN 6 ID Phosphoribosylformylglycinamidine synthase II DN Phosphoribosylformylglycinamidine synthase II (EC 6.3.5.3) RQ 1 EV IPR010073; TIGR01735; sufficient; TG GO:0006189; EV IPR010074; TIGR01736; sufficient; TG GO:0006189; EV IPR010141; TIGR01857; sufficient; TG GO:0006189; -- SN 7 ID Phosphoribosylformylglycinamidine synthase III RQ 0 EV IPR010073; TIGR01735; sufficient; TG GO:0006189; EV IPR003850; TIGR00302; sufficient; TG GO:0006189; EV IPR010141; TIGR01857; sufficient; TG GO:0006189; -- SN 8 ID Phosphoribosylformylglycinamidine cyclo-ligase DN Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) RQ 1 EV IPR004733; TIGR00878; sufficient; TG GO:0006189; -- SN 9 ID Phosphoribosylaminoimidazole carboxylase, catalytic subunit DN Phosphoribosylaminoimidazole carboxylase, catalytic subunit (EC 4.1.1.21) RQ 1 EV IPR000031; TIGR01162; sufficient; TG GO:0006189; -- SN 10 ID Phosphoribosylaminoimidazole carboxylase, ATPase subunit DN Phosphoribosylaminoimidazole carboxylase, ATPase subunit (EC 4.1.1.21) RQ 0 EV IPR005875; TIGR01161; sufficient; TG GO:0006189; -- SN 11 ID Phosphoribosylaminoimidazole-succinocarboxamide synthase DN Phosphoribosylaminoimidazolesuccinocarboxamide synthase (EC 6.3.2.6) RQ 1 EV IPR001636; TIGR00081; sufficient; TG GO:0006189; EV IPR014106; TIGR02735; sufficient; TG GO:0006189; -- SN 12 ID Adenylosuccinate lyase DN Adenylosuccinate lyase (EC 4.3.2.2) RQ 1 EV IPR004769; TIGR00928; sufficient; TG GO:0006189; -- SN 13 ID Phosphoribosylaminoimidazolecarboxamide formyltransferase DN Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3)/IMP cyclohydrolase (EC 3.5.4.10) RQ 0 EV IPR002695; TIGR00355; sufficient; TG GO:0006189; EV IPR002695; PF01808; sufficient; TG GO:0006189; -- SN 14 ID IMP cyclohydrolase DN IMP cyclohydrolase (EC 3.5.4.10) RQ 1 EV IPR002695; TIGR00355; sufficient; TG GO:0006189; EV IPR010191; TIGR01922; sufficient; TG GO:0006189; EV IPR002695; PF01808; sufficient; TG GO:0006189; // AC GenProp0111 DE Proline biosynthesis from glutamate TP PATHWAY AU Haft DH TH 1 DC Proline Biosynthesis DR IUBMB; AminoAcid; Pro; DC Arginine and proline metabolism DR KEGG; map00330; CC The amino acid proline is synthesized in three steps from glutamate via CC L-glutamate-5-semialdehyde which non-enzymatically cyclizes to CC delta-1-pyrroline-5-carboxylate. Glutamate semialdehyde can also arise CC from transamination of ornithine. Proline may also be synthesized CC directly from ornithine by the action of ornithine cyclodeaminase. CC These alternate paths are not covered by this property. -- SN 1 ID Glutamate 5-kinase DN Glutamate 5-kinase (EC 2.7.2.11) RQ 1 EV IPR005715; TIGR01027; sufficient; TG GO:0006561; -- SN 2 ID Glutamate-5-semialdehyde dehydrogenase DN Glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) RQ 1 EV IPR000965; TIGR00407; sufficient; TG GO:0006561; -- SN 3 ID Pyrroline-5-carboxylate reductase DN Pyrroline-5-carboxylate reductase (EC 1.5.1.2) RQ 1 EV IPR000304; TIGR00112; sufficient; TG GO:0006561; // AC GenProp0114 DE Nucleotide excision repair TP SYSTEM AU Haft DH TH 0 DC Nucleotide excision repair DR KEGG; map03420; CC One mechanism of DNA repair is nucleotide excision repair. CC Single-stranded cuts are made on both sides of a DNA lesion and the CC oligomer between the cuts is removed. Very few prokaryotic species lack CC this mechanism, although the insect endosymbiont Buchnera aphidicola is CC an example. In bacteria, the excinuclease UvrABC performs only this CC function, so the presence of any one of the three subunits suggests the CC mechanism is (or was) present. Also required is UvrD or a related CC helicase with similar effect, but this helicase acts in other processes CC as well. The status of nucleotide excision repair in the archaea is CC not fully defined. Eukaryotic NER differs in that many more genes are CC involved, and the characteristic size of the oligomer removed is CC different. -- SN 1 ID Excinuclease ABC subunit A DN Excinuclease ABC subunit A/UvrA (EC 3.1.125.-) RQ 1 EV IPR004602; TIGR00630; sufficient; TG GO:0006289; -- SN 2 ID Excinuclease ABC subunit B DN Excinuclease ABC subunit B/UvrB (EC 3.1.125.-) RQ 1 EV IPR004807; TIGR00631; sufficient; TG GO:0006289; -- SN 3 ID Excinuclease ABC subunit C DN Excinuclease ABC subunit C/UvrC (EC 3.1.125.-) RQ 1 EV IPR004791; TIGR00194; sufficient; TG GO:0006289; -- SN 4 ID DNA helicase II DN DNA helicase II/UvrD (EC 3.6.1.-) RQ 0 EV IPR005753; TIGR01075; sufficient; TG GO:0006289; // AC GenProp0115 DE DNA repair TP CATEGORY AU Haft DH TH 0 CC Any of a number of mechanisms by which damage to DNA is repaired. -- SN 1 ID Nucleotide excision repair RQ 0 EV GenProp0114; -- SN 2 ID RuvABC Holliday junction complex RQ 0 EV GenProp0198; -- SN 3 ID RecBCD pathway RQ 0 EV GenProp0216; -- SN 6 ID SOS response RQ 0 EV GenProp0215; -- SN 7 ID Mismatch repair RQ 0 EV GenProp0225; -- SN 8 ID RecFOR recombination pathway RQ 0 EV GenProp0491; -- SN 9 ID Nonhomologous end-joining, bacterial type RQ 0 EV GenProp0492; -- SN 10 ID AddAB pathway RQ 0 EV GenProp0493; -- SN 11 ID Very short patch repair RQ 0 EV GenProp0767; -- SN 12 ID 8-oxoguanine DNA repair RQ 0 EV GenProp1099; -- SN 13 ID Radical SAM/uracil DNA glycosylase system RQ 0 EV GenProp0903; -- SN 14 ID Ribonucleoside-diphosphate reductase complex RQ 0 EV GenProp1191; -- SN 15 ID TFIIH basal transcription factor RQ 0 EV GenProp2050; // AC GenProp0116 DE DNA metabolism TP CATEGORY AU Haft DH TH 0 CC The chemical reactions and physical changes involving DNA CC (deoxyribonucleic acid), one of the two main types of nucleic acid, CC consisting of a long, unbranched macromolecule formed from one, or CC more commonly two, strands of linked deoxyribonucleotides. -- SN 1 ID DNA repair RQ 0 EV GenProp0115; -- SN 2 ID RuvABC Holliday junction complex RQ 0 EV GenProp0198; -- SN 3 ID DNA polymerase III, bacterial RQ 0 EV GenProp0263; -- SN 4 ID Restriction enzyme system, type I RQ 0 EV GenProp0455; -- SN 5 ID RepABC-type alpha-proteobacterial replicon(s) RQ 0 EV GenProp0487; -- SN 6 ID DNA sulfur modification system dnd RQ 0 EV GenProp0701; -- SN 7 ID DNA ligase/helicase system RQ 0 EV GenProp0977; -- SN 8 ID Replication restart, PriA/PriB primosome pathway RQ 0 EV GenProp1081; -- SN 9 ID Exodeoxyribonuclease VII RQ 0 EV GenProp1095; -- SN 10 ID Replication initiation, bacterial RQ 0 EV GenProp0806; -- SN 11 ID DnaB-DnaC complex RQ 0 EV GenProp1118; -- SN 12 ID DnaB-DnaG complex RQ 0 EV GenProp1123; -- SN 13 ID DnaB-DnaC-DnaT-PriA-PriB complex RQ 0 EV GenProp1130; -- SN 14 ID MukBEF condensin complex RQ 0 EV GenProp1180; -- SN 15 ID DnaB-DnaC-DnaT-PriA-PriC complex RQ 0 EV GenProp1187; -- SN 16 ID DnaA-DnaB-DnaC complex RQ 0 EV GenProp1200; -- SN 17 ID DnaA-HU complex variant 1 RQ 0 EV GenProp1207; -- SN 18 ID DnaB-DnaC-Rep-PriC complex RQ 0 EV GenProp1208; // AC GenProp0117 DE Arginine biosynthesis from ornithine, carbamoyl-p and aspartate TP PATHWAY AU Haft DH TH 1 RN [1] RM 9501170 RT The crystal structure of Pyrococcus furiosus ornithine RT carbamoyltransferase reveals a key role for oligomerization in enzyme RT stability at extremely high temperatures. RA Villeret V, Clantin B, Tricot C, Legrain C, Roovers M, Stalon V, RA Glansdorff N, Van Beeumen J; RL Proc Natl Acad Sci U S A. 1998;95:2801-2806. DC Urea Cycle and Arginine Biosynthesis DR IUBMB; AminoAcid; Arg; DC Arginine biosynthesis DR KEGG; map00220; CC The arginine biosynthesis pathway is a three step process and a part of CC the urea cycle. The first enzyme, ornithine carbamoyltransferase CC (OTCase) carries out the reaction anabolically in arginine CC biosynthesis, but in some cases, it carries out catabolic reactions. CC Most OTCases are homotrimers, but the homotrimers are organized into CC dodecamers built from four trimers in at least two species; the CC catabolic OTCase of Pseudomonas aeruginosa is allosterically regulated, CC while OTCase of the extreme thermophile Pyrococcus furiosus shows both CC allostery and thermophily [1]. The third step of the pathway yields CC L-arginine by argininosuccinate lyase, and the amino acid can be CC cleaved by arginase, yielding urea and reconstituting ornithine. -- SN 1 ID Ornithine carbamoyltransferase DN Ornithine carbamoyltransferase (EC 2.1.3.3) RQ 1 EV IPR002292; TIGR00658; sufficient; TG GO:0042450; -- SN 2 ID Argininosuccinate synthase DN Argininosuccinate synthase (EC 6.3.4.5) RQ 1 EV IPR001518; TIGR00032; sufficient; TG GO:0042450; -- SN 3 ID Argininosuccinate lyase DN Argininosuccinate lyase (EC 4.3.2.1) RQ 1 EV IPR009049; TIGR00838; sufficient; TG GO:0042450; // AC GenProp0118 DE Ornithine biosynthesis from glutamate, acetylated branch TP PATHWAY AU Haft DH TH 0 DC Ornithine Biosynthesis DR IUBMB; AminoAcid; Orn; DC Arginine biosynthesis DR KEGG; map00220; CC This pathway results in the creation of ornithine for use in the CC biosynthesis of arginine and in the urea cycle. Ornithine can also be CC interconverted with glutamate semialdehyde from the proline CC biosynthetic pathway. This pathway represents one of two possible CC branches for the creation of ornithine from glutamate. -- SN 1 ID Glutamate N-acetyltransferase DN Glutamate N-acetyltransferase (EC 2.3.1.35/EC 2.3.1.1) RQ 1 EV IPR002813; TIGR00120; sufficient; TG GO:0006592; EV IPR010167; TIGR01890; sufficient; TG GO:0006592; -- SN 2 ID Acetylglutamate kinase DN Acetylglutamate kinase (EC 2.7.2.8) RQ 1 EV IPR004662; TIGR00761; sufficient; TG GO:0006592; -- SN 3 ID N-acetyl-gamma-glutamyl-phosphate reductase DN N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) RQ 1 EV IPR000706; TIGR01850; sufficient; TG GO:0006592; EV IPR010136; TIGR01851; sufficient; TG GO:0006592; -- SN 4 ID Acetylornithine aminotransferase DN Acetylornithine aminotransferase (EC 2.6.1.11) RQ 1 EV IPR004636; TIGR00707; sufficient; -- SN 5 ID Acetylornithine deacetylase DN Acetylornithine deacetylase (EC 3.5.1.16) RQ 1 EV IPR002813; TIGR00120; sufficient; TG GO:0006592; EV IPR010169; TIGR01892; sufficient; TG GO:0006592; EV IPR010175; TIGR01902; sufficient; EV IPR010182; TIGR01910; sufficient; // AC GenProp0119 DE PTS transport system TP SYSTEM AU Haft DH, Richardson L TH 2 RN [1] RM 28168775 RT Structural characterization of the PTS IIA and IIB proteins associated RT with pneumococcal fucose utilization. RA Higgins MA, Hamilton AM, Boraston AB; RL Proteins. 2017; CC Phosphotransferase system (PTS) is a phosphorylation cascade that allows CC various carbohydrates to be transported accross a membrane at the CC expense of phosphoenolpyruvate (PEP). First, a phosphoryl group is CC donated from PEP to a general (non sugar-specific) enzyme I CC (phosphotransferase system, enzyme I), and then on to a phosphocarrier CC protein (HPr). HPr then dontaes the phosphoryl group to the sugar-specific CC EIIA (enzyme IIA), and then on to EIIB (enzyme IIB), before being CC transferred to the incoming carbohydrate. The carbohydrate is transported CC by EIIC (enzyme IIC), and occasionally EIID (enzyme IID), which are CC sugar-specific transmembrane components [1]. -- SN 1 ID Phosphoenolpyruvate-protein phosphotransferase DN Phosphoenolpyruvate-protein phosphotransferase/ptsI (EC 2.7.3.9) RQ 1 EV IPR006318; TIGR01417; sufficient; TG GO:0009401; -- SN 2 ID Phosphocarrier protein HPr DN Phosphocarrier protein HPr RQ 1 EV IPR000032; TIGR01003; sufficient; TG GO:0009401; -- SN 3 ID HPr(Ser) kinase/phosphatase DN HPr(Ser) kinase/phosphatase RQ 0 EV IPR003755; TIGR00679; sufficient; TG GO:0009401; -- SN 4 ID Phosphotransferase system, EIIA RQ 1 EV IPR003188; PF02255; sufficient; TG GO:0009401; EV IPR004701; PF03610; sufficient; TG GO:0009401; EV IPR004716; PF03829; sufficient; TG GO:0009401; EV IPR013789; TIGR00824; sufficient; TG GO:0009401; EV IPR001127; TIGR00830; sufficient; TG GO:0009401; EV IPR001127; PF00358; sufficient; TG GO:0009401; EV IPR004715; TIGR00848; sufficient; TG GO:0009401; EV IPR018454; TIGR00849; sufficient; TG GO:0009401; EV IPR011297; TIGR01995; sufficient; TG GO:0009401; EV IPR002178; PF00359; sufficient; TG GO:0009401; -- SN 5 ID Phosphotransferase system, EIIB RQ 1 EV IPR003501; PF02302; sufficient; TG GO:0009401; EV IPR003501; PF02302; sufficient; TG GO:0009401; EV IPR004720; PF03830; sufficient; TG GO:0009401; EV IPR004702; TIGR00825; sufficient; TG GO:0009401; EV IPR001996; TIGR00826; sufficient; TG GO:0009401; EV IPR003353; TIGR00829; sufficient; TG GO:0009401; EV IPR013012; TIGR00853; sufficient; TG GO:0009401; EV IPR018455; TIGR00854; sufficient; TG GO:0009401; EV IPR011296; TIGR01992; sufficient; TG GO:0009401; EV IPR011297; TIGR01995; sufficient; TG GO:0009401; EV IPR010973; TIGR01996; sufficient; TG GO:0009401; EV IPR010974; TIGR01998; sufficient; TG GO:0009401; EV IPR011299; TIGR02002; sufficient; TG GO:0009401; EV IPR011300; TIGR02003; sufficient; TG GO:0009401; EV IPR011301; TIGR02004; sufficient; TG GO:0009401; EV IPR010975; TIGR02005; sufficient; TG GO:0009401; EV IPR018113; PF00367; sufficient; TG GO:0009401; -- SN 6 ID Phosphotransferase system, EIIC RQ 1 EV IPR004703; PF03611; sufficient; TG GO:0009401; EV IPR004796; TIGR00359; sufficient; TG GO:0009401; EV IPR004801; TIGR00394; sufficient; TG GO:0009401; EV IPR004501; TIGR00410; sufficient; TG GO:0009401; EV IPR004699; TIGR00821; sufficient; TG GO:0009401; EV IPR004700; TIGR00822; sufficient; TG GO:0009401; EV IPR004702; TIGR00825; sufficient; TG GO:0009401; EV IPR013853; TIGR00827; sufficient; TG GO:0009401; EV IPR004718; TIGR00851; sufficient; TG GO:0009401; EV IPR004719; TIGR00852; sufficient; TG GO:0009401; EV IPR006327; TIGR01427; sufficient; TG GO:0009401; EV IPR011296; TIGR01992; sufficient; TG GO:0009401; EV IPR011297; TIGR01995; sufficient; TG GO:0009401; EV IPR010973; TIGR01996; sufficient; TG GO:0009401; EV IPR010974; TIGR01998; sufficient; TG GO:0009401; EV IPR011299; TIGR02002; sufficient; TG GO:0009401; EV IPR011300; TIGR02003; sufficient; TG GO:0009401; EV IPR011301; TIGR02004; sufficient; TG GO:0009401; EV IPR010975; TIGR02005; sufficient; TG GO:0009401; EV IPR003352; PF02378; sufficient; TG GO:0009401; -- SN 7 ID Phosphotransferase system, EIID RQ 0 EV IPR004704; TIGR00828; sufficient; TG GO:0009401; // AC GenProp0120 DE Pentose phosphate cycle TP PATHWAY AU Haft DH, Richardson L. TH 4 RN [1] RM 28041936 RT The regulation of the pentose phosphate pathway: Remember Krebs. RA Ramos-Martinez JI; RL Arch Biochem Biophys. 2017;614:50-52. DC Pentose Phosphate Pathway (early stages) DR IUBMB; polysacc; PPP1; DC Pentose Phosphate Pathway (later stages) DR IUBMB; polysacc; PPP2; CC The pentose phosphate cycle (also known as the hexose monophosphate CC shunt) is a metabolic pathway that generates NADPH when glucose CC 6-phosphate is oxidised to ribose 5-phosphate. Ribose 5-phosphate is a CC precursor for biosynthesis of nucleotides [1]. NADPH is used in many CC syntheses, including fatty acid synthesis. -- SN 1 ID Glucose-6-phosphate 1-dehydrogenase DN Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) RQ 1 EV IPR001282; TIGR00871; sufficient; TG GO:0006098; -- SN 2 ID 6-phosphogluconolactonase DN 6-phosphogluconolactonase (EC 3.1.1.31) RQ 0 EV IPR005900; TIGR01198; sufficient; TG GO:0006098; -- SN 3 ID 6-phosphogluconate dehydrogenase, decarboxylating DN 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44/EC 1.1.1.343) RQ 1 EV IPR006113; TIGR00873; sufficient; TG GO:0006098; EV IPR004849; TIGR00872; sufficient; TG GO:0006098; -- SN 4 ID Ribose 5-phosphate isomerase DN Ribose 5-phosphate isomerase (EC 5.3.1.6) RQ 1 EV IPR004788; PF06026; sufficient; TG GO:0006098; EV IPR004785; TIGR01120; sufficient; TG GO:0006098; EV IPR011860; TIGR02133; sufficient; TG GO:0006098; -- SN 5 ID Ribulose-phosphate 3-epimerase DN Ribulose-phosphate 3-epimerase (EC 5.1.3.1) RQ 1 EV IPR000056; TIGR01163; sufficient; TG GO:0006098; -- SN 6 ID Transketolase DN Transketolase (EC 2.2.1.1) RQ 1 EV IPR005478; TIGR00232; sufficient; TG GO:0006098; -- SN 7 ID Transaldolase DN Transaldolase (EC 2.2.1.2) RQ 1 EV IPR004730; TIGR00874; sufficient; TG GO:0006098; EV IPR004732; TIGR00876; sufficient; TG GO:0006098; EV IPR011861; TIGR02134; sufficient; TG GO:0006098; -- SN 8 ID Triosephosphate isomerase DN Triosephosphate isomerase (EC 5.3.1.1) RQ 1 EV IPR000652; TIGR00419; sufficient; TG GO:0006098; -- SN 9 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase (EC 4.1.2.13) RQ 1 EV IPR011289; TIGR01859; sufficient; TG GO:0006098; EV IPR000741; PF00274; sufficient; TG GO:0006098; EV IPR006411; TIGR01520; sufficient; TG GO:0006098; EV IPR006412; TIGR01521; sufficient; TG GO:0006098; -- SN 10 ID Fructose bisphosphatase DN Fructose bisphosphatase (EC 3.1.3.11) RQ 0 EV IPR004464; PF03320; sufficient; TG GO:0006098; EV IPR004464; TIGR00330; sufficient; TG GO:0006098; EV IPR009164; PF06874; sufficient; TG GO:0006098; EV IPR033391; PF00316; sufficient; TG GO:0006098; EV IPR002803; PF01950; sufficient; TG GO:0006098; -- SN 11 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; TG GO:0006098; EV IPR010551; PF06560; sufficient; TG GO:0006098; EV IPR011857; TIGR02128; sufficient; TG GO:0006098; // AC GenProp0124 DE Pantothenate biosynthesis from aspartate and 2-oxoisovalerate TP PATHWAY AU Haft DH TH 0 DC Coenzyme A Biosynthesis (early stages) DR IUBMB; misc; CoA1; CC This genome property tracks four proteins of pantothenate biosynthesis CC from aspartate; PanB, PanC, PanD and PanE. In the simplest case PanB CC (3-methyl-2-oxobutanoate hydroxymethyltransferase) makes CC 2-dehydropantoate from 3-methyl-2-oxobutanoate. PanE (2-dehydropantoate CC 2-reductase) makes (R)-pantoate from 2-dehydropantoate. PanD (aspartate CC 1-decarboxylase) makes beta-alanine from L-aspartate, and PanC CC (pantoate--beta-alanine ligase) then produces (R)-pantothenate from CC beta-alanine and (R)-pantoate. The genes for three of the proteins (PanB, CC PanC and PanD) tend to be clustered in bacterial genomes. However, the CC protein family distribution for PanE, is very different. The production CC of (R)-pantoate from 2-dehydropantoate can occur in more than one way CC (NADH or NADPH-dependent), and may be catalyzed by enzymes that have CC additional important substrates (an example is the D-mandelate CC dehydrogenase of Enterococcus faecalis). -- SN 1 ID 3-methyl-2-oxobutanoate hydroxymethyltransferase DN 3-methyl-2-oxobutanoate hydroxymethyltransferase/PanB (EC 2.1.2.11) RQ 1 EV IPR003700; TIGR00222; sufficient; -- SN 2 ID 2-dehydropantoate 2-reductase DN 2-dehydropantoate 2-reductase/PanE (EC 1.1.1.169) RQ 0 EV IPR003710; TIGR00745; sufficient; -- SN 3 ID Aspartate 1-decarboxylase DN Aspartate 1-decarboxylase/PanD (EC 4.1.1.11) RQ 1 EV IPR003190; TIGR00223; sufficient; EV IPR022517; TIGR03799; -- SN 4 ID Pantoate--beta-alanine ligase DN Pantoate--beta-alanine ligase/PanC (EC 6.3.2.1) RQ 1 EV IPR003721; TIGR00018; sufficient; // AC GenProp0125 DE Lysine biosynthesis via diaminopimelate (DAP) TP METAPATH AU Haft DH TH 1 RN [1] RM 17093042 RT L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by RT Chlamydia and plants for synthesis of diaminopimelate/lysine. RA McCoy AJ, Adams NE, Hudson AO, Gilvarg C, Leustek T, Maurelli AT; RL Proc Natl Acad Sci U S A. 2006;103:17909-17914. DC Lysine biosynthesis (early stages) DR IUBMB; AminoAcid; Lys1; DC Lysine biosynthesis (later stages) DR IUBMB; AminoAcid; Lys2; DC Lysine biosynthesis DR KEGG; map00300; DC Lysine biosynthesis I DR MetaCyc; DAPLYSINESYN-PWY; DC Lysine biosynthesis II DR MetaCyc; PWY-2941; CC The basic amino acid lysine is synthesized in most bacteria and plants CC via a nine step pathway from aspartate (via aspartate semialdehyde CC which is also used in a number of other pathways). Most species utilize CC succinate (from succinyl-CoA) to make an important amide linkage in the CC ring-opening of piperidine dicarboxylate. The succinate is then CC hydrolyzed several steps later. Other species carry out analogous CC transformations with acetate (from acetyl-CoA). Chlamydia and CC cyanobacteria have been shown to utilize a direct aminotransferase path CC without the acylation/deacylation steps, and a number of other species CC apparently also use this variant [1]. Each of these variants are included CC within this property. Certain obligate intracellular organisms such as CC Coxiella, Rickettsia and Wolbachia, contain all but the final step CC (diaminopimelate decarboxylase) of this pathway. Presumably these CC organisms have no need of lysine biosynthesis, being able to obtain it CC from their hosts. The products of the penultimate two steps however, CC LL- and meso-diaminopimelate, are required components of the bacterial CC cell wall, and so the rest of the pathway persists. There is a CC possibility that the decarboxylase exists in these organsims but is CC undetected. -- SN 1 ID Source of aspartate-semialdehyde RQ 1 EV GenProp0160; TG GO:0009089; -- SN 2 ID Dihydrodipicolinate synthase DN Dihydrodipicolinate synthase (EC 4.3.3.7) RQ 1 EV IPR005263; TIGR00674; sufficient; TG GO:0009089; -- SN 3 ID Dihydrodipicolinate reductase DN Dihydrodipicolinate reductase (EC 1.17.1.8) RQ 1 EV IPR023940; TIGR00036; sufficient; TG GO:0009089; EV IPR011859; TIGR02130; sufficient; TG GO:0009089; -- SN 4 ID Aminotransferase pathways DN LL-diaminopimelate aminotransferase (EC 2.6.1.83) RQ 0 EV GenProp0787; TG GO:0009089; EV GenProp0786; TG GO:0009089; EV IPR019881; TIGR03540; TG GO:0009089; EV IPR019942; TIGR03542; TG GO:0009089; -- SN 5 ID Diaminopimelate epimerase DN Diaminopimelate epimerase (EC 5.1.1.7) RQ 1 EV IPR001653; TIGR00652; sufficient; TG GO:0009089; -- SN 6 ID Diaminopimelate decarboxylase DN Diaminopimelate decarboxylase (EC 4.1.1.20) RQ 1 EV IPR002986; TIGR01048; sufficient; TG GO:0009089; // AC GenProp0126 DE Amino acid biosynthesis TP CATEGORY AU Haft DH TH 0 CC The synthesis of the basic twenty amino acids found in proteins. -- SN 1 ID Chorismate biosynthesis via shikimate RQ 0 EV GenProp0001; -- SN 2 ID Tryptophan biosynthesis from ribose-5-phosphate RQ 0 EV GenProp0037; -- SN 3 ID Histidine biosynthesis from ribose-5-phosphate RQ 0 EV GenProp0109; -- SN 4 ID Proline biosynthesis from glutamate RQ 0 EV GenProp0111; -- SN 5 ID Arginine biosynthesis from ornithine, carbamoyl-p and aspartate RQ 0 EV GenProp0117; -- SN 6 ID Ornithine biosynthesis from glutamate, acetylated branch RQ 0 EV GenProp0118; -- SN 7 ID Threonine biosynthesis from aspartate semialdehyde RQ 0 EV GenProp0159; -- SN 8 ID Aspartate semialdehyde biosynthesis from aspartate RQ 0 EV GenProp0160; -- SN 9 ID Isoleucine biosynthesis from threonine and pyruvate RQ 0 EV GenProp0162; -- SN 10 ID Valine biosynthesis from pyruvate RQ 0 EV GenProp0163; -- SN 11 ID Leucine biosynthesis from pyruvate and acetyl-CoA RQ 0 EV GenProp0164; -- SN 12 ID Glycine cleavage system RQ 0 EV GenProp0178; -- SN 13 ID Lysine biosynthesis RQ 0 EV GenProp0199; -- SN 14 ID Cysteine biosynthesis, tRNA-dependent RQ 0 EV GenProp0304; -- SN 15 ID Cysteine biosynthesis RQ 0 EV GenProp0305; -- SN 16 ID Methionine salvage from methylthioadenosine RQ 0 EV GenProp0729; -- SN 17 ID Selenocysteinyl-tRNA, PSTK/SepSecS pathway RQ 0 EV GenProp0797; -- SN 18 ID Beta-alanine biosynthesis IV RQ 0 EV GenProp1678; -- SN 19 ID L-ornithine biosynthesis I RQ 0 EV GenProp1466; -- SN 20 ID L-ornithine biosynthesis II RQ 0 EV GenProp1472; -- SN 21 ID L-homocysteine biosynthesis RQ 0 EV GenProp1507; -- SN 22 ID L-homoserine biosynthesis RQ 0 EV GenProp1553; -- SN 23 ID L-alanine biosynthesis I RQ 0 EV GenProp1667; -- SN 24 ID L-asparagine biosynthesis III (tRNA-dependent) RQ 0 EV GenProp1660; -- SN 25 ID L-cysteine biosynthesis IV (fungi) RQ 0 EV GenProp1238; -- SN 26 ID L-methionine salvage from L-homocysteine RQ 0 EV GenProp1719; -- SN 27 ID L-phenylalanine biosynthesis I RQ 0 EV GenProp1708; -- SN 28 ID L-selenocysteine biosynthesis I (bacteria) RQ 0 EV GenProp1499; -- SN 29 ID L-serine biosynthesis RQ 0 EV GenProp1640; -- SN 30 ID L-tryptophan biosynthesis RQ 0 EV GenProp1450; -- SN 31 ID L-tyrosine biosynthesis I RQ 0 EV GenProp1251; -- SN 32 ID L-homoserine and L-methionine biosynthesis RQ 0 EV GenProp1581; -- SN 33 ID 3-Dehydroquinate biosynthesis I RQ 0 EV GenProp1731; -- SN 34 ID Chorismate biosynthesis from 3-dehydroquinate RQ 0 EV GenProp1478; -- SN 35 ID Chorismate biosynthesis I RQ 0 EV GenProp1643; -- SN 36 ID Salicylate biosynthesis I RQ 0 EV GenProp1243; -- SN 37 ID 2,3-Dihydroxybenzoate biosynthesis RQ 0 EV GenProp1336; -- SN 38 ID Carbamoyl phosphate synthetase complex RQ 0 EV GenProp1129; -- SN 39 ID Superpathway of L-tyrosine biosynthesis RQ 0 EV GenProp1234; -- SN 40 ID Superpathway of L-phenylalanine biosynthesis RQ 0 EV GenProp1309; -- SN 41 ID Superpathway of L-alanine biosynthesis RQ 0 EV GenProp1333; -- SN 42 ID Superpathway of L-threonine biosynthesis RQ 0 EV GenProp1358; -- SN 43 ID Superpathway of L-serine and glycine biosynthesis I RQ 0 EV GenProp1386; -- SN 44 ID Superpathway of L-cysteine biosynthesis (mammalian) RQ 0 EV GenProp1399; -- SN 45 ID Superpathway of L-aspartate and L-asparagine biosynthesis RQ 0 EV GenProp1404; -- SN 46 ID Superpathway of branched chain amino acid biosynthesis RQ 0 EV GenProp1405; -- SN 47 ID Superpathway of L-methionine biosynthesis (transsulfuration) RQ 0 EV GenProp1419; -- SN 48 ID Superpathway of L-lysine, L-threonine and L-methionine biosynthesis I RQ 0 EV GenProp1475; -- SN 49 ID Superpathway of L-citrulline metabolism RQ 0 EV GenProp1481; -- SN 50 ID Superpathway of aromatic amino acid biosynthesis RQ 0 EV GenProp1538; -- SN 51 ID Superpathway of L-tryptophan biosynthesis RQ 0 EV GenProp1550; // AC GenProp0127 DE Tat (Sec-independent) protein export TP SYSTEM AU Haft DH TH 0 RN [1] RM 12562823 RT Prokaryotic utilization of the twin-arginine translocation pathway: a RT genomic survey. RA Dilks K, Rose RW, Hartmann E, Pohlschröder M; RL J Bacteriol. 2003;185:1478-1483. RN [2] RM 17901208 RT Structural diversity in twin-arginine signal peptide-binding proteins. RA Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, RA Vuister GW, Sargent F; RL Proc Natl Acad Sci U S A. 2007;104:15641-15646. DC Protein export DR KEGG; map03060; CC The twin-arginine dependent translocation (Tat) system of protein CC transport differs from Sec-dependent translocation in that the Tat CC system transports folded proteins while Sec feeds through unfolded, CC nascent proteins that fold after they cross the membrane. The CC significance is that Tat lets cofactors such as flavins or iron-sulfur CC clusters be retained during transit across the membrane. Targets for CC the system can often be recognized by a characteristic signal sequence CC with an Arg-Arg motif. The target proteins usually are predicted to CC perform redox functions [1]. This property reflects detection of the CC whole system: components of the translocase and at least one example of CC a predicted Tat signal sequence. Every system must have at least one CC TatA homolog (other than TatB) and at least one TatC homolog. TatB CC occurs only in Proteobacteria and is required at least in E. coli. CC Recently, several proteins (TorD, NapD) have been shown to act as CC chaperones that bind the TAT signal peptide of a specific protein and CC delay translocation until the cofactor has bound [2]. -- SN 1 ID TAT signal peptide-binding chaperone RQ 0 EV IPR005623; PF03927; EV IPR020945; PF02613; -- SN 2 ID Twin-Arg translocation proteins TatA/E DN Sec-independent protein translocase protein TatA RQ 1 EV IPR006312; TIGR01411; sufficient; -- SN 3 ID Twin-Arg translocation protein TatB (Proteobacteria) DN Sec-independent protein translocase protein TatB RQ 0 EV IPR018448; TIGR01410; sufficient; -- SN 4 ID Translocase TatC DN Sec-independent protein translocase protein TatC RQ 1 EV IPR002033; TIGR00945; sufficient; EV IPR011532; TIGR01912; sufficient; -- SN 5 ID Has twin-arginine signal sequence DN Tat (twin-arginine translocation) pathway signal sequence domain protein RQ 1 EV IPR019546; TIGR01409; sufficient; // AC GenProp0128 DE F1/F0 ATPase TP SYSTEM AU Haft DH TH 1 CC F1/F0 ATP synthase: F1 and F0 represent two major clusters of CC subunits. F1 is the peripheral membrane associated cluster. The F1 CC subunits: alpha, beta, gamma, delta, epsilon, have the same names both CC in prokaryotes and eukaryotes. F0 is the integral membrane cluster. In CC F0, nomenclatures differ. For example, prokaryotic chain A matches CC eukaryotic chain 6. -- SN 1 ID A subunit of ATP synthase F0 cluster DN ATP synthase subunit A (EC 3.6.3.14) RQ 1 EV IPR000568; TIGR01131; sufficient; -- SN 2 ID B subunit of ATP synthase F0 cluster DN ATP synthase subunit B (EC 3.6.3.14) RQ 1 EV IPR005864; TIGR01144; sufficient; EV IPR002146; PF00430; sufficient; -- SN 3 ID C subunit of ATP synthase F0 cluster DN ATP synthase subunit C (EC 3.6.3.14) RQ 1 EV IPR005953; TIGR01260; sufficient; EV IPR002379; PF00137; sufficient; -- SN 4 ID F1 alpha subunit of F1/F0 ATP synthase DN ATP synthase subunit alpha (EC 3.6.3.14) RQ 1 EV IPR005294; TIGR00962; sufficient; -- SN 5 ID F1 beta subunit of F1/F0 ATP synthase DN ATP synthase subunit beta (EC 3.6.3.14) RQ 1 EV IPR005722; TIGR01039; sufficient; -- SN 6 ID F1 delta subunit of F1/F0 ATP synthase DN ATP synthase subunit delta (EC 3.6.3.14) RQ 1 EV IPR000711; TIGR01145; sufficient; -- SN 7 ID F1 epsilon subunit of F1/F0 ATP synthase DN ATP synthase subunit epsilon (EC 3.6.3.14) RQ 1 EV IPR001469; TIGR01216; sufficient; EV IPR020546; PF02823; sufficient; -- SN 8 ID F1 gamma subunit of F1/F0 ATP synthase DN ATP synthase subunit gamma (EC 3.6.3.14) RQ 1 EV IPR000131; TIGR01146; sufficient; // AC GenProp0129 DE Na+-translocating NADH-quinone reductase TP SYSTEM AU Haft DH TH 2 RN [1] RM 11248187 RT Recent progress in the Na(+)-translocating NADH-quinone reductase from RT the marine Vibrio alginolyticus. RA Hayashi M, Nakayama Y, Unemoto T; RL Biochim Biophys Acta. 2001;1505(1):37-44. CC Na+-translocating NADH:ubiquinone oxidoreductase is found in marine, CC halophilic, and pathogenic Gram-negative bacteria. The NQR complex CC contains six structural subunits and acts as Na(+) pump [1]. -- SN 1 ID A subunit DN NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit (EC: 1.6.5.-) RQ 1 EV IPR008703; TIGR01936; sufficient; TG GO:0006814; -- SN 2 ID B subunit DN NADH:ubiquinone oxidoreductase, Na(+)-translocating, B subunit (EC: 1.6.5.-) RQ 1 EV IPR010966; TIGR01937; sufficient; TG GO:0006814; -- SN 3 ID C subunit DN NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit (EC: 1.6.5.-) RQ 1 EV IPR010204; TIGR01938; sufficient; TG GO:0006814; -- SN 4 ID D subunit DN NADH:ubiquinone oxidoreductase, Na(+)-translocating, D subunit (EC: 1.6.5.-) RQ 1 EV IPR011292; TIGR01939; sufficient; TG GO:0006814; -- SN 5 ID E subunit DN NADH:ubiquinone oxidoreductase, Na(+)-translocating, E subunit (EC: 1.6.5.-) RQ 1 EV IPR010967; TIGR01940; sufficient; TG GO:0006814; -- SN 6 ID F subunit DN NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit (EC: 1.6.5.-) RQ 1 EV IPR010205; TIGR01941; sufficient; TG GO:0006814; // AC GenProp0130 DE Rnf-type electron transport complex TP SYSTEM AU Haft DH TH 1 RN [1] RM 10671439 RT Enhanced nitrogenase activity in strains of Rhodobacter capsulatus that RT overexpress the rnf genes. RA Jeong HS, Jouanneau Y; RL J Bacteriol. 2000;182:1208-1214. RN [2] RM 9154934 RT Membrane localization, topology, and mutual stabilization of the rnfABC RT gene products in Rhodobacter capsulatus and implications for a new RT family of energy-coupling NADH oxidoreductases. RA Kumagai H, Fujiwara T, Matsubara H, Saeki K; RL Biochemistry. 1997;36(18):5509-5521. RN [3] RM 12773378 RT A reducing system of the superoxide sensor SoxR in Escherichia coli. RA Koo MS, Lee JH, Rah SY, Yeo WS, Lee JW, Lee KL, Koh YS, Kang SO, Roe RA JH; RL EMBO J. 2003;22:2614-2622. CC The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an CC apparent NADH oxidoreductase responsible for electron transport to CC nitrogenase, necessary for nitrogen fixation [1,2]. A closely related CC complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the CC 2Fe-2S-containing superoxide sensor SoxR, active as a transcription CC factor when oxidized [3]. This family of putative NADH oxidoreductase CC complexes exists in many of the same species as the related NQR, a CC Na(+)-translocating NADH-quinone reductase, but is distinct. -- SN 1 ID A subunit DN Electron transport complex, RnfABCDGE type, A subunit RQ 1 EV IPR011293; TIGR01943; sufficient; TG GO:0006118; -- SN 2 ID B subunit DN Electron transport complex, RnfABCDGE type, B subunit RQ 1 EV IPR010207; TIGR01944; sufficient; TG GO:0006118; -- SN 3 ID C subunit DN Electron transport complex, RnfABCDGE type, C subunit RQ 1 EV IPR010208; TIGR01945; sufficient; TG GO:0006118; -- SN 4 ID D subunit DN Electron transport complex, RnfABCDGE type, D subunit RQ 1 EV IPR011303; TIGR01946; sufficient; TG GO:0006118; -- SN 5 ID E subunit DN Electron transport complex, RnfABCDGE type, E subunit RQ 1 EV IPR010968; TIGR01948; sufficient; TG GO:0006118; -- SN 6 ID G subunit DN Electron transport complex, RnfABCDGE type, G subunit RQ 1 EV IPR010209; TIGR01947; sufficient; TG GO:0006118; // AC GenProp0131 DE Electron transport TP CATEGORY AU Haft DH TH 0 CC The transport of electrons from an electron donor to an electron CC acceptor. -- SN 1 ID Rnf-type electron transport complex RQ 0 EV GenProp0130; -- SN 2 ID NAD biosynthesis III RQ 0 EV GenProp1296; -- SN 3 ID NAD salvage pathway III RQ 0 EV GenProp1658; -- SN 4 ID NAD phosphorylation and transhydrogenation RQ 0 EV GenProp1305; -- SN 5 ID NAD/NADP-NADH/NADPH cytosolic interconversion (yeast) RQ 0 EV GenProp1502; -- SN 6 ID NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) RQ 0 EV GenProp1677; -- SN 7 ID Trans, trans-farnesyl diphosphate biosynthesis RQ 0 EV GenProp1704; -- SN 8 ID Polyisoprenoid biosynthesis (E. coli) RQ 0 EV GenProp1479; -- SN 9 ID Di-trans,poly-cis-undecaprenyl phosphate biosynthesis RQ 0 EV GenProp1670; -- SN 10 ID Aerobic respiration III (alternative oxidase pathway) RQ 0 EV GenProp1230; -- SN 11 ID NADH to hydrogen peroxide electron transfer RQ 0 EV GenProp1254; -- SN 12 ID Pyruvate to cytochrome bo oxidase electron transfer RQ 0 EV GenProp1256; -- SN 13 ID Pyruvate to cytochrome bd oxidase electron transfer RQ 0 EV GenProp1269; -- SN 14 ID NADH to trimethylamine N-oxide electron transfer RQ 0 EV GenProp1341; -- SN 15 ID D-lactate to cytochrome bo oxidase electron transfer RQ 0 EV GenProp1367; -- SN 16 ID NADH to cytochrome bd oxidase electron transfer II RQ 0 EV GenProp1373; -- SN 17 ID Glycerol-3-phosphate to fumarate electron transfer RQ 0 EV GenProp1391; -- SN 18 ID Proline to cytochrome bo oxidase electron transfer RQ 0 EV GenProp1401; -- SN 19 ID Aerobic respiration II (cytochrome c) (yeast) RQ 0 EV GenProp1426; -- SN 20 ID Succinate to cytochrome bo oxidase electron transfer RQ 0 EV GenProp1493; -- SN 21 ID Succinate to cytochrome bd oxidase electron transfer RQ 0 EV GenProp1515; -- SN 22 ID Formate to trimethylamine N-oxide electron transfer RQ 0 EV GenProp1535; -- SN 23 ID NADH to fumarate electron transfer RQ 0 EV GenProp1537; -- SN 24 ID Glycerol-3-phosphate to cytochrome bo oxidase electron transfer RQ 0 EV GenProp1563; -- SN 25 ID Hydrogen to trimethylamine N-oxide electron transfer RQ 0 EV GenProp1582; -- SN 26 ID NADH to cytochrome bd oxidase electron transfer I RQ 0 EV GenProp1608; -- SN 27 ID Aerobic respiration I (cytochrome c) RQ 0 EV GenProp1637; -- SN 28 ID NADH to cytochrome bo oxidase electron transfer II RQ 0 EV GenProp1641; -- SN 29 ID Hydrogen to fumarate electron transfer RQ 0 EV GenProp1672; -- SN 30 ID Glycerol-3-phosphate to hydrogen peroxide electron transport RQ 0 EV GenProp1729; -- SN 31 ID NADH to cytochrome bo oxidase electron transfer I RQ 0 EV GenProp1751; -- SN 32 ID Respiratory chain complex II RQ 0 EV GenProp1112; -- SN 33 ID Nitrate reductase A complex RQ 0 EV GenProp1122; -- SN 34 ID Formate dehydrogenase N complex RQ 0 EV GenProp1135; -- SN 35 ID Cytochrome bd-I ubiquinol oxidase complex RQ 0 EV GenProp1141; -- SN 36 ID Plasma membrane fumarate reductase complex RQ 0 EV GenProp1143; -- SN 37 ID DMSO reductase complex RQ 0 EV GenProp1148; -- SN 38 ID Respiratory chain complex I RQ 0 EV GenProp1198; -- SN 39 ID Cytochrome bd-II ubiquinol oxidase complex RQ 0 EV GenProp1202; // AC GenProp0132 DE Transcription termination/antitermination Nus factors TP SYSTEM AU Haft DH TH 1 RN [1] RM 16946247 RT Rho-dependent terminators and transcription termination. RA Ciampi MS; RL Microbiology. 2006;152:2515-2528. CC This Genome Property describes the set of Nus factors NusA, NusB, and CC NusG, as well as ribosomal protein S10 which is known as NusE. The name CC Nus, for N-utilization substance, reflects the phenomenology of CC exploitation of N factors for phage lambda in Escherichia coli. Much of CC the literature of these transcription termination/anti-termination CC factors revolves around the interaction with the transcription CC termination factor Rho, but factor Rho and cis-acting Rho-utilization CC sites are less well distributed than the N-factors, which are CC essentially universal in bacteria. In species with Rho, Nus factors CC improve transcriptase turnover speeds. Nus factors can block Rho CC action, a process called anti-termination [1]. See GenProp0812 for CC Rho-dependent transcription termination. -- SN 1 ID Transcription termination factor NusA DN Transcription termination factor NusA RQ 1 EV IPR010213; TIGR01953; sufficient; TG GO:0006353; -- SN 2 ID NusA C-terminal duplication RQ 0 EV IPR010214; TIGR01954; sufficient; -- SN 3 ID Transcription termination-antitermination factor NusB DN Transcription antitermination factor NusB RQ 1 EV IPR011605; TIGR01951; sufficient; TG GO:0006353; -- SN 4 ID Transcription termination-antitermination factor NusG DN Transcription antitermination protein NusG RQ 1 EV IPR001062; TIGR00922; sufficient; TG GO:0006353; EV IPR010216; TIGR01956; sufficient; -- SN 5 ID Ribosomal protein S10, rpsJ/nusE RQ 1 EV IPR001848; TIGR01049; sufficient; TG GO:0006353; // AC GenProp0133 DE Nucleic acid metabolism TP CATEGORY AU Haft DH TH 0 -- SN 1 ID DNA metabolism RQ 0 EV GenProp0116; -- SN 2 ID Transcription termination/antitermination Nus factors RQ 0 EV GenProp0132; -- SN 3 ID Nucleotide biosynthesis RQ 0 EV GenProp0185; -- SN 4 ID Nucleoside catabolism/utilization pathways RQ 0 EV GenProp0816; -- SN 5 ID Nucleotide catabolism/utilization pathways RQ 0 EV GenProp0817; -- SN 6 ID RNA metabolism RQ 0 EV GenProp0819; -- SN 7 ID Ribonucleotide reduction RQ 0 EV GenProp0287; -- SN 8 ID Nucleic acids processing RQ 0 EV GenProp1777; // AC GenProp0135 DE NADH dehydrogenase complex I TP SYSTEM AU Haft DH TH 3 DC Oxidative phosphorylation DR KEGG; map00190; CC Several multichain membrane complexes couple electron transfer CC involving NADH to ion transport. This property represents an NADH CC dehydrogenase termed complex I, whose individual subunits are CC designated A through N. The electron acceptor is a quinone, ubiquinone CC in most bacteria and in the related mitochondrial complex. -- SN 1 ID NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 DN NADH dehydrogenase I, A subunit/NuoA (EC 1.6.5.3) RQ 1 EV IPR000440; PF00507; sufficient; -- SN 2 ID NADH dehydrogenase I, B subunit DN NADH dehydrogenase I, B subunit/NuoB (EC 1.6.5.3) RQ 1 EV IPR006137; PF01058; sufficient; EV IPR006138; TIGR01957; sufficient; -- SN 3 ID NADH dehydrogenase I, C subunit DN NADH dehydrogenase I, C subunit/NuoC (EC 1.6.5.3) RQ 1 EV IPR001268; PF00329; sufficient; EV IPR010218; TIGR01961; sufficient; -- SN 4 ID NADH dehydrogenase I, D subunit DN NADH dehydrogenase I, D subunit/NuoD (EC 1.6.5.3) RQ 1 EV IPR001135; PF00346; sufficient; EV IPR022885; TIGR01962; sufficient; -- SN 5 ID NADH dehydrogenase I, E subunit DN NADH dehydrogenase I, E subunit/NuoE (EC 1.6.5.3) RQ 0 EV IPR002023; TIGR01958; sufficient; -- SN 6 ID NADH dehydrogenase I, F subunit DN NADH dehydrogenase I, F subunit/NuoF (EC 1.6.5.3) RQ 0 EV IPR011538; PF01512; sufficient; EV IPR011537; TIGR01959; sufficient; -- SN 7 ID NADH dehydrogenase I, G subunit DN NADH dehydrogenase I, G subunit/NuoG (EC 1.6.5.3) RQ 0 EV IPR010228; TIGR01973; sufficient; -- SN 8 ID NADH dehydrogenase I, H subunit DN NADH dehydrogenase I, H subunit/NuoH (EC 1.6.5.3) RQ 1 EV IPR001694; PF00146; sufficient; -- SN 9 ID NADH dehydrogenase I, I subunit DN NADH dehydrogenase I, I subunit/NuoI (EC 1.6.5.3) RQ 1 EV IPR010226; TIGR01971; sufficient; -- SN 10 ID NADH dehydrogenase I, J subunit DN NADH dehydrogenase I, J subunit/NuoJ (EC 1.6.5.3) RQ 1 EV IPR001457; PF00499; sufficient; -- SN 11 ID NADH dehydrogenase I, K subunit DN NADH dehydrogenase I, K subunit/NuoK (EC 1.6.5.3) RQ 1 EV IPR001133; PTHR11434; sufficient; -- SN 12 ID NADH dehydrogenase I, L subunit DN NADH dehydrogenase I, L subunit/NuoL (EC 1.6.5.3) RQ 1 EV IPR003945; TIGR01974; sufficient; -- SN 13 ID NADH dehydrogenase I, M subunit DN NADH dehydrogenase I, M subunit/NuoM (EC 1.6.5.3) RQ 1 EV IPR010227; TIGR01972; sufficient; -- SN 14 ID NADH dehydrogenase I, N subunit DN NADH dehydrogenase I, N subunit/NuoN (EC 1.6.5.3) RQ 1 EV IPR010096; TIGR01770; sufficient; // AC GenProp0136 DE Ubiquinone biosynthesis from chorismate, aerobic TP PATHWAY AU Haft DH TH 3 RN [1] RM 10419476 RT Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze RT both O-methyltransferase steps in coenzyme Q biosynthesis. RA Poon WW, Barkovich RJ, Hsu AY, Frankel A, Lee PT, Shepherd JN, Myles RA DC, Clarke CF; RL J Biol Chem. 1999;274(31):21665-72. RN [2] RM 23709220 RT ubiI, a new gene in Escherichia coli coenzyme Q biosynthesis, is RT involved in aerobic C5-hydroxylation. RA Hajj Chehade M, Loiseau L, Lombard M, Pecqueur L, Ismail A, Smadja RA M, Golinelli-Pimpaneau B, Mellot-Draznieks C, Hamelin O, Aussel L, RA Kieffer-Jaquinod S, Labessan N, Barras F, Fontecave M, Pierrel F; RL J Biol Chem. 2013;288(27):20085-20092. RN [3] RM 365223 RT Alternative hydroxylases for the aerobic and anaerobic biosynthesis of RT ubiquinone in Escherichia coli. RA Alexander K, Young IG; RL Biochemistry. 1978;17:4750-4755. RN [4] RM 11583838 RT Ubiquinone biosynthesis in microorganisms. RA Meganathan R; RL FEMS Microbiol Lett. 2001;203:131-139. DC Ubiquinone metabolism DR KEGG; map00130; DC Ubiquinol biosynthesis DR IUBMB; misc; ubiquinol; CC Ubiquinone (also known as coenzyme Q) is an electron and hydrogen CC transport cofactor important for aerobic respiration and photosynthesis. CC It is synthesized in bacteria from chorismate and polyprenyl CC pyrophosphates of varying lengths. The pathway is composed of 10 Ubi CC proteins which are named UbiA-I and UbiX. UbiG catalyses two CC O-methylation steps within the pathway, but with different substrates in CC each case [1]. UbiB is thought to be involved with the fourth step in the CC pathway, catalysed by UbiI [2], but is not included in the pathway CC diagrams. Knock-out of the three hydroxylation steps requiring molecular CC oxygen results in anaerobic synthesis of ubiquinone, indicating the CC presence of an alternative system [3]. In yeast and animals, a different CC pathway exists starting from 4-hydroxyphenylpyruvate, having latter steps CC in common with the bacterial pathway [4]. In addition to ubiquinone, CC bacteria may contain menaquinone and/or phylloquinone which together make CC up their quinone pool. -- SN 1 ID Chorismate-pyruvate lyase DN Chorismate lyase/UbiC (EC 4.1.3.40) RQ 0 EV IPR007440; PF04345; sufficient; -- SN 2 ID 4-hydroxybenzoate prenyltransferase DN 4-hydroxybenzoate prenyltransferase/UbiA (EC 2.5.1.39) RQ 1 EV IPR006371; TIGR01475; sufficient; TG GO:0006744; EV IPR006370; TIGR01474; sufficient; TG GO:0006744; -- SN 3 ID 3-prenyl-4-hydroxybenzoate decarboxylase DN 3-octyprenyl-4-hydroxybenzoate decarboxylase/UbiD/X (EC 4.1.1.98) RQ 1 EV IPR002830; PF01977; sufficient; TG GO:0006744; EV IPR004507; TIGR00421; sufficient; TG GO:0006744; -- SN 4 ID Probable protein kinase UbiB DN Probable protein kinase UbiB (EC 2.7.-.-) RQ 1 EV IPR010232; TIGR01982; sufficient; TG GO:0006744; -- SN 5 ID 3-demethylubiquinone-9 3-methyltransferase DN 3-demethylubiquinone-9 3-methyltransferase/UbiG (EC 2.1.1.222/EC 2.1.1.64) RQ 1 EV IPR010233; TIGR01983; sufficient; TG GO:0006744; -- SN 6 ID Ubiquinone biosynthesis 4-, 5- and 6-hydroxylases DN UbiF/H/I RQ 1 EV IPR010971; TIGR01988; sufficient; TG GO:0006744; EV IPR011566; PF03232; sufficient; TG GO:0006744; -- SN 7 ID Ubiquinone biosynthesis C-methyltransferase DN Ubiquinone biocynthesis C-methyltransferase/UbiE (EC 2.1.1.201) RQ 1 EV IPR004033; TIGR01934; sufficient; // AC GenProp0137 DE Iron-sulfur cluster assembly SUF system TP SYSTEM AU Haft DH TH 1 RN [1] RM 12089140 RT A third bacterial system for the assembly of iron-sulfur clusters with RT homologs in archaea and plastids. RA Takahashi Y, Tokumoto U; RL J Biol Chem. 2002;277:28380-28383. RN [2] RM 12876288 RT Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE RT form a new type of cysteine desulfurase. RA Loiseau L, Ollagnier-de-Choudens S, Nachin L, Fontecave M, Barras F; RL J Biol Chem. 2003;278:38352-38359. RN [3] RM 12554644 RT SufC: an unorthodox cytoplasmic ABC/ATPase required for [Fe-S] RT biogenesis under oxidative stress. RA Nachin L, Loiseau L, Expert D, Barras F; RL EMBO J. 2003;22:427-437. CC The iron-sulfur cluster assembly SUF system is one of three iron-sulfur CC assembly systems present in a wide range of bacteria, archeae, and CC plastids. The other two mechanisms for iron-sulfur cluster assembly are CC the ISC (iron-sulfur cluster) system, composed of at least six CC components and found broadly distributed from bacteria to higher CC eukaryotes, and the NIF (nitrogen fixation) system, which is required CC for nitrogenase maturation [1]. The SUF (mobilization of sulfur) system CC is composed of a six gene cluster with protein complexes responsible CC for cysteine desulfuration of sulfur atoms from cysteine, cytosolic CC ATPase activity, and a protein scaffold for iron and sulfur cluster CC assembly and transfer to protein targets [2]. Operational under CC stressful growth conditions, such as iron limitation and oxidative CC stress, the SUF system has been shown to be an important factor for CC bacterial pathogenicity [3]. -- SN 1 ID Iron-sulfur cluster assembly scaffold SufA RQ 0 EV IPR011298; TIGR01997; sufficient; TG GO:0016226; -- SN 2 ID FeS assembly protein SufB DN FeS assembly protein SufB RQ 1 EV IPR010231; TIGR01980; sufficient; TG GO:0016226; -- SN 3 ID Cytosolic ATPase SufC DN FeS assembly ATPase SufC RQ 1 EV IPR010230; TIGR01978; sufficient; TG GO:0016226; -- SN 4 ID FeS assembly protein SufD DN FeS assembly protein SufD RQ 1 EV IPR011542; TIGR01981; sufficient; TG GO:0016226; -- SN 5 ID Cysteine desulfurase auxiliary chain SufE RQ 0 EV IPR003808; PF02657; sufficient; TG GO:0016226; -- SN 6 ID Transcriptional regulatory SufR RQ 0 EV IPR014075; TIGR02702; sufficient; TG GO:0016226; EV IPR014290; TIGR02944; sufficient; TG GO:0016226; -- SN 7 ID Cysteine desulfurases, SufS subfamily DN Cysteine desulfurase SufS RQ 1 EV IPR010970; TIGR01979; sufficient; -- SN 8 ID Proteobacterial novel SUF protein SufT RQ 0 EV IPR014291; TIGR02945; sufficient; TG GO:0016226; EV IPR017776; TIGR03406; TG GO:0016226; // AC GenProp0138 DE Iron-sulfur cluster assembly iscSUA-hscBA-fdx system TP SYSTEM AU Haft DH TH 0 RN [1] RM 12089140 RT A third bacterial system for the assembly of iron-sulfur clusters with RT homologs in archaea and plastids. RA Takahashi Y, Tokumoto U; RL J Biol Chem. 2002;277:28380-28383. CC At least three different systems have been described for 2Fe-2S cluster CC assembly. The NIF system provides an iron-sulfur cluster to nitrogenase CC in certain nitrogen-fixing species. SUF, described the most recently, CC can operate despite aerobic stress. This property describes the ISC CC system as found in E. coli and many other proteobacteria, containing at CC least the following elements: a characteristic cysteine desulfurase CC IscS, a characteristic ferredoxin, chaperones called heat shock cognate CC proteins A and B, and an assembly scaffold protein resembling the CC N terminus of the scaffold protein of the NIF system [1]. -- SN 1 ID FeS assembly iron donor CyaY DN FeS assembly iron donor CyaY RQ 1 EV IPR002908; TIGR03421; TG GO:0016226; -- SN 2 ID FeS assembly chaperone HscA DN FeS assembly chaperone HscA RQ 1 EV IPR010236; TIGR01991; sufficient; TG GO:0016226; -- SN 3 ID FeS assembly chaperone HscB RQ 1 EV IPR004640; TIGR00714; sufficient; TG GO:0016226; -- SN 4 ID FeS assembly protein IscA DN Iron-sulfur cluster assembly protein IscA RQ 1 EV IPR011302; TIGR02011; sufficient; TG GO:0016226; -- SN 5 ID Iron-sulfur cluster assembly transcription factor IscR DN Iron-sulfur cluster assembly transcription factor IscR RQ 1 EV IPR010242; TIGR02010; sufficient; -- SN 6 ID Cysteine desulfurase RQ 1 EV IPR010240; TIGR02006; sufficient; TG GO:0016226; -- SN 7 ID Iron-sulfur cluster assembly scaffold DN FeS cluster assembly scaffold IscU RQ 1 EV IPR011339; TIGR01999; sufficient; TG GO:0016226; -- SN 8 ID FeS assembly protein IscX/YfhJ RQ 0 EV IPR007479; TIGR03412; TG GO:0016226; -- SN 9 ID Isc-system ferredoxin DN Ferredoxin, 2Fe-2S type, ISC system RQ 1 EV IPR011536; TIGR02007; sufficient; TG GO:0016226; // AC GenProp0139 DE Degradation of tyrosine via homogentisate TP PATHWAY AU Haft DH, Richardson L. TH 0 RN [1] RM 15262943 RT The homogentisate pathway: a central catabolic pathway involved in the RT degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate RT in Pseudomonas putida. RA Arias-Barrau E, Olivera ER, Luengo JM, Fernández C, Galán B, García RA JL, Díaz E, Miñambres B; RL J Bacteriol. 2004;186(15):5062-5077. DC Tyrosine metabolism DR KEGG; map00350; CC Tyrosine is degraded to produce fumarate and acetoacetate via the CC intermediate homogentisate, in a five-step pathway. Tyrosine is CC converted to 4-hydroxyphenylpyruvate by TyrB (tyrosine transaminase CC also known as tyrosine aminotransferase or PhhC) and then to CC homogentisate by Hpd (4-hydroxyphenylpyruvate dioxygenase). The second CC part of the pathway (the catabolism of homogentisate) involves three CC enzymes: HmgA (homogentisate dioxygenase); HmgB (fumarylacetoacetate CC hydrolase, also known as Fah); and HmgC (maleylacetoacetate isomerase, CC also known as Mai) [1]. -- SN 1 ID Tyrosine transaminase DN Tyrosine transaminase/TyrB (EC 2.6.1.5) RQ 0 EV IPR005957; TIGR01264; sufficient; TG GO:0019445; -- SN 2 ID 4-hydroxyphenylpyruvate dioxygenase DN 4-hydroxyphenylpyruvate dioxygenase/Hpd (EC 1.13.11.27) RQ 1 EV IPR005956; TIGR01263; sufficient; TG GO:0019445; -- SN 3 ID Homogentisate 1,2-dioxygenase DN Homogentisate 1,2-dioxygenase/HmgA (EC 1.13.11.5) RQ 1 EV IPR005708; TIGR01015; sufficient; TG GO:0019445; EV IPR005708; PF04209; sufficient; TG GO:0019445; -- SN 4 ID Maleylacetoacetate isomerase DN Maleylacetoacetate isomerase/Mai (EC 5.2.1.2) RQ 1 EV IPR005955; TIGR01262; sufficient; TG GO:0019445; -- SN 5 ID Fumarylacetoacetase DN Fumarylacetoacetase/Fah (EC 3.7.1.2) RQ 1 EV IPR005959; TIGR01266; sufficient; TG GO:0019445; EV IPR011234; PF01557; TG GO:0019445; // AC GenProp0140 DE Iron-sulfur cluster assembly systems TP CATEGORY AU Haft DH TH 0 CC At least three different systems have been described for iron cluster CC assembly, the NIF system provides clusters to nitrogenase, the ISC CC system may provide both 2Fe-2S and 4Fe-4S clusters for various enzymes CC in Proteobacteria and the SUF system is capable of functioning in the CC presence of oxidative stress. -- SN 1 ID Iron-sulfur cluster assembly SUF system RQ 0 EV GenProp0137; -- SN 2 ID Iron-sulfur cluster assembly iscSUA-hscBA-fdx system RQ 0 EV GenProp0138; -- SN 3 ID Iron-sulfur cluster assembly CsdA-CsdE system RQ 0 EV GenProp0739; -- SN 4 ID Iron-sulfur cluster assembly NIF system RQ 0 EV GenProp0742; -- SN 5 ID SufBCD complex RQ 0 EV GenProp1192; // AC GenProp0141 DE Galactose-6-phosphate degradation via tagatose-6-phosphate TP PATHWAY AU Haft DH TH 1 RN 1 RM 1901863 RT Molecular cloning, characterization, and nucleotide sequence of the RT tagatose 6-phosphate pathway gene cluster of the lactose operon of RT Lactococcus lactis. RA van Rooijen RJ, van Schalkwijk S, de Vos WM; RL J Biol Chem. 1991;266(11):7176-7181. DC Galactose metabolism DR KEGG; map00052; DC Lactose and galactose degradation I DR MetaCyc; LACTOSECAT-PWY; CC Galactose-6-phosphate is degraded via the tagatose-6-phosphate pathway, CC which is a 3 step pathway encoded by the lacABCD gene cluster of the CC lactose-PTS (lactose phosphotransferase) operon. The three enzymes in CC the pathway are galactose-6-phosphate isomerase (this requires both CC LacA and LacB subunits for activity), tagatose-6-phosphate kinase CC (LacC), and tagatose 1,6-diphosphate aldolase (LacD)[1]. -- SN 1 ID Galactose-6-phosphate isomerase, LacA subunit DN Galactose-6-phosphate isomerase, LacA subunit (EC 5.3.1.26) RQ 1 EV IPR004783; TIGR01118; sufficient; TG GO:0019320; -- SN 2 ID Galactose-6-phosphate isomerase, LacB subunit DN Galactose-6-phosphate isomerase, LacB subunit (EC 5.3.1.26) RQ 1 EV IPR004784; TIGR01119; sufficient; TG GO:0019320; -- SN 3 ID Tagatose-6-phosphate kinase DN Tagatose-6-phosphate kinase/LacC (EC 2.7.1.144) RQ 1 EV IPR005926; TIGR01231; sufficient; TG GO:0019320; -- SN 4 ID Tagatose 1,6-diphosphate aldolase DN Tagatose 1,6-diphosphate aldolase/LacD (EC 4.1.2.40) RQ 1 EV IPR005927; TIGR01232; sufficient; TG GO:0019320; // AC GenProp0142 DE Catabolism TP CATEGORY AU Haft DH TH 0 CC Any metabolic process involving the breakdown of complex substances CC into smaller products, including the breakdown of carbon compounds with CC the liberation of energy for use by the cell or organism. -- SN 1 ID Polyhydroxyalkanoic acids RQ 0 EV GenProp0055; -- SN 2 ID Galactose-6-phosphate degradation via tagatose-6-phosphate RQ 0 EV GenProp0141; -- SN 3 ID Cyanophycin-like storage polymers RQ 0 EV GenProp0156; -- SN 4 ID Glycogen system RQ 0 EV GenProp0168; -- SN 5 ID 4-hydroxyphenylacetate degradation RQ 0 EV GenProp0231; -- SN 6 ID 2-aminoethylphosphonate catabolism to acetaldehyde RQ 0 EV GenProp0238; -- SN 7 ID Propionyl-CoA catabolism RQ 0 EV GenProp0239; -- SN 8 ID Amino acid catabolism RQ 0 EV GenProp0734; -- SN 9 ID GABA utilization RQ 0 EV GenProp0233; -- SN 10 ID Phosphonate catabolism RQ 0 EV GenProp0241; -- SN 11 ID Trehalose utilization RQ 0 EV GenProp0271; -- SN 12 ID Pyruvate fermentation to acetoin RQ 0 EV GenProp0272; -- SN 13 ID Protocatechuate degradation to beta-ketoadipate RQ 0 EV GenProp0273; -- SN 14 ID Beta-ketoadipate degradation to succinyl-CoA and acetyl-CoA RQ 0 EV GenProp0283; -- SN 15 ID Ethanolamine degradation proteinaceous organelle RQ 0 EV GenProp0294; -- SN 16 ID Rhamnose catabolism RQ 0 EV GenProp0457; -- SN 17 ID Fucose catabolism RQ 0 EV GenProp0458; -- SN 18 ID Ectoine catabolism RQ 0 EV GenProp0653; -- SN 19 ID Malonate decarboxylase RQ 0 EV GenProp0674; -- SN 20 ID Allantoin catabolism to glyoxalate and urea RQ 0 EV GenProp0686; -- SN 21 ID Allantoin catabolism to oxamate and carbamoyl-phosphate RQ 0 EV GenProp0687; -- SN 22 ID Urate catabolism to allantoin RQ 0 EV GenProp0688; -- SN 23 ID Glycolysis RQ 0 EV GenProp0691; -- SN 24 ID Fructose utilization as fructose-1,6-bisphosphate RQ 0 EV GenProp0693; -- SN 25 ID Glucose utilization as fructose-1,6-bisphosphate RQ 0 EV GenProp0694; -- SN 26 ID Purine catabolism via urate, xanthine and allantoin RQ 0 EV GenProp0700; -- SN 27 ID Benzoyl-CoA reductase RQ 0 EV GenProp0702; -- SN 28 ID 4-hydroxybenzoyl-CoA reductase RQ 0 EV GenProp0703; -- SN 29 ID Cyclohexa-1,5-diene-1-carbonyl-CoA to 3-hydroxypimelyl-CoA, dch/had/oah Pathway RQ 0 EV GenProp0706; -- SN 30 ID Catechol meta-cleavage pathway RQ 0 EV GenProp0708; -- SN 31 ID Benzoate catabolism BoxABC pathway RQ 0 EV GenProp0709; -- SN 32 ID Galactarate utilization via tartronate semi-aldehyde RQ 0 EV GenProp0714; -- SN 33 ID Galactarate utilization via 2-oxoglutarate semialdehyde RQ 0 EV GenProp0715; -- SN 34 ID Glucarate utilization via tartronate semi-aldehyde RQ 0 EV GenProp0716; -- SN 35 ID Glucarate utilization via 2-oxoglutarate semialdehyde RQ 0 EV GenProp0717; -- SN 36 ID Oxalate degradation RQ 0 EV GenProp0718; -- SN 37 ID Choline sulfate utilization RQ 0 EV GenProp0749; -- SN 38 ID Encapsulin proteinaceous organelle RQ 0 EV GenProp0810; -- SN 39 ID Pyrimidine utilization RQ 0 EV GenProp0813; -- SN 40 ID Quinohemoprotein amine dehydrogenase RQ 0 EV GenProp0902; -- SN 41 ID Myo-inositol catabolism RQ 0 EV GenProp1071; -- SN 42 ID Cyanase system RQ 0 EV GenProp1072; -- SN 43 ID Choline TMA-lyase system RQ 0 EV GenProp1076; -- SN 44 ID Ethanolamine degradation organelle RQ 0 EV GenProp0292; -- SN 45 ID Catechol ortho-cleavage upper pathway RQ 0 EV GenProp0711; -- SN 46 ID Proposed phosphonate catabolism pathway HpnWXZ RQ 0 EV GenProp0736; -- SN 47 ID Alcohols degradation RQ 0 EV GenProp1768; -- SN 48 ID Amines and polyamines catabolism RQ 0 EV GenProp1769; -- SN 49 ID L-lactaldehyde degradation (aerobic) RQ 0 EV GenProp1662; -- SN 50 ID Methylglyoxal degradation III RQ 0 EV GenProp1263; -- SN 51 ID Methylglyoxal degradation I RQ 0 EV GenProp1578; -- SN 52 ID 3-Phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation to 2-hydroxypentadienoate RQ 0 EV GenProp1287; -- SN 53 ID Cinnamate and 3-hydroxycinnamate degradation to 2-hydroxypentadienoate RQ 0 EV GenProp1458; -- SN 54 ID Urate conversion to allantoin I RQ 0 EV GenProp1652; -- SN 55 ID CO2 fixation into oxaloacetate (anaplerotic) RQ 0 EV GenProp1669; -- SN 56 ID Formate assimilation into 5,10-methylenetetrahydrofolate RQ 0 EV GenProp1613; -- SN 57 ID Heme degradation I RQ 0 EV GenProp1591; -- SN 58 ID Heme degradation VII RQ 0 EV GenProp1688; -- SN 59 ID Glutathione degradation (DUG pathway - yeast) RQ 0 EV GenProp1346; -- SN 60 ID Alkylnitronates degradation RQ 0 EV GenProp1746; -- SN 61 ID Muropeptide degradation RQ 0 EV GenProp1242; -- SN 62 ID Carbohydrates degradation RQ 0 EV GenProp1770; -- SN 63 ID Fatty acid degradation RQ 0 EV GenProp1772; -- SN 64 ID Lipid degradation RQ 0 EV GenProp1773; -- SN 65 ID Secondary metabolites degradation RQ 0 EV GenProp1775; -- SN 66 ID Nucleosides and nucleotides degradation RQ 0 EV GenProp1776; -- SN 67 ID p-aminobenzoyl-glutamate hydrolase RQ 0 EV GenProp1119; -- SN 68 ID Ethanolamine ammonia-lyase complex RQ 0 EV GenProp1167; -- SN 69 ID Carboxylates degradation RQ 0 EV GenProp1771; // AC GenProp0143 DE Leloir pathway (galactose/glucose interconversion) TP PATHWAY AU Haft DH TH 0 DC Galactose metabolism DR KEGG; map00052; CC The Leloir pathway can interconvert galactose and glucose, often for CC galactose degradation. It tends to be found in the Firmicutes. It CC includes aldose 1-epimerase, galactokinase, galactose-1-P CC uridylyltransferase, and UDP-galactose 4-epimerase. -- SN 1 ID Aldose 1-epimerase (mutarotase) DN Aldose 1-epimerase (EC 5.1.3.3) RQ 1 EV IPR013458; TIGR02636; sufficient; -- SN 2 ID Galactokinase DN Galactokinase (EC 2.7.1.6) RQ 1 EV IPR000705; TIGR00131; sufficient; -- SN 3 ID Galactose-1-phosphate uridylyltransferase DN Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) RQ 1 EV IPR001937; TIGR00209; sufficient; EV IPR000766; TIGR01239; sufficient; -- SN 4 ID UDP-glucose 4-epimerase DN UDP-glucose 4-epimerase (EC 5.1.3.2) RQ 1 EV IPR005886; TIGR01179; sufficient; // AC GenProp0144 DE Chlorophyllide a biosynthesis from protoporphyrin IX TP METAPATH AU Haft DH, Richardson L; TH 1 RN [1] RM 17370354 RT Recent advances in chlorophyll biosynthesis. RA Bollivar DW; RL Photosynth Res. 2006;90(2):173-194. DC Heme and Chlorophyll Biosynthesis DR IUBMB; tetrapyr; porphyrin3; DC Chlorophyll Biosynthesis (earlier stages) DR IUBMB; tetrapyr; porphyrin4; DC Chlorophyll Biosynthesis (later stages) DR IUBMB; tetrapyr; porphyrin5; DC Pathway: 3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, DC light-dependent) DR MetaCyc; CHLOROPHYLL-SYN; DC Pathway: 3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light DC independent) DR MetaCyc; PWY-7159; CC Chlorophyllide a is synthesised from protoporphyrin IX as part of the CC chlorophyll biosynthesis pathway. There is an aerobic and an anaerobic CC branch, this property represnts the aerobic branch. The first step CC (Mg-chelatase) has been shown to require three subunits encoded by CC three different genes. The final two steps in this pathway (vinyl CC reductase and protochlorophyllide reductase) can occur in the CC alternate order from that shown. There are two different enzymes that CC can catalyse the final (protochlorophyllide reductase) step; CC light-dependent protochlorophyllide reductase, and light-independent CC protochlorophyllide reductase. Despite catalyzing the same reaction, CC the two enzymes are very different [1]. -- SN 1 ID Mg-chelatase, ChlD-subunit DN Magnesium-chelatase subunit ChlD (EC 6.6.1.1) RQ 1 EV IPR011776; TIGR02031; sufficient; TG GO:0015995; -- SN 2 ID Mg-chelatase, ChlH-subunit DN Magnesium-chelatase subunit ChlH (EC 6.6.1.1) RQ 1 EV IPR011771; TIGR02025; sufficient; TG GO:0015995; -- SN 3 ID Mg-chelatase, ChlI-subunit DN Magnesium-chelatase subunit ChlI (EC 6.6.1.1) RQ 1 EV IPR011775; TIGR02030; sufficient; TG GO:0015995; -- SN 4 ID Magnesium protoporphyrin IX methyltransferase DN Magnesium protoporphyrin IX methyltransferase (EC 2.1.1.11) RQ 1 EV IPR010251; TIGR02021; sufficient; TG GO:0015995; -- SN 5 ID Magnesium protoporphyrin IX monomethylester oxidative cyclase DN Magnesium protoporphyrin IX monomethylester oxidative cyclase (EC 1.14.13.81) RQ 1 EV IPR011772; TIGR02026; sufficient; TG GO:0015995; EV IPR008434; TIGR02029; sufficient; TG GO:0015995; -- SN 6 ID Magnesium-2,4-divinylpheoporphyrin a5-monomethyl ester vinyl reductase DN 3,8-divinyl protochlorophyllide a 8-vinyl-reductase RQ 0 EV IPR010249; TIGR02019; sufficient; TG GO:0015995; -- SN 7 ID Protochlorophyllide reductase DN Protochlorophyllide reductase (EC 1.3.1.33) RQ 1 EV IPR005979; TIGR01289; sufficient; TG GO:0015995; EV GenProp1004; TG GO:0015995; // AC GenProp0146 DE Bacteriochlorophyll biosynthesis from chlorophyllide a TP PATHWAY AU Haft DH TH 2 RN [1] RM 17370354 RT Recent advances in chlorophyll biosynthesis. RA Bollivar DW; RL Photosynth Res. 2006;90(2):173-194. DC Bacteriochlorophyll a biosynthesis DR MetaCyc; PWY-5526; CC Chlorophyllide a is the common branchpoint of the chlorophyll and CC bacteriochlorophyll biosynthetic pathways. This Genome Property CC describes the pathway beyond this branchpoint, which ultimately CC produces bacteriochlorophyll a. Three of the steps in the pathway CC (chlorophyllide reductase, bacteriochlorophyllide a dehydrogenase CC and bacteriochlorophyllide hydratase) can act in multiple orders CC producing different intermediates [1]. -- SN 1 ID 2-vinyl bacteriochlorophyllide hydratase DN 2-vinyl bacteriochlorophyllide hydratase/BchF (EC:4.2.1.-) RQ 1 EV IPR009905; TIGR02020; sufficient; TG GO:0030494; -- SN 2 ID Bacteriochlorophyllide reductase iron protein subunit X DN Chlorophyllide reductase iron protein subunit X/BchX (EC:1.18.6.1) RQ 1 EV IPR010246; TIGR02016; sufficient; TG GO:0030494; -- SN 3 ID Bacteriochlorophyllide reductase subunit Y DN Chlorophyllide reductase subunit Y/BchY (EC:1.18.1.-) RQ 1 EV IPR010245; TIGR02015; sufficient; TG GO:0030494; -- SN 4 ID Bacteriochlorophyllide reductase subunit Z DN Chlorophyllide reductase subunit Z/BchZ (EC:1.18.-.-) RQ 1 EV IPR010244; TIGR02014; sufficient; TG GO:0030494; -- SN 5 ID 2-alpha-hydroxyethylbacteriochlorophyllide reductase DN 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase/BchC (EC:1.-.-.-) RQ 1 EV IPR005903; TIGR01202; sufficient; TG GO:0030494; -- SN 6 ID Geranyl geranyl bacteriochlorophyll synthetase DN Bacteriochlorophyll/chlorophyll a synthase/BchG (EC:2.5.1.-) RQ 1 EV IPR006372; TIGR01476; sufficient; TG GO:0030494; -- SN 7 ID Geranyl geranyl bacteriochlorophyll reductase DN Geranylgeranyl reductase/BchP (EC:1.3.1.-) RQ 1 EV IPR010253; TIGR02023; sufficient; TG GO:0030494; // AC GenProp0147 DE Glycine betaine biosynthesis from choline TP PATHWAY AU Haft DH TH 0 RN [1] RM 1741624 RT Prokaryotic osmoregulation: genetics and physiology. RA Csonka LN, Hanson AD; RL Annu Rev Microbiol. 1991;45:569-606. RN [2] RM 3065456 RT Molecular cloning, physical mapping and expression of the bet genes RT governing the osmoregulatory choline-glycine betaine pathway of RT Escherichia coli. RA Andresen PA, Kaasen I, Styrvold OB, Boulnois G, Strøm AR; RL J Gen Microbiol. 1988;134:1737-1746. RN [3] RM 8752328 RT Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: RT characterization of the gbsAB genes. RA Boch J, Kempf B, Schmid R, Bremer E; RL J Bacteriol. 1996;178:5121-5129. DC Glycine, serine and threonine metabolism DR KEGG; map00260; DC Glycine betaine biosynthesis I (Gram-negative bacteria) DR MetaCyc; BETSYN-PWY; DC Glycine betaine biosynthesis II (Gram-positive bacteria) DR MetaCyc; PWY-3722; CC As a coping mechanism against osmotic stress, prokaryotic organisms CC accumulate osmolytes or osmoprotectants from exogenous sources, to CC counterbalance elevated osmolarities in the environment without CC affecting overall cell metabolism and structural integrity. One of CC the most efficient osmoprotectants found in the environment is the CC compound glycine betaine [1]. Both gram positive and gram negative CC bacteria mediate osmotolerance either by direct uptake of glycine CC betaine from the environment, or by synthesis from exogenously supplied CC choline [2,3]. This genome property refers to the biosynthesis of the CC osmoprotectant glycine betaine from choline. Biosynthesis of CC glycine betaine occurs via a two-step oxidative reaction requiring a CC terminal electron acceptor. Choline dehydrogenase first catalyzes CC the conversion of exogenously supplied choline into the intermediate CC glycine betaine aldehyde, with subsequent oxidization by betaine CC aldehyde dehydrogenase into the osmoprotectant glycine betaine. Both CC choline dehydrogenase and betaine aldehyde dehydrogenase are required CC for conversion of choline into glycine betaine [2,3]. -- SN 1 ID Choline dehydrogenase DN Choline dehydrogenase/BetA (EC 1.1.99.1) RQ 1 EV IPR011533; TIGR01810; sufficient; TG GO:0019285; -- SN 2 ID Glycine betaine dehydrogenase DN Betaine aldehyde dehydrogenase/BetB (EC 1.2.1.8) RQ 1 EV IPR011264; TIGR01804; sufficient; TG GO:0019285; -- SN 3 ID Choline-responsive transcriptional repressor BetI RQ 0 EV IPR017757; TIGR03384; TG GO:0019285; // AC GenProp0150 DE Chlorophyll biosynthesis from chlorophyllide a TP PATHWAY AU Haft DH TH 0 RN [1] RM 17370354 RT Recent advances in chlorophyll biosynthesis. RA Bollivar DW; RL Photosynth Res. 2006;90(2):173-194. DC Chlorophyll Biosynthesis (later stages) DR IUBMB; tetrapyr; porphyrin5; CC Chlorophyll is formed directly from chlorophyllide a by the addition of CC a phytyl side chain, or by addition of a geranylgeranyl side chain and CC subsequent reduction of the side chain. The synthetase and reductase CC responsible for this conversion are closely related to the enzymes CC which carry out the analagous steps of bacteriochlorophyll biosynthesis CC [1]. -- SN 1 ID Chlorophyll synthase DN Clorophyll synthase ChlG (EC 2.5.1.62) RQ 1 EV IPR011799; TIGR02056; sufficient; TG GO:0015995; -- SN 2 ID Geranylgeranyl reductase DN Geranylgeranyl reductase ChlP RQ 1 EV IPR011774; TIGR02028; sufficient; TG GO:0015995; // AC GenProp0151 DE Resistance to mercury TP SYSTEM AU Haft DH TH 1 RN [1] RM 12917805 RT Operon mer: bacterial resistance to mercury and potential for RT bioremediation of contaminated environments. RA Nascimento AM, Chartone-Souza E; RL Genet Mol Res. 2003;2:92-101. CC Detoxification of inorganic and organic mercury compounds involves the CC enzymatic reduction of extracellular mercuric ions or organomercurials CC into less-toxic metallic mercury, which is released into the cytoplasm CC and then volatilizes from the cell. Mercuric ions diffuse across the CC outer membrane by a mer transport system, which binds and transfers CC mercury ions via a pair of cysteine residues to the active site of a CC mercuric reductase. Alternatively, an organomercurial lyase is required CC for hydrolysis of the carbon-mercury bond of organomercurial compounds CC before reduction proceeds. Transcribed separately and divergently, a CC mercury-sensitive transcriptional activator both positively and CC negatively regulates mer expression, while a co-transcribed secondary CC regulatory protein down-regulates this mer operon. This resistance CC system, often encoded on plasmids and transferred via transposons, is CC found in both gram-positive and gram-negative bacteria [1]. -- SN 1 ID Mercuric reductase DN Mercuric reductase (EC 1.16.1.1) RQ 1 EV IPR021179; TIGR02053; sufficient; TG GO:0050787; -- SN 2 ID Organomercurial lyase DN Alkylmercury lyase (EC 4.99.1.2) RQ 0 EV IPR004927; PF03243; sufficient; TG GO:0046689; -- SN 3 ID Mercury transporter, MerC DN Mercuric resistance protein MerC RQ 1 EV IPR004891; PF03203; sufficient; TG GO:0046689; -- SN 4 ID Transcriptional co-regulator, MerD DN Mercuric resistance transcriptional repressor MerD RQ 1 EV IPR011797; TIGR02054; sufficient; TG GO:0046689; -- SN 5 ID Periplasmic mercury binding protein, MerP DN Mercuric transport protein periplasmic component MerP RQ 1 EV IPR011795; TIGR02052; sufficient; TG GO:0050787; -- SN 6 ID Mercury responsive transcriptional activator DN Mercuric-responsive transcriptional activator MerR RQ 1 EV IPR011794; TIGR02051; sufficient; TG GO:0046689; -- SN 7 ID Mercury transporter, MerT DN Mercuric transport protein MerT RQ 1 EV IPR003457; PF02411; sufficient; TG GO:0046689; // AC GenProp0155 DE Dissimilatory sulfate reduction TP PATHWAY AU Haft DH TH 2 RN [1] RM 9308173 RT Towards the phylogeny of APS reductases and sirohaem sulfite reductases RT in sulfate-reducing and sulfur-oxidizing prokaryotes. RA Hipp WM, Pott AS, Thum-Schmitz N, Faath I, Dahl C, Trüper HG; RL Microbiology. 1997;143 ( Pt 9):2891-2902. DC Sulfur metabolism DR KEGG; map00920; DC Dissimilatory sulfate reduction DR MetaCyc; DISSULFRED-PWY; CC During anaerobic respiration, sulfate reducing bacteria catalyze the CC six electron reduction of sulfate to hydrogen sulfide. These sulfate CC reducers comprise both gram-positive and gram-negative bacteria, as CC well as archeae [1]. Sulfur oxidizing bacterium, such as Chromatium CC vinosum, can reversibly catalyze this pathway freeing electrons and CC ATP. -- SN 1 ID Sulfate adenylyltransferase DN Sulfate adenylyltransferase (EC 2.7.7.4) RQ 1 EV IPR002650; TIGR00339; sufficient; TG GO:0019419; -- SN 2 ID Adenylylsulfate reductase, alpha subunit DN Adenylyl-sulfate reductase, subunit A (EC 1.8.99.2) RQ 1 EV IPR011803; TIGR02061; sufficient; TG GO:0019419; -- SN 3 ID Adenylylsulfate reductase, beta subunit DN Adenylyl-sulfate reductase, subunit B (EC 1.8.99.2) RQ 1 EV IPR011802; TIGR02060; sufficient; TG GO:0019419; -- SN 4 ID Sulfite reductase, dissimilatory-type alpha subunit DN Hydrogensulfite reductase, alpha subunit (EC 1.8.99.5) RQ 1 EV IPR011806; TIGR02064; sufficient; TG GO:0019419; -- SN 5 ID Sulfite reductase, dissimilatory-type beta subunit DN Hydrogensulfite reductase, beta subunit (EC 1.8.99.5) RQ 1 EV IPR011808; TIGR02066; sufficient; TG GO:0019419; // AC GenProp0156 DE Cyanophycin-like storage polymers TP SYSTEM AU Haft DH TH 0 CC Cyanophycin is a characteristically Cyanobacterial storage polymer for CC nitrogen, carbon, and energy. It is made by cyanophycin synthetase and CC degraded by cyanophycinase. Cyanophycinase is also found in an CC extracellular form by some species that can utilize exogenous CC cyanophycin. The polymer has a backbone of L-aspartic acid residues CC (Asp), with the side chain COOH linked to the NH2 of arginine (Arg) CC residues. The native cyanobacterial form is insoluble, while CC heterogenously expressed cyanophycin synthetases in E. coli may produce CC a soluble form with some level of Lys substituting for Arg. This CC polymer is analogous to polyhydroxyalkanoic acid biosynthesis systems CC with which it sometimes co-occurs. -- SN 1 ID Cyanophycin synthetase DN Cyanophycin synthase (EC:6.3.2.29/EC:6.3.2.30) RQ 1 EV IPR011810; TIGR02068; sufficient; TG GO:0006112; -- SN 2 ID Cyanophycinase DN Cyanophycinase (EC:3.4.15.6) RQ 1 EV IPR011811; TIGR02069; sufficient; TG GO:0006112; // AC GenProp0157 DE Storage polymer systems TP CATEGORY AU Haft DH TH 0 CC These polymers of various monomer units are used as storage for energy, CC carbon and/or nitrogen. Sometimes these polymers are observed as CC granular inclusions within the cell. These systems may include enzymes CC for the biosynthesis and degradation of the polymer, regulatory CC components as well as proteins associated with the granule surface. -- SN 1 ID Polyhydroxyalkanoic acids RQ 0 EV GenProp0055; -- SN 2 ID Cyanophycin-like storage polymers RQ 0 EV GenProp0156; -- SN 3 ID Glycogen system RQ 0 EV GenProp0168; -- SN 4 ID Polyphosphate kinase/exopolyphosphatase system RQ 0 EV GenProp0840; // AC GenProp0159 DE Threonine biosynthesis from aspartate semialdehyde TP PATHWAY AU Haft DH TH 0 DC Threonine Biosynthesis DR IUBMB; AminoAcid; Thr; DC Glycine, serine and threonine metabolism DR KEGG; map00260; DC Superpathway of L-threonine biosynthesis DR MetaCyc; THRESYN-PWY; CC Threonine is synthesised from aspartate semialdehyde, a branch point CC intermediate in the synthesis of lysine. The aspartate semialdehyde is CC derived from aspartate, which in turn is derived from the Krebs cycle CC intermediate oxaloacetate. Homoserine, an intermediate in this pathway CC is a branchpoint for the biosynthesis of methionine. Threonine itself CC is utilized as a starting point for the biosynthesis of isoleucine. -- SN 1 ID Homoserine dehydrogenase DN Homoserine dehydrogenase (EC 1.1.1.3) RQ 1 EV IPR001342; PF00742; sufficient; TG GO:0009088; -- SN 2 ID Homoserine kinase DN Homoserine kinase (EC 2.7.1.39) RQ 1 EV IPR000870; TIGR00191; sufficient; TG GO:0009088; EV IPR005280; TIGR00938; sufficient; TG GO:0009088; EV IPR011863; TIGR02137; sufficient; TG GO:0009088; -- SN 3 ID Threonine synthase DN Threonine synthase (EC 4.2.3.1) RQ 1 EV IPR004450; TIGR00260; sufficient; TG GO:0009088; // AC GenProp0160 DE Aspartate semialdehyde biosynthesis from aspartate TP PATHWAY AU Haft DH TH 0 RN [1] RM 2892836 RT Structure of the yeast HOM3 gene which encodes aspartokinase. RA Rafalski JA, Falco SC; RL J Biol Chem. 1988;263:2146-2151. DC Glycine, serine and threonine metabolism DR KEGG; map00260; DC Homoserine biosynthesis DR MetaCyc; HOMOSERSYN-PWY; CC Aspartate semialdehyde biosynthesis is a two step pathway. The product CC of this pathway can be used in lysine biosynthesis, or in the pathway CC leading to homoserine, which is involved in threonine, isoleucine and CC methionine biosynthesis. There are three isozymes that differ in their CC sensitivity to regulation by Lys, Met and Thr in Escherichia coli [1]. -- SN 1 ID Aspartate kinase DN Aspartate kinase (EC 2.7.2.4) RQ 1 EV IPR005260; TIGR00656; sufficient; TG GO:0009090; EV IPR001341; TIGR00657; sufficient; TG GO:0009090; EV IPR011819; TIGR02078; sufficient; TG GO:0009090; -- SN 2 ID Aspartate-semialdehyde dehydrogenase DN Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) RQ 1 EV IPR005676; TIGR00978; sufficient; TG GO:0009090; EV IPR005986; TIGR01296; sufficient; TG GO:0009090; EV IPR011534; TIGR01745; sufficient; TG GO:0009090; // AC GenProp0162 DE Isoleucine biosynthesis from threonine and pyruvate TP PATHWAY AU Haft DH TH 1 DC Isoleucine and Valine Biosynthesis DR IUBMB; AminoAcid; IleVal; DC Valine, leucine and isoleucine biosynthesis DR KEGG; map00290; DC L-isoleucine biosynthesis I (from threonine) DR MetaCyc; ILEUSYN-PWY; CC The branched amino acid isoleucine is biosynthesized from the central CC intermediary metabolite pyruvate and the amino acid threonine via a CC five step pathway. Four enzymes in this pathway are common to the CC pathways for the biosynthesis of leucine and valine, although CC specialized versions of these enzymes may exist in certain species CC which have a narrowed substrate range or amino acid-specific regulatory CC mechanisms. Unlike those other two pathways in which two molecules of CC pyruvate are condensed, here threonine is converted first to CC 2-oxobutyrate and then condensed with pyruvate. Thus, the enzymes CC common to the pathways are acting on distinct substrates. CC 2-oxobutyrate for this pathway may also be generated by a separate path CC from glutamate via mesaconate in certain organisms. The penultimate CC intermediate in this pathway, 2-oxo-3-methylvalerate may also be CC incorporated into branched-chain fatty acids -- SN 1 ID Threonine dehydratase DN Threonine dehydratase (EC 4.3.1.19) RQ 1 EV IPR005789; TIGR01127; sufficient; TG GO:0009097; EV IPR005787; TIGR01124; sufficient; TG GO:0009097; EV IPR011820; TIGR02079; sufficient; TG GO:0009097; -- SN 2 ID Acetohydroxyacid synthase, large subunit DN Acetolactate synthase, large subunit (EC 2.2.1.6) RQ 1 EV IPR012846; TIGR00118; sufficient; TG GO:0009097; -- SN 3 ID Acetohydroxyacid synthase, small subunit DN Acetolactate synthase, small subunit (EC 2.2.1.6) RQ 0 EV IPR004789; TIGR00119; sufficient; TG GO:0009097; -- SN 4 ID Ketol-acid reductoisomerase DN Ketol-acid reductoisomerase (EC 1.1.1.86) RQ 1 EV IPR013023; TIGR00465; sufficient; TG GO:0009097; -- SN 5 ID Dihydroxy-acid dehydratase DN Dihydroxy-acid dehydratase (EC 4.2.1.9) RQ 1 EV IPR004404; TIGR00110; sufficient; TG GO:0009097; -- SN 6 ID Branched-chain amino acid aminotransferase DN Branched-chain amino acid aminotransferase (EC 2.6.1.42) RQ 0 EV IPR005785; TIGR01122; sufficient; TG GO:0009097; EV IPR005786; TIGR01123; sufficient; TG GO:0009097; // AC GenProp0163 DE Valine biosynthesis from pyruvate TP PATHWAY AU Haft DH TH 1 DC Isoleucine and Valine Biosynthesis DR IUBMB; AminoAcid; IleVal; DC Valine, leucine and isoleucine biosynthesis DR KEGG; map00290; DC L-valine biosynthesis DR MetaCyc; VALSYN-PWY; CC The branched amino acid valine is biosynthesized from the central CC intermediary metabolite pyruvate via a four step pathway. All four CC enzymes in this pathway are common to the pathways for the biosynthesis CC of isoleucine from 2-oxobutyrate and leucine from pyruvate, although CC specialized versions of these enzymes may exist in certain species CC which have a narrowed substrate range or amino acid-specific regulatory CC mechanisms. The product of the third step in this pathway, CC 2-oxoisovalerate is a branchpoint metabolite required for the CC biosynthesis of Coenzyme A, branched-chain fatty acids, and leucine. CC Similarly, the product of the first step, (S)-2-acetolactate is common CC to the pathway to (R,R)-2,3-butanediol in the mixed-acid fermentation CC of pyruvate. The first step of the pathway, acetolactate synthase, CC requires thiamine pyrophosphate and two molecules of pyruvate, one of CC which is decarboxylated to the acetoacetate adduct, CC 2-(alpha-hydroxyethyl)-ThPP. -- SN 1 ID Acetohydroxyacid synthase, large subunit DN Acetohydroxyacid synthase, large subunit (EC 2.2.1.6) RQ 1 EV IPR012846; TIGR00118; sufficient; TG GO:0009099; -- SN 2 ID Acetohydroxyacid synthase, small subunit DN Acetohydroxyacid synthase, small subunit (EC 2.2.1.6) RQ 0 EV IPR004789; TIGR00119; sufficient; TG GO:0009099; -- SN 3 ID Ketol-acid reductoisomerase DN Ketol-acid reductoisomerase (EC 1.1.1.86) RQ 1 EV IPR013023; TIGR00465; sufficient; TG GO:0009099; -- SN 4 ID Dihydroxy-acid dehydratase DN Dihydroxy-acid dehydratase (EC 4.2.1.9) RQ 1 EV IPR004404; TIGR00110; sufficient; TG GO:0009099; -- SN 5 ID Branched-chain amino acid aminotransferase DN Branched-chain amino acid aminotransferase (EC 2.6.1.42) RQ 0 EV IPR005785; TIGR01122; sufficient; TG GO:0009099; EV IPR005786; TIGR01123; sufficient; TG GO:0009099; // AC GenProp0164 DE Leucine biosynthesis from pyruvate and acetyl-CoA TP PATHWAY AU Haft DH TH 2 DC Valine, leucine and isoleucine biosynthesis DR KEGG; map00290; DC L-leucine biosynthesis DR MetaCyc; LEUSYN-PWY; DC Leucine Biosynthesis DR IUBMB; AminoAcid; Leu; CC The branched amino acid leucine is biosynthesized from the central CC intermediary metabolites pyruvate and acetyl-CoA via a seven step CC pathway. Four of these steps are shared with the valine and isoleucine CC pathways, although specialized versions of these enzymes may exist in CC certain species which have a narrowed substrate range or amino CC acid-specific regulatory mechanisms. The product of the third step in CC this pathway, 2-oxoisovalerate is a branchpoint metabolite required for CC the biosynthesis of Coenzyme A, branched-chain fatty acids and valine. CC Similarly, the product of the first step, (S)-2-acetolactate is common CC to the pathway to (R,R)-2,3-butanediol in the mixed-acid fermentation CC of pyruvate. The first step of the pathway, acetolactate synthase, CC requires thiamine pyrophosphate and two molecules of pyruvate, one of CC which is decarboxylated to the acetoacetate adduct, CC 2-(alpha-hydroxyethyl)-ThPP. The acetyl-CoA required for the fourth CC step, 2-isopropylmalate synthase, may also derive from this ThPP adduct CC by oxidation. -- SN 1 ID Acetohydroxyacid synthase, large subunit DN Acetohydroxyacid synthase, large subunit (EC 2.2.1.6) RQ 1 EV IPR012846; TIGR00118; sufficient; TG GO:0009098; -- SN 2 ID Acetohydroxyacid synthase, small subunit DN Acetohydroxyacid synthase, small subunit (EC 2.2.1.6) RQ 0 EV IPR004789; TIGR00119; sufficient; TG GO:0009098; -- SN 3 ID Ketol-acid reductoisomerase DN Ketol-acid reductoisomerase (EC 1.1.1.86) RQ 1 EV IPR013023; TIGR00465; sufficient; TG GO:0009098; -- SN 4 ID Dihydroxy-acid dehydratase DN Dihydroxy-acid dehydratase (EC 4.2.1.9) RQ 1 EV IPR004404; TIGR00110; sufficient; TG GO:0009098; -- SN 5 ID 2-isopropylmalate synthase DN 2-isopropylmalate synthase (EC 2.3.3.13) RQ 1 EV IPR005671; TIGR00973; sufficient; TG GO:0009098; EV IPR005668; TIGR00970; sufficient; TG GO:0009098; EV IPR011830; TIGR02090; sufficient; -- SN 6 ID 3-isopropylmalate dehydratase, large subunit DN 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33) RQ 1 EV IPR004430; TIGR00170; sufficient; TG GO:0009098; EV IPR011823; TIGR02083; sufficient; TG GO:0009098; EV IPR011826; TIGR02086; sufficient; -- SN 7 ID 3-isopropylmalate dehydratase, small subunit DN 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33) RQ 1 EV IPR004431; TIGR00171; sufficient; TG GO:0009098; EV IPR011824; TIGR02084; sufficient; TG GO:0009098; EV IPR011827; TIGR02087; sufficient; -- SN 8 ID 3-isopropylmalate dehydrogenase DN 3-isopropylmalate dehydrogenase (EC 1.1.1.85) RQ 1 EV IPR004429; TIGR00169; sufficient; TG GO:0009098; EV IPR011828; TIGR02088; sufficient; -- SN 9 ID Branched-chain amino acid aminotransferase DN Branched-chain amino acid aminotransferase (EC 2.6.1.42) RQ 0 EV IPR005785; TIGR01122; sufficient; TG GO:0009098; EV IPR005786; TIGR01123; sufficient; TG GO:0009098; // AC GenProp0165 DE MinCDE system TP SYSTEM AU Haft DH TH 0 RN [1] RM 12766229 RT Division site selection in Escherichia coli involves dynamic RT redistribution of Min proteins within coiled structures that extend RT between the two cell poles. RA Shih YL, Le T, Rothfield L; RL Proc Natl Acad Sci U S A. 2003;100:7865-7870. RN [2] RM 11806906 RT A dynamic model for determining the middle of Escherichia coli. RA Kruse K; RL Biophys J. 2002;82:618-627. CC The MinCDE proteins are organized into extended membrane-associated CC coiled structures that wind around the cell between the two poles. CC These structures, and changes (pole-to-pole oscillations) in the CC distribution of the MinCDE proteins within them over time, are required CC for the proper placement of the cell division septum at midcell [1,2]. -- SN 1 ID MinC protein DN Septum site-determining protein MinC RQ 1 EV IPR013033; TIGR01222; sufficient; TG GO:0000918; -- SN 2 ID MinD protein DN Septum site-determining protein MinD RQ 1 EV IPR010223; TIGR01968; sufficient; TG GO:0000918; -- SN 3 ID MinE protein DN Cell division topological specificity factor MinE RQ 1 EV IPR005527; TIGR01215; sufficient; TG GO:0000918; // AC GenProp0166 DE MreBCD system TP SYSTEM AU Haft DH TH 0 RN [1] RM 14506864 RT Heterospecific expression of the Bacillus subtilis cell shape RT determination genes mreBCD in Escherichia coli. RA Lee JC, Cha JH, Zerbv DB, Stewart GC; RL Curr Microbiol. 2003;47:146-152. RN [2] RM 13678608 RT Bacterial shape: growing off this mortal coil. RA Margolin W; RL Curr Biol. 2003;13:r705-7. RN [3] RM 12867458 RT Essential nature of the mreC determinant of Bacillus subtilis. RA Lee JC, Stewart GC; RL J Bacteriol. 2003;185:4490-4498. RN [4] RM 9063975 RT Bacillus stearothermophilus cell shape determinant gene, mreC and mreD, RT and their stimulation of protease production in Bacillus subtilis. RA Kubo M, Pierro DJ, Mochizuki Y, Kojima T, Yamazaki T, Satoh S, Takizawa RA N, Kiyohara H; RL Biosci Biotechnol Biochem. 1996;60:271-276. RN [5] RM 12809607 RT Control of cell morphogenesis in bacteria: two distinct ways to make a RT rod-shaped cell. RA Daniel RA, Errington J; RL Cell. 2003;113:767-776. CC The bacterial MreBCD proteins are involved in rod shape determination CC and have a postulated role in the regulation of septum-specific CC peptidoglycan synthesis [1]. Members of the actin-like MreB family of CC proteins localize as a helical filament in bacteria and are important CC for determining cylindrical cell shape. Recent results show that new CC cell wall biosynthesis occurs along a helical track dependent on one of CC these actin homologs, providing new insights into bacterial cell CC growth, division and shape [2]. MreC and MreD are membrane-associated CC proteins. MreC is an essential gene in B. subtilis; cells lacking CC sufficient quantities of MreC undergo morphological changes, namely, CC swelling and twisting of the cells, which is followed by cell lysis CC [3]. MreC and MreD may be involved in the regulation of CC cell-shape-related protease expression [4]. There is evidence of the CC existence of a separate rod-shape determining system in rod-shaped CC bacteria lacking the MreBCD system [5]. -- SN 1 ID MreB protein DN Rod shape-determining protein MreB RQ 1 EV IPR004753; TIGR00904; sufficient; TG GO:0008360; -- SN 2 ID MreC protein DN Rod shape-determining protein MreC RQ 1 EV IPR007221; TIGR00219; sufficient; TG GO:0008360; -- SN 3 ID MreD protein DN Rod shape-determining protein MreD RQ 1 EV IPR007227; TIGR03426; sufficient; TG GO:0008360; -- SN 4 ID Penicillin-binding protein 2 RQ 0 EV IPR017790; TIGR03423; TG GO:0008360; -- SN 5 ID Rod shape-determining protein RodA RQ 0 EV IPR011923; TIGR02210; TG GO:0008360; // AC GenProp0167 DE Cellular growth, organization and division TP CATEGORY AU Haft DH TH 0 CC Processes which determine, regulate or alter the physical size, shape CC or organization of the cell. -- SN 1 ID MinCDE system RQ 0 EV GenProp0165; -- SN 2 ID MreBCD system RQ 0 EV GenProp0166; -- SN 3 ID SMC-ScpA-ScpB complex RQ 0 EV GenProp0201; -- SN 4 ID Gas vesicle RQ 0 EV GenProp0460; -- SN 5 ID C-type cytochrome biogenesis, system I RQ 0 EV GenProp0678; -- SN 6 ID C-type cytochrome biogenesis, system II RQ 0 EV GenProp0680; -- SN 7 ID Spore formation RQ 0 EV GenProp0049; -- SN 8 ID FtsQBL complex RQ 0 EV GenProp1142; -- SN 9 ID FtsBL complex RQ 0 EV GenProp1154; // AC GenProp0168 DE Glycogen system TP SYSTEM AU Haft DH TH 1 CC Glycogen and starch are related glucose storage polysaccharides. Alpha CC 1,4 glucan linkages predominate, with some branching using alpha 1,6 CC linkages. The relative level of branching determines whether the CC substance is called glycogen or starch. In bacteria and plants, the CC precursor is ADP-glucose. In animals, the precursor is UDP-glucose. CC Different forms of glycogen synthase are used for the two. This CC property includes the enzyme phosphorylase (glycogen phosphorylase or CC starch phosphorylase, depending on context) necessary to release CC glucose-1-phosphate from the polysaccharide. -- SN 1 ID 4-alpha-glucanotransferase (disproportionating enzyme) DN 4-alpha-glucanotransferase (MalQ) (EC 2.4.1.25) RQ 0 EV IPR003385; TIGR00217; sufficient; TG GO:0005977; -- SN 2 ID 1,4-alpha-glucan branching enzyme DN 1,4-alpha-glucan branching enzyme (GlgB) (EC 2.4.1.18) RQ 1 EV IPR006407; TIGR01515; sufficient; TG GO:0005977; -- SN 3 ID Glycogen debranching enzyme DN Glycogen debranching enzyme RQ 0 EV IPR006421; TIGR01531; sufficient; TG GO:0005977; EV IPR006451; TIGR01561; sufficient; TG GO:0005977; EV IPR011837; TIGR02100; sufficient; TG GO:0005977; -- SN 4 ID Glycogen synthase (ADP) DN Glycogen synthase (EC 2.4.1.21) RQ 1 EV IPR011835; TIGR02095; sufficient; TG GO:0005977; -- SN 5 ID Glucose-1-phosphate adenylyltransferase DN Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) RQ 1 EV IPR011831; TIGR02091; sufficient; TG GO:0005977; -- SN 6 ID Glucose-1-phosphate adenylyltransferase, GlgD subunit DN Glucose-1-phosphate adenylyltransferase, GlgD subunit RQ 0 EV IPR011832; TIGR02092; sufficient; TG GO:0005977; -- SN 7 ID Alpha-glucan phosphorylases DN Alpha-glucan phosphorylase RQ 1 EV IPR011833; TIGR02093; sufficient; TG GO:0005977; // AC GenProp0170 DE Coenzyme PQQ biosynthesis TP SYSTEM AU Haft DH TH 0 RN [1] RM 18371220 RT The pyrroloquinoline quinone biosynthesis pathway revisited: a RT structural approach. RA Puehringer S, Metlitzky M, Schwarzenbacher R; RL BMC Biochem. 2008;9:8. DC Pyrroloquinoline quinone biosynthesis DR MetaCyc; PWY-6420; CC Coenzyme PQQ (coenzyme pyrrolo-quinoline-quinone) is a cofactor of CC certain alcohol dehydrogenases and glucose dehydrogenases. PQQ CC biosynthesis is associated with an operon that includes PqqA, a small CC protein proposed to act as a molecular precursor. At least 6 genes are CC located within the PQQ-operon, all of which are required for PQQ CC biosynthesis, although in some cases the exact mechanism of the gene CC product is not known [1]. -- SN 1 ID PQQ-binding repeats DN PQQ enzyme repeat domain protein RQ 0 EV IPR002372; PF01011; sufficient; -- SN 2 ID PqqA protein DN Coenzyme PQQ biosynthesis protein A RQ 1 EV IPR011725; TIGR02107; sufficient; TG GO:0018189; -- SN 3 ID PqqB protein DN Coenzyme PQQ biosynthesis protein B RQ 1 EV IPR011842; TIGR02108; sufficient; TG GO:0018189; -- SN 4 ID PqqC protein DN Coenzyme PQQ biosynthesis protein C RQ 1 EV IPR011845; TIGR02111; sufficient; TG GO:0018189; -- SN 5 ID PqqD protein DN Coenzyme PQQ biosynthesis protein D RQ 1 EV IPR022479; TIGR03859; TG GO:0018189; -- SN 6 ID PqqE protein DN Coenzyme PQQ biosynthesis protein E RQ 1 EV IPR011843; TIGR02109; sufficient; TG GO:0018189; -- SN 7 ID Peptidase PqqF DN Coenzyme PQQ biosynthesis protein PqqF (EC:3.4.24.-) RQ 0 EV IPR011844; TIGR02110; sufficient; TG GO:0018189; -- SN 8 ID PQQ-dependent enzyme example DN PQQ-dependent dehydrogenase glucose/quinate/shikimate family protein (EC:1.1.5.2) RQ 1 EV IPR017511; TIGR03074; sufficient; TG GO:0018189; EV IPR017512; TIGR03075; sufficient; TG GO:0018189; EV IPR019893; TIGR03606; sufficient; TG GO:0018189; // AC GenProp0171 DE Coenzyme A biosynthesis from pantothenate TP PATHWAY AU Haft DH TH 1 RN [1] RM 15893380 RT Coenzyme A: back in action. RA Leonardi R, Zhang YM, Rock CO, Jackowski S; RL Prog Lipid Res. 2005;44:125-153. DC Coenzyme A Biosynthesis (late stages) DR IUBMB; misc; CoA2; CC This property represents a 5-step pathway for the biosynthesis of CC coenzyme A (CoA) from pantothenate. Most species produce panthothenate CC but some must import it. The first step described here is a CC sodium/pantothenate symporter. The first required step, catalyzed by CC pantothenate kinase, is carried out by at least two different known CC protein families. One is found in most bacteria, including E. coli CC (TIGR00554). Another is present in eukaryotes and in a few CC Gram-positive bacteria (e.g. Staphylococcus aureus, Bacillus anthracis) CC (TIGR00555). The enzyme, if present, has not been identified in a CC number of species. The second and third enzymes are usually found CC together in a multifunctional protein, phosphopantothenoylcysteine CC decarboxylase/phosphopantothenate--cysteine ligase, once thought to CC affect DNA metabolism as well. In Streptococcus and allies, and some CC other species, the enzymes are encoded in tandem genes rather than CC fused. CoaD and CoaE are, respectively, pantetheine-phosphate CC adenylyltransferase and dephospho-CoA kinase [1]. -- SN 1 ID Sodium/pantothenate symporter DN Sodium/pantothenate symporter/panF RQ 0 EV IPR011849; TIGR02119; TG GO:0015937; -- SN 2 ID Pantothenate kinase DN Pantothenate kinase/coaA (EC 2.7.1.33) RQ 0 EV IPR004566; TIGR00554; sufficient; TG GO:0015937; EV IPR004567; TIGR00555; sufficient; TG GO:0015937; EV IPR004619; TIGR00671; TG GO:0015937; -- SN 3 ID Phosphopantothenate--cysteine ligase DN Phosphopantothenate--cysteine ligase/coaB (EC 6.3.2.5) RQ 1 EV IPR005252; TIGR00521; sufficient; TG GO:0015937; EV IPR011848; TIGR02114; sufficient; TG GO:0015937; -- SN 4 ID Phosphopantothenoylcysteine decarboxylase DN Phosphopantothenoylcysteine decarboxylase/coaC (EC 4.1.1.36) RQ 1 EV IPR005252; TIGR00521; sufficient; TG GO:0015937; EV IPR011847; TIGR02113; sufficient; TG GO:0015937; -- SN 5 ID Pantetheine-phosphate adenylyltransferase DN Phosphopantetheine adenylyltransferase/coaD (EC 2.7.7.3) RQ 1 EV IPR001980; TIGR01510; sufficient; TG GO:0015937; -- SN 6 ID Dephospho-CoA kinase DN Dephospho-CoA kinase/coaE (EC 2.7.1.24) RQ 1 EV IPR001977; TIGR00152; sufficient; TG GO:0015937; // AC GenProp0172 DE Potassium-transporting ATPase KdpFABC TP SYSTEM AU Haft DH TH 0 RN [1] RM 14604015 RT The roles and regulation of potassium in bacteria. RA Epstein W; RL Prog Nucleic Acid Res Mol Biol. 2003;75:293-320. RN [2] RM 11248697 RT Analysis of KdpC of the K(+)-transporting KdpFABC complex of RT Escherichia coli. RA Gassel M, Altendorf K; RL Eur J Biochem. 2001;268:1772-1781. DC Two-component system DR KEGG; map02020; CC The Kdp complex is a high affinity P-type ATPase potassium ion CC transport system, found widely distributed among prokaryotes. Regulated CC by increases in osmolarity and/or reduction in external potassium, Kdp CC is the only K+ transport system whose expression is regulated by CC environmental conditions [1]. Kdp is composed of four membrane-bound CC subunits responsible for potassium ion binding and transport, ATP CC hydrolysis, and complex assembly and stability [2]. Not defined by this CC property are the sensor kinase and response regulator components, which CC once stimulated by specific environmental signals, induce expression of CC the adjacent Kdp gene cluster [1,2]. -- SN 1 ID KdpA subunit DN K+-transporting ATPase, A subunit (EC 3.6.3.12) RQ 1 EV IPR004623; TIGR00680; sufficient; TG GO:0010107; -- SN 2 ID KdpB subunit DN K+-transporting ATPase, B subunit (EC 3.6.3.12) RQ 1 EV IPR006391; TIGR01497; sufficient; TG GO:0010107; -- SN 3 ID KdpC subunit DN K+-transporting ATPase, C subunit (EC 3.6.3.12) RQ 1 EV IPR003820; TIGR00681; sufficient; TG GO:0010107; -- SN 4 ID KdpF peptide DN K+-transporting ATPase, F subunit (EC 3.6.3.12) RQ 0 EV IPR011726; TIGR02115; sufficient; TG GO:0010107; // AC GenProp0176 DE TRAP-T (tripartite ATP-independent periplasmic transporters) family transporters TP SYSTEM AU Haft DH TH 0 RN [1] RM 11524131 RT The tripartite ATP-independent periplasmic (TRAP) transporters of RT bacteria and archaea. RA Kelly DJ, Thomas GH; RL FEMS Microbiol Rev. 2001;25:405-424. RN [2] RM 10627041 RT TRAP transporters: an ancient family of extracytoplasmic RT solute-receptor-dependent secondary active transporters. RA Rabus R, Jack DL, Kelly DJ, Saier MH; RL Microbiology. 1999;145 ( Pt 12):3431-3445. CC This property represents the presence of three-subunit transporters CC related to the DctPQM system for dicarboxylate transport in Rhodobacter CC capsulatus. These are secondary transporters, energized by ion CC gradients, rather than primary transporters powered by ATP directly [1]. CC The acronym TRAP, or TRAP-T, stands for Tripartite ATP-independent CC Periplasmic Transporters. The characteristic architecture includes an CC integral membrane protein with 12 predicted transmembrane (TM) regions CC (e.g.DctM) and another with 4 predicted TM regions (e.g. DctQ). These CC two are fused in some species [2]. Also present is an extracytoplasmic CC solute receptor (ESR). In addition to C4 dicarboxylates, substrates CC moved by related transporters appear to include mannitol, aspartate CC derivative ectoine, and other as yet uncharacterized solutes. Some CC bacteria, such as Bradyrhizobium japonicum, may contain over a dozen CC such transporters. -- SN 1 ID DctM-like 12-transmembrane helix protein DN TRAP transporter, DctM subunit RQ 1 EV IPR004681; TIGR00786; sufficient; EV IPR010656; PF06808; sufficient; EV IPR011853; TIGR02123; sufficient; -- SN 2 ID DctQ-like 4-transmembrane helix protein DN TRAP transporter, DctQ-like membrane protein RQ 1 EV IPR007387; PF04290; sufficient; EV IPR011853; TIGR02123; sufficient; -- SN 3 ID TRAP extracytoplasmic solute receptor (ESR) DN TRAP transporter solute receptor, DctP family RQ 1 EV IPR004682; TIGR00787; sufficient; EV IPR018389; PF03480; sufficient; EV IPR011852; TIGR02122; sufficient; // AC GenProp0178 DE Glycine cleavage system TP SYSTEM AU Haft DH TH 1 RN [1] RM 11286922 RT The glycine decarboxylase system: a fascinating complex. RA Douce R, Bourguignon J, Neuburger M, Rebeille F; RL Trends Plant Sci. 2001;6:167-176. DC Glycine Cleavage System DR IUBMB; AminoAcid; GlyCleave; DC Glycine, serine and threonine metabolism DR KEGG; map00260; CC The glycine cleavage system (GCS), also known as the glycine CC decarboxylase system (GDC) consists of a set of four enzymes, CC which are involved in a multi-step reaction to catalyse the CC cleavage of glycine molecules. The constituents enzymes are, P CC protein, H protein, T protein, and L protein (dihydrolipoamide CC dehydrogenase)[1]. -- SN 1 ID Glycine cleavage system H protein DN Glycine cleavage system H protein RQ 1 EV IPR017453; TIGR00527; sufficient; TG GO:0006546; -- SN 2 ID Dihydrolipoamide dehydrogenase DN Dihydrolipoamide dehydrogenase/L protein (EC 1.8.1.4) RQ 1 EV IPR006258; TIGR01350; sufficient; -- SN 3 ID Glycine cleavage system P protein DN Glycine cleavage system P protein (EC 1.4.4.2) RQ 1 EV IPR020581; PF02347; sufficient; TG GO:0006546; -- SN 4 ID Glycine cleavage system T protein DN Glycine cleavage system T protein (EC 2.1.2.10) RQ 1 EV IPR006223; TIGR00528; sufficient; TG GO:0006546; // AC GenProp0179 DE Protein transport TP CATEGORY AU Haft DH TH 0 CC The translocation of proteins across biological membranes or other CC layers. -- SN 1 ID Type III secretion RQ 0 EV GenProp0052; -- SN 2 ID Type II secretion RQ 0 EV GenProp0053; -- SN 3 ID Type I secretion RQ 0 EV GenProp0059; -- SN 4 ID Tat (Sec-independent) protein export RQ 0 EV GenProp0127; -- SN 5 ID Lipoprotein localization system lolABCDE RQ 0 EV GenProp0207; -- SN 6 ID Sec system preprotein translocase RQ 0 EV GenProp0209; -- SN 7 ID Prokaryotic N-terminal cleavage/methylation, type IV pilin-like RQ 0 EV GenProp0295; -- SN 8 ID Protein sorting system, PEP-CTERM/exosortase (generic) RQ 0 EV GenProp0326; -- SN 9 ID Protein sorting system, sortase type, LPXTG/SrtA class RQ 0 EV GenProp0626; -- SN 10 ID Protein sorting system, sortase type, SrtB class RQ 0 EV GenProp0664; -- SN 11 ID Protein sorting system, putative, exosortase G class RQ 0 EV GenProp0669; -- SN 12 ID Type VI secretion RQ 0 EV GenProp0735; -- SN 13 ID OMP chaperone system: SurA-Skp-DegP RQ 0 EV GenProp0928; -- SN 14 ID Protein sorting system, GlyGly-CTERM/rhombosortase RQ 0 EV GenProp0778; -- SN 15 ID Protein sorting system, KxYKxGKxW class RQ 0 EV GenProp0845; -- SN 16 ID Exosporium RQ 0 EV GenProp0847; -- SN 17 ID Protein sorting system, proteobacterial dedicated sortase type RQ 0 EV GenProp0859; -- SN 18 ID Type VII secretion, Actinobacteria form RQ 0 EV GenProp0904; -- SN 19 ID Type VII secretion, Firmicutes form RQ 0 EV GenProp0905; -- SN 20 ID Protein sorting system, SipW class RQ 0 EV GenProp0957; -- SN 21 ID Protein sorting system, PGF-CTERM/archaeosortase A RQ 0 EV GenProp0978; -- SN 22 ID Protein sorting system, PEF-CTERM/archaeosortase C RQ 0 EV GenProp0979; -- SN 23 ID Protein sorting system, putative, exosortase F class RQ 0 EV GenProp0980; -- SN 24 ID Protein sorting system, VPXXXP-CTERM/archaeosortase B RQ 0 EV GenProp0983; -- SN 25 ID Protein sorting system, VPDSG-CTERM/exosortase C RQ 0 EV GenProp0985; -- SN 26 ID Protein sorting system, cyano-PEP-CTERM class RQ 0 EV GenProp0987; -- SN 27 ID Protein sorting system, VPEID-CTERM/exosortase E RQ 0 EV GenProp0989; -- SN 28 ID Protein sorting system, PIP-CTERM/archaeosortase D RQ 0 EV GenProp0993; -- SN 29 ID Protein sorting system, IPTLxxWG-CTERM/exosortase H RQ 0 EV GenProp0996; -- SN 30 ID Por secretion system RQ 0 EV GenProp0999; -- SN 31 ID Protein sorting system, putative, exosortase J class RQ 0 EV GenProp1005; -- SN 32 ID Protein sorting system, MSEP-CTERM/exosortase K RQ 0 EV GenProp1054; -- SN 33 ID Protein sorting system, PEFG-CTERM/thaumarchaeosortase RQ 0 EV GenProp1055; -- SN 34 ID Type V secretion RQ 0 EV GenProp1074; -- SN 35 ID Protein sorting system, vault protein/exosortase N RQ 0 EV GenProp1087; -- SN 36 ID Protein sorting system, CGP-CTERM/unknown of Thermococcaceae RQ 0 EV GenProp1102; -- SN 37 ID Protein sorting system, Synergist-CTERM/unknown of Synergistetes RQ 0 EV GenProp1103; -- SN 38 ID Accessory Sec system, Actinobacterial type RQ 0 EV GenProp1010; // AC GenProp0180 DE Small molecule transport TP CATEGORY AU Haft DH TH 0 CC The translocation of small molecules and ions across biological CC membranes or other layers. -- SN 1 ID PTS transport system RQ 0 EV GenProp0119; -- SN 2 ID Na+-translocating NADH-quinone reductase RQ 0 EV GenProp0129; -- SN 3 ID Potassium-transporting ATPase KdpFABC RQ 0 EV GenProp0172; -- SN 4 ID TRAP-T (tripartite ATP-independent periplasmic transporters) family transporters RQ 0 EV GenProp0176; -- SN 5 ID Phosphate ABC transporter (pstSCAB-phoU) RQ 0 EV GenProp0190; -- SN 6 ID Sulfate/thiosulfate ABC transporter RQ 0 EV GenProp0191; -- SN 7 ID Molybdate ABC transporter RQ 0 EV GenProp0192; -- SN 8 ID Thiamine/TPP ABC transporter ThiBPQ RQ 0 EV GenProp0252; -- SN 9 ID Ion-motive antiporter cycles RQ 0 EV GenProp0873; -- SN 10 ID Phosphonates ABC transport RQ 0 EV GenProp0236; -- SN 11 ID Tol-Pal system RQ 0 EV GenProp0542; -- SN 12 ID TonB-dependent transport RQ 0 EV GenProp0543; -- SN 13 ID Ectoine ABC transporter EhuABCD RQ 0 EV GenProp0651; -- SN 14 ID Fructose utilization as fructose-1,6-bisphosphate RQ 0 EV GenProp0693; -- SN 15 ID Glucose utilization as fructose-1,6-bisphosphate RQ 0 EV GenProp0694; -- SN 16 ID 2-aminoethylphosphonate (AEP) ABC transporter, type I, PhnSTUV RQ 0 EV GenProp0712; -- SN 17 ID 2-aminoethylphosphonate (AEP) ABC transporter, type II RQ 0 EV GenProp0721; -- SN 18 ID Urea ABC transporter UrtABCDE RQ 0 EV GenProp0743; -- SN 19 ID Choline ABC transporter, ChoXWV family RQ 0 EV GenProp0748; -- SN 20 ID Choline sulfate utilization RQ 0 EV GenProp0749; -- SN 21 ID Heme uptake system, NEAT-domain mediated RQ 0 EV GenProp0828; -- SN 22 ID Lantibiotic system, gallidermin/epidermin family RQ 0 EV GenProp0853; -- SN 23 ID Nickel import ABC transporter RQ 0 EV GenProp0494; -- SN 24 ID ATP-dependent methionine-importing complex RQ 0 EV GenProp1114; -- SN 25 ID ProVWX complex RQ 0 EV GenProp1126; -- SN 26 ID Glutathione-regulated potassium-efflux system KefC-KefF complex RQ 0 EV GenProp1160; -- SN 27 ID Glutathione-regulated potassium-efflux system KefB-KefG complex RQ 0 EV GenProp1131; -- SN 28 ID Cytochrome o ubiquinol oxidase complex RQ 0 EV GenProp1164; -- SN 29 ID Cus cation efflux complex RQ 0 EV GenProp1168; -- SN 30 ID BtuCD complex RQ 0 EV GenProp1156; // AC GenProp0182 DE Reduction of oxidized methionine TP GUILD AU Haft DH TH 0 CC Methionine, free or in proteins, is susceptible to oxidation damage. R- CC and S-conformation enantiomers of methionine sulfoxide can be repaired CC by different reductases. MsrB (TIGR00357) was previously designated CC PilB because of altered cytoadherence in a mutant. MsrA and MsrB are CC sometimes expressed as a fusion protein. -- SN 1 ID Methionine-S-sulfoxide reductase DN Methionine-S-sulfoxide reductase/MsrA RQ 1 EV IPR002569; TIGR00401; sufficient; -- SN 2 ID Methionine-R-sulfoxide reductase DN Methionine-R-sulfoxide reductase/MsrB RQ 1 EV IPR002579; TIGR00357; sufficient; // AC GenProp0183 DE dTDP-L-rhamnose biosynthesis from dTDP-4-dehydro-L-rhamnose TP METAPATH AU Haft DH, Richardson L TH 0 RN [1] RM 12773151 RT A structural perspective on the enzymes that convert dTDP-d-glucose RT into dTDP-l-rhamnose. RA Dong C, Beis K, Giraud MF, Blankenfeldt W, Allard S, Major LL, Kerr RA ID, Whitfield C, Naismith JH; RL Biochem Soc Trans. 2003;31:532-536. RN [2] RM 10802738 RT RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of RT epimerase. RA Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH; RL Nat Struct Biol. 2000;7:398-402. DC Streptomycin biosynthesis DR KEGG; map00521; DC dTDP-L-rhamnose biosynthesis I DR MetaCyc; DTDPRHAMSYN-PWY; CC L-rhamnose is a common component of the bacterial capsule and/or CC cell wall, and is important in bacterial survival during infection. CC dTDP-L-rhamnose is the precursor of L-rhamnose[1,2]. dTDP-L-rhamnose CC is synthesized from glucose-1-phosphate and deoxythymidine CC triphosphate (dTTP) via a four-step enzymatic pathway. The four enzymes CC are: glucose-1-phosphate thymidyltransferase (also known as dTDP- CC glucose pyrophosphorylase, gene name rlmA or rfbA); dTDP-D-glucose CC 4,6-dehydratase (gene name rmlB or rfbB); dTDP-4-dehydrorhamnose CC 3,5-epimerase (also known as dTDP-6-deoxy-D-xylo-4-hexulose CC 3,5-epimerase, gene name rmlC or rfbC); and dTDP-4-dehydrorhamnose CC reductase (also known as dTDP-6-deoxy-L-lyxo-4-hexulose reductase CC (gene name rmlD or rfbD)[1,2]. This property refers to the final step CC in this pathway, the conversion of dTDP-4-dehydro-L-rhamose to CC dTDP-L-rhamnose. -- SN 1 ID Source of dTDP-4-dehydro-L-rhamnose RQ 1 EV GenProp1032; -- SN 2 ID dTDP-4-dehydrorhamnose reductase DN dTDP-4-dehydrorhamnose reductase (EC 1.1.1.133) RQ 1 EV IPR005913; TIGR01214; sufficient; // AC GenProp0184 DE Cofactor biosynthesis TP CATEGORY AU Haft DH TH 0 CC The biosynthesis of molecules utilized by enzymes to aid in chemical CC transformations. -- SN 1 ID Chorismate biosynthesis via shikimate RQ 0 EV GenProp0001; -- SN 2 ID Glutathione biosynthesis RQ 0 EV GenProp0030; -- SN 3 ID Biotin biosynthesis RQ 0 EV GenProp0036; -- SN 4 ID Tetrahydrofolate biosynthesis from GTP and PABA RQ 0 EV GenProp0038; -- SN 5 ID NAD(P) biosynthesis from L-aspartate and DHAP RQ 0 EV GenProp0057; -- SN 6 ID Pantothenate biosynthesis from aspartate and 2-oxoisovalerate RQ 0 EV GenProp0124; -- SN 7 ID Ubiquinone biosynthesis from chorismate, aerobic RQ 0 EV GenProp0136; -- SN 8 ID Iron-sulfur cluster assembly systems RQ 0 EV GenProp0140; -- SN 9 ID Coenzyme PQQ biosynthesis RQ 0 EV GenProp0170; -- SN 10 ID Coenzyme A biosynthesis from pantothenate RQ 0 EV GenProp0171; -- SN 11 ID Hydroxyethylthiazole (HET) biosynthesis from 1-deoxy-D-xylulose-5-phosphate, Cysteine, and either Tyr or Gly RQ 0 EV GenProp0250; -- SN 12 ID 5-aminolevulinate biosynthesis RQ 0 EV GenProp0255; -- SN 13 ID Thiamine pyrophosphate (TPP) de novo biosynthesis RQ 0 EV GenProp0261; -- SN 14 ID Photosynthetic cofactor biosynthesis RQ 0 EV GenProp0300; -- SN 15 ID Menaquinone biosynthesis RQ 0 EV GenProp0836; -- SN 16 ID Uroporhyrinogen III biosynthesis from 5-aminolevulinate RQ 0 EV GenProp0220; -- SN 17 ID Protoporphyrin IX biosynthesis from uroporphyrinogen III RQ 0 EV GenProp0221; -- SN 18 ID Protoheme from protoporphyrin IX RQ 0 EV GenProp0222; -- SN 19 ID Molybdopterin biosynthesis RQ 0 EV GenProp0466; -- SN 20 ID Coenzyme F420 biosynthesis RQ 0 EV GenProp0791; -- SN 21 ID 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) biosynthesis RQ 0 EV GenProp0792; -- SN 22 ID Ergothioneine biosynthesis RQ 0 EV GenProp0752; -- SN 23 ID Mycothiol biosynthesis RQ 0 EV GenProp0753; -- SN 24 ID Para-aminobenzoic acid (PABA) biosynthesis from chorismate RQ 0 EV GenProp0759; -- SN 25 ID Tryptophan tryptophylquinone modification of methylamine dehydrogenase RQ 0 EV GenProp0860; -- SN 26 ID Pyridoxal phosphate biosynthesis, PdxA/PdxJ pathway RQ 0 EV GenProp0862; -- SN 27 ID Coenzyme M biosynthesis RQ 0 EV GenProp0891; -- SN 28 ID Mycofactocin system RQ 0 EV GenProp0917; -- SN 29 ID Bacillithiol biosynthesis RQ 0 EV GenProp0927; -- SN 30 ID Ovothiol biosynthesis RQ 0 EV GenProp1064; -- SN 31 ID Coenzyme B12 biosynthesis from cob(II)yrinate diamide RQ 0 EV GenProp0269; -- SN 32 ID Cobyrinic acid diamide biosynthesis, anaerobic pathway RQ 0 EV GenProp0275; -- SN 33 ID Cobalt import system (ABC transporter: 3.A.1.18.1) RQ 0 EV GenProp0277; -- SN 34 ID Coenzyme B/coenzyme M regeneration III (coenzyme F420-dependent) RQ 0 EV GenProp1477; -- SN 35 ID Bis(guanylyl molybdenum cofactor) biosynthesis RQ 0 EV GenProp1409; -- SN 36 ID Factor 420 polyglutamylation RQ 0 EV GenProp1682; -- SN 37 ID Lipoate salvage I RQ 0 EV GenProp1224; -- SN 38 ID Lipoate biosynthesis and incorporation I RQ 0 EV GenProp1237; -- SN 39 ID Lipoate biosynthesis and incorporation II RQ 0 EV GenProp1298; -- SN 40 ID Lipoate biosynthesis and incorporation III (Bacillus) RQ 0 EV GenProp1625; -- SN 41 ID Molybdenum cofactor biosynthesis RQ 0 EV GenProp1711; -- SN 42 ID Erythro-tetrahydrobiopterin biosynthesis I RQ 0 EV GenProp1632; -- SN 43 ID Tetrapyrrole biosynthesis II (from glycine) RQ 0 EV GenProp1525; -- SN 44 ID Tetrapyrrole biosynthesis I (from glutamate) RQ 0 EV GenProp1701; -- SN 45 ID ThiG-ThiH thiazole phosphate synthase complex RQ 0 EV GenProp1127; -- SN 46 ID Molybdopterin synthase RQ 0 EV GenProp1138; -- SN 47 ID Molybdopterin-synthase adenylyltransferase complex RQ 0 EV GenProp1158; -- SN 48 ID Superpathway of coenzyme A biosynthesis III (mammals) RQ 0 EV GenProp1561; -- SN 49 ID Superpathway of coenzyme A biosynthesis I (bacteria) RQ 0 EV GenProp1601; // AC GenProp0185 DE Nucleotide biosynthesis TP CATEGORY AU Haft DH TH 0 CC The biosynthesis of the components pyridine and pyrimidine of DNA and CC RNA. -- SN 1 ID Purine (inosine-5'-phosphate) biosynthesis from ribose-5-phosphate RQ 0 EV GenProp0110; -- SN 2 ID Pyrimidine (uridine-5'-phosphate) de novo biosynthesis RQ 0 EV GenProp0187; -- SN 3 ID Ribulose monophosphate pathway RQ 0 EV GenProp0673; -- SN 4 ID Xanthine utilization as a source of guanine-monophosphate (GMP) RQ 0 EV GenProp0696; -- SN 5 ID Guanine monophosphate (GMP) biosynthesis from inosine monophosphate (IMP) RQ 0 EV GenProp0697; -- SN 6 ID Adenosine monophosphate (AMP) biosynthesis from inosine monophosphate (IMP) RQ 0 EV GenProp0747; -- SN 7 ID Adenosine deoxyribonucleotides de novo biosynthesis II RQ 0 EV GenProp1446; -- SN 8 ID Adenosine deoxyribonucleotides de novo biosynthesis RQ 0 EV GenProp1586; -- SN 9 ID Guanosine deoxyribonucleotides de novo biosynthesis I RQ 0 EV GenProp1227; -- SN 10 ID Guanosine deoxyribonucleotides de novo biosynthesis II RQ 0 EV GenProp1343; -- SN 11 ID Pyrimidine deoxyribonucleotides de novo biosynthesis I RQ 0 EV GenProp1617; -- SN 12 ID Pyrimidine deoxyribonucleotides de novo biosynthesis II RQ 0 EV GenProp1621; -- SN 13 ID 5-Aminoimidazole ribonucleotide biosynthesis I RQ 0 EV GenProp1284; -- SN 14 ID 5-Aminoimidazole ribonucleotide biosynthesis II RQ 0 EV GenProp1628; -- SN 15 ID Inosine-5'-phosphate biosynthesis I RQ 0 EV GenProp1730; -- SN 16 ID Inosine-5'-phosphate biosynthesis II RQ 0 EV GenProp1757; -- SN 17 ID Adenosine ribonucleotides de novo biosynthesis RQ 0 EV GenProp1372; -- SN 18 ID Guanosine ribonucleotides de novo biosynthesis RQ 0 EV GenProp1650; -- SN 19 ID Adenine and adenosine salvage III RQ 0 EV GenProp1235; -- SN 20 ID Adenine salvage RQ 0 EV GenProp1268; -- SN 21 ID Adenine and adenosine salvage II RQ 0 EV GenProp1430; -- SN 22 ID Adenine and adenosine salvage V RQ 0 EV GenProp1741; -- SN 23 ID Guanine and guanosine salvage RQ 0 EV GenProp1528; -- SN 24 ID Purine deoxyribonucleosides salvage RQ 0 EV GenProp1607; -- SN 25 ID Xanthine and xanthosine salvage RQ 0 EV GenProp1611; -- SN 26 ID UMP biosynthesis III RQ 0 EV GenProp1418; -- SN 27 ID UMP biosynthesis I RQ 0 EV GenProp1427; -- SN 28 ID UMP biosynthesis II RQ 0 EV GenProp1614; -- SN 29 ID UTP and CTP de novo biosynthesis RQ 0 EV GenProp1262; -- SN 30 ID Pyrimidine deoxyribonucleosides salvage RQ 0 EV GenProp1221; -- SN 31 ID Pyrimidine nucleobases salvage II RQ 0 EV GenProp1361; -- SN 32 ID Pyrimidine ribonucleosides salvage I RQ 0 EV GenProp1384; -- SN 33 ID Pyrimidine ribonucleosides salvage II RQ 0 EV GenProp1465; -- SN 34 ID Pyrimidine deoxyribonucleotide phosphorylation RQ 0 EV GenProp1494; -- SN 35 ID Pyrimidine ribonucleosides salvage III RQ 0 EV GenProp1540; -- SN 36 ID CMP phosphorylation RQ 0 EV GenProp1634; -- SN 37 ID Aspartate carbamoyltransferase complex RQ 0 EV GenProp1172; -- SN 38 ID Superpathway of pyrimidine deoxyribonucleoside salvage RQ 0 EV GenProp1264; -- SN 39 ID Superpathway of pyrimidine nucleobases salvage RQ 0 EV GenProp1307; -- SN 40 ID Superpathway of pyrimidine ribonucleotides de novo biosynthesis RQ 0 EV GenProp1318; -- SN 41 ID Superpathway of pyrimidine ribonucleosides salvage RQ 0 EV GenProp1369; -- SN 42 ID Superpathway of guanosine nucleotides de novo biosynthesis I RQ 0 EV GenProp1389; -- SN 43 ID Superpathway of purine nucleotides de novo biosynthesis I RQ 0 EV GenProp1406; -- SN 44 ID Superpathway of guanosine nucleotides de novo biosynthesis II RQ 0 EV GenProp1484; -- SN 45 ID Superpathway of purine nucleotides de novo biosynthesis II RQ 0 EV GenProp1592; -- SN 46 ID Superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis RQ 0 EV GenProp1635; -- SN 47 ID Superpathway of 5-aminoimidazole ribonucleotide biosynthesis RQ 0 EV GenProp1689; // AC GenProp0186 DE Storage and structural polymer biosynthesis TP CATEGORY AU Haft DH TH 0 CC The biosynthesis of polymers not including standard protein and CC polynucleotide biosynthesis. -- SN 1 ID Polyhydroxyalkanoic acids RQ 0 EV GenProp0055; -- SN 2 ID Cyanophycin-like storage polymers RQ 0 EV GenProp0156; -- SN 3 ID Glycogen system RQ 0 EV GenProp0168; -- SN 4 ID dTDP-L-rhamnose biosynthesis from dTDP-4-dehydro-L-rhamnose RQ 0 EV GenProp0183; -- SN 5 ID Lipopolysaccharide biosynthesis RQ 0 EV GenProp0297; -- SN 6 ID Exopolysaccharide biosynthesis, exosortase A-associated RQ 0 EV GenProp0652; -- SN 7 ID Exopolysaccharide biosynthesis, exosortase B-associated RQ 0 EV GenProp0655; -- SN 8 ID CMP-N-acetylneuraminate biosynthesis from UDP-N-acetylglucosamine RQ 0 EV GenProp0793; -- SN 9 ID Poly(gamma-glutamic acid) biosynthesis RQ 0 EV GenProp0822; -- SN 10 ID Poly-beta-1,6 N-acetyl-D-glucosamine system, PgaABCD type RQ 0 EV GenProp0907; -- SN 11 ID Cellulose biosynthesis RQ 0 EV GenProp0658; -- SN 12 ID CMP-N-acetylneuraminate biosynthesis I (eukaryotes) RQ 0 EV GenProp1737; -- SN 13 ID Peptidoglycan biosynthesis I (meso-diaminopimelate containing) RQ 0 EV GenProp1480; -- SN 14 ID Poly(glycerol phosphate) wall teichoic acid biosynthesis RQ 0 EV GenProp1398; -- SN 15 ID Poly(3-O-beta-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall teichoic acid biosynthesis RQ 0 EV GenProp1756; -- SN 16 ID UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) RQ 0 EV GenProp1448; -- SN 17 ID Kdo transfer to lipid IVA I RQ 0 EV GenProp1684; -- SN 18 ID Enterobacterial common antigen biosynthesis RQ 0 EV GenProp1270; -- SN 19 ID Lipid IVA biosynthesis RQ 0 EV GenProp1290; -- SN 20 ID Superpathway of (Kdo)2-lipid A biosynthesis RQ 0 EV GenProp1325; // AC GenProp0187 DE Pyrimidine (uridine-5'-phosphate) de novo biosynthesis TP PATHWAY AU Haft DH TH 4 DC Pyrimidine Biosynthesis DR IUBMB; misc; pyrimid; DC Pyrimidine metabolism DR KEGG; map00240; CC De novo pyrimidine biosynthesis procedes from HCO3 (bicarbonate), an NH2 CC group from glutamine or free ammonia, and aspartate. Firstly, CC carbamoyl-phosphate synthase produces carbamoyl phosphate, which is then CC condensed with L-aspartate to produce a ring compound, CC N-carbomoyl-L-aspartate, which is converted in two more steps into orotate. CC The ribose moiety is then added from CC alpha-D-5-P-ribosylpyrophosphate (PRPP), which is also a precursor of CC purines, histidine, and tryptophan. The resulting orotidine CC monophosphate is decarboxylated to uridine monophosphate (UMP), a CC pyrimidine nucleotide from which other pyrimidines are made. The few CC species lacking pyrimidine de novo biosynthesis include some members of CC the Chlamydiae, Mycoplasmatales, Rickettsiales, and Spirochaetes. -- SN 1 ID Ribose-phosphate pyrophosphokinase DN Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) RQ 1 EV IPR005946; TIGR01251; sufficient; TG GO:0006222; -- SN 2 ID Carbamoyl-phosphate synthase, small subunit DN Carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5) RQ 1 EV IPR006274; TIGR01368; sufficient; TG GO:0006222; -- SN 3 ID Carbamoyl-phosphate synthase, large subunit DN Carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5) RQ 1 EV IPR006275; TIGR01369; sufficient; TG GO:0006222; -- SN 4 ID Aspartate carbamoyltransferase DN Aspartate carbamoyltransferase (EC 2.1.3.2) RQ 1 EV IPR002082; TIGR00670; sufficient; TG GO:0006222; -- SN 5 ID Dihydroorotase DN Dihydroorotase (EC 3.5.2.3) RQ 1 EV IPR004721; TIGR00856; sufficient; TG GO:0006222; EV IPR004722; TIGR00857; sufficient; -- SN 6 ID Dihydroorotate dehydrogenase DN Dihydroorotate dehydrogenase/quinone (EC 1.3.5.2) RQ 1 EV IPR005719; TIGR01036; sufficient; TG GO:0006222; EV IPR005720; TIGR01037; sufficient; TG GO:0006222; EV IPR005720; PF01180; sufficient; TG GO:0006222; -- SN 7 ID Orotate phosphoribosyltransferase DN Orotate phosphoribosyltransferase (EC 2.4.2.10) RQ 1 EV IPR004467; TIGR00336; sufficient; TG GO:0006222; EV IPR006273; TIGR01367; sufficient; TG GO:0006222; -- SN 8 ID Orotidine 5'-phosphate decarboxylase DN Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) RQ 1 EV IPR014732; TIGR01740; sufficient; TG GO:0006222; EV IPR011995; TIGR02127; sufficient; TG GO:0006222; -- SN 9 ID Aspartate carbamoyltransferase, regulatory subunit DN Aspartate carbamoyltransferase, regulatory subunit RQ 0 EV IPR002801; TIGR00240; sufficient; TG GO:0006222; // AC GenProp0188 DE GatABC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase complex TP PATHWAY AU Haft DH TH 0 DC Glu-tRNA(Gln) amidotransferase DR MetaCyc; 6.3.5.7-RXN; CC The GatABC heterotrimer acts as an alternative to direct aminoacylation CC of tRNA(Gln), tRNA(Asn), or both with its respective amino acid. CC Rather, the tRNA may be misacylated with Glu in the place of Gln, or CC Asp in the place of Asn. The phylogenetic ranges over which GatABC CC orthologs act on Glu-tRNA(Gln), Asp-tRNA(Asn), or both are not fully CC worked out. It is both in Chlamydia, the Thermus-Deinococcus lineage, CC and Acidithiobacillus ferrooxidans. In the Archaea, GatDE act on CC Glu-tRNA(Gln) while GatABC act on Asp-tRNA(Asn). In Lactobacillus and CC possibly all Firmicutes, GatABC acts on Glu-tRNA(Gln) only. Note that CC the amidotransferase reaction is a mechanism not only to charge a tRNA CC with Asn or Gln, but to complete the synthesis of that amino acid. -- SN 1 ID Glutamyl-tRNA(Gln) amidotransferase, A subunit DN Aspartyl-tRNA(Asn)/glutamyl-tRNA (Gln) amidotransferase subunit A (EC 6.3.5.6/EC 6.3.5.7) RQ 1 EV IPR004412; TIGR00132; sufficient; -- SN 2 ID Glutamyl-tRNA(Gln) amidotransferase, B subunit DN Aspartyl-tRNA(Asn)/glutamyl-tRNA (Gln) amidotransferase subunit B (EC 6.3.5.6/EC 6.3.5.7) RQ 1 EV IPR004413; TIGR00133; sufficient; -- SN 3 ID Glutamyl-tRNA(Gln) amidotransferase, C subunit DN Aspartyl-tRNA(Asn)/glutamyl-tRNA (Gln) amidotransferase subunit C (EC 6.3.5.6/EC 6.3.5.7) RQ 1 EV IPR003837; TIGR00135; sufficient; EV IPR003837; PF02686; sufficient; // AC GenProp0189 DE tRNA-Gln direct aminoacylation TP PATHWAY AU Haft DH TH 0 CC The tRNA for Gln is produced, in different species, in two different CC ways. In some bacteria (including E. coli) and in the eukaryotic CC cytosol, the tRNA for glutamine is charged with glutamine. In the CC majority of sequenced prokaryotes however, tRNA(gln) initially is CC mischarged with glutamate (Glu). Glu is subsequently amidated to Gln CC while on the tRNA(gln), as by GatABC in Bacillus subtilis, resulting in CC Gln biosynthesis from Glu as well as tRNA aminoacylation. This property CC describes the pathway of direct Gln--tRNA ligase activity, performed by CC a single protein, glutaminyl-tRNA synthetase. -- SN 1 ID Glutaminyl-tRNA synthetase DN Glutamine-tRNA ligase (EC 6.1.1.18) RQ 1 EV IPR004514; TIGR00440; sufficient; TG GO:0006425; // AC GenProp0190 DE Phosphate ABC transporter (pstSCAB-phoU) TP SYSTEM AU Haft DH TH 0 RN [1] RM 11489853 RT Characterization of PitA and PitB from Escherichia coli. RA Harris RM, Webb DC, Howitt SM, Cox GB; RL J Bacteriol. 2001;183:5008-5014. CC This property represents an ABC-type transporter for inorganic CC phosphate P(i), consisting of genes related to the pstSCAB genes in CC Escherichia coli. In E. coli, pstSCAB represents a high-affinity CC transporter and is induced by low external P(i) concentrations; a CC constitutive, low affinity transporter PitA, is also found[1]. CC Included in this property is PhoU, a regulatory protein of unknown CC mechanism, generally found adjacent to the pstSCAB genes. -- SN 1 ID Regulatory protein PhoB DN Phosphate regulon transcriptional regulatory protein phoB RQ 0 EV IPR011879; TIGR02154; sufficient; TG GO:0051049; -- SN 2 ID Regulatory protein PhoR DN Phosphate regulon sensor protein phoR (EC 2.7.13.3) RQ 0 EV IPR014310; TIGR02966; sufficient; TG GO:0006817; -- SN 3 ID Regulatory protein PhoU DN Phosphate transport system regulatory protein PhoU RQ 0 EV IPR026022; PF01895; sufficient; TG GO:0051049; EV IPR028366; TIGR02135; sufficient; TG GO:0051049; -- SN 4 ID Permease pstA DN Phosphate ABC transporter, permease protein PtsA RQ 1 EV IPR005672; TIGR00974; sufficient; TG GO:0006817; -- SN 5 ID Phosphate transporter, ATP-binding protein PstB DN Phosphate ABC transporter, ATP-binding protein pstB (EC 3.6.3.27) RQ 1 EV IPR005670; TIGR00972; sufficient; TG GO:0006817; -- SN 6 ID Permease pstC DN Phosphate ABC transporter, permease protein PstC RQ 1 EV IPR011864; TIGR02138; sufficient; TG GO:0006817; -- SN 7 ID Periplasmic protein RQ 1 EV IPR005673; TIGR00975; sufficient; TG GO:0006817; EV IPR011862; TIGR02136; sufficient; TG GO:0006817; EV IPR030980; TIGR04505; TG GO:0006817; // AC GenProp0191 DE Sulfate/thiosulfate ABC transporter TP SYSTEM AU Haft DH TH 0 RN [1] RM 7608089 RT Sulfate and thiosulfate transport in Escherichia coli K-12: evidence RT for a functional overlapping of sulfate- and thiosulfate-binding RT proteins. RA Sirko A, Zatyka M, Sadowy E, Hulanicka D; RL J Bacteriol. 1995;177:4134-4136. RN [2] RM 3897189 RT Single transporter for sulfate, selenate, and selenite in Escherichia RT coli K-12. RA Lindblow-Kull C, Kull FJ, Shrift A; RL J Bacteriol. 1985;163:1267-1269. RN [3] RM 11421278 RT Molybdate transport. RA Self WT, Grunden AM, Hasona A, Shanmugam KT; RL Res Microbiol. 2001;152:311-321. CC This property describes an ATP-binding cassette (ABC) transporter CC complex for sulfate and some related anions. Gene symbols for these CC proteins reflect a role of sulfate import in cysteine biosynthesis. The CC complex consists of four proteins, an ATP-binding protein CysA, two CC homologous permeases CysT and CysW, and a binding protein. In the model CC bacterium Escherichia coli, two binding proteins designated Sbp and CC CysP are present, and appear to facilitate transport of both sulfate CC and thiosulfate ions [1]. Unlike the case for phosphate uptake, ABC CC transport appears to be the only mechanism for sulfate uptake. An older CC report finds the sulfate transporter in E. coli is also the sole CC transporter for selenate and selenite [2], and a review on the CC molybdate ABC transporter notes that, in absense of such a transporter, CC the sulfate transporter can take up molybdate [3]. -- SN 1 ID Sulfate transporter ATP-binding cassette protein CysA DN Sulfate ABC transporter ATP-binding protein CysA (EC 3.6.3.25) RQ 1 EV IPR005666; TIGR00968; sufficient; TG GO:0015709; -- SN 2 ID Sulfate ABC transporter, permease permT DN Sulfate ABC transporter, permease protein CysT RQ 1 EV IPR011865; TIGR02139; sufficient; TG GO:0015709; -- SN 3 ID Sulfate ABC transporter, permease protein CysW DN Sulfate ABC transporter, permease protein CysW RQ 1 EV IPR011866; TIGR02140; sufficient; TG GO:0015709; -- SN 4 ID Sulfate ABC transporter, binding protein DN Thiosulphate/Sulfate-binding protein RQ 1 EV IPR005669; TIGR00971; sufficient; TG GO:0015709; // AC GenProp0192 DE Molybdate ABC transporter TP SYSTEM AU Haft DH TH 0 RN [1] RM 11421278 RT Molybdate transport. RA Self WT, Grunden AM, Hasona A, Shanmugam KT; RL Res Microbiol. 2001;152:311-321. CC The high-affinity molybdate ABC transporter imports molybdate for the CC biosythesis of cofactors such as molybdopterin. Three structural CC components of this typical ABC transporter are the ATPase subunit, CC permease, and binding protein. These structural components appear in CC three gene clusters. A molybdate transport repressor is included as a CC non-required part of the system. It is noted that molybdate can also be CC transported by some sulfate/thiosulfate ABC transporters and CC non-specific anion transporters [1]. -- SN 1 ID Molybdate ABC transporter, ATP-binding protein (EC 3.6.3.29) DN Molybdate ABC transporter, ATP-binding protein (EC 3.6.3.29) RQ 1 EV IPR011868; TIGR02142; sufficient; TG GO:0015689; -- SN 2 ID Molybdate ABC transporter, molybdate binding protein DN Molybdenum ABC transporter, periplasmic binding protein RQ 1 EV IPR005950; TIGR01256; sufficient; TG GO:0015689; -- SN 3 ID Molybdate ABC transporter, permease DN Molybdate ABC transporter, permease protein RQ 1 EV IPR011867; TIGR02141; sufficient; TG GO:0015689; -- SN 4 ID Molybdate transport repressor DN Molybdate transport repressor ModE RQ 0 EV IPR003725; TIGR00637; sufficient; // AC GenProp0193 DE Lysine biosynthesis via alpha-aminoadipate (AAA pathway) TP PATHWAY AU Haft DH TH 6 RN [1] RM 10613839 RT A prokaryotic gene cluster involved in synthesis of lysine through the RT amino adipate pathway: a key to the evolution of amino acid RT biosynthesis. RA Nishida H, Nishiyama M, Kobashi N, Kosuge T, Hoshino T, Yamane H; RL Genome Res. 1999;9:1175-1183. DC L-lysine biosynthesis V DR MetaCyc; PWY-3081; DC Lysine biosynthesis DR KEGG; map00300; CC Lysine biosynthesis in fungi has been characterized and begins with the CC condensation of 2-oxoglutarate and acetyl-CoA to homocitrate and CC continues through the distinctive intermediate, alpha-aminoadipate. CC This pathway is distinct in every respect from the diaminopimelate CC pathway commonly found in bacteria and animals. Recently, an CC alpha-aminoadipate pathway closely related to the fungal version has CC been characterized in Thermus thermophilus [1] and appears to be widely CC distributed among the archaea. -- SN 1 ID Homocitrate synthase DN Homocitrate synthase (EC 2.3.3.14) RQ 1 EV IPR011830; TIGR02090; sufficient; EV IPR011872; TIGR02146; sufficient; -- SN 2 ID Homoaconitate hydratase, LysT subunit DN Homoaconitase/3-isopropylmalate dehydratase, large subunit/LeuC (EC 4.2.1.33) RQ 1 EV IPR011823; TIGR02083; sufficient; EV IPR006251; TIGR01343; sufficient; -- SN 3 ID Homoaconitate hydratase, LysU subunit DN 3-isopropylmalate dehydratase small subunit/LeuD (EC 4.2.1.33) RQ 1 EV IPR011827; TIGR02087; sufficient; -- SN 6 ID Alpha-aminoadipate acylase (proposed) DN Lysine biosynthesis enzyme LysX (EC 6.3.2.-) RQ 1 EV IPR011870; TIGR02144; sufficient; -- SN 7 ID Epsilon-carboxykinase (proposed) DN Acetylglutamate kinase/LysZ RQ 1 EV IPR004662; TIGR00761; sufficient; -- SN 8 ID Epsilon-dehydrogenase (proposed) DN LysW-L-glutamate phosphate reductase/LysY RQ 1 EV IPR000706; TIGR01850; sufficient; -- SN 9 ID Aminotransferase DN Acetylornithine/Succinylornithine transaminase/LysJ RQ 1 EV IPR004636; TIGR00707; sufficient; -- SN 10 ID Acylase DN [LysW]-lysine/[LysW]-ornithine hydrolase/LysK (EC 3.5.1.-) RQ 1 EV IPR010175; TIGR01902; sufficient; // AC GenProp0196 DE Sulfur metabolism TP CATEGORY AU Haft DH TH 0 DC Sulfur metabolism DR KEGG; map00920; CC Processes handling and interconverting sulfur-containing molecules. CC This does not include cysteine and methionine-containing proteins. -- SN 1 ID Glutathione biosynthesis RQ 0 EV GenProp0030; -- SN 2 ID Biotin biosynthesis RQ 0 EV GenProp0036; -- SN 3 ID Iron-sulfur cluster assembly systems RQ 0 EV GenProp0140; -- SN 4 ID Dissimilatory sulfate reduction RQ 0 EV GenProp0155; -- SN 5 ID Reduction of oxidized methionine RQ 0 EV GenProp0182; -- SN 6 ID Sulfate/thiosulfate ABC transporter RQ 0 EV GenProp0191; -- SN 7 ID Sulfite reductase complex, Salmonella/Clostridium type RQ 0 EV GenProp0624; -- SN 8 ID Intracellular sulfur oxidation RQ 0 EV GenProp0654; -- SN 9 ID Methionine salvage from methylthioadenosine RQ 0 EV GenProp0729; -- SN 10 ID Dimethyl sulphone utilization (aerobic) RQ 0 EV GenProp0934; -- SN 11 ID Thiosulfate oxidation to sulfate RQ 0 EV GenProp1088; -- SN 12 ID Sulfate activation for sulfonation RQ 0 EV GenProp1573; // AC GenProp0197 DE Protein biosynthesis TP CATEGORY AU Haft DH TH 0 CC The formation of proteins from amino acid building blocks. -- SN 1 ID Transcription termination/antitermination Nus factors RQ 0 EV GenProp0132; -- SN 2 ID GatABC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase complex RQ 0 EV GenProp0188; -- SN 3 ID tRNA-Gln direct aminoacylation RQ 0 EV GenProp0189; -- SN 4 ID tRNA aminoacylation RQ 0 EV GenProp0258; -- SN 5 ID tRNA-Asn direct aminoacylation RQ 0 EV GenProp0259; -- SN 6 ID Cysteine biosynthesis, tRNA-dependent RQ 0 EV GenProp0304; -- SN 7 ID Sigma-54 (RpoN) systems RQ 0 EV GenProp0634; -- SN 8 ID Selenouridine-containing tRNA RQ 0 EV GenProp0692; -- SN 9 ID tRNA U34 carboxymethylaminomethyl modification RQ 0 EV GenProp0704; -- SN 10 ID Translation initiation, bacterial RQ 0 EV GenProp0740; -- SN 11 ID Translation elongation, bacterial RQ 0 EV GenProp0741; -- SN 12 ID Translation termination, bacterial RQ 0 EV GenProp0746; -- SN 13 ID Rho-dependent termination RQ 0 EV GenProp0812; -- SN 14 ID Ribosome biogenesis proteins, bacteria RQ 0 EV GenProp0802; -- SN 15 ID YgjD-YeaZ-YjeE complex RQ 0 EV GenProp1171; -- SN 16 ID mTORC1 activation RQ 0 EV GenProp2033; -- SN 17 ID mTORC1 pathway RQ 0 EV GenProp2035; // AC GenProp0198 DE RuvABC Holliday junction complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 12423347 RT The RuvABC resolvasome. RA Dickman MJ, Ingleston SM, Sedelnikova SE, Rafferty JB, Lloyd RG, Grasby RA JA, Hornby DP; RL Eur J Biochem. 2002;269:5492-5501. RN [2] RM 12382111 RT Holliday junction-resolving enzymes from eight hyperthermophilic RT archaea differ in reactions with cruciform DNA. RA Neef K, Birkenbihl RP, Kemper B; RL Extremophiles. 2002;6:359-367. RN [3] RM 11251805 RT The X philes: structure-specific endonucleases that resolve Holliday RT junctions. RA Sharples GJ; RL Mol Microbiol. 2001;39:823-834. DC Resolvasome DR MetaCyc; RUVABC-CPLX; CC RuvA, RuvB and RuvC proteins together act on Holliday junctions for CC homologous recombination and DNA repair. RuvAB is the branch migration CC complex and RuvC the resolvase [1]. The system is strictly bacterial; CC proteins with little or no detectable sequence similarity process CC Holliday junctions in Archaea, eukaryotes, and some phage. A variety of CC Holliday junction-cleaving (Hjc) enzymes have been found in the Archaea CC [2]. Holliday junction resolvases, including RuvC, Hjc and CC Hje, CCE1 (yeast) and A22R (poxviruses) are reviewed by Sharples [3]. CC RuvC is replaced by RecU in firmicutes and mollicutes. -- SN 1 ID RuvA subunit, Holliday junction DNA helicase DN Holliday junction DNA helicase RuvA RQ 1 EV IPR000085; TIGR00084; sufficient; TG GO:0006310; -- SN 2 ID RuvB subunit, Holliday junction DNA helicase DN Holliday junction DNA helicase RuvB RQ 1 EV IPR004605; TIGR00635; sufficient; TG GO:0006310; -- SN 3 ID RuvC (or RecU) resolvase DN Crossover junction endodeoxyribonuclease RuvC RQ 1 EV IPR002176; TIGR00228; sufficient; TG GO:0006310; EV IPR004612; TIGR00648; sufficient; TG GO:0006310; // AC GenProp0199 DE Lysine biosynthesis TP METAPATH AU Haft DH TH 0 DC Lysine biosynthesis DR KEGG; map00300; DC Lysine biosynthesis I DR MetaCyc; DAPLYSINESYN-PWY; DC Lysine biosynthesis II DR MetaCyc; PWY-2941; DC Lysine biosynthesis IV DR MetaCyc; LYSINE-AMINOAD-PWY; DC Lysine biosynthesis III DR MetaCyc; PWY-2942; CC The basic amino acid lysine may be synthesized by one of two types of CC pathways in prokaryotes, diaminopimelate (DAP) pathways and the CC alpha-aminoadipate (AAA) pathway. DAP pathways have several variants CC including the dehydrogenase (reductive) pathway which requires ammonia CC and NADPH, and the acetylated and succinylated pathways which do not. CC A non-reductive pathway which uses neither acetate or succinate CC protecting groups is found in plants but has not been observed in CC prokaryotes. The AAA pathway has a variant found in fungi and plants CC which has not been observed in prokaryotes. -- SN 1 ID Lysine biosynthesis pathways RQ 1 EV GenProp0125; EV GenProp0193; EV GenProp0788; // AC GenProp0201 DE SMC-ScpA-ScpB complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 12100548 RT Discovery of two novel families of proteins that are proposed to RT interact with prokaryotic SMC proteins, and characterization of the RT Bacillus subtilis family members ScpA and ScpB. RA Soppa J, Kobayashi K, Noirot-Gros MF, Oesterhelt D, Ehrlich SD, Dervyn RA E, Ogasawara N, Moriya S; RL Mol Microbiol. 2002;45:59-71. RN [2] RM 15009890 RT The bacterial condensin/cohesin-like protein complex acts in DNA repair RT and regulation of gene expression. RA Dervyn E, Noirot-Gros MF, Mervelet P, McGovern S, Ehrlich SD, Polard P, RA Noirot P; RL Mol Microbiol. 2004;51:1629-1640. CC scpA and scpB (segregation and condensation) are proposed [1,2] to act CC with SMC (structural maintenance of chromosome) in chromosome CC organization. SMC is not universal, but is found in Eukaryotes, Archaea, CC and Bacteria. It is homodimeric in Archaea and Bacteria. A mutation CC study [2] has shown a role for scpA in DNA repair in addition to its CC role in chromosome condensation and segregation. Proteins that act with CC SMC may be termed kleisins. Different SMC/kleisin complexes are termed CC cohesins and condensins. ScpA and ScpB are clustered in most bacteria. CC SMC and scpA tend to be clustered in the archaea. -- SN 1 ID Smc protein DN Structural maintenance of chromosomes protein, SMC RQ 1 EV IPR011890; TIGR02168; sufficient; TG GO:0030261; EV IPR011890; TIGR02169; sufficient; TG GO:0030261; -- SN 2 ID ScpA protein DN Segregation and condensation protein A RQ 1 EV IPR003768; PF02616; sufficient; TG GO:0030261; -- SN 3 ID ScpB protein DN Segregation and condensation protein B RQ 1 EV IPR005234; TIGR00281; sufficient; TG GO:0030261; // AC GenProp0202 DE Nitrogen metabolism TP CATEGORY AU Haft DH TH 0 DC Nitrogen metabolism DR KEGG; map00910; CC Processes handling and interconverting nitrogen-containing molecules. -- SN 1 ID Nitrogen fixation RQ 0 EV GenProp0029; -- SN 2 ID Membrane-associated monooxygenase (methane/ammonia) RQ 0 EV GenProp0666; -- SN 3 ID Formate-dependent nitrite reductase, seven-gene type RQ 0 EV GenProp0682; -- SN 4 ID Cytochrome c nitrite reductase NrfHA RQ 0 EV GenProp0683; -- SN 5 ID Urea utilization RQ 0 EV GenProp0814; -- SN 6 ID Nitrile hydratase RQ 0 EV GenProp0899; // AC GenProp0203 DE LPS inner core biosynthesis, ketodeoxyoctonate and heptose type TP PATHWAY AU Haft DH TH 0 RN [1] RM 26981280 RT Synthesis and Evaluation of Mannitol-Based Inhibitors for RT Lipopolysaccharide Biosynthesis. RA Johnsson RE; RL Int J Med Chem. 2016;2016:3475235. CC Lipopolysaccharide (LPS) occurs broadly in Gram-negative bacterial CC outer membrane. Three parts are termed lipid A, the oligosaccharide CC core, and O antigen [1]. If lacking the repeating O-antigen, it may be CC termed Lipooligosaccharide (LOS). The core is often described as having CC inner and outer regions, and is variable among species that contain CC LPS/LOS. This property describes a widely distributed common chemistry CC for the inner core. At least two residues of CC 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) are present, one of which has CC the lipid A moeity is attached. The inner core in E. coli and many CC other bacteria also contains at least two heptose residues, added by CC distinct heptosyltransferases I and II. -- SN 1 ID D-sedoheptulose 7-phosphate isomerase DN D-sedoheptulose 7-phosphate isomerase/GmhA RQ 1 EV IPR004515; TIGR00441; -- SN 2 ID D,D-heptose 1,7-bisphosphate phosphatase DN D,D-heptose 1,7-bisphosphate phosphatase/GmhB RQ 1 EV IPR004446; TIGR00213; -- SN 3 ID ADP-L-glycero-D-mannoheptose-6-epimerase DN ADP-L-glycero-D-mannoheptose-6-epimerase/HldD RQ 1 EV IPR011912; TIGR02197; sufficient; -- SN 4 ID RfaE bifunc, domain II DN RfaE bifunc, domain II/HldE_C RQ 1 EV IPR011914; TIGR02199; sufficient; -- SN 5 ID RfaE bifunc, domain I DN RfaE bifunc, domain I/HldE_N RQ 1 EV IPR011913; TIGR02198; sufficient; -- SN 6 ID Heptosyltransferase I DN Heptosyltransferase I/WaaC RQ 1 EV IPR011908; TIGR02193; sufficient; -- SN 7 ID Heptosyltransferase II DN Heptosyltransferase II/WaaF RQ 1 EV IPR011910; TIGR02195; sufficient; -- SN 8 ID Lipopolysaccharide core biosynthesis protein RfaP DN Lipopolysaccharide core biosynthesis protein RfaP/WaaP RQ 0 EV IPR010440; PF06293; -- SN 9 ID Heptosyltransferase III DN Heptosyltransferase III/WaaQ RQ 0 EV IPR011916; TIGR02201; sufficient; -- SN 10 ID Lipopolysaccharide core biosynthesis protein RfaY DN Lipopolysaccharide core biosynthesis protein RfaY/WaaY RQ 0 EV IPR009330; PF06176; -- SN 11 ID Kdo-III transferase DN Kdo-III transferase/WaaZ RQ 0 EV IPR031026; TIGR04437; // AC GenProp0204 DE KDO(2)-lipid A (Re LPS) biosynthesis and delivery TP METAPATH AU Haft DH TH 0 RN [1] RM 17056748 RT Characterization of lptA and lptB, two essential genes implicated in RT lipopolysaccharide transport to the outer membrane of Escherichia coli. RA Sperandeo P, Cescutti R, Villa R, Di Benedetto C, Candia D, Dehò G, RA Polissi A; RL J Bacteriol. 2007;189:244-253. DC Lipid-A-precursor biosynthesis DR MetaCyc; NAGLIPASYN-PWY; CC Lipid A is a component of the outer leaflet of the outer membrane of CC most gram-negative bacteria. It is one of three regions of bacterial CC lipopolysaccharide (LPS), along with the oligosaccharide core and the CC repeating O-antigen. In some strains, O-antigen may be missing and the CC lipid A-containing material may be designated lipooligosaccharide CC (LOS). Lipid A consists of a disaccharide (often CC beta-D-GlcN-(1-->6)-D-GlcN) with four attached acyl groups. Lipid A is CC attached to a 3-deoxy-D-manno-oct-2-ulosonic acid (KDO), a sugar moeity CC that becomes part of the LPS oligosaccharide inner core. Two of the acyl CC groups of lipid A are then modified by further acylations into branched CC structures; acylation varies somewhat by species, and sometimes CC according to conditions within a species. The inner core typically CC contains at least two KDO and two heptose residues. The outer core and CC O-antigen regions are far more variable, and their biosynthesis is CC modeled in this property. LPS biosynthesis mutational studies have CC shown that in a number of species, lipid A with two KDO residues but CC no additional residues of the inner core, is the minimum required form CC of LPS for viability, called Re LPS or Re endotoxin. This genome CC property describes a set of well-conserved enzymes for the biosynthesis CC of KDO(2)-lipid A that resembles, but is not necessarily identical to CC (nor as active in endotoxin assays as), the Re endotoxin of E. coli, as CC well as a transporter (or flippase) responsible in most Proteobacteria CC for positioning lipid A in the outer membrane. -- SN 1 ID Source of UDP-N-acetylglucosamine DN Source of UDP-N-acetylglucosamine RQ 0 EV GenProp0750; -- SN 2 ID Lipid A exporter MsbA DN Lipid A exporter MsbA RQ 0 EV IPR011917; TIGR02203; sufficient; -- SN 3 ID KDO-8 phosphate synthetase DN KDO-8 phosphate synthetase RQ 1 EV IPR006269; TIGR01362; sufficient; -- SN 4 ID KDO cytidylyltransferase DN KDO cytidylyltransferase RQ 0 EV IPR004528; TIGR00466; sufficient; -- SN 5 ID KDO 8-P phosphatase DN KDO 8-P phosphatase RQ 1 EV IPR010023; TIGR01670; sufficient; -- SN 6 ID UDP-N-acetylglucosamine O-acyltransferase DN Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase RQ 1 EV IPR010137; TIGR01852; sufficient; -- SN 7 ID Lipid-A-disaccharide synthase DN Lipid-A-disaccharide synthase RQ 1 EV IPR003835; TIGR00215; sufficient; -- SN 8 ID UDP-3-0-acyl N-acetylglucosamine deacetylase DN UDP-3-0-acyl N-acetylglucosamine deacetylase RQ 1 EV IPR004463; TIGR00325; sufficient; -- SN 9 ID UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase DN UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase RQ 1 EV IPR007691; TIGR01853; sufficient; -- SN 10 ID UDP-2,3-diacylglucosamine hydrolase DN UDP-2,3-diacylglucosamine hydrolase RQ 1 EV IPR010138; TIGR01854; sufficient; EV IPR010415; PF06230; -- SN 11 ID Tetraacyldisaccharide 4'-kinase DN Tetraacyldisaccharide 4'-kinase RQ 1 EV IPR003758; TIGR00682; sufficient; -- SN 12 ID Add lauroyl to lipid IV-A DN Add lauroyl to lipid IV-A RQ 1 EV IPR011920; TIGR02207; sufficient; EV IPR004960; PF03279; sufficient; -- SN 13 ID Acylate lauroyl-lipid IV-A DN Acylate lauroyl-lipid IV-A RQ 0 EV IPR011921; TIGR02208; sufficient; -- SN 14 ID Temporary_lpxH candidate DN Temporary_lpxH candidate RQ 0 -- SN 15 ID Transferase DN Transferase RQ 1 EV IPR007507; PF04413; sufficient; // AC GenProp0207 DE Lipoprotein localization system lolABCDE TP SYSTEM AU Haft DH TH 0 RN [1] RM 10783239 RT A new ABC transporter mediating the detachment of lipid-modified RT proteins from membranes. RA Yakushi T, Masuda K, Narita S, Matsuyama S, Tokuda H; RL Nat Cell Biol. 2000;2:212-218. RN [2] RM 12823819 RT A mutation in the membrane subunit of an ABC transporter LolCDE complex RT causing outer membrane localization of lipoproteins against their inner RT membrane-specific signals. RA Narita S, Kanamaru K, Matsuyama S, Tokuda H; RL Mol Microbiol. 2003;49:167-177. RN [3] RM 11673422 RT Deletion of lolB, encoding an outer membrane lipoprotein, is lethal for RT Escherichia coli and causes accumulation of lipoprotein localization RT intermediates in the periplasm. RA Tanaka K, Matsuyama SI, Tokuda H; RL J Bacteriol. 2001;183:6538-6542. CC Bacterial lipoproteins have a modified amino terminal Cys residue with CC a covalently attached lipid moiety that serves as a membrane anchor. CC The lol system is responsible for moving lipoproteins from the CC periplasmic side of the inner membrane to the periplasmic side of the CC outer membrane. LolD is homologous to the ATP-binding cassette (ABC) CC transport family [1,2]. LolC and LolE are homologous to each other (in CC species that have both rather than just one) and have several CC membrane-spanning segments, much like ABC transport permeases[3]. However, CC the LolCDE complex differs from other ABC transporters in that is does CC not move a substrate across a membrane. Instead, it detaches CC lipoproteins from the inner membrane. LolA and LolB act to chaperone CC lipoproteins, including LolB itself, to the outer membrane. This system CC is less broadly distributed than the lgt/lsp/lnt system for lipoprotein CC N-terminal modification. -- SN 1 ID Lipoprotein carrier LolA DN Outer membrane lipoprotein carrier protein LolA RQ 1 EV IPR018323; TIGR00547; sufficient; TG GO:0006886; -- SN 2 ID Outer membrane LP LolB DN Outer membrane lipoprotein LolB RQ 1 EV IPR004565; TIGR00548; sufficient; TG GO:0006886; -- SN 3 ID Lipoprotein export, LolC and LolE family DN Lipoprotein releasing system, transmembrane protein, LolC/E family RQ 1 EV IPR011925; TIGR02212; sufficient; TG GO:0006886; -- SN 4 ID Transporter ATP-binding subunit LolD DN Lipoprotein-releasing system ATP-binding protein RQ 1 EV IPR011924; TIGR02211; sufficient; TG GO:0006886; // AC GenProp0208 DE Phage: major features TP GUILD AU Haft DH TH 1 CC Protein families related to head morphogenesis, DNA packaging, tail CC structure, and lysis. -- SN 1 ID Major capsid protein DN Phage major capsid protein RQ 1 EV IPR006441; TIGR01551; sufficient; EV IPR006441; PF05125; sufficient; EV IPR024455; TIGR01554; sufficient; EV IPR005564; PF03864; sufficient; EV IPR003514; PF02305; sufficient; EV IPR024659; PF11651; -- SN 2 ID Any phage holin DN Phage holin RQ 1 EV IPR006479; TIGR01592; sufficient; EV IPR006479; PF04688; sufficient; EV IPR006480; TIGR01593; sufficient; EV IPR006481; TIGR01594; sufficient; EV IPR006481; PF05106; sufficient; EV IPR006485; TIGR01598; sufficient; EV IPR006485; PF04531; sufficient; EV IPR006493; TIGR01606; sufficient; EV IPR006493; PF05102; sufficient; EV IPR007633; PF04550; sufficient; EV IPR009708; PF06946; sufficient; EV IPR010026; TIGR01673; sufficient; -- SN 3 ID Major tail protein DN Major tail protein RQ 0 EV IPR006490; TIGR01603; sufficient; EV IPR006724; PF04630; sufficient; EV IPR011855; TIGR02126; sufficient; EV IPR011855; PF06199; sufficient; -- SN 4 ID Various structural components RQ 0 EV IPR006487; TIGR01600; sufficient; EV IPR006487; PF05100; sufficient; EV IPR006498; TIGR01611; sufficient; EV IPR006498; PF04985; sufficient; EV IPR006521; TIGR01634; sufficient; EV IPR006522; TIGR01635; sufficient; EV IPR006528; PF04233; sufficient; EV IPR006528; TIGR01641; sufficient; EV IPR006949; PF04865; sufficient; EV IPR007119; TIGR01665; sufficient; EV IPR008020; PF05371; sufficient; EV IPR008018; PF05354; sufficient; EV IPR008767; TIGR01563; sufficient; EV IPR008768; PF05396; sufficient; EV IPR009225; PF05926; sufficient; EV IPR009228; PF05929; sufficient; EV IPR009350; TIGR01715; sufficient; EV IPR009493; PF06528; sufficient; EV IPR009636; PF06810; sufficient; EV IPR010027; TIGR01674; sufficient; EV IPR010411; PF06222; sufficient; EV IPR013046; TIGR01644; sufficient; EV IPR021145; PF05133; sufficient; EV IPR035089; PF04984; sufficient; -- SN 5 ID Portal protein DN Phage portal protein RQ 1 EV IPR006427; TIGR01537; sufficient; EV IPR006428; TIGR01538; sufficient; EV IPR006429; TIGR01539; sufficient; EV IPR006429; PF05136; sufficient; EV IPR006430; TIGR01540; sufficient; EV IPR006432; TIGR01542; sufficient; EV IPR006944; PF04860; sufficient; EV IPR021145; PF05133; sufficient; -- SN 6 ID Prohead protease DN Prohead protease RQ 1 EV IPR005082; PF03420; sufficient; EV IPR006433; TIGR01543; sufficient; EV IPR006433; PF04586; sufficient; -- SN 7 ID Replication proteins DN Replication proteins RQ 0 EV IPR006497; TIGR01610; EV IPR019889; TIGR03600; -- SN 8 ID More tail proteins RQ 0 EV IPR005003; PF03335; sufficient; EV IPR005068; PF03406; sufficient; EV IPR005601; PF03903; sufficient; EV IPR005604; PF03906; sufficient; EV IPR006520; TIGR01633; sufficient; EV IPR008861; PF05489; sufficient; EV IPR009312; PF06141; sufficient; EV IPR009678; PF06891; sufficient; EV IPR010027; PF06894; sufficient; EV IPR010265; PF05939; sufficient; EV IPR010633; PF06763; sufficient; EV IPR010654; PF06805; sufficient; EV IPR011748; TIGR02242; sufficient; EV IPR024455; PF05065; sufficient; EV IPR035089; PF04984; sufficient; -- SN 9 ID Tail tape measure protein DN Tail tape measure protein RQ 0 EV IPR006431; TIGR01541; sufficient; EV IPR009302; PF06120; EV IPR009628; PF06791; sufficient; EV IPR010090; TIGR01760; sufficient; EV IPR013491; TIGR02675; sufficient; -- SN 10 ID Terminase, large subunit DN Phage terminase, large subunit RQ 1 EV IPR005021; PF03354; sufficient; EV IPR006437; TIGR01547; sufficient; EV IPR008866; PF05876; sufficient; EV IPR010332; PF06056; sufficient; EV IPR035412; PF04466; sufficient; -- SN 11 ID Terminase, small subunit DN Phage terminase, small subunit RQ 1 EV IPR005335; PF03592; sufficient; EV IPR006448; TIGR01558; sufficient; EV IPR006448; PF05119; sufficient; EV IPR010270; PF05944; sufficient; EV IPR010789; PF07141; sufficient; -- SN 12 ID Uncharacterized phage proteins RQ 0 EV IPR006445; TIGR01555; sufficient; EV IPR006505; TIGR01618; sufficient; EV IPR006517; TIGR01630; sufficient; EV IPR009750; PF07026; sufficient; EV IPR009752; PF07030; sufficient; EV IPR009773; PF07066; sufficient; EV IPR006450; TIGR01560; sufficient; EV IPR010022; TIGR01669; sufficient; EV IPR010024; TIGR01671; sufficient; EV IPR010064; TIGR01725; sufficient; EV IPR010064; PF04883; sufficient; EV IPR010877; PF07409; sufficient; EV IPR011738; TIGR02215; sufficient; EV IPR011739; TIGR02216; sufficient; EV IPR011741; TIGR02220; sufficient; EV IPR014054; TIGR02681; sufficient; // AC GenProp0209 DE Sec system preprotein translocase TP SYSTEM AU Haft DH TH 1 RN [1] RM 22411975 RT The bacterial Sec-translocase: structure and mechanism. RA Lycklama A Nijeholt JA, Driessen AJ; RL Philos Trans R Soc Lond B Biol Sci. 2012;367:1016-1028. CC This property describes the bacterial preprotein translocase Sec[1]. The CC analogous process occurs in eukaryotes and archaea (little studied in CC the archaea), but the component proteins are different enough not to be CC described by the same set of hidden Markov models. SecB is a cytosolic CC export-specific chaperone in E. coli and some related species, but is CC not broadly distributed. SecA, the ATPase that powers the translocase, CC is a peripheral membrane protein. SecY, SecE, and SecG form the CC heterotrimeric translocase, although SecG is not essential at some CC temperatures. SecD, SecG, and YajC form an accessory complex that may CC prevent backsliding of proteins being translocated, and may not be CC essential proteins. -- SN 1 ID Inner membrane protein oxaA DN Membrane insertase Oxa1/YidC RQ 0 EV IPR028053; TIGR03593; EV IPR028055; TIGR03592; EV IPR001708; PF02096; -- SN 2 ID SecA peripheral ATPase DN Preprotein translocase, SecA subunit RQ 1 EV IPR000185; TIGR00963; sufficient; -- SN 3 ID SecB cytosolic chaperone DN Bacterial protein export chaperone SecB RQ 0 EV IPR003708; TIGR00809; sufficient; -- SN 4 ID SecD accessory complex subunit DN Protein translocase subunit SecD RQ 0 EV IPR005791; TIGR01129; sufficient; -- SN 5 ID SecE core heterotrimer subunit DN Preprotein translocase, SecE subunit RQ 1 EV IPR005807; TIGR00964; sufficient; -- SN 6 ID SecF accessory complex subunit DN Protein-export membrane protein SecF RQ 0 EV IPR005665; TIGR00966; sufficient; -- SN 7 ID SecG core heterotrimer subunit DN Preprotein translocase, SecG subunit RQ 1 EV IPR004692; TIGR00810; sufficient; -- SN 8 ID SecY core heterotrimer subunit DN SecY/SEC61-alpha family RQ 1 EV IPR002208; TIGR00967; sufficient; -- SN 9 ID YajC accessory complex subunit DN Preprotein translocase, YajC subunit RQ 0 EV IPR003849; TIGR00739; sufficient; // AC GenProp0213 DE Resistance to Reactive Oxygen Species (ROS) TP GUILD AU Haft DH TH 0 CC A number of systems have evolved to protect cells from reactive oxygen CC species (peroxides, superoxides, hydroxyl radicals, etc.) This CC property creates a list of those genes identified as being related to CC this protective role. -- SN 1 ID Catalases RQ 0 EV IPR011614; PF00199; sufficient; EV IPR007760; PF05067; sufficient; EV IPR000763; TIGR00198; sufficient; -- SN 2 ID Methionine sulfoxide reductases RQ 0 EV IPR002579; TIGR00357; sufficient; EV IPR002569; TIGR00401; sufficient; EV IPR002569; PF01625; sufficient; -- SN 3 ID Peroxidases RQ 0 EV IPR000763; TIGR00198; sufficient; EV IPR004674; TIGR00777; sufficient; EV IPR000028; PF01328; sufficient; EV IPR000889; PF00255; sufficient; EV IPR019791; PF03098; sufficient; EV IPR004852; PF03150; sufficient; EV IPR017559; TIGR03137; sufficient; -- SN 4 ID Superoxide dismutases RQ 0 EV IPR001424; PF00080; sufficient; EV IPR019831; PF00081; sufficient; EV IPR019832; PF02777; sufficient; EV IPR014123; TIGR02753; sufficient; // AC GenProp0214 DE Acetyl-CoA carboxylase complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 12121720 RT Multi-subunit acetyl-CoA carboxylases. RA Cronan JE, Waldrop GL; RL Prog Lipid Res. 2002;41:407-435. CC This property describes the acetyl-CoA carboxylase complex, which CC catalyzes the first committed step of fatty acid biosynthesis, the CC carboxylation of acetyl-CoA to malonyl-CoA. The four-subunit version CC usually found in prokaryotes is described by this property [1]. -- SN 1 ID Acetyl-CoA carboxylase, carboxyl transferase, alpha subunit DN Acetyl-CoA carboxylase, alpha subunit RQ 1 EV IPR001095; TIGR00513; sufficient; TG GO:0009317; -- SN 2 ID Acetyl-CoA carboxylase, biotin carboxyl carrier protein DN Acetyl-CoA biotin carboxyl carrier RQ 1 EV IPR001249; TIGR00531; sufficient; TG GO:0009317; -- SN 3 ID Acetyl-CoA carboxylase, biotin carboxylase DN Acetyl-CoA carboxylase, biotin carboxylase RQ 1 EV IPR004549; TIGR00514; sufficient; TG GO:0009317; -- SN 4 ID Acetyl-CoA carboxylase, carboxyl transferase, beta subunit DN Acetyl-CoA carboxylase carboxyl transferase, beta subunit RQ 1 EV IPR000438; TIGR00515; sufficient; TG GO:0009317; // AC GenProp0215 DE SOS response TP SYSTEM AU Haft DH TH 0 CC The SOS response controls both accurate and potentially mutagenic DNA CC repair functions, and requires the recA and lexA gene products. LexA is CC a repressor protein that binds to a site (the SOS box) located near the CC promoters of the SOS response genes and interferes with the binding of CC RNA polymerase. The recA gene product is required not only for the CC regulation of the SOS response, but also for homologous recombination CC and for various other DNA repair and damage tolerance pathways. -- SN 1 ID LexA repressor DN Transcription regulator LexA RQ 1 EV IPR006200; TIGR00498; sufficient; -- SN 2 ID RecA protein DN DNA recombination and repair protein RecA RQ 1 EV IPR013765; TIGR02012; sufficient; // AC GenProp0216 DE RecBCD pathway TP SYSTEM AU Haft DH TH 0 RN [1] RM 28369478 RT A non-catalytic role of RecBCD in homology directed gap repair and RT translesion synthesis. RA Laureti L, Lee L, Philippin G, Pages V; RL Nucleic Acids Res. 2017;45:5877-5886. RN [2] RM 14604803 RT The genome stability in Corynebacterium species due to lack of the RT recombinational repair system. RA Nakamura Y, Nishio Y, Ikeo K, Gojobori T; RL Gene. 2003;317:149-155. RN [3] RM 12815437 RT RecBCD enzyme is a DNA helicase with fast and slow motors of opposite RT polarity. RA Taylor AF, Smith GR; RL Nature. 2003;423:889-893. CC This property describes the presence of genes for the RecBCD protein CC complex, which participates in at least two different processes. As CC exodeoxyribonuclease V, it degrades linear double-stranded DNA, as CC might occur by cleavage of exogenous DNA by restriction systems. It CC also acts to repair double-stranded breaks in DNA by homologous CC recombination [1]; genera that lack this complex tend to show stronger CC conservation of gene order between species[2]. The RecBCD heterotrimer CC interacts with instances of the DNA sequence GCTGGTGG in E. coli, CC called Chi, which are recombinational hotspots. RecBCD promotes loading CC the strand exchange protein RecA onto chi-containing DNA[3]. CC Double-stranded breaks are processed by AddAB rather than by RecBCD in CC the Firmicutes and in alpha-Proteobacteria. -- SN 1 ID Exodeoxyribonuclease V, beta subunit DN RecBCD enzyme subunit RecB (EC:3.1.11.5) RQ 1 EV IPR004586; TIGR00609; sufficient; TG GO:0000738; -- SN 2 ID Exodeoxyribonuclease V, gamma subunit DN RecBCD enzyme subunit RecC (EC:3.1.11.5) RQ 1 EV IPR006697; TIGR01450; sufficient; TG GO:0000738; -- SN 3 ID Exodeoxyribonuclease V, alpha subunit DN RecBCD enzyme subunit RecD (EC:3.1.11.5) RQ 1 EV IPR006344; TIGR01447; sufficient; TG GO:0000738; // AC GenProp0217 DE 5-aminolevulinate biosynthesis (glutamate pathway) TP PATHWAY AU Haft DH TH 1 RN [1] RM 12196141 RT Structure and function of glutamyl-tRNA reductase involved in RT 5-aminolaevulinic acid formation. RA Moser J, Schubert WD, Heinz DW, Jahn D; RL Biochem Soc Trans. 2002;30:579-584. RN [2] RM 9249985 RT Evolutionary consideration on 5-aminolevulinate synthase in nature. RA Oh-hama T; RL Orig Life Evol Biosph. 1997;27:405-412. RN [3] RM 7883699 RT Regulation of the hemA gene during 5-aminolevulinic acid formation in RT Pseudomonas aeruginosa. RA Hungerer C, Troup B, Römling U, Jahn D; RL J Bacteriol. 1995;177:1435-1443. DC Porphyrin and chlorophyll metabolism DR KEGG; map00860; CC This pathway for the biosynthesis of 5-aminolevulinate, a porphyrin CC precursor, is known as the glutamate or C5 pathway and is found in most CC bacteria. A distinctive feature of this pathway is the utilization of CC an amino acid-charged tRNA as an enzymatic substrate. An alternative CC pathway from succinyl-CoA and glycine utilizing 5-aminolevulinate CC synthase is found in the alphaproteobacteria and eukaryotic CC mitochondria[1,2,3]. -- SN 1 ID APPARENT DISRUPTED READING FRAMES RQ 0 -- SN 2 ID Glutamyl-tRNA synthetase DN Glutamyl-tRNA synthetase/ligase (EC 6.1.1.17) RQ 1 EV IPR004527; TIGR00464; sufficient; TG GO:0006779; EV IPR004526; TIGR00463; sufficient; TG GO:0006779; -- SN 3 ID Glutamyl-tRNA reductase DN Glutamyl-tRNA reductase (EC 1.2.1.70) RQ 1 EV IPR000343; TIGR01035; sufficient; TG GO:0006779; -- SN 4 ID Glutamate-1-semialdehyde-2,1-aminomutase DN Glutamate-1-semialdehyde aminotransferase (EC 5.4.3.8) RQ 1 EV IPR004639; TIGR00713; sufficient; TG GO:0006779; // AC GenProp0218 DE Cysteine biosynthesis from serine TP PATHWAY AU Haft DH TH 0 CC The conversion of L-serine to L-cysteine requires two enzymatic steps as CC described here. The first step involves serine acetyl-transferase, and CC the second step involves acetylserine lyase which forms L-cysteine. -- SN 1 ID Serine O-acetyltransferase DN Serine O-acetyltransferase/cysE RQ 1 EV IPR005881; TIGR01172; sufficient; -- SN 2 ID Cysteine synthase DN Cysteine synthase/cysK RQ 1 EV IPR005858; TIGR01138; sufficient; EV IPR005859; TIGR01139; sufficient; // AC GenProp0219 DE Spermidine biosynthesis from arginine (via agmatine) TP METAPATH AU Haft DH TH 0 CC This pathway uses arginine decarboxylase followed by agmatinase CC (agmatine ureohydrolase) instead of arginase (arginine ureohydrolase) CC followed by ornithine decarboxylase to get to putrescine, the immediate CC precursor of sperimidine. This is part of one of several possible CC arginine degradation pathways. -- SN 1 ID Putrescine biosynthesis from arginine DN Putrescine biosynthesis from arginine RQ 1 EV GenProp0642; -- SN 2 ID Spermidine biosynthesis from putrescine DN Spermidine biosynthesis from putrescine RQ 1 EV GenProp0641; // AC GenProp0220 DE Uroporhyrinogen III biosynthesis from 5-aminolevulinate TP PATHWAY AU Haft DH TH 0 CC This property describes the three step pathway that takes CC 5-aminolevulinate and converts it into uroporhyrinogen III, a compund CC which is used in the biosynthesis of siroheme, coenzyme B12, CC protoporphyrin IX and heme. Protoporphyrin IX is used in the creation CC of chlorophyll. -- SN 1 ID Delta-aminolevulinic acid dehydratase DN Delta-aminolevulinic acid dehydratase/hemB RQ 1 EV IPR001731; PF00490; sufficient; TG GO:0006779; -- SN 2 ID Porphobilinogen deaminase DN Porphobilinogen deaminase/hemC RQ 1 EV IPR000860; TIGR00212; sufficient; TG GO:0006779; -- SN 3 ID Uroporphyrinogen-III synthase DN Uroporphyrinogen-III synthase/hemD RQ 1 EV IPR003754; PF02602; sufficient; TG GO:0006779; // AC GenProp0221 DE Protoporphyrin IX biosynthesis from uroporphyrinogen III TP PATHWAY AU Haft DH TH 0 CC This property describes a three step pathway that converts CC uroporphyrinogen III to protoporphyrin IX, a precursor to both CC protoheme (heme) and chlorophyll. Uroporphyrinogen III can be derived CC from 5-aminolevulinate, as described by GenProp0220. -- SN 1 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase/hemE RQ 1 EV IPR006361; TIGR01464; sufficient; TG GO:0006779; -- SN 2 ID Coproporphyrinogen III oxidase DN Coproporphyrinogen III oxidase/hemF RQ 1 EV IPR001260; PF01218; sufficient; TG GO:0006779; EV IPR004558; TIGR00538; sufficient; TG GO:0006779; -- SN 3 ID Protoporphyrinogen oxidase DN Protoporphyrinogen oxidase/hemG RQ 1 EV IPR004572; TIGR00562; sufficient; TG GO:0006779; // AC GenProp0222 DE Protoheme from protoporphyrin IX TP PATHWAY AU Haft DH TH 0 CC This property is a one-step property describing the production of CC protoheme from protoporphyrin IX. It is designed to be used in CC conjunction with GenProp0220 and GenProp0221 to allow the CC identification of heme biosynthesis from 5-aminolevulinate. -- SN 1 ID Ferrochelatase DN Ferrochelatase/hemH RQ 1 EV IPR001015; TIGR00109; sufficient; TG GO:0006779; // AC GenProp0223 DE 5-aminolevulinate biosynthesis from succinyl-CoA and glycine TP PATHWAY AU Haft DH TH 0 RN [1] RM 11215515 RT Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum. RA Raux E, Schubert HL, Warren MJ; RL Cell Mol Life Sci. 2000;57:1880-1893. CC This property is an alternative to the biosynthesis of CC 5-aminolevulinate through the glutamate pathway. 5-aminolevulinate is CC used in the biosynthesis of uroporphyrinogen III and farther CC downstream, in the biosynthesis of heme[1]. This enzyme appears CC restricted to the alpha Proteobacteria and mitochondrial derivatives. -- SN 1 ID 5-aminolevulinic acid synthase DN 5-aminolevulinic acid synthase RQ 1 EV IPR010961; TIGR01821; sufficient; TG GO:0006783; // AC GenProp0225 DE Mismatch repair TP SYSTEM AU Haft DH TH 0 CC The combination of MutS (the MutS1 branch but not the MutS2 branch of CC the MutS family) and MutL leads to a general mechanism for mismatch CC exision and repair (MMR). Other proteins, recruited by MutS1 and MutL, CC act to clip (MutH or other endonuclease), remove (UvrD), and CC resynthesize one strand in the region containing the mismatch. MMR CC constrasts in its generality with the targeting of specific mismatches CC by various base excision repair (BER) glycosylases and with variants of CC MMR that act on specific mismatches. In Escherichia coli and related CC species that contain the endonuclease MutH and the DNA adenine CC methylation protein Dam, lack of methylation marks the newly CC synthesized strand; the mismatch is resolved by excision, removal, and CC resynthesis of a piece of that strand. MMR is referred to as CC methyl-directed mismatch repair in this subset of species with MMR. -- SN 1 ID MutH (or other) mismatch endonuclease DN DNA mismatch repair protein MutH RQ 0 EV IPR004230; TIGR02248; sufficient; -- SN 2 ID DNA mismatch repair protein MutL DN DNA mismatch repair protein MutL RQ 1 EV IPR002099; TIGR00585; sufficient; -- SN 3 ID DNA mismatch repair protein MutS (mutS1) DN DNA mismatch repair protein MutS RQ 1 EV IPR005748; TIGR01070; sufficient; // AC GenProp0226 DE Integron TP SYSTEM AU Haft DH TH 0 RN [1] RM 14702391 RT Integrons or super integrons? RA Hall RM, Stokes HW; RL Microbiology. 2004;150:3-4. CC An integron is a system that enables capture and expression of small CC mobile elements called cassettes. An integron should contain an intI CC gene, of any of several classes, encoding an integrase. It should CC have a promoter to drive expression, an attI site, ability to CC incorporate cassettes, and multiple attC sites (also called 59-base CC element) flanking the cassettes. The attC sites may exhibit high CC homology to each other in a long integron, but are best recognized by CC imperfect dyad symmetry at their outer ends. A single genome may have CC several integrons, and one integron may contain dozens of cassettes. CC Note that an integron cassette with a defective integron integrase, CC carried by a Tn7 transposon, is called a class 2 integron. -- SN 1 ID Integron integrase DN Integron integrase RQ 1 EV IPR011946; TIGR02249; TG GO:0009294; // AC GenProp0231 DE 4-hydroxyphenylacetate degradation TP PATHWAY AU Haft DH TH 3 RN [1] RM 11729263 RT Biodegradation of aromatic compounds by Escherichia coli. RA Díaz E, Ferrández A, Prieto MA, García JL; RL Microbiol Mol Biol Rev. 2001;65:523-69, table of contents. DC Tyrosine metabolism - reference pathway DR KEGG; map00350; CC 4-hydroxyphenylacetic acid, a degradation product of tyrosine via one CC of several routes, of phenylalanine via phenylacetate, and of CC environmental DDT is metabolized in this pathway to the common CC metabolites succinate and pyruvate via homoprotocatechuate[1]. CC 4-hydroxyphenylacetic acid may also be found in the environment and CC transported into the cell. The genes encoding the components of this CC pathway are often organized into apparent operons which include CC regulatory elements as well as a variety of transport systems. A CC number of genomes show partial evidence of the pathway based on CC homologs of the well-characterized enzymes from other species. Often, CC promising candidates for the missing steps are found in the vicinity. CC These are suggestive of enzymes which have been adapted from ancestral CC sequences having a different function. Of course, the possibility CC exists that it is the entire pathway that has been modified in these CC species and it is other structurally related compounds that are being CC metabolized instead of 4-hydroxyphenylacetic acid. -- SN 1 ID Succinate-semialdehyde dehydrogenase DN Succinate semialdehyde dehydrogenase (EC 1.2.1.-) RQ 1 EV IPR010102; TIGR01780; sufficient; -- SN 2 ID Regulatory protein, HpaA DN 4-hydroxyphenylacetate catabolism regulatory protein HpaA RQ 0 EV IPR011983; TIGR02297; sufficient; TG GO:0009894; -- SN 3 ID 4-hydroxyphenylacetate 3-monooxygenase, large subunit DN 4-HPA 3-monooxygenase large component RQ 1 EV IPR012687; TIGR02309; sufficient; TG GO:0042537; EV IPR012688; TIGR02310; sufficient; TG GO:0042537; -- SN 4 ID 4-hydroxyphenylacetate 3-monooxygenase, small subunit DN 4-hydroxyphenylacetate 3-monooxygenase, reductase component RQ 1 EV IPR011982; TIGR02296; sufficient; TG GO:0042537; -- SN 5 ID 3,4-dihydroxyphenylacetate 2,3-dioxygenase (1.13.11.15) DN 3,4-dihydroxyphenylacetate 2,3-dioxygenase (EC 1.13.11.15) RQ 1 EV IPR011981; TIGR02295; sufficient; TG GO:0042537; EV IPR011984; TIGR02298; sufficient; TG GO:0042537; -- SN 6 ID 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase (1.2.1.60) DN 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60) RQ 1 EV IPR011985; TIGR02299; sufficient; TG GO:0042537; -- SN 7 ID 5-carboxymethyl-2-hydroxymuconate delta-isomerase (5.3.3.10) DN 5-carboxymethyl-2-hydroxymuconate isomerase (EC 5.3.3.10) RQ 1 EV IPR004220; PF02962; sufficient; TG GO:0042537; -- SN 8 ID Bifunctional decarboxylase/isomerase, C-terminal DN 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal RQ 1 EV IPR012684; TIGR02303; sufficient; TG GO:0042537; -- SN 9 ID Bifunctional decarboxylase/isomerase, N-terminal DN 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal RQ 1 EV IPR012686; TIGR02305; sufficient; TG GO:0042537; -- SN 10 ID 2-oxo-hepta-3-ene-1,7-dioate hydratase DN 2-oxo-hepta-4-ene-1,7-dioic acid hydratase RQ 1 EV IPR012690; TIGR02312; sufficient; TG GO:0042537; -- SN 11 ID 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase DN 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase RQ 1 EV IPR012689; TIGR02311; sufficient; TG GO:0042537; EV IPR012691; TIGR02313; sufficient; TG GO:0042537; -- SN 12 ID Regulatory protein, HpaR DN Homoprotocatechuate degradation transcriptional regulator HpaR RQ 0 EV IPR012712; TIGR02337; sufficient; TG GO:0009894; -- SN 13 ID Probable 4-hydroxyphenylacetate transporters DN 4-hydroxyphenylacetate permease RQ 0 EV IPR012707; TIGR02332; sufficient; TG GO:0046942; // AC GenProp0232 DE Phosphonates C-P lyase system TP SYSTEM AU Haft DH TH 2 RN [1] RM 15231805 RT Two C-P lyase operons in Pseudomonas stutzeri and their roles in the RT oxidation of phosphonates, phosphite, and hypophosphite. RA White AK, Metcalf WW; RL J Bacteriol. 2004;186:4730-4739. RN [2] RM 11952414 RT Phosphonates and their degradation by microorganisms. RA Kononova SV, Nesmeyanova MA; RL Biochemistry (Mosc). 2002;67:184-195. CC Phosphonates are compounds similar to phosphates, but in which a direct CC carbon-phosphorous bond replaces a carbon-oxygen-phosphorous linkage. CC They chelate metals, adsorb strongly to surfaces, and are produced and CC used industrially to prevent formation of scale on surfaces. The C-P CC bond is remarkably stable compared to phosphate bonds, and phosphonate CC utilization is rather uncommon. While some enzymes with fairly narrow CC specificity are known that cleave the most common naturally occurring CC phosphonates, this property describes a multisubunit C-P lyase system CC with broad specificity. The specificity may differ from one case to CC another, and two systems with overlapping but non-identical CC specificities may occur in a single genome. -- SN 1 ID ABC transporter phosphonates ATP-binding protein DN ABC transporter, phosphonate import, PhnC RQ 1 EV IPR012693; TIGR02315; TG GO:0019700; -- SN 2 ID ABC transporter phosphonates-binding protein DN Phosphonate ABC transporter, substrate-binding protein RQ 1 EV IPR017797; TIGR03431; TG GO:0019700; -- SN 3 ID ABC transporter phosphonates permease DN ABC transporter, permease PhnE/PtxC RQ 1 EV IPR005769; TIGR01097; TG GO:0019700; -- SN 4 ID Alkylamine acetyltransferase, PhnO DN Alkylamine acetyltransferase, PhnO RQ 0 EV IPR000182; PF00583; TG GO:0019700; -- SN 5 ID Phosphonate metabolism protein, uncharacterized DN Phosphonate metabolism protein, uncharacterized RQ 0 EV IPR009389; TIGR03223; sufficient; TG GO:0019700; -- SN 6 ID Phosphonate metabolism protein, transferase hexapeptide repeat family DN Phosphonate metabolism protein, transferase hexapeptide repeat family RQ 0 EV IPR017694; TIGR03308; sufficient; TG GO:0019700; -- SN 7 ID PhnF transcriptional regulator DN Phosphonate C-P lyase system, transcriptional regulator PhnF RQ 0 EV IPR012702; TIGR02325; sufficient; -- SN 8 ID PhnG unchar. phosphonate metabolism protein DN Phosphonate metabolism PhnG RQ 1 EV IPR009609; PF06754; sufficient; TG GO:0019700; EV IPR009609; TIGR03293; sufficient; TG GO:0019700; -- SN 9 ID PhnH unchar. phosphonate metabolism protein DN Bacterial phosphonate metabolism, PhnH RQ 1 EV IPR008772; PF05845; sufficient; TG GO:0019700; EV IPR008772; TIGR03292; sufficient; TG GO:0019700; -- SN 10 ID PhnI unchar. phosphonate metabolism protein DN Phosphonate metabolism protein PhnI RQ 1 EV IPR008773; PF05861; sufficient; TG GO:0019700; -- SN 11 ID PhnJ unchar. phosphonate metaboism protein DN Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase/phnJ RQ 1 EV IPR010306; PF06007; sufficient; TG GO:0019700; -- SN 12 ID PhnK (ABC-like) C-P lyase protein, putative DN Phosphonate C-P lyase system, PhnK RQ 1 EV IPR012700; TIGR02323; sufficient; TG GO:0019700; -- SN 13 ID Phosphonate C-P lyase system PhnL subunit DN Phosphonate C-P lyase system, PhnL RQ 1 EV IPR012701; TIGR02324; sufficient; TG GO:0019700; -- SN 14 ID PhnM unchar. phosphonate metabolism protein DN Phosphonate metabolism PhnM RQ 1 EV IPR012696; TIGR02318; sufficient; TG GO:0019700; -- SN 15 ID PhnN unchar. phosphonate metabolism protein DN Ribose 1,5-bisphosphate phosphokinase PhnN RQ 0 EV IPR012699; TIGR02322; sufficient; TG GO:0019700; -- SN 16 ID PhnP unchar. phosphonate metabolism protein DN Phosphonate metabolism protein PhnP RQ 0 EV IPR017693; TIGR03307; sufficient; TG GO:0019700; // AC GenProp0233 DE GABA utilization TP PATHWAY AU Haft DH TH 0 CC GABA (gamma-aminobutyric acid also known as 4-aminobutyrate), a CC compound commonly found in plants is utilized by certain organisms. CC GABA is imported with a specific permease, transaminated to succinate CC semialdehyde and oxidized to succinate. -- SN 1 ID Succinic semialdehyde dehydrogenase (1.2.1.16) DN Succinate semialdehyde dehydrogenase RQ 1 EV IPR010102; TIGR01780; sufficient; -- SN 2 ID Hypothesized GABA transporter DN Hypothesized GABA transporter RQ 0 -- SN 3 ID GABA permease DN GABA permease RQ 1 EV IPR011265; TIGR01773; sufficient; -- SN 4 ID GABA transaminase (2.6.1.19) DN 4-aminobutyrate transaminase RQ 1 EV IPR004632; TIGR00700; sufficient; EV IPR004631; TIGR00699; sufficient; // AC GenProp0236 DE Phosphonates ABC transport TP SYSTEM AU Haft DH TH 0 CC Phosphonates are a varied class of compound with a direct C-P bond that CC can be significantly more stable than indirect C-O-P bond of organic CC phosphates. Phosphonates may be toxic but also may be utilized as a CC sorce of phosphorus, carbon, and energy. Some species appear to have a CC (sometimes two) membrane-associated C-P lyase complex, PhnGHIJKLM, for CC degradation of many different (but not all) phosphonates, while other CC species have single gene-encoded phosphonatases active on specific CC compounds. This property represents the presence of transporters for CC phosphonates and related C-P bond-containing compounds (e.g. CC phosphites); it should be found in association with either the C-P CC lysase membrane complex or specific phoshonatases, but not all of the CC latter are known. -- SN 1 ID ABC transporter phosphonates ATP-binding protein DN ABC transporter, phosphonate import, PhnC RQ 1 EV IPR012693; TIGR02315; -- SN 2 ID ABC transporter phosphonates-binding protein DN Phosphonate ABC transporter, substrate-binding protein RQ 1 EV IPR017797; TIGR03431; -- SN 3 ID ABC transporter phosphonates permease DN ABC transporter, permease PhnE/PtxC RQ 1 EV IPR005769; TIGR01097; // AC GenProp0238 DE 2-aminoethylphosphonate catabolism to acetaldehyde TP PATHWAY AU Haft DH TH 0 RN [1] RM 12107130 RT The 2-aminoethylphosphonate-specific transaminase of the RT 2-aminoethylphosphonate degradation pathway. RA Kim AD, Baker AS, Dunaway-Mariano D, Metcalf WW, Wanner BL, Martin BM; RL J Bacteriol. 2002;184:4134-4140. DC Aminophosphonate metabolism DR KEGG; map00440; CC The enzyme 2-aminoethylphosphonate--pyruvate transaminase (AEPT) CC interconverts 2-aminoethylphosphonate plus pyruvate with CC 2-phosphonoacetaldehyde plus alanine. The enzyme phosphonoacetaldehyde CC hydrolase, a HAD superfamily hydrolase, breaks the C-P bond, yielding CC acetaldehyde plus inorganic phosphate[1]. In species that appear to CC encode a phosphonate ABC transporter, this property is likely to be CC present only when the large phosphonate operon proposed to encode a CC multisubunit C-P lyase, as found in Escherichia coli, is not found. -- SN 1 ID 2-aminoethylphosphonate--pyruvate transaminase DN 2-aminoethylphosphonate--pyruvate transaminase (EC:2.6.1.37) RQ 1 EV IPR012703; TIGR02326; sufficient; TG GO:0019635; -- SN 2 ID Phosphonoacetaldehyde hydrolase DN Phosphonoacetaldehyde hydrolase (EC:3.11.1.1) RQ 1 EV IPR006323; TIGR01422; sufficient; TG GO:0019635; // AC GenProp0239 DE Propionyl-CoA catabolism TP CATEGORY AU Haft DH TH 0 CC At least five pathways exist for propionate catabolism in prokaryotes: CC the malonic semialdehyde-CoA pathway, acrylate pathway, CC methylmalonyl-CoA mutase pathway, alpha-hydroxyglutaric acid pathway, CC and methylcitric acid cycle pathway. -- SN 1 ID Propionyl-CoA catabolism via methylcitric acid RQ 0 EV GenProp0240; // AC GenProp0240 DE Propionyl-CoA catabolism via methylcitric acid TP PATHWAY AU Haft DH TH 0 CC This property describes one of at least five pathways for propionyl-CoA CC catabolism in prokaryotes. This pathway requires oxaloacetate and later CC releases succinate, both of which are TCA cycle intermediates. TCA CC cycle enzymes convert succinate back to oxaloacetate, and so this CC pathway is a cycle. Propionyl-CoA may derive from propionate, CC propionaldehyde, or other compounds. Propionyl-CoA plus oxaloacetate is CC converted by PrpC to 2-methylcitrate, which is then converted in two CC steps, by PrpD and an aconitase, to 2-methylisocitrate. CC 2-methylisocitrate is cleaved by PrpB to pyruvate and succinate. The CC TCA cycle enzymes needed to complete the cycle are not modelled here as CC part of the pathway -- SN 1 ID 2-methylisocitrate dehydratase DN 2-methylisocitrate dehydratase AcnD RQ 1 EV IPR012708; TIGR02333; sufficient; -- SN 2 ID Methylisocitrate lyase PrpB DN 2-methylisocitrate lyase RQ 1 EV IPR012695; TIGR02317; sufficient; -- SN 3 ID 2-methylcitrate synthase family DN 2-methylcitrate synthase/citrate synthase type I RQ 1 EV IPR011278; TIGR01800; sufficient; -- SN 4 ID 2-methylcitrate dehydratase DN 2-methylcitrate dehydratase PrpD RQ 1 EV IPR012705; TIGR02330; sufficient; -- SN 5 ID AcnD-accessory protein PrpF DN 2-methyl-aconitate isomerase PrpF RQ 1 EV IPR012709; TIGR02334; sufficient; -- SN 6 ID Propionate catabolism operon regulator PrpR DN Propionate catabolism, transcriptional regulator PrpR RQ 0 EV IPR012704; TIGR02329; sufficient; // AC GenProp0241 DE Phosphonate catabolism TP METAPATH AU Haft DH TH 0 RN [1] RM 1556070 RT Evidence for two phosphonate degradative pathways in Enterobacter RT aerogenes. RA Lee KS, Metcalf WW, Wanner BL; RL J Bacteriol. 1992;174:2501-2510. RN [2] RM 8335257 RT Evidence for a fourteen-gene, phnC to phnP locus for phosphonate RT metabolism in Escherichia coli. RA Metcalf WW, Wanner BL; RL Gene. 1993;129:27-32. RN [3] RM 15231805 RT Two C-P lyase operons in Pseudomonas stutzeri and their roles in the RT oxidation of phosphonates, phosphite, and hypophosphite. RA White AK, Metcalf WW; RL J Bacteriol. 2004;186:4730-4739. RN [4] RM 11952414 RT Phosphonates and their degradation by microorganisms. RA Kononova SV, Nesmeyanova MA; RL Biochemistry (Mosc). 2002;67:184-195. CC The capability to degrade phosphonates is believed to consist minimally CC of a system for transporting phosphonate compounds (those with CC carbon-PO3 linkages) coupled with a pathway for the hydrolysis of such CC bonds. Two classes of system are known, those that handle broad classes CC of phosphonate compounds and those that handle specific molecules. This CC property describes species utilizing either system. -- SN 1 ID Phosphonate catabolism operons associated proteins DN Phosphonate catabolism operons associated proteins RQ 0 EV IPR017741; TIGR03364; sufficient; TG GO:0019700; EV IPR017670; TIGR03276; sufficient; TG GO:0019700; -- SN 2 ID Phosphonate utilization systems DN Phosphonate utilization systems RQ 1 EV GenProp0232; TG GO:0019700; EV GenProp0720; TG GO:0019700; // AC GenProp0242 DE Phosphorus metabolism TP CATEGORY AU Haft DH TH 0 CC The transport and transformations of biomolecules containing the CC phosphorus atom. -- SN 1 ID Phosphate ABC transporter (pstSCAB-phoU) RQ 0 EV GenProp0190; -- SN 2 ID ATP synthases RQ 0 EV GenProp0243; -- SN 3 ID Phosphonate catabolism RQ 0 EV GenProp0241; -- SN 4 ID Phosphonoacetaldehyde biosynthesis from phosphoenolpyruvate RQ 0 EV GenProp0724; -- SN 5 ID Generic phosphonates utilization RQ 0 EV GenProp0710; -- SN 6 ID Proposed phosphonate catabolism pathway HpnWXZ RQ 0 EV GenProp0736; // AC GenProp0243 DE ATP synthases TP CATEGORY AU Haft DH TH 0 CC Systems which generate ATP from ADP and inorganic phosphate by CC utilizing membrane potential or chemical gradients. -- SN 1 ID F1/F0 ATPase RQ 0 EV GenProp0128; -- SN 2 ID A1/A0 ATPase RQ 0 EV GenProp0629; // AC GenProp0244 DE Chaperone system: DnaK-DnaJ-GrpE TP SYSTEM AU Haft DH TH 0 RN [1] RM 15102842 RT Influence of GrpE on DnaK-substrate interactions. RA Brehmer D, Gässler C, Rist W, Mayer MP, Bukau B; RL J Biol Chem. 2004;279:27957-27964. CC DnaK, DnaJ, and GrpE form a chaperone system. DnaK has ATPase activity. CC DnaJ and GrpE are co-chaperones for DnaK, that is, stimulate this CC activity[1]. This system is also called the hsp70 heat-shock system. CC Excluded from this system are the heat shock cognate (Hsc) homologs, CC which are associated specifically with iron-sulfur cluster biosynthesis CC (see GenProp0138, the iron-sulfur cluster assembly iscSUA-hscBA-fdx CC system). The heat shock repressor HrcA is found in about half of CC bacterial genomes with the DnaK-DnaJ-GrpE heat shock system, usually CC encoded upstream in a heat shock operon; it is included here as an CC optional component. -- SN 1 ID Co-chaperone DnaJ DN Molecular chaperone DnaJ RQ 1 EV IPR012724; TIGR02349; sufficient; TG GO:0006457; -- SN 2 ID Chaperone DnaK DN Molecular chaperone DnaK RQ 1 EV IPR012725; TIGR02350; sufficient; TG GO:0006457; -- SN 3 ID Co-chaperone GrpE DN Molecular chaperone/nucleotide exchange factor GrpE RQ 1 EV IPR000740; PF01025; sufficient; TG GO:0006457; -- SN 4 ID Heat shock gene repressor HrcA DN Heat-inducible transcription repressor HrcA RQ 0 EV IPR002571; TIGR00331; sufficient; TG GO:0045892; // AC GenProp0245 DE Chaperone system: GroEL/GroES TP SYSTEM AU Haft DH TH 0 RN [1] RM 9759498 RT Structure and function in GroEL-mediated protein folding. RA Sigler PB, Xu Z, Rye HS, Burston SG, Fenton WA, Horwich AL; RL Annu Rev Biochem. 1998;67:581-608. RN [2] RM 12796498 RT Coexistence of group I and group II chaperonins in the archaeon RT Methanosarcina mazei. RA Klunker D, Haas B, Hirtreiter A, Figueiredo L, Naylor DJ, Pfeifer G, RA Müller V, Deppenmeier U, Gottschalk G, Hartl FU, Hayer-Hartl M; RL J Biol Chem. 2003;278:33256-33267. CC GroEL and GroES comprise the bacterial group I chaperonin, a toroidal CC complex involved in folding or refolding proteins in the cytosol[1]. CC Archaea and Eukaryotes have instead (with a few rare cases of overlap) CC a group II chaperonin complex, usually called the thermosome in the CC Archaea and CCT in the Eukaryota. At least one member of the archaeal CC genus Methanosarcina, has both[2]. -- SN 1 ID Chaperonin GroEL DN Chaperonin GroEL/Cpn60 RQ 1 EV IPR001844; TIGR02348; sufficient; TG GO:0006457; -- SN 2 ID Co-chaperonin GroES DN Chaperonin GroES/Cpn10 RQ 1 EV IPR020818; PF00166; sufficient; TG GO:0006457; // AC GenProp0246 DE Chaperone system: thermosome/prefoldin TP SYSTEM AU Haft DH TH 0 RN [1] RM 10550210 RT Group II chaperonins: new TRiC(k)s and turns of a protein folding RT machine. RA Gutsche I, Essen LO, Baumeister W; RL J Mol Biol. 1999;293:295-312. RN [2] RM 9678597 RT The thermosome: archetype of group II chaperonins. RA Klumpp M, Baumeister W; RL FEBS Lett. 1998;430:73-77. CC The archaeal thermosome system is a group II chaperonin, closely CC related to the CCT complex of eukaryotes. Thermosome subunits show CC clear remote sequence similarity to GroEL of the bacterial group I CC chaperonin system[1,2]. Prefoldin, with alpha and beta subunits, works CC with the chaperonin. The number of distinct but homologous genes for CC subunits of the thermosome ranges from one to five in the archaea. -- SN 1 ID Prefoldin, alpha subunit DN Prefoldin, alpha subunit RQ 1 EV IPR011599; TIGR00293; sufficient; TG GO:0006457; -- SN 2 ID Prefoldin, beta subunit DN Prefoldin, beta subunit RQ 1 EV IPR012713; TIGR02338; sufficient; TG GO:0006457; -- SN 3 ID Thermosome subunit(s) DN Thermosome subunit RQ 1 EV IPR012714; TIGR02339; sufficient; TG GO:0006457; // AC GenProp0247 DE Protein metabolism TP CATEGORY AU Haft DH TH 0 CC The chemical reactions and physical changes involving the synthesis, CC modification and degradation of proteins. -- SN 1 ID Protein modification, prosthetic groups and cofactors RQ 0 EV GenProp0075; -- SN 2 ID Protein transport RQ 0 EV GenProp0179; -- SN 3 ID Protein biosynthesis RQ 0 EV GenProp0197; -- SN 4 ID Protein folding RQ 0 EV GenProp0248; -- SN 5 ID Protein degradation RQ 0 EV GenProp0301; -- SN 6 ID Protein repair RQ 0 EV GenProp0302; // AC GenProp0248 DE Protein folding TP CATEGORY AU Haft DH TH 0 CC The transformation of polypeptide chains between the unfolded, CC misfolded and folded (active) states. -- SN 1 ID Chaperone system: DnaK-DnaJ-GrpE RQ 0 EV GenProp0244; -- SN 2 ID Chaperone system: GroEL/GroES RQ 0 EV GenProp0245; -- SN 3 ID Chaperone system: thermosome/prefoldin RQ 0 EV GenProp0246; -- SN 4 ID Outer membrane protein assembly complex RQ 0 EV GenProp0725; -- SN 5 ID OMP chaperone system: SurA-Skp-DegP RQ 0 EV GenProp0928; -- SN 6 ID GroEL-GroES complex RQ 0 EV GenProp1181; // AC GenProp0250 DE Hydroxyethylthiazole (HET) biosynthesis from 1-deoxy-D-xylulose-5-phosphate, Cysteine, and either Tyr or Gly TP PATHWAY AU Haft DH TH 1 RN [1] RM 12376536 RT Comparative genomics of thiamin biosynthesis in procaryotes. New genes RT and regulatory mechanisms. RA Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS; RL J Biol Chem. 2002;277:48949-48959. RN [2] RM 12410317 RT Thiamine derivatives bind messenger RNAs directly to regulate bacterial RT gene expression. RA Winkler W, Nahvi A, Breaker RR; RL Nature. 2002;419:952-956. CC This property describes de novo synthesis of the thiazole moiety of CC thiamine, hydroxyethylthiazole (HET). This requires more distinct CC proteins than that of the pyrimidine moeity, hydromethylpyrimidine CC (HMP). Phosphorylated forms of HET and HMP are connected by ThiE as CC thiamine phosphate and converted eventually to the active form thiamine CC pyrophosphate, TPP. HET biosynthesis requires the small ThiS protein, CC the C terminus of which becomes modified transiently by a sulfur atom CC from cysteine [1]. ThiG is required, along with either ThiH in species CC where tyrosine is a precursor or ThiO in species where glycine is a CC precursor. ThiF, although required biosynthetically, is not readily CC separated from MoeB, a molybdopterin biosynthesis protein, and so is CC not considered a required component. The ThiI gene is required, but CC also serves in formation of a tRNA modified site in species that do CC not make HET [2]. This property represents and alternative to HET CC uptake as a means to obtain the thiazole component for thiamine CC biosynthesis. -- SN 1 ID ThiH (Tyr) or ThiO (Gly) RQ 1 EV IPR012727; TIGR02352; sufficient; TG GO:0018131; EV IPR012726; TIGR02351; sufficient; TG GO:0018131; -- SN 2 ID ThiF protein RQ 0 EV IPR012729; TIGR02354; sufficient; TG GO:0018131; EV IPR012731; TIGR02356; sufficient; TG GO:0018131; -- SN 3 ID ThiG protein DN Thiazole biosynthesis protein ThiG RQ 1 EV IPR033983; PF05690; sufficient; TG GO:0018131; -- SN 4 ID ThiI protein DN Thiamine biosynthesis protein ThiI RQ 1 EV IPR026340; TIGR04271; sufficient; TG GO:0018131; -- SN 5 ID ThiS protein DN Thiamine biosynthesis protein ThiS RQ 1 EV IPR010035; TIGR01683; sufficient; TG GO:0018131; // AC GenProp0251 DE ClpXP degradation machine TP SYSTEM AU Haft DH TH 0 CC This property describes an energy-dependent protease, one of whose CC tasks is degradation of abortively translated proteins tagged by the CC tmRNA trans-translation system. ClpX is an ATPase that unfolds target CC proteins for degradation; ClpP is a protease in complex with ClpX. SspB CC is an example of an adaptor that brings targets, including but not CC restricted to proteins tagged by trans-translation, to the ClpXP CC machine. -- SN 1 ID Adaptor SspB DN Stringent starvation protein B RQ 0 EV IPR007481; PF04386; sufficient; -- SN 2 ID Temp clpA DN ATP-dependent Clp protease ATP-binding subunit ClpA RQ 0 EV IPR013461; TIGR02639; sufficient; -- SN 3 ID Clp protease proteolytic subunit ClpP DN ATP-dependent Clp protease RQ 1 EV IPR001907; TIGR00493; sufficient; -- SN 4 ID Temp clpS DN Adaptor protein ClpS RQ 0 EV IPR003769; PF02617; sufficient; -- SN 5 ID Clp protease ATP-binding subunit ClpX DN Clp protease ATP-binding subunit ClpX RQ 1 EV IPR004487; TIGR00382; sufficient; // AC GenProp0252 DE Thiamine/TPP ABC transporter ThiBPQ TP SYSTEM AU Haft DH TH 0 RN [1] RM 9535878 RT thiBPQ encodes an ABC transporter required for transport of thiamine RT and thiamine pyrophosphate in Salmonella typhimurium. RA Webb E, Claas K, Downs D; RL J Biol Chem. 1998;273:8946-8950. DC Thiamine metabolism DR KEGG; map00730; CC This property describes a three-component ABC transporter, ThiBPQ, for CC thiamine and/or thiamine derivatives. It is demonstrated experimentally CC in Salmonella typhimurium and E. coli[1], and is inferred from gene CC location next to genes for thiamine salvage enzymes in Brucella suis and CC Sinorhizobium meliloti. All known examples are in Proteobacteria. -- SN 1 ID Thiamine binding protein DN Proteobacterial thiamine ABC transporter, periplasmic binding protein RQ 1 EV IPR005967; TIGR01276; sufficient; TG GO:0030974; -- SN 2 ID Thiamine transporter permease DN Thiamine/thiamine pyrophosphate ABC transporter, permease protein RQ 1 EV IPR005947; TIGR01253; sufficient; TG GO:0030974; -- SN 3 ID Thiamine transporter ATP-binding protein DN Thiamine ABC transporter, ATP-binding protein ThiQ RQ 1 EV IPR005968; TIGR01277; sufficient; TG GO:0030974; // AC GenProp0253 DE Hydroxymethylpyrimidine pyrophosphate (HMP-P) biosynthesis from aminoimidazole ribotide TP PATHWAY AU Haft DH TH 1 RN [1] RM 12376536 RT Comparative genomics of thiamin biosynthesis in procaryotes. New genes RT and regulatory mechanisms. RA Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS; RL J Biol Chem. 2002;277:48949-48959. CC Hydroxymethylpyrimidine pyrophosphate (HMP-PP) and hydroxyethylthiazole CC phosphate (HET-P) are the two components attached by ThiE to yield CC thiamine phosphate, which is subsequently converted to the active form CC thiamine pyrophosphate (TPP). HMP and HET may be imported and converted CC to HMP-PP and HET-P, respectively, as an alternative to de novo CC biosynthesis. This property reflects known steps of HMP-P de novo CC biosynthesis from the purine biosynthesis metabolite aminoimidazole CC ribotide (AIR), starting with the ThiC enzyme [1]. -- SN 1 ID Thiamine biosynthesis protein ThiC DN Phosphomethylpyrimidine synthase RQ 1 EV IPR002817; TIGR00190; sufficient; -- SN 2 ID TenA domain/protein DN Thiaminase-2/PQQC RQ 0 EV IPR004305; PF03070; sufficient; -- SN 3 ID Phosphomethylpyrimidine kinase/ThiD DN Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase/ThiD RQ 1 EV IPR004399; TIGR00097; sufficient; // AC GenProp0254 DE Thiamine pyrophosphate (TPP) biosynthesis from HMP-PP and HET-P TP PATHWAY AU Haft DH TH 0 RN [1] RM 12376536 RT Comparative genomics of thiamin biosynthesis in procaryotes. New genes RT and regulatory mechanisms. RA Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS; RL J Biol Chem. 2002;277:48949-48959. CC Thiamine pyrophosphate (TPP) is an essential cofactor for several CC carbohydrate metabolism enzymes. Hydroxymethylpyrimidine pyrophosphate CC (HMP-PP) may be obtained by de novo synthesis, or by import or salvage CC of hydroxymethylpyrimidine followed by phosphorylation. Likewise, CC hydroxyethylthiazole phosphate (HET-P) may come from synthesis, import, CC or salvage. The two heterocylic compounds are ligated by ThiE to thiamine CC phosphate. Thiamine phosphate then undegoes either dephosphorylation CC followed by pyrophosphorylation or direct phosphorylation [1]. -- SN 1 ID Thiamine-phosphate diphosphorylase DN Thiamine phosphate synthase RQ 1 EV IPR034291; TIGR00693; sufficient; TG GO:0009228; -- SN 2 ID TPP riboswitch (THI element) RQ 0 -- SN 3 ID ThiL or pyrophosphokinase DN Thiamine-monophosphate kinase/Thiamin pyrophosphokinase RQ 1 EV IPR006283; TIGR01379; sufficient; TG GO:0009228; EV IPR006282; TIGR01378; sufficient; TG GO:0009228; // AC GenProp0255 DE 5-aminolevulinate biosynthesis TP METAPATH AU Haft DH TH 0 CC 5-aminolevulinate, a heme precursor, may be biosynthesized by one of CC two pathways. The C5 (or Glutamate) pathway is more common [GenProp0217], CC while alphaproteobacteria utilize the enzyme 5-aminolevulinate synthase CC to make the molecule from succinyl-CoA and glycine [GenProp0223]. -- SN 1 ID 5-aminolevulinate biosynthesis pathway RQ 1 EV GenProp0217; TG GO:0006783; EV GenProp0223; TG GO:0006783; // AC GenProp0258 DE tRNA aminoacylation TP GUILD AU Haft DH TH 1 CC In all species, it is presumed that tRNA molecules for all 20 common CC amino acids exist and become charged with the correct amino acid. Most CC are charged directly by a known ligase that is a single polypeptide CC chain, but not all. -- SN 1 ID Alanyl-tRNA synthetase DN Alanine-tRNA ligase/Ala RQ 1 EV IPR002318; TIGR00344; sufficient; -- SN 2 ID Arginyl-tRNA synthetase DN Arginine-tRNA ligase/Arg RQ 1 EV IPR001278; TIGR00456; sufficient; EV IPR035684; PF00750; sufficient; -- SN 3 ID Asn direct aminoacylation DN Asparagine-tRNA ligase/Asn RQ 1 EV IPR004522; TIGR00457; sufficient; -- SN 4 ID Aspartyl-tRNA synthetase DN Aspartate-tRNA synthetase/Asp RQ 1 EV IPR004523; TIGR00458; sufficient; EV IPR004524; TIGR00459; sufficient; -- SN 5 ID Cysteinyl-tRNA synthetase DN Cysteine-tRNA ligase/Cys RQ 1 EV IPR015803; TIGR00435; sufficient; -- SN 6 ID Gln direct aminoacylation DN Glutamine-tRNA synthetase/Gln RQ 1 EV IPR004514; TIGR00440; sufficient; -- SN 7 ID Glutamyl-tRNA synthetase DN Glutamate-tRNA ligase/Glu RQ 1 EV IPR004527; TIGR00464; sufficient; EV IPR004526; TIGR00463; sufficient; -- SN 8 ID Glycyl-tRNA synthetase, alpha subunit DN Glycine-tRNA ligase, alpha subunit/Gly_A RQ 1 EV IPR002310; TIGR00388; sufficient; -- SN 9 ID Glycyl-tRNA synthetase, beta subunit DN Glycine-tRNA ligase, beta subunit/Gly_B RQ 1 EV IPR015944; TIGR00211; sufficient; -- SN 10 ID Glycyl-tRNA synthetase DN Glycyl-tRNA synthetase/Gly RQ 1 EV IPR002315; TIGR00389; sufficient; -- SN 11 ID Histidyl-tRNA synthetase DN Histidine-tRNA ligase/His RQ 1 EV IPR015807; TIGR00442; sufficient; -- SN 12 ID Isoleucyl-tRNA synthetase DN Isoleucine-tRNA ligase/Ile RQ 1 EV IPR002301; TIGR00392; sufficient; -- SN 13 ID Leucyl-tRNA synthetase DN Leucyl-tRNA synthetase/Leu RQ 1 EV IPR004493; TIGR00395; sufficient; EV IPR002302; TIGR00396; sufficient; -- SN 14 ID Lysyl-tRNA synthetase DN Lysine-tRNA ligase/Lys RQ 1 EV IPR002904; TIGR00467; sufficient; EV IPR002313; TIGR00499; sufficient; -- SN 15 ID Methionyl-tRNA synthetase DN Methionyl-tRNA synthetase/Met RQ 1 EV IPR014758; TIGR00398; sufficient; -- SN 16 ID Methionyl-tRNA synthetase, beta subunit DN Methionyl-tRNA synthetase, beta subunit/Met_B RQ 0 EV IPR004495; TIGR00399; sufficient; -- SN 17 ID Phenylalanyl-tRNA synthetase, alpha subunit DN Phenylalanyl-tRNA synthetase, alpha subunit/Phe_A RQ 1 EV IPR004529; TIGR00468; sufficient; -- SN 18 ID Phenylalanyl-tRNA synthetase, beta subunit DN Phenylalanyl-tRNA synthetase, beta subunit/Phe_B RQ 1 EV IPR004531; TIGR00471; sufficient; EV IPR004532; TIGR00472; sufficient; -- SN 19 ID Prolyl-tRNA synthetase DN Proline-tRNA ligase/Pro RQ 1 EV IPR004499; TIGR00408; sufficient; EV IPR004500; TIGR00409; sufficient; -- SN 20 ID Seryl-tRNA synthetase DN Serine-tRNA ligase/Ser RQ 1 EV IPR002317; TIGR00414; sufficient; EV IPR004503; TIGR00415; sufficient; -- SN 21 ID Threonyl-tRNA synthetase DN Threonine-tRNA ligase/Thr RQ 1 EV IPR002320; TIGR00418; sufficient; -- SN 22 ID Tryptophanyl-tRNA synthetase DN Tryptophan-tRNA ligase/Trp RQ 1 EV IPR002306; TIGR00233; sufficient; -- SN 23 ID Tyrosyl-tRNA synthetase DN Tyrosine-tRNA ligase/Tyr RQ 1 EV IPR002307; TIGR00234; sufficient; -- SN 24 ID Valyl-tRNA synthetase DN Valine-tRNA ligase/Val RQ 1 EV IPR002303; TIGR00422; sufficient; -- SN 25 ID GatA subunit, glutamyl-tRNA(Gln) amidotransferase DN Glutamyl-tRNA(Gln) amidotransferase A subunit/gatA RQ 1 EV IPR004412; TIGR00132; sufficient; -- SN 26 ID GatA as aspartyl-tRNA(Asn) complex candidate DN GatA as aspartyl-tRNA(Asn) complex candidate/gatA_N RQ 1 EV IPR004412; TIGR00132; sufficient; -- SN 27 ID GatB subunit, glutamyl-tRNA(Gln) amidotransferase DN Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit/gatB RQ 1 EV IPR004413; TIGR00133; sufficient; -- SN 28 ID GatB as aspartyl-tRNA(Asn) complex candidate DN GatB as aspartyl-tRNA(Asn) complex candidate/gatB_N RQ 1 EV IPR004413; TIGR00133; sufficient; -- SN 29 ID GatC subunit, glutamyl-tRNA(Gln) amidotransferase DN Glu-tRNAGln amidotransferase C subunit/gatC RQ 1 EV IPR003837; TIGR00135; sufficient; -- SN 30 ID GatC as aspartyl-tRNA(Asn) complex candidate DN GatC as aspartyl-tRNA(Asn) complex candidate/gatC_N RQ 1 EV IPR003837; TIGR00135; sufficient; -- SN 31 ID GatD subunit, archaeal glutamyl-tRNA(Gln) amidotransferase DN Glutamyl-tRNA(Gln) amidotransferase subunit D/gatD RQ 1 EV IPR011878; TIGR02153; sufficient; -- SN 32 ID GatE subunit, archaeal glutamyl-tRNA(Gln) amidotransferase DN Glutamyl-tRNA(Gln) amidotransferase subunit E/gatE RQ 1 EV IPR004414; TIGR00134; sufficient; // AC GenProp0259 DE tRNA-Asn direct aminoacylation TP PATHWAY AU Haft DH TH 0 CC The tRNA for Asn can be produced in either of two ways: direct CC aminoacylation with Asn, and misacylation with Asp that is subsequently CC amidated to Asn. This is analogous to the system for charging tRNA with CC Gln, and may share some of the same machinery. This property describes CC a single polypeptide chain tRNA ligase responsible for direct CC aminoacylation with Asn. -- SN 1 ID Source of asparagine DN Aspartate--ammonia ligase/Asparagine synthase RQ 0 EV IPR004618; TIGR00669; EV IPR006426; TIGR01536; -- SN 2 ID Asparaginyl-tRNA synthetase DN Asparagine-tRNA ligase RQ 1 EV IPR004522; TIGR00457; sufficient; // AC GenProp0261 DE Thiamine pyrophosphate (TPP) de novo biosynthesis TP METAPATH AU Haft DH TH 0 RN [1] RM 12376536 RT Comparative genomics of thiamin biosynthesis in procaryotes. New genes RT and regulatory mechanisms. RA Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS; RL J Biol Chem. 2002;277:48949-48959. CC This property describes de novo synthesis of teh essential cofactor CC thiamine pyrophosphate (TPP) [1]. The process consists of the synthesis of CC hydroxyethylthiazole phosphate (HET-P), the synthesis of CC hydroxymethylpyrimidine pyrophosphate (HMP-PP), and their ligation and CC conversion to TPP. -- SN 1 ID Hydroxyethylthiazole (HET) biosynthesis RQ 1 EV GenProp0250; TG GO:0018131; -- SN 2 ID Hydroxymethylpyrimidine pyrophosphate (HMP-P) biosynthesis RQ 1 EV GenProp0253; -- SN 3 ID Thiamine pyrophosphate (TPP) biosynthesis from HMP-PP and HET-P RQ 1 EV GenProp0254; TG GO:0009228; // AC GenProp0262 DE RNA polymerase, bacterial TP SYSTEM AU Haft DH TH 0 RN [1] RM 12949700 RT The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, RT gyrB, rpoC1 and rpoD1 gene sequences. RA Seo PS, Yokota A; RL J Gen Appl Microbiol. 2003;49:191-203. RN [2] RM 12426327 RT The rpoZ gene, encoding the RNA polymerase omega subunit, is required RT for antibiotic production and morphological differentiation in RT Streptomyces kasugaensis. RA Kojima I, Kasuga K, Kobayashi M, Fukasawa A, Mizuno S, Arisawa A, RA Akagawa H; RL J Bacteriol. 2002;184:6417-6423. DC RNA polymerase DR KEGG; map03020; CC This property describes the bacterial multisubunit DNA-directed RNA CC polymerase (EC 2.7.7.6). This property does not include sigma factors CC which are regulatory and varied, and so by definition this property CC describes the core enzyme rather than the holoenzyme. Subunit CC stochiometry is two alpha subunits to one each of beta and beta'. In CC Cyanobacteria and plastids, beta' is replaced by two proteins, one like CC the N-term of beta' (called gamma in Cyanobacteria and, confusingly, CC beta' in plastids) and one like the C-term of beta' (called beta' in CC Cyanobacteria and beta'' in plastids)[1]. -- SN 1 ID RNA polymerase delta DN DNA-directed RNA polymerase, delta subunit RQ 0 EV IPR029757; TIGR04567; sufficient; -- SN 2 ID RNA polymerase alpha DN DNA-directed RNA polymerase, alpha subunit RQ 1 EV IPR011773; TIGR02027; sufficient; -- SN 3 ID RNA polymerase beta DN DNA-directed RNA polymerase, beta subunit RQ 1 EV IPR010243; TIGR02013; sufficient; -- SN 4 ID RNA polymerase beta', C-terminal region DN DNA-directed RNA polymerase beta' C/subunit beta''(plastid)/beta'(cyanobacteria) RQ 1 EV IPR012756; TIGR02388; sufficient; EV IPR012754; TIGR02386; sufficient; -- SN 5 ID RNA polymerase beta', N-terminal region DN DNA-directed RNA polymerase beta' N/subunit beta'(plastid)/gamma(cyanobacteria) RQ 1 EV IPR012755; TIGR02387; sufficient; EV IPR012754; TIGR02386; sufficient; -- SN 6 ID RNA polymerase omega DN DNA-directed RNA polymerase, omega subunit RQ 0 EV IPR003716; TIGR00690; sufficient; // AC GenProp0263 DE DNA polymerase III, bacterial TP SYSTEM AU Haft DH TH 0 RN [1] RM 11432857 RT The delta and delta ' subunits of the DNA polymerase III holoenzyme are RT essential for initiation complex formation and processive elongation. RA Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry RA CS; RL J Biol Chem. 2001;276:35165-35175. RN [2] RM 10878011 RT The DNA replication machine of a gram-positive organism. RA Bruck I, O'Donnell M; RL J Biol Chem. 2000;275:28971-28983. CC This property represents bacterial DNA polymerase III, a multisubunit CC replicative enzyme. In addition to core subunits, various bacteria may CC have accessory proteins that confer special properties such as greater CC speed and processivity. The single subunit in Gram-positive bacteria CC that carries polymerase and 3'-5' proofreading exonuclease activities CC corresponds to separate alpha (dnaE) and epsilon (dnaQ) subunits in E. CC coli. The polymerase works together with a clamp (beta, dnaN) and a CC clamp-loading complex of delta, delta-prime, and tau. In some species, CC a gamma subunit is related to tau by a translational frameshift from CC the same gene, dnaX. Some known accessory subunits include chi, psi, CC and theta. -- SN 1 ID DNA polymerase III, alpha subunit (DnaE) DN DNA polymerase III, alpha subunit/dnaE RQ 1 EV IPR004805; TIGR00594; sufficient; -- SN 2 ID DNA polymerase III, beta subunit (dnaN) DN DNA polymerase III, beta sliding clamp/dnaN RQ 1 EV IPR001001; TIGR00663; sufficient; -- SN 3 ID DNA polymerase III, epsilon subunit (dnaQ) DN DNA polymerase III, epsilon subunit/dnaQ RQ 1 EV IPR006309; TIGR01406; sufficient; -- SN 4 ID DNA polymerase III, gamma and tau subunits (dnaX) DN DNA polymerase III, subunit gamma/ tau/dnaX RQ 1 EV IPR012763; TIGR02397; sufficient; -- SN 5 ID DNA polymerase III, delta subunit DN DNA polymerase III, delta subunit/holA RQ 1 EV IPR005790; TIGR01128; sufficient; -- SN 6 ID DNA polymerase III, delta prime subunit DN DNA polymerase III, delta prime subunit/holB RQ 1 EV IPR004622; TIGR00678; sufficient; -- SN 7 ID DNA polymerase III, chi subunit (holC) DN DNA polymerase III chi subunit, HolC RQ 1 EV IPR007459; PF04364; sufficient; -- SN 8 ID DNA polymerase III, psi subunit (holD) DN DNA polymerase III, psi subunit/holD RQ 1 EV IPR018382; TIGR00664; sufficient; -- SN 9 ID DNA polymerase III, theta subunit (holE) DN DNA polymerase III-theta/holE RQ 0 EV IPR009052; PF06440; sufficient; -- SN 10 ID DNA polymerase III, alpha subunit, PolC-type DN DNA polymerase III, alpha subunit, Gram-positive type/polC RQ 0 EV IPR006308; TIGR01405; sufficient; // AC GenProp0264 DE Glucosylglycerol biosynthesis TP PATHWAY AU Haft DH TH 1 RN [1] RM 9733686 RT The ggpS gene from Synechocystis sp. strain PCC 6803 encoding RT glucosyl-glycerol-phosphate synthase is involved in osmolyte synthesis. RA Marin K, Zuther E, Kerstan T, Kunert A, Hagemann M; RL J Bacteriol. 1998;180:4843-4849. CC Glucosylglycerol is an osmolyte, a solute compatible with biological CC function inside cells that serves as an osmoprotectant. Other osmolytes CC include trehalose, sucrose, glycine betaine, and other betaines. CC Betaines offer stronger osmoprotection than glucosylglycerol but are CC nitrogen-requiring. The key enzyme, glucosylglycerol-phosphate CC synthase, uses ADP-glucose + sn-glycerol 3-phosphate. CC Glucose-1-phosphate adenylyltransferase, which synthesizes ADP-glucose, CC is therefore included in this property although it also has other CC roles, such as in glycogen biosynthesis. -- SN 1 ID Glucose-1-phosphate adenylyltransferase DN Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) RQ 1 EV IPR011831; TIGR02091; sufficient; TG GO:0006970; -- SN 2 ID Glucosylglycerol 3-phosphatase DN Glucosylglycerol 3-phosphatase (EC 3.1.3.69) RQ 1 EV IPR012765; TIGR02399; sufficient; TG GO:0006970; -- SN 3 ID Glucosylglycerol-phosphate synthase DN Glucosylglycerol-phosphate synthase (EC 2.4.1.213) RQ 1 EV IPR012764; TIGR02398; sufficient; TG GO:0006970; // AC GenProp0265 DE Trehalose biosynthesis, OtsAB pathway TP PATHWAY AU Haft DH TH 0 RN [1] RM 12890033 RT Three pathways for trehalose metabolism in Corynebacterium glutamicum RT ATCC13032 and their significance in response to osmotic stress. RA Wolf A, Krämer R, Morbach S; RL Mol Microbiol. 2003;49:1119-1134. RN [2] RM 8045430 RT Analysis of the otsBA operon for osmoregulatory trehalose synthesis in RT Escherichia coli and homology of the OtsA and OtsB proteins to the RT yeast trehalose-6-phosphate synthase/phosphatase complex. RA Kaasen I, McDougall J, Strøm AR; RL Gene. 1994;145:9-15. CC Trehalose is compatible solute, an osmolyte that protects cells against CC osmotic stress. It is built from two glucose molecules in an CC alpha,alpha linkage, and can be made by at least three different CC pathways. In the OtsAB pathway (ots stands for osmotically regulated CC trehalose synthesis), OtsA (EC 2.4.1.15) makes trehalose-6-phosphate CC from UDP-glucose and D-glucose 6-phosphate. OtsB (EC 3.1.3.12) removes CC the phosphate. -- SN 1 ID Trehalose-6-phosphate synthase DN Alpha,alpha-trehalose-phosphate synthase (UDP-forming)/OtsA (EC 2.4.1.15) RQ 1 EV IPR012766; TIGR02400; sufficient; TG GO:0006970; -- SN 2 ID Trehalose-phosphatase DN Trehalose-phosphatase/OtsB (EC 3.1.3.12) RQ 1 EV IPR003337; TIGR00685; sufficient; TG GO:0006970; // AC GenProp0266 DE Trehalose biosynthesis, TreYZ pathway TP PATHWAY AU Haft DH TH 0 RN [1] RM 10658666 RT Three pathways for trehalose biosynthesis in mycobacteria. RA De Smet KA, Weston A, Brown IN, Young DB, Robertson BD; RL Microbiology. 2000;146 ( Pt 1):199-208. RN [2] RM 12626396 RT New insights on trehalose: a multifunctional molecule. RA Elbein AD, Pan YT, Pastuszak I, Carroll D; RL Glycobiology. 2003;13:17r-27r. CC Trehalose is an alpha,alpha glucose disaccharide that serves as a CC highly protective osmoprotectant in many species in all three domains CC of life. Trehalose may also be a component of more complex molecules CC such as cell wall glycolipids in Actinomycetes. The TreYZ is one of CC several pathways for trehalose biosynthesis and is dependent on the CC presence of glycogen-like glucose polymers. It is alternative to the CC OtsAB (osmotically regulated trehalose synthesis A and B) system. In CC some species with both, the TreYZ rather then the OtsAB system is CC induced by osmotic stress. -- SN 1 ID Maltooligosyltrehalose synthase DN (1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase/TreY (EC 5.4.99.15) RQ 1 EV IPR012767; TIGR02401; sufficient; TG GO:0006970; -- SN 2 ID Malto-oligosyltrehalose trehalohydrolase DN 4-alpha-D-{(1->4)-alpha-D-glucano} trehalose trehalohydrolase/TreZ (EC 3.2.1.141) RQ 1 EV IPR012768; TIGR02402; sufficient; TG GO:0006970; // AC GenProp0267 DE Osmolyte biosynthesis TP CATEGORY AU Haft DH TH 0 RN [1] RM 9818351 RT Uptake and synthesis of compatible solutes as microbial stress RT responses to high-osmolality environments. RA Kempf B, Bremer E; RL Arch Microbiol. 1998;170:319-330. CC Cells can resist dessication, high salt, and other osmotic stresses by CC modulating levels of osmolytes, compatible solutes that can exists in CC high concentrations without damaging cells. Some osmolytes may have CC secondary functions for carbon and energy storage molecules or for CC further biosynthetic reactions. Widely distributed compatible solutes CC induced by osmotic stress include trehalose, glucosylglycerol, sucrose, CC mannitol, glycine betaine and other betaines, ectoine and CC hydroxyectoine, glutamate, N-acetylglutaminylglutamine amide, etc. -- SN 1 ID Glycine betaine biosynthesis from choline RQ 0 EV GenProp0147; -- SN 2 ID Glucosylglycerol biosynthesis RQ 0 EV GenProp0264; -- SN 3 ID Trehalose biosynthesis, OtsAB pathway RQ 0 EV GenProp0265; -- SN 4 ID Trehalose biosynthesis, TreYZ pathway RQ 0 EV GenProp0266; -- SN 5 ID Ectoine biosynthesis RQ 0 EV GenProp0268; -- SN 6 ID Mannosylglycerate biosynthesis RQ 0 EV GenProp0281; -- SN 7 ID N(epsilon)-acetyl-beta-lysine biosynthesis RQ 0 EV GenProp0878; -- SN 8 ID Beta-glutamate biosynthesis RQ 0 EV GenProp1070; // AC GenProp0268 DE Ectoine biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 11823218 RT Osmotically regulated synthesis of the compatible solute ectoine in RT Bacillus pasteurii and related Bacillus spp. RA Kuhlmann AU, Bremer E; RL Appl Environ Microbiol. 2002;68:772-783. RN [2] RM 22885758 RT Ectoine biosynthesis in Mycobacterium smegmatis. RA Ofer N, Wishkautzan M, Meijler M, Wang Y, Speer A, Niederweis M, Gur E; RL Appl Environ Microbiol. 2012;78:7483-7486. CC Ectoine is a compatible solute used as an osmoprotectant by a number of CC bacterial species, including Vibrio cholerae, Halomonas variabilis, CC Bacillus pasteurii, and Mycobacterium smegmatis. Key enzymes are CC diaminobutyric acid acetyltransferase (EctA), diaminobutyric acid CC aminotransferase (EctB), and ectoine synthase (EctC). Ectoine is CC 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid. Many CC ectoine-producing species contain the enzyme ectoine hydroxylase CC (EctD), and also produce hydroxyectoine. -- SN 1 ID Diaminobutyrate acetyltransferase DN Diaminobutyrate acetyltransferase/EctA (EC 2.3.1.178) RQ 1 EV IPR012772; TIGR02406; sufficient; TG GO:0019491; -- SN 2 ID Diaminobutyrate--2-oxoglutarate transaminase DN Diaminobutyrate--2-oxoglutarate transaminase/EctB (EC 2.6.1.76) RQ 1 EV IPR012773; TIGR02407; sufficient; TG GO:0019491; -- SN 3 ID Ectoine synthase DN Ectoine synthase/EctC (EC 4.2.1.108) RQ 1 EV IPR010462; PF06339; sufficient; TG GO:0019491; -- SN 4 ID Ectoine hydroxylase DN Ectoine hydroxylase/EctD (EC 1.17.-.-) RQ 0 EV IPR012774; TIGR02408; sufficient; // AC GenProp0269 DE Coenzyme B12 biosynthesis from cob(II)yrinate diamide TP PATHWAY AU Haft DH TH 1 CC This property covers the main branch of the latter part of the Coenzyme CC B12 (5-deoxyadenosyl cobalamin) biosynthesis pathway from CC cob(II)yrinate diamide, which is the product of cobalt chelatase. CC Additionally, in order to have a complete pathway, an organism must CC have the capability to synthesize (or otherwise obtain) CC 1-amino-2-propanol and alpha-ribazole. -- SN 1 ID Adenosylcobinamide-phosphate synthase DN Cobalamin biosynthesis CobD/CbiB RQ 0 EV IPR004485; TIGR00380; sufficient; -- SN 2 ID Cobyrinate adenosyltransferases (BtuR, PduO, EutT) DN ATP:cob(I)alamin adenosyltransferases (BtuR, PduO, EutT) RQ 1 EV IPR003724; TIGR00708; sufficient; EV IPR029499; TIGR00636; sufficient; EV IPR016030; PF01923; sufficient; -- SN 3 ID Alpha-ribazole-5`-phosphate phosphatase DN Alpha-ribazole phosphatase, CobZ/CobC RQ 0 EV IPR017577; TIGR03161; sufficient; EV IPR017578; TIGR03162; sufficient; -- SN 4 ID Adenosylcobinamide synthase (CobD) DN Cobalamin biosynthesis CobD/CbiB RQ 1 EV IPR004485; PF03186; sufficient; -- SN 5 ID Cobyric acid synthase (CobQ/CbiP) DN Cobyric acid synthase CobQ RQ 1 EV IPR004459; TIGR00313; sufficient; -- SN 6 ID Cobalamine 5-phosphate synthase (alpha ribazole transferase) (CobV) DN Adenosylcobinamide-GDP ribazoletransferase (CobS) RQ 1 EV IPR003805; PF02654; sufficient; EV IPR003805; TIGR00317; sufficient; -- SN 7 ID Nicotinate nucleotide-DBI P-ribosyltransferase DN Nicotinate nucleotide-DBI P-ribosyltransferase RQ 1 EV IPR017846; TIGR03160; sufficient; -- SN 8 ID Bifunctional cobinamide kinase, cobinamide phosphate guanylyltransferase (CobP) DN Cobinamide kinase/cobinamide phosphate guanylyltransferase RQ 1 EV IPR003203; PF02283; sufficient; -- SN 9 ID Threonine-phosphate decarboxylase DN L-threonine-O-3-phosphate decarboxylase RQ 0 EV IPR005860; TIGR01140; sufficient; // AC GenProp0271 DE Trehalose utilization TP SYSTEM AU Haft DH TH 0 CC This system consists of three components, typically in a single operon. CC First is a PTS system transporter by which trehalose enters the cell as CC trehalose-6-phosphate. Second is trehalose-6-phosphate hydrolase, or CC alpha,alpha-phosphotrehalase. Third is a transcriptional repressor for CC the operon, with different families in E.coli and Bacillus. -- SN 1 ID PTS system, trehalose-specific IIBC component DN Phosphotransferase system, trehalose-specific IIBC component/PTS RQ 1 EV IPR011296; TIGR01992; sufficient; -- SN 2 ID Trehalose-6-phosphate hydrolase DN Trehalose-6-phosphate hydrolase RQ 1 EV IPR012769; TIGR02403; sufficient; -- SN 3 ID Trehalose operon repressor DN Trehalose operon transcriptional repressor RQ 1 EV IPR012770; TIGR02404; sufficient; EV IPR012771; TIGR02405; sufficient; // AC GenProp0272 DE Pyruvate fermentation to acetoin TP PATHWAY AU Haft DH TH 0 CC Energy metabolism from sugars leads to flux through pyruvate. Pyruvate CC metabolism under limited oxygen may lead to fermentation with acidic CC end products. Pyruvate may be converted to acetoin in two steps, and in CC some species from acetoin to 2,3-butanediol, a neutral compound, so CC homeostasis can be maintained. This property describes the catabolic CC form of acetolactate synthase (distinguished from forms used in CC branched chain amino acid biosynthesis) and alpha-acetolactate CC decarboxylase. -- SN 1 ID Acetolactate decarboxylase DN Alpha-acetolactate decarboxylase RQ 1 EV IPR005128; TIGR01252; sufficient; -- SN 2 ID Acetolactate synthase, catabolic DN Acetolactate synthase, catabolic RQ 1 EV IPR012782; TIGR02418; sufficient; // AC GenProp0273 DE Protocatechuate degradation to beta-ketoadipate TP PATHWAY AU Haft DH TH 0 RN [1] RM 15006791 RT Diverse organization of genes of the beta-ketoadipate pathway in RT members of the marine Roseobacter lineage. RA Buchan A, Neidle EL, Moran MA; RL Appl Environ Microbiol. 2004;70:1658-1668. CC This pathway represents the bacterial version of degradation of CC protocatechuate to beta-ketoadipate. It is often referred to as the CC protocatechuate branch of the beta-ketoadipate pathway, in contrast to CC the catechol branch. Protocatechuate can be reached in one step from CC 3-hydroxybenzoate, 4-hydroxybenzoate, vanillate, etc., and in two steps CC from benzoate, and from other aromatic compounds. Note that catechol is CC another common intermediate in the degradation of aromatic compounds. CC The two branches converge at beta-ketoadipate. From there, CC beta-ketoadipate is degraded in a two-step pathway to succinyl-CoA and CC acetyl-CoA. -- SN 1 ID Protocatechuate 3,4-dioxygenase, alpha subunit DN Protocatechuate 3,4-dioxygenase, alpha subunit (EC 1.13.11.3) RQ 1 EV IPR012786; TIGR02423; sufficient; TG GO:0019619; -- SN 2 ID Protocatechuate 3,4-dioxygenase, beta subunit DN Protocatechuate 3,4-dioxygenase, beta subunit (EC 1.13.11.3) RQ 1 EV IPR012785; TIGR02422; sufficient; TG GO:0019619; -- SN 3 ID 3-carboxy-cis,cis-muconate cycloisomerase DN 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) RQ 1 EV IPR012789; TIGR02426; sufficient; TG GO:0019619; -- SN 4 ID 4-carboxymuconolactone decarboxylase DN 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) RQ 1 EV IPR012788; TIGR02425; sufficient; TG GO:0019619; -- SN 5 ID 3-oxoadipate enol-lactonase DN 3-oxoadipate enol-lactonase 1/2 (EC 3.1.1.24) RQ 1 EV IPR026968; TIGR02427; sufficient; TG GO:0019619; -- SN 6 ID Pca operon transcriptional regulator PcaQ DN Pca transcription factor PcaQ RQ 0 EV IPR012787; TIGR02424; sufficient; -- SN 7 ID Regulators, PcaR/PcaU/PobR family DN Beta-ketoadipate pathway transcriptional regulator, PcaR/PcaU/PobR RQ 0 EV IPR012794; TIGR02431; sufficient; // AC GenProp0275 DE Cobyrinic acid diamide biosynthesis, anaerobic pathway TP PATHWAY AU Haft DH TH 3 RN [1] RM 12869542 RT Comparative genomics of the vitamin B12 metabolism and regulation in RT prokaryotes. RA Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS; RL J Biol Chem. 2003;278:41148-41159. CC This property covers that part of the Vitamin B12 (cobalamin) CC biosynthesis pathway in which uroporphyrinogen III is converted to CC cobyrinic acid diamide under anaerobic conditions. This process CC differs from the aerobic version in several key respects. The most CC striking is the fact that here the cobalt atom is inserted early in the CC process (after the formation of the branchpoint compound precorrin-2 by CC CbiK or CbiX) in an ATP-independent manner, as opposed to the aerobic CC pathway in which the cobalt is inserted at the end by a multimeric CC ATP-hydrolyzing system. Another distinctive feature is the nature of CC the enzyme catalyzing the oxidative ring contraction. In the aerobic CC pathway, this is carried out by an oxygenase (CobG), while the CC as-of-yet uncharacterized anaerobic enzyme clearly must utilize some CC other mechanism. Finally, the methylation at position C-1 at the point CC of the ring contraction is carried out by CobF in the aerobic pathway, CC and by an as-of-yet uncharacterized enzyme in the anaerobic pathway CC (presumably because the proximity of this carbon to the cobalt changes CC the chemistry somewhat). Two genes (CbiD and CbiG) are found in most CC anaerobic B12 biosynthetic clusters and have been shown to be essential CC to the pathway. CbiD is homologous to methylases and is likely to CC catalyze the C-1 methylation. CbiG then, by process of elimination and CC (coupled with unique nature of the chemical transformation) its lack of CC homology to other known classes of enzyme, is likely to catalyze the CC ring contraction. CbiJ, the analog of precorrin-6x reductase (CobK), CC is not found in deltaproteobacteria, a number of archaea and some other CC species, often this is the only component missing. Most likely, an CC unknown reductase replaces CbiJ/CobK in these species. For this reason CC the detection of this component is not a required step in this property. CC The majority of genomes for which some evidence has been asserted, are CC missing evidence of the CbiK or CbiX chelatase. This step is still CC required for the assertion of the YES state since it is part of the CC suite of components which are diagnostic for the anaerobic pathway. The CC evidence for the anaerobic pathway is nonetheless quite strong when CC this is the only component missing, especially when the aerobic pathway CC is not supported. -- SN 1 ID Cobyrinate diamide synthase (CbiA) DN Cobyrinic acid a,c-diamide synthase CbiA RQ 1 EV IPR004484; TIGR00379; sufficient; TG GO:0019251; -- SN 2 ID C-11, C-12 mutase (CbiC) DN Cobalamin biosynthesis precorrin-8X methylmutase CobH/CbiC RQ 1 EV IPR003722; PF02570; sufficient; TG GO:0019251; -- SN 3 ID CbiD DN Cobalt-precorrin-5B C(1)-methyltransferase CbiD RQ 1 EV IPR002748; TIGR00312; sufficient; TG GO:0019251; EV IPR002748; PF01888; sufficient; TG GO:0019251; -- SN 4 ID C-5,15 methylase/C-12 decarboxylase (CbiE) DN Cobalamin (vitamin B12) biosynthesis CbiE, precorrin-6Y methyltransferase RQ 1 EV IPR012818; TIGR02467; sufficient; TG GO:0019251; -- SN 5 ID C-11 methylase (CbiF) DN Cobalamin (vitamin B12) biosynthesis CobM/CbiF, precorrin-4 C11-methyltransferase RQ 1 EV IPR006362; TIGR01465; sufficient; TG GO:0019251; -- SN 6 ID CbiG DN CobE/GbiG C-terminal domain RQ 1 EV IPR002750; PF01890; sufficient; TG GO:0019251; -- SN 7 ID C-17 methylase (CbiH) DN Precorrin-3B C17-methyltransferase domain RQ 1 EV IPR006363; TIGR01466; sufficient; TG GO:0019251; -- SN 8 ID Co-precorrin 6 reductase (CbiJ) DN Precorrin-6x reductase (CbiJ) RQ 0 EV IPR003723; TIGR00715; sufficient; TG GO:0019251; EV IPR003723; PF02571; sufficient; TG GO:0019251; -- SN 9 ID Cobaltochelatase, monomeric DN Cobalamin (vitamin B12) biosynthesis CbiX RQ 1 EV IPR010388; PF06180; sufficient; TG GO:0019251; EV IPR002762; PF01903; sufficient; TG GO:0019251; -- SN 10 ID C-20 methylase (CbiL) DN Precorrin-2 C(20)-methyltransferase domain (CbiL) RQ 1 EV IPR006364; TIGR01467; sufficient; TG GO:0019251; -- SN 11 ID C-5,15 methylase/C-12 decarboxylase (CbiT) DN Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit RQ 1 EV IPR014008; TIGR02469; sufficient; TG GO:0019251; -- SN 12 ID Cobalt reductase DN Cobalt reductase/Co_red RQ 0 -- SN 13 ID Uroporphyrinogen methyltransferase DN Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) RQ 1 EV IPR006366; TIGR01469; sufficient; TG GO:0019251; // AC GenProp0277 DE Cobalt import system (ABC transporter: 3.A.1.18.1) TP SYSTEM AU Haft DH TH 2 RN [1] RM 12869542 RT Comparative genomics of the vitamin B12 metabolism and regulation in RT prokaryotes. RA Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS; RL J Biol Chem. 2003;278:41148-41159. CC This ABC transporter is important for the import of cobalt ions CC essential for the biosynthesis of coenzyme B12. In this complex, the CC solute-binding (CbiN), permease (CbiQ) and ATP-binding (CbiO) subunits CC are accompanied by a fourth subunit (CbiM) of unknown function, CC although it is believed to be a membrane-spanning protein. -- SN 1 ID Cobalt ECF transporter S component CbiM DN Cobalamin (vitamin B12) biosynthesis protein CbiM RQ 1 EV IPR018024; TIGR00123; sufficient; TG GO:0006824; -- SN 2 ID Cobalt transporter, subunit CbiN DN Cobalt transport protein CbiN RQ 1 EV IPR003705; TIGR01165; sufficient; TG GO:0006824; -- SN 3 ID Cobalt ECF transporter ATPase CbiO DN Cobalt transport protein ATP-binding subunit RQ 1 EV IPR005876; TIGR01166; sufficient; TG GO:0006824; -- SN 4 ID Cobalt ECF transporter T component CbiQ DN Cobalt ECF transporter T component CbiQ RQ 1 EV IPR012809; TIGR02454; sufficient; TG GO:0006824; // AC GenProp0281 DE Mannosylglycerate biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 12788726 RT The bacterium Thermus thermophilus, like hyperthermophilic archaea, RT uses a two-step pathway for the synthesis of mannosylglycerate. RA Empadinhas N, Albuquerque L, Henne A, Santos H, da Costa MS; RL Appl Environ Microbiol. 2003;69:3272-3279. CC Mannosylglycerate is a compatible solute (cf. trehalose, ectoine, CC sucrose, glucosylglycerol, etc.) that tends to be found in highly CC thermophilic prokaryotes of various lineages. The more common CC biosynthetic pathway is a two-step pathway. Mannosyl-3-phosphoglycerate CC synthase (EC 2.4.1.217) combines GDP-mannose with CC 3-phospho-D-glycerate. The resultant mannosyl-3-phosphoglycerate is CC dephosphorylated by mannosyl-3-phosphoglycerate phosphatase (EC CC 3.1.3.70). The two enzymes are fused in Dehalococcoides ethenogenes, a CC rare mesophile to have this pathway. -- SN 1 ID Mannosyl-3-phosphoglycerate synthase DN Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) RQ 1 EV IPR012812; TIGR02460; sufficient; -- SN 2 ID Mannosyl-3-phosphoglycerate phosphatase DN Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) RQ 1 EV IPR033980; TIGR02461; sufficient; // AC GenProp0283 DE Beta-ketoadipate degradation to succinyl-CoA and acetyl-CoA TP PATHWAY AU Haft DH TH 0 CC The beta-ketoadipate pathway is the general term for pathways that CC degrade aromatic compounds, via either catechol or protocatechuate, to CC beta-ketoadipate and then to succinyl-CoA plus acetyl-CoA. This CC property represents the shared final two steps, from beta-ketoadipate CC to succinyl- and acetyl-CoA. -- SN 1 ID Beta-ketoadipyl CoA thiolase DN Beta-ketoadipyl CoA thiolase/pcaF RQ 1 EV IPR012793; TIGR02430; sufficient; EV IPR002155; TIGR01930; -- SN 2 ID CoA-transferase, A subunit DN 3-oxoacid CoA-transferase, subunit A/pcaI RQ 1 EV IPR012792; TIGR02429; sufficient; -- SN 3 ID CoA-transferase, B subunit DN 3-oxoacid CoA-transferase, subunit B/pcaJ RQ 1 EV IPR012791; TIGR02428; sufficient; // AC GenProp0287 DE Ribonucleotide reduction TP METAPATH AU Haft DH TH 0 RN [1] RM 15158709 RT Structure, function, and mechanism of ribonucleotide reductases. RA Kolberg M, Strand KR, Graff P, Andersson KK; RL Biochim Biophys Acta. 2004;1699:1-34. RN [2] RM 12714050 RT Di-iron-tyrosyl radical ribonucleotide reductases. RA Stubbe J; RL Curr Opin Chem Biol. 2003;7:183-188. RN [3] RM 11802741 RT Crystal structure of the di-iron/radical protein of ribonucleotide RT reductase from Corynebacterium ammoniagenes. RA Högbom M, Huque Y, Sjöberg BM, Nordlund P; RL Biochemistry. 2002;41:1381-1389. RN [4] RM 9818192 RT The function of adenosylcobalamin in the mechanism of ribonucleoside RT triphosphate reductase from Lactobacillus leichmannii. RA Lawrence CC, Stubbe J; RL Curr Opin Chem Biol. 1998;2:650-655. RN [5] RM 12206460 RT Deoxyribonucleotide synthesis in anaerobic microorganisms: the class RT III ribonucleotide reductase. RA Fontecave M, Mulliez E, Logan DT; RL Prog Nucleic Acid Res Mol Biol. 2002;72:95-127. RN [6] RM 15949864 RT Identification of a bacterial regulatory system for ribonucleotide RT reductases by phylogenetic profiling. RA Rodionov DA, Gelfand MS; RL Trends Genet. 2005;21:385-389. DC Purine metabolism DR KEGG; map00230; DC Pyrimidine metabolism DR KEGG; map00240; CC The reduction of the ribose sugar of ribonucleotide triphosphates to CC deoxyribose is one of the essential steps in the biosynthesis of DNA. CC This chemically challenging step is carried out be a number of CC distinctly different enzyme systems [1]. Each of these systems utilizes CC a different mechanism for the generation of a transient cysteine-thiyl CC radical which initiates the reduction of the substrate. Class I enzymes CC utilize a diferric non-heme iron cluster to generate a stable tyrosine CC radical [2]. Note that earlier reports of a manganese-based class IV CC system related to class I in high GC gram positive species was proved CC to be spurious [3]. Class II enzymes utilize adenosylcobalamin CC (vitamin B12) [4]. Class III enzymes utilize radical-SAM domain CC proteins to generate stable glycine radicals [5]. A very small CC number of genomes appear to be devoid of ribonucleotide reductase CC sequences, Mycoplasma arthritidis 158L3-1, Mycoplasma bovis Donetta CC PG45, Ureaplasma urealyticum parvum biovar serovar 3, Borrelia CC burgdorferi B31 and Borrelia garinii PBi. Each of these is a reduced CC genome with a limited metabolic portfolio, however other mycoplasma CC species do contain RNRs. Three possibilities are likely, 1) these CC genomes harbor a non-orthologous RNR, 2) these genes are located on CC plasmids or small chromosomes which were lost prior to genomic CC sequencing (Borrelia, in particular has a number of small chromosomes CC and plasmids which were sequenced) or 3) these species strictly rely on CC import of deoxyribonucleic acid from the host environment. -- SN 1 ID Class I (aerobic) ribonucleotide reductase: GenProp0289 DN Class I (aerobic) ribonucleotide reductase: GenProp0289 RQ 1 EV GenProp0289; TG GO:0009265; -- SN 2 ID Class II (B12-dependent) ribonucleotide reductase: GenProp0290 DN Class II (B12-dependent) ribonucleotide reductase: GenProp0290 RQ 1 EV GenProp0290; TG GO:0009265; -- SN 3 ID Class III (anaerobic) ribonucleotide reductase: GenProp0291 DN Class III (anaerobic) ribonucleotide reductase: GenProp0291 RQ 1 EV GenProp0291; TG GO:0009265; -- SN 4 ID Transcriptional regulator NrdR DN Ribonucleotide reductase regulator NrdR-like RQ 0 EV IPR003796; TIGR00244; sufficient; TG GO:0009265; // AC GenProp0288 DE Tetrahydromethanopterin S-methyltransferase complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 10338124 RT The energy conserving methyltetrahydromethanopterin:coenzyme M RT methyltransferase complex from methanogenic archaea: function of the RT subunit MtrH. RA Hippler B, Thauer RK; RL FEBS Lett. 1999;449:165-168. CC This complex of eight subunits, MtrA-H, effects the transfer of a CC methyl group from tetrahydromethanopterin to coenzyme M using a CC cobalamin (B12) cofactor residing on MtrA. This transfer is coupled to CC an energy-driven sodium-ion pump. Methane is subsequently released by CC a two-electron reduction of the methyl-coenzyme M by the enzyme CC methyl-coenzyme M reductase. -- SN 1 ID Subunit A, cobalamin-containing DN Tetrahydromethanopterin S-methyltransferase subunit A/MtrA RQ 1 EV IPR005778; TIGR01111; sufficient; -- SN 2 ID Tetrahydromethanopterin S-methyltransferase subunit B DN Tetrahydromethanopterin S-methyltransferase subunit B/MtrB RQ 1 EV IPR008690; TIGR04166; sufficient; -- SN 3 ID Tetrahydromethanopterin S-methyltransferase, subunit C DN Tetrahydromethanopterin S-methyltransferase, subunit C/MtrC RQ 1 EV IPR005865; TIGR01148; sufficient; -- SN 4 ID Tetrahydromethanopterin S-methyltransferase, subunit D DN Tetrahydromethanopterin S-methyltransferase, subunit D/MtrD RQ 1 EV IPR005779; TIGR01112; sufficient; -- SN 5 ID Tetrahydromethanopterin S-methyltransferase, subunit E DN Tetrahydromethanopterin S-methyltransferase, subunit E/MtrE RQ 1 EV IPR005780; TIGR01113; sufficient; -- SN 6 ID Tetrahydromethanopterin S-methyltransferase, F subunit DN Tetrahydromethanopterin S-methyltransferase, F subunit/MtrF RQ 1 EV IPR013347; TIGR02507; sufficient; -- SN 7 ID Tetrahydromethanopterin S-methyltransferase, subunit G DN Tetrahydromethanopterin S-methyltransferase, subunit G/MtrG RQ 1 EV IPR005866; TIGR01149; sufficient; -- SN 8 ID Subunit H, pterin:cobalamin transferase DN Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H/MtrH RQ 1 EV IPR023467; TIGR01114; sufficient; // AC GenProp0289 DE Class I (aerobic) ribonucleotide reductase TP SYSTEM AU Haft DH TH 0 RN [1] RM 12714050 RT Di-iron-tyrosyl radical ribonucleotide reductases. RA Stubbe J; RL Curr Opin Chem Biol. 2003;7:183-188. RN [2] RM 11802741 RT Crystal structure of the di-iron/radical protein of ribonucleotide RT reductase from Corynebacterium ammoniagenes. RA Högbom M, Huque Y, Sjöberg BM, Nordlund P; RL Biochemistry. 2002;41:1381-1389. RN [3] RM 11441020 RT Structural basis for the thioredoxin-like activity profile of the RT glutaredoxin-like NrdH-redoxin from Escherichia coli. RA Stehr M, Schneider G, Aslund F, Holmgren A, Lindqvist Y; RL J Biol Chem. 2001;276:35836-35841. CC Ribonucleotide reductases (RNRs) are responsible for the conversion of CC the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the CC rate-limiting step of DNA biosynthesis. The class I RNRs [1] consist of CC two subunits, alpha and beta (also known as the large and small CC subunbits, respectively). Class I RNRs generate the required radical CC (on tyrosine) via a non-heme iron cofactor which resides in the beta CC subunit. The alpha subunit contains the catalytic and allosteric CC regulatory sites. The most common gene symbols for these genes are NrdE CC (alpha) and NrdF (beta), althought the first characterized complex from CC E.coli (NrdAB) turns out to be one of a pair in gammaproteobacteria and CC the more divergent one at that. Where multiple class I enzymes exist in CC a single organism they are presumed to be under differential CC regulation. Note that earlier reports of a manganese-based class IV CC system related to class I in high GC gram positive species was proved CC to be spurious [2]. Electrons for this reduction are supplied by CC glutaredoxin-like (NrdH, in some species [3]), or flavodoxins specific CC to this system which are in turn reduced by oxygen via thioredoxin CC reductase. Certain class I RNRs are associated with a gene of unknown CC function (NrdI). NrdI shows up more frequently, but not exclusively in CC species with more than one class I RNR, so it may be involved in CC regulation in some way. -- SN 1 ID Aerobic RNR, alpha (large) chain DN Ribonucleotide reductase alpha chain RQ 1 EV IPR013346; TIGR02506; sufficient; TG GO:0009265; EV IPR013350; TIGR02510; sufficient; TG GO:0009265; -- SN 2 ID Aerobic RNR, beta (small) chain DN Ribonucleotide reductase small subunit family RQ 1 EV IPR000358; PF00268; sufficient; TG GO:0009265; -- SN 3 ID Ribonucleotide reductase Class Ib, NrdI DN Ribonucleotide reductase Class Ib, NrdI RQ 0 EV IPR004465; TIGR00333; sufficient; TG GO:0009265; -- SN 4 ID Redoxin, ribonucleotide-reductase related DN Ribonucleotide reductase-associated flavodoxin/Glutaredoxin-like protein NrdH RQ 0 EV IPR011909; TIGR02194; sufficient; TG GO:0009265; EV IPR010088; TIGR01754; sufficient; TG GO:0009265; // AC GenProp0290 DE Class II (B12-dependent) ribonucleotide reductase TP SYSTEM AU Haft DH TH 0 RN [1] RM 9818192 RT The function of adenosylcobalamin in the mechanism of ribonucleoside RT triphosphate reductase from Lactobacillus leichmannii. RA Lawrence CC, Stubbe J; RL Curr Opin Chem Biol. 1998;2:650-655. CC Ribonucleotide reductases (RNRs) are responsible for the conversion of CC the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the CC rate-limiting step of DNA biosynthesis. The class II RNRs consist of a CC single subunit and generate the required radical via an CC adenosylcobalamin (B12) cofactor. The most common gene symbols for CC this gene is NrdJ, although the gene in mycobacterium is called NrdZ. CC The first characterized NrdJ gene, from Lactobacillus leichmannii, CC acted specifically on nucleoside triphosphates like the class III CC enzymes (1.17.4.2) and unlike the class I enzymes which act on the CC diphosphates (1.17.4.1). However, as further B12-dependent RNRs were CC characterized, it became clear that this is the exception rather than CC the rule. This property captures both types. -- SN 1 ID B12-dependent ribonucleotide reductase DN Ribonucleoside-triphosphate reductase/NrdJ/Z (EC:1.17.4.2) RQ 1 EV IPR013345; TIGR02505; sufficient; TG GO:0009265; EV IPR013344; TIGR02504; sufficient; TG GO:0009265; // AC GenProp0291 DE Class III (anaerobic) ribonucleotide reductase TP SYSTEM AU Haft DH TH 0 RN [1] RM 12206460 RT Deoxyribonucleotide synthesis in anaerobic microorganisms: the class RT III ribonucleotide reductase. RA Fontecave M, Mulliez E, Logan DT; RL Prog Nucleic Acid Res Mol Biol. 2002;72:95-127. CC Ribonucleotide reductases (RNRs) are responsible for the conversion of CC the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the CC rate-limiting step of DNA biosynthesis. The class III RNRs consist of CC two components, the catalytic enzyme (NrdD) and a radical-SAM domain CC enzyme (NrdG) which activates the catalytic enzyme by the generation of CC a protein-centered radical. -- SN 1 ID Anaerobic ribonucleoside-triphosphate reductase DN Ribonucleoside-triphosphate reductase (EC:1.17.4.2) RQ 1 EV IPR012833; TIGR02487; sufficient; TG GO:0009265; EV IPR012833; TIGR02827; sufficient; TG GO:0009265; -- SN 2 ID Activating protein for anaerobic ribonucleotide triphosphate reductase DN Ribonucleoside-triphosphate reductase activating enzyme (EC:1.97.1.4) RQ 1 EV IPR012837; TIGR02491; sufficient; TG GO:0009265; EV IPR012840; TIGR02495; sufficient; TG GO:0009265; EV IPR014191; TIGR02826; sufficient; TG GO:0009265; // AC GenProp0292 DE Ethanolamine degradation organelle TP SYSTEM AU Haft DH TH 4 RN [1] RM 1550360 RT Overexpression, purification, and some properties of the RT AdoCbl-dependent ethanolamine ammonia-lyase from Salmonella RT typhimurium. RA Faust LP, Babior BM; RL Arch Biochem Biophys. 1992;294:50-54. RN [2] RM 15466038 RT Identification of a reactivating factor for adenosylcobalamin-dependent RT ethanolamine ammonia lyase. RA Mori K, Bando R, Hieda N, Toraya T; RL J Bacteriol. 2004;186:6845-6854. RN [3] RM 15516577 RT Evidence that a B12-adenosyl transferase is encoded within the RT ethanolamine operon of Salmonella enterica. RA Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth JR; RL J Bacteriol. 2004;186:7635-7644. RN [4] RM 15466042 RT A pH-sensitive function and phenotype: evidence that EutH facilitates RT diffusion of uncharged ethanolamine in Salmonella enterica. RA Penrod JT, Mace CC, Roth JR; RL J Bacteriol. 2004;186:6885-6890. RN [5] RM 23585538 RT Evidence that a metabolic microcompartment contains and recycles RT private cofactor pools. RA Huseby DL, Roth JR; RL J Bacteriol. 2013;195:2864-2879. DC Glycerophospholipid metabolism DR KEGG; map00564; CC Ethanolamine can be broken down to acetaldehyde by the action of CC ethanolamine ammonia lyase, an adenosyl cobalamin (vitamin B12) CC dependent enzyme. In its simplest form this system consists only of the CC two subunits of the enzyme, but ususally also includes a transporter CC for ethanolamine and may include a coexpressed acetaldehyde CC dehydrogenase to ensure that the toxic aldehyde is efficiently CC converted to acetyl-CoA. This property encompasses the more complex CC version of this system which includes additional genes coding for the CC proteinaceous coat of a specialized organelle as well as other genes CC for the efficienct maintenance and regulation of the lyase, handling of CC the product and import of the substrate. Presumably, this organellar CC system in organisms which may rely on ethanolamine as a primary carbon CC source. -- SN 1 ID Phosphotransacetylase DN Phosphate acetyl/butaryl transferase RQ 0 EV IPR002505; PF01515; TG GO:0046336; -- SN 2 ID Conserved hypothetical in ethanolamine operon DN Ethanolamine utilization, putative RQ 0 EV IPR013372; TIGR02536; sufficient; TG GO:0046336; -- SN 3 ID Reactivating factor for ethanolamine ammonia lyase DN Ethanolamine utilisation EutA RQ 1 EV IPR009377; PF06277; sufficient; TG GO:0046336; -- SN 4 ID Ethanolamine ammonia lyase, large subunit DN Ethanolamine ammonia lyase large subunit/eutB RQ 1 EV IPR010628; PF06751; sufficient; TG GO:0046336; -- SN 5 ID Ethanolamine ammonia lyase, small subunit DN Ethanolamine ammonia-lyase light chain/eutC RQ 1 EV IPR009246; PF05985; sufficient; TG GO:0046336; -- SN 6 ID Acetaldehyde dehydrogenase (acetylating) DN Acetaldehyde dehydrogenase, acetylating/eutE RQ 1 EV IPR013357; TIGR02518; TG GO:0046336; EV IPR015590; PF00171; TG GO:0046336; -- SN 7 ID Alcohol dehydrogenase, ethanolamine operon related DN Alcohol dehydrogenase, iron-type/glycerol dehydrogenase gldA/eutG RQ 1 EV IPR001670; PF00465; TG GO:0046336; -- SN 8 ID Ethanolamine permease DN Ethanolamine permease/eutH RQ 1 EV IPR004757; TIGR00908; sufficient; TG GO:0046336; EV IPR007441; PF04346; sufficient; TG GO:0046336; -- SN 9 ID Ethanolamine utilization protein EutJ DN Ethanolamine utilisation EutJ RQ 0 EV IPR013366; TIGR02529; sufficient; TG GO:0046336; -- SN 10 ID Microcompartment coat protein DN Microcompartment protein/eutM RQ 1 EV IPR000249; PF00936; TG GO:0046336; -- SN 11 ID Carboxysome coat protein homolog DN Ethanolamine utilization protein EutN/carboxysome structural protein Ccml RQ 1 EV IPR004992; PF03319; TG GO:0046336; -- SN 12 ID Ethanolamine utilization protein, EutP DN Ethanolamine/propanediol utilisation protein, EutP/PduV RQ 0 EV IPR012381; TIGR02528; TG GO:0046336; -- SN 13 ID Ethanolamine utilization protein, PduL homolog DN Phosphate propanoyltransferase RQ 0 EV IPR008300; PF06130; TG GO:0046336; -- SN 14 ID Carboxysome coat protein homolog DN Ethanolamine utilization protein, PduT-related RQ 0 EV IPR013501; TIGR02526; sufficient; TG GO:0046336; -- SN 15 ID Ethanolamine utilization protein, EutQ DN Ethanolamine utilisation EutQ RQ 0 EV IPR010424; PF06249; TG GO:0046336; -- SN 16 ID Cob(I)alamin adenosyltransferase DN Cobalamin adenosyltransferase-like/eutT RQ 0 EV IPR016030; PF01923; TG GO:0046336; -- SN 17 ID Regulatory components DN Regulatory components RQ 0 EV IPR006208; PF00007; TG GO:0046336; EV IPR011495; PF07568; TG GO:0046336; EV IPR001789; PF00072; TG GO:0046336; EV IPR018060; PF00165; TG GO:0046336; // AC GenProp0294 DE Ethanolamine degradation proteinaceous organelle TP SYSTEM AU Haft DH TH 1 RN [1] RM 3045078 RT Ethanolamine utilization in Salmonella typhimurium. RA Roof DM, Roth JR; RL J Bacteriol. 1988;170:3855-3863. CC Ethanolamine can be broken down to acetaldehyde by the action of CC ethanolamine ammonia lyase, an adenosyl cobalamin (vitamin B12) CC dependent enzyme. In its simplest form this system consists only of CC the two subunits of the enzyme, but ususally also includes a CC transporter for ethanolamine and may include a coexpressed acetaldehyde CC dehydrogenase to ensure that the toxic aldehyde is efficiently CC converted to acetyl-CoA. A more complex version of this system exists CC (GenProp0292) which includes additional genes coding for the CC proteinaceous coat of a specialized organelle, as well as other genes CC for the efficienct maintenance and regulation of the lyase, handling of CC the product and import of the substrate. Presumably this organellar CC system in organisms which may rely on ethanolamine as a primary carbon CC source. -- SN 1 ID Ethanolamine ammonia-lyase, large subunit DN Ethanolamine ammonia-lyase, large subunit (EC 4.3.1.7) RQ 1 EV IPR010628; PF06751; sufficient; TG GO:0046336; -- SN 2 ID Ethanolamine ammonia-lyase, small subunit DN Ethanolamine ammonia-lyase, small subunit (EC 4.3.1.7) RQ 1 EV IPR009246; PF05985; sufficient; TG GO:0046336; -- SN 3 ID Putative acetaldehyde dehydrogenase (acetylating) DN Putative acetaldehyde dehydrogenase (acetylating) RQ 0 EV IPR013357; TIGR02518; sufficient; TG GO:0046336; EV IPR015590; PF00171; TG GO:0046336; -- SN 4 ID Ethanolamine diffusion facilitator DN Ethanolamine permease/Ethanolamine utilisation protein EutH RQ 0 EV IPR004757; TIGR00908; sufficient; TG GO:0046336; EV IPR007441; PF04346; sufficient; TG GO:0046336; // AC GenProp0295 DE Prokaryotic N-terminal cleavage/methylation, type IV pilin-like TP SYSTEM AU Haft DH TH 0 CC This property describes the system found in many prokaryotes for CC recognition, leader peptide cleavage, and N-terminal methylation of CC sequences targeted to the cell surface, as found in type IV pilus CC components, competence proteins, type II secretion proteins, and some CC other systems. -- SN 1 ID Prepilin peptidase DN Prepilin type IV endopeptidase, peptidase domain RQ 1 EV IPR000045; PF01478; sufficient; -- SN 2 ID N-term residue-methylating domain DN Peptidase A24A, N-terminal RQ 1 EV IPR010627; PF06750; sufficient; -- SN 3 ID Prokaryotic N-term cleave/methyl site DN Prokaryotic N-terminal methylation site RQ 1 EV IPR012902; TIGR02532; sufficient; // AC GenProp0297 DE Lipopolysaccharide biosynthesis TP CATEGORY AU Haft DH TH 0 RN [1] RM 28551077 RT Lipopolysaccharide Detection across the Kingdoms of Life. RA Kagan JC; RL Trends Immunol. 2017; [Epub ahead of print] CC Lipopolysaccharide (also known as LPS, lipoglycan and endotoxin) is the CC major component of the Gram-negative bacterial cell wall. Lipopolysaccharide CC is composed of three parts, lipid A, a core oligosaccharide, and the CC O-antigen [1]. -- SN 1 ID LPS inner core biosynthesis, ketodeoxyoctonate and heptose type RQ 0 EV GenProp0203; -- SN 2 ID KDO(2)-lipid A (Re LPS) biosynthesis and delivery RQ 0 EV GenProp0204; // AC GenProp0298 DE Fermentation TP CATEGORY AU Haft DH TH 0 CC The generation of energy, usually in the form of ATP, from the breakdown CC of exogenous compounds into simpler compounds. -- SN 1 ID Pyruvate fermentation to acetoin RQ 0 EV GenProp0272; -- SN 2 ID Butyryl-CoA to butyrate, phosphotransbutyrylase pathway RQ 0 EV GenProp0910; -- SN 3 ID Butyryl-CoA to butyrate, acetate CoA-transferase pathway RQ 0 EV GenProp0911; -- SN 4 ID Citrate lyase system RQ 0 EV GenProp0672; -- SN 5 ID Pyruvate fermentation to acetoin III RQ 0 EV GenProp1485; -- SN 6 ID Pyruvate fermentation to ethanol II RQ 0 EV GenProp1226; -- SN 7 ID Mixed acid fermentation RQ 0 EV GenProp1267; -- SN 8 ID Pyruvate fermentation to ethanol I RQ 0 EV GenProp1425; -- SN 9 ID Pyruvate fermentation to isobutanol (engineered) RQ 0 EV GenProp1342; -- SN 10 ID Homolactic fermentation RQ 0 EV GenProp1580; // AC GenProp0299 DE Fatty acid biosynthesis TP CATEGORY AU Haft DH TH 0 CC The formation of fatty acids (any of the aliphatic monocarboxylic acids CC that can be liberated by hydrolysis from naturally occurring fats and oils) CC from simpler components. Fatty acids are predominantly straight-chain acids CC of 4 to 24 carbon atoms, which may be saturated or unsaturated. Branched CC fatty acids and hydroxy fatty acids also occur, and very long chain acids CC of over 30 carbons are found in waxes. -- SN 1 ID Acetyl-CoA carboxylase complex RQ 0 EV GenProp0214; -- SN 2 ID Fatty acid biosynthesis from acetyl-CoA RQ 0 EV GenProp0681; -- SN 3 ID Acyl carrier protein phosphopantetheinylation RQ 0 EV GenProp1104; -- SN 4 ID Alpha-linolenate biosynthesis I (plants and red algae) RQ 0 EV GenProp1339; -- SN 5 ID Gamma-linolenate biosynthesis II (animals) RQ 0 EV GenProp1452; -- SN 6 ID Linoleate biosynthesis I (plants) RQ 0 EV GenProp1761; -- SN 7 ID Oleate biosynthesis II (animals and fungi) RQ 0 EV GenProp1587; -- SN 8 ID Pinolenate and coniferonate biosynthesis RQ 0 EV GenProp1597; -- SN 9 ID Fatty acid biosynthesis initiation II RQ 0 EV GenProp1220; -- SN 10 ID Fatty acid biosynthesis initiation III RQ 0 EV GenProp1315; -- SN 11 ID Very long chain fatty acid biosynthesis II RQ 0 EV GenProp1376; -- SN 12 ID Fatty acid biosynthesis initiation I RQ 0 EV GenProp1512; -- SN 13 ID Fatty acid salvage RQ 0 EV GenProp1562; -- SN 14 ID Very long chain fatty acid biosynthesis I RQ 0 EV GenProp1569; -- SN 15 ID Acetyl-CoA carboxylase complex RQ 0 EV GenProp1111; -- SN 16 ID Superpathway of fatty acid biosynthesis initiation (E. coli) RQ 0 EV GenProp1415; -- SN 17 ID Superpathway of mycolate biosynthesis RQ 0 EV GenProp1436; // AC GenProp0300 DE Photosynthetic cofactor biosynthesis TP CATEGORY AU Haft DH TH 0 CC The biosynthesis of compounds which assist in the harvesting of light CC energy, such as chlorophyll and bacteriochlorophyll. -- SN 1 ID Chlorophyllide a biosynthesis from protoporphyrin IX RQ 0 EV GenProp0144; -- SN 2 ID Bacteriochlorophyll biosynthesis from chlorophyllide a RQ 0 EV GenProp0146; -- SN 3 ID Chlorophyll biosynthesis from chlorophyllide a RQ 0 EV GenProp0150; -- SN 4 ID Light-independent protochlorophyllide reductase RQ 0 EV GenProp1004; // AC GenProp0301 DE Protein degradation TP CATEGORY AU Haft DH TH 0 CC The breakdown of proteins and polypeptides into smaller pieces. -- SN 1 ID 19S proteasome cap RQ 0 EV GenProp2012; -- SN 2 ID ClpXP degradation machine RQ 0 EV GenProp0251; -- SN 3 ID Proteasome-targeting modification by pupylation RQ 0 EV GenProp0833; -- SN 4 ID Proteasome, bacterial RQ 0 EV GenProp0834; -- SN 5 ID ATP-dependent protease HslVU RQ 0 EV GenProp0835; -- SN 6 ID FtsH/HflKC protease complex RQ 0 EV GenProp0684; -- SN 7 ID Endopeptidase ClpXP complex RQ 0 EV GenProp1108; -- SN 8 ID Endopeptidase ClpAP complex RQ 0 EV GenProp1137; -- SN 9 ID Fibrinolysis RQ 0 EV GenProp2010; -- SN 10 ID 26S proteasome RQ 0 EV GenProp2013; -- SN 11 ID Immunoproteasome RQ 0 EV GenProp2014; -- SN 12 ID Thymoproteasome RQ 0 EV GenProp2015; -- SN 13 ID Mammalian spermatoproteasome RQ 0 EV GenProp2016; -- SN 14 ID Initiator caspases of the apoptosis extrinsic pathway RQ 0 EV GenProp2018; -- SN 15 ID Executor caspases of apoptosis RQ 0 EV GenProp2019; -- SN 16 ID KICSTOR complex RQ 0 EV GenProp2026; // AC GenProp0302 DE Protein repair TP CATEGORY AU Haft DH TH 0 CC The process of restoring a protein to its original state after damage CC by such things as oxidation or spontaneous decomposition of residues. -- SN 1 ID Reduction of oxidized methionine RQ 0 EV GenProp0182; // AC GenProp0303 DE Detoxification TP CATEGORY AU Haft DH TH 0 CC The process of making deleterious compounds, whether exogenous or CC generated within the cell, less dangerous via the mechanisms of chemical CC conversion, transport or sequestration. -- SN 1 ID Resistance to mercury RQ 0 EV GenProp0151; -- SN 2 ID Resistance to Reactive Oxygen Species (ROS) RQ 0 EV GenProp0213; -- SN 3 ID Arsenical resistance system RQ 0 EV GenProp0474; -- SN 4 ID Superoxide dismutase, nickel-type RQ 0 EV GenProp0488; -- SN 5 ID Formaldehyde detoxification, glutathione-dependent RQ 0 EV GenProp0562; -- SN 6 ID Ribulose monophosphate pathway RQ 0 EV GenProp0673; -- SN 7 ID Alkylhydroperoxide reductase AhpCF (peroxiredoxin) RQ 0 EV GenProp0676; -- SN 8 ID Glyoxalase pathway, glutathione dependent RQ 0 EV GenProp0744; -- SN 9 ID Superoxide radicals degradation RQ 0 EV GenProp1598; -- SN 10 ID D-galactose detoxification RQ 0 EV GenProp1459; // AC GenProp0304 DE Cysteine biosynthesis, tRNA-dependent TP PATHWAY AU Haft DH TH 0 RN [1] RM 15790858 RT RNA-dependent cysteine biosynthesis in archaea. RA Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, RA Yates JR, Ibba M, Söll D; RL Science. 2005;307:1969-1972. CC Methanocaldococcus jannaschii is a model archaeal species that lacks a CC direct cys--tRNA ligase. In a system analogous to pyrrolysine and (in CC many species) asparagine tRNA aminoacylation, the tRNA is misacylated CC and then the attached amino acid is modified. This two-step pathway is CC conducted by proteins in the families of MJ1660 (sepS) and MJ1678 CC (pscS). This pathway assumes 0-phosphoserine, whose biosynthesis is CC proposed to require D-3-phosphoglycerate dehydrogenase (TIGR01327) and CC an unidentified aminotransferase. -- SN 1 ID Sep-tRNA:Cys-tRNA synthase DN O-phosphoseryl-tRNA:Cys-tRNA synthase/pscS RQ 1 EV IPR013375; TIGR02539; sufficient; TG GO:0019344; -- SN 2 ID O-phosphoseryl-tRNA synthetase DN O-phosphoseryl-tRNA(Cys) ligase/sepS RQ 1 EV IPR005246; TIGR00470; sufficient; TG GO:0019344; // AC GenProp0305 DE Cysteine biosynthesis TP METAPATH AU Haft DH TH 0 CC The biosynthesis of the amino acid cysteine may be achieved via several CC routes. Most commonly serine is the starting point (GenProp0218), CC while in the archaea a mis-charged cys-tRNA bearing O-phosphoserine is CC modified (GenProp0304). -- SN 1 ID Cysteine biosynthesis DN Cysteine biosynthesis RQ 1 EV GenProp0218; TG GO:0019344; EV GenProp0304; TG GO:0019344; // AC GenProp0309 DE Arginine catabolism to glutamate via arginine succinyltransferase (AST) TP PATHWAY AU Haft DH TH 0 RN [1] RM 9696779 RT Arginine catabolism and the arginine succinyltransferase pathway in RT Escherichia coli. RA Schneider BL, Kiupakis AK, Reitzer LJ; RL J Bacteriol. 1998;180:4278-4286. CC The AST pathway converts the carbon skeleton of arginine into CC glutamate, with the concomitant production of ammonia, and conversion of CC succinyl-CoA to succinate and CoA. -- SN 1 ID Arginine N-succinyltransferase DN Arginine N-succinyltransferase RQ 1 EV IPR017650; TIGR03244; sufficient; TG GO:0019544; -- SN 2 ID Succinylarginine dihydrolase DN Succinylarginine dihydrolase RQ 1 EV IPR007079; TIGR03241; sufficient; TG GO:0019544; -- SN 3 ID Succinylornithine transaminase DN Acetyl/Succinylornithine transaminase RQ 1 EV IPR017652; TIGR03246; TG GO:0019544; -- SN 4 ID Succinylglutamic semialdehyde dehydrogenase DN Succinylglutamate-semialdehyde dehydrogenase RQ 1 EV IPR017649; TIGR03240; sufficient; TG GO:0019544; -- SN 5 ID Succinylglutamate desuccinylase DN Succinylglutamate desuccinylase RQ 1 EV IPR016681; TIGR03242; sufficient; TG GO:0019544; // AC GenProp0310 DE CRISPR system, I-F/Ypest subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 15822923 RT Predicted roles for hypothetical proteins in the low-temperature RT expressed proteome of the Antarctic archaeon Methanococcoides burtonii. RA Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli RA R; RL J Proteome Res. 2005;4:464-472. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. RN [3] RM 15758212 RT CRISPR elements in Yersinia pestis acquire new repeats by preferential RT uptake of bacteriophage DNA, and provide additional tools for RT evolutionary studies. RA Pourcel C, Salvignol G, Vergnaud G; RL Microbiology. 2005;151:653-663. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Ypest subtype, so named CC because this subtype is the only one found in the genome of Yersinia CC pestis, consists of cas1, cas3 and the subtype specific genes csy1-4. CC The cas3 gene of this subtype is sufficiently diverged from the cas3 CC gene of other CRISPR subtypes that it is identified by a separate HMM. CC The spacers of these CRISPRs have been analyzed and some have been CC shown to have been captured from extrachromosomal sources [3]. The CC repeats associated with this subtype tend to have a periodicity of 60 CC nucleotides. This subtype is found only in the Proteobacteria. -- SN 1 ID Cas1, Ypest region DN CRISPR-associated protein Cas1, YPEST subtype RQ 1 EV IPR019857; TIGR03637; -- SN 2 ID Cas3, Ypest subtype variant DN Helicase Cas3, CRISPR-associated, Yersinia-type RQ 1 EV IPR013395; TIGR02562; sufficient; -- SN 3 ID Csy1 DN CRISPR-associated protein Csy1 RQ 1 EV IPR013397; TIGR02564; sufficient; -- SN 4 ID Csy2 DN CRISPR-associated protein Csy2 RQ 1 EV IPR013398; TIGR02565; sufficient; -- SN 5 ID Csy3 DN CRISPR-associated protein Csy3 RQ 1 EV IPR013399; TIGR02566; sufficient; -- SN 6 ID CRISPR-derived RNA endonuclease Csy4 DN CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST RQ 1 EV IPR013396; TIGR02563; sufficient; // AC GenProp0311 DE Competence-related genes TP SYSTEM AU Haft DH TH 0 RN [1] RM 8901420 RT Who's competent and when: regulation of natural genetic competence in RT bacteria. RA Solomon JM, Grossman AD; RL Trends Genet. 1996;12:150-155. CC Competence is the ability of a cell to take up exogenous DNA from its CC environment, resulting in transformation. It is widespread among bacteria CC and is probably an important mechanism for the horizontal transfer of CC genes. DNA usually becomes available by the death and lysis of other cells. CC Competent bacteria use components of extracellular filaments called type 4 CC pili to create pores in their membranes and pull DNA through the pores into CC the cytoplasm. This process, including the development of competence and CC the expression of the uptake machinery, is regulated in response to CC cell-cell signalling and/or nutritional conditions [1]. -- SN 1 ID Competence protein ComE/CelA DN Competence protein ComE/CelA/ComEA RQ 1 EV IPR004509; TIGR00426; sufficient; -- SN 2 ID ComEB: CTP/dCTP deaminase family protein DN ComEB: CTP/dCTP deaminase family protein/ComEB RQ 0 EV IPR013404; TIGR02571; sufficient; -- SN 3 ID DNA internalization-related competence protein ComEC/Rec2 DN DNA internalization-related competence protein ComEC/Rec2 RQ 1 EV IPR004797; TIGR00361; sufficient; -- SN 5 ID ComF DN ComF RQ 0 EV IPR005222; TIGR00201; sufficient; -- SN 6 ID ComK DN ComK RQ 0 EV IPR010461; PF06338; sufficient; // AC GenProp0313 DE CRISPR system, I-C/Dvulg subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. RN [3] RM 22942283 RT Double-stranded endonuclease activity in Bacillus halodurans clustered RT regularly interspaced short palindromic repeats (CRISPR)-associated RT Cas2 protein. RA Nam KH, Ding F, Haitjema C, Huang Q, DeLisa MP, Ke A; RL J Biol Chem. 2012;287:35943-35952. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Dvulg subtype, so named CC because this subtype is the only one found in the genome of CC Desulfovibrio vulgaris, also called type I-C, consists of cas1-5 and CC the subtype specific genes csd1-2. The repeats associated with this CC subtype tend to have a periodicity of 66 nucleotides. This subtype is CC found in a wide variety of bacteria and never in the Archaea. Cas2 in CC this system has been shown to act as an endonuclease for dsDNA rather CC than ssRNA. -- SN 1 ID Cas1, Dvulg region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Dvulg region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, Dvulg region DN Helicase Cas3, CRISPR-associated, core RQ 1 EV IPR006474; TIGR01587; -- SN 4 ID Cas4, Dvulg region DN CRISPR-associated protein Cas4 RQ 1 EV IPR013343; TIGR00372; -- SN 5 ID Cas5, Dvulg specific variant DN CRISPR pre-crRNA endoribonuclease Cas5d RQ 1 EV IPR010155; TIGR01876; sufficient; -- SN 6 ID Csd1 DN CRISPR-associated protein, Csd1-type RQ 1 EV IPR010144; TIGR01863; sufficient; -- SN 7 ID Csd2 DN CRISPR-associated protein Csd2 RQ 1 EV IPR013418; TIGR02589; sufficient; // AC GenProp0314 DE CRISPR system, II/Nmeni subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 15822923 RT Predicted roles for hypothetical proteins in the low-temperature RT expressed proteome of the Antarctic archaeon Methanococcoides burtonii. RA Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli RA R; RL J Proteome Res. 2005;4:464-472. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats. The repeats vary in size from 24 to 48 bp, CC interspaced by similarly sized non-repetitive sequences. These spacers CC often are derived from phage and other exogenous DNA, are transcribed CC into RNA, and confer resistance to those same phage. Several CC CRISPR-associated sequences (cas genes) are nearly as widespread as CC CRISPR itself and nearly always are found near repeat loci. Others CC represent minor cas genes that serve as markers for specific subtypes CC of CRISPR/cas system, each with characteristic cas gene makeup, repeat CC structure, and spacer length. The Nmeni subtype, so named because this CC subtype is the only one found in the genome of Neisseria meningitidis, CC consists of cas1 and cas2 and the subtype specific genes csn1-2. This CC subtype has the most limited suite of cas core genes of any subtype CC defined thus far. The repeats associated with this subtype tend to CC have a periodicity of 66 nucleotides. This subtype is found only in CC Bacteria, and notably it would seem only in known or potential (i.e. CC containing virulence genes) vertebrate pathogens. -- SN 1 ID Cas1, Nmeni region DN CRISPR-associated protein Cas1, NMENI subtype RQ 1 EV IPR019855; TIGR03639; -- SN 2 ID Cas2, Nmeni region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID RNA-guided endonuclease Cas9/Csn1 DN CRISPR-associated endonuclease Cas9 RQ 1 EV IPR028629; TIGR01865; sufficient; -- SN 4 ID Csn2 DN CRISPR-associated protein, Csn2-type RQ 0 EV IPR010146; TIGR01866; sufficient; // AC GenProp0315 DE CRISPR system, I-E/Ecoli subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. RN [3] RM 15822923 RT Predicted roles for hypothetical proteins in the low-temperature RT expressed proteome of the Antarctic archaeon Methanococcoides burtonii. RA Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli RA R; RL J Proteome Res. 2005;4:464-472. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Ecoli subtype, so named CC because this subtype is the only one found in the genome of Escherichia CC coli, consists of cas1-3, a subtype-specific variant of cas5 and the CC subtype specific genes cse1-4. The repeats associated with this subtype CC tend to have a periodicity of 61 nucleotides and a repeat size of 29 CC nucleotides. This subtype is found in a wide variety of bacteria and has CC also been reported to be present in an archaeon [3]. -- SN 1 ID Cas1, Ecoli region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Ecoli specific variant DN CRISPR-associated protein Cas2 subtype RQ 1 EV IPR010152; TIGR01873; sufficient; -- SN 3 ID Cas3, Ecoli region DN Helicase Cas3, CRISPR-associated, core RQ 1 EV IPR006474; TIGR01587; -- SN 4 ID Cas5, Ecoli specific variant DN CRISPR-associated protein, CasD RQ 1 EV IPR010147; TIGR01868; sufficient; -- SN 5 ID Cse1 DN CRISPR-associated protein Cse1 RQ 1 EV IPR013381; TIGR02547; sufficient; -- SN 6 ID Cse2 DN CRISPR-associated protein Cse2 RQ 1 EV IPR013382; TIGR02548; sufficient; -- SN 7 ID Cse3 DN CRISPR-associated protein Cse3 RQ 1 EV IPR010179; TIGR01907; sufficient; -- SN 8 ID Cse4 DN CRISPR-associated protein, CT1975/Cse4 RQ 1 EV IPR010148; TIGR01869; sufficient; // AC GenProp0316 DE CRISPR system, III-B/RAMP module subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 15822923 RT Predicted roles for hypothetical proteins in the low-temperature RT expressed proteome of the Antarctic archaeon Methanococcoides burtonii. RA Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli RA R; RL J Proteome Res. 2005;4:464-472. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. The repeats vary in size from 24 to 48 bp, CC interspaced by similarly sized non-repetitive sequences. Variants of CC CRISP/Cas loci (subtypes) have been described [2] in which certain CC groups of subtype-specific genes are found in addition to CC characteristic sets of the more widely distributed cas genes. These CC subtype-specific genes are found proximal to the cas core genes and the CC CRISPR repeats. Unlike these, the set of CRISPR-associated genes CC represented here are always found in in genomes which also contain CC CRISPRs, but may be located at a remote site on the genome from the CC core genes and repeats. Several of these genes belong to the RAMP CC (Repeat-Associated Mystery Protein) family, so this 6-gene cassette is CC called the CRISPR RAMP module. -- SN 1 ID Cmr1 DN CRISPR-associated protein TM1795/Cmr1 RQ 1 EV IPR007522; TIGR01894; sufficient; -- SN 2 ID Cmr2 DN CRISPR-associated protein Cmr2 RQ 1 EV IPR013407; TIGR02577; sufficient; -- SN 3 ID Cmr3 DN CRISPR-associated protein, TM1793/Cmr3 RQ 1 EV IPR010165; TIGR01888; sufficient; -- SN 4 ID Cmr4 DN CRISPR-associated RAMP Cmr4 RQ 1 EV IPR013410; TIGR02580; sufficient; -- SN 5 ID Cmr5 DN CRISPR-associated protein, Cmr5 RQ 1 EV IPR010160; TIGR01881; sufficient; -- SN 6 ID Cmr6 DN CRISPR-associated protein, TM1791/Cmr6 RQ 1 EV IPR010172; TIGR01898; sufficient; // AC GenProp0317 DE CRISPR system, I-B subtype, Tneap branch TP SYSTEM AU Haft DH TH 0 RN [1] RM 15822923 RT Predicted roles for hypothetical proteins in the low-temperature RT expressed proteome of the Antarctic archaeon Methanococcoides burtonii. RA Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli RA R; RL J Proteome Res. 2005;4:464-472. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Tneap subtype, so named CC because this subtype is the only one found in the genome of Thermotoga CC neapolitana DSM4359, consists of cas1-5 and the subtype specific genes CC cst1-2. The repeats associated with this subtype tend to have a CC periodicity of 66 nucleotides. This subtype is found both in Archaea and CC Bacteria (with the notable exclusion of the Proteobacteria). -- SN 1 ID Cas1, Tneap region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Tneap region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, Tneap region DN Helicase Cas3, CRISPR-associated RQ 1 EV IPR006483; TIGR01596; EV IPR006474; TIGR01587; -- SN 4 ID Cas4, Tneap region DN CRISPR-associated protein Cas4 RQ 1 EV IPR013343; TIGR00372; -- SN 5 ID Cas5, Tneap specific variant DN CRISPR-associated protein Cas5, Tneap type RQ 1 EV IPR013337; TIGR01895; sufficient; -- SN 6 ID Cas6, Tneap region DN CRISPR-associated protein, Cas6 RQ 1 EV IPR010156; TIGR01877; -- SN 7 ID Cst1 DN CRISPR-associated protein, CXXC-CXXC RQ 1 EV IPR010180; TIGR01908; sufficient; -- SN 8 ID Cst2, DevR family regulator DN CRISPR-associated protein Cas7, subtype I-B/Tneap RQ 1 EV IPR013414; TIGR02585; // AC GenProp0318 DE CRISPR system, III-A/Mtube subtype TP SYSTEM AU Haft DH TH 3 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Mtube subtype, so named CC because this subtype is the only one found in the genome of CC Mycobacterium tuberculosis, consists of cas1, cas2, and the subtype CC specific genes csm1-5. Csm3, 4 and 5 are members of the RAMP CC superfamily, and this subtype shares some similarities with the CRISPR CC RAMP module in that it tends to be associated with other subtypes and CC often forms hybrid-subtype loci. -- SN 1 ID Cas1, Mtube region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Mtube region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas6, Mtube region DN CRISPR-associated protein, Cas6 RQ 1 EV IPR010156; TIGR01877; -- SN 4 ID Csm1 DN CRISPR-associated protein Csm1 RQ 1 EV IPR013408; TIGR02578; sufficient; -- SN 5 ID Csm2 DN CRISPR-associated protein, Csm2 Type III-A RQ 1 EV IPR010149; TIGR01870; sufficient; -- SN 6 ID Csm3 DN CRISPR-associated RAMP Csm3 RQ 1 EV IPR013412; TIGR02582; sufficient; -- SN 7 ID Csm4 DN CRISPR type III-associated RAMP protein Csm4 RQ 1 EV IPR005510; TIGR01903; sufficient; -- SN 8 ID Csm5 DN CRISPR-associated protein, TM1807/Csm5 RQ 1 EV IPR010173; TIGR01899; sufficient; -- SN 9 ID Csm6 DN CRISPR-associated protein Csm6 RQ 0 EV IPR013489; TIGR02672; sufficient; // AC GenProp0319 DE CRISPR system, I-A/Apern subtype TP SYSTEM AU Haft DH TH 4 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Apern subtype, so named CC because this subtype is the only one found in the genome of Archaeoglobus CC pernix, consists of cas1-6, the subtype specific genes csa1-3 and either CC csa4 or csa5. The repeats associated with this subtype tend to have a CC periodicity of 66 nucleotides. This subtype is found exclusively in CC Archaea, primarily in the Chrenarchaeota. -- SN 1 ID Cas1, Apern region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Apern region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, Apern region DN Helicase Cas3, CRISPR-associated RQ 1 EV IPR006474; TIGR01587; -- SN 4 ID Cas3b, Apern region DN CRISPR-associated Cas3-HD domain RQ 1 EV IPR006483; TIGR01596; -- SN 5 ID Cas4, Apern region DN CRISPR-associated protein Cas4 RQ 1 EV IPR013343; TIGR00372; -- SN 6 ID Cas5, Apern specific variant DN CRISPR-associated protein, Cas5a type RQ 1 EV IPR010153; TIGR01874; sufficient; -- SN 7 ID Cas6, Apern region DN CRISPR-associated protein, Cas6 RQ 1 EV IPR010156; TIGR01877; -- SN 8 ID Csa1 DN CRISPR-associated exonuclease Csa1 RQ 1 EV IPR009260; TIGR01896; sufficient; -- SN 9 ID Csa2, regulatory protein DN CRISPR-associated protein Cas7/Cst2/DevR, subtype I-a/Apern RQ 1 EV IPR002764; TIGR02583; sufficient; -- SN 10 ID Csa3, DNA-binding protein DN CRISPR locus-related putative DNA-binding protein Csa3 RQ 1 EV IPR010163; TIGR01884; sufficient; -- SN 11 ID Csa4 DN CRISPR-associated protein, MJ0385/Csx9/Csa4 RQ 0 EV IPR010184; TIGR01914; sufficient; EV IPR013488; TIGR02671; -- SN 12 ID Csa5 DN CRISPR type I-A/APERN-associated protein Csa5 RQ 0 EV IPR010157; TIGR01878; sufficient; -- SN 13 ID CRISPR-associated protein, CsaX family DN CRISPR-associated protein, CsaX RQ 0 EV IPR022297; TIGR03876; // AC GenProp0320 DE CRISPR system, I-B subtype, Hmari branch TP SYSTEM AU Haft DH TH 0 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Jansen, et al. describe CRISPR loci as CC having direct repeats, varying in size from 21 to 37 bp, interspaced by CC similarly sized non-repetitive sequences. Variants of CRISP/Cas loci CC (subtypes) have been described [2] in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed cas genes. The Hmari subtype, so named CC because this subtype is the only one found in the genome of Haloarcula CC marismortui ATCC 43049, consists of cas1-6 and the subtype specific CC genes csh1-2. The repeats associated with this subtype tend to have a CC periodicity of 66 nucleotides. This subtype is found both in Archaea CC and Bacteria. -- SN 1 ID Cas1, Hmari region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Hmari region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, Hmari region DN Helicase Cas3, CRISPR-associated RQ 1 EV IPR006474; TIGR01587; -- SN 4 ID Cas4, Hmari region DN CRISPR-associated protein Cas4 RQ 1 EV IPR013343; TIGR00372; -- SN 5 ID Cas5, Hmari subtype specific variant DN CRISPR-associated protein Cas5, HALMA RQ 1 EV IPR013421; TIGR02592; sufficient; -- SN 6 ID Cas6, Hmari region DN CRISPR-associated protein, Cas6 RQ 1 EV IPR010156; TIGR01877; -- SN 7 ID Csh1 family, TIGR02591 DN CRISPR-associated protein Csh1 RQ 1 EV IPR013420; TIGR02591; sufficient; -- SN 8 ID Csh2 family, TIGR02590 DN CRISPR-associated protein Csh2 RQ 1 EV IPR013419; TIGR02590; sufficient; // AC GenProp0321 DE Toxin-antitoxin system, type II TP GUILD AU Haft DH TH 0 CC Pairs of genes are often found to maintain plasmids by a mechanism of CC post-segregational killing. One protein is a short-lived antidote, the CC other a long-lived toxin, and the two encoded together. Loss of the CC gene pair, as from a cell division in which one of the daughter cells CC does not receive a copy of the plasmid, leads to loss of the antidote CC faster than the toxin, and therefore to cell death. Such pairs are CC called addition modules, and may be chromosomal rather than plasmid. CC Chromosomal pairs frequently have mRNA-cleaving activity with CC bacteriostatic rather than bacteriocidal activity, and may benefit the CC host cell by enabling a persister state in response to certain CC challenges. -- SN 1 ID Antidote partner (various) DN Antidote partner (various) RQ 1 EV IPR006442; PF02604; sufficient; EV IPR009956; PF07362; sufficient; EV IPR007337; TIGR02384; sufficient; EV IPR007337; PF04221; sufficient; EV IPR022789; PF03693; EV IPR022789; TIGR02606; sufficient; EV IPR001387; PF01381; EV IPR013432; TIGR02609; sufficient; EV IPR013430; TIGR02607; sufficient; -- SN 2 ID Killing partner DN Killing partner RQ 1 EV IPR007712; PF05016; sufficient; EV IPR007712; TIGR02385; sufficient; EV IPR007711; PF05015; sufficient; EV IPR009614; TIGR02116; sufficient; EV IPR004386; TIGR00053; sufficient; EV IPR002712; PF01845; sufficient; EV IPR003812; PF02661; sufficient; EV IPR006440; TIGR01550; sufficient; EV IPR033439; PF03882; sufficient; EV IPR012556; PF08085; sufficient; EV IPR003477; PF02452; EV IPR002850; TIGR00305; EV IPR009241; PF05973; -- SN 3 ID Unassigned role in predicted module DN Unassigned role in predicted module RQ 0 EV IPR013406; TIGR02574; sufficient; // AC GenProp0322 DE Addiction module, Hig class TP SYSTEM AU Haft DH TH 0 CC This addiction module consists of homologs of the killer HigB and the CC antidote HigA. It is unusual in that the killer protein is encoded by CC the upstream gene. -- SN 1 ID Antidote protein HigA DN Toxin-antitoxin system, antidote protein, HigA RQ 1 EV IPR013430; TIGR02607; sufficient; -- SN 2 ID Killer protein HigB DN Toxin HigB-1 RQ 1 EV IPR007711; PF05015; sufficient; // AC GenProp0323 DE Addiction module, ParE class TP SYSTEM AU Haft DH, Richardson L TH 0 RN [1] RM 20487277 RT Interaction specificity, toxicity and regulation of a paralogous set RT of ParE/RelE-family toxin-antitoxin systems. RA Fiebig A, Castro Rojas CM, Siegal-Gaskins D, Crosson S; RL Mol Microbiol. 2010;77:236-251. CC Toxin-antitoxin gene pairs, called addiction modules, are found often CC on plasmids but also on the chromosome. These modules can promote CC plasmid stability in populations by killing daughter cells that don't CC receive a copy of the plasmid during cell division. The phenomenon, CC called post-segregational killing, occurs because the antitoxin has a CC shorter biological half-life than the toxin. Some chromosomal CC toxin-antitoxin gene pairs appear to act in regulation of cellular CC processes and are not necessarily selfish genetic elements. The CC antitoxin generally is a transcription factor. The toxin may act in CC several ways. This addiction module property describes the ParE system CC where ParE inhibits gyrase and thereby blocks chromosome replication CC [1]. -- SN 1 ID Antidote TIGR02606 DN Antidote TIGR02606/A-Par RQ 1 EV IPR022789; TIGR02606; sufficient; -- SN 2 ID Killer ParE - PF05016 DN Killer ParE - PF05016/K-ParE RQ 1 EV IPR007712; PF05016; // AC GenProp0324 DE Addiction module, RelE-RelB class TP SYSTEM AU Haft DH TH 0 RN [1] RM 11717402 RT RelE, a global inhibitor of translation, is activated during RT nutritional stress. RA Christensen SK, Mikkelsen M, Pedersen K, Gerdes K; RL Proc Natl Acad Sci U S A. 2001;98:14328-14333. CC Toxin-antitoxin gene pairs, called addiction modules, are found often CC on plasmids but also on the chromosome. These modules can promote CC plasmid stability in populations by killing daughter cells that don't CC receive a copy of the plasmid during cell division. The phenomenon, CC called post-segregational killing, occurs because the antitoxin has a CC shorter biological half-life than the toxin. Some chromosomal CC toxin-antitoxin gene pairs appear to act in regulation of cellular CC processes and are not necessarily selfish genetic elements. The CC antitoxin generally is a transcription factor. The toxin may act in CC several ways. This addiction module property describes the RelE system, CC where RelE acts by cleaving ribosome-associated transcripts. -- SN 1 ID Antidote RelB DN RelB antitoxin/Antitoxin DinJ RQ 1 EV IPR007337; PF04221; sufficient; -- SN 2 ID Toxin RelE DN Toxin-antitoxin system, RelE/ParE toxin family RQ 1 EV IPR007712; TIGR02385; sufficient; // AC GenProp0326 DE Protein sorting system, PEP-CTERM/exosortase (generic) TP SYSTEM AU Haft DH TH 0 RN [1] RM 16930487 RT Exopolysaccharide-associated protein sorting in environmental RT organisms: the PEP-CTERM/EpsH system. Application of a novel RT phylogenetic profiling heuristic. RA Haft DH, Paulsen IT, Ward N, Selengut JD; RL BMC Biol. 2006;4:29. CC This Genome Property describes a proposed protein sorting system CC associated with exopolysaccharide loci in many Gram-negative bacteria. CC One hallmark is the presence of a paralogous domain at the C-termini of CC a substantial number of proteins in a single genome, usually from four CC to sixty-five. Features of this domain, described by TIGRFAMs model CC TIGR02595, are a conserved motif PEP, a transmembrane domain, and a CC cluster of basic residues for a total length of about 24 amino acids. CC We call this domain PEP-CTERM, and note that is shares a number of CC properties with the the LPXTG-type Gram-positive cell-wall targeting CC sequence. Another hallmark of this system is the presence of one or CC more homologs of EpsH (TIGR02602), a highly hydrophobic protein that CC spans the membrane eight or more times. Its surrounding genes nearly CC always pertain to exopolysaccharide biosynthesis. We have proposed that CC TIGR02602 models a transpeptidase that cleaves PEP-CTERM proteins, CC attaches them transiently to an active site Cys, then attaches them CC covalently to an unknown substrate for sorting to the outer surface of CC the cell, closely analogous to the action of sortase in Gram-positive CC bacteria. We suggest the name exosortase for EpsH homologs involved in CC this process. In Proteobacterial species with a the PEP-CTERM/exsortase CC system, a sensor histidine kinase (TIGR02916) and a sigma-54-dependent CC DNA-binding response regulator (TIGR02915) are present and appear to CC bind a conserved regulatory site found upstream of most PEP-CTERM CC genes. -- SN 1 ID PEP-CTERM motif DN PEP-CTERM protein-sorting domain RQ 1 EV IPR013424; TIGR02595; sufficient; EV IPR013424; PF07589; sufficient; -- SN 2 ID EpsH family 8TM protein DN Exosortase, EpsH RQ 1 EV IPR013426; TIGR02602; sufficient; -- SN 3 ID EpsI protein/fusion DN Methanolan biosynthesis EpsI RQ 0 EV IPR014263; TIGR02914; sufficient; // AC GenProp0455 DE Restriction enzyme system, type I TP SYSTEM AU Haft DH TH 0 RN [1] RM 15121719 RT S-Adenosyl-L-methionine-dependent restriction enzymes. RA Sistla S, Rao DN; RL Crit Rev Biochem Mol Biol. 2004;39:1-19. RN [2] RM 12595133 RT Complex restriction enzymes: NTP-driven molecular motors. RA Bourniquel AA, Bickle TA; RL Biochimie. 2002;84:1047-1059. CC Type I restriction endonucleases are components of prokaryotic DNA CC restriction-modification mechanisms that protects the organism against CC invading foreign DNA. Type I enzymes have three different subunits, CC M (modification), S (specificity), and R (restriction), that form CC multifunctional enzymes with restriction, methylase, and ATPase activities CC [1,2]. -- SN 1 ID M modification methylase DN DNA methylase, adenine-specific/M RQ 1 EV IPR003356; PF02384; sufficient; -- SN 2 ID R restriction DN Restriction endonuclease, type I, HsdR RQ 1 EV IPR007409; PF04313; sufficient; -- SN 3 ID S specificity DN Restriction endonuclease, type I, HsdS RQ 1 EV IPR000055; PF01420; sufficient; // AC GenProp0456 DE Attenuation system: tryptophanase TP SYSTEM AU Haft DH TH 0 RN [1] RM 9045840 RT Regulation of the Escherichia coli tna operon: nascent leader peptide RT control at the tnaC stop codon. RA Konan KV, Yanofsky C; RL J Bacteriol. 1997;179:1774-1779. CC This property is characterized by two components. One is the enzyme CC tryptophanase, capabable of degrading tryptophan. The other is the CC tryptophanase leader peptide, TnaC, encoded upstream of the enzyme. The CC ribosome that translates the leader peptide may stall at either of two CC points: the trp codon (when trp is scarce) or the stop codon. The CC leader peptide may interact with ribosome to delay release at its stop CC codon. Whether the ribosome stalls at the trp codon or continues to the CC stop codon controls what mRNA secondary structure may form as the CC trytophanase message is synthesized. When trp is scarce, and the enzyme CC should not be made, a terminator forms and transcription ends. Examples CC of this mechanism for controlling transcription at termination are called CC transcriptional attenuation. -- SN 1 ID Tryptophanase TnaA DN Tryptophanase (EC:4.1.99.1) RQ 1 EV IPR013440; TIGR02617; sufficient; -- SN 2 ID Tryptophanase leader pep TnaC DN Tryptophanese operon leader peptide RQ 1 EV IPR012620; TIGR02616; sufficient; // AC GenProp0457 DE Rhamnose catabolism TP SYSTEM AU Haft DH TH 1 RN [1] RM 9893952 RT The metabolism of 6-deoxyhexoses in bacterial and animal cells. RA Tonetti M, Sturla L, Bisso A, Zanardi D, Benatti U, De Flora A; RL Biochimie. 1998;80:923-931. RN [2] RM 15576793 RT A genetic locus necessary for rhamnose uptake and catabolism in RT Rhizobium leguminosarum bv. trifolii. RA Richardson JS, Hynes MF, Oresnik IJ; RL J Bacteriol. 2004;186:8433-8442. RN [3] RM 8384447 RT Proton-linked L-rhamnose transport, and its comparison with L-fucose RT transport in Enterobacteriaceae. RA Muiry JA, Gunn TC, McDonald TP, Bradley SA, Tate CG, Henderson PJ; RL Biochem J. 1993;290 ( Pt 3):833-842. RN [4] RM 3316663 RT Positive regulation of the Escherichia coli L-rhamnose operon is RT mediated by the products of tandemly repeated regulatory genes. RA Tobin JF, Schleif RF; RL J Mol Biol. 1987;196:789-799. RN [5] RM 3275622 RT Metabolism of L-fucose and L-rhamnose in Escherichia coli: RT aerobic-anaerobic regulation of L-lactaldehyde dissimilation. RA Baldomà L, Aguilar J; RL J Bacteriol. 1988;170:416-421. RN [6] RM 15876375 RT Structural insights into the monosaccharide specificity of Escherichia RT coli rhamnose mutarotase. RA Ryu KS, Kim JI, Cho SJ, Park D, Park C, Cheong HK, Lee JO, Choi BS; RL J Mol Biol. 2005;349:153-162. DC rhamnose catabolism DR KEGG; map00051; CC L-rhamnose, (aka 6-deoxy-L-mannose) is a common sugar synthesized and CC utilized in oligosaccharides and glcyolipids by many bacteria [1]. The CC monosaccharide is available in various environments and thus CC regulatory, transport and enzymatic systems have also evolved for its CC breakdown and use as a carbon source. The system modeled here includes CC specific transporters, ketose-aldose isomerases, kinases, and aldolases CC which result in the production of lactaldehyde and glycerone-phosphate. CC As these genes are generally organized into operons, assignments can be CC made for regulatory components as well as transport and enzymatic CC components which, by homology alone, cannot be assigned a specific CC substrate. Certain of the enzymes in this system are similar enough to CC cognate enzymes in the fucose catabolism system (GenProp0458) as to CC have caused gene naming errors in the past (i.e. CC fuculokinase/rhamnokinase). The system in certain rhizobial species [2] CC has been reported to vary from the canonical pathway in that the sugar CC may be phosphorylated prior to isomerization (i.e. the rhamnulokinase CC may in fact be a rhamnokinase and the rhamnose isomerase may be a CC rhamnose-1-phosphate isomerase), although this has not yet been CC independantly verified. In addition to the characterized CC rhamnose:proton symporter [3], rhamnose catabolism operons contain CC transporters from the ABC, and major facilitator families. Regulators CC are generally members of the DeoR and AraC [4] families. The product of CC both rhamnose and fucose catabolism is lactaldehyde, and subsequently CC alcohol and aldehyde dehydrogenases are often present in those operons CC to convert it to either 1,2-propane diol or lactate depending on CC oxidation conditions [5]. Rhamnose operons also often contain an CC epimerase (mutarotase) enzyme which has been proposed to be essential CC only under limiting L-rhamnose conditions [6]. Partial rhamnose CC catabolism operons have been detected in Thermotoga species which CC appear to handle the import and cleavage of rhamnose-containing CC oligosaccharides. -- SN 1 ID Clustered alcohol/aldehyde dehydrogenases DN Clustered alcohol/aldehyde dehydrogenases RQ 0 EV IPR001670; PF00465; TG GO:0019301; EV IPR015590; PF00171; TG GO:0019301; EV IPR002347; PF00106; TG GO:0019301; -- SN 2 ID Rhamnulose-1-P aldolase (RhaD) DN Rhamnulose-1-P aldolase (RhaD) RQ 1 EV IPR013447; TIGR02624; sufficient; TG GO:0019301; EV IPR013454; TIGR02632; sufficient; TG GO:0019301; -- SN 3 ID Rhamnose epimerase DN L-rhamnose mutarotase RQ 0 EV IPR008000; PF05336; TG GO:0019301; EV IPR013448; TIGR02625; sufficient; TG GO:0019301; -- SN 4 ID L-rhamnose isomerase (RhaA/RhaI) DN L-rhamnose isomerase (RhaA/RhaI) RQ 1 EV IPR009308; PF06134; sufficient; TG GO:0019301; EV IPR009308; TIGR01748; sufficient; TG GO:0019301; EV IPR013451; TIGR02629; sufficient; TG GO:0019301; EV IPR013457; TIGR02635; sufficient; TG GO:0019301; -- SN 5 ID Rhamnulokinase (RhaB/RhuK) DN Rhamnulokinase (RhaB/RhuK) RQ 1 EV IPR018484; PF00370; TG GO:0019301; EV IPR013449; TIGR02627; sufficient; TG GO:0019301; -- SN 6 ID Clustered regulatory components DN Clustered regulatory components RQ 0 EV IPR018060; PF00165; TG GO:0043463; EV IPR014036; PF00455; TG GO:0043463; EV IPR001761; PF00532; TG GO:0043463; EV IPR001387; PF01381; TG GO:0043463; EV IPR000843; PF00356; TG GO:0043463; -- SN 7 ID Rhamnose transporters (RhaSTPQ) DN Rhamnose transporters (RhaSTPQ) RQ 1 EV IPR011701; PF07690; TG GO:0019301; EV IPR005828; PF00083; TG GO:0019301; EV IPR004673; PF06379; sufficient; TG GO:0019301; EV IPR001851; PF02653; TG GO:0019301; EV IPR003439; PF00005; TG GO:0019301; EV IPR013459; TIGR02637; sufficient; TG GO:0019301; // AC GenProp0458 DE Fucose catabolism TP SYSTEM AU Haft DH TH 1 RN [1] RM 3325779 RT The organization of the fuc regulon specifying L-fucose dissimilation RT in Escherichia coli K12 as determined by gene cloning. RA Chen YM, Zhu Y, Lin EC; RL Mol Gen Genet. 1987;210:331-337. CC This property describes the catabolism of fucose by the following CC route. L-fucose to fuculose by L-fucose ketol-isomerase, then to CC L-fuculose 1P by L-fuculokinase, then to L-lactaldehyde and CC glycerone phosphate by L-fuculose-phosphate aldolase. The property CC also includes a transporter to import fucose and transcription factors. -- SN 1 ID Lactaldehyde oxidoreductases DN Alcohol dehydrogenase, iron-type/glycerol dehydrogenase gldA/ADH RQ 0 EV IPR001670; PF00465; TG GO:0019317; -- SN 2 ID L-fuculose-phosphate aldolase DN L-fuculose-phosphate aldolase (EC 4.1.2.17) RQ 1 EV IPR004782; TIGR01086; sufficient; TG GO:0019317; EV IPR001303; PF00596; TG GO:0019317; -- SN 3 ID L-fucose isomerase DN L-fucose isomerase (EC 5.3.1.25) RQ 1 EV IPR005763; TIGR01089; sufficient; TG GO:0019317; -- SN 4 ID L-fuculokinase DN L-fuculokinase (EC 2.7.1.51) RQ 1 EV IPR013450; TIGR02628; sufficient; TG GO:0019317; EV IPR018484; PF00370; TG GO:0019317; -- SN 5 ID Clustered regulatory genes DN Clustered regulatory genes RQ 0 EV IPR014036; PF00455; TG GO:0043468; EV IPR018060; PF00165; TG GO:0043468; EV IPR000524; PF00392; TG GO:0043468; -- SN 6 ID Fucose transport components DN Fucose transport components RQ 1 EV IPR005275; TIGR00885; sufficient; TG GO:0019317; EV IPR007721; PF05025; TG GO:0019317; // AC GenProp0460 DE Gas vesicle TP SYSTEM AU Haft DH TH 0 CC Gas vesicles are gas-filled hollow protein structures, visible by CC phase-contrast microscopy, that confer bouyancy. They occur in CC cyanobacteria, anoxyphototrophic bacteria, halophilic archaea, and at CC least one soil bacterium (Bacillus megaterium). GvpA and GvpC are the CC characterized structural proteins, but it seems at least 10 genes are CC required. -- SN 1 ID Gas vesicle structural protein GvpC DN Gas vesicle structural protein GvpC RQ 1 EV IPR002003; PF01304; sufficient; EV IPR002003; TIGR02641; sufficient; EV IPR008639; PF05465; sufficient; -- SN 2 ID Gas vesicle protein, GvpG family DN Gas vesicle protein, GvpG family RQ 0 EV IPR007804; PF05120; sufficient; -- SN 3 ID Gas vesicle protein, GvpK family DN Gas vesicle protein, GvpK family RQ 0 EV IPR007805; PF05121; sufficient; -- SN 4 ID Gas vesicle protein GvpN DN Gas vesicle protein GvpN RQ 0 EV IPR013462; TIGR02640; sufficient; -- SN 5 ID Gas vesicle protein, GvpO family DN Gas vesicle protein, GvpO family RQ 0 EV IPR008634; PF05800; sufficient; -- SN 6 ID Gas vesicle protein, GvpL/GvpF family DN Gas vesicle protein, GvpL/GvpF family RQ 0 EV IPR009430; PF06386; sufficient; -- SN 7 ID Gas vesicle major structural protein GvpA DN Gas vesicle major structural protein GvpA RQ 1 EV IPR000638; PF00741; sufficient; // AC GenProp0462 DE Response to stress TP CATEGORY AU Haft DH TH 0 CC A change in state or activity of a cell (in terms of movement, CC secretion, enzyme production, gene expression, etc.) as a result of the CC perception of a stress condition. -- SN 1 ID Phage shock protein regulon RQ 0 EV GenProp0648; -- SN 2 ID Cascade complex RQ 0 EV GenProp1179; -- SN 3 ID Cas1-Cas2 complex RQ 0 EV GenProp1196; -- SN 4 ID UvrAB complex RQ 0 EV GenProp1109; -- SN 6 ID ProVWX complex RQ 0 EV GenProp1126; -- SN 7 ID TRCF-UvrA complex RQ 0 EV GenProp1153; -- SN 8 ID HslUV protease complex RQ 0 EV GenProp1173; -- SN 9 ID Exodeoxyribonuclease V complex RQ 0 EV GenProp1188; -- SN 10 ID UvrBC complex RQ 0 EV GenProp1190; -- SN 11 ID Hydrogenase-1 complex RQ 0 EV GenProp1209; // AC GenProp0465 DE Circadian clock system KaiABC TP SYSTEM AU Haft DH TH 0 CC Cyanobacteria have a system of proteins, KaiABC, capable of generating CC rhythmic oscillations in the expression of other genes with a period of CC about a day. KaiC performs autophosphorylations, modulated by its CC interactions with the other clock proteins, and appears to act as CC transcriptional repressor. This remarkable system can continue its CC oscillations even in the absence of transcription and translation of CC kaiABC itself. KaiB and KaiC, at least, may be universal among the CC Cyanobacteria. Homologs outside the Cyanobacteria and paralogs within, CC both with uncertain function, occur for KaiB and KaiC. -- SN 1 ID Circadian clock protein KaiA DN Circadian clock protein KaiA RQ 1 EV IPR020856; PF07688; sufficient; -- SN 2 ID Circadian clock protein KaiB DN Circadian clock protein KaiB RQ 1 EV IPR013474; TIGR02654; sufficient; -- SN 3 ID Circadian clock protein KaiC DN Circadian clock protein KaiC RQ 1 EV IPR013503; TIGR02655; sufficient; // AC GenProp0466 DE Molybdopterin biosynthesis TP PATHWAY AU Haft DH TH 1 RN [1] RM 15632135 RT In vitro molybdenum ligation to molybdopterin using purified RT components. RA Nichols JD, Rajagopalan KV; RL J Biol Chem. 2005;280:7817-7822. CC Molybdenum, in every enzyme containing it except nitrogenase, is a CC single atom coordinated by the two sulfur atoms of molybdopterin (MPT). CC MoaA and MoaC synthesize precursor Z from guanine. MoaD (supported by CC MoeB) and MoaE synthesize MPT from precursor Z. MoeA and MogA add CC molybdenum to the dithiolene of MPT. A molybdenum transport system (see CC GenProp0192) must also be present. In bacteria, MPT most often occurs CC as the derivative molybdopterin guanine dinucleotide (MGG); MobA CC catalyzes the addition of GMP to MPT. In hyperthermophiles, tungsten CC may substitute for molybdenum. In species with a member of family CC TIGR03309 (YqeB family), selenium can substitute for sulfur. -- SN 1 ID Molybdenum cofactor biosynthesis protein A DN Molybdenum cofactor biosynthesis protein A/moaA RQ 1 EV IPR013483; TIGR02666; sufficient; TG GO:0032324; EV IPR013485; TIGR02668; sufficient; TG GO:0032324; -- SN 2 ID Molybdenum cofactor biosynthesis protein B DN Molybdenum cofactor biosynthesis protein B/moaB RQ 0 EV IPR013484; TIGR02667; sufficient; TG GO:0032324; -- SN 3 ID Molybdenum cofactor biosynthesis protein C DN Molybdenum cofactor biosynthesis protein C/moaC RQ 1 EV IPR023045; TIGR00581; sufficient; TG GO:0032324; -- SN 4 ID Molybdopterin converting factor, subunit 1 DN Molybdopterin converting factor, subunit 1/moaD RQ 1 EV IPR010034; TIGR01682; sufficient; TG GO:0032324; -- SN 5 ID Molybdopterin converting factor, subunit 2 DN Molybdopterin converting factor, subunit 2/moaE RQ 1 EV IPR003448; PF02391; sufficient; TG GO:0032324; -- SN 6 ID Molybdopterin-guanine dinucleotide biosynthesis protein A DN Molybdenum cofactor guanylyltransferase/mobA RQ 0 EV IPR013482; TIGR02665; sufficient; TG GO:0032324; -- SN 7 ID Molybdopterin-guanine dinucleotide biosynthesis protein B DN Molybdopterin-guanine dinucleotide biosynthesis protein B/mobB RQ 1 EV IPR004435; TIGR00176; sufficient; TG GO:0032324; // AC GenProp0468 DE Entner-Doudoroff pathway TP PATHWAY AU Haft DH TH 0 CC Glucose (in the first two steps of the pentose phosphate pathway) or CC gluconate (in one step) can be converted to 6-phospho-D-gluconate. The CC Entner-Doudoroff pathway is the degradation of 6-phospho-D-gluconate in CC two steps to pyruvate and D-glyceraldehyde 3-phosphate. The CC D-glyceraldehyde 3-phosphate can then be converted to pyruvate by CC enzymes from glycolysis. This bacterial pathway is less widespread than CC glycolysis and is an alternative to the early steps of glycolysis. -- SN 1 ID 2-dehydro-3-deoxyphosphogluconate aldolase DN KDPG/KHG aldolase RQ 1 EV IPR000887; TIGR01182; -- SN 2 ID 6-phosphogluconate dehydratase DN 6-phosphogluconate dehydratase RQ 1 EV IPR004786; TIGR01196; sufficient; // AC GenProp0469 DE CRISPR system, Dpsyc subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 21756346 RT Unification of Cas protein families and a simple scenario for the RT origin and evolution of CRISPR-Cas systems. RA Makarova KS, Aravind L, Wolf YI, Koonin EV; RL Biol Direct. 2011;6:38. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats, described by Jansen [1]. Certain proteins, CC including Cas1 to Cas4, are found only in genomes with CRISPR repeats, CC and are near these repeats. Haft, et al. [2] have since found multiple CC subtypes of CRISPR/cas systems. This property describes a subtype found CC in Desulfotalea psychrophila LSv54, Geobacter sulfurreducens PCA, CC Gemmata obscuriglobus UQM 2246, Verrucomicrobium spinosum DSM 4136, and CC Actinomyces naeslundii MG1. Cas1 tends to be fused with Cas4 in this CC type. Repeats typically are 37 base pairs long. -- SN 1 ID Cas1, Dpsyc region DN CRISPR-associated protein Cas1 RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Dpsyc region DN CRISPR-associated endonuclease Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, Dpsyc subtype variant DN Helicase Cas3, CRISPR-associated RQ 1 EV IPR013444; TIGR02621; sufficient; -- SN 4 ID Cas4, Dpsyc region DN CRISPR-associated protein Cas4 RQ 1 EV IPR013343; TIGR00372; -- SN 5 ID Csb1 (GSU0053) DN CRISPR-associated protein GSU0053/csb1 RQ 1 EV IPR013403; TIGR02570; sufficient; -- SN 6 ID Csb2 (GSU0054) DN CRISPR-associated protein, GSU0054/csb2 RQ 1 EV IPR019089; TIGR02165; sufficient; -- SN 7 ID Csb3 (GSU0052) DN CRISPR-associated protein GSU0052/csb3 RQ 0 EV IPR026391; TIGR04106; -- SN 8 ID CRISPR-associated protein Csx17, subtype Dpsyc DN CRISPR-associated protein Csx17, subtype Dpsyc RQ 0 EV IPR026483; TIGR04113; // AC GenProp0470 DE Sporadically distributed four-gene operon TP SYSTEM AU Haft DH TH 0 CC A conserved gene four-gene neighborhood is found sporadically in a CC phylogenetically broad range of bacteria: Nocardia farcinica, CC Symbiobacterium thermophilum, and Streptomyces avermitilis CC (Actinobacteria), Geobacillus kaustophilus (Firmicutes), and Azoarcus CC sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). It is found CC near CRISPR repeats in Geobacillus kaustophilus HTA426, whose genome CC has no identified Cas proteins. It is found near a cas gene cluster and CC its CRISPR repeats in another species. -- SN 1 ID Sporadic operon protein A DN Conserved hypothetical protein CHP02677 RQ 1 EV IPR013493; TIGR02677; sufficient; -- SN 2 ID Sporadic operon protein B DN Conserved hypothetical protein CHP02678 RQ 1 EV IPR013494; TIGR02678; sufficient; -- SN 3 ID Sporadic operon protein C DN Conserved hypothetical protein CHP02680 RQ 1 EV IPR013496; TIGR02680; sufficient; -- SN 4 ID Sporadic operon protein D DN Conserved hypothetical protein CHP02679 RQ 1 EV IPR013495; TIGR02679; sufficient; // AC GenProp0471 DE Uncharacterized gene pair TIGR02683/TIGR02684 TP SYSTEM AU Haft DH TH 0 CC This uncharacterized operon may be an addiction module. Both member CC proteins average under 100 amino acids. In one example so far the CC genes are fused. This bacterial gene pair usually but not always CC occurs in prophage or integrated plasmid regions of the genome. -- SN 1 ID Downstream DN Addiction module antidote protein, HI1420 RQ 1 EV IPR014057; TIGR02684; sufficient; -- SN 2 ID Upstream/kill DN Addiction module killer protein, predicted RQ 1 EV IPR014056; TIGR02683; sufficient; // AC GenProp0472 DE Uncharacterized gene pair TIGR02687/TIGR02688 TP SYSTEM AU Haft DH TH 0 CC This property describes an uncharacterized gene pair, sporadically CC distributed in archaea and bacteria, consisting of an upstream protein CC of about 880 amino acids (family TIGR02687) and a downstream protein of CC about 470 amino acids (TIGR02688). The downstream member is CC occasionally annotated (apparently incorrectly) as ATP-dependent CC protease La. -- SN 1 ID Downstream DN Conserved hypothetical protein CHP02688 RQ 1 EV IPR014061; TIGR02688; sufficient; -- SN 2 ID Upstream DN Conserved hypothetical protein CHP02687 RQ 1 EV IPR014060; TIGR02687; sufficient; // AC GenProp0473 DE Arsenite oxidase TP PATHWAY AU Haft DH TH 0 RN [1] RM 12679550 RT Arsenite oxidase, an ancient bioenergetic enzyme. RA Lebrun E, Brugna M, Baymann F, Muller D, Lièvremont D, Lett MC, RA Nitschke W; RL Mol Biol Evol. 2003;20:686-693. CC The enzyme designated arsenate reductase (azurin), acts in the CC biological process of arsenite oxidation for energy metabolism, CC rather than in the reduction of intracellular arsenate to facilitate CC transport as is the case for arsenate reductases of arsenical CC resistance systems. The large subunit contains a molybdopterin CC cofactor, while the small subunit is a Rieske iron-sulfur protein. CC Azurin is present in some but not all species with arsenite oxidase; it CC may be replaced by auracyanin or an unrelated redox partner. -- SN 1 ID Arsenite oxidase, small (Rieske) subunit DN Arsenite oxidase, small subunit RQ 1 EV IPR014067; TIGR02694; sufficient; TG GO:0015975; -- SN 2 ID Azurin DN Azurin (EC 1.20.9.1) RQ 0 EV IPR014068; TIGR02695; sufficient; TG GO:0015975; -- SN 3 ID Arsenite oxidase, large subunit DN Arsenite oxidase, large subunit RQ 1 EV IPR014066; TIGR02693; sufficient; TG GO:0015975; // AC GenProp0474 DE Arsenical resistance system TP SYSTEM AU Haft DH TH 0 CC A characteristic four-gene system for arsenic (and antimony) resistance CC is found in many prokaryotic genomes. The system includes a pump for CC extrusion of arsenite, an arsenate reductase that converts arsenate to CC arsenite for transport, a protein ArsH of unknown function that is CC sometimes not required, and a regulatory protein. Several distinct CC families are known for the arsenate reductase, ArsC, which may be CC dependent on glutaredoxin or thioredoxin in different instances. -- SN 1 ID Arsenical resistance protein ArsH DN Arsenical resistance protein ArsH RQ 1 EV IPR014063; TIGR02690; sufficient; -- SN 2 ID Arsenical resistance regulator ArsR DN HTH ArsR-type DNA-binding domain RQ 1 EV IPR001845; PF01022; -- SN 3 ID Arsenite efflux transporter ArsB DN Arsenical-resistance protein Acr3/Arsenical pump membrane protein/ArsB RQ 1 EV IPR004706; TIGR00832; sufficient; EV IPR000802; TIGR00935; sufficient; -- SN 4 ID Arsenate reductase DN Arsenate reductase RQ 1 EV IPR014064; TIGR02691; sufficient; EV IPR014062; TIGR02689; sufficient; EV IPR006659; TIGR00014; EV IPR023485; PF01451; // AC GenProp0475 DE Unknown biological process TP CATEGORY AU Haft DH TH 0 CC Groups of homologous genes may be associated by their proximity and CC co-directionality in a number of phylogenetically diverse genomes. A CC reasonable hypothesis is that these genes act in a related biological CC process. When none of the genes in such a syntenic grouping have a CC characterized biological process they may still be used to create a CC Genome Property and will be children of this category. -- SN 1 ID Sporadically distributed four-gene operon RQ 0 EV GenProp0470; -- SN 2 ID Uncharacterized gene pair TIGR02683/TIGR02684 RQ 0 EV GenProp0471; -- SN 3 ID Uncharacterized gene pair TIGR02687/TIGR02688 RQ 0 EV GenProp0472; -- SN 4 ID Peptide chain release operon, RctB-like/PrfH RQ 0 EV GenProp0665; -- SN 5 ID Acidobacterial ADOP/PadR gene pairs RQ 0 EV GenProp0751; -- SN 6 ID Sporadic pair TIGR03545/TIGR03546 RQ 0 EV GenProp0790; -- SN 7 ID Enterococcus/Aeromonas extended locus RQ 0 EV GenProp0798; -- SN 8 ID Integral membrane mystery pair RQ 0 EV GenProp0830; -- SN 9 ID ParB-rel/ThiF-rel cassette PRTRC RQ 0 EV GenProp0854; -- SN 10 ID Actinobacterial uncharacterized trio RQ 0 EV GenProp0894; -- SN 11 ID Radical SAM/uncharacterized protein TIGR03936 system RQ 0 EV GenProp0916; -- SN 12 ID Metallo-mystery pair RQ 0 EV GenProp0940; -- SN 13 ID Memo/AMMECR1/rSAM family trio system RQ 0 EV GenProp1063; -- SN 14 ID Verrucomicrobium/Chthoniobacter four-plus-PEP_CTERM cassette RQ 0 EV GenProp0663; -- SN 15 ID Acetyltransferase/synthase/peptidase cassette RQ 0 EV GenProp0668; -- SN 16 ID Uptake/catabolism system KPN_01854/KPN_01858 RQ 0 EV GenProp0935; -- SN 17 ID RSAM-containing biosynthetic cluster, MSMEG_0568 system RQ 0 EV GenProp0939; -- SN 18 ID Radical SAM/lipoprotein system RQ 0 EV GenProp0981; -- SN 19 ID Mobile element associated three-Cys-motif pair RQ 0 EV GenProp1100; // AC GenProp0476 DE Protein-coding palindromic elements TP GUILD AU Haft DH TH 1 RN [1] RM 15936655 RT Discovery of protein-coding palindromic repeats in Wolbachia. RA Ogata H, Suhre K, Claverie JM; RL Trends Microbiol. 2005;13:253-255. RN [2] RM 11030655 RT Selfish DNA in protein-coding genes of Rickettsia. RA Ogata H, Audic S, Barbe V, Artiguenave F, Fournier PE, Raoult D, RA Claverie JM; RL Science. 2000;290:347-350. CC Two different classes are known, so far, of mobile palindromic elements CC that insert in-frame into genes of certain obligate intracellular CC bacteria and code for an amino acid insert in the host protein. In CC contrast to inteins, the insert is relatively small and does not get CC spliced out. Rather, it appears the affected protein continues to CC function because the location of the insert is not destructive to CC correct protein folding. The two classes described so far are CC designated RPE, discovered in Rickettsia, and WPE, discovered in CC Wolbachia. -- SN 1 ID Rickettsia palindromic element (RPE) DN Rickettsial palindromic element/RPE1 RQ 0 EV IPR005728; TIGR01045; sufficient; -- SN 2 ID Rickettsial palindromic element RPE2 domain DN Rickettsia palindromic element RPE2 RQ 0 EV IPR022436; TIGR03774; -- SN 3 ID Rickettsial palindromic element RPE3 domain DN Rickettsia palindromic element RPE3 RQ 0 EV IPR022437; TIGR03775; -- SN 4 ID Rickettsial palindromic element RPE4 domain DN Rickettsia palindromic element RPE4 RQ 0 EV IPR022439; TIGR03777; -- SN 5 ID Rickettsial palindromic element RPE5 domain DN Rickettsia palindromic element RPE5 RQ 0 EV IPR022438; TIGR03776; -- SN 6 ID Wolbachia palindromic element (WPE) DN Wolbachia palindromic element (WPE) RQ 0 EV IPR014070; TIGR02697; sufficient; // AC GenProp0478 DE Acetyl-CoA -- acetate interconversion via acetyl phosphate TP PATHWAY AU Haft DH TH 1 RN [1] RM 13221579 RT Enzymatic phosphorylation of acetate. RA ROSE IA, GRUNBERG-MANAGO M, KOREY SR, OCHOA S; RL J Biol Chem. 1954;211:737-756. RN [2] RM 10894724 RT Regulation of acetyl coenzyme A synthetase in Escherichia coli. RA Kumari S, Beatty CM, Browning DF, Busby SJ, Simel EJ, Hovel-Miner G, RA Wolfe AJ; RL J Bacteriol. 2000;182:4173-4179. RN [3] RM 10074080 RT Purification and characterization of two extremely thermostable RT enzymes, phosphate acetyltransferase and acetate kinase, from the RT hyperthermophilic eubacterium Thermotoga maritima. RA Bock AK, Glasemacher J, Schmidt R, Schönheit P; RL J Bacteriol. 1999;181:1861-1867. CC Acetate and acetyl-CoA can be interconverted by any of several routes. CC This pathway utilizes acetyl phosphate as an intermediate. This system CC is used in E. coli and other bacteria for the utilization of acetate as CC a carbon source [1]. Alternatively, the reactions may be run in the CC catabolic direction in fermentations in order to produce ATP and CC excrete acetate. -- SN 1 ID Phosphate acetyltransferase DN Phosphate acetyltransferase RQ 1 EV IPR004614; TIGR00651; sufficient; TG GO:0019427; -- SN 2 ID Acetyl kinase DN Acetate/propionate kinase RQ 1 EV IPR004372; TIGR00016; sufficient; TG GO:0019427; // AC GenProp0479 DE Acetate -- acetyl-CoA interconversions TP METAPATH AU Haft DH TH 0 CC Acetate and acetyl-CoA can be interconverted for a number of purposes CC including utilization of acetate as in acetate fermentation, excretion CC of acetate in the fermentation of other compounds and the biosynthesis CC of acetyl-CoA for other purposes. Several different single-step and CC multi-step pathways are summarized in this property. -- SN 1 ID Direct with ATP/AMP: GenProp0480 DN Direct with ATP/AMP: GenProp0480 RQ 1 EV GenProp0480; -- SN 2 ID Via acetyl phosphate: GenProp0478 DN Via acetyl phosphate: GenProp0478 RQ 1 EV GenProp0478; // AC GenProp0480 DE Acetyl-CoA biosynthesis from acetate, direct TP PATHWAY AU Haft DH TH 0 RN [1] RM 13367067 RT Acyl adenylates; an enzymatic mechanism of acetate activation. RA BERG P; RL J Biol Chem. 1956;222:991-1013. CC This property's sole component is the enzyme acetyl-CoA ligase which CC hydrolyses ATP to AMP in the process of ligating acetate to coenzyme A. CC This enzyme acts essentially irreversibly in the direction of AcCoA CC biosynthesis and utilizes an enzyme-bound acyl-adeylate (AMP-Ac) CC intermediate [1]. -- SN 1 ID Acetate--CoA ligase DN Acetate--CoA ligase RQ 1 EV IPR011904; TIGR02188; sufficient; TG GO:0019427; // AC GenProp0481 DE Urea carboxylase/allophanate hydrolase pathway TP PATHWAY AU Haft DH TH 0 RN [1] RM 15090492 RT Enzymatic characterization of a prokaryotic urea carboxylase. RA Kanamori T, Kanou N, Atomi H, Imanaka T; RL J Bacteriol. 2004;186:2532-2539. CC This two-step, ATP-dependent pathway for urea hydrolysis is an CC alternative to urease. Urease requires a transporter and accessory CC proteins to produce its nickel metallocenter, while this two-step CC system uses biotin. Urea carboxylase acts first in this pathway, CC requiring ATP and bicarbonate as substrates. Allophanate hydrolase acts CC next, but note that this enzyme may be found in systems that do not CC contain a urea carboxylase. In yeasts such as Saccaromyces cerevisiae, CC the two activities of this pathway are encoded in a fusion protein, CC designated urea amidolyase. This pathway appears to function primarily CC for the purpose of obtaining nitrogen in the form of ammonia. A pair of CC uncharacterized, tandem, homologous genes, restricted to organisms with CC this system and adjacent to the known genes, have been added to this CC Genome Property. -- SN 1 ID ABC transporter periplasmic binding protein, urea carboxylase region DN ABC transporter, urea utilisation-associated, substrate-binding protein RQ 0 EV IPR017793; TIGR03427; TG GO:0043419; -- SN 2 ID Allophanate hydrolase DN Allophanate hydrolase (EC:3.5.1.54) RQ 1 EV IPR014085; TIGR02713; sufficient; TG GO:0043419; -- SN 3 ID Urea carboxylase DN UreA carboxylase (EC:6.3.4.6) RQ 1 EV IPR014084; TIGR02712; sufficient; TG GO:0043419; -- SN 4 ID Urea carboxylase-associated protein 1 DN UreA carboxylase-associated protein 1 RQ 1 EV IPR017791; TIGR03424; TG GO:0043419; -- SN 5 ID Urea carboxylase-associated protein 2 DN UreA carboxylase-associated protein 2 RQ 1 EV IPR017792; TIGR03425; TG GO:0043419; // AC GenProp0483 DE Cytochrome c oxidase, cbb3-type TP SYSTEM AU Haft DH TH 0 RN [1] RM 16343536 RT Multi-step assembly pathway of the cbb3-type cytochrome c oxidase RT complex. RA Kulajta C, Thumfart JO, Haid S, Daldal F, Koch HG; RL J Mol Biol. 2006;355:989-1004. CC Cytochrome cbb(3) oxidase belongs to the family of heme-copper oxidases CC and couples using oxygen as a terminal electron acceptor with pumping CC protons across the membrane. This oxidase is related to, yet CC signficantly different from the mitochondrial cytochrome c oxidase and CC is largely restricted to the Proteobacteria. -- SN 1 ID Subunit I (CcoN) DN Cytochrome c oxidase cbb3-type, subunit I RQ 1 EV IPR004677; TIGR00780; sufficient; -- SN 2 ID Subunit II (CcoO) DN Cytochrome c oxidase, monohaem subunit/FixO RQ 1 EV IPR003468; TIGR00781; sufficient; -- SN 3 ID Subunit III (CcoP) DN Cytochrome c oxidase cbb3-type, subunit III RQ 1 EV IPR004678; TIGR00782; sufficient; -- SN 4 ID Subunit CcoQ DN Cytochrome c oxidase cbb3-type, CcoQ RQ 0 EV IPR008621; PF05545; sufficient; EV IPR014107; TIGR02736; sufficient; -- SN 5 ID Insertion/maturation protein CcoS DN Cytochrome oxidase maturation protein cbb3-type RQ 1 EV IPR004714; TIGR00847; sufficient; -- SN 6 ID Accessory, ferredoxin-like, FixG DN Cytochrome c oxidase cbb3 type, accessory protein FixG RQ 1 EV IPR014116; TIGR02745; sufficient; // AC GenProp0484 DE F-type conjugation system (type IV secretion) specific components TP SYSTEM AU Haft DH TH 1 RN [1] RM 16138100 RT Mobile genetic elements: the agents of open source evolution. RA Frost LS, Leplae R, Summers AO, Toussaint A; RL Nat Rev Microbiol. 2005;3:722-732. RN [2] RM 12855161 RT F factor conjugation is a true type IV secretion system. RA Lawley TD, Klimke WA, Gubbins MJ, Frost LS; RL FEMS Microbiol Lett. 2003;224:1-15. RN [3] RM 15292150 RT Tra proteins characteristic of F-like type IV secretion systems RT constitute an interaction group by yeast two-hybrid analysis. RA Harris RL, Silverman PM; RL J Bacteriol. 2004;186:5480-5485. CC A system for the transfer of plasmid DNA between cells via a pilus. CC This system is a specialized type-IV secretion system. -- SN 1 ID TraF pilus assembly protein DN Type-F conjugative transfer system pilin assembly protein TraF RQ 1 EV IPR014110; TIGR02739; sufficient; TG GO:0009291; -- SN 2 ID Possible alternate TraF or TrbB DN Type IV conjugative transfer system protein TraF RQ 0 EV IPR014111; TIGR02740; sufficient; TG GO:0009291; -- SN 3 ID TraH pilus assembly protein DN Type IV conjugative transfer system protein TraH RQ 1 EV IPR010927; PF06122; sufficient; TG GO:0009291; -- SN 4 ID TraI plasmid relaxase/helicase protein DN Conjugative transfer relaxase protein TraI RQ 1 EV IPR014129; TIGR02760; sufficient; TG GO:0009291; -- SN 5 ID TraN outer membrane mating-pair stabilization protein DN Type-F conjugative transfer system mating-pair stabilisation protein TraN RQ 1 EV IPR014121; PF06986; sufficient; TG GO:0009291; EV IPR014121; TIGR02750; sufficient; TG GO:0009291; -- SN 6 ID TraQ pilin inner membrane chaperone DN Type-F conjugative transfer system pilin chaperone TraQ RQ 0 EV IPR014112; TIGR02741; sufficient; TG GO:0009291; -- SN 7 ID TraU mating-pair stabilization protein DN TraU mating-pair stabilization protein RQ 1 EV IPR009649; PF06834; sufficient; TG GO:0009291; -- SN 8 ID TraW pilus assembly protein DN Type-F conjugative transfer system protein TraW RQ 1 EV IPR014114; TIGR02743; sufficient; TG GO:0009291; -- SN 9 ID TraX pilin acetylase DN TType-F conjugative transfer system pilin acetylase TraX RQ 0 EV IPR014125; TIGR02755; sufficient; TG GO:0009291; -- SN 10 ID TrbB pilus assembly disulfide isomerase DN Type-F conjugative transfer system pilin assembly thiol-disulphide isomerase TrbB RQ 1 EV IPR014109; TIGR02738; sufficient; TG GO:0009291; -- SN 12 ID TrbC pilus assembly protein DN Type-F conjugative transfer system pilin assembly protein TrbC RQ 1 EV IPR014113; TIGR02742; sufficient; TG GO:0009291; -- SN 13 ID TrbI pilus assembly protein DN Type-F conjugative transfer system protein TrbI RQ 0 EV IPR014115; TIGR02744; sufficient; TG GO:0009291; // AC GenProp0485 DE F and P-type conjugation systems (type IV secretion), common components TP SYSTEM AU Haft DH TH 1 CC Both the F-type (F factor like) and P-type (Ti plasmid like) CC conjucation systems use a core set of structures for the elaboration of CC a conjugative pilus. Components specific to these two systems are CC found in related Genome Properties. -- SN 2 ID Pilin, TraA/TrbC/VirB2 DN Conjugal transfer TrbC/type IV secretion VirB2/TraA RQ 1 EV IPR008873; PF05513; sufficient; TG GO:0009291; EV IPR008873; TIGR02758; sufficient; TG GO:0009291; EV IPR007039; PF04956; sufficient; TG GO:0009291; -- SN 3 ID T4SS protein TraB/TrbI/VirB10 DN Type IV secretion system, VirB10/TraB/TrbI RQ 1 EV IPR005498; PF03743; sufficient; TG GO:0009291; EV IPR005498; PF03743; sufficient; TG GO:0009291; -- SN 4 ID ATPase, TraC/TrbE/VirB4 DN Type-IV secretion system protein TraC/CagE/TrbE/VirB RQ 1 EV IPR014117; TIGR02746; sufficient; TG GO:0009291; EV IPR004346; TIGR00929; sufficient; TG GO:0009291; EV IPR018145; PF03135; sufficient; TG GO:0009291; -- SN 5 ID Coupling factor, DNA-pumping ATPase TraD DN Type IV conjugative transfer system, coupling protein TraD RQ 1 EV IPR014128; TIGR02759; sufficient; TG GO:0009291; -- SN 6 ID T4SS protein TraE/TrbJ/VirB5 DN Pilus assembly TraE/Type IV conjugative transfer protein TrbJ RQ 1 EV IPR007973; PF05309; sufficient; TG GO:0009291; EV IPR007973; TIGR02761; sufficient; TG GO:0009291; EV IPR014147; TIGR02780; sufficient; TG GO:0009291; EV IPR014158; TIGR02791; sufficient; TG GO:0009291; -- SN 7 ID Mate-pair stab. TraG/TrbL/VirB6 DN Conjugal transfer, TraG/TrbL/VirB6 RQ 1 EV IPR012931; PF07916; sufficient; TG GO:0009291; EV IPR007688; PF04610; sufficient; TG GO:0009291; EV IPR014150; TIGR02783; sufficient; TG GO:0009291; -- SN 8 ID T4SS protein TraK/TrbG/VirB9 DN P-type conjugative transfer protein TraK/TrbG/VirB9 RQ 1 EV IPR010563; PF06586; sufficient; TG GO:0009291; EV IPR014126; TIGR02756; sufficient; TG GO:0009291; EV IPR014142; TIGR02775; sufficient; TG GO:0009291; EV IPR014148; TIGR02781; sufficient; TG GO:0009291; -- SN 9 ID T4SS protein TraL/TrbD/VirB3 DN Type IV conjugative transfer system, protein TraL/TrbD/VirB3 RQ 1 EV IPR009838; PF07178; sufficient; TG GO:0009291; EV IPR009838; TIGR02762; sufficient; TG GO:0009291; EV IPR007792; PF05101; sufficient; TG GO:0009291; -- SN 10 ID T4SS protein TraV/TrbH/VirB7 DN Type IV conjugative transfer system protein TraV RQ 1 EV IPR014118; TIGR02747; sufficient; TG GO:0009291; // AC GenProp0487 DE RepABC-type alpha-proteobacterial replicon(s) TP SYSTEM AU Haft DH TH 0 RN [1] RM 15659174 RT The expression of a novel antisense gene mediates incompatibility RT within the large repABC family of alpha-proteobacterial plasmids. RA MacLellan SR, Smallbone LA, Sibley CD, Finan TM; RL Mol Microbiol. 2005;55:611-623. CC Plasmids and second chromosomes in the alpha-proteobacteria, that is CC replicons other than main chromosome, are often maintained by repABC CC systems (an example of an alternative system is replicator region type CC A). RepA and RepB are partitioning proteins, while RepC is a CC replication protein. In species with multiple plasmids, different CC classes of repABC system work in parallel; it appears that the CC incompatability system that separates the different RepABC subtypes is CC mediated by an untranslated RNA gene, IncA, encoded between repB and CC repC and transcribed in the antisense direction [1]. IncA is not CC modelled as part of this Genome Property. Note that homologs to RepA CC and RepB occur as gene pairs in smaller replicons outside the CC alpha-proteobacteria, such as on the smaller chromosome of Vibrio CC cholerae (a gamma-proteobacterium). These more distantly related CC systems, however, fall outside the definition of repABC systems as CC adapted here from literature. -- SN 1 ID RepA plasmid partitioning protein DN Plasmid partitioning protein, RepA RQ 1 EV IPR017818; TIGR03453; -- SN 2 ID RepB plasmid partitioning protein DN Plasmid partitioning protein, RepB RQ 1 EV IPR017819; TIGR03454; sufficient; -- SN 3 ID RepC replication initiator protein DN Replication protein C/RepC RQ 1 EV IPR005090; PF03428; sufficient; // AC GenProp0488 DE Superoxide dismutase, nickel-type TP SYSTEM AU Haft DH TH 0 CC This property consists of a nickel-dependent superoxide dismutase and a CC cognate protease necessary to process an N-terminal sequence. -- SN 1 ID Superoxide dismutase [Ni] DN Superoxide dismutase, Nickel-type RQ 1 EV IPR014123; TIGR02753; sufficient; -- SN 2 ID SOD [Ni] protease DN Peptidase S26A, superoxide dismutase maturation protease, nickel-type RQ 1 EV IPR014124; TIGR02754; sufficient; // AC GenProp0489 DE F-type conjugation system TP METAPATH AU Haft DH TH 0 RN [1] RM 16138100 RT Mobile genetic elements: the agents of open source evolution. RA Frost LS, Leplae R, Summers AO, Toussaint A; RL Nat Rev Microbiol. 2005;3:722-732. RN [2] RM 12855161 RT F factor conjugation is a true type IV secretion system. RA Lawley TD, Klimke WA, Gubbins MJ, Frost LS; RL FEMS Microbiol Lett. 2003;224:1-15. RN [3] RM 15292150 RT Tra proteins characteristic of F-like type IV secretion systems RT constitute an interaction group by yeast two-hybrid analysis. RA Harris RL, Silverman PM; RL J Bacteriol. 2004;186:5480-5485. CC F-type plasmid conjugation systems are those distinctive of the CC F-plasmid first described in E.coli. This system consists of a type-IV CC pilus specialized for plasmid DNA transduction as well as specialized CC machinery for mating-type recognition in the recipient cell and a CC relaxosome and coupling protein system for initiating and providing CC energy for the transfer. Two genome properties, GenProp0484 and CC GenProp0485, encapsulate the F-type-specific and generic components CC repectively. The generic components are found in non-F-type CC conjugative systems such as the P and I-like systems. -- SN 1 ID GenProp0485: conjugation common component DN GenProp0485: conjugation common component RQ 1 EV GenProp0485; TG GO:0009291; -- SN 3 ID GenProp0484: F-type specific components DN GenProp0484: F-type specific components RQ 1 EV GenProp0484; TG GO:0009291; // AC GenProp0490 DE Ti-type conjugation system TP SYSTEM AU Haft DH TH 0 RN [1] RM 8763953 RT The tra region of the nopaline-type Ti plasmid is a chimera with RT elements related to the transfer systems of RSF1010, RP4, and F. RA Farrand SK, Hwang I, Cook DM; RL J Bacteriol. 1996;178:4233-4247. CC This type IV secretion system for the exchange of plasmid DNA is found CC in the Agrobacterium tumefaciens Ti plasmid. This (tra/trb) system is CC separate from the vir system which is responsible for targetting the CC T-region DNA to eukaryotic host cells in the process of tumor CC formation. -- SN 1 ID Ti conjugation system relaxase TraA DN Ti conjugation system relaxase TraA RQ 1 EV IPR014136; TIGR02768; sufficient; TG GO:0009291; -- SN 2 ID Ti conjugation system protein TraB DN Conjugal transfer, TraB RQ 0 EV IPR016707; PIRSF017932; sufficient; TG GO:0009291; -- SN 3 ID Ti conjugation system protein TraC DN TraC-like RQ 0 EV IPR012930; PF07820; sufficient; TG GO:0009291; -- SN 4 ID Ti conjugation system protein TraD DN Conjugal transfer, TraD RQ 0 EV IPR009444; PF06412; sufficient; TG GO:0009291; -- SN 5 ID Ti conjugation system signal peptidase TraF DN Peptidase S26C, conjugative transfer signal peptidase TraF RQ 0 EV IPR014139; TIGR02771; sufficient; TG GO:0009291; -- SN 6 ID Ti conjugation system protein TraG DN Ti-type conjugative transfer system, TraG RQ 1 EV IPR014135; TIGR02767; sufficient; TG GO:0009291; -- SN 7 ID Ti conjugation system protein TraH DN TraH-2 RQ 0 EV IPR010680; PF06871; sufficient; TG GO:0009291; -- SN 8 ID Ti/vir system protein TrbB/VirB11 DN Conjugative transfer TrbB/Type IV secretion system protein VirB11 RQ 0 EV IPR014149; TIGR02782; sufficient; TG GO:0009291; EV IPR014155; TIGR02788; sufficient; TG GO:0009291; -- SN 9 ID Ti/vir system protein TrbF/VirB8 DN Bacterial virulence protein VirB8 RQ 1 EV IPR007430; PF04335; sufficient; TG GO:0009291; EV IPR007430; PF04335; sufficient; TG GO:0009291; // AC GenProp0491 DE RecFOR recombination pathway TP SYSTEM AU Haft DH TH 0 RN [1] RM 16132081 RT Comparative and evolutionary analysis of the bacterial homologous RT recombination systems. RA Rocha EP, Cornet E, Michel B; RL PLoS Genet. 2005;1:e15. RN [2] RM 15687199 RT Effects of recJ, recQ, and recFOR mutations on recombination in RT nuclease-deficient recB recD double mutants of Escherichia coli. RA Ivancic-Bace I, Salaj-Smic E, Brcic-Kostic K; RL J Bacteriol. 2005;187:1350-1356. CC RecFOR is a system for homologous recombination, a nearly universal CC housekeeping process especially important for repair. RecFOR acts CC independently from the RecBCD system, or the AddAB system that replaces CC RecBCD in certain lineages, and the presence of RecFOR is actually CC positively correlated with the presence of RecBCD/AddAB, so these two CC presynaptic systems that act in loading RecA may be regarded as CC complementary. RecFOR especially repairs single-stranded gaps while CC RecBCD/AddAB repairs double-stranded DNA ends, although roles for CC RecFOR in double stranded break repair are shown in discussion of RecN CC and RecQ function and of recBCD mutants. RecFOR systems often are CC assisted in an early step by the exonuclease RecJ. Following strand CC exchange by RecA, Holliday junction resolution may be done by RuvABC or CC RecG. The action of the RecFOR pathway involves formation of RecOR CC complexes, and RecFR complexes, but no complex of all three. Of the CC three genes, either RecO or RecF may be missing while the other two CC components are present, but RecR must be present in genomes with any CC part of this system. -- SN 1 ID RecF DN DNA replication and repair protein RecF RQ 1 EV IPR001238; TIGR00611; sufficient; TG GO:0000724; -- SN 2 ID Exonuclease RecJ DN Single-stranded-DNA-specific exonuclease RecJ (EC 3.1.-.-) RQ 1 EV IPR004610; TIGR00644; sufficient; TG GO:0000724; -- SN 3 ID RecN DN DNA repair protein RecN RQ 0 EV IPR004604; TIGR00634; sufficient; TG GO:0000724; -- SN 4 ID RecO DN DNA repair protein RecO RQ 1 EV IPR003717; TIGR00613; sufficient; TG GO:0000724; -- SN 5 ID Helicase RecQ DN ATP-dependent DNA helicase RecQ (EC 3.6.1.-) RQ 0 EV IPR006293; TIGR01389; sufficient; TG GO:0000724; -- SN 6 ID RecR DN Recombination protein RecR RQ 1 EV IPR000093; TIGR00615; sufficient; TG GO:0000724; // AC GenProp0492 DE Nonhomologous end-joining, bacterial type TP SYSTEM AU Haft DH TH 0 RN [1] RM 16132081 RT Comparative and evolutionary analysis of the bacterial homologous RT recombination systems. RA Rocha EP, Cornet E, Michel B; RL PLoS Genet. 2005;1:e15. RN [2] RM 16046407 RT Essential constituents of the 3'-phosphoesterase domain of bacterial RT DNA ligase D, a nonhomologous end-joining enzyme. RA Zhu H, Wang LK, Shuman S; RL J Biol Chem. 2005;280:33707-33715. CC This property describes nonhomologous end-joining (NHEJ), a mechanism CC for DNA repair of double-stranded breaks that appears significantly CC less common in bacteria than, and uncorrelated with, recombinational CC repair. The bacterial Ku protein typically is encoded next to the CC multidomain, multifunctional DNA ligase, LidD. The domains of LigD, CC which may be permuted, carry separable 3'-phosphoesterase (PE), DNA CC ligase, and polymerase activities. -- SN 1 ID Ku protein, bacterial type DN Ku protein, bacterial type RQ 1 EV IPR009187; TIGR02772; sufficient; TG GO:0006303; -- SN 2 ID 3-prime phosphoesterase domain DN 3-prime phosphoesterase domain RQ 0 EV IPR014144; TIGR02777; sufficient; TG GO:0006303; -- SN 3 ID Ligase domain DN Ligase domain RQ 1 EV IPR014146; TIGR02779; sufficient; TG GO:0006303; -- SN 4 ID Polymerase domain DN Polymerase domain RQ 1 EV IPR014145; TIGR02778; sufficient; TG GO:0006303; // AC GenProp0493 DE AddAB pathway TP SYSTEM AU Haft DH TH 0 CC The recBCD pathway, important in double stranded break DNA repair by CC homologous recombination, is replaced by AddAB in several bacterial CC lineages. The AddAB gene pairs are quite distant, in terms of sequence CC similarity, between that of Gram-positive bacteria and that of CC alphaproteobacteria. Note that an alternative, less common method of CC repair of double stranded breaks is nonhomologous end-joining (NHEJ), CC and that pathway may coexist with AddAB in a genome. In some species, CC AddAB is called RexAB. -- SN 1 ID AddA protein DN DNA helicase subunit AddA RQ 1 EV IPR014151; TIGR02784; sufficient; TG GO:0000724; EV IPR014152; TIGR02785; sufficient; TG GO:0000724; -- SN 2 ID AddB protein DN DNA helicase subunit AddB RQ 1 EV IPR014153; TIGR02786; sufficient; TG GO:0000724; EV IPR014140; TIGR02773; sufficient; TG GO:0000724; EV IPR014141; TIGR02774; sufficient; TG GO:0000724; // AC GenProp0494 DE Nickel import ABC transporter TP SYSTEM AU Haft DH TH 0 RN [1] RM 7934931 RT The nik operon of Escherichia coli encodes a periplasmic RT binding-protein-dependent transport system for nickel. RA Navarro C, Wu LF, Mandrand-Berthelot MA; RL Mol Microbiol. 1993;9:1181-1191. RN [2] RM 23139401 RT Helicobacter hepaticus NikR controls urease and hydrogenase RT activities via the NikABDE and HH0418 putative nickel import RT proteins. RA Benoit SL, Seshadri S, Lamichhane-Khadka R, Maier RJ; RL Microbiology. 2013;159:136-146. RN [3] RM 9882686 RT Isolation and characterization of the nikR gene encoding a RT nickel-responsive regulator in Escherichia coli. RA De Pina K, Desjardin V, Mandrand-Berthelot MA, Giordano G, Wu LF; RL J Bacteriol. 1999;181:670-674. CC Nickel is an essential trace element, but is also toxic at high levels. CC This genome property descibes a specifc ABC transporter that is responsible CC for the uptake of nickel. The transporter is encoded by the nikABCDE operon. CC This property also includes nikR which has been shown to function as a CC regulator for this transporter [1,2,3]. -- SN 1 ID Periplasmic binding protein NikA DN Periplasmic binding protein NikA/NikA RQ 1 EV IPR011980; TIGR02294; sufficient; -- SN 2 ID Permease NikB DN Permease NikB/NikB RQ 1 EV IPR014156; TIGR02789; sufficient; -- SN 3 ID Permease NikC DN Permease NikC/NikC RQ 1 EV IPR014157; TIGR02790; sufficient; -- SN 4 ID ATP-binding protein NikD DN ATP-binding protein NikD/NikD RQ 1 EV IPR014138; TIGR02770; sufficient; -- SN 5 ID ATP-binding protein NikE DN ATP-binding protein NikE/NikE RQ 1 EV IPR014137; TIGR02769; sufficient; -- SN 6 ID Nickel-responsive transcriptional regulator DN Nickel-responsive transcriptional regulator/nikR RQ 0 EV IPR014160; TIGR02793; sufficient; // AC GenProp0542 DE Tol-Pal system TP SYSTEM AU Haft DH TH 0 RN [1] RM 11200223 RT Organisation and evolution of the tol-pal gene cluster. RA Sturgis JN; RL J Mol Microbiol Biotechnol. 2001;3:113-122. RN [2] RM 16207916 RT Tol-Pal proteins are critical cell envelope components of Erwinia RT chrysanthemi affecting cell morphology and virulence. RA Dubuisson JF, Vianney A, Hugouvieux-Cotte-Pattat N, Lazzaroni JC; RL Microbiology. 2005;151:3337-3347. RN [3] RM 12486055 RT Transcriptional organization of the Pseudomonas putida tol-oprL genes. RA Llamas MA, Ramos JL, Rodríguez-Herva JJ; RL J Bacteriol. 2003;185:184-195. RN [4] RM 11959124 RT The YbgC protein encoded by the ybgC gene of the tol-pal gene cluster RT of Haemophilus influenzae catalyzes acyl-coenzyme A thioester RT hydrolysis. RA Zhuang Z, Song F, Martin BM, Dunaway-Mariano D; RL FEBS Lett. 2002;516:161-163. RN [5] RM 11722743 RT The TolQ-TolR proteins energize TolA and share homologies with the RT flagellar motor proteins MotA-MotB. RA Cascales E, Lloubès R, Sturgis JN; RL Mol Microbiol. 2001;42:795-807. RN [6] RM 14731286 RT Deletion analyses of the peptidoglycan-associated lipoprotein Pal RT reveals three independent binding sequences including a TolA box. RA Cascales E, Lloubès R; RL Mol Microbiol. 2004;51:873-885. RN [7] RM 12896989 RT Role of Pseudomonas putida tol-oprL gene products in uptake of solutes RT through the cytoplasmic membrane. RA Llamas MA, Rodríguez-Herva JJ, Hancock RE, Bitter W, Tommassen J, RA Ramos JL; RL J Bacteriol. 2003;185:4707-4716. CC A complex of TolQ, TolR, and TolA in the inner membrane, interacting CC through TolA with a complex of TolB and Pal (also called OprL) present CC at the outer membrane, is pivotal to maintaining morphology and outer CC membrane integrity in many Gram-negative bacteria. The tol operon(s) CC routinely also contain ybgC (orf1) and ybgF (orf2) genes, although CC these are not clearly associated with mutant phenotypes. The TolA CC protein, homologous to TonB from a similar complex, is the most CC divergent, as it consists largely of very low complexity sequence. TolB CC contains a variable number of beta-propellar repeats. -- SN 1 ID Tol-pal system protein Pal (OprL) DN Peptidoglycan-associated lipoprotein/Pal/OprL RQ 1 EV IPR014169; TIGR02802; sufficient; -- SN 2 ID TolA DN Tol-Pal system, TolA RQ 1 EV IPR014161; TIGR02794; sufficient; -- SN 3 ID TolB DN Tol-Pal system beta propeller repeat-containing protein, TolB RQ 1 EV IPR014167; TIGR02800; sufficient; -- SN 4 ID TolQ DN Tol-Pal system, TolQ RQ 1 EV IPR014163; TIGR02796; sufficient; -- SN 5 ID TolR DN Biopolymer transport, TolR RQ 1 EV IPR014168; TIGR02801; sufficient; -- SN 6 ID Tol-pal region thioesterase YbgC DN Tol-Pal system-associated acyl-CoA thioesterase/YbgC RQ 0 EV IPR014166; TIGR02799; sufficient; -- SN 7 ID Tol-pal region protein YbgF DN Cell division coordinator CpoB/YbgF RQ 0 EV IPR014162; TIGR02795; sufficient; // AC GenProp0543 DE TonB-dependent transport TP SYSTEM AU Haft DH TH 0 CC The components of a TonB-dependent transport system include ExbB, ExbD, CC and TonB, respectively homologous to TolQ, TolR, and TolA of related CC tol-pal system. But while the tol-pal system includes seven genes CC altogether, including the peptidoglycan associated lipoprotein Pal, and CC seems required for maintaining integrity of the outer membrane, TonB CC systems tend to be required for siderophore or B12 uptake when mutant CC phenotypes are observed. At least two different exbB/exbD gene pair CC families exist, and two different pairs of HMMs currently model two CC different classes. The capacity for TonB-dependent transport is also CC marked by the presence of TonB-dependent transporters, which share a CC region of homology and may number more than 50 in a single genome. -- SN 1 ID TonB C-terminal domain DN TonB C-terminal domain RQ 1 EV IPR006260; TIGR01352; -- SN 2 ID Barrel domain, tonB-dependent receptor DN Barrel domain, tonB-dependent receptor RQ 0 EV IPR000531; PF00593; sufficient; -- SN 3 ID TonB-system energizer ExbB DN TonB-system energizer ExbB RQ 1 EV IPR014164; TIGR02797; sufficient; EV IPR014172; TIGR02805; sufficient; -- SN 4 ID TonB-system energizer ExbD DN onB system transport protein ExbD RQ 1 EV IPR014170; TIGR02803; sufficient; EV IPR014171; TIGR02804; sufficient; -- SN 5 ID Plug domain, tonB-dependent receptor DN Plug domain, tonB-dependent receptor RQ 0 EV IPR012910; PF07715; sufficient; // AC GenProp0551 DE Gene regulatory systems TP CATEGORY AU Haft DH TH 0 CC Properties that describe various systems for the regulation of gene CC activity. This may occur at the level of DNA modification, translation CC to RNA, RNA stability, RNA conformation, RNA degradation, transcription CC to protein, protein conformation, protein stability and/or protein CC degradation. -- SN 1 ID Attenuation system: tryptophanase RQ 0 EV GenProp0456; -- SN 2 ID Circadian clock system KaiABC RQ 0 EV GenProp0465; -- SN 3 ID Regulation of biological processes RQ 0 EV GenProp1212; // AC GenProp0562 DE Formaldehyde detoxification, glutathione-dependent TP PATHWAY AU Haft DH TH 0 CC Formaldehyde, a toxic metabolite because it reacts easily with protein CC or DNA, naturally combines with reduced glutathione (GSH) to form CC S-hydroxymethyl-glutathione. In some species, this reaction is CC accelerated by the enzyme S-(hydroxymethyl)glutathione synthase, also CC called glutathione-dependent formaldehyde activating enzyme. A class CC III alcohol dehydrogenase, with activity for a variety of medium chain CC alcohols (but poor activity for ethanol) can convert CC S-(hydroxymethyl)glutathione to S-formylglutathione, and therefore has CC been called glutathione-dependent formaldehyde dehydrogenase but is CC more properly called S-(hydroxymethyl)glutathione dehydrogenase for CC this activity. Finally, S-formylglutathione is converted to glutathione CC and formate by S-formylglutathione hydrolase, which has a dual role as CC a broadly specific esterase, called esterase D in animals. While the CC two essential enzymes of this pathway both have broad specificities, CC the pairing in operons in so many genomes demonstrates the recurring CC importance of formaldehyde detoxification. -- SN 1 ID S-(hydroxymethyl)glutathione synthase DN S-(hydroxymethyl)glutathione synthase RQ 0 EV IPR014185; TIGR02820; sufficient; -- SN 2 ID S-formylglutathione hydrolase DN S-formylglutathione hydrolase RQ 1 EV IPR014186; TIGR02821; sufficient; -- SN 3 ID S-(hydroxymethyl)glutathione dehydrogenase DN S-(hydroxymethyl)glutathione dehydrogenase RQ 1 EV IPR014183; TIGR02818; sufficient; // AC GenProp0603 DE Lifestyle TP CATEGORY AU Haft DH TH 0 CC Genome Properties in this category describe the different modes, CC styles and strategies by which organisms live. Lifestyles describe CC distinguishing characteristics by which these organisms may be CC grouped, and generally will have an underlying metabolic basis. -- SN 1 ID Nitrogen fixation RQ 0 EV GenProp0029; // AC GenProp0610 DE Endospore formation marker gene set TP SYSTEM AU Haft DH TH 0 RN [1] RM 16311624 RT Life in hot carbon monoxide: the complete genome sequence of RT Carboxydothermus hydrogenoformans Z-2901. RA Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, RA Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, RA Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA; RL PLoS Genet. 2005;1:e65. CC An article by Wu, et al.[1] on Carboxydothermus hydrogenoformans Z-2901 CC describes a minimal set of genes whose phylogenetic profile appears to CC exactly match the assignment of endospore formation capability. The CC list corresponds to a fairly small fraction of sporulation and CC germination-related genes in Bacillus subtilis. This property reflects CC those genes for which identifying hidden Markov models (HMMs) with CC appropriate scope are available. Also included in this property, as CC optional rather than mandatory components, are various classes of CC small, acid-soluble spore protein, or SASP, where one class may expand CC into a paralogous family while another class is lost in any given CC genome. -- SN 1 ID Stage 0 sporulation protein A DN Stage 0 sporulation protein A RQ 1 EV IPR012052; TIGR02875; sufficient; -- SN 2 ID Dipicolinic acid synthetase, A subunit DN Dipicolinic acid synthetase, A subunit RQ 0 EV IPR014215; TIGR02853; sufficient; -- SN 3 ID Dipicolinic acid synthetase, B subunit DN Dipicolinic acid synthetase, B subunit RQ 0 EV IPR014214; TIGR02852; sufficient; -- SN 4 ID Germination protease DN Germination protease RQ 1 EV IPR005080; TIGR01441; sufficient; -- SN 5 ID Stage III sporulation protein AA DN Stage III sporulation protein AA RQ 1 EV IPR014217; TIGR02858; sufficient; -- SN 6 ID Stage III sporulation protein AB DN Stage III sporulation protein AB RQ 1 EV IPR014198; TIGR02833; sufficient; -- SN 7 ID Stage III sporulation protein AC DN Stage III sporulation protein AC RQ 1 EV IPR009570; TIGR02848; sufficient; -- SN 8 ID Stage III sporulation protein AD DN Stage III sporulation protein AD RQ 1 EV IPR014211; TIGR02849; sufficient; -- SN 9 ID Stage III sporulation protein AE (TIGR02829) DN Stage III sporulation protein AE (TIGR02829) RQ 1 EV IPR014194; TIGR02829; sufficient; -- SN 10 ID Stage III sporulation protein AF DN Stage III sporulation protein AF RQ 1 EV IPR014245; TIGR02896; sufficient; -- SN 11 ID Stage III sporulation protein AG DN Stage III sporulation protein AG RQ 1 EV IPR014195; TIGR02830; sufficient; -- SN 12 ID Transcriptional regulator SpoIIID DN Transcriptional regulator SpoIIID RQ 1 EV IPR014208; TIGR02844; sufficient; -- SN 13 ID Anti-anti-sigma-F DN Anti-anti-sigma-F RQ 1 EV IPR014237; TIGR02886; sufficient; -- SN 14 ID Anti-sigma-F DN Anti-sigma-F RQ 1 EV IPR010194; TIGR01925; sufficient; -- SN 15 ID Sigma-F DN Sigma-F RQ 1 EV IPR014236; TIGR02885; sufficient; -- SN 16 ID Stage II sporulation protein D DN Stage II sporulation protein D RQ 1 EV IPR014225; TIGR02870; sufficient; -- SN 17 ID Stage II sporulation protein E DN Stage II sporulation protein E RQ 1 EV IPR014221; TIGR02865; sufficient; -- SN 18 ID Sigma-E protease SpoIIGA DN Sigma-E protease SpoIIGA RQ 1 EV IPR005081; TIGR02854; sufficient; -- SN 19 ID Stage II sporulation protein M DN Stage II sporulation protein M RQ 1 EV IPR014196; TIGR02831; sufficient; -- SN 20 ID Stage II sporulation protein P DN Stage II sporulation protein P RQ 1 EV IPR010897; TIGR02867; sufficient; -- SN 21 ID Stage II sporulation protein R DN Stage II sporulation protein R RQ 1 EV IPR014202; TIGR02837; sufficient; -- SN 22 ID Stage IV sporulation protein A DN Stage IV sporulation protein A RQ 1 EV IPR014201; TIGR02836; sufficient; -- SN 23 ID Stage IV sporulation protein B DN Stage IV sporulation protein B RQ 1 EV IPR014219; TIGR02860; sufficient; -- SN 24 ID SASP, alpha/beta type DN SASP, alpha/beta type RQ 1 EV IPR001448; PF00269; sufficient; -- SN 25 ID SASP, gamma type DN SASP, gamma type RQ 0 EV IPR006341; TIGR01442; sufficient; -- SN 26 ID SASP, SspH-type DN SASP, SspH-type RQ 0 EV IPR012610; TIGR02861; sufficient; -- SN 27 ID Stage VI sporulation protein D DN Stage VI sporulation protein D RQ 0 EV IPR014256; TIGR02907; sufficient; -- SN 28 ID Stage V sporulation protein AC DN Stage V sporulation protein AC RQ 1 EV IPR014203; TIGR02838; sufficient; -- SN 29 ID Stage V sporulation protein AD DN Stage V sporulation protein AD RQ 1 EV IPR010894; TIGR02845; sufficient; -- SN 30 ID Stage V sporulation protein AE DN Stage V sporulation protein AE RQ 1 EV IPR014204; TIGR02839; sufficient; -- SN 31 ID Stage V sporulation protein B DN Stage V sporulation protein B RQ 0 EV IPR014249; TIGR02900; sufficient; -- SN 32 ID Stage V sporulation protein K DN Stage V sporulation protein K RQ 0 EV IPR014232; TIGR02881; sufficient; -- SN 33 ID Stage V sporulation protein T DN Stage V sporulation protein T RQ 1 EV IPR014213; TIGR02851; sufficient; -- SN 34 ID Germination lipoprotein, YhcN/YlaJ family DN Germination lipoprotein, YhcN/YlaJ family RQ 0 EV IPR014247; TIGR02898; sufficient; -- SN 35 ID Spore coat protein, CotS family DN Spore coat protein, CotS family RQ 0 EV IPR014255; TIGR02906; sufficient; -- SN 36 ID GerKA-like paralogous family DN GerKA-like paralogous family RQ 1 EV IPR004995; PF03323; sufficient; -- SN 37 ID GerKB-like paralogous family DN GerKB-like paralogous family RQ 1 EV IPR004761; TIGR00912; sufficient; -- SN 38 ID GerKC-like paralogous family DN GerKC-like paralogous family RQ 1 EV IPR008844; TIGR02887; sufficient; -- SN 39 ID ATP-dependent protease LonB DN ATP-dependent protease LonB RQ 0 EV IPR014251; TIGR02902; sufficient; -- SN 40 ID Spore coat assembly protein SafA (yrbB) DN Spore coat assembly protein SafA (yrbB) RQ 0 EV IPR014248; TIGR02899; sufficient; -- SN 41 ID Sigma-E DN Sigma-E RQ 1 EV IPR014200; TIGR02835; sufficient; -- SN 42 ID Sigma-G DN Sigma-G RQ 1 EV IPR014212; TIGR02850; sufficient; -- SN 43 ID Sigma-H DN Sigma-H RQ 1 EV IPR014218; TIGR02859; sufficient; -- SN 44 ID Sigma-I (heat shock-induced) DN Sigma-I (heat shock-induced) RQ 0 EV IPR014244; TIGR02895; sufficient; -- SN 45 ID Sigma-K DN Sigma-K RQ 1 EV IPR014209; TIGR02846; sufficient; -- SN 46 ID Spore coat assembly protease YabG DN Spore coat assembly protease YabG RQ 1 EV IPR008764; TIGR02855; sufficient; -- SN 47 ID Sporulation protein YabP DN Sporulation protein YabP RQ 1 EV IPR012504; TIGR02892; sufficient; -- SN 48 ID Sporulation protein YabQ DN Sporulation protein YabQ RQ 1 EV IPR014242; TIGR02893; sufficient; -- SN 49 ID Sporulation protein YlbJ DN Sporulation protein YlbJ RQ 1 EV IPR014226; TIGR02871; sufficient; -- SN 50 ID Sporulation protein, YlmC/YmxH family DN Sporulation protein, YlmC/YmxH family RQ 1 EV IPR014238; TIGR02888; sufficient; -- SN 51 ID Germination protein YpeB DN Germination protein YpeB RQ 1 EV IPR014239; TIGR02889; sufficient; -- SN 52 ID Sporulation protein YqfC DN Sporulation protein YqfC RQ 1 EV IPR022477; TIGR02856; sufficient; -- SN 53 ID Sporulation protein YqfD DN Sporulation protein YqfD RQ 1 EV IPR010690; TIGR02876; sufficient; -- SN 54 ID Spore coat protein YsxE DN Spore coat protein YsxE RQ 0 EV IPR014253; TIGR02904; sufficient; -- SN 55 ID Sporulation protein YtaF DN Sporulation protein YtaF RQ 1 EV IPR014205; TIGR02840; sufficient; -- SN 56 ID Sporulation protein YtfJ DN Sporulation protein YtfJ RQ 1 EV IPR014229; TIGR02874; sufficient; -- SN 57 ID Sporulation protein YtvI DN Sporulation protein YtvI RQ 1 EV IPR014227; TIGR02872; sufficient; -- SN 58 ID Sporulation protein YtxC DN Sporulation protein YtxC RQ 1 EV IPR014199; TIGR02834; sufficient; -- SN 59 ID Sporulation protein YunB DN Sporulation protein YunB RQ 1 EV IPR014197; TIGR02832; sufficient; -- SN 60 ID Spore coat protein YutH DN Spore coat protein YutH RQ 0 EV IPR014254; TIGR02905; sufficient; -- SN 61 ID Putative sporulation protease YyaC DN Putative sporulation protease YyaC RQ 1 EV IPR009665; TIGR02841; sufficient; // AC GenProp0611 DE Aerobic respiration TP METAPATH AU Haft DH TH 0 CC Aerobic respiration is the complex series of pathways in which a common CC organic intermediate (generally pyruvate) is broken down into carbon CC dioxide (CO2) and water (H20) with the concomitant production of ATP in CC the presence of oxygen. Pyruvate is generated from glucose via CC glycolysis. The first step of this process is conversion of pyruvate to CC acetyl-CoA which then enters the Krebs (or, TCA) cycle. Acetyl-CoA may CC also be generated independently of pyruvate via the breakdown of other CC organic compounds. The TCA cycle generates reducing equivalents in the CC form of NADH. NADH, in turn delivers the electrons to the top of the CC electron transport chain (oxidative phosphorylation). This chain CC results in the pumping of protons (and/or sodium ions) to form a CC gradient. Ions flowing back with this gradient power the ATP-generation CC machines of the cell. Oxygen acts as the terminal electron acceptor for CC the electron-transport chain. -- SN 1 ID A1/A0 ATPase/F1/F0 ATPase DN A1/A0 ATPase/F1/F0 ATPase RQ 1 EV GenProp0128; EV GenProp0629; -- SN 2 ID Aerobic electron transfer (transport) chain, ETC DN Aerobic electron transfer (transport) chain, ETC RQ 1 EV GenProp0612; -- SN 3 ID TCA cycle DN TCA cycle RQ 1 EV GenProp0033; // AC GenProp0612 DE Aerobic electron transfer (transport) chain, ETC TP METAPATH AU Haft DH TH 0 CC These complexes act in the process of oxidative phosphorylation to CC create a proton gradient which powers the ATP synthase complex. CC Reducing equivalents in the form of NADH and quinone from the TCA cycle CC stepped down in potential finally resulting in a reduced cytochrome c CC which, in cytochrome oxidase, pairs with oxygen as a terminal elextron CC acceptor. -- SN 1 ID Quinone re-oxidation, oxygen reduction DN Quinone re-oxidation, oxygen reduction RQ 1 EV GenProp0615; EV GenProp0616; -- SN 2 ID Quinone reduction (NADH dehydrogenases) DN Quinone reduction (NADH dehydrogenases) RQ 1 EV GenProp0135; EV GenProp0129; // AC GenProp0613 DE Cytochrome c reductase TP SYSTEM AU Haft DH TH 1 CC The component of the oxidative phosphorylation electron transfer chain CC responsible for transferring electrons from quinones to cytochrome c. -- SN 1 ID Iron-sulfur cluster subunit DN Iron-sulfur cluster subunit RQ 1 EV IPR006317; TIGR01416; sufficient; EV IPR017941; PF00355; sufficient; -- SN 2 ID Cytochrome b subunit DN Cytochrome b subunit RQ 1 EV IPR005798; PF00032; sufficient; EV IPR005797; PF00033; sufficient; -- SN 3 ID Cytochrome c subunit DN Cytochrome c subunit RQ 1 EV IPR002326; PF02167; sufficient; EV IPR009056; PF00034; sufficient; // AC GenProp0614 DE Cytochrome c oxidase, mitochondrial, caa3-type TP SYSTEM AU Haft DH TH 0 RN [1] RM 1847686 RT The Bacillus subtilis cytochrome-c oxidase. Variations on a conserved RT protein theme. RA Saraste M, Metso T, Nakari T, Jalli T, Lauraeus M, Van der Oost J; RL Eur J Biochem. 1991;195:517-525. RN [2] RM 9380672 RT Structure at 2.7 A resolution of the Paracoccus denitrificans RT two-subunit cytochrome c oxidase complexed with an antibody FV RT fragment. RA Ostermeier C, Harrenga A, Ermler U, Michel H; RL Proc Natl Acad Sci U S A. 1997;94:10547-10553. CC The cytochrome c oxidase complex is responsible for coupling the CC oxidation of the reduced cytochrome c protein to the reduction of CC molecular oxygen to form water with the concomitant pumping of protons CC out of the cell. This complex is the type found in mitochondria and CC prokaryotes which utilize mitochondrial-type aerobic respiration. The CC complex in Bacilli [1] is somewhat different but included here and CC carrys the gene symbols CtaD/CtaC. -- SN 1 ID Oxidase subunit I CoxA/CtaD/Cox1 DN Oxidase subunit I CoxA/CtaD/Cox1 RQ 1 EV IPR014241; TIGR02891; sufficient; -- SN 2 ID Oxidase subunit II, CoxB DN Oxidase subunit II, CoxB RQ 1 EV IPR014222; TIGR02866; sufficient; -- SN 3 ID Oxidase subunit III, CoxC DN Oxidase subunit III, CoxC RQ 1 EV IPR024791; PTHR11403; sufficient; -- SN 4 ID Oxidase subunit IV, CoxD DN Oxidase subunit IV, CoxD RQ 0 EV IPR011743; TIGR02229; sufficient; EV IPR005171; PF03626; sufficient; -- SN 5 ID Protoheme IX farnesyltransferase, CtaB/Cox10 DN Protoheme IX farnesyltransferase, CtaB/Cox10 RQ 0 EV IPR006369; TIGR01473; sufficient; -- SN 6 ID Assembly protein CoxG/CtaG/Cox11 DN Assembly protein CoxG/CtaG/Cox11 RQ 0 EV IPR007533; PF04442; sufficient; -- SN 7 ID Assembly protein CoxW/CtaA/Cox15 DN Assembly protein CoxW/CtaA/Cox15 RQ 0 EV IPR003780; PF02628; sufficient; // AC GenProp0615 DE Cytochrome c based oxygen reduction and quinone re-oxidation TP METAPATH AU Haft DH TH 0 CC Mitochondria and many aerobic bacteria utilize cytochrome c as a mobile CC electron carrier to couple the processes of oxygen reduction to water CC and quinone re-oxidation. These two processes occur on two separate CC complexes, cytochrome c oxidase and cytochrome c reductase, CC respectively. Both of these processes also result in the pumping of CC protons across the cell membrane to generate the proton gradient CC necessary for ATP generation. -- SN 1 ID A cytochrome c oxidase DN A cytochrome c oxidase RQ 1 EV GenProp0483; EV GenProp0614; -- SN 2 ID A cytochrome c reductase DN A cytochrome c reductase RQ 1 EV GenProp0613; // AC GenProp0616 DE Single complex oxygen reduction and quinone re-oxidation TP METAPATH AU Haft DH TH 0 CC Many aerobic bacteria have complexes for the reduction of oxygen that CC are independent of cytochrome c (as found in mitochondria). These CC complexes carry out the conversion of oxygen to water, the oxidation of CC reduced quinones and the pumping of protons to generate the proton CC gradient for ATP generateion. Examples include the cytochrome bd CC complex and the cytochrome bo complex. -- SN 1 ID Single complex cytochrome (quinone) oxidase DN Single complex cytochrome (quinone) oxidase RQ 1 EV GenProp0617; EV GenProp0618; EV GenProp0620; // AC GenProp0617 DE Cytochrome (quinone) oxidase, bd type TP SYSTEM AU Haft DH TH 0 RN [1] RM 14749831 RT The strict anaerobe Bacteroides fragilis grows in and benefits from RT nanomolar concentrations of oxygen. RA Baughn AD, Malamy MH; RL Nature. 2004;427:441-444. RN [2] RM 16299377 RT Mass spectrometric analysis of the ubiquinol-binding site in cytochrome RT bd from Escherichia coli. RA Matsumoto Y, Murai M, Fujita D, Sakamoto K, Miyoshi H, Yoshida M, Mogi RA T; RL J Biol Chem. 2006;281:1905-1912. RN [3] RM 15474037 RT Interaction of the bacterial terminal oxidase cytochrome bd with nitric RT oxide. RA Borisov VB, Forte E, Konstantinov AA, Poole RK, Sarti P, Giuffrè A; RL FEBS Lett. 2004;576:201-204. CC The cytochrome bd complex is a quinol oxidase, oxygen reductase. CC Usually this complex functions to couple the reduced quinone pool to CC the oxygen terminal electron acceptor in aerobic respiration. It has CC been reported that certain anaerobes or microaerophiles may utilize CC this system to reduce the amount of oxygen present in their local CC environment [1]. The complex is composed of two subunits: Subunit I CC (CydA) contains the quinone binding site [2] and is also a component of CC the cytochrome b0 complex. Subunit II (CydB) contains the binding site CC for heme b558. Additionally, the complex contains two other hemes, CC b595 and d which make up the oxygen reduction site [3]. -- SN 1 ID Subunit I, CydA DN Cytochrome ubiquinol oxidase subunit 1 RQ 1 EV IPR002585; PF01654; sufficient; -- SN 2 ID Subunit II, CydB DN Cytochrome ubiquinol oxidase subunit 2 RQ 1 EV IPR003317; PF02322; sufficient; EV IPR003317; TIGR00203; sufficient; -- SN 3 ID Transporter for assembly, CydC DN Transporter for assembly, CydC RQ 0 EV IPR014223; TIGR02868; sufficient; -- SN 4 ID Transporter for assembly, CydD DN Transporter for assembly, CydD RQ 0 EV IPR014216; TIGR02857; sufficient; -- SN 5 ID Cyd operon protein YbgT (Proteobacterial) DN Cyd operon protein YbgT (Proteobacterial) RQ 0 EV IPR011724; TIGR02106; sufficient; // AC GenProp0618 DE Cytochrome (quinone) oxidase, bo type TP SYSTEM AU Haft DH TH 1 RN [1] RM 2162835 RT The sequence of the cyo operon indicates substantial structural RT similarities between the cytochrome o ubiquinol oxidase of Escherichia RT coli and the aa3-type family of cytochrome c oxidases. RA Chepuri V, Lemieux L, Au DC, Gennis RB; RL J Biol Chem. 1990;265:11185-11192. CC The cytochrome bo complex is a quinol oxidase, oxygen reductase which CC functions in the electron transfer chain of aerobic respiration in CC bacteria. The bo complex contains two heme b (protoheme IX) molecules CC designated b562 and b595 as well as an active site copper atom. This CC complex is structurally analagous to the aa3-type cytochrome c oxidases CC [1] which contains cytochromes a and copper. -- SN 1 ID Subunit II, CyoA DN Cytochrome o ubiquinol oxidase subunit II RQ 1 EV IPR006333; TIGR01433; sufficient; -- SN 2 ID Subunit I, CyoB DN Cytochrome o ubiquinol oxidase, subunit I RQ 1 EV IPR014207; TIGR02843; sufficient; -- SN 3 ID Subunit III, CyoC DN Cytochrome o ubiquinol oxidase, subunit III RQ 1 EV IPR014206; TIGR02842; sufficient; -- SN 4 ID Subunit IV, CyoD DN Cytochrome o ubiquinol oxidase subunit IV RQ 1 EV IPR014210; TIGR02847; sufficient; -- SN 5 ID Protoheme IX farnesyltransferase, CyoE DN Protohaem IX farnesyltransferase RQ 1 EV IPR006369; TIGR01473; sufficient; // AC GenProp0620 DE Cytochrome (quinone) oxidase, aa3 type, QoxABCD TP SYSTEM AU Haft DH TH 0 RN [1] RM 7575098 RT Properties of the menaquinol oxidase (Qox) and of qox deletion mutants RT of Bacillus subtilis. RA Lemma E, Simon J, Schägger H, Kröger A; RL Arch Microbiol. 1995;163:432-438. CC The cytochrome (quinone) oxidase complex QoxABCD is closely related CC to the bacillus cytochrome c oxidase of the caa3 type. This complex CC couples the reduction of oxidized quinones with the reduction of CC molecular oxygen to water and the pumping of protons. -- SN 1 ID Subunit II, QoxA DN Quinol oxidase subunit II RQ 1 EV IPR006332; TIGR01432; sufficient; -- SN 2 ID Subunit I, QoxB DN Quinol oxidase subunit I RQ 1 EV IPR014233; TIGR02882; sufficient; -- SN 3 ID Subunit III, QoxC DN Quinol oxidase subunit III RQ 1 EV IPR014246; TIGR02897; sufficient; -- SN 4 ID Subunit IV, QoxD DN Quinol oxidase subunit IV RQ 1 EV IPR014250; TIGR02901; sufficient; // AC GenProp0624 DE Sulfite reductase complex, Salmonella/Clostridium type TP PATHWAY AU Haft DH TH 0 RN [1] RM 2656637 RT Characterization of anaerobic sulfite reduction by Salmonella RT typhimurium and purification of the anaerobically induced sulfite RT reductase. RA Hallenbeck PC, Clark MA, Barrett EL; RL J Bacteriol. 1989;171:3008-3015. CC Several different types of enzyme complex are designated sulfite CC reductase, and each may resemble some enzyme with differing specificity CC more closely than they resemble each other. This property represents a CC bacterial three subunit type as found in several species of Clostridium CC and in Salmonella. In Salmonella, it is described as a CC siroheme-containing sulfite reductase, reversibly inhibited by oxygen, CC that can produce H2S from sulfite under anaerobic conditions when CC provided with a fermentable sugar. -- SN 1 ID Sulfite reductase, subunit A DN Sulfite reductase, subunit A RQ 1 EV IPR014259; TIGR02910; sufficient; -- SN 2 ID Sulfite reductase, subunit B DN Sulfite reductase, subunit B RQ 1 EV IPR014260; TIGR02911; sufficient; -- SN 3 ID Sulfite reductase, subunit C DN Sulfite reductase, subunit C RQ 1 EV IPR014261; TIGR02912; sufficient; // AC GenProp0626 DE Protein sorting system, sortase type, LPXTG/SrtA class TP SYSTEM AU Haft DH TH 0 CC This property describes the common subtype of the sortase system for CC targeting cell wall proteins in the Firmicutes by recognition of the CC LPXTG C-terminal motif. The presence of one or more sortases and their CC target sequences should be universal in Gram-positive organisms with CC cell walls. Sortase is a transpeptidase; sortases belonging to this CC Genome Property resemble SrtA, and the sorting signal generally CC resembles LPXTG. Several SrtA paralogs can be found in some genomes, as CC well as the substantially different SrtB and other families of sortase CC and their cognate sequences. -- SN 1 ID LPXTG-like C-terminal region DN LPXTG cell wall anchor domain RQ 1 EV IPR019931; TIGR01167; sufficient; -- SN 2 ID Sortase (transpeptidase) DN Sortase family RQ 1 EV IPR005754; TIGR01076; sufficient; // AC GenProp0629 DE A1/A0 ATPase TP SYSTEM AU Haft DH TH 0 RN [1] RM 8702544 RT Subunit structure and organization of the genes of the A1A0 ATPase from RT the Archaeon Methanosarcina mazei Gö1. RA Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Müller V; RL J Biol Chem. 1996;271:18843-18852. RN [2] RM 12782317 RT Defined subcomplexes of the A1 ATPase from the archaeon Methanosarcina RT mazei Gö1: biochemical properties and redox regulation. RA Lemker T, Grüber G, Schmid R, Müller V; RL FEBS Lett. 2003;544:206-209. RN [3] RM 14988401 RT Three-dimensional organization of the archaeal A1-ATPase from RT Methanosarcina mazei Gö1. RA Coskun U, Radermacher M, Müller V, Ruiz T, Grüber G; RL J Biol Chem. 2004;279:22759-22764. RN [4] RM 10340845 RT Structure and function of the A1A0-ATPases from methanogenic Archaea. RA Müller V, Ruppert C, Lemker T; RL J Bioenerg Biomembr. 1999;31:15-27. RN [5] RM 9642200 RT The A1A0 ATPase from Methanosarcina mazei: cloning of the 5' end of the RT aha operon encoding the membrane domain and expression of the RT proteolipid in a membrane-bound form in Escherichia coli. RA Ruppert C, Wimmers S, Lemker T, Müller V; RL J Bacteriol. 1998;180:3448-3452. CC This ATP synthase is the archaebacterial version of the F1/F0 ATP CC synthase found in bacteria in the sense that it functions in the ATP CC synthetic direction [1], although it also has similarities to the V1/V0 CC (V-type, vacuolar) ATPase in eucarya which hydrolyzes ATP in order to CC acidify cellular compartments. -- SN 1 ID A1 stalk complex, A subunit DN ATP synthase alpha chain, archaea RQ 1 EV IPR005726; TIGR01043; sufficient; -- SN 2 ID A1 stalk complex, B subunit DN ATPase, A1 complex, beta subunit RQ 1 EV IPR005724; TIGR01041; sufficient; -- SN 3 ID A1 stalk complex, C subunit DN ATPase, V0 complex, c subunit RQ 1 EV IPR014272; TIGR02923; sufficient; -- SN 4 ID A1 stalk complex, D subunit DN ATPase, V1 complex, subunit D RQ 1 EV IPR002699; TIGR00309; sufficient; -- SN 5 ID A1 stalk complex, E subunit DN ATPase, V1/A1 complex, subunit E RQ 1 EV IPR002842; PF01991; sufficient; -- SN 6 ID A1 stalk complex, F subunit DN ATPase, V1 complex, subunit F RQ 1 EV IPR008218; PF01990; sufficient; -- SN 8 ID H subunit DN ATPase, A1A0, subunit H RQ 0 EV IPR014275; TIGR02926; sufficient; // AC GenProp0630 DE 2-oxoglutarate dehydrogenase system TP SYSTEM AU Haft DH TH 0 RN [1] RM 16321804 RT Alpha-ketoglutarate dehydrogenase: a target and generator of RT oxidative stress. RA Tretter L, Adam-Vizi V; RL Philos Trans R Soc Lond B Biol Sci. 2005;360:2335-2345. CC This enzyme system utilizes three components E1 (thiamine CC pyrophosphate-binding subunit, SucA), E2 (dihydrolipoamide CC succinyltransferase, SucB) and E3 (dihydrolipoamide dehydrogenase, CC LpdA) for the interconversion of 2-oxoglutarate (alpha-ketoglutarate) CC and succinyl-CoA. In addition to lipoate and thiamine pyrophosphate, CC FAD is also involved. In the course of the reaction CO2 is released CC and one molecule of NAD+ is converted to NADH. This reaction is an CC essential component of the TCA (Krebs) cycle [1]. -- SN 1 ID Thiamine pyrophosphate-binding subunit, SucA (E1) RQ 1 EV IPR011603; TIGR00239; sufficient; -- SN 2 ID Dihydrolipoamide succinyltransferase, SucB (E2) RQ 1 EV IPR006255; TIGR01347; sufficient; -- SN 3 ID Dihydrolipoamide dehydrogenase, LpdA (E3) RQ 1 EV IPR006258; TIGR01350; sufficient; // AC GenProp0631 DE Nitrogenase, Fe-only TP SYSTEM AU Haft DH TH 0 RN [1] RM 25139995 RT Reconstruction and minimal gene requirements for the alternative RT iron-only nitrogenase in Escherichia coli. RA Yang J, Xie X, Wang X, Dixon R, Wang YP; RL Proc Natl Acad Sci U S A. 2014;111:E3718-E3725. CC There are three homologous types of nitrogenase; the common CC molybdenum-containing, the alternative vanadium (V)-containing, and the CC alterantive iron (Fe)-only. This Genome Property represents the Fe-only CC nitrogenase system (which acts in nitrogen fixation) and its accessory CC proteins. Fe-only nitrogenase is composed of 2 copies each of an alpha, CC beta and delta subunit, forming a hexameric structure. The exact CC function of the accessory protein included in this property is not yet CC known [1]. -- SN 1 ID Fe-only nitrogenase, alpha subunit RQ 1 EV IPR011290; TIGR01861; sufficient; -- SN 2 ID Fe-only nitrogenase, beta subunit RQ 1 EV IPR014280; TIGR02931; sufficient; -- SN 3 ID Fe-only nitrogenase, delta subunit RQ 1 EV IPR014278; TIGR02929; sufficient; -- SN 4 ID Fe-only nitrogenase, anfO/anf1 accessory protein RQ 0 EV IPR014287; TIGR02940; sufficient; // AC GenProp0632 DE Nitrogenase, V-containing TP SYSTEM AU Haft DH TH 0 RN [1] RM 2743980 RT Structural genes for the vanadium nitrogenase from Azotobacter RT chroococcum. RA Robson RL, Woodley PR, Pau RN, Eady RR; RL EMBO J. 1989;8:1217-1224. CC There are three homologous types of nitrogenase; the common CC molybdenum-containing, the alternative vanadium (V)-containing, and the CC alterantive iron (Fe)-only. This Genome Property represents the CC V-containing nitrogenase, which acts in nitrogen fixation. V-containing CC nitrogenase is composed of three subunits encoded by three genes within CC an operon: subunit alpha (vnfD), subunit beta (vnfK) and subunit delta CC (vnfG) [1]. -- SN 1 ID V-containing nitrogenase, alpha subunit RQ 1 EV IPR010142; TIGR01860; sufficient; -- SN 2 ID V-containing nitrogenase, beta subunit RQ 1 EV IPR014281; TIGR02932; sufficient; -- SN 3 ID V-containing nitrogenase, delta subunit RQ 1 EV IPR014279; TIGR02930; sufficient; // AC GenProp0633 DE Nitrogenase, Mo-containing TP SYSTEM AU Haft DH TH 0 RN [1] RM 25139995 RT Reconstruction and minimal gene requirements for the alternative RT iron-only nitrogenase in Escherichia coli. RA Yang J, Xie X, Wang X, Dixon R, Wang YP; RL Proc Natl Acad Sci U S A. 2014;111:E3718-E3725. CC There are three distict types of nitrogenase system that exist in CC bacteria and archea, acting in nitrogen fixation. The most common CC type of nitrogenase contains molybdenum as well as iron (MoFe CC nitrogenase). Alternative nitrogenases with homologous alpha and CC beta subunits, but somewhat different sets of accessory proteins, CC use vanadium and iron, or just iron. All species studied so far CC with one or more alternative nitrogenases, also contain a MoFe CC nitrogenase. This genome property consists of the structural CC subunits of the MoFe nitrogenase [1]. -- SN 1 ID Nitrogenase, molybdenum-iron protein, alpha subunit RQ 1 EV IPR005972; TIGR01282; sufficient; -- SN 2 ID Nitrogenase, molybdenum-iron protein, beta subunit RQ 1 EV IPR005976; TIGR01286; sufficient; // AC GenProp0634 DE Sigma-54 (RpoN) systems TP SYSTEM AU Haft DH TH 0 RN [1] RM 15231786 RT Helicobacter pylori FlgR is an enhancer-independent activator of RT sigma54-RNA polymerase holoenzyme. RA Brahmachary P, Dashti MG, Olson JW, Hoover TR; RL J Bacteriol. 2004;186:4535-4542. RN [2] RM 7934866 RT In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma RT N). RA Merrick MJ; RL Mol Microbiol. 1993;10:903-909. RN [3] RM 10894718 RT The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription RT factor. RA Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD; RL J Bacteriol. 2000;182:4129-4136. RN [4] RM 11528004 RT Metabolic context and possible physiological themes of RT sigma(54)-dependent genes in Escherichia coli. RA Reitzer L, Schneider BL; RL Microbiol Mol Biol Rev. 2001;65:422-44, table of contents. CC A sigma factor is a DNA-binding protein that binds to the DNA-directed CC RNA polymerase core, to produce the holoenzyme capable of initiating CC transcription at specific sites. Different sigma factors act in CC vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. CC This model represents the clade of sigma factors called sigma-54, or CC RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is CC responsible for enhancer-dependent transcription, and its presence CC characteristically is associated with varied panels of activators, most CC of which are enhancer-binding proteins [1]. RpoN may be responsible for CC transcription of nitrogen fixation genes, flagellins, pilins, etc., and CC synonyms for the gene symbol rpoN, such as ntrA, reflect these observations. -- SN 1 ID Sigma-54 interacting protein, activator DN RNA polymerase sigma factor 54 interaction domain RQ 1 EV IPR002078; PF00158; sufficient; -- SN 2 ID Sigma-54 (RpoN) DN RNA polymerase sigma factor 54 RQ 1 EV IPR000394; TIGR02395; sufficient; // AC GenProp0636 DE Respiratory nitrate reductase TP SYSTEM AU Haft DH TH 0 CC The nitrate reductase enzyme complex allows bacteria to use nitrate as CC an electron acceptor during anaerobic growth. -- SN 1 ID Nitrate reductase molybdenum cofactor assembly chaperone DN Nitrate reductase molybdenum cofactor assembly chaperone RQ 1 EV IPR003765; TIGR00684; sufficient; -- SN 2 ID Respiratory nitrate reductase, alpha subunit DN Respiratory nitrate reductase, alpha subunit RQ 1 EV IPR006468; TIGR01580; sufficient; -- SN 3 ID Respiratory nitrate reductase, beta subunit DN Respiratory nitrate reductase, beta subunit RQ 1 EV IPR006547; TIGR01660; sufficient; -- SN 4 ID Respiratory nitrate reductase, gamma subunit DN Respiratory nitrate reductase, gamma subunit RQ 1 EV IPR003816; TIGR00351; sufficient; // AC GenProp0637 DE Anaerobic dimethyl sulfoxide reductase TP SYSTEM AU Haft DH TH 0 RN [1] RM 16221580 RT Microbial dimethylsulfoxide and trimethylamine-N-oxide respiration. RA McCrindle SL, Kappler U, McEwan AG; RL Adv Microb Physiol. 2005;50:147-198. RN [2] RM 27656177 RT The Two Sets of DMSO Respiratory Systems of Shewanella piezotolerans RT WP3 Are Involved in Deep Sea Environmental Adaptation. RA Xiong L, Jian H, Zhang Y, Xiao X; RL Front Microbiol. 2016;7:1418. CC This property describes the dimethyl sulfoxide (DMSO) reductase complex, CC which reduces DMSO to DMS (dimethyl sulfide). The complex consists of three CC functional proteins encoded by the DmsABC operon. DmsA is a molybdopterin CC cofactor-containing subunit, DmsB is an ion-sulfur subunit, and DmsC is a CC NapC-like integral membrane anchor, that anchors the complex to the CC periplasmic side of the inner membrane [1,2]. -- SN 1 ID Anaerobic dimethylsulfoxide reductase, chain A DN Anaerobic dimethylsulfoxide reductase, chain A/dmsA RQ 1 EV IPR011888; TIGR02166; sufficient; -- SN 2 ID Anaerobic dimethylsulfoxide reductase, chain B DN Anaerobic dimethylsulfoxide reductase, chain B/dmsB RQ 1 EV IPR014297; TIGR02951; sufficient; -- SN 3 ID Anaerobic dimethylsulfoxide reductase, chain C DN Anaerobic dimethylsulfoxide reductase, chain C/dmsC RQ 1 EV IPR007059; PF04976; sufficient; // AC GenProp0639 DE Arginine degradation via citrulline, ATP-generating TP PATHWAY AU Haft DH TH 0 RN [1] RM 15006749 RT Characterization of the arginine deiminase operon of Streptococcus RT rattus FA-1. RA Griswold A, Chen YY, Snyder JA, Burne RA; RL Appl Environ Microbiol. 2004;70:1321-1327. CC Arginine may be degraded to generate ammonia, ATP and ornithine via CC citrulline and carbamoyl phosphate. The ornithine may be further CC processed via putrescine. -- SN 1 ID Arginine deiminase DN Arginine deiminase RQ 1 EV IPR003876; TIGR01078; sufficient; -- SN 2 ID Ornithine carbamoyltransferase DN Ornithine carbamoyltransferase RQ 1 EV IPR002292; TIGR00658; sufficient; -- SN 3 ID Carbamate kinase DN Carbamate kinase RQ 0 EV IPR003964; TIGR00746; sufficient; -- SN 4 ID Arginine-ornithine antiporter DN Arginine-ornithine antiporter RQ 0 EV IPR022461; TIGR03810; // AC GenProp0640 DE Xanthine dehydrogenase TP SYSTEM AU Haft DH TH 0 RN [1] RM 16597619 RT Rhodobacter capsulatus XdhC is involved in molybdenum cofactor binding RT and insertion into xanthine dehydrogenase. RA Neumann M, Schulte M, Jünemann N, Stöcklein W, Leimkühler S; RL J Biol Chem. 2006;281:15701-15708. CC Xanthine dehydrogenase is a molydbopterin-containing enzyme. It CC converts xanthine, from the purine pool, to urate, which is CC subsequently degraded. In bacteria, the enzyme usually is encoded as a CC small subunit, XdhA, that contains FAD and 2Fe2S cofactors and a large CC subunit, XdhB, that contains the molybdopterin cofactor. The accessory CC protein XdhC is usually but not always encoded next to the XdhAB gene CC pair. -- SN 1 ID Xanthine dehydrogenase, 2Fe2S/FAD subunit DN Xanthine dehydrogenase, 2Fe2S/FAD subunit RQ 1 EV IPR014307; TIGR02963; sufficient; -- SN 2 ID Xanthine dehydrogenase, molybdopterin subunit DN Xanthine dehydrogenase, molybdopterin subunit RQ 1 EV IPR014309; TIGR02965; sufficient; -- SN 3 ID Xanthine dehydrogenase accessory protein XdhC DN Xanthine dehydrogenase accessory protein XdhC RQ 1 EV IPR014308; TIGR02964; sufficient; // AC GenProp0641 DE Spermidine biosynthesis from putrescine and S-adenosylmethionine TP PATHWAY AU Haft DH TH 0 CC Spermine, spermidine and putrescine are a family of polyamines CC (positively charged organic polycations) that are important for CC cellular growth, most likely by stabilizing polynucleotides and CC membranes. Spermidine is derived from putrescine and the CC 4-aminobutyrate moiety of methionine (indirectly via S-adenosyl CC methionine). Spermine is synthesized by a second addition of CC 4-aminobutyrate to spermidine, and is more commonly found in CC eukaryotes. -- SN 1 ID S-adenosylmethionine decarboxylase DN S-adenosylmethionine decarboxylase/speD RQ 1 EV IPR003826; PF02675; sufficient; -- SN 2 ID Spermidine synthase DN Spermidine synthase/speE RQ 1 EV IPR001045; TIGR00417; sufficient; // AC GenProp0642 DE Putrescine biosynthesis from arginine utilizing agmatinase TP PATHWAY AU Haft DH TH 0 CC L-arginine can be converted to the polyamine putrescine via this CC pathway, either for the purposes of arginine catabolism or for the CC biosynthesis of spermidine. This version of the pathway utilizes CC agmatinase while an alternative pathway does the same reaction in CC two steps via carbamoylputrescine. -- SN 1 ID Arginine decarboxylase DN Arginine decarboxylase/SpeA RQ 1 EV IPR002985; TIGR01273; sufficient; -- SN 2 ID Agmatinase DN Agmatinase/SpeB RQ 1 EV IPR005925; TIGR01230; sufficient; // AC GenProp0643 DE Putrescine biosynthesis from arginine via ornithine TP METAPATH AU Haft DH TH 0 CC An alternative to the SpeAB pathway to synthesise putrescine from arginine CC via agmatine (GenProp0642) involves ornithine decarboxylase (SpeC or SpeF). CC Ornithine can be generated via several amino acids including glutamate CC (GenProp0118) and possibly proline as well as the pathways from CC arginine represented here. A pathway found only in eukaryotes for the CC biosynthesis of creatine also incidentally generates ornithine (and CC guanidinoacetate) from arginine and glycine. -- SN 1 ID Ornithine decarboxylase DN Ornithine decarboxylase SpeC/SpeF RQ 1 EV IPR027568; TIGR04301; sufficient; -- SN 2 ID Conversion of arginine to ornithine DN Arginase/Conversion of arginine to ornithine RQ 1 EV GenProp0639; EV IPR014033; TIGR01229; sufficient; // AC GenProp0644 DE Putrescine biosynthesis from glutamate via ornithine TP METAPATH AU Haft DH TH 0 CC Putrescine may be generated from ornithine by ornithine decarboxylase. CC Orninthine may in turn come from glutamate (GenProp0118) or arginine CC utilizing arginase or via citrulline (SpeAB, GenProp0639). This CC Property detects the potential for the biosynthesis of putrescine from CC glutamate via ornithine. -- SN 1 ID Ornithine decarboxylase DN Ornithine decarboxylase SpeF RQ 1 EV IPR027568; TIGR04301; -- SN 2 ID Conversion of glutamate to ornithine DN Conversion of glutamate to ornithine RQ 1 EV GenProp0118; // AC GenProp0645 DE Putrescine biosynthesis TP METAPATH AU Haft DH TH 0 CC The polyamine putrescine is both the precursor of the essential growth CC factor spermidine as well as an intermediate for the degradation of CC arginine and ornithine (and those compounds which may be converted to CC ornithine). Putrescine may be generated from glutamate and arginine CC via a number of pathways. -- SN 1 ID Putrescine biosynthesis pathways DN Putrescine biosynthesis pathways RQ 1 EV GenProp0642; EV GenProp0643; EV GenProp0644; EV GenProp1733; // AC GenProp0648 DE Phage shock protein regulon TP SYSTEM AU Haft DH TH 0 RN [1] RM 1712397 RT Characterization and sequence of the Escherichia coli stress-induced RT psp operon. RA Brissette JL, Weiner L, Ripmaster TL, Model P; RL J Mol Biol. 1991;220:35-48. RN [2] RM 8606168 RT Identification, nucleotide sequence, and characterization of PspF, the RT transcriptional activator of the Escherichia coli stress-induced psp RT operon. RA Jovanovic G, Weiner L, Model P; RL J Bacteriol. 1996;178:1936-1945. RN [3] RM 15485810 RT Identification of a new member of the phage shock protein response in RT Escherichia coli, the phage shock protein G (PspG). RA Lloyd LJ, Jones SE, Jovanovic G, Gyaneshwar P, Rolfe MD, Thompson A, RA Hinton JC, Buck M; RL J Biol Chem. 2004;279:55707-55714. RN [4] RM 16709570 RT Induction and function of the phage shock protein extracytoplasmic RT stress response in Escherichia coli. RA Jovanovic G, Lloyd LJ, Stumpf MP, Mayhew AJ, Buck M; RL J Biol Chem. 2006;281:21147-21161. RN [5] RM 16707685 RT 6S RNA regulation of pspF transcription leads to altered cell survival RT at high pH. RA Trotochaud AE, Wassarman KM; RL J Bacteriol. 2006;188:3936-3943. CC This property describes a regulon present in E. coli and a number of CC other species induced by various stresses including osmotic shock, CC ethanol, heat, and expression of various secretins, as occurs with CC infection by certain filamentous phage. A common thread to these CC stressors may be compromise of the inner membrane and decrease of the CC protonmotive force. Most proteins of the regulon occur in a single CC operon, but at least one member, pspG, is located elsewhere in most CC genomes. The signature genes of the the phage shock regulon are the CC sigma-54-dependent positive regulator PspF, PspA which binds to and CC inhibits PspF, and PspB and PspC which act together as both regulatory CC and effector proteins of the phage shock regulon. PspG occurs in most CC but not all phage shock-positive genomes, while PspD and PspE are found CC only in a minority of phage shock operons. -- SN 1 ID Phage shock protein PspA DN Phage shock protein PspA RQ 1 EV IPR014319; TIGR02977; sufficient; TG GO:0006950; -- SN 2 ID Phage shock protein PspB DN Phage shock protein PspB RQ 1 EV IPR009554; TIGR02976; sufficient; TG GO:0006950; -- SN 3 ID Phage shock protein PspC DN Phage shock protein PspC RQ 1 EV IPR014320; TIGR02978; sufficient; TG GO:0006950; -- SN 4 ID Phage shock protein PspD DN Phage shock protein PspD RQ 0 EV IPR014321; TIGR02979; sufficient; TG GO:0006950; -- SN 5 ID Rhodanese PspE DN Phage shock protein PspE RQ 0 EV IPR014323; TIGR02981; sufficient; TG GO:0006950; -- SN 6 ID Signa-54-dependent activagtor PspF DN Transcription activator PspF RQ 1 EV IPR014317; TIGR02974; sufficient; TG GO:0006950; -- SN 7 ID Phage shock protein PspG (YjbO) DN Phage shock protein, PspG RQ 0 EV IPR014318; TIGR02975; sufficient; TG GO:0006950; // AC GenProp0649 DE Heterocyst-related ABC exporter DevBCA TP SYSTEM AU Haft DH TH 0 RN [1] RM 11371545 RT NtcA-dependent expression of the devBCA operon, encoding a RT heterocyst-specific ATP-binding cassette transporter in Anabaena spp. RA Fiedler G, Muro-Pastor AM, Flores E, Maldener I; RL J Bacteriol. 2001;183:3795-3799. CC Most genomes in which the set of three tandemly-encoded genes for the CC ATP-binding cassette (ABC) exporter complex similar to the DevBCA CC complex of Anabaena are Cyanobacteria capable of heterocyst formation. CC Roughly every tenth cell in colonies of certain species of CC cyanobacteria differentiate into heterocysts under conditions of CC nitrogen starvation, with a loss of CO2 fixation, reduction of O2 CC permeability, and development of the ability to fix nitrogen. The CC DevBCA transporter most likely acts by exporting a glycolipid (or an CC enzyme) specific to heterocyst formation. -- SN 1 ID ABC exporter ATP-binding subunit, DevA family DN ABC exporter ATP-binding subunit, DevA family RQ 1 EV IPR014324; TIGR02982; sufficient; -- SN 2 ID ABC exporter membrane fusion protein, DevB family DN ABC exporter membrane fusion protein, DevB family RQ 1 EV IPR014315; TIGR02971; sufficient; -- SN 3 ID ABC exporter, DevC family protein DN ABC exporter, DevC family protein RQ 1 EV IPR005891; TIGR01185; sufficient; // AC GenProp0651 DE Ectoine ABC transporter EhuABCD TP SYSTEM AU Haft DH TH 0 RN [1] RM 15687193 RT Ectoine-induced proteins in Sinorhizobium meliloti include an Ectoine RT ABC-type transporter involved in osmoprotection and ectoine catabolism. RA Jebbar M, Sohn-Bösser L, Bremer E, Bernard T, Blanco C; RL J Bacteriol. 2005;187:1293-1304. CC Ectoine, and its derivative hydroxyectoine, are nitrogen-containing CC compatible solutes that protect enzymes from the stress of high CC osmolarity. Bacteria may synthesize or import it, or both. This CC transporter was partially characterized in Sinorhizobium, where it is CC encoded along with genes for ectoine catabolism. All subunits are CC homologous to various amino acid transporter subunits. -- SN 1 ID Ectoine ABC transporter, ATP-binding protein DN Ectoine/hydroxyectoine ABC transporter, ATP-binding protein EhuA RQ 1 EV IPR014343; TIGR03005; sufficient; TG GO:0051470; -- SN 2 ID Ectoine ABC transporter, solute-binding protein DN Ectoine/hydroxyectoine ABC transporter solute-binding protein EhuB RQ 1 EV IPR014337; TIGR02995; sufficient; TG GO:0051470; -- SN 3 ID Ectoine ABC transporter, permease protein EhuC DN Ectoine/hydroxyectoine ABC transporter, permease protein EhuC RQ 1 EV IPR014342; TIGR03004; sufficient; TG GO:0051470; -- SN 4 ID Ectoine ABC transporter, permease protein EhuD DN Ectoine/hydroxyectoine ABC transporter, permease protein EhuD RQ 1 EV IPR014341; TIGR03003; sufficient; TG GO:0051470; // AC GenProp0652 DE Exopolysaccharide biosynthesis, exosortase A-associated TP SYSTEM AU Haft DH TH 0 RN [1] RM 16930487 RT Exopolysaccharide-associated protein sorting in environmental RT organisms: the PEP-CTERM/EpsH system. Application of a novel RT phylogenetic profiling heuristic. RA Haft DH, Paulsen IT, Ward N, Selengut JD; RL BMC Biol. 2006;4:29. CC At least 30 different bacterial species known so far have the CC PEP-CTERM/exosortase system believed to process proteins analogously to CC the LPXTG/sortase system. Genes associated with this processing are CC found among exopolysaccharide biosynthesis genes, suggesting that CC PEP-CTERM proteins are part of this exopolysaccharide system, and CC therefore are likely to be transported across the outer membrane. This CC property represents a panel of exopolysaccharide biosynthesis genes CC where each belongs to a subfamily that marks its host gene as carrying CC the PEP-CTERM/exopolysaccharide system. -- SN 1 ID ATPase, exosortase type 1 region DN ATPase, exosortase type 1 region RQ 1 EV IPR017466; TIGR03015; sufficient; -- SN 2 ID Exosortase EpsH, type 1 DN Exosortase EpsH, type 1 RQ 1 EV IPR013426; TIGR02602; EV IPR017540; TIGR03109; sufficient; -- SN 3 ID EpsI DN EpsI RQ 0 EV IPR014263; TIGR02914; -- SN 4 ID Hydrolases (1 and 2), exosortase system type 1 associated DN Hydrolases (1 and 2), exosortase system type 1 associated RQ 0 EV IPR017531; TIGR03100; sufficient; EV IPR017532; TIGR03101; sufficient; -- SN 5 ID Uncharacterized protein, EpsL-related DN Uncharacterized protein, EpsL-related RQ 1 EV IPR017467; TIGR03016; sufficient; -- SN 6 ID Acyl-CoA ligase, PEP-CTERM/EpsH1 associated DN Acyl-CoA ligase, PEP-CTERM/EpsH1 associated RQ 0 EV IPR017529; TIGR03098; sufficient; -- SN 7 ID Clustered asparagine synthase homolog DN Clustered asparagine synthase homolog RQ 0 EV IPR006426; TIGR01536; EV IPR017539; TIGR03108; sufficient; -- SN 8 ID Putative transmembrane histidine kinase, PEP-CTERM system DN Putative transmembrane histidine kinase, PEP-CTERM system RQ 1 EV IPR014265; TIGR02916; sufficient; -- SN 9 ID Putative response regulator, PEP-CTERM system DN Putative response regulator, PEP-CTERM system RQ 1 EV IPR014264; TIGR02915; sufficient; -- SN 10 ID TPR repeat putative lipoprotein, PEP-CTERM system DN TPR repeat putative lipoprotein, PEP-CTERM system RQ 1 EV IPR014266; TIGR02917; sufficient; -- SN 11 ID Decarboxylase, exosortase system type 1 associated DN Decarboxylase, exosortase system type 1 associated RQ 0 EV IPR017530; TIGR03099; sufficient; -- SN 12 ID Polysaccharide deacetylase DN Polysaccharide deacetylase RQ 1 EV IPR014344; TIGR03006; sufficient; -- SN 13 ID Polysaccharide export protein DN Polysaccharide export protein RQ 1 EV IPR017477; TIGR03027; sufficient; -- SN 14 ID FemAB-related protein DN FemAB-related protein RQ 1 EV IPR017469; TIGR03019; sufficient; -- SN 15 ID Sugar transferase DN Sugar transferase RQ 1 EV IPR017464; TIGR03013; sufficient; -- SN 16 ID Sugar transferase, PEP-CTERM/EpsH1-associated DN Sugar transferase, PEP-CTERM/EpsH1-associated RQ 0 EV IPR017521; TIGR03087; sufficient; -- SN 17 ID Sugar transferase, PEP-CTERM/EpsH1-associated DN Sugar transferase, PEP-CTERM/EpsH1-associated RQ 0 EV IPR017522; TIGR03088; sufficient; -- SN 18 ID Sugar transferase, PEP-CTERM/exosortase 1-associated DN Sugar transferase, PEP-CTERM/exosortase 1-associated RQ 0 EV IPR024004; TIGR04063; -- SN 21 ID Probable O-glycosylation ligase DN Probable O-glycosylation ligase RQ 0 EV IPR017528; TIGR03097; sufficient; -- SN 22 ID Tryosine autokinase DN Tryosine autokinase RQ 1 EV IPR031045; TIGR03018; sufficient; -- SN 23 ID Polysaccharide chain length determinant DN Polysaccharide chain length determinant RQ 1 EV IPR014345; TIGR03007; sufficient; // AC GenProp0653 DE Ectoine catabolism TP PATHWAY AU Haft DH TH 0 RN [1] RM 15687193 RT Ectoine-induced proteins in Sinorhizobium meliloti include an Ectoine RT ABC-type transporter involved in osmoprotection and ectoine catabolism. RA Jebbar M, Sohn-Bösser L, Bremer E, Bernard T, Blanco C; RL J Bacteriol. 2005;187:1293-1304. CC This property describes a set of five genes, found together in an CC operon in a number of bacteria, for ectoine catabolism. In CC Sinorhizobium meliloti, where the system is partially characterized, CC these genes occur together with four genes for an ectoine/hydroxyectoine CC ABC transporter for ectoine uptake. -- SN 1 ID Ectoine utilization protein EutA DN Ectoine utilization protein EutA RQ 1 EV IPR014332; TIGR02990; sufficient; TG GO:0042400; -- SN 2 ID Ectoine utilization protein EutB DN Ectoine utilization protein EutB RQ 1 EV IPR014333; TIGR02991; sufficient; TG GO:0042400; -- SN 3 ID Ectoine utilization protein EutC DN Ectoine utilization protein EutC RQ 1 EV IPR014334; TIGR02992; sufficient; TG GO:0042400; -- SN 4 ID Ectoine utilization protein EutD DN Ectoine utilization protein EutD RQ 1 EV IPR014335; TIGR02993; sufficient; TG GO:0042400; -- SN 5 ID Ectoine utilization protein EutE DN Ectoine utilization protein EutE RQ 1 EV IPR014336; TIGR02994; sufficient; TG GO:0042400; // AC GenProp0654 DE Intracellular sulfur oxidation TP SYSTEM AU Haft DH TH 0 RN [1] RM 16387657 RT Mechanistic insights into sulfur relay by multiple sulfur mediators RT involved in thiouridine biosynthesis at tRNA wobble positions. RA Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T; RL Mol Cell. 2006;21:97-108. RN [2] RM 15687204 RT Novel genes of the dsr gene cluster and evidence for close interaction RT of Dsr proteins during sulfur oxidation in the phototrophic sulfur RT bacterium Allochromatium vinosum. RA Dahl C, Engels S, Pott-Sperling AS, Schulte A, Sander J, Lübbe Y, RA Deuster O, Brune DC; RL J Bacteriol. 2005;187:1392-1404. CC This system, usually associated with the dissimatory sulfite reductase CC (dsr) locus, includes proteins DsrE, DsrF, DshH, and DsrC, which are CC small, soluble proteins required for the oxidation of intracellular CC sulfur. -- SN 1 ID Putative dissimilatory sulfite reductase gamma subunit DN Putative dissimilatory sulfite reductase gamma subunit/DsrC RQ 0 EV IPR007453; TIGR03342; -- SN 2 ID DsrE protein DN DsrE protein RQ 1 EV IPR017463; TIGR03012; sufficient; -- SN 3 ID DsrF protein DN DsrF protein RQ 1 EV IPR017462; TIGR03010; sufficient; -- SN 4 ID DsrH protein DN DsrH protein RQ 1 EV IPR007215; TIGR03011; sufficient; // AC GenProp0655 DE Exopolysaccharide biosynthesis, exosortase B-associated TP SYSTEM AU Haft DH TH 0 RN [1] RM 12624205 RT Genes involved in the synthesis of the exopolysaccharide methanolan by RT the obligate methylotroph Methylobacillus sp strain 12S. RA Yoshida T, Ayabe Y, Yasunaga M, Usami Y, Habe H, Nojiri H, Omori T; RL Microbiology. 2003;149:431-444. RN [2] RM 16930487 RT Exopolysaccharide-associated protein sorting in environmental RT organisms: the PEP-CTERM/EpsH system. Application of a novel RT phylogenetic profiling heuristic. RA Haft DH, Paulsen IT, Ward N, Selengut JD; RL BMC Biol. 2006;4:29. CC At least 30 different bacterial species known so far have the CC PEP-CTERM/exosortase system believed to process proteins analogously to CC the LPXTG/sortase system. Genes associated with this processing are CC found among exopolysaccharide biosynthesis genes, suggesting that CC PEP-CTERM proteins are part of this exopolysaccharide system, and CC therefore are likely to be transported across the outer membrane. This CC property represents a panel of exopolysaccharide biosynthesis genes CC where each belongs to a subfamily that marks its host gene as carrying CC the PEP-CTERM/exopolysaccharide system. This type 2 version of the CC system is found in Methylobacillus sp. strain 12S where it is embedded CC in a region for the biosynthesis of the exopolysaccharide mthanolan. -- SN 1 ID Transcriptional regulator EpsA DN Transcriptional regulator EpsA RQ 0 EV IPR017470; TIGR03020; sufficient; -- SN 2 ID Undecaprenyl-phosphate glucose phosphotransferase EpsB DN Undecaprenyl-phosphate glucose phosphotransferase EpsB RQ 1 EV IPR017473; TIGR03023; -- SN 3 ID Polysaccharide export protein DN Polysaccharide export protein/EpsE RQ 1 EV IPR017478; TIGR03028; sufficient; -- SN 4 ID Chain length determinant protein EpsF DN Chain length determinant protein EpsF RQ 1 EV IPR017468; TIGR03017; sufficient; -- SN 5 ID Protein tyrosine kinase EpsG DN Protein tyrosine kinase EpsG RQ 1 EV IPR017479; TIGR03029; sufficient; -- SN 6 ID Exosortase 2 DN Exosortase 2 RQ 1 EV IPR017544; TIGR03113; sufficient; -- SN 7 ID EpsL protein DN EpsL protein RQ 1 EV IPR017465; TIGR03014; sufficient; // AC GenProp0658 DE Cellulose biosynthesis TP SYSTEM AU Haft DH TH 2 RN [1] RM 2030672 RT Cellulose biosynthesis and function in bacteria. RA Ross P, Mayer R, Benziman M; RL Microbiol Rev. 1991;55:35-58. RN [2] RM 8083166 RT Characterization of genes in the cellulose-synthesizing operon (acs RT operon) of Acetobacter xylinum: implications for cellulose RT crystallization. RA Saxena IM, Kudlicka K, Okuda K, Brown RM; RL J Bacteriol. 1994;176:5735-5752. RN [3] RM 16585767 RT A CsgD-independent pathway for cellulose production and biofilm RT formation in Escherichia coli. RA Da Re S, Ghigo JM; RL J Bacteriol. 2006;188:3073-3087. RN [4] RM 11929533 RT Genetic analysis of Salmonella enteritidis biofilm formation: critical RT role of cellulose. RA Solano C, García B, Valle J, Berasain C, Ghigo JM, Gamazo C, Lasa I; RL Mol Microbiol. 2002;43:793-808. CC Cellulose, a homopolymer of glucose featuring uniform beta-1,4 CC linkages, is synthesized in bacteria by cellulose synthase [1,2]. CC Bacterial cellulose may have further modifications such as acetylation. CC The synthase consists of two subunits (or domains in the frequent cases CC where it is encoded as a single polypeptide), a catalytic domain and CC regulatory domain which binds the allosteric activator cyclic-di-GMP. CC The protein is membrane-embedded and probably assembles into multimers CC such that the individual cellulose strands can self-assemble into CC multi-strand fibrils. The purpose of the endoglucanase which is always CC present in the same operon with the synthase is not known. Control of CC the levels of c-diGMP is via pppGpG cyclases and c-diGMP and pGpG CC phosphodiesterases. All genomes expressing this system have numerous CC cyclase and phosphodiesterase domain proteins and multiple regulatory CC circuits are possible. In E. coli strains, at least three regulatory CC systems are indicated [3], whose genes typically are not clustered with CC the biosynthetic genes. -- SN 1 ID Cellulose synthase, catalytic subunit CelA DN Cellulose synthase, catalytic subunit CelA RQ 1 EV IPR003919; TIGR03030; sufficient; TG GO:0030244; -- SN 2 ID Cellulose synthase, regulatory subunit CelB DN Cellulose synthase, regulatory subunit CelB RQ 1 EV IPR018513; PF03170; sufficient; TG GO:0030244; -- SN 3 ID Cellulose biosynthesis protein BcsE/YhjS DN Cellulose biosynthesis protein BcsE/YhjS RQ 0 EV IPR017745; TIGR03369; TG GO:0030244; -- SN 4 ID Cellulose biosynthesis operon protein BcsF/YhjT DN Cellulose biosynthesis operon protein BcsF/YhjT RQ 0 EV IPR019995; TIGR03493; TG GO:0030244; -- SN 5 ID Cellulose biosynthesis protein BcsG/YhjU DN Cellulose biosynthesis protein BcsG/YhjU RQ 0 EV IPR017744; TIGR03368; TG GO:0030244; -- SN 6 ID Cellulose synthase operon protein C DN Cellulose synthase operon protein C RQ 1 EV IPR008410; PF05420; sufficient; TG GO:0030244; -- SN 7 ID Cellulose synthase operon protein YhjQ DN Cellulose synthase operon protein YhjQ RQ 0 EV IPR017746; TIGR03371; TG GO:0030244; -- SN 8 ID Clustered endoglucanase (cellulase?) DN Clustered endoglucanase (cellulase?) RQ 0 EV IPR002037; PF01270; TG GO:0030244; // AC GenProp0659 DE Tryptophan degradation to anthranilate TP PATHWAY AU Haft DH TH 0 CC Tryptophan 2,3-dioxygenase converts Trp to L-formylkynurenine. CC Arylformamidase converts the product to L-kynurenine + formate. CC Kynureninase converts L-kynurenine + H(2)O = anthranilate + CC L-alanine. -- SN 1 ID Tryptophan 2,3-dioxygenase DN Tryptophan 2,3-dioxygenase (EC 1.13.11.11) RQ 1 EV IPR017485; TIGR03036; sufficient; -- SN 2 ID Arylformamidase DN Arylformamidase (EC 3.5.1.9) RQ 1 EV IPR017484; TIGR03035; sufficient; -- SN 3 ID Kynureninase DN Kynureninase (EC 3.7.1.3) RQ 1 EV IPR010111; TIGR01814; sufficient; // AC GenProp0660 DE Photosystem I TP SYSTEM AU Haft DH TH 0 RN [1] RM 3333014 RT Structure, function and organization of the Photosystem I reaction RT center complex. RA Golbeck JH; RL Biochim Biophys Acta. 1987;895:167-204. CC Photosystem I is a membrane complex found in the chloroplasts of plants and CC cyanobacteria. It uses light energy to transfer electrons from plastocyanin CC to ferredoxin. The core proteins of photosystem I are PsaA and PsaB, CC homologous integral membrane proteins that form a heterodimer that binds CC the electron-donating chlorophyll dimer P700, as well as chlorophyll, CC phylloquinone, and 4FE-4S electron acceptors [1]. -- SN 1 ID Photosystem I core protein PsaA DN Photosystem I core protein PsaA/psaA RQ 1 EV IPR006243; TIGR01335; sufficient; TG GO:0030094; -- SN 2 ID Photosystem I core protein PsaB DN Photosystem I core protein PsaB/psaB RQ 1 EV IPR006244; TIGR01336; sufficient; TG GO:0030094; -- SN 3 ID Photosystem I iron-sulfur center DN Photosystem I iron-sulfur center/psaC RQ 1 EV IPR017491; TIGR03048; sufficient; TG GO:0030094; -- SN 4 ID Photosystem I reaction center subunit II DN Photosystem I reaction center subunit II/psaD RQ 1 EV IPR003685; PF02531; sufficient; TG GO:0030094; -- SN 5 ID Photosystem I reaction center subunit IV DN Photosystem I reaction center subunit IV/psaE RQ 1 EV IPR003375; PF02427; sufficient; TG GO:0030094; -- SN 6 ID Photosystem I reaction center subunit III DN Photosystem I reaction center subunit III/psaF RQ 1 EV IPR003666; PF02507; sufficient; TG GO:0030094; -- SN 7 ID Photosystem I reaction center subunit VI DN Photosystem I reaction center subunit VI/psaH RQ 0 EV IPR004928; PF03244; sufficient; TG GO:0030094; -- SN 8 ID Photosystem I reaction center subunit VIII DN Photosystem I reaction center subunit VIII/psaI RQ 1 EV IPR001302; TIGR03052; sufficient; TG GO:0030094; -- SN 9 ID Photosystem I reaction center subunit IX DN Photosystem I reaction center subunit IX/psaJ RQ 1 EV IPR002615; PF01701; sufficient; TG GO:0030094; -- SN 10 ID Photosystem I reaction center subunit X DN Photosystem I reaction center subunit X/psaK RQ 1 EV IPR017492; TIGR03049; sufficient; TG GO:0030094; -- SN 11 ID Photosystem I reaction center subunit XI DN Photosystem I reaction center subunit XI/psaL RQ 1 EV IPR003757; PF02605; sufficient; TG GO:0030094; -- SN 12 ID Photosystem I protein M DN Photosystem I protein M/psaM RQ 1 EV IPR010010; TIGR03053; sufficient; TG GO:0030094; -- SN 13 ID Photosystem I reaction centre subunit N DN Photosystem I reaction centre subunit N/psaN RQ 0 EV IPR008796; PF05479; sufficient; TG GO:0030094; // AC GenProp0661 DE Photosystem II TP SYSTEM AU Haft DH TH 0 CC Photosystem II is found in cyanobacteria and in chloroplasts. It CC oxidizes water (removes hydrogen) to evolve 02, and the protein CC families in this model are all markers for oxygenic photosynthesis. CC Most components of this property are shared from Synechocystis to CC vascular plants. Variant forms of photosystem II in those Cyanobacteria CC that lack thylakoid lack some proteins otherwise expected. Photosystem CC II is found in the same species as photosystem I but assembles into a CC different supracomplex; both may receive light energy from CC light-harvesting antennae. -- SN 1 ID Photosystem II S4 domain protein DN Photosystem II S4 domain protein RQ 1 EV IPR017506; TIGR03069; sufficient; -- SN 2 ID Photosystem II protein Psb27 DN Photosystem II protein Psb27 RQ 1 EV IPR017488; TIGR03044; sufficient; -- SN 3 ID Photosystem II reaction center protein Psb28 DN Photosystem II reaction center protein Psb28 RQ 1 EV IPR005610; TIGR03047; sufficient; -- SN 4 ID Photosystem II biogenesis protein Psp29 DN Photosystem II biogenesis protein Psp29 RQ 1 EV IPR017499; TIGR03060; sufficient; -- SN 5 ID Photosystem II, DI subunit DN Photosystem II, DI subunit RQ 1 EV IPR005867; TIGR01151; sufficient; -- SN 6 ID Photosystem II chlorophyll-binding protein CP47 DN Photosystem II chlorophyll-binding protein CP47 RQ 1 EV IPR017486; TIGR03039; sufficient; -- SN 7 ID Photosystem II, 44K reaction center protein DN Photosystem II, 44K reaction center protein RQ 1 EV IPR005869; TIGR01153; sufficient; -- SN 8 ID Photosystem II, D2 subunit DN Photosystem II, D2 subunit RQ 1 EV IPR005868; TIGR01152; sufficient; -- SN 9 ID Cytochrome b559, alpha subunit DN Cytochrome b559, alpha subunit RQ 1 EV IPR006217; TIGR01332; sufficient; -- SN 10 ID Cytochrome b559, beta subunit DN Cytochrome b559, beta subunit RQ 1 EV IPR006241; TIGR01333; sufficient; -- SN 11 ID Photosystem II, 10 kd phosphoprotein PsbH DN Photosystem II, 10 kd phosphoprotein PsbH RQ 1 EV IPR001056; PF00737; sufficient; -- SN 12 ID Photosystem II reaction center protein PsbI DN Photosystem II reaction center protein PsbI RQ 1 EV IPR003686; PF02532; sufficient; -- SN 13 ID Photosystem II protein PsbJ DN Photosystem II protein PsbJ RQ 1 EV IPR002682; PF01788; sufficient; -- SN 14 ID Photosystem II 4 kDa reaction center protein DN Photosystem II 4 kDa reaction center protein RQ 1 EV IPR003687; PF02533; sufficient; -- SN 15 ID Photosystem II protein PsbL DN Photosystem II protein PsbL RQ 1 EV IPR003372; PF02419; sufficient; -- SN 16 ID Photosystem II reaction center protein M DN Photosystem II reaction center protein M RQ 1 EV IPR007826; TIGR03038; sufficient; -- SN 17 ID Photosystem II reaction center protein PsbN DN Photosystem II reaction center protein PsbN RQ 1 EV IPR003398; PF02468; sufficient; -- SN 18 ID Photosystem II extrinsic protein PsbO DN Photosystem II extrinsic protein PsbO RQ 1 EV IPR002628; PF01716; sufficient; -- SN 19 ID Photosystem II extrinsic protein PsbP DN Photosystem II extrinsic protein PsbP RQ 1 EV IPR002683; PF01789; sufficient; -- SN 20 ID Photosystem II protein PsbQ DN Photosystem II protein PsbQ RQ 1 EV IPR017487; TIGR03042; sufficient; -- SN 21 ID Photosystem II 10 kDa polypeptide PsbR DN Photosystem II 10 kDa polypeptide PsbR RQ 0 EV IPR006814; PF04725; sufficient; -- SN 22 ID Photosystem II reaction center T protein DN Photosystem II reaction center T protein RQ 1 EV IPR001743; PF01405; sufficient; -- SN 23 ID Photosystem II 12 kDa extrinsic protein PsbU DN Photosystem II 12 kDa extrinsic protein PsbU RQ 1 EV IPR010527; PF06514; sufficient; -- SN 24 ID Cytochrome c-550 DN Cytochrome c-550 RQ 1 EV IPR017851; TIGR03045; sufficient; -- SN 25 ID Photosystem II reaction center protein PsbW DN Photosystem II reaction center protein PsbW RQ 1 EV IPR005610; PF03912; sufficient; -- SN 26 ID Photosystem II reaction center protein (plant) DN Photosystem II reaction center protein (plant) RQ 0 EV IPR009806; PF07123; sufficient; -- SN 27 ID Photosystem II reaction center protein PsbX DN Photosystem II reaction center protein PsbX RQ 1 EV IPR009518; PF06596; sufficient; -- SN 28 ID Photosystem II protein PsbY DN Photosystem II protein PsbY RQ 1 EV IPR009388; PF06298; sufficient; -- SN 29 ID Photosystem II reaction center protein PsbZ DN Photosystem II reaction center protein PsbZ RQ 1 EV IPR002644; TIGR03043; sufficient; // AC GenProp0662 DE Photosynthetic reaction center, alphaproteobacterial type TP SYSTEM AU Haft DH TH 0 RN [1] RM 6744416 RT Nucleotide and deduced polypeptide sequences of the photosynthetic RT reaction-center, B870 antenna, and flanking polypeptides from R. RT capsulata. RA Youvan DC, Bylina EJ, Alberti M, Begusch H, Hearst JE; RL Cell. 1984;37:949-957. CC This alphaproteobacterial-type photosynthetic reaction center is found CC in Rhodobacterales, Rhodospirillales, and Rhizobiales. A similar CC complex is found in the Chloroflexi, which do not belong to the CC alphaproteobacteria. This complex is associated with nonoxygenic CC photosynthesis. It differs from photosystems I and II of the CC cyanobacteria and plants. The core complex of the reaction center is a CC heterotrimer of L, M, and H subunits. -- SN 1 ID Putative photosynthetic complex assembly protein DN Putative photosynthetic complex assembly protein RQ 1 EV IPR017495; TIGR03054; sufficient; -- SN 2 ID Putative photosynthetic complex assembly protein 2 DN Putative photosynthetic complex assembly protein 2 RQ 1 EV IPR017496; TIGR03055; sufficient; -- SN 3 ID Photosynthetic reaction center L subunit DN Photosynthetic reaction center L subunit RQ 1 EV IPR005871; TIGR01157; sufficient; -- SN 4 ID Photosynthetic reaction center M subunit DN Photosynthetic reaction center M subunit RQ 1 EV IPR005781; TIGR01115; sufficient; -- SN 5 ID Photosynthetic reaction center H subunit DN Photosynthetic reaction center H subunit RQ 1 EV IPR005652; TIGR01150; sufficient; // AC GenProp0663 DE Verrucomicrobium/Chthoniobacter four-plus-PEP_CTERM cassette TP SYSTEM AU Haft DH TH 0 CC Verrucomicrobium spinosum DSM 4136 and Chthoniobacter flavus Ellin428, CC both members of the Verrucomicrobia, have multiple homologous operons CC featuring four proteins with similarly narrow species distributions. CC Three of these families have N-terminal signal sequences typical of CC type IV pilus modification target proteins (see TIGR02523). The fourth CC is a large protein, usually > 1300 residues. The majority of these CC four-gene cassettes are adjacent to a PEP-CTERM protein (see CC TIGR02595), among the largest PEP-CTERM proteins from any species, with CC repetitive structure that suggests outer membrane autotransporter CC function (see TIGR02601). The surface structures that these cassettes CC may form are not yet understood. -- SN 1 ID Operon position FOUR protein DN Verru/Chthon cassette protein D RQ 1 EV IPR019836; TIGR02596; sufficient; -- SN 2 ID V. spinosum long paralogous protein DN Verru/Chthon cassette protein A RQ 1 EV IPR019840; TIGR02600; sufficient; -- SN 3 ID Mid-operon protein DN Verru/Chthon cassette protein C RQ 1 EV IPR019839; TIGR02599; sufficient; -- SN 4 ID V. spinosum short paralogous protein DN Verru/Chthon cassette protein B RQ 1 EV IPR019838; TIGR02598; sufficient; // AC GenProp0664 DE Protein sorting system, sortase type, SrtB class TP SYSTEM AU Haft DH TH 0 RN [1] RM 15028680 RT Sortase B, a new class of sortase in Listeria monocytogenes. RA Bierne H, Garandeau C, Pucciarelli MG, Sabet C, Newton S, Garcia-del RA Portillo F, Cossart P, Charbit A; RL J Bacteriol. 2004;186:1972-1982. RN [2] RM 16247833 RT Identification of substrates of the Listeria monocytogenes sortases A RT and B by a non-gel proteomic analysis. RA Pucciarelli MG, Calvo E, Sabet C, Bierne H, Cossart P, Garcia-del RA Portillo F; RL Proteomics. 2005;5:4808-4817. RN [3] RM 11914350 RT Differential recognition of surface proteins in Streptococcus RT pyogenes by two sortase gene homologs. RA Barnett TC, Scott JR; RL J Bacteriol. 2002;184:2181-2191. RN [4] RM 15317792 RT A novel sortase, SrtC2, from Streptococcus pyogenes anchors a surface RT protein containing a QVPTGV motif to the cell wall. RA Barnett TC, Patel AR, Scott JR; RL J Bacteriol. 2004;186:5865-5875. CC This is a family of sortases and their substrates, less abundant than CC the housekeeping sortase, SrtA, and the LPXTG-like target sequences [1]. CC SrtB in Listeria monocytogenes appears to process two classes of signal, CC NXZTN and NPKXZ [2]. Note that the protein called SrtB in Streptococcus CC pyogenes [3] is a member of the SrtA family, not the family described CC here, while the protein called SrtC2 is a member of the SrtB family [4]. -- SN 1 ID Sortase, SrtB family DN Sortase, SrtB family RQ 1 EV IPR009835; TIGR03064; sufficient; -- SN 2 ID Sortase B target sequence DN Sortase B target sequence RQ 1 EV IPR017502; TIGR03063; sufficient; EV IPR017503; TIGR03065; sufficient; EV IPR017505; TIGR03068; sufficient; // AC GenProp0665 DE Peptide chain release operon, RctB-like/PrfH TP SYSTEM AU Haft DH TH 0 RN [1] RM 16970810 RT Diverse bacterial genomes encode an operon of two genes, one of which RT is an unusual class-I release factor that potentially recognizes RT atypical mRNA signals other than normal stop codons. RA Baranov PV, Vestergaard B, Hamelryck T, Gesteland RF, Nyborg J, Atkins RA JF; RL Biol Direct. 2006;1:28. CC This genome property describes a novel two-gene operon that consists of CC PrfH, which is a member of the bacterial class I peptide chain release CC factors, and a homolog of RctB, which is a protein of unknown function CC thought suggest to act in RNA processing. -- SN 1 ID Peptide chain release factor H DN Peptide chain release factor H RQ 1 EV IPR017509; TIGR03072; sufficient; -- SN 2 ID Translationally-coupled RctB family protein DN Translationally-coupled RctB family protein RQ 1 EV IPR017510; TIGR03073; sufficient; // AC GenProp0666 DE Membrane-associated monooxygenase (methane/ammonia) TP SYSTEM AU Haft DH TH 0 CC This property represents a membrane-associated three-protein enzyme CC complex. The enzyme, designated methane monooxygenase shows a broad CC specificiy for methane (to methanol), ammonia (to hydroxylamine), and CC various alkanes and alkenes. However, this enzyme is commonly named CC according to its relavant biological role in species in which it CC occurs: methane monooxygenase in methanotrophs, ammonia monooxygenase CC in nitrifiers. -- SN 1 ID Methane monooxygenase/ammonia monooxygenase, subunit A DN Methane monooxygenase/ammonia monooxygenase, subunit A RQ 1 EV IPR003393; TIGR03080; sufficient; -- SN 2 ID Methane monooxygenase/ammonia monooxygenase, subunit B DN Methane monooxygenase/ammonia monooxygenase, subunit B RQ 1 EV IPR006833; TIGR03079; sufficient; -- SN 3 ID Methane monooxygenase/ammonia monooxygenase, subunit C DN Methane monooxygenase/ammonia monooxygenase, subunit C RQ 1 EV IPR006980; TIGR03078; sufficient; // AC GenProp0668 DE Acetyltransferase/synthase/peptidase cassette TP SYSTEM AU Haft DH TH 0 CC This genome property represents an uncharacterized three gene cassette. CC One gene resembles GNAT-family acetyltransferases, another resembles a CC peptidase, and a third resembles glutamine-hydrolyzing asparagine CC synthases. This cassette is sparsely and somewhat broadly distributed, CC occurring in the Mycobacteria and a member of the Chlorobi as well as CC in numerous alpha, beta, and gamma Proteobacteria. -- SN 1 ID GNAT-family acetyltransferase TIGR03103 DN GNAT-family acetyltransferase TIGR03103 RQ 1 EV IPR017534; TIGR03103; sufficient; -- SN 2 ID Asparagine synthase family amidotransferase DN Asparagine synthase family amidotransferase RQ 1 EV IPR017535; TIGR03104; sufficient; -- SN 3 ID Putative peptidase DN Putative peptidase RQ 1 EV IPR017537; TIGR03106; sufficient; // AC GenProp0669 DE Protein sorting system, putative, exosortase G class TP SYSTEM AU Haft DH TH 0 CC For several non-pathogenic Gram-positive bacteria, a protein family CC showing considerable sequence similarity to the proposed exosortases CC of Gram-negative bacteria occurs in a conserved gene neighborhood. CC This property describes that neighborhood, which also includes a CC glycosyltransferase and a domain related to 6-pyruvoyl tetrahydropterin CC synthases. These regions also include a family of proteins in the which CC the well-conserved C-terminal region (TIGR04145) resembles PEP-CTERM and CC LPXTG protein C-terminal regions. This last family may be the CC protein-sorting target. -- SN 1 ID Putative glycosyltransferase DN Putative glycosyltransferase RQ 1 EV IPR017542; TIGR03111; sufficient; -- SN 2 ID Conserved hypothetical integral membrane protein DN Conserved hypothetical integral membrane protein RQ 0 EV IPR021200; TIGR03766; -- SN 3 ID EpsH core region-related protein DN EpsH core region-related protein RQ 1 EV IPR017541; TIGR03110; sufficient; -- SN 4 ID 6-pyruvoyl tetrahydropterin synthase-related domain DN 6-pyruvoyl tetrahydropterin synthase-related domain RQ 1 EV IPR017543; TIGR03112; sufficient; -- SN 5 ID Firmicu-CTERM domain DN Firmicu-CTERM domain RQ 1 EV IPR026409; TIGR04145; // AC GenProp0670 DE CRISPR system, Aferr subtype TP SYSTEM AU Haft DH TH 0 CC At least ten different systems of proteins associated with CRISPR CC (Clustered Regularly Interspaced Short Palindromic Repeats) have CC been described, such as the Ecoli, Ypest, Nmeni, and Dvulg subtypes. We CC designate this type Aferr, after Acidithiobacillus ferrooxidans ATCC CC 23270, where this system is carried on the chromosome rather than on a CC plasmid, and where it is the only CRISPR subtype in the species. None CC of the familiar core cas genes, cas1-cas4, are found in A. ferrooxidans, CC making this type of CRISPR/cas locus unusual. -- SN 1 ID CRISPR-associated protein, Csf1 DN CRISPR-associated protein, Csf1 RQ 1 EV IPR017545; TIGR03114; sufficient; -- SN 2 ID CRISPR-associated protein, Csf2 DN CRISPR-associated protein, Csf2 RQ 1 EV IPR017546; TIGR03115; sufficient; -- SN 3 ID CRISPR-associated protein, Csf3 DN CRISPR-associated protein, Csf3 RQ 1 EV IPR017547; TIGR03116; sufficient; -- SN 4 ID CRISPR-associated DEAH-box helicase Csf4 DN CRISPR-associated DEAH-box helicase Csf4 RQ 1 EV IPR017548; TIGR03117; sufficient; // AC GenProp0671 DE H4MPT-linked C1 transfer pathway TP PATHWAY AU Haft DH TH 0 CC Tetrahydromethanopterin (H4MPT) is a chemical analog of CC tetrahydrofolate (H4F). It acts as a C-1 carrier for interconversions CC of formate, formaldehyde, and methanol, and was once thought to occur CC only in methanogenic archaea. -- SN 1 ID Formaldehyde-activating enzyme DN Formaldehyde-activating enzyme RQ 1 EV IPR014826; TIGR03126; sufficient; -- SN 2 ID Formylmethanofuran--tetrahydromethanopterin N-formyltransferase DN Formylmethanofuran--tetrahydromethanopterin N-formyltransferase RQ 1 EV IPR014053; TIGR03119; sufficient; -- SN 3 ID Formylmethanofuran dehydrogenase, subunit A DN Formylmethanofuran dehydrogenase, subunit A RQ 1 EV IPR012027; TIGR03121; sufficient; -- SN 4 ID Formylmethanofuran dehydrogenase, subunit B DN Formylmethanofuran dehydrogenase, subunit B RQ 1 EV IPR016457; TIGR03129; sufficient; -- SN 5 ID Formylmethanofuran dehydrogenase, subunit C DN Formylmethanofuran dehydrogenase, subunit C RQ 1 EV IPR017550; TIGR03122; sufficient; -- SN 6 ID Methenyltetrahydromethanopterin cyclohydrolase DN Methenyltetrahydromethanopterin cyclohydrolase RQ 1 EV IPR003209; TIGR03120; sufficient; // AC GenProp0672 DE Citrate lyase system TP SYSTEM AU Haft DH TH 0 RN [1] RM 9457870 RT Purification of Leuconostoc mesenteroides citrate lyase and cloning RT and characterization of the citCDEFG gene cluster. RA Bekal S, Van Beeumen J, Samyn B, Garmyn D, Henini S, Divies C, RA Prevost H; RL J Bacteriol. 1998;180:647-654. CC Citrate lyase is a holoenzyme composed of alpha (citrate:acetyl-ACP CC transferase), beta (citryl-S-ACP lyase), and gamma (acyl carrier protein) CC subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an CC enzyme which converts citrate to oxaloacetate. In bacteria, this reaction CC is involved in citrate fermentation [1]. -- SN 1 ID [citrate (pro-3S)-lyase] ligase DN [citrate (pro-3S)-lyase] ligase/citC RQ 1 EV IPR005216; TIGR00124; sufficient; -- SN 2 ID Citrate lyase acyl carrier protein DN Citrate lyase acyl carrier protein/citD RQ 1 EV IPR006495; TIGR01608; sufficient; -- SN 3 ID Citrate lyase, beta subunit DN Citrate lyase, beta subunit/citE RQ 1 EV IPR006475; TIGR01588; sufficient; -- SN 4 ID Citrate lyase, alpha subunit DN Citrate lyase, alpha subunit/citF RQ 1 EV IPR006472; TIGR01584; sufficient; -- SN 5 ID Triphosphoribosyl-dephospho-CoA synthase DN Triphosphoribosyl-dephospho-CoA synthase/citG RQ 1 EV IPR017551; TIGR03125; sufficient; -- SN 6 ID Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase DN Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase/citX RQ 1 EV IPR005551; TIGR03124; sufficient; // AC GenProp0673 DE Ribulose monophosphate pathway TP PATHWAY AU Haft DH TH 0 RN [1] RM 16788179 RT The ribulose monophosphate pathway substitutes for the missing pentose RT phosphate pathway in the archaeon Thermococcus kodakaraensis. RA Orita I, Sato T, Yurimoto H, Kato N, Atomi H, Imanaka T, Sakai Y; RL J Bacteriol. 2006;188:4698-4704. RN [2] RM 16237021 RT Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs RT in the absence of a pentose-phosphate pathway. RA Grochowski LL, Xu H, White RH; RL J Bacteriol. 2005;187:7382-7389. RN [3] RM 15978081 RT HxlR, a member of the DUF24 protein family, is a DNA-binding protein RT that acts as a positive regulator of the formaldehyde-inducible hxlAB RT operon in Bacillus subtilis. RA Yurimoto H, Hirai R, Matsuno N, Yasueda H, Kato N, Sakai Y; RL Mol Microbiol. 2005;57:511-519. CC The ribulose monophosphate pathway consists of two enzyme, CC 3-hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexuloisomerase CC (PHI). In one direction, this pathway removes the toxic metabolite CC formaldehyde by assimilation. In the other direction, in certain CC species lacking the complete pentose phosphate pathway, this pathway CC releases formaldehyde in order to produce ribulose-5-phosphate, CC essential for nucleotide biosynthesis. The two enzymes may occur as a CC fusion protein, as in Thermococcus kodakaraensis. -- SN 1 ID 3-hexulose-6-phosphate synthase DN 3-hexulose-6-phosphate synthase/HPS RQ 1 EV IPR017553; TIGR03128; sufficient; -- SN 2 ID 6-phospho-3-hexuloisomerase DN 6-phospho-3-hexuloisomerase/PHI RQ 1 EV IPR017552; TIGR03127; sufficient; // AC GenProp0674 DE Malonate decarboxylase TP SYSTEM AU Haft DH TH 0 RN [1] RM 11902724 RT Enzymic and genetic basis for bacterial growth on malonate. RA Dimroth P, Hilbi H; RL Mol Microbiol. 1997;25:3-10. RN [2] RM 12619701 RT Functions of malonate decarboxylase subunits from Pseudomonas putida. RA Chohnan S, Akagi K, Takamura Y; RL Biosci Biotechnol Biochem. 2003;67:214-217. CC Malonate decarboxylase as found in Klebsiella pneumoniae is a CC multi-subunit water-soluble enzyme. In some species, such as CC Malonomonas rubra, soluble components are linked to membrane-bound CC enzymes and the system on the whole acts as a sodium pump. This CC property contains (as required steps) the subunits of the CC water-soluble enzyme and accessory proteins for biosynthesis and CC attachment of the 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic CC group. The sodium pumping form can be recognized by the presence of a CC carboxybiotin decarboxylase subunit (step 1) in the operon. -- SN 1 ID Na+-transporting malonate decarboxylase, carboxybiotin decarboxylase subunit DN Na+-transporting malonate decarboxylase, carboxybiotin decarboxylase subunit RQ 0 EV IPR017558; TIGR03136; sufficient; -- SN 2 ID Malonate transporter, MadL subunit DN Malonate transporter, MadL subunit RQ 0 EV IPR004690; TIGR00807; sufficient; -- SN 3 ID Malonate transporter, MadM subunit DN Malonate transporter, MadM subunit RQ 0 EV IPR004691; TIGR00808; sufficient; -- SN 4 ID Malonate decarboxylase, alpha subunit DN Malonate decarboxylase, alpha subunit RQ 1 EV IPR005777; TIGR01110; sufficient; -- SN 5 ID Triphosphoribosyl-dephospho-CoA synthase MdcB DN Triphosphoribosyl-dephospho-CoA synthase MdcB RQ 1 EV IPR017555; TIGR03132; sufficient; -- SN 6 ID Malonate decarboxylase acyl carrier protein DN Malonate decarboxylase acyl carrier protein RQ 1 EV IPR009662; TIGR03130; sufficient; -- SN 7 ID Malonate decarboxylase, beta subunit DN Malonate decarboxylase, beta subunit RQ 1 EV IPR017556; TIGR03133; sufficient; -- SN 8 ID Malonate decarboxylase, gamma subunit DN Malonate decarboxylase, gamma subunit RQ 1 EV IPR009648; TIGR03134; sufficient; -- SN 9 ID Holo ACP synthase MdcG DN Holo ACP synthase MdcG RQ 1 EV IPR017557; TIGR03135; sufficient; -- SN 10 ID Malonate decarboxylase, epsilon subunit DN Malonate decarboxylase, epsilon subunit RQ 1 EV IPR017554; TIGR03131; sufficient; // AC GenProp0676 DE Alkylhydroperoxide reductase AhpCF (peroxiredoxin) TP SYSTEM AU Haft DH TH 0 RN [1] RM 10482511 RT Role of the alkyl hydroperoxide reductase (ahpCF) gene in oxidative RT stress defense of the obligate Anaerobe bacteroides fragilis. RA Rocha ER, Smith CJ; RL J Bacteriol. 1999;181:5701-5710. CC This two-gene peroxiredoxin consists of ahpC and ahpF, ususally as CC tandem genes in an apparent operon. Peroxiredoxin detoxifies alkyl CC hydroperoxides by catalyzing the oxidation of an active site cysteine CC (on AhpC) to a sulfenic acid. This subsequently becomes a disulfide CC which is then resolved by reduction. AhpF contains an FAD-binding CC domain along with a NAD(P)H binding domain (PF07992). -- SN 1 ID Subunit C DN Subunit C/ahpC RQ 1 EV IPR017559; TIGR03137; sufficient; TG GO:0006800; -- SN 2 ID Subunit F DN Subunit F/ahpF RQ 1 EV IPR012081; TIGR03140; sufficient; TG GO:0006800; EV IPR017561; TIGR03143; sufficient; TG GO:0006800; // AC GenProp0677 DE Queuosine (Q-tRNA) biosynthesis from preQ0 TP PATHWAY AU Haft DH TH 0 RN [1] RM 15767583 RT From cyclohydrolase to oxidoreductase: discovery of nitrile reductase RT activity in a common fold. RA Van Lanen SG, Reader JS, Swairjo MA, de Crécy-Lagard V, Lee B, RA Iwata-Reuyl D; RL Proc Natl Acad Sci U S A. 2005;102:4264-4269. RN [2] RM 18931107 RT Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role RT for GTP cyclohydrolase I. RA Phillips G, El Yacoubi B, Lyons B, Alvarez S, Iwata-Reuyl D, de RA Crécy-Lagard V; RL J Bacteriol. 2008;190:7876-7884. RN [3] RM 21502530 RT Discovery of epoxyqueuosine (oQ) reductase reveals parallels between RT halorespiration and tRNA modification. RA Miles ZD, McCarty RM, Molnar G, Bandarian V; RL Proc Natl Acad Sci U S A. 2011;108:7368-7372. CC preQ0 (7-cyano-7-deazaguanine) is the last common intermediate in the CC biosyntheses of queuosine (in bacteria and eukarya) and archaeosine (in CC archaea). preQ0 is converted to queuosine by the action of at least CC four enzymes, two reductases, a tRNA(GUN) transferase and an CC adenosylmethionine ribosyl transferase-isomerase. -- SN 1 ID PreQ1 tRNA transferase DN PreQ1 tRNA transferase (EC 2.4.2.29) RQ 1 EV IPR004803; TIGR00430; sufficient; TG GO:0008616; -- SN 3 ID PreQ1-tRNA adenosyl methionine ribosyl transferase isomerase DN PreQ1-tRNA adenosyl methionine ribosyl transferase isomerase (EC 2.4.99.17) RQ 1 EV IPR003699; TIGR00113; sufficient; TG GO:0008616; -- SN 4 ID PreQ0 reductase DN PreQ0 reductase (EC 1.7.1.13) RQ 1 EV IPR016428; TIGR03138; sufficient; TG GO:0008616; EV IPR016856; TIGR03139; sufficient; TG GO:0008616; -- SN 5 ID Epoxyqueuosine reductase DN Epoxyqueuosine reductase (EC 1.17.99.6) RQ 1 EV IPR004453; TIGR00276; TG GO:0008616; // AC GenProp0678 DE C-type cytochrome biogenesis, system I TP SYSTEM AU Haft DH TH 0 RN [1] RM 15513913 RT CcmD is involved in complex formation between CcmC and the heme RT chaperone CcmE during cytochrome c maturation. RA Ahuja U, Thöny-Meyer L; RL J Biol Chem. 2005;280:236-243. CC Assembling c-type cytochromes outside the bacterial inner membrane CC requires apocytochome export, heme export, heme ligation, and CC chaperones for both heme and apocytochromes. Of three different c-type CC cytochrome biogenesis systems, this is system I. It features the operon CC ccmABCDEFGHI in Escherichia coli and the equivalent genes in many other CC bacterial species. -- SN 1 ID Heme ABC exporter, ATP-binding protein CcmA DN Heme ABC exporter, ATP-binding protein CcmA RQ 1 EV IPR005895; TIGR01189; sufficient; -- SN 2 ID Heme exporter protein CcmB DN Heme exporter protein CcmB RQ 1 EV IPR026031; TIGR01190; sufficient; -- SN 3 ID Heme exporter protein CcmC DN Heme exporter protein CcmC RQ 1 EV IPR003557; TIGR01191; sufficient; -- SN 4 ID Heme exporter protein CcmD DN Heme exporter protein CcmD RQ 1 EV IPR007078; PF04995; sufficient; EV IPR030888; TIGR04391; sufficient; -- SN 5 ID Cytochrome c-type biogenesis protein CcmE DN Cytochrome c-type biogenesis protein CcmE RQ 1 EV IPR004329; PF03100; sufficient; -- SN 6 ID Cytochrome c-type biogenesis protein CcmF DN Cytochrome c-type biogenesis protein CcmF RQ 1 EV IPR003568; TIGR00353; sufficient; -- SN 7 ID CcmG protein DN CcmG protein RQ 1 EV IPR004799; TIGR00385; sufficient; -- SN 8 ID Cytochrome C biogenesis protein CcmH/CycL/NrfF/Ccl2 DN Cytochrome C biogenesis protein CcmH/CycL/NrfF/Ccl2 RQ 1 EV IPR005616; PF03918; sufficient; -- SN 9 ID Cytochrome c-type biogenesis protein CcmI DN Cytochrome c-type biogenesis protein CcmI RQ 0 EV IPR017560; TIGR03142; sufficient; // AC GenProp0680 DE C-type cytochrome biogenesis, system II TP SYSTEM AU Haft DH TH 0 CC This property is system II for c-type cytochrome biosynthesis, one CC among three such systems described, and one of two described in CC bacteria. The two genes critical even in the presence of the added CC disulfide bond reducing compounds, are CcsA (or ResB) and CcsB (or CC ResC). This system is much simpler than the CcmABCDEFGH system, system CC I. -- SN 1 ID Cytochrome c-type biogenesis protein CcsA DN Cytochrome c-type biogenesis protein CcsA RQ 1 EV IPR007816; PF05140; sufficient; -- SN 2 ID Cytochrome c-type biogenesis protein CcsB DN Cytochrome c-type biogenesis protein CcsB RQ 1 EV IPR017562; TIGR03144; sufficient; // AC GenProp0681 DE Fatty acid biosynthesis from acetyl-CoA TP PATHWAY AU Haft DH TH 0 CC This property describes the formation of fatty acids from acetyl-CoA. CC Fatty acids are any of the aliphatic monocarboxylic acids that can be CC liberated by hydrolysis from naturally occurring fats and oils. Fatty CC acids are predominantly straight-chain acids of 4 to 24 carbon atoms, CC which may be saturated or unsaturated; branched fatty acids and hydroxy CC fatty acids also occur, and very long chain acids of over 30 carbons CC are found in waxes. -- SN 1 ID Acyl carrier protein DN Acyl carrier protein/ACP RQ 1 EV GenProp1104; -- SN 2 ID Acetyl-CoA carboxylase complex DN Acetyl-CoA carboxylase complex/AccABCD RQ 1 EV GenProp0214; -- SN 3 ID 3-hydroxyacyl-[ACP] dehydratase FabA DN 3-hydroxyacyl-[ACP] dehydratase FabA RQ 1 EV IPR010083; TIGR01749; sufficient; -- SN 4 ID Malonyl CoA--(ACP) transacylase DN Malonyl CoA--(ACP) transacylase/fabD RQ 1 EV IPR004410; TIGR00128; sufficient; -- SN 5 ID 3-oxoacyl-[ACP] synthase II DN 3-oxoacyl-[ACP] synthase II/fabF RQ 1 EV IPR017568; TIGR03150; sufficient; -- SN 6 ID 3-oxoacyl-[ACP] reductase DN 3-oxoacyl-[ACP] reductase/fabG RQ 1 EV IPR011284; TIGR01830; sufficient; -- SN 7 ID 3-oxoacyl-[ACP] synthase III DN 3-oxoacyl-[ACP] synthase III/fabH RQ 1 EV IPR004655; TIGR00747; sufficient; -- SN 8 ID Enoyl-[ACP] reductase DN Enoyl-[ACP] reductase/fabI RQ 0 EV IPR017569; TIGR03151; sufficient; -- SN 9 ID 3-hydroxyacyl-[ACP] dehydratase FabZ DN 3-hydroxyacyl-[ACP] dehydratase FabZ RQ 1 EV IPR010084; TIGR01750; sufficient; // AC GenProp0682 DE Formate-dependent nitrite reductase, seven-gene type TP SYSTEM AU Haft DH TH 0 CC This property describes a multiheme enzyme, cytochrome c nitrite CC reductase, and accessory proteins that may or may not be present. This CC enzyme allows formate-dependent nitrite reduction all the way to CC ammonia. Three of the accessory proteins are closely homologous to CC three genes of system I for c-type cytochrome biogenesis. This property CC describes the system as encoded by a seven-gene operon in Escherichia CC coli, six of which are modeled explicitly for this property. Several of CC the genes occur as paralogs of genes from the CcmABCDEFGH c-type CC cytochrome biogenesis system present in the same genomes. The most CC distinctive protein from this system is a pentaheme cytochrome c, NrfB. -- SN 1 ID Cytochrome c552 DN Cytochrome c552/NrfA RQ 1 EV IPR003321; PF02335; sufficient; -- SN 2 ID Penta-heme cytochrome c DN Penta-heme cytochrome c/NrfB RQ 1 EV IPR017564; TIGR03146; sufficient; -- SN 3 ID Cytochrome c nitrite reductase, NrfC subunit DN Cytochrome c nitrite reductase, NrfC subunit/NrfC RQ 1 EV IPR017567; TIGR03149; sufficient; -- SN 4 ID Cytochrome c nitrite reductase, NrfD subunit DN Cytochrome c nitrite reductase, NrfD subunit/NrfD RQ 1 EV IPR017566; TIGR03148; sufficient; -- SN 5 ID Accessory protein NrfE DN Accessory protein NrfE/NrfE RQ 0 EV IPR017563; TIGR03145; sufficient; -- SN 6 ID Accessory protein NrfF DN Accessory protein NrfF/NrfF RQ 1 EV IPR017565; TIGR03147; sufficient; // AC GenProp0683 DE Cytochrome c nitrite reductase NrfHA TP SYSTEM AU Haft DH TH 0 CC This property describes a heterodimeric cytochrome c nitrite reductase. CC NrfA, or cytochrome c552, is the catalytic subunit. NrfH, the small CC subunit, is a tetraheme cytochrome c that binds NrfA, anchors it to the CC membrane, and couples the enzyme to the quinone pool for electron CC transport. -- SN 1 ID Cytochrome c nitrite reductase, c552 subunit DN Cytochrome c nitrite reductase, c552 subunit/NrfA RQ 1 EV IPR003321; PF02335; -- SN 2 ID Cytochrome c nitrate reductase, small subunit DN Cytochrome c nitrate reductase, small subunit/NrfH RQ 1 EV IPR017571; TIGR03153; sufficient; // AC GenProp0684 DE FtsH/HflKC protease complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 9636708 RT Different pathways for protein degradation by the FtsH/HflKC RT membrane-embedded protease complex: an implication from the RT interference by a mutant form of a new substrate protein, YccA. RA Kihara A, Akiyama Y, Ito K; RL J Mol Biol. 1998;279:175-188. CC FtsH/HflKC protease complex is a membrane-embedded protease CC complex that degrades uncomplexed forms of the SecY subunit of CC protein translocase. It is composed of FtsH (HflB), an CC ATP-dependent zinc-metalloproteinase, HflK and HflC. HflK and CC HflC are periplasmically exposed membrane proteins, which CC together form a complex (HflKC) which in turn complexes with CC FtsH [1]. -- SN 1 ID ATP-dependent metallopeptidase FtsH (HflB) DN ATP-dependent metallopeptidase FtsH (HflB)/HflB RQ 1 EV IPR005936; TIGR01241; sufficient; -- SN 2 ID HflC protein DN HflC protein/HflC RQ 1 EV IPR010200; TIGR01932; sufficient; -- SN 3 ID HflK protein DN HflK protein/HflK RQ 1 EV IPR010201; TIGR01933; sufficient; // AC GenProp0685 DE CRISPR system, I-D/Cyano subtype TP SYSTEM AU Haft DH TH 0 CC This property describes a set of CRISPR-Associated Sequence (Cas) CC proteins found in at least three Cyanobacteria, as well as in a diverse CC set of Archaea. Associated repeats are typically 35-37 nucleotides CC long. -- SN 1 ID CRISPR-associated protein Cas1, Cyano-type DN CRISPR-associated protein Cas1, Cyano-type RQ 1 EV IPR002729; TIGR00287; EV IPR023843; TIGR04093; -- SN 2 ID CRISPR-associated helicase, Cyano-type DN CRISPR-associated helicase, Cyano-type RQ 1 EV IPR017575; TIGR03158; sufficient; -- SN 3 ID CRISPR-associated protein Csc1 DN CRISPR-associated protein Csc1 RQ 1 EV IPR017576; TIGR03159; sufficient; -- SN 4 ID CRISPR-associated protein Csc2 DN CRISPR-associated protein Csc2 RQ 1 EV IPR017574; TIGR03157; sufficient; -- SN 5 ID CRISPR-associated protein Csc3 DN CRISPR-associated protein Csc3 RQ 0 EV IPR017589; TIGR03174; sufficient; // AC GenProp0686 DE Allantoin catabolism to glyoxalate and urea TP METAPATH AU Haft DH TH 0 RN [1] RM 10601204 RT Genetic analysis of a chromosomal region containing genes required for RT assimilation of allantoin nitrogen and linked glyoxylate metabolism in RT Escherichia coli. RA Cusa E, Obradors N, Baldomà L, Badía J, Aguilar J; RL J Bacteriol. 1999;181:7479-7484. CC (S)-allantoin ([(4S)-2,5-dioxoimidazolidin-4-yl]urea) is a breakdown CC product of urate that may be obtained by an endogenous urate catabolism CC pathway or by transport from the environment. Catabolism of allantoate CC consists of a three-step pathway resulting in glyoxalate. This is CC further processed to tartronate semi-aldehyde CC (2-hydroxy-3-oxopropanoate) and subsequently to either CC phyosphoglycerate or glycoaldehyde (in the pathway to the pyridoxine CC component of vitamin B6). Since many pathways result in glyoxalate, CC this genome property terminates at that compound although the downsream CC enzymes may be grouped into apparent operons in many organisms (i.e. E. CC coli). Degradation of allantoin results in the production of two CC molecules of urea which may be excreted or used as a source of ammonia CC in urease-containing organisms. -- SN 1 ID Source of (S)-allantoin DN Source of (S)-allantoin RQ 0 EV IPR012681; TIGR00800; TG GO:0009442; EV GenProp0688; TG GO:0009442; -- SN 2 ID Ureidoglycolate lyase (4.3.2.3) DN Ureidoglycolate lyase (4.3.2.3) RQ 1 EV IPR007247; PF04115; sufficient; TG GO:0009442; -- SN 3 ID Allantoinase (3.5.2.5) DN Allantoinase (3.5.2.5) RQ 1 EV IPR017593; TIGR03178; sufficient; TG GO:0009442; -- SN 4 ID Allantoin hydrolysis, final DN Allantoin hydrolysis, final RQ 0 EV IPR005164; TIGR02961; sufficient; TG GO:0009442; -- SN 5 ID Allantoin hydrolysis, initial DN Allantoin hydrolysis, initial RQ 1 EV IPR005164; TIGR02961; sufficient; TG GO:0009442; EV IPR017591; TIGR03176; sufficient; TG GO:0009442; -- SN 6 ID Cupin domain protein, unknown function DN Cupin domain protein, unknown function RQ 0 EV IPR017627; TIGR03214; sufficient; TG GO:0009442; // AC GenProp0687 DE Allantoin catabolism to oxamate and carbamoyl-phosphate TP PATHWAY AU Haft DH TH 1 RN [1] RM 10601204 RT Genetic analysis of a chromosomal region containing genes required for RT assimilation of allantoin nitrogen and linked glyoxylate metabolism in RT Escherichia coli. RA Cusa E, Obradors N, Baldomà L, Badía J, Aguilar J; RL J Bacteriol. 1999;181:7479-7484. CC Allantoin ([(4S)-2,5-dioxoimidazolidin-4-yl]urea) is a breakdown CC product of urate and may be obtained by an endogenous urate catabolism CC pathway or by transport from the environment. This catabolism pathway CC avoids the production of urea (as in the pathway to glyoxalate -- CC GenProp0686) and instead produces ammonia by the action of allantoate CC amidohydrolase and the breakdown of carbamoyl-phosphate by carbamate CC kinase. A by-product of this pathway is oxamate (oxalic monoamide) CC which is presumably excreted. -- SN 1 ID Carbamate kinase (EC 2.7.2.2) DN Carbamate kinase (EC 2.7.2.2) RQ 1 EV IPR003964; TIGR00746; sufficient; -- SN 2 ID Source of allantoin DN Source of allantoin RQ 0 EV IPR012681; TIGR00800; EV GenProp0688; -- SN 3 ID Allantoinase (EC 3.5.2.5) DN Allantoinase (EC 3.5.2.5) RQ 1 EV IPR017593; TIGR03178; sufficient; -- SN 4 ID Allantoate amidohydrolase (EC 3.5.3.9) DN Allantoate amidohydrolase (EC 3.5.3.9) RQ 1 EV IPR010158; TIGR01879; EV IPR017591; TIGR03176; sufficient; EV IPR005164; TIGR02961; sufficient; -- SN 5 ID Ureidoglycolate dehydrogenase (EC 1.1.1.54) DN Ureidoglycolate dehydrogenase (EC 1.1.1.54) RQ 1 EV IPR017590; TIGR03175; sufficient; -- SN 6 ID Cupin domain protein, unknown function DN Cupin domain protein, unknown function RQ 0 EV IPR017627; TIGR03214; sufficient; // AC GenProp0688 DE Urate catabolism to allantoin TP PATHWAY AU Haft DH TH 0 RN [1] RM 16787778 RT The crystal structure of the transthyretin-like protein from Salmonella RT dublin, a prokaryote 5-hydroxyisourate hydrolase. RA Hennebry SC, Law RH, Richardson SJ, Buckle AM, Whisstock JC; RL J Mol Biol. 2006;359:1389-1399. RN [2] RM 15790071 RT Identification, cloning and expression of Pseudomonas aeruginosa Ps-x RT putative urate oxidase gene in Escherichia coli. RA Saeed HM, Abdel-Fattah YR, Berekaa MM, Gohar YM, Elbaz MA; RL Pol J Microbiol. 2004;53:227-236. RN [3] RM 16462750 RT Completing the uric acid degradation pathway through phylogenetic RT comparison of whole genomes. RA Ramazzina I, Folli C, Secchi A, Berni R, Percudani R; RL Nat Chem Biol. 2006;2:144-148. CC Urate is the product of xanthine catabolism by either the xanthine CC dehydrogenase complex or xanthine oxidase. The purine ring system of CC urate is oxidized by uricase (urate oxidase) and the 6-membered ring CC is opened by hydroxyisourate hydrolase. The hydrolase may be CC unnecessary in some organisms as the hydroxyisourate will hydrolyze CC spontaneously, albeit an a slow rate. The resulting product (OHCU) CC then spontaneously decarboxylates, resulting in a mixture of CC (S)- and (R)-allantoin. For further catabolism, generally only CC (S)-allantoin is processed, so allantoin racemace is also typically CC found. An OHCU carboxylase has been discovered in Mus musculus which CC does have homologs in prokaryotes. -- SN 2 ID Urate oxidase (EC 1.7.3.3) DN Urate oxidase (EC 1.7.3.3) RQ 1 EV IPR002042; PF01014; sufficient; TG GO:0019628; -- SN 3 ID OHCU decarboxylase DN OHCU decarboxylase RQ 1 EV IPR017580; TIGR03164; sufficient; TG GO:0019628; EV IPR017595; TIGR03180; sufficient; TG GO:0019628; -- SN 4 ID Hydroxyisourate hydrolase (EC 3.5.2.17) DN Hydroxyisourate hydrolase (EC 3.5.2.17) RQ 1 EV IPR014306; TIGR02962; sufficient; TG GO:0019628; -- SN 5 ID UraD N-terminal domain/upstream protein DN UraD N-terminal domain/upstream protein RQ 0 EV IPR017625; TIGR03212; sufficient; TG GO:0019628; // AC GenProp0689 DE Glyoxalate conversion to phosphoglycerate TP PATHWAY AU Haft DH TH 0 CC Glyoxalate is a common intermediate produced by a number of catabolic CC and anapleurotic pathways, notably the breakdown for allantoate, CC proline and glycine and the glyoxalate shunt. This pathway is initiated CC by the incorporation of carbon dioxide utilizing the TPP-dependent CC enzyme, tartronate-semialdehyde synthase (aka glyoxalate carbo-ligase, CC gcl). Note that this is not a carbon-fixation pathway. For instance, CC in the case of allantoate catabolism, the production of glyoxalate also CC produces one or more molecules of carbon dioxide. Intermediates in CC this pathway (tartronate semialdehyde, and glycerate) may be diverted CC to other final products involved, for instance in covactor CC biosynthesis. Phosphoglycerate may be put to a large number of CC metabolic uses. -- SN 1 ID Glyoxalate carbo-ligase DN Glyoxalate carbo-ligase RQ 1 EV IPR006397; TIGR01504; sufficient; -- SN 2 ID Glycerate kinase (EC 2.7.1.31) DN Glycerate kinase/glxK (EC 2.7.1.31) RQ 1 EV IPR004381; TIGR00045; sufficient; -- SN 3 ID Tartronate semialdehyde reductase (EC 1.1.1.60) DN Tartronate semialdehyde reductase/glxR (EC 1.1.1.60) RQ 1 EV IPR006398; TIGR01505; sufficient; -- SN 4 ID Hydroxypyruvate isomerase DN Hydroxypyruvate isomerase RQ 0 EV IPR017643; TIGR03234; sufficient; // AC GenProp0691 DE Glycolysis TP PATHWAY AU Haft DH TH 0 CC Various monosaccharides can be converted into fructose-1,6-bisphosphate CC and subsequently broken down to three carbon units (i.e. pyruvate) via CC this pathway for utilization in basic metabolism. -- SN 1 ID Phosphopyruvate hydratase DN Phosphopyruvate hydratase RQ 1 EV IPR000941; TIGR01060; sufficient; TG GO:0006096; -- SN 2 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase RQ 1 EV IPR000741; PF00274; sufficient; TG GO:0006096; EV IPR006411; TIGR01520; sufficient; TG GO:0006096; -- SN 3 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase RQ 1 EV IPR006424; TIGR01534; sufficient; TG GO:0006096; EV IPR006436; TIGR01546; sufficient; TG GO:0006096; -- SN 4 ID Phosphoglycerate mutase DN Phosphoglycerate mutase RQ 1 EV IPR005995; TIGR01307; sufficient; TG GO:0006096; EV IPR004456; TIGR00306; sufficient; TG GO:0006096; EV IPR005952; TIGR01258; sufficient; TG GO:0006096; -- SN 5 ID Phosphoglycerate kinase DN Phosphoglycerate kinase RQ 1 EV IPR001576; PF00162; sufficient; TG GO:0006096; -- SN 6 ID Pyruvate kinase DN Pyruvate kinase RQ 1 EV IPR001697; TIGR01064; sufficient; TG GO:0006096; -- SN 7 ID Triosephosphate isomerase DN Triosephosphate isomerase RQ 1 EV IPR000652; TIGR00419; sufficient; TG GO:0006096; EV IPR000652; PF00121; sufficient; TG GO:0006096; -- SN 8 ID Source(s) of fructose-1,6-bisphosphate DN Source(s) of fructose-1,6-bisphosphate RQ 1 EV GenProp0693; TG GO:0006096; EV GenProp0694; TG GO:0006096; // AC GenProp0692 DE Selenouridine-containing tRNA TP PATHWAY AU Haft DH TH 1 RN [1] RM 14594807 RT Functional diversity of the rhodanese homology domain: the Escherichia RT coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine RT synthase. RA Wolfe MD, Ahmed F, Lacourciere GM, Lauhon CT, Stadtman TC, Larson TJ; RL J Biol Chem. 2004;279:1801-1809. RN [2] RM 16086848 RT Evolution of selenium utilization traits. RA Romero H, Zhang Y, Gladyshev VN, Salinas G; RL Genome Biol. 2005;6:r66. RN [3] RM 22293502 RT Selenomodification of tRNA in archaea requires a bipartite rhodanese RT enzyme. RA Su D, Ojo TT, Söll D, Hohn MJ; RL FEBS Lett. 2012;586:717-721. CC Selenium may occur in cells both in proteins, in the form of CC selenocysteine, and in tRNA, in the form of 2-selenouridine. The two CC incorporation systems both rely on the selenium donor protein, CC selenide-water dikinase. This property describes the two-gene CC combination of selenide-water dikinase and tRNA 2-selenouridine CC synthase. Note that an initial sulfurtransferase reaction must proceed CC the action of 2-selenouridine synthase; the enzyme(s) responsible is CC not currently included in the definition of this Genome Property. -- SN 1 ID Selenide, water dikinase DN Selenide, water dikinase RQ 1 EV IPR004536; TIGR00476; sufficient; TG GO:0006400; -- SN 2 ID 2-selenouridine synthase DN 2-selenouridine synthase RQ 1 EV IPR017582; TIGR03167; sufficient; TG GO:0006400; // AC GenProp0693 DE Fructose utilization as fructose-1,6-bisphosphate TP SYSTEM AU Haft DH TH 0 CC Fructose may be imported into the cell as a carbon source via the CC fructose-specific phosphotransferase system (PTS) and converted to the CC glycolysis pathway intermediate fructose-1,6-bisphosphate by the action CC of 1-phosphofructokinase. -- SN 1 ID PTS core components DN PTS core components RQ 1 EV GenProp0119; -- SN 2 ID PTS IIA, fructose-specific DN PTS IIA, fructose-specific RQ 1 EV IPR004715; TIGR00848; sufficient; -- SN 3 ID PTS IIB, fructose-specific DN PTS IIB, fructose-specific RQ 1 EV IPR003353; TIGR00829; sufficient; -- SN 4 ID PTS IIC, fructose-specific DN PTS IIC, fructose-specific RQ 1 EV IPR006327; TIGR01427; sufficient; -- SN 5 ID 1-phosphofructokinase DN 1-phosphofructokinase RQ 1 EV IPR017583; TIGR03168; EV IPR022463; TIGR03828; sufficient; // AC GenProp0694 DE Glucose utilization as fructose-1,6-bisphosphate TP SYSTEM AU Haft DH TH 0 CC Glucose may be imported into the cell as a carbon source via the CC glucose-specific phosphotransferase system (PTS) and converted to the CC glycolysis pathway intermediate fructose-1,6-bisphosphate by the action CC of phosphoglucose isomerase (PGI) and 6-phosphofructokinase (6-PFK). -- SN 1 ID 6-Phosphofructokinase DN 6-Phosphofructokinase/6-PFK RQ 1 EV IPR009161; TIGR02478; sufficient; EV IPR012828; TIGR02482; sufficient; -- SN 2 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase/PGI RQ 1 EV IPR001672; PF00342; sufficient; EV IPR011857; TIGR02128; sufficient; // AC GenProp0695 DE Cytochrome b558/566 TP SYSTEM AU Haft DH TH 0 RN [1] RM 15632423 RT Respiratory gene clusters of Metallosphaera sedula - differential RT expression and transcriptional organization. RA Kappler U, Sly LI, McEwan AG; RL Microbiology. 2005;151:35-43. CC Cytochrome b558/566 is a heterodimeric, highly glycosylated, mono-heme CC cytochrome. It was described originally in Sulfolobus acidocaldarius, a CC hyperthermoacidophilic member of the Crenarchaeota, and is found also CC in related Crenarchaeota. It is suggested to work in a system analogous CC to cytochrome bc1. -- SN 1 ID Cytochrome b558/566, subunit A DN Cytochrome b558/566, subunit A RQ 1 EV IPR017572; TIGR03154; sufficient; -- SN 2 ID Cytochrome b558/566, subunit B DN Cytochrome b558/566, subunit B RQ 1 EV IPR017573; TIGR03155; sufficient; -- SN 3 ID Rieske iron-sulphur protein SoxL2 DN Rieske iron-sulphur protein SoxL2 RQ 0 EV IPR017586; TIGR03171; sufficient; // AC GenProp0696 DE Xanthine utilization as a source of guanine-monophosphate (GMP) TP SYSTEM AU Haft DH TH 0 CC Xanthine may be imported into the cell and converted to GMP by the CC route described by this property. -- SN 1 ID GMP synthase, C-term DN GMP synthase, C-term RQ 1 EV IPR001674; TIGR00884; sufficient; -- SN 2 ID GMP synthase, N-term DN GMP synthase, N-term RQ 1 EV IPR004739; TIGR00888; sufficient; -- SN 3 ID Xanthine import DN Xanthine import RQ 1 EV IPR017588; TIGR03173; sufficient; -- SN 4 ID Xanthine phosphoribosyltransferase DN Xanthine phosphoribosyltransferase RQ 1 EV IPR010079; TIGR01744; sufficient; // AC GenProp0697 DE Guanine monophosphate (GMP) biosynthesis from inosine monophosphate (IMP) TP PATHWAY AU Haft DH TH 0 DC Purine Metabolism: GMP Biosynthesis DR KEGG; map00230; CC Inosine monophosphate (IMP) can be used as a source of guanosine CC monophosphate (GMP) via this pathway in which xanthosine monophosphate CC (XMP) is an intermediate. IMP may come from de novo biosynthesis CC or by the import of inosine derivatives. -- SN 1 ID GMP synthase, C-term DN GMP synthase, C-term RQ 1 EV IPR001674; TIGR00884; sufficient; TG GO:0006177; -- SN 2 ID GMP synthase, N-term DN GMP synthase, N-term RQ 1 EV IPR004739; TIGR00888; sufficient; TG GO:0006177; -- SN 3 ID Inosine-5'-phosphate dehydrogenase DN Inosine-5'-phosphate dehydrogenase RQ 1 EV IPR005990; TIGR01302; sufficient; TG GO:0006177; // AC GenProp0698 DE Xanthine catabolism to urate TP METAPATH AU Haft DH TH 0 CC The committed step in the catabolism of purines is the oxidation of the CC purine ring of xanthine (via hypoxanthine) to urate (uric acid). The CC xanthine may result from the deamination of guanine (or hypoxanthine CC from adenine), or may be imported via a permease. Several systems CC exist for the conversion of xanthine to urate including the XdhABC CC xanthine dehydrogenase complex, xanthine oxidase and other less CC well-described oxidoreductases. -- SN 1 ID Xanthine conversion to urate (uric acid) DN Xanthine conversion to urate (uric acid) RQ 1 EV GenProp0640; -- SN 2 ID Source of xanthine DN Source of xanthine RQ 1 EV IPR017588; TIGR03173; sufficient; EV IPR006679; TIGR01178; sufficient; EV IPR014311; TIGR02967; sufficient; // AC GenProp0699 DE DNA gyrase TP SYSTEM AU Haft DH TH 0 CC The term DNA gyrase is synonymous with type II DNA topoisomerase. The CC enzymes consists of A and B subunits. -- SN 1 ID DNA gyrase, A subunit DN DNA gyrase, A subunit RQ 1 EV IPR005743; MF_01897; sufficient; -- SN 2 ID DNA gyrase, B subunit DN DNA gyrase, B subunit RQ 1 EV IPR011557; TIGR01059; sufficient; // AC GenProp0700 DE Purine catabolism via urate, xanthine and allantoin TP METAPATH AU Haft DH TH 0 CC This property is an overview of the complete catabolic pathways leading CC from intracellular guanine, adenine or extracellular xanthine, through CC to the breakdown products of allantoin, oxamate or glyoxalate. -- SN 1 ID Urate biosynthesis via xanthine DN Urate biosynthesis via xanthine RQ 1 EV GenProp0698; -- SN 2 ID Urate catabolism to allantoin DN Urate catabolism to allantoin RQ 1 EV GenProp0688; -- SN 3 ID Allantoin catabolism DN Allantoin catabolism RQ 1 EV GenProp0687; EV GenProp0686; // AC GenProp0701 DE DNA sulfur modification system dnd TP SYSTEM AU Haft DH TH 0 RN [1] RM 17439960 RT DNA modification by sulfur: analysis of the sequence recognition RT specificity surrounding the modification sites. RA Liang J, Wang Z, He X, Li J, Zhou X, Deng Z; RL Nucleic Acids Res. 2007;35:2944-2954. RN [2] RM 16102010 RT A novel DNA modification by sulphur. RA Zhou X, He X, Liang J, Li A, Xu T, Kieser T, Helmann JD, Deng Z; RL Mol Microbiol. 2005;57:1428-1438. RN [3] RM 19232083 RT DNA phosphorothioation in Streptomyces lividans: mutational analysis of RT the dnd locus. RA Xu T, Liang J, Chen S, Wang L, He X, You D, Wang Z, Li A, Xu Z, Zhou X, RA Deng Z; RL BMC Microbiol. 2009;9:41. CC Several bacteria have an unusual DNA phenotype, Dnd (degradation during CC electrophoresis). This property results from a sulfur modification on a CC G residue, shown in one example to occur at a rate of about one sulfur CC per 6000 base pairs. Study of Streptomyces lividans 1326 showed a CC stringent requirement for a core motif GGCC within a longer recognition CC region represented as cGGCCgccg [1]. Five characteristic genes, CC including a predicted cysteine sulfurtransferase related to IscS, appear CC responsible for the dnd phenotype. Through comparative genomic studies, CC we find that, beyond a core set of three genes dndC, dndD, and dndE, CC other proteins may be associated. That is, they show up specifically in CC genomes that carry dndCDE and occur nearby, but do not show up in all CC such genomes. -- SN 1 ID Dnd system cysteine sulfurtransferase DN Aminotransferase class V domain (EC 2.8.1.7) RQ 0 EV IPR000192; PF00266; EV IPR017644; TIGR03235; sufficient; -- SN 2 ID Dnd operon putative ATPase DndB DN DNA sulfur modification protein DndB RQ 0 EV IPR017642; TIGR03233; sufficient; -- SN 3 ID Dnd operon putative sulfurtransferase DndC DN Putative sulfurtransferase DndC RQ 1 EV IPR017598; TIGR03183; sufficient; -- SN 4 ID Dnd operon putative ATPase DndD DN DNA sulphur modification protein DndD RQ 1 EV IPR017599; TIGR03185; sufficient; -- SN 5 ID Dnd operon putative carboxylase DndE DN DNA sulphur modification protein DndE RQ 1 EV IPR014969; TIGR03184; sufficient; -- SN 6 ID DNA phosphorothioation-dependent restriction protein DptF DN Dnd system-associated protein 3 RQ 0 EV IPR017647; TIGR03238; sufficient; -- SN 7 ID DNA phosphorothioation-dependent restriction protein DptG DN Dnd system-associated protein 1 RQ 0 EV IPR017645; TIGR03236; sufficient; -- SN 8 ID DNA phosphorothioation-dependent restriction protein DptH DN Dnd system-associated protein 2 RQ 0 EV IPR017646; TIGR03237; sufficient; -- SN 9 ID Dnd system-associated protein 4 DN Dnd system-associated protein 4 RQ 0 EV IPR023983; TIGR04062; // AC GenProp0702 DE Benzoyl-CoA reductase TP SYSTEM AU Haft DH TH 0 CC This model describes an ATP-dependent four-subunit enzyme, benzoyl-CoA CC reductase, that dearomatizes benzoyl-CoA to CC cyclohexa-1,5-diene-1-carbonyl-CoA. This enzyme acts under anaerobic CC conditions. -- SN 1 ID Benzoyl-CoA reductase, subunit A DN Benzoyl-CoA reductase, subunit A RQ 1 EV IPR011954; TIGR02259; sufficient; -- SN 2 ID Benzoyl-CoA reductase, subunit B DN Benzoyl-CoA reductase, subunit B RQ 1 EV IPR011955; TIGR02260; sufficient; -- SN 3 ID Benzoyl-CoA reductase, subunit C DN Benzoyl-CoA reductase, subunit C RQ 1 EV IPR011958; TIGR02263; sufficient; -- SN 4 ID Benzoyl-CoA reductase, subunit D DN Benzoyl-CoA reductase, subunit D RQ 1 EV IPR011956; TIGR02261; sufficient; // AC GenProp0703 DE 4-hydroxybenzoyl-CoA reductase TP SYSTEM AU Haft DH TH 0 CC This property represents an enzyme, 4-hydroxybenzoyl-CoA reductase, CC that occurs as alpha2,beta2,gamma2 heterohexamer. This enzyme converts CC 4-hydroxybenzoyl-CoA, a metabolite of phenolic compounds, to CC benzoyl-CoA. -- SN 1 ID 4-hydroxybenzoyl-CoA reductase, alpha subunit DN 4-hydroxybenzoyl-CoA reductase, alpha subunit RQ 1 EV IPR017607; TIGR03194; sufficient; -- SN 2 ID 4-hydroxybenzoyl-CoA reductase, beta subunit DN 4-hydroxybenzoyl-CoA reductase, beta subunit RQ 1 EV IPR017608; TIGR03195; sufficient; -- SN 3 ID 4-hydroxybenzoyl-CoA reductase, gamma subunit DN 4-hydroxybenzoyl-CoA reductase, gamma subunit RQ 1 EV IPR017606; TIGR03193; sufficient; // AC GenProp0704 DE tRNA U34 carboxymethylaminomethyl modification TP PATHWAY AU Haft DH TH 0 CC GidA and MnmE act as a heterotetramer for the cmnmU34 modification in CC bacteria and eukarya. They are absent from the Archaea. Their action CC may be followed by that of the bifunctional MnmC (YfcK) protein. -- SN 1 ID U34 modification protein GidA DN U34 modification protein GidA RQ 1 EV IPR004416; TIGR00136; sufficient; -- SN 2 ID Cysteine desulfurase IscS DN Cysteine desulfurase IscS RQ 1 EV IPR010240; TIGR02006; sufficient; -- SN 3 ID tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase DN tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase/MnmA RQ 1 EV IPR004506; TIGR00420; sufficient; -- SN 4 ID MnmC, C-term model DN MnmC, C-term model RQ 0 EV IPR017610; TIGR03197; sufficient; -- SN 5 ID U34 modification protein MnmE DN U34 modification protein MnmE RQ 1 EV IPR004520; TIGR00450; sufficient; // AC GenProp0705 DE Xanthine dehydrogenase, bacillus type (pucABCDE) TP SYSTEM AU Haft DH TH 0 RN [1] RM 11344136 RT Functional analysis of 14 genes that constitute the purine catabolic RT pathway in Bacillus subtilis and evidence for a novel regulon RT controlled by the PucR transcription activator. RA Schultz AC, Nygaard P, Saxild HH; RL J Bacteriol. 2001;183:3293-3302. CC This xanthine dehydrogenase complex is particular to a small number of CC organisms including Bacillus subtilis, where it has been characterized. -- SN 1 ID Accessory factor PucA DN Accessory factor PucA RQ 0 EV IPR003777; PF02625; sufficient; -- SN 2 ID PucB gene DN PucB gene RQ 0 EV IPR017615; TIGR03202; sufficient; -- SN 3 ID FAD-binding domain, PucC DN FAD-binding domain, PucC RQ 1 EV IPR017612; TIGR03199; sufficient; -- SN 4 ID Molybdopterin-binding subunit, pucD DN Molybdopterin-binding subunit, pucD RQ 1 EV IPR017609; TIGR03196; sufficient; -- SN 5 ID Fe-S cluster-binding subunit, PucE DN Fe-S cluster-binding subunit, PucE RQ 1 EV IPR017611; TIGR03198; sufficient; // AC GenProp0706 DE Cyclohexa-1,5-diene-1-carbonyl-CoA to 3-hydroxypimelyl-CoA, dch/had/oah Pathway TP PATHWAY AU Haft DH TH 0 CC This property describes degradation of CC cyclohexa-1,5-diene-1-carbonyl-CoA, which is the product of benzoyl-CoA CC reductase activity, to 3-hydroxypimelyl-CoA, as occurs in Thauera CC aromatica and several other species. A different pathway occurs in CC Rhodopseudomonas palustris. This pathway serves the anaerobic CC metabolism of a number of different aromatic compounds. -- SN 1 ID Cyclohexa-1,5-dienecarbonyl-CoA hydratase DN Cyclohexa-1,5-dienecarbonyl-CoA hydratase RQ 1 EV IPR017602; TIGR03189; sufficient; TG GO:0019439; -- SN 2 ID 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase DN 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase RQ 1 EV IPR017614; TIGR03201; sufficient; TG GO:0019439; -- SN 3 ID 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase DN 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase RQ 1 EV IPR017613; TIGR03200; sufficient; TG GO:0019439; // AC GenProp0707 DE Botulinum toxin system TP SYSTEM AU Haft DH TH 0 CC Clostridium botulinum contains a virulence cassette encoding a potent CC neurotoxin called BoNT. Also found in this operon are several CC hemagglutinin proteins and a regulatory sigma-70 gene. -- SN 1 ID Neurotoxin component DN Neurotoxin component/BoNT RQ 1 EV IPR013104; PF07951; sufficient; EV IPR012500; PF07952; sufficient; -- SN 2 ID Sigma-70 factor regulator DN Sigma-70 factor regulator RQ 1 EV IPR017622; TIGR03209; sufficient; -- SN 3 ID Haemagglutinin HA17 DN Haemagglutinin HA17 RQ 1 EV IPR033982; PF05588; sufficient; -- SN 4 ID Haemagglutinin HA33 DN Haemagglutinin HA33 RQ 1 EV IPR000772; cd00161; sufficient; -- SN 5 ID Haemagglutinin HA70 DN Haemagglutinin HA70 RQ 1 EV IPR003897; PF03505; sufficient; -- SN 6 ID Non-toxin, non-haemaglutinin component DN Non-toxin, non-haemaglutinin component RQ 1 EV IPR013677; PF08470; sufficient; // AC GenProp0708 DE Catechol meta-cleavage pathway TP PATHWAY AU Haft DH TH 0 CC The metabolism of many aromatic compounds proceeds by way of catechol, CC a compound chemically similar to benzene except that a pair of adjacent CC H atoms of benzene are replaced by OH groups of catechol. This property CC describes the meta-cleavage pathway, in which catechol 2,3-dioxygenase CC cleaves the ring at the meta position. Degradation continues to CC pyruvate and acetyl-CoA. Some compounds degraded by way of catechol and CC this pathway, include benzoate, toluene, salicylate, phenol, napthalene, CC and 3,4-dimethylphenol (dmp). -- SN 1 ID Catechol 2,3-dioxygenase DN Catechol 2,3-dioxygenase RQ 1 EV IPR017624; TIGR03211; sufficient; -- SN 3 ID 2-hydroxymuconic semialdehyde dehydrogenase DN 2-hydroxymuconic semialdehyde dehydrogenase RQ 1 EV IPR017628; TIGR03216; sufficient; -- SN 4 ID 4-oxalocrotonate isomerase DN 4-oxalocrotonate isomerase RQ 1 EV IPR018191; TIGR00013; sufficient; -- SN 5 ID 4-oxalocrotonate decarboxylase DN 4-oxalocrotonate decarboxylase RQ 1 EV IPR017630; TIGR03218; sufficient; -- SN 6 ID 2-oxopent-4-enoate hydratase DN 2-oxopent-4-enoate hydratase RQ 1 EV IPR017632; TIGR03220; sufficient; -- SN 7 ID 2-oxo-4-hydroxypentanoate aldolase DN 2-oxo-4-hydroxypentanoate aldolase RQ 1 EV IPR017629; TIGR03217; sufficient; -- SN 8 ID Acetaldehyde dehydrogenase (acetylating) DN Acetaldehyde dehydrogenase (acetylating) RQ 1 EV IPR003361; TIGR03215; sufficient; // AC GenProp0709 DE Benzoate catabolism BoxABC pathway TP PATHWAY AU Haft DH TH 0 CC In the presence of molecular oxygen, BoxAB acts as a benzoyl-CoA CC oxygenase. Formate is then hydrolyzed from its product by BoxC. -- SN 1 ID Benzoyl-CoA oxidase, BoxA subunit DN Benzoyl-CoA oxidase, BoxA subunit RQ 1 EV IPR017634; TIGR03224; sufficient; -- SN 2 ID Benzoyl-CoA oxidase, BoxB subunit DN Benzoyl-CoA oxidase, BoxB subunit RQ 1 EV IPR017635; TIGR03225; sufficient; -- SN 3 ID Benzoyl-CoA-dihydrodiol lyase DN Benzoyl-CoA-dihydrodiol lyase RQ 1 EV IPR017633; TIGR03222; sufficient; // AC GenProp0710 DE Generic phosphonates utilization TP METAPATH AU Haft DH TH 0 CC Phosphonates, compounds with carbon-phosphorous bonds, may be CC specifically imported with a transport system and the CP-bond lysed by CC the C-P lyase system. -- SN 1 ID Phosphonate degradation system DN Phosphonate degradation system RQ 1 EV GenProp0232; -- SN 2 ID Phosphonate import system DN Phosphonate import system RQ 1 EV GenProp0236; // AC GenProp0711 DE Catechol ortho-cleavage upper pathway TP PATHWAY AU Haft DH TH 1 RN [1] RM 18836712 RT Induction of ortho- and meta-cleavage pathways in Pseudomonas in RT biodegradation of high benzoate concentration: MS identification of RT catabolic enzymes. RA Cao B, Geng A, Loh KC; RL Appl Microbiol Biotechnol. 2008;81:99-107. CC Catechol is an intermediate in the degradation of a number of CC aromatic compounds, including benzoate. Cleavage of the catechol CC ring can occur either by the ortho- or the meta-cleavage pathways. CC This property describes the initial steps in the ortho-cleavage CC pathway. Catechol is cleaved between two ring hydroxyls by catechol CC 1,2-dioxygenase (catA) to produce cis,cis-muconate. cis,cis-muconate CC is then metabolised (via the three steps catB, catC and catD) to form  CC 3-oxoadipate (the end-point of this upper part of the pathway)[1]. -- SN 1 ID Catechol 1,2-dioxygenase DN Catechol 1,2-dioxygenase/catA RQ 1 EV IPR012801; TIGR02439; sufficient; EV IPR012800; TIGR02438; sufficient; -- SN 2 ID Muconate cycloisomerase DN Muconate cycloisomerase/catB RQ 1 EV IPR013370; TIGR02534; sufficient; -- SN 3 ID Muconolactone delta-isomerase DN Muconolactone delta-isomerase/catC RQ 1 EV IPR003464; TIGR03221; sufficient; -- SN 4 ID 3-oxoadipate enol-lactonase DN 3-oxoadipate enol-lactonase/catD RQ 1 EV IPR026968; TIGR02427; sufficient; // AC GenProp0712 DE 2-aminoethylphosphonate (AEP) ABC transporter, type I, PhnSTUV TP SYSTEM AU Haft DH TH 0 RN [1] RM 7592415 RT Molecular cloning, mapping, and regulation of Pho regulon genes for RT phosphonate breakdown by the phosphonatase pathway of Salmonella RT typhimurium LT2. RA Jiang W, Metcalf WW, Lee KS, Wanner BL; RL J Bacteriol. 1995;177:6411-6421. CC A multisubunit ABC transporter for the import of CC 2-aminoethylphosphonate (AEP, ciliatine) which is then subject to CC catabolism. -- SN 1 ID Periplasmic AEP binding protein DN Putative 2-aminoethylphosphonate binding protein, ABC transporter RQ 1 EV IPR017637; TIGR03227; sufficient; -- SN 2 ID ATP-binding component DN 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT RQ 1 EV IPR017662; TIGR03258; sufficient; -- SN 3 ID Permease component DN 2-aminoethylphosphonate ABC transporter system, permease protein phnU RQ 1 EV IPR017636; TIGR03226; sufficient; -- SN 4 ID Permease component DN 2-aminoethylphosphonate ABC transport system, membrane component PhnV RQ 1 EV IPR017661; TIGR03255; sufficient; // AC GenProp0713 DE 2-aminoethylphosphonate catabolism via phosphonoacetate TP PATHWAY AU Haft DH TH 1 CC This AEP degradation pathway utilizes PhnA, phosphonoacetate hydrolase, CC generating acetate and inorganic phosphate as products. -- SN 1 ID Phosphonoacetate hydrolase DN Phosphonoacetate hydrolase RQ 1 EV IPR012710; TIGR02335; sufficient; -- SN 2 ID 2-aminoethylphosphonate--pyruvate transaminase DN 2-aminoethylphosphonate--pyruvate transaminase RQ 1 EV IPR012703; TIGR02326; sufficient; -- SN 3 ID Aldehyde dehydrogenase DN Phosphonoacetaldehyde dehydrogenase RQ 1 EV IPR017656; TIGR03250; sufficient; -- SN 4 ID Clustered regulatory genes DN Clustered regulatory genes RQ 0 EV IPR000524; PF00392; EV IPR014036; PF00455; -- SN 5 ID 2-aminoethylphosphonate transporters DN 2-aminoethylphosphonate transporters RQ 0 EV GenProp0712; EV GenProp0721; // AC GenProp0714 DE Galactarate utilization via tartronate semi-aldehyde TP SYSTEM AU Haft DH TH 2 CC D-galactarate (D-Mucic acid, 2,3,4,5-tetrahydroxyhexanedioic acid) may CC be utilized by this pathway involving the lyase GarL which produces CC pyruvate and tartronate semi-aldehyde (which may then be further CC converted to 3-phosphoglycerate). -- SN 1 ID Galactarate dehydratase (EC 4.2.1.42) DN Galactarate dehydratase (EC 4.2.1.42) RQ 1 EV IPR007392; PF04295; sufficient; TG GO:0046392; -- SN 2 ID Glycerate kinase (EC 2.7.1.31) DN Glycerate kinase (EC 2.7.1.31) RQ 1 EV IPR004381; TIGR00045; TG GO:0046392; -- SN 3 ID 5-dehydro-4-deoxy-D-glucarate lyase (EC 4.1.2.20) DN 5-dehydro-4-deoxy-D-glucarate lyase (EC 4.1.2.20) RQ 1 EV IPR017648; TIGR03239; sufficient; TG GO:0046392; -- SN 4 ID Tartronate semialdehyde reductase (EC 1.1.1.60) DN Tartronate semialdehyde reductase (EC 1.1.1.60) RQ 1 EV IPR006398; TIGR01505; sufficient; TG GO:0046392; -- SN 6 ID D-galactarate transporter, putative DN D-galactarate transporter, putative RQ 0 EV IPR004681; TIGR00786; TG GO:0046392; EV IPR007387; PF04290; TG GO:0046392; EV IPR004682; TIGR00787; TG GO:0046392; EV IPR004744; TIGR00893; TG GO:0046392; // AC GenProp0715 DE Galactarate utilization via 2-oxoglutarate semialdehyde TP SYSTEM AU Haft DH TH 1 CC This pathway converts D-galactarate to alpha-ketoglutarate via CC 2-oxoglutarate semialdehyde, -- SN 1 ID Galactarate dehydratase (EC 4.2.1.42) DN Galactarate dehydratase (EC 4.2.1.42) RQ 1 EV IPR007392; PF04295; sufficient; -- SN 2 ID 5-dehydro-4-deoxyglucarate dehydratase DN 5-dehydro-4-deoxyglucarate dehydratase RQ 1 EV IPR002220; PF00701; EV IPR017655; TIGR03249; sufficient; -- SN 3 ID 2-oxoglutarate semialdehyde dehydrogenase DN 2-oxoglutarate semialdehyde dehydrogenase RQ 0 EV IPR015590; PF00171; -- SN 4 ID D-galactarate transorter, putative DN D-galactarate transorter, putative RQ 0 EV IPR004744; TIGR00893; // AC GenProp0716 DE Glucarate utilization via tartronate semi-aldehyde TP SYSTEM AU Haft DH TH 1 RN [1] RM 9772162 RT Evolution of enzymatic activities in the enolase superfamily: RT characterization of the (D)-glucarate/galactarate catabolic pathway in RT Escherichia coli. RA Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA; RL Biochemistry. 1998;37:14369-14375. CC D-glucarate may be utilized by this pathway involving the lyase CC (aldolase) GarL which produces pyruvate and tartronate semi-aldehyde, CC which may then be further converted to 3-phosphoglycerate. GarD, the CC dehydratase, and GarR the reductase, may be present in the absence of CC GarL and where each is part of different processes. -- SN 1 ID Glycerate kinase (EC 2.7.1.31) DN Glycerate kinase (EC 2.7.1.31) RQ 0 EV IPR004381; TIGR00045; sufficient; TG GO:0019394; EV IPR004381; TIGR00045; sufficient; TG GO:0019394; -- SN 2 ID 5-dehydro-4-deoxy-D-glucarate lyase (EC 4.1.2.20) DN 5-dehydro-4-deoxy-D-glucarate lyase (EC 4.1.2.20) RQ 1 EV IPR017648; TIGR03239; sufficient; TG GO:0019394; -- SN 3 ID Tartronate semialdehyde reductase (EC 1.1.1.60) DN Tartronate semialdehyde reductase (EC 1.1.1.60) RQ 1 EV IPR006398; TIGR01505; sufficient; TG GO:0019394; -- SN 4 ID Glucarate dehydratase (EC 4.2.1.40) DN Glucarate dehydratase (EC 4.2.1.40) RQ 1 EV IPR017653; TIGR03247; sufficient; TG GO:0019394; -- SN 5 ID D-glucarate transporter, putative DN D-glucarate transporter, putative RQ 0 EV IPR004744; TIGR00893; TG GO:0019394; // AC GenProp0717 DE Glucarate utilization via 2-oxoglutarate semialdehyde TP SYSTEM AU Haft DH TH 0 CC This pathway converts D-glucarate to alpha-ketoglutarate via CC 2-oxoglutarate. -- SN 1 ID Glucarate dehydratase (EC 4.2.1.40) DN Glucarate dehydratase (EC 4.2.1.40) RQ 1 EV IPR017653; TIGR03247; sufficient; TG GO:0019394; -- SN 2 ID 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) DN 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) RQ 1 EV IPR002220; PF00701; TG GO:0019394; EV IPR017655; TIGR03249; sufficient; TG GO:0019394; -- SN 3 ID 2-oxoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) DN 2-oxoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) RQ 1 EV IPR015590; PF00171; TG GO:0019394; -- SN 4 ID D-glucarate transorter, putative DN D-glucarate transorter, putative RQ 0 EV IPR004744; TIGR00893; TG GO:0019394; EV IPR011701; PF07690; TG GO:0019394; // AC GenProp0718 DE Oxalate degradation TP PATHWAY AU Haft DH TH 0 RN [1] RM 16517636 RT Transcriptional and functional analysis of oxalyl-coenzyme A (CoA) RT decarboxylase and formyl-CoA transferase genes from Lactobacillus RT acidophilus. RA Azcarate-Peril MA, Bruno-Bárcena JM, Hassan HM, Klaenhammer TR; RL Appl Environ Microbiol. 2006;72:1891-1899. RN [2] RM 12844490 RT The crystal structure of the Escherichia coli YfdW gene product reveals RT a new fold of two interlaced rings identifying a wide family of CoA RT transferases. RA Gruez A, Roig-Zamboni V, Valencia C, Campanacci V, Cambillau C; RL J Biol Chem. 2003;278:34582-34586. CC A two-enzyme pathway degrades oxalate, a toxic metabolite. Formyl-CoA CC transferase transfers coenzyme A from formyl-CoA to oxalate, leaving CC formate. Oxalyl-CoA decarboxylase, a TPP-containing enzyme, removes C02 CC to regenerate formyl-CoA. The net result is conversion of oxalate to CC formate and CO2. This system was originally described in Oxalobacter CC formigenes from the human gut, and is found in a number of other gut CC bacteria. -- SN 1 ID Formyl-CoA transferase DN Formyl-CoA transferase RQ 1 EV IPR017659; TIGR03253; sufficient; -- SN 2 ID Oxalyl-CoA decarboxylase DN Oxalyl-CoA decarboxylase RQ 1 EV IPR017660; TIGR03254; sufficient; // AC GenProp0719 DE Methyl-coenzyme M reductase TP SYSTEM AU Haft DH TH 0 CC Methyl-coenzyme M reductase is a nickel-containing, alpha2/beta2/gamma2 CC hexameric enzyme that catalyzes the final step in methanogenesis. This CC enzyme has several novel post-translational modifications; it is found CC in methanogenic archaea, many of which are hyperthermophiles. Many CC archaea have two versions of this enzyme. It appears that some Archaea CC are methanotrophic; homologous proteins act in the anaerobic oxidation CC of methane rather than in methanogenesis. -- SN 1 ID Methyl-coenzyme M reductase, alpha subunit DN Methyl-coenzyme M reductase, alpha subunit RQ 1 EV IPR016212; TIGR03256; sufficient; -- SN 2 ID Methyl-coenzyme M reductase, beta subunit DN Methyl-coenzyme M reductase, beta subunit RQ 1 EV IPR003179; TIGR03257; sufficient; -- SN 3 ID Methyl-coenzyme M reductase, gamma subunit DN Methyl-coenzyme M reductase, gamma subunit RQ 1 EV IPR003178; TIGR03259; sufficient; -- SN 4 ID Methyl coenzyme M reductase system, component A2 DN Methyl coenzyme M reductase system, component A2 RQ 1 EV IPR017669; TIGR03269; sufficient; -- SN 5 ID Methyl-coenzyme M reductase I operon protein C DN Methyl-coenzyme M reductase I operon protein C RQ 1 EV IPR007687; TIGR03264; sufficient; -- SN 6 ID Methyl-coenzyme M reductase operon protein D DN Methyl-coenzyme M reductase operon protein D RQ 1 EV IPR003901; TIGR03260; sufficient; // AC GenProp0720 DE 2-aminoethylphosphonate utilization TP METAPATH AU Haft DH TH 0 CC 2-aminoethylphosphonate (2-AEP) is a common phosphonate compound found CC in the environment. At least two related pathways are known for its CC catabolism. The critical enzyme, PhnW (2-AEP:pyruvate CC aminotransferase) is found in both of these pathways as well as CC (working in the opposite direction), biosynthetic pathways. CC Additionally, two different ABC transporter complexes are likely CC responsible for the import of 2-AEP. -- SN 1 ID 2-aminoethylphosphonate catabolic pathways DN 2-aminoethylphosphonate catabolic pathways RQ 1 EV GenProp0238; EV GenProp0713; -- SN 2 ID 2-aminoethylphosphonate transport systems DN 2-aminoethylphosphonate transport systems RQ 1 EV GenProp0712; EV GenProp0721; -- SN 3 ID Associated FAD-dependent oxidoreductase DN Putative aminophosphonate oxidoreductase RQ 0 EV IPR017715; TIGR03329; -- SN 4 ID Associated transcriptional regulators DN Associated transcriptional regulators RQ 0 EV IPR017722; TIGR03337; EV IPR017723; TIGR03338; EV IPR017724; TIGR03339; // AC GenProp0721 DE 2-aminoethylphosphonate (AEP) ABC transporter, type II TP SYSTEM AU Haft DH TH 0 CC This ABC transporter is found in a number of genomes in operon-like CC contexts, strongly suggesting a substrate specificity for CC 2-aminoethylphosphonate (2-AEP, ciliatine). The characterized PhnSTUV CC system is absent in the genomes in which this system is found. These CC genomes encode systems for the catabolism of 2-AEP, making the need for CC a 2-AEP-specific transporter likely. -- SN 1 ID Periplasmic AEP binding protein DN ABC transport system, 1-aminoethylphosphonate-binding protein/PhnS2 RQ 1 EV IPR017663; TIGR03261; sufficient; -- SN 2 ID ATP-binding protein DN 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT2 RQ 1 EV IPR017666; TIGR03265; sufficient; -- SN 3 ID Permease protein DN 2-aminoethylphosphonate ABC transport system, permease protein/PhnU2 RQ 1 EV IPR017664; TIGR03262; sufficient; // AC GenProp0722 DE Methanogenesis marker set TP SYSTEM AU Haft DH TH 0 RN [1] RM 16385054 RT The genome sequence of Methanosphaera stadtmanae reveals why this human RT intestinal archaeon is restricted to methanol and H2 for methane RT formation and ATP synthesis. RA Fricke WF, Seedorf H, Henne A, Krüer M, Liesegang H, Hedderich R, RA Gottschalk G, Thauer RK; RL J Bacteriol. 2006;188:642-658. CC Members of this genome property are largely uncharacterized proteins CC that appear to represent marker proteins for methanogenic archaea, as CC detected by partial phylogenetic profiling. Substrates that can be CC reduced wih H2 to methane may include methanol only, as in Methanosphaera CC stadtmanae, or carbon dioxide and other compounds. This Genome Property CC represents proteins that are universal (in the first ten completed genomes CC of archaeal methanogens) and can serve as markers for methanogenesis (they CC are found nowhere else). These markers have the same phylogenetic CC distribution, among completely sequenced genomes, as the enzyme CC methyl-coenzyme M reductase, whose components are represented in a separate CC Genome Property (GenProp0719). This analysis was performed without the CC availability of an anaerobic methane-oxidizing archaeal genome sequence, CC and it is unclear how such a genome would affect the results. -- SN 1 ID CoB--CoM heterodisulfide reductase, subunit B DN CoB--CoM heterodisulfide reductase, subunit B RQ 1 EV IPR017678; TIGR03288; sufficient; -- SN 2 ID CoB--CoM heterodisulfide reductase, subunit C DN CoB--CoM heterodisulfide reductase, subunit C RQ 1 EV IPR017680; TIGR03290; sufficient; -- SN 3 ID Methyl coenzyme M reductase system, component A2 DN Methyl coenzyme M reductase system, component A2 RQ 1 EV IPR017669; TIGR03269; -- SN 4 ID Methyl-coenzyme M reductase, alpha subunit DN Methyl-coenzyme M reductase, alpha subunit RQ 1 EV IPR016212; TIGR03256; sufficient; -- SN 5 ID Methyl-coenzyme M reductase, beta subunit DN Methyl-coenzyme M reductase, beta subunit RQ 1 EV IPR003179; TIGR03257; sufficient; -- SN 6 ID Methyl-coenzyme M reductase I operon protein C DN Methyl-coenzyme M reductase I operon protein C RQ 1 EV IPR007687; TIGR03264; -- SN 7 ID Methyl-coenzyme M reductase operon protein D DN Methyl-coenzyme M reductase operon protein D RQ 1 EV IPR003901; TIGR03260; -- SN 8 ID Methyl-coenzyme M reductase, gamma subunit DN Methyl-coenzyme M reductase, gamma subunit RQ 1 EV IPR003178; TIGR03259; sufficient; -- SN 9 ID Tetrahydromethanopterin S-methyltransferase, subunit A DN Tetrahydromethanopterin S-methyltransferase, subunit A RQ 1 EV IPR005778; TIGR01111; -- SN 10 ID Tetrahydromethanopterin S-methyltransferase, subunit B DN Tetrahydromethanopterin S-methyltransferase, subunit B RQ 1 EV IPR008690; TIGR04166; -- SN 11 ID Tetrahydromethanopterin S-methyltransferase, subunit C DN Tetrahydromethanopterin S-methyltransferase, subunit C RQ 1 EV IPR005865; TIGR01148; -- SN 12 ID Tetrahydromethanopterin S-methyltransferase, subunit D DN Tetrahydromethanopterin S-methyltransferase, subunit D RQ 1 EV IPR005779; TIGR01112; -- SN 13 ID Tetrahydromethanopterin S-methyltransferase, subunit E DN Tetrahydromethanopterin S-methyltransferase, subunit E RQ 1 EV IPR005780; TIGR01113; -- SN 14 ID Tetrahydromethanopterin S-methyltransferase, subunit F DN Tetrahydromethanopterin S-methyltransferase, subunit F RQ 1 EV IPR013347; TIGR02507; -- SN 15 ID Tetrahydromethanopterin S-methyltransferase, subunit G DN Tetrahydromethanopterin S-methyltransferase, subunit G RQ 1 EV IPR005866; TIGR01149; -- SN 16 ID Tetrahydromethanopterin S-methyltransferase, subunit H DN Tetrahydromethanopterin S-methyltransferase, subunit H RQ 1 EV IPR023467; TIGR01114; -- SN 17 ID Methanogenesis marker protein 1 DN Methanogenesis marker protein 1 RQ 1 EV IPR017667; TIGR03266; sufficient; -- SN 18 ID Methanogenesis marker protein 2 DN Methanogenesis marker protein 2 RQ 1 EV IPR017668; TIGR03267; sufficient; -- SN 19 ID Methanogenesis marker protein 3 DN Methanogenesis marker protein 3 RQ 1 EV IPR016466; TIGR03268; sufficient; -- SN 20 ID Methanogenesis marker protein 4 DN Methanogenesis marker protein 4 RQ 1 EV IPR016764; TIGR03270; sufficient; -- SN 21 ID Methanogenesis marker protein 5 DN Methanogenesis marker protein 5 RQ 1 EV IPR012356; TIGR03271; sufficient; -- SN 22 ID Methanogenesis marker protein 6 DN Methanogenesis marker protein 6 RQ 1 EV IPR012025; TIGR03272; sufficient; -- SN 23 ID Methanogenesis marker protein 7 DN Methanogenesis marker protein 7 RQ 1 EV IPR011312; TIGR03274; sufficient; -- SN 24 ID Methanogenesis marker protein 8 DN Methanogenesis marker protein 8 RQ 1 EV IPR009181; TIGR03275; sufficient; -- SN 25 ID Methanogenesis marker domain 9 DN Methanogenesis marker domain 9 RQ 1 EV IPR017671; TIGR03277; sufficient; -- SN 26 ID Methanogenesis radical SAM marker protein DN Methanogenesis radical SAM marker protein RQ 1 EV IPR017672; TIGR03278; sufficient; -- SN 27 ID Methanogenesis imperfect marker 11 DN Methanogenesis imperfect marker 11 RQ 1 EV IPR017674; TIGR03280; sufficient; -- SN 28 ID Methanogenesis marker protein 12 DN Methanogenesis marker protein 12 RQ 1 EV IPR016735; TIGR03281; sufficient; -- SN 29 ID Methanogenesis marker 13 metalloprotein DN Methanogenesis marker 13 metalloprotein RQ 1 EV IPR017675; TIGR03282; sufficient; -- SN 30 ID Methanogenesis marker protein 14 DN Methanogenesis marker protein 14 RQ 1 EV IPR008303; TIGR03285; sufficient; -- SN 31 ID Methanogenesis marker protein 15 DN Methanogenesis marker protein 15 RQ 1 EV IPR017676; TIGR03286; sufficient; -- SN 32 ID Methanogenesis marker 16 metalloprotein DN Methanogenesis marker 16 metalloprotein RQ 1 EV IPR017677; TIGR03287; sufficient; -- SN 33 ID Methanogenesis marker protein 17 DN Methanogenesis marker protein 17 RQ 1 EV IPR016762; TIGR03291; sufficient; // AC GenProp0723 DE Hydrogenase, nickel and F420-dependent TP SYSTEM AU Haft DH TH 0 RN [1] RM 2207102 RT Cloning, sequence determination, and expression of the genes encoding RT the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing RT hydrogenase from Methanobacterium thermoautotrophicum delta H. RA Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT; RL Biochemistry. 1990;29:7237-7244. CC This nickel hydrogenase reduces coenzyme F420 (8-hydroxy-5-deazaflavin) CC and is found exclusively, but not universally, in methanogenic archaea. CC It is lacking in at least four Methanosarcinales. F420 reducing CC hydrogenase (FRH) is composed of three subuints, aplpha, beta and CC gamma, which are encoded by the genes frhA, frhB, and frhG respectively. CC A forth gene in the same cluster, frhD, encodes a delta subunit, which CC is not part of the active FRH heterotrimer, but may be required for CC maturation [1]. -- SN 1 ID Coenzyme F420 hydrogenase, subunit alpha DN Coenzyme F420 hydrogenase, subunit alpha (EC 1.12.98.1) RQ 1 EV IPR017682; TIGR03295; sufficient; -- SN 2 ID Coenzyme F420 hydrogenase, subunit beta DN Coenzyme F420 hydrogenase, subunit beta (EC 1.12.98.1) RQ 1 EV IPR017679; TIGR03289; sufficient; -- SN 3 ID Coenzyme F420 hydrogenase, maturation protease DN Peptidase A31, coenzyme F420-reducing hydrogenase delta subunit RQ 1 EV IPR004411; TIGR00130; sufficient; -- SN 4 ID Coenzyme F420 hydrogenase, subunit gamma DN Coenzyme F420 hydrogenase, subunit gamma (EC 1.12.98.1) RQ 1 EV IPR017681; TIGR03294; sufficient; // AC GenProp0724 DE Phosphonoacetaldehyde biosynthesis from phosphoenolpyruvate TP PATHWAY AU Haft DH TH 0 RN [1] RM 1337066 RT Studies on the biosynthesis of bialaphos (SF-1293). 14. Nucleotide RT sequence of phosphoenolpyruvate phosphomutase gene isolated from a RT bialaphos producing organism, Streptomyces hygroscopicus, and its RT expression in Streptomyces lividans. RA Hidaka T, Hidaka M, Seto H; RL J Antibiot (Tokyo). 1992;45:1977-1980. RN [2] RM 9673017 RT Isolation and characterization of the PEP-phosphomutase and the RT phosphonopyruvate decarboxylase genes from the phosphinothricin RT tripeptide producer Streptomyces viridochromogenes Tü494. RA Schwartz D, Recktenwald J, Pelzer S, Wohlleben W; RL FEMS Microbiol Lett. 1998;163:149-157. RN [3] RM 11035722 RT Bacteroides fragilis NCTC9343 produces at least three distinct capsular RT polysaccharides: cloning, characterization, and reassignment of RT polysaccharide B and C biosynthesis loci. RA Coyne MJ, Kalka-Moll W, Tzianabos AO, Kasper DL, Comstock LE; RL Infect Immun. 2000;68:6176-6181. CC Phosphonacetaldehyde is a precursor of natural products, lipids and CC polysaccharides containing phosphonates (C-P linkages). Often this is CC converted by an aminotransferase to the most common naturally occuring CC phosphonate, 2-aminoethylphosphonate. -- SN 1 ID PEP phosphomutase DN PEP phosphomutase RQ 1 EV IPR012698; TIGR02320; sufficient; TG GO:0006796; -- SN 2 ID Phosphonopyruvate decarboxylase DN Phosphonopyruvate decarboxylase RQ 1 EV IPR017684; TIGR03297; sufficient; TG GO:0006796; -- SN 3 ID 2-aminophosphonate transaminase DN 2-aminophosphonate transaminase RQ 0 EV IPR012703; TIGR03301; EV IPR012703; TIGR02326; -- SN 4 ID Proximal marker of exopolysaccharide biosynthesis DN Proximal marker of exopolysaccharide biosynthesis RQ 0 EV IPR002797; PF01943; -- SN 5 ID Proximal marker of lipid biosynthesis DN Proximal marker of lipid biosynthesis RQ 0 EV IPR000462; PF01066; -- SN 6 ID Proximal marker of natural products biosynthesis DN Squalene cyclase RQ 0 EV IPR018333; TIGR01787; -- SN 7 ID Proximal nucleotidyltransferase domain DN Proximal nucleotidyltransferase domain RQ 0 EV IPR004821; PF01467; EV IPR005835; PF00483; EV IPR003329; PF02348; -- SN 8 ID Proximal oxidoreductases/oxygenases DN Proximal oxidoreductases/oxygenases RQ 0 EV IPR001670; PF00465; EV IPR017656; TIGR03250; EV IPR005123; PF03171; // AC GenProp0725 DE Outer membrane protein assembly complex TP METAPATH AU Haft DH TH 0 RN [1] RM 16824102 RT YfiO stabilizes the YaeT complex and is essential for outer membrane RT protein assembly in Escherichia coli. RA Malinverni JC, Werner J, Kim S, Sklar JG, Kahne D, Misra R, Silhavy TJ; RL Mol Microbiol. 2006;61:151-164. RN [2] RM 17090219 RT Assembly factor Omp85 recognizes its outer membrane protein substrates RT by a species-specific C-terminal motif. RA Robert V, Volokhina EB, Senf F, Bos MP, Van Gelder P, Tommassen J; RL PLoS Biol. 2006;4:e377. RN [3] RM 17015657 RT Differential effects of yfgL mutation on Escherichia coli outer RT membrane proteins and lipopolysaccharide. RA Charlson ES, Werner JN, Misra R; RL J Bacteriol. 2006;188:7186-7194. RN [4] RM 20378773 RT Reconstitution of outer membrane protein assembly from purified RT components. RA Hagan CL, Kim S, Kahne D; RL Science. 2010;328:890-892. CC Correct assembly of proteins in the bacterial outer membrane is CC facilitated by a protein complex, consisting largely of lipoproteins, CC plus a member of the Omp85 protein family, named YaeT in Escherichia CC coli. -- SN 1 ID OMP insertion complex protein BamA/YaeT DN OMP insertion complex protein BamA/YaeT RQ 1 EV IPR023707; TIGR03303; sufficient; TG GO:0061077; -- SN 2 ID OMP insertion complex lipoprotein BamB/YfgL DN OMP insertion complex lipoprotein BamB/YfgL RQ 0 EV IPR017687; TIGR03300; sufficient; TG GO:0061077; -- SN 3 ID OMP insertion complex lipoprotein BamC/NlpB DN OMP insertion complex lipoprotein BamC/NlpB RQ 0 EV IPR010653; PF06804; sufficient; TG GO:0061077; -- SN 4 ID OMP insertion complex lipoprotein BamD/YfiO DN OMP insertion complex lipoprotein BamD/YfiO RQ 1 EV IPR017689; TIGR03302; sufficient; TG GO:0061077; -- SN 5 ID OMP insertion complex lipoprotein BamE/SmpA DN OMP insertion complex lipoprotein BamE/SmpA RQ 0 EV IPR007450; PF04355; TG GO:0061077; -- SN 6 ID OMP insertion C-terminal signal DN OMP insertion C-terminal signal RQ 0 EV IPR017690; TIGR03304; sufficient; -- SN 7 ID OMP chaperone system: SurA-Skp-DegP DN OMP chaperone system: SurA-Skp-DegP RQ 1 EV GenProp0928; TG GO:0061077; // AC GenProp0726 DE Selenium-dependent molybdenum hydroxylase system TP SYSTEM AU Haft DH TH 1 RN [1] RM 10860985 RT Selenium-dependent metabolism of purines: A selenium-dependent purine RT hydroxylase and xanthine dehydrogenase were purified from Clostridium RT purinolyticum and characterized. RA Self WT, Stadtman TC; RL Proc Natl Acad Sci U S A. 2000;97:7208-7213. RN [2] RM 14503889 RT Cofactor determination and spectroscopic characterization of the RT selenium-dependent purine hydroxylase from Clostridium purinolyticum. RA Self WT, Wolfe MD, Stadtman TC; RL Biochemistry. 2003;42:11382-11390. RN [3] RM 10430865 RT Crystal structure and mechanism of CO dehydrogenase, a molybdo RT iron-sulfur flavoprotein containing S-selanylcysteine. RA Dobbek H, Gremer L, Meyer O, Huber R; RL Proc Natl Acad Sci U S A. 1999;96:8884-8889. RN [4] RM 21257770 RT A selenium-dependent xanthine dehydrogenase triggers biofilm RT proliferation in Enterococcus faecalis through oxidant production. RA Srivastava M, Mallard C, Barke T, Hancock LE, Self WT; RL J Bacteriol. 2011;193:1643-1652. CC The enzyme selenide, water dikinase (SelD) activates selenium for use in CC bacteria as selenocysteine to be incorporated during protein CC translation, or as the modified base selenouridine in certain tRNAs. CC However, SelD occurs in some genomes with neither of those traits, and CC instead acts in the post-translational addition of a labile selenium to CC a molybdenum-containing cofactor. A bioinformatic analysis showed that CC the family of TIGRFAMs model TIGR03309 represents a third CC selenium-dependent bacterial trait, and that it is quite widespread. CC The current version of this Genome Property includes both selenium CC cofactor maturation proteins and subunits of predicted labile selenium CC cofactor enzymes. -- SN 1 ID Diaminopropionate ammonia-lyase DN Diaminopropionate ammonia-lyase RQ 0 EV IPR019871; TIGR03528; -- SN 2 ID Selenium-dependent molybdenum hydroxylase, protein 1 DN Selenium-dependent molybdenum hydroxylase, protein 1 RQ 1 EV IPR017695; TIGR03309; -- SN 3 ID Selenium-dependent molybdenum hydroxylase, protein 3 DN Selenium-dependent molybdenum hydroxylase, protein 3 RQ 1 EV IPR017587; TIGR03172; -- SN 4 ID Molybdenum cofactor cytidylyltransferase DN Molybdenum cofactor cytidylyltransferase RQ 1 EV IPR017696; TIGR03310; -- SN 5 ID Selenide, water dikinase DN Selenide, water dikinase RQ 0 EV IPR004536; TIGR00476; -- SN 6 ID Selenium metabolism protein YedF DN Selenium metabolism protein YedF RQ 0 EV IPR019870; TIGR03527; -- SN 7 ID Selenium-dependent xanthine dehydrogenase DN Selenium-dependent xanthine dehydrogenase RQ 0 EV IPR017697; TIGR03311; -- SN 8 ID Probable selenate reductase, FAD-binding subunit DN Probable selenate reductase, FAD-binding subunit RQ 0 EV IPR017698; TIGR03312; -- SN 9 ID Probable selenate reductase, molybdenum subunit DN Probable selenate reductase, molybdenum subunit RQ 0 EV IPR017699; TIGR03313; -- SN 10 ID Probable selenate reductase, YgfK subunit DN Probable selenate reductase, YgfK subunit RQ 0 EV IPR017701; TIGR03315; -- SN 11 ID Putative selenium metabolism hydrolase DN Putative selenium metabolism hydrolase RQ 0 EV IPR017706; TIGR03526; // AC GenProp0728 DE AMP metabolism using type III Rubisco TP PATHWAY AU Haft DH TH 0 RN [1] RM 17303759 RT Archaeal type III RuBisCOs function in a pathway for AMP metabolism. RA Sato T, Atomi H, Imanaka T; RL Science. 2007;315:1003-1006. CC Lee, et al. [1] have described an archaeal pathway for the conversion CC of AMP to 3-phosphoglycerate with the release of adenine. This pathway CC includes an AMP phosphorylase previously annotated as a probable CC thymidine phosphorylase, and a ribose-1,5-bisphosphate isomerase CC previously annotated as a translation initation factor. -- SN 1 ID AMP phosphorylase DN AMP phosphorylase RQ 1 EV IPR017713; TIGR03327; -- SN 2 ID Ribose-1,5-bisphosphate isomerase DN Ribose-1,5-bisphosphate isomerase RQ 1 EV IPR005250; TIGR00511; -- SN 3 ID Rubisco, type III DN Rubisco, type III RQ 1 EV IPR017712; TIGR03326; // AC GenProp0729 DE Methionine salvage from methylthioadenosine TP METAPATH AU Haft DH TH 0 RN [1] RM 15102328 RT Bacterial variations on the methionine salvage pathway. RA Sekowska A, Dénervaud V, Ashida H, Michoud K, Haas D, Yokota A, RA Danchin A; RL BMC Microbiol. 2004;4:9. CC Methylthioadenosine (MTA) is a sulfur-containing by-product from the CC use of S-adenosylmethionine in spermidine or polyamine biosynthesis and CC certain other pathways. A series of reactions, with considerable CC species-specific variation, recycles MTA to methionine in a wide range CC of organisms. In a new nomenclature, these genes are now designated mtn CC (MethylThioNucleoside). An interesting enzyme in this system is MtnD, CC the aci-reductone dioxygenase. This enzyme has two different enzymatic CC activities, depending on whether Ni2+ or Fe2+ is bound. The action of CC the single enzyme MtnP is replaced by two enzymes, MtnN and MtnK in CC some species. Likewise, the enolase-phosphatase MtnC is replaced by CC MtnW and MtnX in the Bacillus lineage. The final step in the pathway, a CC transamination that generates methionine from CC 2-keto-4-methylthiobutyrate, apparantly can be catalyzed by a large CC number of functional analogs using different amino donors, and so is CC not included explicitly in the reconstruction. -- SN 1 ID Methylthioribose-1-phosphate isomerase DN Methylthioribose-1-phosphate isomerase/mtnA RQ 1 EV IPR005251; TIGR00512; TG GO:0019509; -- SN 2 ID Methylthioribulose-1-phosphate dehydratase DN Methylthioribulose-1-phosphate dehydratase/mtnB RQ 1 EV IPR017714; TIGR03328; TG GO:0019509; -- SN 3 ID 2,3-diketo-5-methylthiopentyl-1-P to aci-reductone DN 2,3-diketo-5-methylthiopentyl-1-P to aci-reductone/mtnC RQ 1 EV IPR023943; TIGR01691; TG GO:0019509; EV GenProp0732; TG GO:0019509; -- SN 4 ID Aci-reductone dioxygenase DN Aci-reductone dioxygenase/mtnD RQ 1 EV IPR004313; PF03079; TG GO:0019509; -- SN 5 ID MTA to MTR-1-P DN MTA to MTR-1-P/mtnP RQ 1 EV IPR010044; TIGR01694; TG GO:0019509; EV GenProp0730; TG GO:0019509; // AC GenProp0730 DE Methylthioadenosine to methylthioribose-1-phosphate via MTR TP PATHWAY AU Haft DH TH 0 CC This property exists to describe a branch in the methionine salvage CC pathway in which MtnN followed by MtnK replaces the single step of CC MtnP. -- SN 1 ID 5-methylthioribose kinase DN 5-methylthioribose kinase/mtnK RQ 1 EV IPR009212; TIGR01767; -- SN 2 ID Methylthioadenosine nucleosidase DN Methylthioadenosine nucleosidase/mtnN RQ 1 EV IPR010049; TIGR01704; // AC GenProp0731 DE Amino acid metabolism TP CATEGORY AU Haft DH TH 0 CC The chemical reactions and pathways involving amino acids (organic CC acids containing one or more amino substituents). -- SN 1 ID Amino acid biosynthesis RQ 0 EV GenProp0126; -- SN 2 ID Amino acid salvage RQ 0 EV GenProp0733; -- SN 3 ID Amino acid catabolism RQ 0 EV GenProp0734; -- SN 4 ID Homocysteine regeneration from S-adenosylhomocysteine RQ 0 EV GenProp0789; -- SN 5 ID Aspartate superpathway RQ 0 EV GenProp1250; -- SN 6 ID D-serine metabolism RQ 0 EV GenProp1274; -- SN 7 ID Superpathway of chorismate metabolism RQ 0 EV GenProp1291; // AC GenProp0732 DE Methionine salvage enolase-phosphate pair MtnW/MtnX TP PATHWAY AU Haft DH TH 0 CC In many species with methionine salvage from methylthioadenosine, a CC single protein (MtnC) acts as an enolase-phosphatase. However, in CC Bacillus subtilis and related species, the enolase and phosphate are CC separate proteins designated MtnW and MtnX. The former resembles CC RuBisCO and the latter belongs to the HAD superfamily hydrolases. -- SN 1 ID 2,3-diketo-5-methylthiopentyl-1-phosphate enolase DN 2,3-diketo-5-methylthiopentyl-1-phosphate enolase/mtnW RQ 1 EV IPR017717; TIGR03332; -- SN 2 ID 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase DN 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase/mtnX RQ 1 EV IPR017718; TIGR03333; // AC GenProp0733 DE Amino acid salvage TP CATEGORY AU Haft DH TH 0 CC Any process which produces an amino acid from derivatives of it, CC without de novo synthesis. -- SN 1 ID Reduction of oxidized methionine RQ 0 EV GenProp0182; -- SN 2 ID Methionine salvage from methylthioadenosine RQ 0 EV GenProp0729; // AC GenProp0734 DE Amino acid catabolism TP CATEGORY AU Haft DH TH 0 CC The chemical reactions and pathways resulting in the breakdown of amino CC acids (organic acids containing one or more amino substituents). -- SN 1 ID Degradation of tyrosine via homogentisate RQ 0 EV GenProp0139; -- SN 2 ID Arginine catabolism to glutamate via arginine succinyltransferase (AST) RQ 0 EV GenProp0309; -- SN 3 ID Attenuation system: tryptophanase RQ 0 EV GenProp0456; -- SN 4 ID Arginine degradation via citrulline, ATP-generating RQ 0 EV GenProp0639; -- SN 5 ID Tryptophan degradation to anthranilate RQ 0 EV GenProp0659; -- SN 6 ID L-glutamate degradation II RQ 0 EV GenProp1233; -- SN 7 ID Uracil degradation I (reductive) RQ 0 EV GenProp1371; -- SN 8 ID L-arginine degradation I (arginase pathway) RQ 0 EV GenProp1428; -- SN 9 ID L-citrulline degradation RQ 0 EV GenProp1357; -- SN 10 ID Glycine cleavage RQ 0 EV GenProp1275; -- SN 11 ID L-alanine degradation I RQ 0 EV GenProp1626; -- SN 12 ID L-arginine degradation II (AST pathway) RQ 0 EV GenProp1280; -- SN 13 ID L-arginine degradation III (arginine decarboxylase/agmatinase pathway) RQ 0 EV GenProp1282; -- SN 14 ID L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) RQ 0 EV GenProp1431; -- SN 15 ID L-asparagine degradation III (mammalian) RQ 0 EV GenProp1365; -- SN 16 ID L-aspartate degradation II RQ 0 EV GenProp1584; -- SN 17 ID L-cysteine degradation III RQ 0 EV GenProp1681; -- SN 18 ID L-histidine degradation I RQ 0 EV GenProp1619; -- SN 19 ID L-isoleucine degradation II RQ 0 EV GenProp1328; -- SN 20 ID L-isoleucine degradation I RQ 0 EV GenProp1533; -- SN 21 ID L-leucine degradation III RQ 0 EV GenProp1334; -- SN 22 ID L-leucine degradation I RQ 0 EV GenProp1673; -- SN 23 ID L-lysine degradation XI (mammalian) RQ 0 EV GenProp1487; -- SN 24 ID L-methionine degradation III RQ 0 EV GenProp1655; -- SN 25 ID L-phenylalanine degradation I (aerobic) RQ 0 EV GenProp1679; -- SN 26 ID L-phenylalanine degradation III RQ 0 EV GenProp1698; -- SN 27 ID L-threonine degradation V RQ 0 EV GenProp1223; -- SN 28 ID L-threonine degradation IV RQ 0 EV GenProp1445; -- SN 29 ID L-threonine degradation II RQ 0 EV GenProp1646; -- SN 30 ID L-tryptophan degradation VIII (to tryptophol) RQ 0 EV GenProp1292; -- SN 31 ID L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde RQ 0 EV GenProp1503; -- SN 32 ID L-tryptophan degradation X (mammalian, via tryptamine) RQ 0 EV GenProp1551; -- SN 33 ID L-tyrosine degradation III RQ 0 EV GenProp1245; -- SN 34 ID L-tyrosine degradation I RQ 0 EV GenProp1375; -- SN 35 ID L-valine degradation II RQ 0 EV GenProp1467; -- SN 36 ID IscS-ThiL complex RQ 0 EV GenProp1144; -- SN 37 ID Superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation RQ 0 EV GenProp1279; // AC GenProp0735 DE Type VI secretion TP SYSTEM AU Haft DH TH 2 RN [1] RM 16432199 RT Identification of a conserved bacterial protein secretion system in RT Vibrio cholerae using the Dictyostelium host model system. RA Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, Nelson WC, RA Heidelberg JF, Mekalanos JJ; RL Proc Natl Acad Sci U S A. 2006;103:1528-1533. RN [2] RM 17558395 RT Threonine phosphorylation post-translationally regulates protein RT secretion in Pseudomonas aeruginosa. RA Mougous JD, Gifford CA, Ramsdell TL, Mekalanos JJ; RL Nat Cell Biol. 2007;9:797-803. RN [3] RM 16930487 RT Exopolysaccharide-associated protein sorting in environmental RT organisms: the PEP-CTERM/EpsH system. Application of a novel RT phylogenetic profiling heuristic. RA Haft DH, Paulsen IT, Ward N, Selengut JD; RL BMC Biol. 2006;4:29. RN [4] RM 16763151 RT A virulence locus of Pseudomonas aeruginosa encodes a protein secretion RT apparatus. RA Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, Gifford CA, Goodman AL, RA Joachimiak G, Ordoñez CL, Lory S, Walz T, Joachimiak A, Mekalanos JJ; RL Science. 2006;312:1526-1530. RN [5] RM 15228535 RT Use of proteomics to identify novel virulence determinants that are RT required for Edwardsiella tarda pathogenesis. RA Rao PS, Yamada Y, Tan YP, Leung KY; RL Mol Microbiol. 2004;53:573-586. RN [6] RM 20865170 RT Burkholderia type VI secretion systems have distinct roles in RT eukaryotic and bacterial cell interactions. RA Schwarz S, West TE, Boyer F, Chiang WC, Carl MA, Hood RD, Rohmer L, RA Tolker-Nielsen T, Skerrett SJ, Mougous JD; RL PLoS Pathog. 2010;6:e1001068. CC The protein secretion system now called type VI (T6SS) has been described CC by Pukatzki, et al. [1], Mougous. et al. [2] and others. Two components of CC the system resemble components of type IV secretion systems (T4SS). Many CC species that carry this system have known pathogenic activity, but T6SS CC may be directed against other bacteria rather than eukaryotic cells. In CC addition to protein families for this system identified in various CC publications, several were identified by the partial phylogenetic CC programming algorithm [3], supported by proximity to other type VI CC secretion genes. -- SN 1 ID Type VI secretion system DotU family protein DN Type VI secretion system DotU family protein RQ 1 EV IPR017732; TIGR03349; TG GO:0033103; -- SN 2 ID Type VI secretion protein, VC_A0108 family DN Type VI secretion protein, VC_A0108 family RQ 1 EV IPR010269; TIGR03355; TG GO:0033103; -- SN 3 ID Type VI secretion system FHA domain protein DN Type VI secretion system FHA domain protein RQ 1 EV IPR017735; TIGR03354; TG GO:0033103; -- SN 4 ID IcmF3-like protein DN IcmF3-like protein RQ 1 EV IPR017731; TIGR03348; TG GO:0033103; -- SN 5 ID Type VI secretion system OmpA/MotB domain DN Type VI secretion system OmpA/MotB domain RQ 0 EV IPR017733; TIGR03350; TG GO:0033103; -- SN 6 ID Type VI secretion ATPase ClpV1 DN Type VI secretion ATPase ClpV1 RQ 1 EV IPR017729; TIGR03345; TG GO:0033103; -- SN 7 ID Type VI secretion target, Hcp family DN Type VI secretion target, Hcp family RQ 1 EV IPR008514; TIGR03344; TG GO:0033103; -- SN 8 ID Type VI secretion lipoprotein, VC_A0113 family DN Type VI secretion lipoprotein, VC_A0113 family RQ 1 EV IPR017734; TIGR03352; TG GO:0033103; -- SN 9 ID Type VI secretion system Vgr family protein DN Type VI secretion system Vgr family protein RQ 1 EV IPR017847; TIGR03361; TG GO:0033103; -- SN 10 ID Type VI secretion protein, VC_A0111 family DN Type VI secretion protein, VC_A0111 family RQ 1 EV IPR010732; TIGR03347; TG GO:0033103; -- SN 11 ID Type VI secretion protein, VC_A0114 family DN Type VI secretion protein, VC_A0114 family RQ 1 EV IPR010263; TIGR03353; TG GO:0033103; -- SN 12 ID Type VI secretion protein, VC_A0107 family DN Type VI secretion protein, VC_A0107 family RQ 1 EV IPR008312; TIGR03358; TG GO:0033103; -- SN 13 ID Type VI secretion protein, VC_A0110 family DN Type VI secretion protein, VC_A0110 family RQ 1 EV IPR010272; TIGR03359; TG GO:0033103; -- SN 14 ID Type VI secretion system lysozyme-like protein DN Type VI secretion system lysozyme-like protein RQ 1 EV IPR017737; TIGR03357; TG GO:0033103; -- SN 15 ID Type VI secretion-associated protein, VC_A0118 family DN Type VI secretion-associated protein, VC_A0118 family RQ 0 EV IPR017738; TIGR03360; -- SN 16 ID Type VI secretion-associated protein, VC_A0119 family DN Type VI secretion-associated protein, VC_A0119 family RQ 0 EV IPR017739; TIGR03362; -- SN 17 ID Type VI secretion-associated protein, BMA_A0402 family DN Type VI secretion-associated protein, BMA_A0402 family RQ 0 EV IPR017740; TIGR03363; -- SN 18 ID Type VI secretion-associated protein, BMA_A0400 DN Type VI secretion-associated protein, BMA_A0400 RQ 0 EV IPR017748; TIGR03373; // AC GenProp0736 DE Proposed phosphonate catabolism pathway HpnWXZ TP PATHWAY AU Haft DH TH 0 CC Phosphonatase (PhnX) is an enzyme that catalyzes the hydrolysis of CC phosphonoacetaldehyde via a bicatalytic mechanism involving a specific CC enzyme lysine which forms a Shiff base with the aldehyde, and a CC magnesium-aspartate (HAD-type) nucleophile to cleave the phosphonate CC carbon-phosphorous bond. The PhnW enzyme provides the substrate for this CC reaction. HpnX (closely related to PhnX) shares a significant degree of CC similarity at critical catalytic sites suggesting that it also acts as a CC phosphonatase on a beta-phosphonoaldehyde. HpnX genes are often found in CC the vicinity of a family of FAD-dependent oxidoreductases (HpnW). These CC genes may act in an analagous fashion to PhnW by converting an CC aminophosphonate into an aldehyde, here by oxidative deamination. HpnW CC genes are members of a larger family of genes including enzymes with amino CC acid deaminating oxidase activities. These genes (HpnX and HpnW) are often CC associated with a family of Zn++ dependent alcohol dehydrogenases. Other CC genes in the vicinity indicate a phosphonate-related context and are CC typically observed near other phosphonate catabolic pathways such as genes CC of the HDIG domain family, certain GntR-type transcriptional regulators and CC phosphonate-related transporters. -- SN 1 ID Associated GntR-family transcriptional regulator DN Associated GntR-family transcriptional regulator/GntR RQ 0 EV IPR000524; PF00392; -- SN 2 ID Associated HDIG-domain protein DN Associated HDIG-domain protein/HDIG RQ 0 EV IPR017670; TIGR03276; -- SN 3 ID Proposed aminophosphonate deaminating oxidase DN Proposed aminophosphonate deaminating oxidase/HpnW RQ 1 EV IPR017741; TIGR03364; -- SN 4 ID Proposed phosphonoacetaldehyde-like hydrolase DN Proposed phosphonoacetaldehyde-like hydrolase/HpnX RQ 1 EV IPR022468; TIGR03351; -- SN 5 ID Phosphonate-associated alcohol dehydrogenase DN Phosphonate-associated alcohol dehydrogenase/HpnZ RQ 0 EV IPR017743; TIGR03366; // AC GenProp0737 DE Anaerobic glycerol-3-phosphate dehydrogenase complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 3286606 RT Nucleotide sequence and gene-polypeptide relationships of the glpABC RT operon encoding the anaerobic sn-glycerol-3-phosphate dehydrogenase of RT Escherichia coli K-12. RA Cole ST, Eiglmeier K, Ahmed S, Honore N, Elmes L, Anderson WF, Weiner RA JH; RL J Bacteriol. 1988;170:2448-2456. CC A three-protein complex, the anaerobic glycerol-3-phosphate CC dehydrogenase, which is a product of the glpABC genes, is found CC in Escherichia coli and related species. GlpA and GlpB are catalytic, CC while GlpC anchors the complex to the plasma membrane. -- SN 1 ID Glycerol-3-phosphate dehydrogenase, anaerobic, A subunit DN Glycerol-3-phosphate dehydrogenase, anaerobic, A subunit/glpA RQ 1 EV IPR017752; TIGR03377; -- SN 2 ID Glycerol-3-phosphate dehydrogenase, anaerobic, B subunit DN Glycerol-3-phosphate dehydrogenase, anaerobic, B subunit/glpB RQ 1 EV IPR009158; TIGR03378; -- SN 3 ID Glycerol-3-phosphate dehydrogenase, anaerobic, anchor subunit DN Glycerol-3-phosphate dehydrogenase, anaerobic, anchor subunit/glpC RQ 1 EV IPR017753; TIGR03379; // AC GenProp0738 DE Agmatine to putrescine via N-carbamoylputrescine TP PATHWAY AU Haft DH TH 0 CC Agmatine deiminase (aguA) converts agmatine to N-carbamoylputrescine. CC N-carbamoylputrescine amidase (aguB) then releases CO2 and NH4+ to CC yield putrescine. The aguAB pathway replaces agmatinase (speB), which CC simply releases urea from agmatine to yield putrescine. -- SN 1 ID Agmatine deiminase DN Agmatine deiminase/aguA RQ 1 EV IPR017754; TIGR03380; TG GO:0009445; -- SN 2 ID N-carbamoylputrescine amidase DN N-carbamoylputrescine amidase/aguB RQ 1 EV IPR017755; TIGR03381; TG GO:0009445; // AC GenProp0739 DE Iron-sulfur cluster assembly CsdA-CsdE system TP SYSTEM AU Haft DH TH 0 RN [1] RM 15901727 RT Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting RT Fe-S cluster biogenesis in Escherichia coli. RA Loiseau L, Ollagnier-de Choudens S, Lascoux D, Forest E, Fontecave M, RA Barras F; RL J Biol Chem. 2005;280:26760-26769. CC The heteromeric complex of CsdA and CsdE plays a role in iron-sulfur CC (Fe-S) cluster biosynthesis, as do the better-known systems ISC, SUF, CC and NIF. CdsA, a homolog of SufS, IscS, and NifS, is a cysteine CC desulfurase catalytic subunit. CdsE, a SufE homolog, physically CC interacts and accepts a sulfur at Cys-61 (numbered as in Escherichia CC coli). In contrast to sulfur-accepting components such as NifU and CC IscU, CsdE does not bind iron and is not viewed as a scaffold on which CC Fe-S cluster biosynthesis can be completed prior to transfer to other CC proteins. Rather, the simplicity of this system may reflect a limited CC role for the maturation of specific Fe-S cluster-containing proteins. -- SN 1 ID Cysteine desulfurase, catalytic subunit CdsA DN Cysteine desulfurase, catalytic subunit CdsA (EC 2.8.1.7) RQ 1 EV IPR022471; TIGR03392; TG GO:0016226; -- SN 2 ID Cysteine desulfurase, sulfur acceptor subunit CsdE DN Cysteine desulfurase, sulfur acceptor subunit CsdE RQ 1 EV IPR017763; TIGR03391; TG GO:0016226; // AC GenProp0740 DE Translation initiation, bacterial TP SYSTEM AU Haft DH TH 0 RN [1] RM 15755955 RT Initiation of protein synthesis in bacteria. RA Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU; RL Microbiol Mol Biol Rev. 2005;69:101-123. CC Essential housekeeping genes of bacterial translation initiation. -- SN 1 ID Translation initiation factor IF-1 DN Translation initiation factor IF-1 RQ 1 EV IPR004368; TIGR00008; -- SN 2 ID Translation initiation factor IF-2 DN Translation initiation factor IF-2 RQ 1 EV IPR000178; TIGR00487; -- SN 3 ID Translation initiation factor IF-3 DN Translation initiation factor IF-3 RQ 1 EV IPR001288; TIGR00168; // AC GenProp0741 DE Translation elongation, bacterial TP SYSTEM AU Haft DH TH 0 CC Essential housekeeping genes of bacterial translation elongation. -- SN 1 ID Translation elongation factor G DN Translation elongation factor G RQ 1 EV IPR004540; TIGR00484; -- SN 2 ID Translation elongation factor P DN Translation elongation factor P RQ 1 EV IPR011768; TIGR00038; -- SN 3 ID Translation elongation factor Ts DN Translation elongation factor Ts RQ 1 EV IPR001816; TIGR00116; -- SN 4 ID Translation elongation factor Tu DN Translation elongation factor Tu RQ 1 EV IPR004541; TIGR00485; // AC GenProp0742 DE Iron-sulfur cluster assembly NIF system TP SYSTEM AU Haft DH TH 0 RN [1] RM 10639125 RT NifS-directed assembly of a transient [2Fe-2S] cluster within the NifU RT protein. RA Yuvaniyama P, Agar JN, Cash VL, Johnson MK, Dean DR; RL Proc Natl Acad Sci U S A. 2000;97:599-604. RN [2] RM 15667274 RT NifU and NifS are required for the maturation of nitrogenase and cannot RT replace the function of isc-gene products in Azotobacter vinelandii. RA Johnson DC, Dos Santos PC, Dean DR; RL Biochem Soc Trans. 2005;33:90-93. CC Iron-sulfur (FeS) cluster assembly systems include the NIF system, CC which is part of nitrogen fixation clusters in a number of bacteria, as CC well as the ISC and SUF systems. The latter two make FeS clusters for a CC wide variety of proteins, while NIF and a related system called CC CsdA-CsdE may produce FeS clusters for only a small range of target CC proteins. The defining components of the NIF-type systems described CC here are the cysteine desulfurase NifS and the FeS cluster assembly CC scaffold protein NifU. The terms NifS and NifU are applied not only to CC components of nitrogen fixation systems, but also to tandem gene pairs CC in other organisms such as Helicobacter pylori. These NifU-like and CC NifS-like proteins largely fall into separate clades, and are best CC modeled by separate HMMs, but are included in this Genome Property as CC components of NIF-type systems. NifS/NifU or NifS-like/NifU-like pairs CC may produce FeS clusters for a limited range of target proteins, as in CC Azotobacter vinelandii, or uniquely within the cell, as in Helicobacter CC pylori. -- SN 1 ID Cysteine desulfurase NifS DN Cysteine desulfurase NifS RQ 1 EV IPR017772; TIGR03402; TG GO:0016226; EV IPR017773; TIGR03403; TG GO:0016226; -- SN 2 ID FeS cluster formation protein NifU DN FeS cluster formation protein NifU RQ 1 EV IPR010238; TIGR02000; sufficient; TG GO:0016226; EV IPR017787; TIGR03419; TG GO:0016226; // AC GenProp0743 DE Urea ABC transporter UrtABCDE TP SYSTEM AU Haft DH TH 0 RN [1] RM 16930487 RT Exopolysaccharide-associated protein sorting in environmental RT organisms: the PEP-CTERM/EpsH system. Application of a novel RT phylogenetic profiling heuristic. RA Haft DH, Paulsen IT, Ward N, Selengut JD; RL BMC Biol. 2006;4:29. RN [2] RM 11929526 RT An ABC-type, high-affinity urea permease identified in cyanobacteria. RA Valladares A, Montesinos ML, Herrero A, Flores E; RL Mol Microbiol. 2002;43:703-715. CC This property represents a conserved five-gene operon for an ABC CC transporter with a substrate-binding protein, two permeases, and two CC ATP-binding cassette proteins. All five genes from this operon are CC detected in Burkholderia mallei, at very high confidence levels, by CC means of the partial phylogenetic profiling algorithm [1] vs. a CC profile for urease, and the operon occurs next to urease genes in CC B. mallei and most other species. In Cyanobacteria, high-affinity urea CC transport is shown to be eliminated by mutations to any of several CC different proteins in this system [2]. -- SN 1 ID Urea ABC transporter, periplasmic binding protein DN Urea ABC transporter, periplasmic binding protein RQ 1 EV IPR017777; TIGR03407; TG GO:0015840; EV IPR019968; TIGR03669; TG GO:0015840; -- SN 2 ID Urea ABC transporter, permease protein UrtB DN Urea ABC transporter, permease protein UrtB RQ 1 EV IPR017779; TIGR03409; TG GO:0015840; EV IPR019924; TIGR03622; TG GO:0015840; -- SN 3 ID Urea ABC transporter, permease protein UrtC DN Urea ABC transporter, permease protein UrtC RQ 1 EV IPR017778; TIGR03408; TG GO:0015840; EV IPR022497; TIGR03727; TG GO:0015840; -- SN 4 ID Urea ABC transporter, ATP-binding protein UrtD DN Urea ABC transporter, ATP-binding protein UrtD RQ 1 EV IPR017781; TIGR03411; TG GO:0015840; -- SN 5 ID Urea ABC transporter, ATP-binding protein UrtE DN Urea ABC transporter, ATP-binding protein UrtE RQ 1 EV IPR017780; TIGR03410; TG GO:0015840; // AC GenProp0744 DE Glyoxalase pathway, glutathione dependent TP PATHWAY AU Haft DH TH 0 RN [1] RM 16958620 RT Trypanothione-dependent glyoxalase I in Trypanosoma cruzi. RA Greig N, Wyllie S, Vickers TJ, Fairlamb AH; RL Biochem J. 2006;400:217-223. RN [2] RM 17196158 RT Escherichia coli glyoxalase II is a binuclear zinc-dependent RT metalloenzyme. RA O'Young J, Sukdeo N, Honek JF; RL Arch Biochem Biophys. 2007;459:20-26. CC Glyoxalase I and glyoxalase II are the enzymes lactoylglutathione lyase CC and hydroxyacylglutathione hydrolase, respectively. This system CC detoxifies methylglyoxal and other highly reactive aldehydes. CC Glutathione serves as a cofactor; variants of this CC pathway may occur where glutathione is replaced by another cofactor CC such as trypanothione in Trypanosoma cruzi [1]. -- SN 1 ID Lactoylglutathione lyase (glyoxalase I) DN Lactoylglutathione lyase (glyoxalase I) (EC 4.4.1.5) RQ 1 EV IPR004361; TIGR00068; TG GO:0051596; -- SN 2 ID Hydroxyacylglutathione hydrolase (glyoxalase II) DN Hydroxyacylglutathione hydrolase (glyoxalase II) (EC 3.1.2.6) RQ 1 EV IPR017782; TIGR03413; TG GO:0051596; // AC GenProp0745 DE Lipoyl-protein attachment TP SYSTEM AU Haft DH TH 0 CC This property consists of two enzymes, lipoic acid synthetase and CC lipoate-protein ligase. Lipoamide-containing proteins include the CC glycine cleavage system and 2-osoacid dehydrogenase complexes. -- SN 1 ID Lipoic acid synthetase DN Lipoic acid synthetase/lipA RQ 1 EV IPR003698; TIGR00510; -- SN 2 ID Lipoyltransferase DN Lipoyltransferase/lipB RQ 1 EV IPR000544; TIGR00214; // AC GenProp0746 DE Translation termination, bacterial TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes the basic set of bacterial transcription CC termination factors. Release factor 1 (RF-1, PrfA) should be both CC universal among bacteria and univerally detected, as should release CC factor 3 (RF-3). Release factor 2 is a special case. It is truly absent CC in the Mycoplasmatales, including Mycoplasma genitalium. Its absence CC means TGA is not recognized as a stop coodon. It codes for Trp instead. CC However, release factor 2 in most bacteria is encoded by a gene with a CC programmed frameshift about 25 amino acids from the N-terminus. It may CC be annotated incorrectly as a truncated or disrupted gene and therefore CC not detected by its HMM, TIGR00020. A fourth protein included in this CC genome property is the ribosome recycling factor, which also partipates CC in processes at the conclusion of bacterial protein translation. This CC property does not include PrfH, part of a specialized system present CC only in some bacteria, as it is intended for essentially univeral CC bacterial termination factors. -- SN 1 ID Release factor methylase DN Release factor methylase/hemK RQ 1 EV IPR019874; TIGR03534; EV IPR004556; TIGR00536; -- SN 2 ID Peptide chain release factor 1 DN Peptide chain release factor 1/prfA RQ 1 EV IPR004373; TIGR00019; -- SN 3 ID Peptide chain release factor 2 DN Peptide chain release factor 2/prfB RQ 1 EV IPR004374; TIGR00020; -- SN 4 ID Peptide chain release factor 3 DN Peptide chain release factor 3/prfC RQ 1 EV IPR004548; TIGR00503; -- SN 5 ID Ribosome recycling factor DN Ribosome recycling factor RQ 1 EV IPR002661; TIGR00496; // AC GenProp0747 DE Adenosine monophosphate (AMP) biosynthesis from inosine monophosphate (IMP) TP PATHWAY AU Haft DH TH 0 CC This two-step pathway in purine biosynthesis begins with IMP (inosine CC monophosphate), a branch point in purine de novo biosynthesis. CC Adenylosuccinate synthetase, product of the PurA gene, catalyzes the CC first committed step to AMP. Adenylosuccinate lyase, product of the CC purB gene, catalyzes the second and final step, but it also catalyzes CC the eighth step in IMP biosynthesis. -- SN 1 ID Adenylosuccinate synthetase DN Adenylosuccinate synthetase/purA (EC 6.3.4.4) RQ 1 EV IPR001114; TIGR00184; TG GO:0006167; -- SN 2 ID Adenylosuccinate lyase DN Adenylosuccinate lyase/purB (EC 4.3.2.2) RQ 1 EV IPR004769; TIGR00928; TG GO:0006167; // AC GenProp0748 DE Choline ABC transporter, ChoXWV family TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a family of quaternary amine CC transporters that appears, based on physical characterization in CC Sinorhizobium meliloti and on bioinformatic methods, to import choline. CC The presence of paralogs in some bacteria and their association with CC choline sulfatase genes suggests choline sulfate may also be a CC substrate. -- SN 1 ID Choline ABC transporter, ATP-binding protein DN Choline ABC transporter, ATP-binding protein RQ 1 EV IPR022473; TIGR03415; -- SN 2 ID Choline ABC transporter, periplasmic binding protein DN Choline ABC transporter, periplasmic binding protein RQ 1 EV IPR017783; TIGR03414; -- SN 3 ID Choline ABC transporter, permease protein DN Choline ABC transporter, permease protein RQ 1 EV IPR017784; TIGR03416; // AC GenProp0749 DE Choline sulfate utilization TP SYSTEM AU Haft DH TH 0 CC This property describes a gene pair for choline sulfate utilization. CC Choline is a precursor to the osmoprotectant glycine-betaine and to CC acetylcholine, and can be used as an energy source. One member of the CC gene pair is a choline-sulfatase, as in Sinorhizobium meliloti and CC Pseudomonas aeruginosa PAO1. The other gene is a periplasmic binding CC protein for the ABC transporters responsible for choline uptake. It CC appears that several different periplasmic binding proteins interact CC with the same permease and ATP-binding subunit. -- SN 1 ID Putative choline sulfate transcription factor DN Putative choline sulfate transcription factor RQ 1 EV IPR017786; TIGR03418; -- SN 2 ID Choline sulfate periplasmic binding protien DN Choline sulfate periplasmic binding protien RQ 1 EV IPR017783; TIGR03414; -- SN 3 ID Choline-sulfatase DN Choline-sulfatase RQ 1 EV IPR017785; TIGR03417; // AC GenProp0750 DE UDP-N-acetylglucosamine biosynthesis from fructose-6-phosphate TP PATHWAY AU Haft DH TH 0 RN [1] RM 8407787 RT Identification of the glmU gene encoding RT N-acetylglucosamine-1-phosphate uridyltransferase in Escherichia coli. RA Mengin-Lecreulx D, van Heijenoort J; RL J Bacteriol. 1993;175:6150-6157. CC This pathway converts fructose-6-phosphate in four steps to activated CC N-acetylglucosamine. GlmS produces glucosamine-6-phosphate. GlmM CC isomerizes this product to glucosamine-1-phosphate. GlmU, which is CC bifunctional, adds an acetyl group from acetyl-CoA, then acts as CC N-acetylglucosamine-1-phosphate uridylyltransferase [1]. The product, CC UDP-N-acetyl-D-glucosamine, is then used both for murein biosynthesis CC and (in species with LPS) for lipopolysaccharide biosynthesis. -- SN 1 ID Phosphoglucosamine mutase DN Phosphoglucosamine mutase/glmM (EC 5.4.2.10) RQ 1 EV IPR006352; TIGR01455; EV IPR024086; TIGR03990; -- SN 2 ID Glutamine--fructose-6-phosphate transaminase (isomerizing) DN Glucosamine-fructose-6-phosphate aminotransferase, isomerising/glmS (EC 2.6.1.16) RQ 1 EV IPR005855; TIGR01135; -- SN 3 ID Glucosamine-1-phosphate N-acetyltransferase/UDP-N-acetylglucosamine diphosphorylase DN Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase/glmU (EC 2.3.1.157/EC 2.7.7.23) RQ 1 EV IPR005882; TIGR01173; EV IPR023917; TIGR03991; // AC GenProp0751 DE Acidobacterial ADOP/PadR gene pairs TP SYSTEM AU Haft DH TH 0 CC This property represents the presence of a characteristic gene pair, CC found in large paralogous families in several species of Acidobacteria. CC One component is a putative transcriptional regulator related to PadR. CC The other is ADOP, or Acidobacterial duplicated orphan permease, an CC integral membrane protein related to ABC transporter permease CC components such as LolC, MacB, and FtsX, but orphaned in the sense of CC not being found next to ATP-binding cassette (ABC) proteins. The CC function is unknown. -- SN 1 ID Acidobacterial duplicated orphan permease DN Acidobacterial duplicated orphan permease RQ 1 EV IPR017800; TIGR03434; -- SN 2 ID Transcriptional regulator, Acidobacterial, PadR-family DN Transcriptional regulator, Acidobacterial, PadR-family RQ 1 EV IPR017799; TIGR03433; // AC GenProp0752 DE Ergothioneine biosynthesis TP SYSTEM AU Haft DH TH 0 RN [1] RM 20420449 RT In vitro reconstitution of Mycobacterial ergothioneine biosynthesis. RA Seebeck FP; RL J Am Chem Soc. 2010;132:6632-6633. CC In actinobacteria, ergothioneine biosynthesis begins with EgtD, a CC SAM-dependent enzyme that trimethylates the histidine alpha-amino group CC to produce hercynine, the histidine-betaine. EgtA gamma-ligates Cys to CC Glu, as occurs in glutathione biosynthesis. Next, EgtB attaches CC hercynine to gammaglutamyl cysteine, with sulfur attachment to the CC histidine-derived ring. EgtC then releases glutamate. Finally EgtE, a CC pyridoxal phosphate-dependent enzyme related to selenocysteine lyase, CC cleaves the hercynylcysteine sulfoxide to leave ergothioneine. CC Ergothioneine production is known also in cyanobacteria and mushrooms, CC and is predicted to be more widely distributed. -- SN 1 ID Glutamate--cysteine ligase family protein DN Glutamate--cysteine ligase family protein RQ 0 EV IPR017809; TIGR03444; TG GO:0052699; -- SN 2 ID Ergothioneine biosynthesis protein EgtB DN Ergothioneine biosynthesis protein EgtB RQ 1 EV IPR017806; TIGR03440; TG GO:0052699; -- SN 3 ID Ergothioneine biosynthesis protein EgtC DN Ergothioneine biosynthesis protein EgtC RQ 0 EV IPR017808; TIGR03442; TG GO:0052699; -- SN 4 ID Ergothioneine biosynthesis methyltransferase EgtD DN Ergothioneine biosynthesis methyltransferase EgtD RQ 1 EV IPR017804; TIGR03438; TG GO:0052699; -- SN 5 ID Ergothioneine biosynthesis PLP-binding protein EgtE DN Ergothioneine biosynthesis PLP-binding protein EgtE RQ 0 EV IPR027563; TIGR04343; TG GO:0052699; // AC GenProp0753 DE Mycothiol biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 16674910 RT A coupled spectrophotometric assay for l-cysteine:1-D-myo-inosityl RT 2-amino-2-deoxy-alpha-D-glucopyranoside ligase and its application for RT inhibitor screening. RA Newton GL, Ta P, Sareen D, Fahey RC; RL Anal Biochem. 2006;353:167-173. CC Mycothiol is a thiol, a glutathione analog, found in Mycobacterium CC tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and CC related species. Four genes associated with its biosynthesis, CC designated mshA, mshB, mshC, and mshD, are scattered in the M. CC tuberculosis genome rather than arranged as an operon. A fifth reaction CC associated with this biosynthesis, a phosphatase designated MsaA2, has CC been described but not yet assigned to a specific protein. Genomes with CC this biosynthesis system will have other proteins that make use of CC mycothiol. -- SN 1 ID D-inositol-3-phosphate glycosyltransferase DN Mycothiol biosynthesis glycosyltransferase, MshA (EC 2.4.1.-) RQ 1 EV IPR017814; TIGR03449; TG GO:0010125; -- SN 2 ID Mycothiol biosynthesis protein B DN Mycothiol biosynthesis protein B/MshB (EC 2.4.1.-) RQ 1 EV IPR017810; TIGR03445; TG GO:0010125; -- SN 3 ID Mycothiol biosynthesis Cys ligase DN Cysteinyl-tRNA ligase/MshC (EC 6.1.1.-) RQ 1 EV IPR017812; TIGR03447; TG GO:0010125; -- SN 4 ID Mycothiol biosynthesis acetyltransferase DN Mycothiol biosynthesis acetyltransferase protein, MshD (EC 2.3.1.-) RQ 1 EV IPR017813; TIGR03448; TG GO:0010125; // AC GenProp0754 DE Acetate production from acetylphosphate TP PATHWAY AU Haft DH TH 0 RN [1] RM 172079 RT Acetate kinase (pyrophosphate). A fourth pyrophosphate-dependent kinase RT from Entamoeba histolytica. RA Reeves RE, Guthrie JD; RL Biochem Biophys Res Commun. 1975;66:1389-1395. RN [2] RM 16080684 RT Characterization of the acetate-producing pathways in Escherichia coli. RA Dittrich CR, Bennett GN, San KY; RL Biotechnol Prog. 2005;21:1062-1067. CC Acetate may be generated from acetyl phosphate by hydrolysis (EC 3.6.1.7, CC acylphosphatase) or by a reversible ATP-dependent reaction (EC 2.7.2.1, CC ATP:acetate phosphohydrolase). The literature also refers to a reversible CC pyrophophate-dependent reaction in Entamoeba histolytica [1] although the CC sequence of the enzyme responsible is not yet known. -- SN 1 ID Acetetylphosphate dephosphorylation DN Acetetylphosphate dephosphorylation RQ 1 EV IPR004372; TIGR00016; EV IPR001792; PF00708; // AC GenProp0756 DE Fumarate reductase complex TP SYSTEM AU Haft DH TH 1 CC Fumarate reductase reversibly converts succinate to fumarate with the CC concomitant production of FADH2. It consists of four components, a CC flavoprotein, an iron-sulfur protein, and two other subunits. It is a CC component of the reverse TCA carbon fixation pathway as well as certain CC fermentation pathways. Although reversible, certain enzymes have CC evolved to prefer one direction over the other, this property captures CC those which are likely to function in the process of fumarate CC reduction. -- SN 1 ID Flavoprotein subunit DN Flavoprotein subunit/FrdA RQ 1 EV IPR011280; TIGR01811; EV IPR005884; TIGR01176; -- SN 2 ID Iron-sulfur protein subunit DN Iron-sulfur protein subunit/FrdB RQ 1 EV IPR004489; TIGR00384; -- SN 3 ID Subunit C DN Subunit C/FrdC RQ 1 EV IPR003510; PF02300; -- SN 4 ID Subunit D DN Subunit D/FrdD RQ 1 EV IPR003418; PF02313; // AC GenProp0757 DE Quorum-sensing, autoinducer-2 system TP SYSTEM AU Haft DH TH 0 RN [1] RM 16101288 RT Mutational analysis of a nucleosidase involved in quorum-sensing RT autoinducer-2 biosynthesis. RA Lee JE, Luong W, Huang DJ, Cornell KA, Riscoe MK, Howell PL; RL Biochemistry. 2005;44:11049-11057. RN [2] RM 15456522 RT Is autoinducer-2 a universal signal for interspecies communication: a RT comparative genomic and phylogenetic analysis of the synthesis and RT signal transduction pathways. RA Sun J, Daniel R, Wagner-Döbler I, Zeng AP; RL BMC Evol Biol. 2004;4:36. CC S-ribosylhomocysteine lyase (LuxS) is an iron(2+)-containing protein. CC Its immediate product, 4,5-dihydroxypentan-2,3-dione, cyclizes CC spontaneously and binds borate to become autoinducer-2 (AI-2), a CC quorum-sensing molecule produced and recognized by a wide range of CC bacteria. LuxS serves as a marker for this system, while MTA/SAH CC nucleosidase is essential both for this and other systems. -- SN 1 ID S-ribosylhomocysteine lyase DN S-ribosylhomocysteine lyase (EC 4.4.1.21)/LuxS RQ 1 EV IPR003815; PF02664; TG GO:0009372; -- SN 2 ID Methylthioadenosine nucleosidase/adenosylhomocysteine nucleosidase DN Methylthioadenosine nucleosidase (EC 3.2.2.16)/adenosylhomocysteine nucleosidase (EC 3.2.2.9) RQ 1 EV IPR010049; TIGR01704; TG GO:0009372; // AC GenProp0758 DE Lycopene biosynthesis from IPP TP METAPATH AU Haft DH TH 2 RN [1] RM 16669779 RT Vitamin synthesis in plants: tocopherols and carotenoids. RA DellaPenna D, Pogson BJ; RL Annu Rev Plant Biol. 2006;57:711-738. CC Lycopene is one of the most commonly occurring carotenes (nonoxygenated CC carotenoids). Carotenoids are synthesized via the isoprenoid biosynthetic CC pathway, of which isopetenylpyrophosphate (IPP) is an intermediate. IPP CC undergoes a series of condensation reactions to form geranylgeranyl CC diphosphate (GGDP), a key intermediate in the synthesis of carotenoids. In CC plants, the first committed step in carotenoid synthesis is the CC condensation of two GGDP molecules, producing phytoene. Multiple CC desaturation steps then occur to yield lycopene. These desaturation steps CC vary slightly between plant and bacterial pathways [1]. -- SN 1 ID Source of IPP DN Source of IPP RQ 0 EV GenProp0048; EV GenProp0047; -- SN 2 ID Phytoene synthase (2.5.1.32) DN Phytoene synthase (2.5.1.32)/crtB RQ 1 EV IPR002060; PF00494; -- SN 3 ID Lycopene cyclases DN Lycopene cyclases/crtLY RQ 0 EV IPR010108; TIGR01790; EV IPR017825; TIGR03462; -- SN 5 ID Isopentenyl-diphosphate delta-isomerase (5.3.3.2) DN Isopentenyl-diphosphate delta-isomerase (5.3.3.2)/idi RQ 0 EV IPR011876; TIGR02150; EV IPR011179; TIGR02151; -- SN 6 ID Geranylgeranyl pyrophosphate synthase DN Geranylgeranyl pyrophosphate synthase/ispA RQ 1 EV IPR000092; PF00348; -- SN 7 ID Uncharacterized syntenic membrane protein DN Uncharacterized syntenic membrane protein RQ 0 EV IPR017822; TIGR03459; EV IPR017823; TIGR03460; -- SN 8 ID Phytoene desaturase (1.14.99.-) DN Phytoene desaturase (1.14.99.-)/pds RQ 1 EV IPR014102; TIGR02731; EV IPR014105; TIGR02734; -- SN 9 ID Zeta-carotene desaturase (1.14.99.30) DN Zeta-carotene desaturase (1.14.99.30)/zds RQ 1 EV IPR014103; TIGR02732; EV IPR014105; TIGR02734; // AC GenProp0759 DE Para-aminobenzoic acid (PABA) biosynthesis from chorismate TP PATHWAY AU Haft DH TH 0 CC PABA, or para-aminobenzoic acid biosynthesis, is a precursor of folate CC biosynthesis. It is synthesized from the branch point metabolite CC chorismate and glutamine. Aminodeoxychorismate synthase (EC 2.6.1.85) CC component I is PabA, aminodeoxychorismate synthase component II is CC PabB, and 4-amino-4-deoxychorismate lyase (EC 4.1.3.38) is PabC. -- SN 1 ID Aminodeoxychorismate synthase, component I DN Aminodeoxychorismate synthase, component I/PabA (EC 2.6.1.85) RQ 1 EV IPR010117; TIGR01823; -- SN 2 ID Aminodeoxychorismate synthase, component II DN Aminodeoxychorismate synthase, component II/PabB (EC 2.6.1.85) RQ 1 EV IPR005802; TIGR00553; EV IPR010118; TIGR01824; EV IPR010117; TIGR01823; -- SN 3 ID Aminodeoxychorismate lyase DN Aminodeoxychorismate lyase/PabC (EC 4.1.3.38) RQ 1 EV IPR017824; TIGR03461; // AC GenProp0764 DE DMSO reductase family type II enzyme TP SYSTEM AU Haft DH TH 0 CC This genome property refers to several related molybdopterin-containing CC enzymes for a distinct class within the broader set of DMSO reductase CC family enzymes. The most distinct feature is the heme b-containing gamma CC subunit. However, both the molybdopterin-containing alpha subunit and the CC iron-sulfur cluster-containing beta subunit are readily separable by CC phylogenetic analysis from multiple sequence alignments. Many of these CC complexes act in anaerobic respiration, including a selenate reductase, CC a chlorate reductase, and a nitrate reductase. -- SN 1 ID DMSO reductase family type II enzyme, molybdopterin subunit DN DMSO reductase family type II enzyme, molybdopterin subunit RQ 1 EV IPR017840; TIGR03479; -- SN 2 ID DMSO reductase family type II enzyme, iron-sulfur subunit DN DMSO reductase family type II enzyme, iron-sulfur subunit RQ 1 EV IPR017839; TIGR03478; -- SN 3 ID DMSO reductase family type II enzyme chaperone DN DMSO reductase family type II enzyme chaperone RQ 0 EV IPR017843; TIGR03482; -- SN 4 ID DMSO reductase family type II enzyme, heme b subunit DN DMSO reductase family type II enzyme, heme b subunit RQ 1 EV IPR017838; TIGR03477; // AC GenProp0766 DE Anhydro-N-acetylmuramic acid to N-acetylglucosamine-phosphate TP PATHWAY AU Haft DH TH 0 RN [1] RM 15901686 RT Recycling of the anhydro-N-acetylmuramic acid derived from cell wall RT murein involves a two-step conversion to N-acetylglucosamine-phosphate. RA Uehara T, Suefuji K, Valbuena N, Meehan B, Donegan M, Park JT; RL J Bacteriol. 2005;187:3643-3649. RN [2] RM 16452451 RT MurQ Etherase is required by Escherichia coli in order to metabolize RT anhydro-N-acetylmuramic acid obtained either from the environment or RT from its own cell wall. RA Uehara T, Suefuji K, Jaeger T, Mayer C, Park JT; RL J Bacteriol. 2006;188:1660-1662. CC Components of the bacterial murein cell wall, including CC 1,6-anhydro-N-acetylmuramic acid (anhMurNAc), N-acetyl-D-glucosamine CC (GlcNAc), D-alanine, and murein tripeptide are released during in CC murein recycling as bacteria grow. Pathways exist to recycle these CC components for the biosynthesis of new cell wall. This pathway CC describes a two-enzyme pathway for converting anhMurNAc into CC N-acetylglucosamine-phosphate. -- SN 1 ID Anhydro-N-acetylmuramic acid kinase DN Anhydro-N-acetylmuramic acid kinase/anmK RQ 1 EV IPR005338; PF03702; TG GO:0009254; -- SN 2 ID N-acetylmuramic acid-phosphate etherase DN N-acetylmuramic acid-phosphate etherase/murQ RQ 1 EV IPR005488; TIGR00274; TG GO:0009254; // AC GenProp0767 DE Very short patch repair TP SYSTEM AU Haft DH TH 0 RN [1] RM 8736526 RT Very short patch repair: reducing the cost of cytosine methylation. RA Lieb M, Bhagwat AS; RL Mol Microbiol. 1996;20:467-473. CC Very short patch (VSP) repair is a repair system that recognizes CC mismatches caused by deamination of 5-methylcytosine (5meC). Cytosine CC is modified to 5meC by the product of the dcm gene. Vsr is an CC endonuclease that creates a nick to allow the repair. In Escherichia CC coli, the second C of the DNA motif CCWGG (where W is A or T) is CC methylated; deamination yields T:G mispairs reccognized by the vsr gene CC product. The vsr gene typically is found very close to the dcm gene, CC and is essentially restricted to a subset of those genomes that carry CC dcm. -- SN 1 ID DNA-cytosine methyltransferase DN DNA-cytosine methyltransferase/dcm RQ 1 EV IPR001525; TIGR00675; -- SN 2 ID Very short patch repair DN Very short patch repair/vsr RQ 1 EV IPR004603; TIGR00632; // AC GenProp0768 DE CRISPR system, Pging subtype TP SYSTEM AU Haft DH TH 0 RN [1] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats. Certain proteins are found only in genomes with CC CRISPR repeats and are near these repeats. We have shown that certain CC families of CRISPR-associated (cas) proteins, unlike the cas1-cas4 CC genes common to nearly all loci, are relatively uncommon and mark CC distinct subclasses of CRISPR/cas system. This Genome Property CC describes a rare CRISPR/cas subtype, named Pging for its occurence in CC Porphyromonas gingivalis W83. -- SN 1 ID Cas1, Pging region DN Cas1, Pging region RQ 1 EV IPR002729; TIGR00287; -- SN 2 ID Cas2, Pging region DN Cas2, Pging region RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, Pging region DN Cas3, Pging region RQ 1 EV IPR006474; TIGR01587; -- SN 4 ID Cas4, Pging region DN Cas4, Pging region RQ 1 EV IPR013343; TIGR00372; -- SN 5 ID Cas5, Pging subtype variant DN Cas5, Pging subtype variant RQ 1 EV IPR020031; TIGR03488; -- SN 6 ID Cas6, Pging region DN Cas6, Pging region RQ 1 EV IPR010156; TIGR01877; -- SN 7 ID Csp1 family TIGR03489 DN Csp1 family TIGR03489 RQ 1 EV IPR020032; TIGR03489; -- SN 8 ID Csp2 family TIGR03487 DN Csp2 family TIGR03487 RQ 1 EV IPR020029; TIGR03487; // AC GenProp0778 DE Protein sorting system, GlyGly-CTERM/rhombosortase TP SYSTEM AU Haft DH TH 0 RN [1] RM 22194940 RT GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal RT in a many-to-one pairing with a rhomboid family intramembrane serine RT protease. RA Haft DH, Varghese N; RL PLoS One. 2011;6:e28886. RN [2] RM 21385872 RT Proteomic analysis of the Vibrio cholerae type II secretome reveals new RT proteins, including three related serine proteases. RA Sikora AE, Zielke RA, Lawrence DA, Andrews PC, Sandkvist M; RL J Biol Chem. 2011;286:16555-16566. CC The GlyGly-CTERM domain, previously called the gammaproteobacterial CC enzyme C-terminal transmembrane domain or rhombotail, appears to be a CC protein sorting signal analogous to LPXTG and PEP-CTERM. Every genome CC that encodes a set of GlyGly-CTERM proteins also encodes a rhomboid CC family enzyme, designated rhombosortase, in a many-to-one relationship. CC Rhomboid proteases are serine proteases with the active site Ser within CC the membrane, and they are capable of cleaving hydrophobic CC transmembrane segments. In general, genomes that encode GlyGly-CTERM CC proteins and rhombosortase also encode a type 2 secretion system CC (T2SS). Several GlyGly-CTERM proteins have been shown to undergo CC T2SS-mediated secretion. -- SN 1 ID GlyGly-CTERM sorting domain DN GlyGly-CTERM sorting domain/GGcterm RQ 1 EV IPR020008; TIGR03501; EV IPR021206; TIGR03867; -- SN 2 ID Rhombosortase DN Rhombosortase/rhomsort RQ 1 EV IPR023826; TIGR03902; // AC GenProp0781 DE Gliding motility, Bacteroidetes type TP SYSTEM AU Haft DH TH 0 RN [1] RM 16199564 RT Flavobacterium johnsoniae gliding motility genes identified by mariner RT mutagenesis. RA Braun TF, Khubbar MK, Saffarini DA, McBride MJ; RL J Bacteriol. 2005;187:6943-6952. CC The Bacteroidetes phylum includes many organisms capable of gliding CC motility over surfaces. This has been studied most thoroughly in CC Flavobacterium johnsoniae. The precise mechanism of the motility has CC yet to be determined, but a number of the genes involved have been CC identified by mutagenesis. The gliding phenotype is linked to the CC utilization of the insoluble polysaccharide chitin as well as CC susceptability to certain bacteriophage. -- SN 1 ID ABC transporter, ATP-binding protein, GldA DN ABC transporter, ATP-binding protein, GldA/GldA RQ 1 EV IPR019864; TIGR03522; -- SN 2 ID Lipoprotein, GldB DN Lipoprotein, GldB/GldB RQ 1 EV IPR019853; TIGR03514; -- SN 3 ID Unknown protein, GldC DN Unknown protein, GldC/GldC RQ 0 EV IPR019854; TIGR03515; -- SN 4 ID Lipoprotein, GldD DN Lipoprotein, GldD/GldD RQ 1 EV IPR019850; TIGR03512; -- SN 5 ID Unknown protein, GldE DN Unknown protein, GldE/GldE RQ 0 EV IPR019862; TIGR03520; -- SN 6 ID ABC transporter membrane protein, GldF DN ABC transporter membrane protein, GldF/GldF RQ 1 EV IPR019860; TIGR03518; -- SN 7 ID Proposed ABC transporter component, GldG DN Proposed ABC transporter component, GldG/GldG RQ 1 EV IPR019863; TIGR03521; -- SN 8 ID Lipoprotein, GldH DN Lipoprotein, GldH/GldH RQ 1 EV IPR020018; TIGR03511; -- SN 9 ID Lipoprotein, GldI DN Lipoprotein, GldI/GldI RQ 1 EV IPR019869; TIGR03516; -- SN 10 ID Lipoprotein, GldJ DN Lipoprotein, GldJ/GldJ RQ 1 EV IPR019865; TIGR03524; EV IPR019868; TIGR03530; -- SN 11 ID Lipoprotein, GldK DN Lipoprotein, GldK/GldK RQ 1 EV IPR019866; TIGR03525; EV IPR019867; TIGR03529; -- SN 12 ID Unknown protein, GldL DN Unknown protein, GldL/GldL RQ 1 EV IPR019852; TIGR03513; -- SN 13 ID Unknown protein, GldM DN Unknown protein, GldM/GldM RQ 1 EV IPR019859; TIGR03517; -- SN 14 ID Unknown protein, GldN DN Unknown protein, GldN/GldN RQ 1 EV IPR019847; TIGR03523; -- SN 15 ID Bacteroidetes multicopy membrane protein DN Bacteroidetes multicopy membrane protein/gld_xxx RQ 0 EV IPR019861; TIGR03519; -- SN 16 ID Bacteroidetes multicopy C-terminal domain DN Bacteroidetes multicopy C-terminal domain/gld_yyy RQ 0 EV IPR026341; TIGR04131; // AC GenProp0786 DE Lysine biosynthesis via diaminopimelate (DAP), succinylated branch TP PATHWAY AU Haft DH TH 0 RN [1] RM 20418392 RT Methanococci use the diaminopimelate aminotransferase (DapL) pathway RT for lysine biosynthesis. RA Liu Y, White RH, Whitman WB; RL J Bacteriol. 2010;192(13):3304-3310. DC Lysine Biosynthesis DR KEGG; map00300; CC There are four known variations (branches) of the lysine biosynthesis CC pathway via diaminopimelate (DAP). The variations occur in the steps CC converting L-2,3,4,5-tetrahydrodipicolinate (THDPA) to CC LL-2,6-diaminopimelate. This property refers to the succinylated CC branch of this pathway. This branch acylates THDPA with succinyl-CoA CC to generate N-succinyl-ll-2-amino-6-ketopimelate and forms meso-DAP CC by subsequent transamination, desuccinylation, and epimerization. This CC branch is utilized by proteobacteria as well as many firmicutes and CC actinobacteria [1]. -- SN 1 ID 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase DN 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase/DapD (EC 2.3.1.117) RQ 1 EV IPR005664; TIGR00965; sufficient; EV IPR019875; TIGR03535; EV IPR019876; TIGR03536; -- SN 2 ID Succinyl-diaminopimelate transaminase DN Succinyl-diaminopimelate transaminase/DapC (EC 2.6.1.17) RQ 0 EV IPR019877; TIGR03537; EV IPR019878; TIGR03538; EV IPR019880; TIGR03539; -- SN 3 ID Succinyl-diaminopimelate desuccinylase (DapE) DN Succinyl-diaminopimelate desuccinylase/DapE (EC 3.5.1.18) RQ 1 EV IPR005941; TIGR01246; sufficient; EV IPR010174; TIGR01900; sufficient; // AC GenProp0787 DE Lysine biosynthesis via diaminopimelate (DAP), acetylated branch TP PATHWAY AU Haft DH TH 0 RN [1] RM 20418392 RT Methanococci use the diaminopimelate aminotransferase (DapL) pathway RT for lysine biosynthesis. RA Liu Y, White RH, Whitman WB; RL J Bacteriol. 2010;192(13):3304-3310. DC Lysine Biosynthesis DR KEGG; map00300; CC There are four known variations (branches) of the lysine biosynthesis CC pathway via diaminopimelate (DAP). The variations occur in the steps CC converting L-2,3,4,5-tetrahydrodipicolinate (THDPA) to CC LL-2,6-diaminopimelate. This property refers to the acetylated branch CC of this pathway which generates N-acetyl intermediates. This branch CC is limited to certain Bacillus species [1]. -- SN 1 ID Acetyl-diaminopimelate deacetylase DN Acetyl-diaminopimelate deacetylase (EC 3.5.1.47) RQ 1 EV IPR023905; MF_01692; -- SN 2 ID Acetyl-diaminopimelate transaminase DN Acetyl-diaminopimelate transaminase (EC 2.6.1.-) RQ 0 -- SN 3 ID 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase DN 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase (EC 2.3.1.89) RQ 1 EV IPR019873; TIGR03532; // AC GenProp0788 DE Lysine biosynthesis via diaminopimelate (DAP) utilizing ammonia and NADPH TP METAPATH AU Haft DH TH 4 RN [1] RM 1906065 RT A functionally split pathway for lysine synthesis in Corynebacterium RT glutamicium. RA Schrumpf B, Schwarzer A, Kalinowski J, Pühler A, Eggeling L, Sahm H; RL J Bacteriol. 1991;173:4510-4516. DC Lysine biosynthesis DR KEGG; map00300; CC This pathway for the biosynthesis of L-lysine differs from the more CC common diaminopimelate pathway by the action of diaminopimelate CC dehydrogenase (ddh). This enzyme requires both ammonia as a nitrogen CC source (instead of an amino acid via a transaminase) and reductive CC power in the form of NADPH. Additionally, this pathway does not require CC the acetyl/succinyl protecting group transformations found in the CC standard pathway, nor does it require the action of diaminopimelate CC epimerase. This enzyme has been best characterized in Corynebacterium CC glutamicum and Bacillus sphaericus. One should note that the ddh CC enzyme is shown acting on the compound L-2-amino-6-oxoheptanedioate in CC EC and KEGG representations. This is merely the ring-opened form of CC 2,3,4,5-tetrahydropicolinate with which it is in equilibrium, and upon CC which the acyltransferases of the common pathway act. -- SN 1 ID Source of aspartate-semialdehyde RQ 1 EV GenProp0160; TG GO:0033361; -- SN 2 ID Diaminopimelate decarboxylase DN Diaminopimelate decarboxylase/LysA (EC 4.1.1.20) RQ 1 EV IPR002986; TIGR01048; TG GO:0033361; -- SN 3 ID Dihydrodipicolinate reductase DN Dihydrodipicolinate reductase (EC 1.17.1.8) RQ 1 EV IPR023940; TIGR00036; TG GO:0033361; -- SN 4 ID Dihydrodipicolinate synthase DN 4-hydroxy-tetrahydrodipicolinate synthase/DapA (EC 4.3.3.7) RQ 1 EV IPR005263; TIGR00674; TG GO:0033361; -- SN 5 ID Diaminopimelate dehydrogenase DN Diaminopimelate dehydrogenase/Ddh (EC 1.4.1.16) RQ 1 EV IPR010190; TIGR01921; TG GO:0033361; // AC GenProp0789 DE Homocysteine regeneration from S-adenosylhomocysteine TP METAPATH AU Haft DH TH 0 CC S-adenosylmethionine (SAM) is used in cells as a methyl donor by a CC large guild of methyltransferases, leaving S-adenosylhomocysteine CC (SAH). SAH can be cleaved in one step to adenosine and homocysteine by CC adenosylhomocysteinase (EC 3.3.1.1). The homocysteine can then be used CC to regenerate methionine. Alternatively, it can be cleaved in two CC steps. First adenine is removed by adenosylhomocysteine nucleosidase CC (EC 3.2.2.9) to leave S-ribosylhomocysteine. Next, CC S-ribosylhomocysteinase acts to produce homocysteine and CC 4,5-dihydroxypentan-2,3-dione, which cyclizes spontaneously and binds CC borate to become autoinducer-2 (AI-2), a quorum-sensing molecule CC produced and recognized by a wide range of bacteria. This property CC represents the presence of at least one of these two mechanisms to CC regenerate homocysteine. -- SN 1 ID SAH to homocysteine DN SAH to homocysteine RQ 1 EV IPR000043; TIGR00936; EV GenProp0757; -- SN 2 ID Methionine adenosyltransferase DN Methionine adenosyltransferase RQ 1 EV IPR002133; TIGR01034; EV IPR027790; PF01941; // AC GenProp0790 DE Sporadic pair TIGR03545/TIGR03546 TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes an uncommon two-gene pair, sporadically CC distributed in and restricted to bacteria that possess an outer CC membrane. Fused forms do occur. Bacteria with this system include CC Treponema denticola ATCC 35405, Bdellovibrio bacteriovorus, Hahella CC chejuensis KCTC 2396, Rhodopirellula baltica SH 1, Thiomicrospira CC crunogena, etc. -- SN 1 ID Sporadic gene pair, small protein DN Sporadic gene pair, small protein RQ 1 EV IPR019935; TIGR03546; -- SN 2 ID Sporadic gene pair, large protein DN Sporadic gene pair, large protein RQ 1 EV IPR019934; TIGR03545; // AC GenProp0791 DE Coenzyme F420 biosynthesis TP METAPATH AU Haft DH TH 1 RN [1] RM 18260642 RT Identification and characterization of the 2-phospho-L-lactate RT guanylyltransferase involved in coenzyme F420 biosynthesis. RA Grochowski LL, Xu H, White RH; RL Biochemistry. 2008;47:3033-3037. RN [2] RM 12911320 RT CofE catalyzes the addition of two glutamates to F420-0 in F420 RT coenzyme biosynthesis in Methanococcus jannaschii. RA Li H, Graupner M, Xu H, White RH; RL Biochemistry. 2003;42:9771-9778. RN [3] RM 11717263 RT Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based RT selection system to demonstrate a requirement for fbiA and fbiB in RT coenzyme F(420) biosynthesis by Mycobacterium bovis BCG. RA Choi KP, Bair TB, Bae YM, Daniels L; RL J Bacteriol. 2001;183:7058-7066. RN [4] RM 11888293 RT Characterization of the 2-phospho-L-lactate transferase enzyme involved RT in coenzyme F(420) biosynthesis in Methanococcus jannaschii. RA Graupner M, Xu H, White RH; RL Biochemistry. 2002;41:3754-3761. CC Coenzyme F420 is a hydride carrier cofactor functioning in CC methanogenesis [1]. The chromophore of coenzyme F420 is CC 7,8-didemethyl-8-hydroxy-5-deazaflavin (otherwise known as FO), which is CC also used in a cyanobacterial DNA photoreactivating enzyme. Modification of CC FO to create coenzyme F420 includes the GTP-dependent addition of two CC glutamate residues in Methanococcus jannaschii [2] and five or six in CC Mycobacterium bovis [3]. CofF, which caps the gamma-glutamyl tail after two CC glutamates, occurs only the archaea. -- SN 1 ID FO biosynthesis RQ 1 EV GenProp0792; TG GO:0009108; -- SN 2 ID Lactoylphosphate guanylyltransferase DN 2-phospho-L-lactate guanylyltransferase, CofC (EC 2.7.7.68) RQ 1 EV IPR002835; TIGR03552; TG GO:0009108; -- SN 3 ID LPPG:Fo 2-phospho-L-lactate transferase DN 2-phospho-L-lactate transferase/CofD (EC 2.7.8.28) RQ 1 EV IPR010115; TIGR01819; TG GO:0009108; -- SN 4 ID F420-O:gamma-glutamyl ligase DN Coenzyme F420:L-glutamate ligase/CofE (EC 6.3.2.31/EC 6.3.2.34) RQ 1 EV IPR008225; TIGR01916; TG GO:0009108; -- SN 5 ID Coenzyme gamma-F420-2:alpha-L-glutamate ligase DN Coenzyme gamma-F420-2:alpha-L-glutamate ligase/CofF RQ 0 EV IPR031039; TIGR04443; TG GO:0009108; -- SN 6 ID F420 biosynthesis protein FbiB, C-terminal domain DN Coenzyme F420 biosynthesis protein FbiB, C-terminal (EC 6.3.2.31/EC 6.3.2.34) RQ 0 EV IPR019943; TIGR03553; TG GO:0009108; -- SN 7 ID NADPH-dependent F420 reductase DN NADPH-dependent F420 reductase (EC 1.5.1.40) RQ 0 EV IPR010185; TIGR01915; // AC GenProp0792 DE 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 2110564 RT DNA photoreactivating enzyme from the cyanobacterium Anacystis RT nidulans. RA Eker AP, Kooiman P, Hessels JK, Yasui A; RL J Biol Chem. 1990;265:8009-8015. RN [2] RM 14593448 RT Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin RT synthase required for coenzyme F(420) biosynthesis. RA Graham DE, Xu H, White RH; RL Arch Microbiol. 2003;180:455-464. RN [3] RM 11948155 RT Demonstration that fbiC is required by Mycobacterium bovis BCG for RT coenzyme F(420) and FO biosynthesis. RA Choi KP, Kendrick N, Daniels L; RL J Bacteriol. 2002;184:2420-2428. CC 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO, is the chromophore CC of coenzyme F420. Several enzymatic steps convert FO to F420 (see CC GenProp0791). FO is also the chromophore of a cyanobacterial DNA CC photoreactivating enzyme [1]. The two key enzymes of this pathway, CC encoded by CofG and CofH in Methanocaldococcus jannaschii, are encoded CC by fusion proteins in certain lineages. The fusion protein in CC Mycobacterium smegmatis is designated FbiC (F420 BIosynthesis C). The CC precursors are a pyrimidine intermediate from riboflavin biosynthesis CC and the 4-hydroxyphenylpyruvate precursor of tyrosine, so expressing CC FbiC in Escherichia coli is sufficient for FO biosynthesis [2]. -- SN 1 ID 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) synthase, CofG subunit DN CofG family (EC 2.5.1.77) RQ 1 EV IPR019939; TIGR03550; TG GO:0009108; -- SN 2 ID 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) synthase, CofH subunit DN CofH family (EC 2.5.1.77) RQ 1 EV IPR019940; TIGR03551; TG GO:0009108; // AC GenProp0793 DE CMP-N-acetylneuraminate biosynthesis from UDP-N-acetylglucosamine TP METAPATH AU Haft DH TH 0 RN [1] RM 15629947 RT Structural and genetic characterization of enterohemorrhagic RT Escherichia coli O145 O antigen and development of an O145 RT serogroup-specific PCR assay. RA Feng L, Senchenkova SN, Tao J, Shashkov AS, Liu B, Shevelev SD, Reeves RA PR, Xu J, Knirel YA, Wang L; RL J Bacteriol. 2005;187:758-764. DC Aminosugars Metabolism DR KEGG; map00530; CC CMP-N5-acetylneuraminate (CMP-Neu5Ac) is the activated version of a CC sugar unit found in certain glycolipids and glycoproteins. Neuraminic CC acid is also commonly known as sialic acid. In particular, Neu5Ac is CC observed in certain versions of the E. coli O-antigen [1]. CMP-Neu5Ac CC is synthesized in three steps: isomerization of UDP-GlcNAc to CC N-Acetyl-D-Mannosamine (ManNAc) catalyzed by NeuC, a condensation with CC phosphoenolpyruvate to form NeuNAc catalyzed by NeuB, and an activation CC with CTPcatalyzed by NeuA. A fourth gene product, NeuD is believed to CC carry out O-acetyltransfers onto sialic acid but is often missing and CC is also found more broadly than NeuABC -- SN 1 ID CTP:N-acylneuraminate cytidyltransferase (2.7.7.43) DN CTP:N-acylneuraminate cytidyltransferase (EC 2.7.7.43)/NeuA RQ 1 EV IPR003329; PF02348; TG GO:0006054; -- SN 2 ID N-acetylneuraminate synthase (2.5.1.56) DN N-acetylneuraminate synthase (EC 2.5.1.56)/NeuB RQ 1 EV IPR020007; TIGR03569; TG GO:0006054; -- SN 3 ID UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing DN UDP-N-acetyl-D-glucosamine 2-epimerase (EC 5.1.3.14)/NeuC RQ 1 EV IPR020004; TIGR03568; TG GO:0006054; -- SN 4 ID Sialic acid O-acetyltransferase NeuD DN Sialic acid O-acetyltransferase NeuD RQ 0 EV IPR020019; TIGR03570; TG GO:0006054; -- SN 5 ID Source of UDP-N-acetyl-D-glucosamine DN Source of UDP-N-acetyl-D-glucosamine/UGlcNAc RQ 0 EV GenProp0750; TG GO:0006054; // AC GenProp0794 DE Proposed N-acetyl sugar amidation module WbuXYZ TP SYSTEM AU Haft DH TH 0 RN [1] RM 18156256 RT lfnA from Pseudomonas aeruginosa O12 and wbuX from Escherichia coli RT O145 encode membrane-associated proteins and are required for RT expression of 2,6-dideoxy-2-acetamidino-L-galactose in RT lipopolysaccharide O antigen. RA King JD, Mulrooney EF, Vinogradov E, Kneidinger B, Mead K, Lam JS; RL J Bacteriol. 2008;190:1671-1679. RN [2] RM 16684771 RT Functional characterization of the flagellar glycosylation locus in RT Campylobacter jejuni 81-176 using a focused metabolomics approach. RA McNally DJ, Hui JP, Aubry AJ, Mui KK, Guerry P, Brisson JR, Logan SM, RA Soo EC; RL J Biol Chem. 2006;281:18489-18498. RN [3] RM 15629947 RT Structural and genetic characterization of enterohemorrhagic RT Escherichia coli O145 O antigen and development of an O145 RT serogroup-specific PCR assay. RA Feng L, Senchenkova SN, Tao J, Shashkov AS, Liu B, Shevelev SD, Reeves RA PR, Xu J, Knirel YA, Wang L; RL J Bacteriol. 2005;187:758-764. CC The WbuX protein from E. coli and its homologs in P. aeruginosa (IfnA) CC and C. jejuni (PseA) have been proposed to function as N-acetyl sugar CC amidotransferases, forming the positively charged acetamidino moitey on CC both O-antigens and glycosylated flagellins [1,2]. These WbuX homologs CC are invariably associated with homologs of the HisH and HisF proteins CC (WbuYZ) which are proposed to act as a glutaminase and ammonium channel, CC to provide sufficient ammonium ion under limiting conditions [3]. CC Occasionally the WbuX protein is found in multiple (tandem) copies CC which may indicate multiple substrates or multiple N-acetyl groups CC being modified on the same substrate. -- SN 1 ID N-acetyl sugar amidotransferase DN N-acetyl sugar amidotransferase/WbuX (EC 6.3.4.-) RQ 1 EV IPR020022; TIGR03573; -- SN 2 ID HisH-like glutaminase WbuY DN HisH-like glutaminase WbuY (EC 2.4.2.-) RQ 1 EV IPR010139; TIGR01855; -- SN 3 ID HisF-like proposed ammonium channel protein WbuZ DN HisF-like proposed ammonium channel protein WbuZ RQ 1 EV IPR020021; TIGR03572; // AC GenProp0795 DE Carbohydrate biosynthesis TP CATEGORY AU Haft DH TH 0 CC Processes related to the biosynthesis and modification of sugars CC (saccharides). These may then be utilized in central metabolism, the CC modification of cellular stuctures and/or incorporated into complex CC polymers. -- SN 1 ID dTDP-L-rhamnose biosynthesis from dTDP-4-dehydro-L-rhamnose RQ 0 EV GenProp0183; -- SN 2 ID Lipopolysaccharide biosynthesis RQ 0 EV GenProp0297; -- SN 3 ID Glucosylglycerol biosynthesis RQ 0 EV GenProp0264; -- SN 4 ID UDP-N-acetylglucosamine biosynthesis from fructose-6-phosphate RQ 0 EV GenProp0750; -- SN 5 ID Anhydro-N-acetylmuramic acid to N-acetylglucosamine-phosphate RQ 0 EV GenProp0766; -- SN 6 ID CMP-N-acetylneuraminate biosynthesis from UDP-N-acetylglucosamine RQ 0 EV GenProp0793; -- SN 7 ID Proposed N-acetyl sugar amidation module WbuXYZ RQ 0 EV GenProp0794; -- SN 8 ID CMP-pseudaminic acid biosynthesis from UDP-N-acetylglucosamine RQ 0 EV GenProp0796; -- SN 9 ID S-layer homology domain-mediated cell wall binding RQ 0 EV GenProp0811; -- SN 10 ID dTDP-4-acetamido-4,6-dideoxy-D-galactose (dTDP-Fuc4NAc) biosynthesis RQ 0 EV GenProp0972; -- SN 11 ID dTDP-4-dehydro-6-deoxy-alpha-D-glucose biosynthesis from glucose-1-phosphate RQ 0 EV GenProp0950; -- SN 12 ID GDP-4-keto-6-deoxymannose biosynthesis from beta-D-fructose-6-phosphate RQ 0 EV GenProp0930; -- SN 13 ID Biosynthesis of undecaprenyl phosphate (Und-P) RQ 0 EV GenProp0971; -- SN 14 ID Biosynthesis of UDP-N-acetyl-D-mannosamine (UDP-ManNAc) RQ 0 EV GenProp0975; -- SN 15 ID GDP-D-mannose biosynthesis from b-D-fructose-6-phosphate RQ 0 EV GenProp1017; -- SN 16 ID Glycogen biosynthesis I (from ADP-D-Glucose) RQ 0 EV GenProp1247; -- SN 17 ID Glycogen biosynthesis II (from UDP-D-Glucose) RQ 0 EV GenProp1483; -- SN 18 ID Chondroitin sulfate biosynthesis RQ 0 EV GenProp1526; -- SN 19 ID Heparan sulfate biosynthesis RQ 0 EV GenProp1595; -- SN 20 ID Glycosaminoglycan-protein linkage region biosynthesis RQ 0 EV GenProp1699; -- SN 21 ID Protein O-[N-acetyl]-glucosylation RQ 0 EV GenProp1442; -- SN 22 ID Complex N-linked glycan biosynthesis (plants) RQ 0 EV GenProp1444; -- SN 23 ID Protein O-mannosylation III (mammals, core M3) RQ 0 EV GenProp1455; -- SN 24 ID Complex N-linked glycan biosynthesis (vertebrates) RQ 0 EV GenProp1524; -- SN 25 ID i antigen and I antigen biosynthesis RQ 0 EV GenProp1545; -- SN 26 ID Protein N-glycosylation processing phase (yeast) RQ 0 EV GenProp1706; -- SN 27 ID Mucin core 1 and core 2 O-glycosylation RQ 0 EV GenProp1712; -- SN 28 ID Cis-alkene biosynthesis RQ 0 EV GenProp1473; -- SN 29 ID Hentriaconta-3,6,9,12,15,19,22,25,28-nonaene biosynthesis RQ 0 EV GenProp1364; -- SN 30 ID Gluconeogenesis I RQ 0 EV GenProp1344; -- SN 31 ID Gluconeogenesis III RQ 0 EV GenProp1612; -- SN 32 ID ADP-L-glycero-β-D-manno-heptose biosynthesis RQ 0 EV GenProp1239; -- SN 33 ID dTDP-N-acetylthomosamine biosynthesis RQ 0 EV GenProp1403; -- SN 34 ID GDP-L-fucose biosynthesis I (from GDP-D-mannose) RQ 0 EV GenProp1429; -- SN 35 ID UDP-N-acetyl-D-glucosamine biosynthesis II RQ 0 EV GenProp1222; -- SN 36 ID UDP-N-acetyl-D-glucosamine biosynthesis I RQ 0 EV GenProp1443; -- SN 37 ID UDP-alpha-D-xylose biosynthesis RQ 0 EV GenProp1260; -- SN 38 ID UDP-beta-L-arabinose biosynthesis II (from beta-L-arabinose) RQ 0 EV GenProp1330; -- SN 39 ID UDP-alpha-D-glucuronate biosynthesis (from myo-inositol) RQ 0 EV GenProp1347; -- SN 40 ID UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronate biosynthesis RQ 0 EV GenProp1468; -- SN 41 ID UDP-N-acetyl-alpha-D-mannosaminouronate biosynthesis RQ 0 EV GenProp1549; -- SN 42 ID UDP-beta-L-rhamnose biosynthesis RQ 0 EV GenProp1713; -- SN 43 ID UDP-alpha-D-glucose biosynthesis I RQ 0 EV GenProp1743; -- SN 44 ID Colanic acid building blocks biosynthesis RQ 0 EV GenProp1648; // AC GenProp0796 DE CMP-pseudaminic acid biosynthesis from UDP-N-acetylglucosamine TP METAPATH AU Haft DH TH 3 RN [1] RM 3104041 RT Somatic antigens of Pseudomonas aeruginosa. The structure of O-specific RT polysaccharide chains of the lipopolysaccharides from P. aeruginosa O5 RT (Lányi) and immunotype 6 (Fisher). RA Knirel YA, Kocharova NA, Shashkov AS, Dmitriev BA, Kochetkov NK, RA Stanislavsky ES, Mashilova GM; RL Eur J Biochem. 1987;163:639-652. RN [2] RM 16286454 RT Functional characterization of dehydratase/aminotransferase pairs from RT Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic RT acid and bacillosamine biosynthetic pathways. RA Schoenhofen IC, McNally DJ, Vinogradov E, Whitfield D, Young NM, Dick RA S, Wakarchuk WW, Brisson JR, Logan SM; RL J Biol Chem. 2006;281:723-732. RN [3] RM 11119490 RT Role of flm locus in mesophilic Aeromonas species adherence. RA Gryllos I, Shaw JG, Gavín R, Merino S, Tomás JM; RL Infect Immun. 2001;69:65-74. RN [4] RM 16684771 RT Functional characterization of the flagellar glycosylation locus in RT Campylobacter jejuni 81-176 using a focused metabolomics approach. RA McNally DJ, Hui JP, Aubry AJ, Mui KK, Guerry P, Brisson JR, Logan SM, RA Soo EC; RL J Biol Chem. 2006;281:18489-18498. CC Pseudaminic acid is a component of the O-antigen of certain pseudomonas CC strains [1] as well as the glycosylation modification of Campylobacter CC and Helicobacter flagellins [2], but is clearly more widely CC distributed. The proposed biosynthetic pathway involves the CC dehydration/isomerization of UDP-D-GlcNAc to UDP-4-keto-6-deoxy-GlcNAc CC by PseB, and a transamination at position 4 by PseC. The PseH protein is CC similar to acetyltransferases and is presumed to carry out transfer to CC the C-4 amine. PseH itself is occasionally missing. Often in this CC case, the PseG protein contains a passable acetyltransferase domain. CC The function of PseG when PseH is present is unknown, it may complex CC with PseH, or it may be responsible for the UDP-hydrolysis that clearly CC must happen, but is not currently assigned to an enzyme with a conserved CC domain for this reaction. PseI carries out the condensation with CC phosphoenolpyruvate to create pseudaminic acid, a reaction analagous to CC that carried out by NeuB in the biosynthesis of neuraminic acid. CC PseF carries out the transfer of CMP onto pseudaminic CC acid to yield the most common product. In Campylobacter, the CC biosynthetic cluster is accompanied by the PseA protein, a homolog of CC WbuX and is responsible for the conversion of the N-acetyl group at CC position 7 into the acetimidino group. PseA is accompanied by two CC genes, WbuY and WbuZ which are reported to provide ammonia for the CC reaction. Other proteins are found associated with this cluster CC including methylases and possible formyltransferases and CC deacetylases. Thus, a range of closely related structures are likely CC produced as mature products in various lineages. -- SN 1 ID CMP-pseudaminic acid C7-N-acetyl amidotransferase DN N-acetyl sugar amidotransferase (EC: 6.3.4.-)/PseA RQ 0 EV IPR020022; TIGR03573; -- SN 2 ID UDP-GlcNAc C6-dehydratase/C4-reductase DN UDP-N-acetylglucosamine 4,6-dehydratase (EC:4.2.1.-)/PseB RQ 1 EV IPR020025; TIGR03589; -- SN 3 ID Pseudaminic acid biosynthesis aminotransferase PseC DN UDP-4-keto-6-deoxy-N-acetylglucosamine 4-aminotransferase (EC: 2.6.1.-)/PseC RQ 1 EV IPR020026; TIGR03588; -- SN 4 ID Pseudaminic acid CMP-transferase DN Pseudaminic acid CMP-transferase (EC:2.7.7.-)/PseF RQ 1 EV IPR020039; TIGR03584; EV IPR003329; PF02348; -- SN 5 ID Possible pseudaminic acid biosynthesis UDP hydrolase DN Pseudaminic acid biosynthesis-associated protein PseG/PseG RQ 0 EV IPR020023; TIGR03590; -- SN 6 ID Possible pseudaminic acid biosynthesis N-acetyl transferase DN Pseudaminic acid biosynthesis N-acetyl transferase/PseH RQ 1 EV IPR020036; TIGR03585; EV IPR000182; PF00583; -- SN 7 ID Pseudaminic acid synthase (pyruvate condensing enzyme) DN Pseudaminic acid synthase (EC:2.5.1.-)/PseI RQ 1 EV IPR020030; TIGR03586; -- SN 8 ID Pseudaminic acid biosynthesis associated methylase DN Pseudaminic acid biosynthesis associated methylase/PseM RQ 0 EV IPR020027; TIGR03587; -- SN 9 ID Source of UDP-N-acetyl-D-glucosamine DN Source of UDP-N-acetyl-D-glucosamine/UGlcNAc RQ 0 EV GenProp0750; // AC GenProp0797 DE Selenocysteinyl-tRNA, PSTK/SepSecS pathway TP PATHWAY AU Haft DH TH 0 RN [1] RM 18174226 RT Characterization and evolutionary history of an archaeal kinase RT involved in selenocysteinyl-tRNA formation. RA Sherrer RL, O'Donoghue P, Söll D; RL Nucleic Acids Res. 2008;36:1247-1259. RN [2] RM 15317934 RT Identification and characterization of phosphoseryl-tRNA[Ser]Sec RT kinase. RA Carlson BA, Xu XM, Kryukov GV, Rao M, Berry MJ, Gladyshev VN, Hatfield RA DL; RL Proc Natl Acad Sci U S A. 2004;101:12848-12853. CC This pathway is the archaeal and eukaryotic system for converting the CC serine on selenocysteine-tRNA to selenocysteine. This first enzyme is a CC kinase, L-seryl-tRNA(Sec) kinase (PSTK). The second is CC Sep-tRNA:Sec-tRNA synthase (SepSecS). In bacteria, this two-enzyme CC pathway is replaced by SelA (TIGR00474). -- SN 1 ID L-seryl-tRNA(Sec) kinase DN L-seryl-tRNA(Sec) kinase (EC 2.7.1.-) RQ 1 EV IPR020024; TIGR03574; TG GO:0016260; -- SN 2 ID O-phosphoseryl-tRNA(Sec) selenium transferase DN O-phosphoseryl-tRNA(Sec) selenium transferase (EC 2.9.1.-) RQ 1 EV IPR019872; TIGR03531; TG GO:0016260; // AC GenProp0798 DE Enterococcus/Aeromonas extended locus TP SYSTEM AU Haft DH TH 0 CC This Genome Property represents an uncharacterized, sporadically CC distributed eight-gene system. A somewhat broader set of bacteria CC contain three core genes from this system including a probable CC amidohydrolase (TIGR03583), a pyridoxal phosphate-dependent enzyme CC related to SelA (TIGR01437), and an uncharacterized protein CC (TIGR03581). Species with the eight-gene system include Aeromonas CC hydrophila ATCC7966, Salmonella typhimurium LT2, and Vibrio fischeri CC ES114 among the Proteobacteria, and Enterococcus faecalis V583 and CC Bacillus clausii KSM-K16 among the Firmicutes. The three-gene core is CC found also in Lactobacillus plantarum WCFS1, Bacillus anthracis, and CC Clostridium difficile QCD-32g58. Neighboring genes, including CC PTS-family transport genes and a member of the carbohydrate kinases, CC tend to suggest a role in carbohydrate catabolism. -- SN 1 ID PRD domain protein EF_0829/AHA_3910 DN PRD domain protein EF_0829/AHA_3910 RQ 1 EV IPR020044; TIGR03582; -- SN 2 ID Conserved hypothetical protein EF_0830/AHA_3911 DN Conserved hypothetical protein EF_0830/AHA_3911 RQ 1 EV IPR020034; TIGR03577; -- SN 3 ID Conserved hypothetical protein EF_0831/AHA_3912 DN Conserved hypothetical protein EF_0831/AHA_3912 RQ 1 EV IPR020037; TIGR03578; -- SN 4 ID Conserved hypothetical protein EF_0832/AHA_3913 DN Conserved hypothetical protein EF_0832/AHA_3913 RQ 1 EV IPR020042; TIGR03580; -- SN 5 ID Conserved hypothetical protein EF_0833/AHA_3914 DN Conserved hypothetical protein EF_0833/AHA_3914 RQ 1 EV IPR025456; TIGR03579; -- SN 6 ID Probable amidohydrolase EF_0837/AHA_3915 DN Probable amidohydrolase EF_0837/AHA_3915 RQ 1 EV IPR020043; TIGR03583; -- SN 7 ID Pyridoxal phosphate-dependent enzyme EF_0838/AHA_3916 DN Pyridoxal phosphate-dependent enzyme EF_0838/AHA_3916 RQ 1 EV IPR006337; TIGR01437; -- SN 8 ID Conserved hypothetical protein EF_0839/AHA_3917 DN Conserved hypothetical protein EF_0839/AHA_3917 RQ 1 EV IPR010763; TIGR03581; // AC GenProp0802 DE Ribosome biogenesis proteins, bacteria TP SYSTEM AU Haft DH TH 0 CC A number of well-conserved bacterial proteins, including various CC members of a family of GTPases, appear to aid in ribosome biogenesis in CC bacteria. This Genome Property collects some of these together and CC allows analysis of the degree to which each can be considered part of CC the universal bacterial core genome. -- SN 1 ID Obg family GTPase CgtA DN Obg family GTPase CgtA RQ 1 EV IPR014100; TIGR02729; -- SN 2 ID Ribosome biogenesis GTPase Der (EngA) DN Ribosome biogenesis GTPase Der (EngA) RQ 1 EV IPR016484; TIGR03594; -- SN 3 ID Ribosome biogenesis GTPase Era DN Ribosome biogenesis GTPase Era RQ 0 EV IPR005662; TIGR00436; -- SN 4 ID Ribosome biogenesis GTPase RsgA DN Ribosome biogenesis GTPase RsgA RQ 0 EV IPR004881; TIGR00157; -- SN 5 ID Ribosome biogenesis GTPase YlqF DN Ribosome biogenesis GTPase YlqF RQ 0 EV IPR019991; TIGR03596; -- SN 6 ID Ribosome biogenesis GTPase YqeH DN Ribosome biogenesis GTPase YqeH RQ 0 EV IPR019988; TIGR03597; -- SN 7 ID Ribosome biogenesis GTPase YsxC DN Ribosome biogenesis GTPase YsxC RQ 0 EV IPR019987; TIGR03598; -- SN 8 ID RRNA small subunit methyltransferase A DN RRNA small subunit methyltransferase A RQ 1 EV IPR011530; TIGR00755; -- SN 9 ID 16S RNA methyltransferase RsmG DN 16S RNA methyltransferase RsmG RQ 0 EV IPR003682; TIGR00138; -- SN 10 ID 16S rRNA methyltransferase RsmH DN 16S rRNA methyltransferase RsmH RQ 0 EV IPR002903; TIGR00006; -- SN 11 ID Ribosome maturation protein RimM DN Ribosome maturation protein RimM RQ 1 EV IPR011961; TIGR02273; -- SN 12 ID Ribosome maturation protein RimP DN Ribosome maturation protein RimP RQ 0 EV IPR003728; PF02576; // AC GenProp0806 DE Replication initiation, bacterial TP SYSTEM AU Haft DH TH 0 RN [1] RM 16036556 RT Protein--protein interactions in the eubacterial replisome. RA Schaeffer PM, Headlam MJ, Dixon NE; RL IUBMB Life. 2005;57:5-12. CC Replication of DNA involves three distinct stages: initiation, elongation, CC and termination. This genome propery describes the system of proteins CC required to initiate DNA replication in bacteria. -- SN 1 ID Chromosomal replication initiator protein DnaA DN Chromosomal replication initiator protein DnaA/DnaA RQ 1 EV IPR001957; TIGR00362; -- SN 2 ID Replicative DNA helicase DN Replicative DNA helicase/DnaB RQ 1 EV IPR007692; TIGR00665; -- SN 3 ID DNA primase DN DNA primase/DnaG RQ 1 EV IPR006295; TIGR01391; // AC GenProp0809 DE Bacteriocin system, lactococcin 972 group TP SYSTEM AU Haft DH TH 0 RN [1] RM 10589723 RT Synthesis of lactococcin 972, a bacteriocin produced by Lactococcus RT lactis IPLA 972, depends on the expression of a plasmid-encoded RT bicistronic operon. RA Martínez B, Fernández M, Suárez JE, Rodríguez A; RL Microbiology. 1999;145 ( Pt 11):3155-3161. CC Bacteriocins are bacterial products, toxic typically to closely related CC bacteria, derived from polypeptide precursors. This Genome Property CC represents a recognizable subclass of bacteriocin-biosynthesis and CC export system with a characteristic immunity protein modeled by CC TIGR01654. -- SN 1 ID Bacteriocin export protein, lactococcin 972 group DN Bacteriocin export protein, lactococcin 972 group RQ 1 EV IPR019895; TIGR03608; -- SN 2 ID Bacteriocin putative immunity protein, lactococcin 972 group DN Bacteriocin putative immunity protein, lactococcin 972 group RQ 1 EV IPR006541; TIGR01654; -- SN 3 ID Bacteriocin, lactococcin 972 group DN Bacteriocin, lactococcin 972 group RQ 1 EV IPR006540; TIGR01653; // AC GenProp0810 DE Encapsulin proteinaceous organelle TP SYSTEM AU Haft DH TH 0 RN [1] RM 22046962 RT Self-assembling, protein-based intracellular bacterial organelles: RT emerging vehicles for encapsulating, targeting and delivering RT therapeutical cargoes. RA Corchero JL, Cedano J; RL Microb Cell Fact. 2011;10:92. CC The protein previously called linocin M18 is now recognized as CC encapsulin, a self-assembling protein that associates with an CC enzyme (typically a peroxidase) and forms a proteinaceous organelle. CC Two quite different families, one a peroxidase, the other resembling CC ferritins, can be packaged by encapsulin and have a similar C-terminal CC motif, resembling DGSL[SGN]IGSL[KR], separated by a disordered region CC from their respective core homology regions. -- SN 1 ID Encapsulin DN Encapsulin RQ 1 EV IPR007544; PF04454; -- SN 2 ID Encapsulin-associated protein DN Encapsulin-associated protein RQ 0 EV IPR006314; TIGR01413; EV IPR030907; TIGR04535; EV IPR030909; TIGR04536; // AC GenProp0811 DE S-layer homology domain-mediated cell wall binding TP SYSTEM AU Haft DH TH 0 RN [1] RM 10970841 RT Bacterial SLH domain proteins are non-covalently anchored to the cell RT surface via a conserved mechanism involving wall polysaccharide RT pyruvylation. RA Mesnage S, Fontaine T, Mignot T, Delepierre M, Mock M, Fouet A; RL EMBO J. 2000;19:4473-4484. CC Two classes of S-layer homology domain (SLH) proteins are S-layer CC proteins themselves and porin-like outer membrane proteins with CC N-terminal SLH domains. Mesnage, et al. [1] have shown that CsaB (cell CC surface anchoring B) in Bacillus anthracis catalyzes a pyruvyl group CC addition to an LPS-associated polysaccharide, an addition that enables CC non-covalent binding by SLH domain proteins to the cell wall. CC the larger family described by Pfam model PF04230, and find that it -- SN 1 ID S-layer homology domain DN S-layer homology domain RQ 1 EV IPR001119; PF00395; -- SN 2 ID Polysaccharide pyruvyl transferase DN S-layer domain protein RQ 1 EV IPR019896; TIGR03609; TG GO:0042545; // AC GenProp0812 DE Rho-dependent termination TP METAPATH AU Haft DH TH 0 RN [1] RM 16554712 RT Rho-dependent transcription termination: more questions than answers. RA Banerjee S, Chalissery J, Bandey I, Sen R; RL J Microbiol. 2006;44:11-22. CC Transcriptional termination in bacteria occurs in two modes, one of CC them dependent on the termination factor Rho. Rho occurs in the CC overwhelming majority of bacteria, and is an essential protein in most CC but not all of those species. When Rho is present, the Nus factors CC (NusA, NusB, and NusG) participate in Rho-dependent termination, CC although those proteins have other functions as well and are more CC nearly universal than Rho itself. -- SN 1 ID Nus factors (NusA, NusB, NusG, and NexE/S10) DN Nus factors (NusA, NusB, NusG, and NexE/S10) RQ 1 EV GenProp0132; TG GO:0003715; -- SN 2 ID Rho termination factor DN Rho termination factor RQ 1 EV IPR004665; TIGR00767; TG GO:0003715; // AC GenProp0813 DE Pyrimidine utilization TP PATHWAY AU Haft DH TH 0 RN [1] RM 16540542 RT A previously undescribed pathway for pyrimidine catabolism. RA Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, RA Parales R, Zhou Z, Inwood W, Kustu S; RL Proc Natl Acad Sci U S A. 2006;103:5114-5119. CC This seven-gene operon described in E. coli K-12 [1] is responsible for CC the degradation of uracil, and to a lesser extent, thymine. This has CC been determined by growth and mutation experiments. The operon contains CC a luciferase family member (RutA) which likely catalyzes the CC FMN-dependent critical oxidation for the ring opening as well as RutF CC which may be involved in recycling the FMN cofactor. Other seemingly CC essential components are an isochorismate mutase family protein (RutB), CC a hydrolase (RutD) and a member of the L-PSP endoribonuclease family CC (RutC) and a regulatory protein (RutR). The transporter RutG found in CC E. coli is not found in all genomes harboring the rest of the operon CC and may be replaced by other non-homologous transporters located CC elsewhere in the genomes. This property appears to be limited to the CC alpha and gamma proteobacteria. -- SN 1 ID FMN-dependent luciferase family monoxygenase RutA DN FMN-dependent luciferase family monoxygenase RutA RQ 1 EV IPR019914; TIGR03612; -- SN 2 ID Isochorismate mutase family protein RutB DN Isochorismate mutase family protein RutB RQ 1 EV IPR019916; TIGR03614; -- SN 3 ID L-PSP endoribonuclease family protein RutC DN L-PSP endoribonuclease family protein RutC RQ 1 EV IPR019898; TIGR03610; -- SN 4 ID Hydrolase protein RutD DN Hydrolase protein RutD RQ 1 EV IPR019913; TIGR03611; -- SN 5 ID Nitroreductase family protein RutE DN Nitroreductase family protein RutE RQ 0 EV IPR029479; PF00881; -- SN 6 ID Flavin reductase RutF DN Flavin reductase RutF RQ 1 EV IPR019917; TIGR03615; -- SN 7 ID Uracil-xanthine permease family protein RutG DN Uracil-xanthine permease family protein RutG RQ 0 EV IPR019918; TIGR03616; -- SN 8 ID Clustered regulatory protein DN Clustered regulatory protein RQ 0 EV IPR019915; TIGR03613; // AC GenProp0814 DE Urea utilization TP METAPATH AU Haft DH TH 0 CC This property encompasses two separate urea catabolism pathways, the CC nickel-dependent urease pathway and the urea carboxylase/allophanate CC hydrolase pathway. -- SN 1 ID A urea transporter DN A urea transporter RQ 0 EV GenProp0743; EV IPR004937; PF03253; -- SN 2 ID A urea degradation pathway DN A urea degradation pathway RQ 1 EV GenProp0481; EV GenProp0051; // AC GenProp0816 DE Nucleoside catabolism/utilization pathways TP CATEGORY AU Haft DH TH 0 CC Properties in this category are pathways for the degradation and reuse CC of nucleosides. Pathways utilizing the bases and the sugar moieties are CC included. -- SN 1 ID AMP metabolism using type III Rubisco RQ 0 EV GenProp0728; // AC GenProp0817 DE Nucleotide catabolism/utilization pathways TP CATEGORY AU Haft DH TH 0 CC Properties in this category are pathways for the degradation and reuse CC of nucleotides. -- SN 1 ID Xanthine dehydrogenase RQ 0 EV GenProp0640; -- SN 2 ID Xanthine utilization as a source of guanine-monophosphate (GMP) RQ 0 EV GenProp0696; -- SN 3 ID Purine catabolism via urate, xanthine and allantoin RQ 0 EV GenProp0700; -- SN 4 ID Xanthine dehydrogenase, bacillus type (pucABCDE) RQ 0 EV GenProp0705; -- SN 5 ID Pyrimidine utilization RQ 0 EV GenProp0813; // AC GenProp0819 DE RNA metabolism TP CATEGORY AU Haft DH TH 0 CC The chemical reactions and physical changes involving RNA (ribonucleaic CC acid), one of the two main types of nucleic acid. RNA is a long unbranched CC macromolecule, formed from one strand of linked ribonucleotides. -- SN 1 ID RNA polymerase, bacterial RQ 0 EV GenProp0262; -- SN 2 ID tRNA aminoacylation RQ 0 EV GenProp0258; -- SN 3 ID Queuosine (Q-tRNA) biosynthesis from preQ0 RQ 0 EV GenProp0677; -- SN 4 ID Selenouridine-containing tRNA RQ 0 EV GenProp0692; -- SN 5 ID tRNA U34 carboxymethylaminomethyl modification RQ 0 EV GenProp0704; -- SN 6 ID RNA ligase/unknown protein pair RQ 0 EV GenProp0898; -- SN 7 ID RNA repair, Hen1/Pnkp system RQ 0 EV GenProp0948; -- SN 8 ID tRNA N6-threonylcarbamoyladenosine modification RQ 0 EV GenProp1060; -- SN 9 ID tRNA(Pro) cmo5UGG modification RQ 0 EV GenProp1077; -- SN 10 ID 16S rRNA C1402 m(4)Cm modification RQ 0 EV GenProp1082; -- SN 11 ID Degradosome RQ 0 EV GenProp1166; // AC GenProp0820 DE Iron metabolism TP CATEGORY AU Haft DH TH 0 CC Properties in this catergory cover processes that import, export and CC transform the chemical state of the iron atom. -- SN 1 ID Iron-sulfur cluster assembly systems RQ 0 EV GenProp0140; -- SN 3 ID Protoheme from protoporphyrin IX RQ 0 EV GenProp0222; -- SN 4 ID Heme uptake system, NEAT-domain mediated RQ 0 EV GenProp0828; -- SN 5 ID Heme metabolism pair HutWX RQ 0 EV GenProp0961; // AC GenProp0821 DE Putative Na:solute symporter two-gene cassette TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes an unusual two-gene cassette for a CC probable transporter system. The longer protein belongs to the CC sodium:solute symporter family. The shorter protein, found almost CC invariably immediately upstream, is highly hydrophobic but CC uncharacterized. The pair is found in about one in six completed CC prokaryotic genomes. -- SN 1 ID Na+/solute symporter, large subunit DN Na+/solute symporter, large subunit RQ 1 EV IPR019899; TIGR03648; -- SN 2 ID Na+/solute symporter, small subunit DN Na+/solute symporter, small subunit RQ 1 EV IPR019886; TIGR03647; // AC GenProp0822 DE Poly(gamma-glutamic acid) biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 16267300 RT CapE, a 47-amino-acid peptide, is necessary for Bacillus anthracis RT polyglutamate capsule synthesis. RA Candela T, Mock M, Fouet A; RL J Bacteriol. 2005;187:7765-7772. RN [2] RM 19483793 RT Fusobacterium nucleatum, the first Gram-negative bacterium demonstrated RT to produce polyglutamate. RA Candela T, Moya M, Haustant M, Fouet A; RL Can J Microbiol. 2009;55:627-632. CC Poly(gamma-glutamic acid) (PGA) is an extracellular structural polymer CC found in Bacillus subtilis and a number of other species. Differences in CC stereochemistry are reported, with poly-(gamma-D-glutamate) in Bacillus CC anthracis but a mixture of D- and L-glutamates in Bacillus subtilis CC 168, Staphylococcus epidermidis ATCC 12228, and Bacillus licheniformis CC ATCC 14580. Because the gene symbol pgsA (nomenclature from Bacillus CC subtilis natto) refers to a different gene in Bacillus subtilis 168, we CC will use instead capB (pgsB, ywsC), capC (pgsC, ywtA), capA (pgsA, CC ywtB), etc. This property describes only the biosynthesis (PgsB and CC PgsC), and not the export or attachment machinery that differs between CC Gram-positive and Gram-negative systems, and between capsule-forming CC and secretory forms of system. -- SN 1 ID Poly-gamma-glutamate synthase DN Poly-gamma-glutamate synthase RQ 1 EV IPR008337; TIGR04012; TG GO:0070501; -- SN 2 ID Poly-gamma-glutamate biosynthesis protein PgsC DN Poly-gamma-glutamate biosynthesis protein PgsC RQ 1 EV IPR008338; TIGR04011; TG GO:0070501; // AC GenProp0828 DE Heme uptake system, NEAT-domain mediated TP SYSTEM AU Haft DH TH 0 RN [1] RM 18676371 RT Demonstration of the iron-regulated surface determinant (Isd) heme RT transfer pathway in Staphylococcus aureus. RA Muryoi N, Tiedemann MT, Pluym M, Cheung J, Heinrichs DE, Stillman MJ; RL J Biol Chem. 2008;283:28125-28136. RN [2] RM 17229211 RT Haem recognition by a Staphylococcus aureus NEAT domain. RA Grigg JC, Vermeiren CL, Heinrichs DE, Murphy ME; RL Mol Microbiol. 2007;63:139-149. RN [3] RM 18725935 RT Bacillus anthracis secretes proteins that mediate heme acquisition from RT hemoglobin. RA Maresso AW, Garufi G, Schneewind O; RL PLoS Pathog. 2008;4:e1000132. RN [4] RM 14570922 RT IsdG and IsdI, heme-degrading enzymes in the cytoplasm of RT Staphylococcus aureus. RA Skaar EP, Gaspar AH, Schneewind O; RL J Biol Chem. 2004;279:436-443. CC This system is found in certain lineages of the Bacillus/Clostridium CC group, including a number of pathogenic species. In order to obtain CC iron, this system utilizes a number of NEAT domain containing proteins CC to scavenge heme from host hemoproteins and convey them across the CC cell wall to an ABC transporter in the cytoplasmic membrane. Cell CC wall localization of these components is generally mediated by CC sortases, SrtB being particularly critical to this system in many CC organisms. Heme is often oxidized to biliverdin by heme oxygenases in CC the cytoplasm, releasing iron. Genes of this system are generally CC given "isd" gene symbols where isd stands for Iron-regulated Surface CC Determinant proteins. -- SN 1 ID Heme oxygenase DN Heme oxygenase RQ 1 EV IPR007138; PF03992; TG GO:0015886; EV IPR016053; PF01126; TG GO:0015886; -- SN 2 ID Heme ABC transporter, heme-binding protein IsdE DN Heme ABC transporter, heme-binding protein IsdE RQ 1 EV IPR019957; TIGR03659; TG GO:0015886; -- SN 3 ID Heme ABC transporter, permease protein IsdF DN Heme ABC transporter, permease protein IsdF RQ 1 EV IPR000522; PF01032; TG GO:0015886; -- SN 4 ID NEAT-domain proteins DN NEAT-domain proteins RQ 1 EV IPR006635; PF05031; TG GO:0015886; -- SN 5 ID Heme ABC transporter, ATP-binding protein DN Heme ABC transporter, ATP-binding protein RQ 0 EV IPR003439; PF00005; TG GO:0015886; -- SN 6 ID Multi-NEAT, srt-signal component DN Multi-NEAT, srt-signal component RQ 0 EV IPR019930; TIGR03658; TG GO:0015886; EV IPR019929; TIGR03657; TG GO:0015886; -- SN 8 ID Single-NEAT, srt-signal component DN Single-NEAT, srt-signal component RQ 1 EV IPR019909; TIGR03656; TG GO:0015886; // AC GenProp0829 DE Menaquinone biosynthesis via futalosine TP PATHWAY AU Haft DH TH 2 RN [1] RM 18801996 RT An alternative menaquinone biosynthetic pathway operating in RT microorganisms. RA Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi RA T; RL Science. 2008;321:1670-1673. CC This pathway for the biosynthesis of menaquinone begins with CC chorismate, and progresses via the intermediate futalosine. This is CC completely separate to the well-known E. coli menaquinone synthesis CC pathway (GenProp0058), which also starts with chorismate [1]. -- SN 1 ID Prenyltransferase DN 4-hydroxybenzoate polyprenyltransferase-related RQ 1 EV IPR006371; TIGR01475; TG GO:0009234; -- SN 2 ID Futalosine synthase DN Menaquinone biosynthesis enzyme RQ 1 EV IPR003773; PF02621; TG GO:0009234; -- SN 3 ID Futalosine hydrolase DN Futalosine hydrolase RQ 1 EV IPR019963; TIGR03664; TG GO:0009234; -- SN 4 ID De-hypoxanthine futalosine (DHFL) cyclase DN Cyclic dehypoxanthine futalosine synthase RQ 1 EV IPR022431; TIGR03699; TG GO:0009234; -- SN 5 ID 1,4-dihydroxy-6-naphthoate (DHN) synthase DN 1,4-dihydroxy-6-naphtoate synthase RQ 1 EV IPR030869; MF_00996; TG GO:0009234; -- SN 6 ID Decarboxylase DN 4-hydroxybenzoate decarboxylase subunit C RQ 1 EV IPR022390; TIGR03701; TG GO:0009234; -- SN 7 ID Putative menaquinone biosynthesis protein, SCO4494 family DN Aminodeoxyfutalosine synthase RQ 1 EV IPR022432; TIGR03700; TG GO:0009234; // AC GenProp0830 DE Integral membrane mystery pair TP SYSTEM AU Haft DH TH 0 CC This Genome Property represents a pair of families of probable CC multi-membrane-spanning enzymes, one with some similarity to CC glycosyltransferase family. The sporadic distribution includes a number CC of members of the Archaea and the Chloroflexi. The members of the two CC families are sometimes clustered, confirming a functional link. The CC function is unknown. -- SN 1 ID Integral membrane mystery pair protein 1 DN Integral membrane mystery pair protein 1 RQ 1 EV IPR018746; TIGR03662; -- SN 2 ID Integral membrane mystery pair protein 2 DN Integral membrane mystery pair protein 2 RQ 1 EV IPR019962; TIGR03663; // AC GenProp0833 DE Proteasome-targeting modification by pupylation TP SYSTEM AU Haft DH TH 0 RN [1] RM 18832610 RT Ubiquitin-like protein involved in the proteasome pathway of RT Mycobacterium tuberculosis. RA Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH; RL Science. 2008;322:1104-1107. RN [2] RM 17277063 RT Characterization of the proteasome accessory factor (paf) operon in RT Mycobacterium tuberculosis. RA Festa RA, Pearce MJ, Darwin KH; RL J Bacteriol. 2007;189:3044-3050. CC Pupylation is the process by which the small protein Pup is conjugated CC to proteins through its C-terminus to a lysine epsilon-amino group of CC the target. This modification, analogous to ubiquitination in CC eukaryotes, targets proteins for degradation by archaeal-type CC proteasomes in Mycobacterium tuberculosis and related Actinobacteria. -- SN 1 ID 20S proteasome DN 20S proteasome RQ 1 EV GenProp0834; TG GO:0019941; -- SN 2 ID Ubiquitin-like protein Pup DN Ubiquitin-like protein Pup RQ 1 EV IPR008515; TIGR03687; TG GO:0019941; -- SN 3 ID AAA family ATPase, pupylation-associated DN AAA family ATPase, pupylation-associated RQ 1 EV IPR022482; TIGR03689; TG GO:0019941; -- SN 4 ID Pup ligase DN Pup ligase RQ 1 EV IPR022279; TIGR03686; TG GO:0019941; EV IPR022366; TIGR03688; TG GO:0019941; // AC GenProp0834 DE Proteasome, bacterial TP SYSTEM AU Haft DH TH 0 CC The proteasome, a large complex formed of alpha and beta subunits, CC performs protein degradation in eukaryotes, archaea, and bacteria. This CC Genome Property describes a bacterial 20S proteasome that approximates CC being restricted to and universal in the Actinobacteria. Nearly all CC bacteria with this proteasomal system use pupylation to tag proteins CC as proteasomal targets. The HslVU system in many bacteria is related, CC with HslV homologous to the proteasome beta subunit, but that system is CC outside the scope of the archaeal-type bacterial 20S proteasome CC described here. -- SN 1 ID Proteasome, alpha subunit DN Proteasome, alpha subunit RQ 1 EV IPR022296; TIGR03691; TG GO:0010498; -- SN 2 ID Proteasome, beta subunit DN Proteasome, beta subunit RQ 1 EV IPR022483; TIGR03690; TG GO:0010498; // AC GenProp0835 DE ATP-dependent protease HslVU TP SYSTEM AU Haft DH TH 0 RN [1] RM 9288941 RT The heat-shock protein HslVU from Escherichia coli is a RT protein-activated ATPase as well as an ATP-dependent proteinase. RA Seol JH, Yoo SJ, Shin DH, Shim YK, Kang MS, Goldberg AL, Chung CH; RL Eur J Biochem. 1997;247:1143-1150. CC HslVU, also known as ClpQY, is an ATP-dependent protease that resembles CC proteasomes. The ATPase HslU acts in protein unfolding, while the CC threonine-type endopeptidase HslV is homologous to the proteasome beta CC subunit and acts in protein degradation. Members of this family CC frequently are described as heat shock proteins. -- SN 1 ID ATP-dependent protease HslVU, ATPase subunit DN ATP-dependent protease HslVU, ATPase subunit RQ 1 EV IPR004491; TIGR00390; TG GO:0006510; -- SN 2 ID ATP-dependent protease HslVU, peptidase subunit DN ATP-dependent protease HslVU, peptidase subunit RQ 1 EV IPR022281; TIGR03692; TG GO:0006510; // AC GenProp0836 DE Menaquinone biosynthesis TP METAPATH AU Haft DH TH 0 CC Menaquinone may be synthesized by one of two independent pathways. The CC better known pathway, which includes MenA, MenB, etc., as found in CC Escherichia coli, passes through the intermediate SEPHCHC (see CC GenProp0058). An alternate pathway, found in both Helicobacter pylori CC and Streptomyces coelicolor, involves the intermediate futalosine (see CC GenProp0829). -- SN 1 ID Menaquinone biosynthesis: SEPHCHC or futalosine RQ 1 EV GenProp0058; EV GenProp0829; // AC GenProp0837 DE 1-acylglycerol-3-phosphate biosynthesis, PlsX/Y pathway TP PATHWAY AU Haft DH TH 0 RN [1] RM 17645809 RT Involvement of the YneS/YgiH and PlsX proteins in phospholipid RT biosynthesis in both Bacillus subtilis and Escherichia coli. RA Yoshimura M, Oshima T, Ogasawara N; RL BMC Microbiol. 2007;7:69. CC This two-enzyme pathway for 1-acylglycerol-3-phosphate biosynthesis can CC replace the enzyme glycerol-3-phosphate O-acyltransferase of E. coli, CC and is more widely distributed. PlsX synthesizes the acylphosphate from CC an acyl group on a carrier (CoA or acyl carrier protein), and PlsY (YgiH, CC YneS) transfers the acyl group to glycerol-3-phosphate. -- SN 1 ID PlsX DN PlsX RQ 1 EV IPR012281; TIGR00182; sufficient; TG GO:0006654; -- SN 2 ID Acylphosphate:glycerol 3-phosphate acyltransferase DN Acylphosphate:glycerol 3-phosphate acyltransferase RQ 1 EV IPR003811; TIGR00023; TG GO:0006654; // AC GenProp0838 DE Lipid biosynthesis TP CATEGORY AU Haft DH TH 0 CC The chemical reactions and pathways resulting in the formation of CC lipids (compounds soluble in an organic solvent but not, or sparingly, CC in an aqueous solvent). These include but are not limited to: CC isoprenoids, steroids, fatty acids, membrane lipids and CC lipopolysaccharides. -- SN 1 ID IPP biosynthesis RQ 0 EV GenProp0046; -- SN 2 ID Ubiquinone biosynthesis from chorismate, aerobic RQ 0 EV GenProp0136; -- SN 3 ID Lipopolysaccharide biosynthesis RQ 0 EV GenProp0297; -- SN 4 ID Fatty acid biosynthesis RQ 0 EV GenProp0299; -- SN 5 ID Menaquinone biosynthesis RQ 0 EV GenProp0836; -- SN 6 ID 1-acylglycerol-3-phosphate biosynthesis, PlsX/Y pathway RQ 0 EV GenProp0837; -- SN 7 ID Lycopene biosynthesis from IPP RQ 0 EV GenProp0758; -- SN 8 ID Galactolipid biosynthesis I RQ 0 EV GenProp1302; -- SN 9 ID Glycolipid desaturation RQ 0 EV GenProp1690; -- SN 10 ID Cardiolipin biosynthesis III RQ 0 EV GenProp1252; -- SN 11 ID Cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) RQ 0 EV GenProp1453; -- SN 12 ID Cardiolipin biosynthesis I RQ 0 EV GenProp1627; -- SN 13 ID Phosphatidylcholine biosynthesis I RQ 0 EV GenProp1351; -- SN 14 ID Phosphatidylcholine biosynthesis V RQ 0 EV GenProp1516; -- SN 15 ID Phospholipid remodeling (phosphatidylcholine, yeast) RQ 0 EV GenProp1718; -- SN 16 ID Phosphatidylethanolamine biosynthesis I RQ 0 EV GenProp1542; -- SN 17 ID Phospholipid remodeling (phosphatidylethanolamine, yeast) RQ 0 EV GenProp1575; -- SN 18 ID Phosphatidate biosynthesis (yeast) RQ 0 EV GenProp1316; -- SN 19 ID D-myo-inositol-5-phosphate metabolism RQ 0 EV GenProp1511; -- SN 20 ID 3-Phosphoinositide biosynthesis RQ 0 EV GenProp1758; -- SN 21 ID Globo-series glycosphingolipids biosynthesis RQ 0 EV GenProp1304; -- SN 22 ID Sphingolipid biosynthesis (yeast) RQ 0 EV GenProp1423; -- SN 23 ID Ganglio-series glycosphingolipids biosynthesis RQ 0 EV GenProp1517; -- SN 24 ID Lacto-series glycosphingolipids biosynthesis RQ 0 EV GenProp1518; -- SN 25 ID Neolacto-series glycosphingolipids biosynthesis RQ 0 EV GenProp1539; -- SN 26 ID Sphingolipid biosynthesis (mammals) RQ 0 EV GenProp1665; -- SN 27 ID Ceramide de novo biosynthesis RQ 0 EV GenProp1671; -- SN 28 ID Ergosterol biosynthesis I RQ 0 EV GenProp1609; -- SN 29 ID Zymosterol biosynthesis RQ 0 EV GenProp1246; -- SN 30 ID Allopregnanolone biosynthesis RQ 0 EV GenProp1552; -- SN 31 ID Sterol:steryl ester interconversion (yeast) RQ 0 EV GenProp1558; -- SN 32 ID (Kdo)2-lipid A biosynthesis I RQ 0 EV GenProp1397; -- SN 33 ID Sulfoquinovosyl diacylglycerol biosynthesis RQ 0 EV GenProp1546; -- SN 34 ID Lipid A-core biosynthesis RQ 0 EV GenProp1651; -- SN 35 ID Epoxysqualene biosynthesis RQ 0 EV GenProp1683; -- SN 36 ID Superpathway of cholesterol biosynthesis RQ 0 EV GenProp1530; -- SN 37 ID Superpathway of ergosterol biosynthesis I RQ 0 EV GenProp1594; -- SN 38 ID Superpathway of lipopolysaccharide biosynthesis RQ 0 EV GenProp1647; // AC GenProp0839 DE 2-oxoacid:ferredoxin oxidoreductase, multisubunit form TP SYSTEM AU Haft DH TH 0 CC This complex can serve as an alternative to the 2-oxoglutarate CC dehydrogenase system of the TCA cycle. -- SN 1 ID Alpha subunit (TPP binding domain) DN Alpha subunit (TPP binding domain) RQ 1 EV IPR002880; PF01855; -- SN 2 ID Beta subunit (TPP enzyme) DN Beta subunit (TPP enzyme) RQ 1 EV IPR011766; PF02775; EV IPR011896; TIGR02177; -- SN 3 ID Ferredoxin (4Fe-4S binding domain) DN Ferredoxin (4Fe-4S binding domain) RQ 0 EV IPR017896; PF00037; -- SN 4 ID Gamma subunit DN Gamma subunit RQ 1 EV IPR019752; PF01558; // AC GenProp0840 DE Polyphosphate kinase/exopolyphosphatase system TP SYSTEM AU Haft DH TH 0 RN [1] RM 15520374 RT Inorganic polyphosphate in the origin and survival of species. RA Brown MR, Kornberg A; RL Proc Natl Acad Sci U S A. 2004;101:16085-16087. CC This property describes systems for polyphosphate metabolism, featuring CC a polyphosphate kinase (PPK1) and an exopolyphosphatase that often are CC encoded by adjacent genes. Polyphosphate can provide functions of CC phosphate and energy storage, and may form granules. Genes from this CC system are often found next to genes of the inorganic phosphate CC transport system. Performing comparative genomics for this system is CC tricky in part because of numbers of numerous apparent bifunctional CC proteins, exopolyphosphatase/guanosine pentaphosphate phosphohydrolase. CC Proteins of the polyphosphate kinase 2 (PPK2) family are largely CC restricted to species with PPK1 and help produce GTP from GDP and CC polyphosphate. -- SN 1 ID Polyphosphate kinase 1 DN Polyphosphate kinase 1/PP_ppk1 RQ 1 EV IPR024953; PF02503; EV IPR003414; TIGR03705; -- SN 2 ID Exopolyphosphatase DN Exopolyphosphatase/PP_ppx RQ 1 EV IPR022371; TIGR03706; EV IPR003695; PF02541; -- SN 3 ID Polyphosphate kinase 2, PA0141 family DN Polyphosphate kinase 2, PA0141 family/PP_useA RQ 0 EV IPR022486; TIGR03707; -- SN 4 ID Polyphosphate:AMP phosphotransferase DN Polyphosphate:AMP phosphotransferase/PP_useB RQ 0 EV IPR022489; TIGR03708; -- SN 5 ID Putative polyphosphate kinase DN Putative polyphosphate kinase/PP_useC RQ 0 EV IPR022300; TIGR03709; -- SN 6 ID Polyphosphate kinase 2 DN Polyphosphate kinase 2/PP_useX RQ 0 EV IPR022488; PF03976; // AC GenProp0841 DE 2-oxoacid:ferredoxin oxidoreductase TP METAPATH AU Haft DH TH 0 CC This complex can serve as an alternative to the 2-oxoglutarate CC dehydrogenase system of the TCA cycle, but may also function CC in other systems, for instance as a NifJ component acting on CC pyruvate, supplying electrons to the nitrogenase system. -- SN 1 ID 2-oxoacid:ferredoxin oxidoreductase DN 2-oxoacid:ferredoxin oxidoreductase RQ 1 EV IPR011895; TIGR02176; EV GenProp0839; // AC GenProp0842 DE 2-oxoacid:acceptor oxidoreductase, 2 subunit form TP SYSTEM AU Haft DH TH 0 CC This form of 2-oxoacid:acceptor oxidoreductase has been shown to CC possess 2-oxoglutarate oxidoreductase (succinyl-CoA forming) activity CC in a number of species and likely replaces the lipoate-based E1/E2/E3 CC system in many organisms lacking it. -- SN 1 ID Ferredoxin, or other gene clustered electron acceptor DN Ferredoxin, or other gene clustered electron acceptor/acceptor RQ 0 EV IPR017896; PF00037; EV IPR008331; PF00210; EV IPR003251; PF02915; -- SN 2 ID 2-oxoacid:acceptor oxidoreductase, alpha subunit DN 2-oxoacid:acceptor oxidoreductase, alpha subunit/alpha RQ 1 EV IPR022367; TIGR03710; -- SN 3 ID 2-oxoacid:acceptor oxidoreductase, beta subuni DN 2-oxoacid:acceptor oxidoreductase, beta subuni/beta RQ 1 EV IPR011896; TIGR02177; EV IPR011766; PF02775; // AC GenProp0845 DE Protein sorting system, KxYKxGKxW class TP SYSTEM AU Haft DH TH 0 CC Analogous to YSIRK, this property describes a subclass of N-terminal CC signal sequence in Firmicutes (low-GC Gram-positive bacteria). As with CC YSIRK, many proteins with this N-terminal domain have an LPXTG CC C-terminal anchor. However, most of these proteins have extended CC regions of low-complexity sequence, usually serine-rich. We propose CC that this signal domain is recognized by cellular machinery that delays CC protein translocation until glycosylation or other post-translational CC modifications are complete. -- SN 1 ID KxYKxGKxW motif signal peptide DN KxYKxGKxW motif signal peptide RQ 1 EV IPR022263; TIGR03715; -- SN 2 ID Putative linked putative esterase TIGR03729 DN Putative linked putative esterase TIGR03729 RQ 0 EV IPR022302; TIGR03729; // AC GenProp0847 DE Exosporium TP SYSTEM AU Haft DH TH 0 RN [1] RM 18761690 RT Targeting of the BclA and BclB proteins to the Bacillus anthracis spore RT surface. RA Thompson BM, Stewart GC; RL Mol Microbiol. 2008;70:421-434. RN [2] RM 23411372 RT A genetic approach for the identification of exosporium assembly RT determinants of Bacillus anthracis. RA Spreng KA, Thompson BM, Stewart GC; RL J Microbiol Methods. 2013;93:58-67. CC The exosporium is an outermost extra surface layer of spores formed by CC some members of the genus Bacillus, including pathogens B. anthracis CC and B. cereus. It consists of a basal layer and a nap of hair-like CC filaments. -- SN 1 ID Exosporium leader peptide DN Exosporium leader peptide RQ 1 EV IPR021201; TIGR03720; TG GO:0043592; // AC GenProp0853 DE Lantibiotic system, gallidermin/epidermin family TP SYSTEM AU Haft DH TH 0 CC A specialized ABC transporter occurs both in species that make CC lantibiotics in the gallidermin family and as orphans in species that CC lack both the lantibiotic precursor molecule and the corresponding CC synthases. It appears these transporters are responsible for CC self-protection in species that make lantibiotics, and defense in those CC that do not. -- SN 1 ID Lantibiotic protection ABC transporter, MutE family permease subunit DN Lantibiotic protection ABC transporter, MutE family permease subunit RQ 1 EV IPR021205; TIGR03732; -- SN 2 ID Lantibiotic protection ABC transporter, MutG family permease subunit DN Lantibiotic protection ABC transporter, MutG family permease subunit RQ 1 EV IPR022294; TIGR03733; -- SN 3 ID Lantibiotic protection ABC transporter, ATP-binding subunit DN Lantibiotic protection ABC transporter, ATP-binding subunit RQ 1 EV IPR022501; TIGR03740; -- SN 4 ID Lantibiotic precursor, gallidermin/epidermin family DN Lantibiotic precursor, gallidermin/epidermin family RQ 1 EV IPR006079; TIGR03731; // AC GenProp0854 DE ParB-rel/ThiF-rel cassette PRTRC TP SYSTEM AU Haft DH TH 0 CC A novel genetic system characterized by six major proteins, including a CC ParB homolog and a ThiF homolog, is designated PRTRC, or CC ParB-Related,ThiF-Related Cassette. It is often found on plasmids. -- SN 1 ID PRTRC system ParB family protein DN PRTRC system ParB family protein RQ 1 EV IPR022396; TIGR03734; -- SN 2 ID PRTRC system protein E DN PRTRC system protein E RQ 1 EV IPR022273; TIGR03741; -- SN 3 ID PRTRC system protein C DN PRTRC system protein C RQ 1 EV IPR022289; TIGR03738; -- SN 4 ID PRTRC system protein F DN PRTRC system protein F RQ 1 EV IPR022283; TIGR03742; -- SN 5 ID PRTRC system protein B DN PRTRC system protein B RQ 1 EV IPR022280; TIGR03737; -- SN 6 ID PRTRC system protein A DN PRTRC system protein A RQ 1 EV IPR022499; TIGR03735; -- SN 7 ID PRTRC system ThiF family protein DN PRTRC system ThiF family protein RQ 1 EV IPR022500; TIGR03736; -- SN 8 ID PRTRC system protein D DN PRTRC system protein D RQ 0 EV IPR022389; TIGR03739; // AC GenProp0855 DE Integrating conjugative element, PFGI-1 class TP SYSTEM AU Haft DH TH 0 RN [1] RM 19144133 RT Mobile genetic elements in the genome of the beneficial rhizobacterium RT Pseudomonas fluorescens Pf-5. RA Mavrodi DV, Loper JE, Paulsen IT, Thomashow LS; RL BMC Microbiol. 2009;9:8. RN [2] RM 12107144 RT Genomic and functional analyses of SXT, an integrating antibiotic RT resistance gene transfer element derived from Vibrio cholerae. RA Beaber JW, Hochhut B, Waldor MK; RL J Bacteriol. 2002;184:4259-4269. CC This Genome Property represents a collection of mostly uncharacterized CC proteins typical of integrative conjugative elements (ICE) in the CC class of PFGI-1 of Pseudomonas fluorescens Pf-5. -- SN 1 ID Integrating conjugative element ParB-related protein DN Integrating conjugative element ParB-related protein RQ 1 EV IPR022304; TIGR03764; -- SN 2 ID Integrating conjugative element protein, PFL_4669 family DN Integrating conjugative element protein, PFL_4669 family RQ 1 EV IPR014996; TIGR03761; -- SN 3 ID Integrating conjugative element protein PilL, PFGI-1 class DN Integrating conjugative element protein PilL, PFGI-1 class RQ 1 EV IPR022260; TIGR03748; -- SN 4 ID Integrating conjugative element protein PFL4693 DN Integrating conjugative element protein PFL4693 RQ 1 EV IPR022293; TIGR03759; -- SN 5 ID Integrating conjugative element protein, PFL4695 family DN Integrating conjugative element protein, PFL4695 family RQ 1 EV IPR021300; TIGR03765; -- SN 6 ID Integrating conjugative element TraD protein, PFGI-1 class DN Integrating conjugative element TraD protein, PFGI-1 class RQ 1 EV IPR022503; TIGR03754; -- SN 7 ID Integrating conjugative element membrane protein PFL4697 DN Integrating conjugative element membrane protein PFL4697 RQ 1 EV IPR022266; TIGR03747; -- SN 8 ID Integrating conjugative element protein, RAQPRD family DN Integrating conjugative element protein, RAQPRD family RQ 1 EV IPR019110; TIGR01690; -- SN 9 ID Integrating conjugative element protein membrane PFL4701 DN Integrating conjugative element protein membrane PFL4701 RQ 1 EV IPR021676; TIGR03758; -- SN 10 ID Integrating conjugative element membrane protein PFL4702 DN Integrating conjugative element membrane protein PFL4702 RQ 1 EV IPR021356; TIGR03745; -- SN 11 ID Integrating conjugative element protein, PFL4703 family DN Integrating conjugative element protein, PFL4703 family RQ 1 EV IPR021548; TIGR03746; -- SN 12 ID Integrating conjugative element protein, PFL4704 family DN Integrating conjugative element protein, PFL4704 family RQ 1 EV IPR021844; TIGR03749; -- SN 13 ID Integrating conjugative element protein, PFL4705 family DN Integrating conjugative element protein, PFL4705 family RQ 1 EV IPR021207; TIGR03752; -- SN 14 ID Conjugative transfer ATPase, PFL_4706 family DN Conjugative transfer ATPase, PFL_4706 family RQ 1 EV IPR022303; TIGR03744; -- SN 15 ID Integrating conjugative element protein PFL4709 DN Integrating conjugative element protein PFL4709 RQ 1 EV IPR011090; TIGR03757; -- SN 16 ID Integrating conjugative element protein, PFL4710 family DN Integrating conjugative element protein, PFL4710 family RQ 1 EV IPR026331; TIGR03756; -- SN 17 ID Integrating conjugative element protein, PFL4711 family DN Integrating conjugative element protein, PFL4711 family RQ 1 EV IPR021204; TIGR03755; -- SN 18 ID Integrating conjugative element relaxase, PFGI-1 class DN Integrating conjugative element relaxase, PFGI-1 class RQ 1 EV IPR022391; TIGR03760; -- SN 19 ID Conjugative transfer region protein, TIGR03750 DN Conjugative transfer region protein, TIGR03750 RQ 0 EV IPR021877; TIGR03750; -- SN 20 ID Conjugative transfer region protein, TIGR03751 family DN Conjugative transfer region protein, TIGR03751 family RQ 0 EV IPR022262; TIGR03751; // AC GenProp0857 DE Anchored repeat-class ABC transporter, P. acnes type TP SYSTEM AU Haft DH TH 0 CC Model TIGR03769 describes a protein region that occurs several times CC per genome in several Actinobacteria. Typically, it occurs once in an CC ABC transporter substrate binding protein and two to three times in a CC neighboring gene that is anchored to the Gram-positive cell wall by a CC sortase/LPXTG system. This genome property describes the three genes of CC the ABC transporter cassette and the neighboring LPXTG-anchored repeat CC protein. This system is analogous to the NEAT domain system found in CC some pathogenic Firmicutes. -- SN 1 ID Anchored repeat ABC transporter, ATP-binding subunit DN Anchored repeat ABC transporter, ATP-binding subunit RQ 1 EV IPR022508; TIGR03771; -- SN 2 ID Anchored repeat ABC transporter, permease subunit DN Anchored repeat ABC transporter, permease subunit RQ 1 EV IPR022392; TIGR03770; -- SN 3 ID Anchored repeat ABC transporter, anchored relay protein DN Anchored repeat ABC transporter, anchored relay protein RQ 1 EV IPR022395; TIGR03773; -- SN 4 ID Anchored repeat ABC transporter, substrate-binding subunit DN Anchored repeat ABC transporter, substrate-binding subunit RQ 1 EV IPR022434; TIGR03772; -- SN 5 ID Actinobacterial surface-anchored domain protein DN Actinobacterial surface-anchored domain protein RQ 1 EV IPR022435; TIGR03769; // AC GenProp0858 DE Conjugative transposon, Bacteroides type TP SYSTEM AU Haft DH TH 0 RN [1] RM 10869083 RT Integration and excision of a Bacteroides conjugative transposon, RT CTnDOT. RA Cheng Q, Paszkiet BJ, Shoemaker NB, Gardner JF, Salyers AA; RL J Bacteriol. 2000;182:4035-4043. CC This property describes a class of conjugative transposon, including CC CTnDOT and related elements, from various Bacteroides and related CC species. These self-transmissable elements can be fairly large, 50-100 CC Kb, and contain proteins required for integration, excision, and CC conjugation. A single genome, such as Bacteroides thetaiotaomicron CC VPI-5482, may contain several such elements. -- SN 1 ID Bacteroides conjugative transposon TraG protein DN Bacteroides conjugative transposon TraG protein RQ 1 EV IPR022509; TIGR03783; -- SN 2 ID Bacteroides conjugative transposon TraJ protein DN Bacteroides conjugative transposon TraJ protein RQ 1 EV IPR022393; TIGR03782; -- SN 3 ID Bacteroides conjugative transposon TraK protein DN Bacteroides conjugative transposon TraK protein RQ 1 EV IPR022276; TIGR03781; -- SN 4 ID Bacteroides conjugative transposon TraM protein DN Bacteroides conjugative transposon TraM protein RQ 1 EV IPR022187; TIGR03779; -- SN 5 ID Bacteroides conjugative transposon TraN protein DN Bacteroides conjugative transposon TraN protein RQ 1 EV IPR022298; TIGR03780; // AC GenProp0859 DE Protein sorting system, proteobacterial dedicated sortase type TP SYSTEM AU Haft DH TH 0 CC This property represents a specialization of SrtA-like sortase systems CC in the Proteobacteria, including many marine species. In contrast to CC sortase A systems in the Firmicutes, where a single transpeptidase CC serves multiple target proteins, this system is characterized by a CC single sorting target protein, conserved across species, adjacent to CC the sorting enzyme itself. In a majority of species with this system, CC the sortase and target pair are accompanied by a histidine kinase and CC response regulator pair. -- SN 1 ID Proteobacterial dedicated sortase system histidine kinase DN Proteobacterial dedicated sortase system histidine kinase RQ 0 EV IPR022510; TIGR03785; -- SN 2 ID LPXTG-anchored VIT/VWA domain protein DN LPXTG-anchored VIT/VWA domain protein RQ 1 EV IPR022440; TIGR03788; -- SN 3 ID Proteobacterial dedicated sortase system response regulator DN Proteobacterial dedicated sortase system response regulator RQ 0 EV IPR022305; TIGR03787; -- SN 4 ID Sortase, proteobacterial dedicated type DN Sortase, proteobacterial dedicated type RQ 1 EV IPR022445; TIGR03784; // AC GenProp0860 DE Tryptophan tryptophylquinone modification of methylamine dehydrogenase TP SYSTEM AU Haft DH TH 0 RN [1] RM 19196017 RT Kinetic mechanism for the initial steps in MauG-dependent tryptophan RT tryptophylquinone biosynthesis. RA Lee S, Shin S, Li X, Davidson VL; RL Biochemistry. 2009;48:2442-2447. RN [2] RM 22314272 RT Tryptophan tryptophylquinone biosynthesis: a radical approach to RT posttranslational modification. RA Davidson VL, Liu A; RL Biochim Biophys Acta. 2012;1824:1299-1305. CC The maturation enzyme MauG completes the modification and cross-linking CC of a pair of Trp residues into the novel cofactor tryptophan CC tryptophylquinone (TTQ) in the light chain (MauA) of methylamine CC dehydrogenase. While some analogous enzyme cofactors are produced CC autocatalytically from amino acids in the precursor polypeptide, TTQ is CC produced with aid of the maturation enzyme MauG. MauG is a di-heme CC enzyme with peroxidase activity, similar to di-heme cytochrome c CC peroxidases of other biological systems. Interestingly, the pair of CC modified Trp residues are conserved in MauA homologs in species that CC have no MauG homolog in the vicinity, suggesting no modification, CC autocatalytic modification, or a different modification enzyme. -- SN 1 ID Methylamine dehydrogenase, light chain DN Methylamine dehydrogenase, light chain RQ 1 EV IPR004229; TIGR02659; -- SN 2 ID Methylamine dehydrogenase heavy chain DN Methylamine dehydrogenase heavy chain RQ 1 EV IPR013476; TIGR02658; -- SN 3 ID Methylamine dehydrogenase accessory protein MauD DN Methylamine dehydrogenase accessory protein MauD RQ 1 EV IPR013478; TIGR02661; -- SN 4 ID TTQ maturation di-heme protein MauG DN TTQ maturation di-heme protein MauG RQ 1 EV IPR022394; TIGR03791; // AC GenProp0861 DE Bacteriocin system, NHLP (nif11/nitrile hydratase leader peptide) transport group TP SYSTEM AU Haft DH TH 0 CC Model TIGR03793 describes a leader peptide region (homologous to the CC nitrile hydratase alpha subunit) for peptides subject to modification CC by bacteriocin-like maturation enzyme clusters, typically including CC either a cyclodehydratase and a dehydrogenase (producing TOMMS - CC Thiazole/Oxazole-Modified Microcins) or a lantibiotic synthase. Radical CC SAM enzymes are commonly found as well. While sequences of the mature CC peptides are highly variable, as are their modification clusters, the CC leader peptide region shows a close phylogenetic correlation to a three CC gene transporter operon, one subunit of which includes a protease CC domain for cleavage at the Gly-Gly motif at the end of the leader CC peptide region. This property describes the transport operon as well as CC the leader peptide family. -- SN 1 ID Bacteriocin, nitrile hydratase-homologous leader family DN Bacteriocin, nitrile hydratase-homologous leader family RQ 1 EV IPR022513; TIGR03793; EV IPR022516; TIGR03798; TG GO:0043213; -- SN 2 ID NHLP bacteriocin system ABC transporter, peptidase/ATP-binding protein DN NHLP bacteriocin system ABC transporter, peptidase/ATP-binding protein RQ 1 EV IPR022515; TIGR03797; TG GO:0043213; -- SN 3 ID NHLP class bacteriocin export protein, HlyD family DN NHLP class bacteriocin export protein, HlyD family RQ 1 EV IPR022275; TIGR03794; TG GO:0043213; -- SN 4 ID NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein DN NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein RQ 1 EV IPR022514; TIGR03796; TG GO:0043213; -- SN 5 ID NHLP bacteriocin system radical SAM enzyme DN NHLP bacteriocin system radical SAM enzyme RQ 0 EV IPR023984; TIGR03975; TG GO:0043213; EV IPR024016; TIGR04064; TG GO:0043213; // AC GenProp0862 DE Pyridoxal phosphate biosynthesis, PdxA/PdxJ pathway TP PATHWAY AU Haft DH TH 0 CC This genome property represents pyridoxal 5-prime phosphate CC biosynthesis as it occurs in Escherichia coli, from deoxyxylulose CC 5-phosphate and 4-phosphohydroxy-L-threonine. The key proteins are PdxA CC and PdxJ. This pathway contrasts with the Pdx1 and Pdx2 pathway, as CC found in Bacillus subtilis. -- SN 1 ID 4-hydroxythreonine-4-phosphate dehydrogenase DN 4-hydroxythreonine-4-phosphate dehydrogenase/pdxA RQ 1 EV IPR005255; TIGR00557; TG GO:0042823; -- SN 3 ID Pyridoxal phosphate synthase DN Pyridoxal phosphate synthase/pdxJ RQ 1 EV IPR004569; TIGR00559; TG GO:0042823; // AC GenProp0864 DE Response to external environment TP CATEGORY AU Haft DH TH 0 CC Mechanisms by which cells sense the external environment and alter CC their motion, behavior, shape, metabolism or other properties in CC response to those conditions. -- SN 1 ID Response to stress RQ 0 EV GenProp0462; -- SN 2 ID Response to acidic (low pH) environment RQ 0 EV GenProp0874; -- SN 4 ID Cus cation efflux complex RQ 0 EV GenProp1168; // AC GenProp0866 DE Carbon metabolism TP CATEGORY AU Haft DH TH 0 CC Processes involved in the handling and processing of small, primarily CC 1-carbon compounds. This category includes carbon fixation, CC C1-compound interconversion and excretion processes. -- SN 2 ID H4MPT-linked C1 transfer pathway RQ 0 EV GenProp0671; -- SN 3 ID CO2 fixation into oxaloacetate (anaplerotic) RQ 0 EV GenProp1669; -- SN 4 ID Formate assimilation into 5,10-methylenetetrahydrofolate RQ 0 EV GenProp1613; // AC GenProp0867 DE Decarboxylation/antiport proton-motive cycle: aspartate-alanine TP SYSTEM AU Haft DH TH 0 RN [1] RM 12003930 RT Plasmid-encoded asp operon confers a proton motive metabolic cycle RT catalyzed by an aspartate-alanine exchange reaction. RA Abe K, Ohnishi F, Yagi K, Nakajima T, Higuchi T, Sano M, Machida M, RA Sarker RI, Maloney PC; RL J Bacteriol. 2002;184:2906-2913. CC This Genome Property represents a proton-motive cycle. A cycle of CC decarboxylating an aspartate to alanine plus CO2, then exchanging the CC cytosolic alanine for an extracellular asparate, has the net effect of CC consuming one proton. Analogous systems for antiport of substrates CC related by decarboxylation include the pairing of an acid-induced CC arginine decarboxylase with an arginine-agmatine antiporter as in CC Escherichia coli. -- SN 1 ID Aspartate 4-decarboxylase DN Aspartate 4-decarboxylase RQ 1 EV IPR022518; TIGR03801; TG GO:0010248; -- SN 2 ID Aspartate-alanine antiporter DN Aspartate-alanine antiporter RQ 1 EV IPR022457; TIGR03802; TG GO:0010248; // AC GenProp0871 DE Decarboxylation/antiport proton-motive cycle: ornithine-putrescine TP SYSTEM AU Haft DH TH 0 RN [1] RM 1584788 RT Excretion of putrescine by the putrescine-ornithine antiporter encoded RT by the potE gene of Escherichia coli. RA Kashiwagi K, Miyamoto S, Suzuki F, Kobayashi H, Igarashi K; RL Proc Natl Acad Sci U S A. 1992;89:4529-4533. RN [2] RM 17578420 RT Gene organization of the ornithine decarboxylase-encoding region in RT Morganella morganii. RA de las Rivas B, Marcobal A, Muñoz R; RL J Appl Microbiol. 2007;102:1551-1560. RN [3] RM 22247134 RT Evidence of two functionally distinct ornithine decarboxylation systems RT in lactic acid bacteria. RA Romano A, Trip H, Lonvaud-Funel A, Lolkema JS, Lucas PM; RL Appl Environ Microbiol. 2012;78:1953-1961. CC The decarboxylation of L-ornithine to putrescine consumes a proton. CC Exchange of putrescine for L-ornithine by an antiporter completes a CC cycle that effectively removes a cytosolic protein. CC Decarboxylation/antiporter systems for this and other (e.g. CC aspartate-alanine) substrate pairs can provide protection against CC acidic pH. -- SN 1 ID Ornithine-putrescine antiporter DN Ornithine-putrescine antiporter RQ 1 EV IPR027566; TIGR04299; TG GO:0010248; -- SN 2 ID Ornithine decarboxylase DN Ornithine decarboxylase RQ 1 EV IPR027568; TIGR04301; TG GO:0010248; // AC GenProp0872 DE Decarboxylation/antiport proton-motive cycle: histidine-histamine TP SYSTEM AU Haft DH TH 0 RN [1] RM 15817789 RT Sequencing, characterization and transcriptional analysis of the RT histidine decarboxylase operon of Lactobacillus buchneri. RA Martín MC, Fernández M, Linares DM, Alvarez MA; RL Microbiology. 2005;151:1219-1228. CC The decarboxylation of histidine to histamine consumes a proton. CC Exchange of histamine for histadine by an antiporter completes a cycle CC that effectively removes a cytosolic proton. Decarboxylation/antiporter CC systems for this and other (e.g. aspartate-alanine) substrate pairs can CC provide protection against acidic pH. -- SN 1 ID Histidine decarboxylase DN Histidine decarboxylase RQ 1 EV IPR003427; TIGR00541; TG GO:0010248; -- SN 2 ID Histidine-histamine antiporter DN Histidine-histamine antiporter RQ 1 EV IPR027562; TIGR04298; TG GO:0010248; // AC GenProp0873 DE Ion-motive antiporter cycles TP CATEGORY AU Haft DH TH 0 CC Properties in this category describe the general class of biological system CC in which an essentially irreversible enzymatic process (such as CC decarboxylation) converts one substrate of an antiporter into the CC other, so that extrusion of the enzymatic product leads to import of CC new substrate. An example of such a system is the pairing of asparate CC decarboxylase (which produces alanine plus CO2) with an aspartate CC alanine antiporter. The net result of each cycle is removal of one CC cytosolic proton, therefore such systems can and do confer acid resistance. -- SN 1 ID Arginine degradation via citrulline, ATP-generating RQ 0 EV GenProp0639; -- SN 2 ID Decarboxylation/antiport proton-motive cycle: aspartate-alanine RQ 0 EV GenProp0867; -- SN 3 ID Decarboxylation/antiport proton-motive cycle: ornithine-putrescine RQ 0 EV GenProp0871; -- SN 4 ID Decarboxylation/antiport proton-motive cycle: histidine-histamine RQ 0 EV GenProp0872; -- SN 5 ID Decarboxylation/antiport proton-motive cycle: oxalate-formate RQ 0 EV GenProp1034; // AC GenProp0874 DE Response to acidic (low pH) environment TP CATEGORY AU Haft DH TH 0 CC A process which allows an organism to cope with the deleterious effects CC of an acidic external environment. Such processes may be regulated to CC respond to changes in external pH or, in the case of acidophiles, may CC be constitutive. -- SN 1 ID Decarboxylation/antiport proton-motive cycle: aspartate-alanine RQ 0 EV GenProp0867; -- SN 2 ID Decarboxylation/antiport proton-motive cycle: ornithine-putrescine RQ 0 EV GenProp0871; -- SN 3 ID Decarboxylation/antiport proton-motive cycle: histidine-histamine RQ 0 EV GenProp0872; // AC GenProp0877 DE Flagellar motor stator complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 15629949 RT Evidence for two flagellar stators and their role in the motility of RT Pseudomonas aeruginosa. RA Toutain CM, Zegans ME, O'Toole GA; RL J Bacteriol. 2005;187:771-777. CC The MotAB complex functions as the stator producing torque in the CC mobile flagellar rotor complex. The stator changes conformation in CC response to the passage of protons across the cytoplasmic membrane. CC This complex is also necessarily a force-generating proton transporter. CC The stator complex contains MotA and MotB subunits in a 4:2 ratio and CC several stators are associated with each motor, each generating torque CC independently. -- SN 1 ID Flagellar motor stator protein MotA DN Flagellar motor stator protein MotA RQ 1 EV IPR002898; PF01618; EV IPR022522; TIGR03818; -- SN 2 ID Flagellar motor stator protein MotB DN Flagellar motor stator protein MotB RQ 1 EV IPR006665; PF00691; // AC GenProp0878 DE N(epsilon)-acetyl-beta-lysine biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 10629195 RT Lysine 2,3-aminomutase from Clostridium subterminale SB4: mass RT spectral characterization of cyanogen bromide-treated peptides and RT cloning, sequencing, and expression of the gene kamA in Escherichia RT coli. RA Ruzicka FJ, Lieder KW, Frey PA; RL J Bacteriol. 2000;182:469-476. RN [2] RM 14532061 RT Lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of RT methanogenic archaea are salt induced and are essential for the RT biosynthesis of Nepsilon-acetyl-beta-lysine and growth at high RT salinity. RA Pflüger K, Baumann S, Gottschalk G, Lin W, Santos H, Müller V; RL Appl Environ Microbiol. 2003;69:6047-6055. CC N(epsilon)-acetyl-beta-lysine is a compatible solute produced in CC methanogenic archaea under salt stress. Note that the first enzyme in CC this two-step pathway can instead serve as the first step in lysine CC catabolism, as in Clostridium subterminale SB4 [1]. -- SN 1 ID Lysine-2,3-aminomutase DN Lysine-2,3-aminomutase RQ 1 EV IPR022459; TIGR03820; TG GO:0042398; -- SN 2 ID Beta-lysine acetyltransferase DN Beta-lysine acetyltransferase RQ 1 EV IPR022525; TIGR03827; TG GO:0042398; // AC GenProp0879 DE Flagellar export apparatus TP SYSTEM AU Haft DH TH 0 CC The assembly of the bacterial flagellum requires the export of CC flagellar components through the cytoplasmic membrane. This is an CC ATP-driven process mediated by a series of subunits similar to elements CC of type III secretion complexes. -- SN 1 ID Flagellar biosynthesis protein FlhA DN Flagellar biosynthesis protein FlhA RQ 1 EV IPR006301; TIGR01398; sufficient; -- SN 2 ID Flagellar biosynthetic protein FlhB DN Flagellar biosynthetic protein FlhB RQ 1 EV IPR006136; TIGR00328; sufficient; -- SN 3 ID Flagellar assembly protein FliH DN Flagellar assembly protein FliH RQ 1 EV IPR018035; PF02108; sufficient; EV IPR022524; TIGR03825; -- SN 4 ID Flagellum-specific ATP synthase FliI DN Flagellum-specific ATP synthase FliI RQ 1 EV IPR020005; TIGR03496; EV IPR022425; TIGR03497; EV IPR022426; TIGR03498; -- SN 5 ID Flagellar export protein FliJ DN Flagellar export protein FliJ RQ 1 EV IPR012823; TIGR02473; sufficient; -- SN 6 ID Flagellar assembly protein FliO DN Flagellar assembly protein FliO RQ 1 EV IPR022781; PF04347; sufficient; EV IPR022781; TIGR03500; -- SN 7 ID Flagellar biosynthetic protein FliP DN Flagellar biosynthetic protein FliP RQ 1 EV IPR005837; TIGR01103; sufficient; -- SN 8 ID Flagellar biosynthetic protein FliQ DN Flagellar biosynthetic protein FliQ RQ 1 EV IPR006305; TIGR01402; sufficient; -- SN 9 ID Flagellar biosynthetic protein FliR DN Flagellar biosynthetic protein FliR RQ 1 EV IPR006303; TIGR01400; sufficient; // AC GenProp0880 DE Flagellar basal body complex TP SYSTEM AU Haft DH TH 0 CC The flagellar basal body is that portion of the bacterial flagellum CC proximal to the cell, passing through the cytoplasmic and outer CC membranes. The basal body includes the proximal and distal basal body CC rod, the MS, P and L rings and (for the purposes of this property) CC excludes the rotor (switch), stator and export apparatus. -- SN 1 ID Flagellar basal body rod protein FlgB DN Flagellar basal-body rod protein FlgB RQ 1 EV IPR006300; TIGR01396; sufficient; -- SN 2 ID Flagellar basal body rod protein FlgC DN Flagellar basal-body rod protein FlgC RQ 1 EV IPR006299; TIGR01395; sufficient; -- SN 3 ID Flagellar basal body rod protein FlgF DN Flagellar basal body rod protein FlgF RQ 1 EV IPR012836; TIGR02490; sufficient; -- SN 4 ID Flagellar basal body rod protein FlgG DN Flagellar basal-body rod protein FlgG RQ 1 EV IPR012834; TIGR02488; sufficient; -- SN 5 ID Flagellar basal body L-ring protein FlgH DN Flagellar L-ring protein FlgH RQ 1 EV IPR000527; PF02107; sufficient; -- SN 6 ID Flagellar basal body P-ring protein FlgI DN Flagellar P-ring protein FlgI RQ 1 EV IPR001782; PF02119; sufficient; -- SN 7 ID Flagellar basal body protein FliE DN Flagellar hook-basal body complex protein FliE RQ 1 EV IPR001624; TIGR00205; sufficient; -- SN 8 ID Flagellar basal-body MS-ring and collar protein FliF DN Flagellar M-ring protein FliF RQ 1 EV IPR000067; TIGR00206; sufficient; // AC GenProp0881 DE Flagellar assembly apparatus TP SYSTEM AU Haft DH TH 0 CC The bacterial flagellum requires a number of assembly cofactors, CC chaperones and scaffold proteins which are not incorporated into the CC assembled flagellum. This property describes that assembly apparatus. -- SN 1 ID Flagellar basal-body P-ring assembly protein FlgA DN Flagella basal body P-ring formation protein FlgA RQ 1 EV IPR017585; TIGR03170; sufficient; -- SN 2 ID Flagellar hook assembly protein FlgD DN Flagellar hook assembly protein FlgD RQ 1 EV IPR005648; PF03963; sufficient; -- SN 3 ID Flagellar biosynthesis protein FlgN DN Flagellar biosynthesis protein FlgN RQ 1 EV IPR007809; PF05130; sufficient; -- SN 4 ID Flagellar hook-length control protein FliK DN Flagellar hook-length control protein FliK RQ 1 EV IPR021136; PF02120; sufficient; -- SN 5 ID Flagellar biosynthesis chaperone FliS DN Flagellar protein FliS RQ 1 EV IPR003713; TIGR00208; sufficient; -- SN 6 ID Flagellar biosynthesis protein FliT DN Flagellar biosynthesis protein FliT RQ 0 EV IPR008622; PF05400; sufficient; -- SN 7 ID Flagellar assembly factor FliW DN Flagellar assembly factor FliW RQ 0 EV IPR003775; PF02623; // AC GenProp0882 DE Flagellar filament and hook complex TP SYSTEM AU Haft DH TH 0 CC The external rotating components of the bacterial flagellum consist of CC a cell proximal bent hook structure, and a long, whip-like filament. CC Additional structures are a cap and a hook/filament juncture. -- SN 1 ID Flagellar hook protein FlgE DN Flagellar hook protein FlgE RQ 0 EV IPR011491; PF07559; sufficient; -- SN 2 ID Flagellar hook-filament junction protein 1 (FlgK) DN Flagellar hook-filament junction protein 1 (FlgK) RQ 1 EV IPR002371; TIGR02492; sufficient; -- SN 3 ID Flagellar hook-filament junction protein FlgL DN Flagellar hook-filament junction protein FlgL RQ 0 EV IPR013384; TIGR02550; -- SN 4 ID Flagellar filament structural protein FliC, C-terminal domain DN Flagellar filament structural protein FliC, C-terminal domain RQ 1 EV IPR001029; PF00700; sufficient; -- SN 5 ID Flagellar filament structural protein FliC, N-terminal domain DN Flagellar filament structural protein FliC, N-terminal domain RQ 1 EV IPR001029; PF00669; sufficient; -- SN 6 ID Flagellar filament capping protein FliD DN Flagellar hook-associated protein FliD RQ 1 EV IPR003481; PF02465; sufficient; // AC GenProp0883 DE Flagellar motor switch (rotor) complex TP SYSTEM AU Haft DH TH 0 CC The flagellar rotor complex consists of the FliG, FliM and FliN CC proteins. This complex is also known as the flagellar motor switch, CC due to its role in determining the clockwise or counter-clockwise CC rotation of the flagellum. The complex is located at the inner end of CC the basal body. The FliG protein interacts with the stator complex CC protein MotA. The FliM protein interacts with phosphorylated CheY from CC the chemotaxis response regulation system allowing the transduction of CC the directional switching signal. The subunits of this structure are CC predicted to be in a 26:34:100 (FliG:FliM:FliN) ratio per motor CC complex. -- SN 1 ID Flagellar motor switch (rotor) protein FliG DN Flagellar motor switch protein FliG RQ 1 EV IPR000090; TIGR00207; sufficient; -- SN 2 ID Flagellar motor switch (rotor) protein FliM DN Flagellar motor switch protein FliM RQ 1 EV IPR001689; TIGR01397; sufficient; -- SN 3 ID Flagellar motor switch (rotor) protein FliN DN Flagellar motor switch (rotor) protein FliN RQ 0 EV IPR012826; TIGR02480; sufficient; // AC GenProp0885 DE Flagellar post-translational modification components TP SYSTEM AU Haft DH TH 0 CC Certain flagellar proteins, particularly the flagellin subunits CC themselves as well as other components with access to the CC extracellular environment, may be post-translationally altered by this CC group of proteins. -- SN 1 ID Flagellar rod assembly protein/muramidase FlgJ DN Flagellar rod assembly protein/muramidase FlgJ RQ 1 EV IPR013377; TIGR02541; sufficient; EV IPR012823; PF02050; sufficient; // AC GenProp0886 DE Flagellar components of unknown function TP GUILD AU Haft DH TH 0 CC These components are members of flagellar operons and, based on CC experimental evidence (i.e. mutational analysis or physical binding) CC are associated with flagella. Insufficient evidence has been CC determined to further classify which flagellar subsystem is the CC appropriate category to place these components. -- SN 1 ID Flagellar biosynthesis protein FlhF DN Flagellar biosynthesis protein FlhF RQ 1 EV IPR020006; TIGR03499; -- SN 2 ID Flagellar basal body-associated protein FliL DN Flagellar basal body-associated protein FliL RQ 1 EV IPR005503; PF03748; sufficient; // AC GenProp0891 DE Coenzyme M biosynthesis TP SYSTEM AU Haft DH TH 0 RN [1] RM 19761441 RT Convergent evolution of coenzyme M biosynthesis in the RT Methanosarcinales: cysteate synthase evolved from an ancestral RT threonine synthase. RA Graham DE, Taylor SM, Wolf RZ, Namboori SC; RL Biochem J. 2009;424:467-478. RN [2] RM 10940029 RT Identification of the gene encoding sulfopyruvate decarboxylase, an RT enzyme involved in biosynthesis of coenzyme M. RA Graupner M, Xu H, White RH; RL J Bacteriol. 2000;182:4862-4867. RN [3] RM 21402221 RT 2-oxoacid metabolism in methanogenic CoM and CoB biosynthesis. RA Graham DE; RL Methods Enzymol. 2011;494:301-326. CC Coenzyme M (2-mercaptoethanesulfonic acid) acts in methanogenesis in CC methanogenic archaea. It is also used as a carrier in a bacterium CC (Xanthobacter autotrophicus Py2) in aerobic propylene metabolism. CC Pathways differ from Methanococcus jannaschi to Methanosarcina CC acetivorans, and again to Xanthobacter autotrophicus Py2. This Genome CC Property represents the parent property. -- SN 1 ID Sulfopyruvate biosynthesis DN Sulfopyruvate biosynthesis RQ 1 EV GenProp0893; -- SN 2 ID Sulfopyruvate decarboxylase, alpha subunit DN Sulfopyruvate decarboxylase, alpha subunit RQ 1 EV IPR022502; TIGR03845; -- SN 3 ID Sulfopyruvate decarboxylase, beta subunit DN Sulfopyruvate decarboxylase, beta subunit RQ 1 EV IPR022494; TIGR03846; // AC GenProp0893 DE Sulfopyruvate biosynthesis via L-cysteate TP PATHWAY AU Haft DH TH 0 CC Two different pathways for coenzyme M biosynthesis pass through the CC intermediate sulfopyruvate. This Genome Property describes a pathway CC for the creation of sulfopyruvate via L-cysteate. Cysteate synthase CC converts L-phosphoserine to L-cysteate. An aspartate aminotransferase CC (not represented explicitly in this Genome Property) can then convert CC L-cysteate to sulfopyruvate. -- SN 1 ID Cysteate synthase DN Cysteate synthase RQ 1 EV IPR022401; TIGR03844; // AC GenProp0894 DE Actinobacterial uncharacterized trio TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a three-gene cassette common among the CC Actinobacteria. The system includes a putative kinase (similar to CC phosphatidylinositol kinase), a putative phosphomutase (similar to CC phosphoglycerate mutase), and an uncharacterized protein. -- SN 1 ID Probable kinase, MSMEG_4191 family DN Probable kinase, MSMEG_4191 family RQ 1 EV IPR022292; TIGR03843; -- SN 2 ID MSMEG_4192 family protein DN MSMEG_4192 family protein RQ 1 EV IPR021441; TIGR03847; -- SN 3 ID Probable phosphomutase, MSMEG_4193 family DN Probable phosphomutase, MSMEG_4193 family RQ 1 EV IPR022492; TIGR03848; // AC GenProp0895 DE Alcohol ABC transporter, PedABC-type TP SYSTEM AU Haft DH TH 0 RN [1] RM 18177365 RT Genetic analyses and molecular characterization of the pathways RT involved in the conversion of 2-phenylethylamine and 2-phenylethanol RT into phenylacetic acid in Pseudomonas putida U. RA Arias S, Olivera ER, Arcos M, Naharro G, Luengo JM; RL Environ Microbiol. 2008;10:413-432. CC A conserved four-gene operon, found regularly in genomes with PQQ CC biosynthesis and with PQQ-dependent enzymes for catabolism of various CC alcohols, appears to represent an alcohol import ABC transporter. This CC conclusion is based partly on recognizing one member of the operon as a CC likely periplasmic substrate-binding protein. An earlier view [1] CC suggests this system to be an efflux transporter for removal of toxic CC intermediates during catabolism. -- SN 1 ID Alcohol ABC transporter, substrate-binding subunit DN Alcohol ABC transporter, substrate-binding subunit RQ 1 EV IPR022478; TIGR03863; -- SN 2 ID Alcohol ABC transporter, beta-propeller protein DN Alcohol ABC transporter, beta-propeller protein RQ 1 EV IPR022456; TIGR03866; -- SN 3 ID Alcohol ABC transporter, ATP-binding subunit DN Alcohol ABC transporter, ATP-binding subunit RQ 1 EV IPR022467; TIGR03864; -- SN 4 ID Alcohol ABC transporter, permease subunit DN Alcohol ABC transporter, permease subunit RQ 1 EV IPR022403; TIGR03861; // AC GenProp0896 DE Proposed F420-0 transporter TP SYSTEM AU Haft DH TH 0 CC This small clade of ABC-type transporters are found in Actinobacteria CC containing numerous genes requiring the coenzyme F420. This property CC was defined based on five such organisms, four of which are lacking all CC F420 biosynthetic capability save the final side-chain polyglutamate CC attachment step (via the gene cofE). In Jonesia denitrificans DSM 20603 CC and marine actinobacterium PHSC20C1, this cassette is in an apparent CC operon with the cofE gene and, in PHSC20C1, also with a F420-dependent CC glucose-6-phosphate dehydrogenase. Based on these observations we CC propose that this is an F420-0 (F420 lacking only the polyglutamate CC tail) ABC transporter. -- SN 1 ID Proposed F420-0 transporter ATP-binding protein DN Proposed F420-0 transporter ATP-binding protein RQ 1 EV IPR022286; TIGR03873; -- SN 2 ID Proposed F420-0 periplasmic binding protein DN Proposed F420-0 periplasmic binding protein RQ 1 EV IPR022287; TIGR03868; -- SN 3 ID Proposed F420-0 permease DN Proposed F420-0 permease RQ 1 EV IPR022410; TIGR03869; // AC GenProp0898 DE RNA ligase/unknown protein pair TP SYSTEM AU Haft DH TH 0 CC This property describes the pairing of two proteins, one of which is CC characterized as a ligase capable of circularizing RNA. The genes for CC the two proteins are only occasionally near to each other on the CC chromosome and then not in the form of an operon. -- SN 1 ID RNA ligase, Pab1020 family DN RNA ligase, Pab1020 family RQ 1 EV IPR001072; TIGR01209; -- SN 2 ID RNA ligase partner, MJ_0950 family DN RNA ligase partner, MJ_0950 family RQ 1 EV IPR014856; TIGR03875; // AC GenProp0899 DE Nitrile hydratase TP SYSTEM AU Haft DH TH 0 RN [1] RM 15096062 RT Fe(III) and Co(III) centers with carboxamido nitrogen and modified RT sulfur coordination: lessons learned from nitrile hydratase. RA Harrop TC, Mascharak PK; RL Acc Chem Res. 2004;37:253-260. CC The enzyme nitrile hydratase (EC 4.2.1.84) catalyzes the CC interconversion of an aliphatic amide to a nitrile plus H20. The enzyme CC is closely related to thiocyanate hydrolase (EC 3.5.5.8). The nitrile CC hydratase alpha subunit contains active site Cys residues that undergo CC covalent modification, after which it binds either Fe(III) or Co(III). CC A CXCC-containing protein related to the cobalamin biosynthesis protein CC CobW is described as a nitrile hydratase activator and is often found CC in the nitrile hydratase operon. However, the protein family described CC by TIGR03889, also commonly annotated as a nitrile hydratase accessory CC protein, is found in a larger fraction of nitrile hydratase operons. -- SN 1 ID Nitrile hydratase activator, CobW family DN Nitrile hydratase activator, CobW family RQ 0 EV IPR003495; PF02492; -- SN 2 ID Nitrile hydratase accessory protein DN Nitrile hydratase accessory protein RQ 0 EV IPR023808; TIGR03889; -- SN 3 ID Nitrile hydratase, alpha subunit DN Nitrile hydratase, alpha subunit RQ 1 EV IPR018141; TIGR01323; -- SN 4 ID Nitrile hydratase, beta subunit DN Nitrile hydratase, beta subunit RQ 1 EV IPR003168; TIGR03888; // AC GenProp0901 DE Post-ribosomal natural product synthesis system, Burkholderia TOMM-type TP SYSTEM AU Haft DH TH 0 RN [1] RM 20500830 RT Expansion of ribosomally produced natural products: a nitrile RT hydratase- and Nif11-related precursor family. RA Haft DH, Basu MK, Mitchell DA; RL BMC Biol. 2010;8:70. CC This system describes a novel system of a bacteriocin-like metabolite CC found in multiple species of Burkholderia (in Acidovorax avenae subsp. CC citrulli AAC00-1 and Delftia acidovorans SPH-1, and in multiple copies CC in Sorangium cellulosum). It features a probable two-chain bacteriocin CC precursor, a fused cyclodehydratase/docking scaffold fusion protein, CC and a kinase and cyclase homology domain-containing multidomain protein. -- SN 1 ID Cyclodeydratase/docking scaffold fusion protein DN Cyclodeydratase/docking scaffold fusion protein RQ 1 EV IPR022291; TIGR03882; -- SN 2 ID TOMM system kinase/cyclase multidomain protein DN TOMM system kinase/cyclase multidomain protein RQ 1 EV IPR023889; TIGR03903; -- SN 3 ID TOMM precursor subunit, Burkholderia type DN TOMM precursor subunit, Burkholderia type RQ 1 EV IPR022261; TIGR03795; // AC GenProp0902 DE Quinohemoprotein amine dehydrogenase TP SYSTEM AU Haft DH TH 0 RN [1] RM 16546999 RT Involvement of a putative [Fe-S]-cluster-binding protein in the RT biogenesis of quinohemoprotein amine dehydrogenase. RA Ono K, Okajima T, Tani M, Kuroda S, Sun D, Davidson VL, Tanizawa K; RL J Biol Chem. 2006;281:13672-13684. RN [2] RM 11704672 RT Crystal structure of quinohemoprotein amine dehydrogenase from RT Pseudomonas putida. Identification of a novel quinone cofactor encaged RT by multiple thioether cross-bridges. RA Satoh A, Kim JK, Miyahara I, Devreese B, Vandenberghe I, Hacisalihoglu RA A, Okajima T, Kuroda S, Adachi O, Duine JA, Van Beeumen J, Tanizawa K, RA Hirotsu K; RL J Biol Chem. 2002;277:2830-2834. CC This system is characterized by three subunits of the mature enzyme, CC plus one radical SAM protein involved in modification of the gamma CC subunit. The gamma subunit contains two unusual modifications. One is a CC cysteine tryptophylquinone, which unlike PQQ is derived from the CC polypeptide precursor. The other is intrapeptidyl thioether CC cross-linking. -- SN 1 ID Quinohemoprotein amine dehydrogenase maturation protein DN Quinohemoprotein amine dehydrogenase maturation protein RQ 1 EV IPR023886; TIGR03906; TG GO:0043687; -- SN 2 ID Quinohemoprotein amine dehydrogenase, alpha subunit DN Quinohemoprotein amine dehydrogenase, alpha subunit RQ 1 EV IPR023887; TIGR03908; TG GO:0030058; -- SN 3 ID Quinohemoprotein amine dehydrogenase, beta subunit DN Quinohemoprotein amine dehydrogenase, beta subunit RQ 1 EV IPR023879; TIGR03907; TG GO:0030058; -- SN 4 ID Quinohemoprotein amine dehydrogenase, gamma subunit DN Quinohemoprotein amine dehydrogenase, gamma subunit RQ 1 EV IPR015084; PF08992; TG GO:0030058; // AC GenProp0903 DE Radical SAM/uracil DNA glycosylase system TP SYSTEM AU Haft DH TH 0 CC This property represents a possible DNA modification and/or repair CC system. One component is a protein of about 400 amino acids in length, CC in which the N-terminal half is a radical SAM domain and the C-terminal CC half is an undescribed domain. Another component is an adjacent CC conserved hypothetical protein, TIGR03915. About forty percent of the CC members of TIGR03915 have a C-terminal uracil-DNA glycosylase homology CC domain, suggesting a role for this cassette in DNA repair, CC modification, or both. -- SN 1 ID Putative uracil-DNA glycosylase, rSAM/UDG system DN Putative uracil-DNA glycosylase, rSAM/UDG system RQ 0 EV IPR005273; TIGR03914; -- SN 2 ID Uncharacterized protein, rSAM/UDG system DN Uncharacterized protein, rSAM/UDG system RQ 1 EV IPR023875; TIGR03915; -- SN 3 ID Radical SAM protein, rSAM/UDG syste DN Radical SAM protein, rSAM/UDG syste RQ 1 EV IPR023874; TIGR03916; // AC GenProp0904 DE Type VII secretion, Actinobacteria form TP SYSTEM AU Haft DH TH 0 RN [1] RM 19876390 RT Systematic genetic nomenclature for type VII secretion systems. RA Bitter W, Houben EN, Bottai D, Brodin P, Brown EJ, Cox JS, Derbyshire RA K, Fortune SM, Gao LY, Liu J, Gey van Pittius NC, Pym AS, Rubin EJ, RA Sherman DR, Cole ST, Brosch R; RL PLoS Pathog. 2009;5:e1000507. CC Type VII secretion (T7S) (also called ESAT-6-, SNM-, or ESX-secretion) CC occurs in Mycobacterium. Mycobacterium has an impermeable cell CC envelope that contains long-chain mycolic acids in an outer CC membrane; T7S provides a means to transport proteins through this CC barrier. Multiple T7S loci can occur in one species, with different CC secretion targets for different systems. The system includes a CC subtilisin-like protease called mycosin and membrane proteins with a CC new nomenclature starting with ecc (esx conserved component). -- SN 1 ID Type VII secretion AAA-ATPase EccA DN Type VII secretion AAA-ATPase EccA RQ 1 EV IPR023835; TIGR03922; -- SN 2 ID Type VII secretion transmembrane protein EccB DN Type VII secretion transmembrane protein EccB RQ 1 EV IPR007795; TIGR03919; -- SN 3 ID Type VII secretion protein EccC DN Type VII secretion protein EccC RQ 1 EV IPR023836; TIGR03924; EV IPR023837; TIGR03925; -- SN 4 ID Type VII secretion integral membrane protein EccD DN Type VII secretion integral membrane protein EccD RQ 1 EV IPR006707; TIGR03920; -- SN 5 ID Type VII secretion transmembrane protein EccE DN Type VII secretion transmembrane protein EccE RQ 1 EV IPR021368; TIGR03923; -- SN 6 ID WXG100 family type VII secretion target DN WXG100 family type VII secretion target RQ 1 EV IPR010310; PF06013; EV IPR010310; TIGR03930; -- SN 7 ID Type VII secretion-associated protein, Rv3446c family DN Type VII secretion-associated protein, Rv3446c family RQ 0 EV IPR023840; TIGR03931; -- SN 8 ID Mycosin DN Mycosin RQ 1 EV IPR023834; TIGR03921; // AC GenProp0905 DE Type VII secretion, Firmicutes form TP SYSTEM AU Haft DH TH 0 RN [1] RM 18723613 RT ESAT-6-like protein secretion in Bacillus anthracis. RA Garufi G, Butler E, Missiakas D; RL J Bacteriol. 2008;190:7004-7011. RN [2] RM 18554323 RT EsaC substrate for the ESAT-6 secretion pathway and its role in RT persistent infections of Staphylococcus aureus. RA Burts ML, DeDent AC, Missiakas DM; RL Mol Microbiol. 2008;69:736-746. CC This Genome Property describes the Firmicutes secretion system related CC to the well-described type VII secretion system of Actinobacteria such CC as Mycobacterium tuberculosis. In both systems, members of the WXG100 CC family are targets, and a homolog of EccC is present. Otherwise, CC differences appear to be profound. -- SN 1 ID Type VII secretion protein EsaA DN Type VII secretion protein EsaA RQ 0 EV IPR023838; TIGR03929; -- SN 2 ID Type VII secretion protein EssA DN Type VII secretion protein EssA RQ 1 EV IPR018920; TIGR03927; -- SN 3 ID Type VII secretion protein EssC DN Type VII secretion protein EssC RQ 1 EV IPR023839; TIGR03928; -- SN 4 ID Type VII secretion target, WXG100 family DN Type VII secretion target, WXG100 family RQ 1 EV IPR010310; PF06013; EV IPR010310; TIGR03930; EV IPR021477; TIGR04197; -- SN 5 ID Type VII secretion protein EsaB DN Type VII secretion protein EsaB RQ 1 EV IPR024962; PF08817; -- SN 6 ID Type VII secretion protein EssB DN Type VII secretion protein EssB RQ 1 EV IPR018778; TIGR03926; // AC GenProp0907 DE Poly-beta-1,6 N-acetyl-D-glucosamine system, PgaABCD type TP SYSTEM AU Haft DH TH 0 RN [1] RM 18359807 RT Roles of pgaABCD genes in synthesis, modification, and export of the RT Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine. RA Itoh Y, Rice JD, Goller C, Pannuri A, Taylor J, Meisner J, Beveridge RA TJ, Preston JF, Romeo T; RL J Bacteriol. 2008;190:3670-3680. CC This property describes the biosynthesis and delivery of a CC polysaccharide adhesin based on poly-beta-1,6-N-acetyl-D-glucosamine, CC partially N-deacetylated, as the system occurs in Gram-negative CC bacteria with a requirement for transit across the outer membrane. A CC related system, termed PIA (polysaccharide intercellular adhesin), CC occurs in certain Gram-positive species. -- SN 1 ID Poly-beta-1,6 N-acetyl-D-glucosamine export porin DN Poly-beta-1,6 N-acetyl-D-glucosamine export porin/PgaA RQ 1 EV IPR023870; TIGR03939; TG GO:0042710; -- SN 2 ID Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase DN Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase/PgaB RQ 1 EV IPR023854; TIGR03938; TG GO:0045226; -- SN 3 ID Poly-beta-1,6 N-acetyl-D-glucosamine synthase DN Poly-beta-1,6 N-acetyl-D-glucosamine synthase/PgaC RQ 1 EV IPR023853; TIGR03937; TG GO:0045226; -- SN 4 ID Poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD DN Poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD RQ 1 EV IPR023829; TIGR03940; TG GO:0045226; // AC GenProp0908 DE 2,3-diaminopropionic acid biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 19775248 RT Molecular characterization of staphyloferrin B biosynthesis in RT Staphylococcus aureus. RA Cheung J, Beasley FC, Liu S, Lajoie GA, Heinrichs DE; RL Mol Microbiol. 2009;74:594-608. CC L-2,3-diaminopropionic acid (Dap) is an intermediate in the CC biosynthesis of a number of metabolites, such as the siderophore CC staphyloferrin B. Cheung, et al. [1] cite their own unpublished CC results that SbnA and SbnB produce Dap. SbnA is a pyridoxal CC phosphate-dependent enzyme distantly related to diaminopropionate CC ammonia-lyase. SbnB shows homology to an NAD-dependent alanine CC dehydrogenase of Archaeoglobus fulgidus. The two occasionally occur as CC a fusion protein. -- SN 1 ID 2,3-diaminopropionate biosynthesis protein SbnA DN 2,3-diaminopropionate biosynthesis protein SbnA RQ 1 EV IPR023927; TIGR03945; -- SN 2 ID 2,3-diaminopropionate biosynthesis protein SbnB DN 2,3-diaminopropionate biosynthesis protein SbnB RQ 1 EV IPR023866; TIGR03944; // AC GenProp0909 DE Capreomycidine biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 19490124 RT Structural basis for the erythro-stereospecificity of the L-arginine RT oxygenase VioC in viomycin biosynthesis. RA Helmetag V, Samel SA, Thomas MG, Marahiel MA, Essen LO; RL FEBS J. 2009;276:3669-3682. RN [2] RM 15368582 RT Conversion of (2S)-arginine to (2S,3R)-capreomycidine by VioC and VioD RT from the viomycin biosynthetic pathway of Streptomyces sp. strain RT ATCC11861. RA Ju J, Ozanick SG, Shen B, Thomas MG; RL Chembiochem. 2004;5:1281-1285. CC (2S,3R)-capreomycidine is made as a relatively rare precursor for CC non-ribosomal peptide synthesis. The first enzyme (VioC), an CC alpha-ketoglutarate-dependent and Fe(II)-dependent L-arginine CC beta-hydroxylase, produces (2S,3S)-hydroxyarginine. The second enzyme CC (VioD), capreomycidine synthase, converts the product to CC (2S,3R)-capreomycidine. -- SN 1 ID Arginine oxygenase VioC DN Arginine oxygenase VioC RQ 1 EV IPR023966; TIGR03946; TG GO:0042398; -- SN 2 ID Capreomycidine synthase DN Capreomycidine synthase/VioD RQ 1 EV IPR023965; TIGR03947; TG GO:0042398; // AC GenProp0910 DE Butyryl-CoA to butyrate, phosphotransbutyrylase pathway TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a pathway that operates in CC butyrate-producing bacteria. A central pathway converts acetyl-CoA to CC butyryl-CoA. This Property represents one alternative pathway from CC butyryl-CoA to butyrate. The first enzyme, phosphate CC butyryltransferase, transfers butyrate from coenzyme A to an inorganic CC phosphate. The second enzyme, butyrate kinase, transfers the phosphate CC from butryate onto ADP, producing ATP. -- SN 1 ID Butyrate kinase DN Butyrate kinase RQ 1 EV IPR011245; TIGR02707; -- SN 2 ID Phosphate butyryltransferase DN Phosphate butyryltransferase RQ 1 EV IPR014079; TIGR02706; // AC GenProp0911 DE Butyryl-CoA to butyrate, acetate CoA-transferase pathway TP SYSTEM AU Haft DH TH 0 CC This pathway describes one of two well-desribed pathways for the CC conversion of butyryl-CoA to butyrate, a one-step pathway of CoA CC transfer to acetate. An alternative two-step pathway transfers butyrate CC from CoA to inorganic phosphate, after which a butyrate kinase CC transfers the phosphate to ADP. The two pathways can coexist in a CC species, and the pathway described here appears to be the more CC significant in bacteria of the human colon. -- SN 1 ID Butyryl-CoA:acetate CoA-transferase DN Butyryl-CoA:acetate CoA-transferase RQ 1 EV IPR023990; TIGR03948; // AC GenProp0914 DE Hydrogenase, [FeFe]-dependent TP SYSTEM AU Haft DH TH 0 RN [1] RM 15082711 RT Discovery of two novel radical S-adenosylmethionine proteins required RT for the assembly of an active [Fe] hydrogenase. RA Posewitz MC, King PW, Smolinski SL, Zhang L, Seibert M, Ghirardi ML; RL J Biol Chem. 2004;279:25711-25720. RN [2] RM 19855833 RT Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] RT hydrogenase activation. RA Kuchenreuther JM, Stapleton JA, Swartz JR; RL PLoS One. 2009;4:e7565. CC This system consists of two radical SAM proteins and a GTP-binding CC protein involved in [Fe] hydrogenase maturation. -- SN 1 ID Iron hydrogenase, large subunit DN Iron hydrogenase, large subunit RQ 1 EV IPR013352; TIGR02512; -- SN 2 ID Iron hydrogenase, small subunit DN Iron hydrogenase, small subunit RQ 1 EV IPR003149; PF02256; -- SN 3 ID Hydrogenase accessory rSAM protein HydE DN Hydrogenase accessory rSAM protein HydE RQ 1 EV IPR024021; TIGR03956; TG GO:0051188; -- SN 4 ID Hydrogenase accessory GTP-binding protein HydF DN Hydrogenase accessory GTP-binding protein HydF RQ 1 EV IPR023873; TIGR03918; TG GO:0051188; -- SN 5 ID Hydrogenase accessory rSAM protein HydG DN Hydrogenase accessory rSAM protein HydG RQ 1 EV IPR024007; TIGR03955; TG GO:0051188; -- SN 6 ID Hydrogenase putative regulator DN Hydrogenase putative regulator RQ 0 EV IPR023860; TIGR03959; // AC GenProp0915 DE Hydrogenase, mono-iron type TP SYSTEM AU Haft DH TH 1 RN [1] RM 19897660 RT Identification and characterization of a novel member of the radical RT AdoMet enzyme superfamily and implications for the biosynthesis of the RT Hmd hydrogenase active site cofactor. RA McGlynn SE, Boyd ES, Shepard EM, Lange RK, Gerlach R, Broderick JB, RA Peters JW; RL J Bacteriol. 2010;192:595-598. RN [2] RM 18407624 RT Characterization of the Fe site in iron-sulfur cluster-free hydrogenase RT (Hmd) and of a model compound via nuclear resonance vibrational RT spectroscopy (NRVS). RA Guo Y, Wang H, Xiao Y, Vogt S, Thauer RK, Shima S, Volkers PI, RA Rauchfuss TB, Pelmenschikov V, Case DA, Alp EE, Sturhahn W, Yoda Y, RA Cramer SP; RL Inorg Chem. 2008;47:3969-3977. CC This property describes 5,10-methenyltetrahydromethanopterin CC hydrogenase (HmdA, also called mono-iron hydrogenase or iron-sulfur CC cluster-free hydrogenase), together with a few of its accessory CC proteins: HmdB (a radical SAM protein) and HmdC. The enzyme contains a CC novel cofactor with an Fe ion ligated by two CO molecules, a cysteine CC side chain, a guanylyl pyridinol cofactor, and an uncharacterized CC additional ligand. -- SN 1 ID 5,10-methenyltetrahydromethanopterin hydrogenase DN 5,10-methenyltetrahydromethanopterin hydrogenase RQ 1 EV IPR010062; TIGR01723; -- SN 2 ID HmdA cofactor biosynthesis rSAM protein HmdB DN HmdA cofactor biosynthesis rSAM protein HmdB RQ 1 EV IPR023858; TIGR03957; -- SN 3 ID HmdA cofactor biosynthesis protein HmdC DN HmdA cofactor biosynthesis protein HmdC RQ 1 EV IPR016760; TIGR03958; // AC GenProp0916 DE Radical SAM/uncharacterized protein TIGR03936 system TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a two-gene system, usually occurring as CC a fusion protein. One member is an uncharacterized radical SAM protein. CC The other member is uncharacterized protein TIGR03936. -- SN 1 ID Uncharacterized protein TIGR03936 DN Uncharacterized protein TIGR03936 RQ 1 EV IPR018768; TIGR03936; -- SN 2 ID Uncharacterized radical SAM protein DN Uncharacterized radical SAM protein RQ 1 EV IPR023862; TIGR03960; // AC GenProp0917 DE Mycofactocin system TP SYSTEM AU Haft DH TH 0 RN [1] RM 21223593 RT Bioinformatic evidence for a widely distributed, ribosomally produced RT electron carrier precursor, its maturation proteins, and its RT nicotinoprotein redox partners. RA Haft DH; RL BMC Genomics. 2011;12:21. RN [2] RM 9249038 RT Tetrazolium-dye-linked alcohol dehydrogenase of the methylotrophic RT actinomycete Amycolatopsis methanolica is a three-component complex. RA Bystrykh LV, Govorukhina NI, Dijkhuizen L, Duine JA; RL Eur J Biochem. 1997;247:280-287. CC This Genome Property describes the proposed mycofactocin system, in CC which the four absolutely conserved elements are a radical SAM protein, CC a glycosyltransferase, a small protein with a strongly conserved CC central motif, and a very small protein with an invariant C-terminal CC motif GCVY. This last component, the proposed mycofactocin precursor CC MftA, often is not apparent because of faulty gene calling. Species CC with this system always have in addition at least a few examples CC (usually co-clustered) of nicotinoproteins with tightly bound NAD(P) CC cofactors that cannot be exchanged, requiring an extrinsic mechanism CC (such as the artifical electron acceptor NDMA) to be able to cycle. CC Mycofactocin is proposed to undergo modification and become the CC required electron exchange cofactor. -- SN 1 ID Oxidoreductase, FAD/FMN-binding DN Oxidoreductase, FAD/FMN-binding RQ 0 EV IPR023987; TIGR03997; TG GO:0055114; EV IPR023967; TIGR03996; TG GO:0051188; -- SN 2 ID Dehydrogenase, Rv0697 family DN Dehydrogenase, Rv0697 family RQ 0 EV IPR023978; TIGR03970; TG GO:0055114; EV IPR030900; TIGR04542; TG GO:0051188; -- SN 3 ID Mycofactocin precursor DN Mycofactocin precursor/MftA RQ 1 EV IPR023988; TIGR03969; TG GO:0051188; -- SN 4 ID RPExGFAL protein DN RPExGFAL protein RQ 1 EV IPR023850; TIGR03967; TG GO:0051188; -- SN 5 ID Radical SAM mycofactocin maturase DN Radical SAM mycofactocin maturase RQ 1 EV IPR023913; TIGR03962; TG GO:0051188; -- SN 6 ID Heme/FMN protein DN Heme/FMN protein RQ 1 EV IPR023989; TIGR03966; TG GO:0055114; -- SN 7 ID Creatininase family protein DN Creatininase family protein RQ 1 EV IPR023871; TIGR03964; TG GO:0051188; -- SN 8 ID Glycosyltransferase DN Glycosyltransferase RQ 1 EV IPR023981; TIGR03965; TG GO:0051188; -- SN 9 ID Mycofactocin system transcriptional regulator DN Mycofactocin system transcriptional regulator RQ 0 EV IPR023851; TIGR03968; TG GO:0051193; -- SN 10 ID Dehydrogenase, SDR family DN Dehydrogenase, SDR family RQ 0 EV IPR023985; TIGR03971; TG GO:0055114; EV IPR030981; TIGR04504; TG GO:0051188; -- SN 11 ID Dehydrogenase, Rxyl_3153 family DN Dehydrogenase, Rxyl_3153 family RQ 1 EV IPR023921; TIGR03989; TG GO:0055114; -- SN 12 ID Dehydrogenase, iron-activated family DN Dehydrogenase, iron-activated family RQ 0 EV IPR001670; PF00465; TG GO:0055114; EV IPR026338; TIGR04266; TG GO:0055114; // AC GenProp0918 DE Anaerobic sulfatase/maturase system TP SYSTEM AU Haft DH TH 0 CC This property indicates the presence of gene pairs, where one member is CC a sulfatase, the other a radical SAM enzyme for its anaerobic CC maturation. -- SN 1 ID Sulfatase maturase DN Sulfatase maturase RQ 1 EV IPR023867; TIGR03942; -- SN 2 ID Anaerobic sulfatase DN Anaerobic sulfatase RQ 1 EV IPR000917; PF00884; // AC GenProp0919 DE SCIFF/radical SAM Clostridial gene pair TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This property describes a radical SAM protein and its 45-amino acid CC partner with six conserved cysteine residues. The system appears to be CC universal in the Clostridia, and rare outside the Clostridia. This CC pattern suggests a house-keeping role rather than a role such as CC bacteriocin production. Meanwhile, among all characterized radical SAM CC proteins, those closest by homology to the member of this system are CC modification enzymes for short peptides. -- SN 1 ID Six-Cys-in-45 protein DN Six-Cys-in-45 protein RQ 1 EV IPR023975; TIGR03973; -- SN 2 ID Six-Cys-in-45 modification radical SAM protein DN Six-Cys-in-45 modification radical SAM protein RQ 1 EV IPR024025; TIGR03974; // AC GenProp0920 DE Radical SAM Y_X(10)_GDL system TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This Genome Property consists of radical SAM protein family TIGR03913 CC and its presumptive target family PF08898, which may exist in multiple CC copies. -- SN 1 ID Y_X(10)_GDL-associated radical SAM protein DN Y_X(10)_GDL-associated radical SAM protein RQ 1 EV IPR023820; TIGR03913; -- SN 2 ID Y_X(10)_GDL domain protein DN Y_X(10)_GDL domain protein RQ 1 EV IPR014994; PF08898; // AC GenProp0921 DE Radical SAM pair and His-Xaa-Ser repeats peptide TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This Genome Property represents a pair of radical SAM proteins that CC occur as tandem genes in bacteria. The most likely function for this CC system is post-translational modification of ribosomally produced CC peptides. TIGR03979 describes a family with low levels of sequence CC similarity overall, a C-terminal putative peptidoglycan-binding domain, CC but also a striking region with five to seven repeats of His-Xaa-Ser. CC This family only occurs next to the radical SAM pair. Surprisingly, a CC search based on the His-Xaa-Ser repeat region and just a few flanking CC amino acids finds that essentially every radical SAM pair has a CC His-Xaa-Ser repeats region peptide nearby. TIGR03976 describes an CC additional protein in this system, including one branch of the family CC with the signature motif LLNDYxLRE. -- SN 1 ID Conserved hypothetical protein TIGR03982 DN Conserved hypothetical protein TIGR03982 RQ 0 EV IPR023814; TIGR03982; -- SN 2 ID Putative quinone modification maturase DN Putative quinone modification maturase RQ 0 EV IPR023893; TIGR03981; -- SN 3 ID LLNDYxLRE motif rSAM-associated protein DN LLNDYxLRE motif rSAM-associated protein RQ 1 EV IPR023974; TIGR03976; -- SN 4 ID His/Ser-rich radical SAM pair-associated protein DN His/Ser-rich radical SAM pair-associated protein RQ 0 EV IPR023928; TIGR03979; -- SN 5 ID Upstream radical SAM protein DN Upstream radical SAM protein RQ 1 EV IPR024023; TIGR03978; -- SN 6 ID Downstream radical SAM protein DN Downstream radical SAM protein RQ 1 EV IPR024032; TIGR03977; // AC GenProp0922 DE CRISPR system, Myxan subtype TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a subtype of CRISPR/Cas system as found CC in Myxococcus xanthus near locus MXAN_7263, in Leptospira interrogans, CC in Anabaena variabilis ATCC 29413, Lyngbya sp. PCC 8106, Cyanothece, CC etc. Repeats average about 36 base pairs in length. A typical repeat is CC GTGCCGCTCGCCGTGATGCCGGAAGGCGTTGAGCAC. Interestingly, this system CC includes the DevR and DevS proteins of Myxococcus, which have been CC recruited to demonstrable roles in fruiting body development. -- SN 1 ID CRISPR-associated protein Cas1, MYXAN subtype DN CRISPR-associated protein Cas1, MYXAN subtype RQ 1 EV IPR023844; TIGR03983; -- SN 2 ID CRISPR-associated protein Cas2, MYXAN subtype DN CRISPR-associated protein Cas2, MYXAN subtype RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas3, MYXAN region DN Cas3, MYXAN region RQ 1 EV IPR006474; TIGR01587; -- SN 4 ID CRISPR-associated protein Cas4, MYXAN subtype DN CRISPR-associated protein Cas4, MYXAN subtype RQ 1 EV IPR013343; TIGR00372; -- SN 5 ID CRISPR-associated protein Csx13, C-terminal region DN CRISPR-associated protein Csx13, C-terminal region RQ 1 EV IPR027811; TIGR03486; -- SN 6 ID CRISPR-associated protein Csx13, N-terminal region DN CRISPR-associated protein Csx13, N-terminal region RQ 1 EV IPR019989; TIGR03485; -- SN 7 ID CRISPR-associated protein DevS DN CRISPR-associated protein DevS RQ 1 EV IPR013415; TIGR02586; -- SN 8 ID CRISPR-associated protein Cas6, MYXAN subtype DN CRISPR-associated protein Cas6, MYXAN subtype RQ 1 EV IPR014174; TIGR02807; -- SN 9 ID CRISPR-associated autoregulator, MYXAN subtype DN CRISPR-associated autoregulator, MYXAN subtype RQ 1 EV IPR010154; TIGR01875; // AC GenProp0923 DE Mycothiol system TP SYSTEM AU Haft DH TH 0 RN [1] RM 17286835 RT Mycothiol-dependent proteins in actinomycetes. RA Rawat M, Av-Gay Y; RL FEMS Microbiol Rev. 2007;31:278-292. CC Mycothiol is a glutathione analog common in the Actinobacteria, but not CC found elsewhere. This Genome Property provides a higher-level view of CC mycothiol metabolism that includes its synthesis, the regeneration of CC mycothiol from mycothione (its disulfide-bonded dimer) by NADPH-dependent CC reduction, and a guild of mycothiol-dependent enzymes, the discovery of CC which is incomplete. -- SN 1 ID Anti-sigma-R factor RsrA DN Anti-sigma-R factor RsrA RQ 1 EV IPR024020; TIGR03988; -- SN 2 ID Mycothione reductase DN Mycothione reductase RQ 1 EV IPR017817; TIGR03452; TG GO:0010126; -- SN 3 ID Mycothiol-dependent enzyme DN Mycothiol-dependent enzyme RQ 1 EV IPR017811; TIGR03446; TG GO:0010126; EV IPR017816; TIGR03451; -- SN 4 ID Mycothiol biosynthesis DN Mycothiol biosynthesis RQ 1 EV GenProp0753; // AC GenProp0927 DE Bacillithiol biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 20308541 RT Biosynthesis and functions of bacillithiol, a major RT low-molecular-weight thiol in Bacilli. RA Gaballa A, Newton GL, Antelmann H, Parsonage D, Upton H, Rawat M, RA Claiborne A, Fahey RC, Helmann JD; RL Proc Natl Acad Sci U S A. 2010;107:6482-6486. RN [2] RM 20799687 RT Characterization of the N-acetyl-α-D-glucosaminyl l-malate synthase RT and deacetylase functions for bacillithiol biosynthesis in Bacillus RT anthracis . RA Parsonage D, Newton GL, Holder RC, Wallace BD, Paige C, Hamilton CJ, RA Dos Santos PC, Redinbo MR, Reid SD, Claiborne A; RL Biochemistry. 2010;49:8398-8414. CC This property describes the biosynthesis of bacillithiol, a thiol CC analog of glutathione and mycothiol. Bacillithiol is a 398-Da CC alpha-anomeric glycoside of L-cysteinyl-D-glucosamine with L-malic acid. -- SN 1 ID Glycosyltransferase BshA DN Glycosyltransferase BshA RQ 1 EV IPR023881; TIGR03999; TG GO:0071793; -- SN 2 ID N-acetylhydrolase BshB DN N-acetylhydrolase BshB RQ 1 EV IPR023841; TIGR04000; TG GO:0071793; EV IPR023842; TIGR04001; TG GO:0071793; -- SN 3 ID Cysteine-adding enzyme BshC DN Cysteine-adding enzyme BshC RQ 1 EV IPR011199; TIGR03998; TG GO:0071793; // AC GenProp0928 DE OMP chaperone system: SurA-Skp-DegP TP SYSTEM AU Haft DH TH 0 RN [1] RM 17908933 RT Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in RT Escherichia coli. RA Sklar JG, Wu T, Kahne D, Silhavy TJ; RL Genes Dev. 2007;21:2473-2484. CC Outer membrane beta-barrel proteins are translocated into the periplasm CC by the Sec system and subsequently properly folded and inserted into CC the outer membrane by the beta-barrel assembly machine (Bam). In the CC periplasm, chaperones prevent misfolding and aggregation, and facilitate CC the transit across the periplasmic space. The SurA protein appears to CC be the primary chaperone, at least in E. coli [1], while Skp and DegP CC may act to rescue any OMPs which fall off of the SurA complex. -- SN 1 ID Chaperone DegP DN Chaperone DegP RQ 1 EV IPR011782; TIGR02037; TG GO:0006886; -- SN 2 ID Chaperone Skp DN Chaperone Skp RQ 1 EV IPR005632; PF03938; TG GO:0006886; -- SN 3 ID Chaperone SurA DN Chaperone SurA RQ 1 EV IPR015391; PF09312; TG GO:0006886; // AC GenProp0930 DE GDP-4-keto-6-deoxymannose biosynthesis from beta-D-fructose-6-phosphate TP METAPATH AU Haft DH TH 0 CC The sugar intermediate GDP-4-keto-6-deoxymannose is produced in a CC 4-step pathway from beta-D-fructose-6-phosphate using the ManABC and CC Gmd gene products. Mannose may be produced as a side-product of this CC pathway by the inclusion of the Gmm gene product (GDP-mannose mannosyl CC hydrolase). GDP-4-keto-6-deoxymannose may be converted to GDP-L-fucose CC by the Fcl gene product, to perosamine by Per, or to colicin by ColCD. -- SN 1 ID Source of GDP-D-mannose DN Source of GDP-D-mannose RQ 1 EV GenProp1017; -- SN 2 ID GDP-mannose-4,6-dehydratase DN GDP-mannose-4,6-dehydratase/Gmd RQ 1 EV IPR006368; TIGR01472; // AC GenProp0933 DE Bacillithiol utilization TP GUILD AU Haft DH TH 0 RN [1] RM 20308541 RT Biosynthesis and functions of bacillithiol, a major RT low-molecular-weight thiol in Bacilli. RA Gaballa A, Newton GL, Antelmann H, Parsonage D, Upton H, Rawat M, RA Claiborne A, Fahey RC, Helmann JD; RL Proc Natl Acad Sci U S A. 2010;107:6482-6486. CC This property describes the guild of proteins dependent on bacillithiol CC in microbial genomes. Bacillithiol, a thiol analog of glutathione and CC mycothiol, is a 398-Da alpha-anomeric glycoside of CC L-cysteinyl-D-glucosamine with L-malic acid. A separate property CC describes the biosynthesis of bacillithiol. -- SN 1 ID Putative bacillithiol TDOR, YpdA family DN Putative bacillithiol TDOR, YpdA family RQ 0 EV IPR023856; TIGR04018; TG GO:0071792; -- SN 2 ID Putative bacillithiol TDOR, YphP/YqiW family DN Putative bacillithiol TDOR, YphP/YqiW family RQ 0 EV IPR009474; PF06491; TG GO:0071792; -- SN 3 ID Putative bacillithiol TDOR, YtxJ family DN Putative bacillithiol TDOR, YtxJ family RQ 0 EV IPR022551; TIGR04019; TG GO:0071792; // AC GenProp0934 DE Dimethyl sulphone utilization (aerobic) TP SYSTEM AU Haft DH TH 0 CC A pathway has been described in which two FMNH2-dependent members of CC the bacterial luciferase-like monooxygenase (LLM) family convert CC dimethyl sulfone (DMS02) first to methanesulfonate (MSA), then from MSA CC to inorganic form. The enzymes are the dimethyl sulphone monooxygenase CC SfnG and methanesulfonate sulfonatase (an alkanesulfonate monooxygenase) CC SsuD. -- SN 1 ID Acyl-CoA dehydrogenase family protein, SfnB type DN Acyl-CoA dehydrogenase family protein, SfnB type RQ 1 EV IPR023922; TIGR04022; -- SN 2 ID Dimethyl sulphone monooxygenase SfnG DN Dimethyl sulphone monooxygenase SfnG RQ 1 EV IPR024014; TIGR04021; -- SN 3 ID Methanesulfonate sulfonatase SsuD DN Methanesulfonate sulfonatase SsuD RQ 1 EV IPR019911; TIGR03565; // AC GenProp0935 DE Uptake/catabolism system KPN_01854/KPN_01858 TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes an uncharacterized system with an ABC CC transporter both co-clustered and phylogenetically co-distributed CC (although not perfectly) with a putative FMN-dependent luciferase-like CC monooxygenase (LLM). This system is distributed sporadically from CC Gram-negative (e.g. Klebsiella pneumoniae) to Gram-positive (e.g. CC Kineococcus radiotolerans). -- SN 1 ID Alkylhydroperoxidase domain protein, Avi_7169 family DN Alkylhydroperoxidase domain protein, Avi_7169 family RQ 1 EV IPR023923; TIGR04030; -- SN 2 ID Utilization system luciferase-like monooxygenase DN Utilization system luciferase-like monooxygenase RQ 1 EV IPR024003; TIGR04027; -- SN 3 ID CMD domain protein, Avi_7170 family DN CMD domain protein, Avi_7170 family RQ 1 EV IPR023982; TIGR04029; -- SN 4 ID Utilization system ABC transporter substrate binding protein DN Utilization system ABC transporter substrate binding protein RQ 1 EV IPR023920; TIGR04028; // AC GenProp0936 DE Bacteriocin system, sporulation delay protein group TP SYSTEM AU Haft DH TH 0 RN [1] RM 19775247 RT Cannibalism enhances biofilm development in Bacillus subtilis. RA López D, Vlamakis H, Losick R, Kolter R; RL Mol Microbiol. 2009;74:609-618. CC This Genome Property describes a three-gene system of antimicrobial CC peptide and two export proteins modeled on SdpC (sporulation delay CC protein C) from Bacillus subtilis, a killing peptide that allows CC cannibalism to obtain nutrients and avoid the irreversible sporulation CC cascade. Related systems are sparsely but widely distributed. CC Additional components of the SdpABC system itself, such as immunity CC protein SdpI and regulatory proteins, were not recognized as universal CC to such systems by phylogenetic profiling mechanisms and are not CC modeled within this Genome Property. -- SN 1 ID Antimicrobial peptide system protein, SdpA family DN Antimicrobial peptide system protein, SdpA family RQ 1 EV IPR023902; TIGR04034; TG GO:0030152; -- SN 2 ID Antimicrobial peptide system protein, SdpB family DN Antimicrobial peptide system protein, SdpB family RQ 1 EV IPR023894; TIGR04033; TG GO:0030152; -- SN 3 ID Antimicrobial peptide, SdpC family DN Antimicrobial peptide, SdpC family RQ 1 EV IPR023888; TIGR04032; TG GO:0030152; // AC GenProp0938 DE Glycine radical enzyme system, YjjI/YjjW pair TP SYSTEM AU Haft DH TH 0 CC This system, analogous to pyruvate formate-lyase and its activase, CC contains an enzyme of unknown function from the family of glycine CC radical enzymes, and the adjacent gene for a matched radical SAM enzyme CC that generates the active site. -- SN 1 ID Glycine radical enzyme YjjI DN Glycine radical enzyme YjjI RQ 1 EV IPR016905; TIGR04040; -- SN 2 ID Radical SAM family activase YjjW DN Radical SAM family activase YjjW RQ 1 EV IPR023912; TIGR04041; // AC GenProp0939 DE RSAM-containing biosynthetic cluster, MSMEG_0568 system TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a broadly but sparsely distributed gene CC cluster that appears to be biosynthetic. The cluster includes a radical CC SAM protein, an N-acetyltransferase, a probable nitrilase, a CC flavin-dependent oxidoreductase, and several uncharacterized CC proteins.This assortment of functions suggests a biosynthetic rather CC than catabolic role for the cluster. -- SN 1 ID Glycosyltransferase, MSMEG_0565 family DN Glycosyltransferase, MSMEG_0565 family RQ 0 EV IPR023986; TIGR04047; -- SN 2 ID AIR synthase-related protein, sll0787 family DN AIR synthase-related protein, sll0787 family RQ 1 EV IPR024030; TIGR04049; EV IPR023911; TIGR04050; -- SN 3 ID GNAT class N-acetyltransferase, MSMEG_0567 family DN GNAT class N-acetyltransferase, MSMEG_0567 family RQ 1 EV IPR024035; TIGR04045; -- SN 4 ID Radical SAM protein, MSMEG_0568 family DN Radical SAM protein, MSMEG_0568 family RQ 1 EV IPR016779; TIGR04043; -- SN 5 ID Flavin-dependent oxidoreductase, MSMEG_0569 family DN Flavin-dependent oxidoreductase, MSMEG_0569 family RQ 1 EV IPR024000; TIGR04046; -- SN 6 ID MSMEG_0570 family protein DN MSMEG_0570 family protein RQ 1 EV IPR023846; TIGR04042; -- SN 7 ID MSMEG_0572 family protein DN MSMEG_0572 family protein RQ 1 EV IPR023847; TIGR04044; -- SN 8 ID Biosynthetic protein, Pnap_2097 family DN Biosynthetic protein, Pnap_2097 family RQ 0 EV IPR024092; TIGR04099; -- SN 9 ID Putative nitrilase, sll0784 family DN Putative nitrilase, sll0784 family RQ 1 EV IPR023919; TIGR04048; // AC GenProp0940 DE Metallo-mystery pair TP SYSTEM AU Haft DH TH 0 CC The two genes described here are a subfamily related to MauG and to CC di-heme cytochrome c peroxidase, and an adjacent gene family in which CC members share a four-Cys motif. Additional homologs to this second CC protein family exist in which the four Cys residues motif is not CC preserved. Some members are found near TonB-dependent transporter CC system proteins and/or copper transport ATPases. -- SN 1 ID Metallo-mystery pair system di-heme enzyme DN Metallo-mystery pair system di-heme enzyme RQ 1 EV IPR023929; TIGR04039; -- SN 2 ID Metallo-mystery pair system AZL_007920/MXAN_0976 family protein DN Metallo-mystery pair system AZL_007920/MXAN_0976 family protein RQ 1 EV IPR023977; TIGR04052; // AC GenProp0941 DE TonB-dependent nutrient uptake pairs, RagAB/SusCD type TP SYSTEM AU Haft DH TH 0 CC A set of gene pairs almost entirely restricted to the Bacteroidetes, CC and with up to 100 pairs per genome, consists of TonB-linked outer CC membrane protein related to RagA and SusC, and its neighbor related to CC RagB and SusD. -- SN 1 ID TonB-linked outer membrane protein, SusC/RagA family DN TonB-linked outer membrane protein, SusC/RagA family RQ 1 EV IPR023996; TIGR04056; -- SN 2 ID Outer membrane protein, SusD/RagB family DN Outer membrane protein, SusD/RagB family RQ 1 EV IPR012944; PF07980; EV IPR033985; PF14322; // AC GenProp0942 DE Alkane biosynthesis, cyanobacterial TP PATHWAY AU Haft DH TH 0 RN [1] RM 20671186 RT Microbial biosynthesis of alkanes. RA Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB; RL Science. 2010;329:559-562. CC This two gene system converts even-numbered saturated and unsaturated CC fatty acids (largely C16 and C18) into n-1 odd-numbered alkanes or CC alkenes. The most commonly observed alkanes in cyanobacteria, where CC this system is found, are heptadecane, pentadecane and CC methyl-heptadecane [1]. Fatty acyl-acyl carrier protein (ACP) CC substrates are first converted to fatty aldehydes by the action of an CC NAD(P)H-dependent Acyl-ACP reductase. This reductase is distantly CC related to the short-chain dehydrogenase or reductase (SDR) family. CC The fatty aldehyde is subsequently converted to hydrocarbons by an CC aldehyde decarbonylase, releasing CO. This decarbonylase is distantly CC related to a family of di-iron-containing reductases including CC ribonucleotide reductase. -- SN 1 ID Acyl-ACP reductase DN Acyl-ACP reductase RQ 1 EV IPR016836; TIGR04058; TG GO:0043447; -- SN 2 ID Aldehyde decarbonylase DN Aldehyde decarbonylase RQ 1 EV IPR022612; TIGR04059; TG GO:0043447; // AC GenProp0943 DE Pyruvate formate-lyase system TP SYSTEM AU Haft DH TH 0 RN [1] RM 11444864 RT YfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous RT glycyl radical cofactors reconstituting the catalytic center of RT oxygen-fragmented pyruvate formate-lyase. RA Wagner AF, Schultz S, Bomke J, Pils T, Lehmann WD, Knappe J; RL Biochem Biophys Res Commun. 2001;285:456-462. CC This property consists of the glycine radical enzyme, pyruvate-formate CC lyase (also called formate C-acetyltransferase) and its activating CC enzyme, [Formate-C-acetyltransferase]-activating enzyme. In most CC Proteobacteria, the gene pair is accompanied by the formate channel CC gene FocA. FocA forms a pentameric channel that can CC pass formate but not water, and that belongs to the same transporter CC family as nitrate transporter NirC. -- SN 1 ID Pyruvate formate-lyase DN Pyruvate formate-lyase (EC 2.3.1.54) RQ 1 EV IPR010098; TIGR01774; EV IPR005949; TIGR01255; -- SN 2 ID Pyruvate formate-lyase activating enzyme DN Pyruvate formate-lyase activating enzyme (EC 1.97.1.4) RQ 1 EV IPR012838; TIGR02493; -- SN 3 ID Formate transporter DN Formate transporter/FocA RQ 0 EV IPR000292; PF01226; -- SN 4 ID Autonomous glycyl radical cofactor DN Autonomous glycyl radical cofactor RQ 0 EV IPR011140; TIGR04365; // AC GenProp0944 DE Cohesin/dockerin (cellulosome-like) system TP SYSTEM AU Haft DH TH 0 CC The signature proteins of the cellulosome include cohesins and dockerins. -- SN 1 ID Cohesin DN Cohesin RQ 1 EV IPR002102; PF00963; -- SN 2 ID Dockerin DN Dockerin RQ 1 EV IPR002105; PF00404; // AC GenProp0945 DE Radical SAM maturase bacteriocin system, CLI_3235 type TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This Genome Property represents mostly Clostridial bacteriocin CC precursors adjacent to a radical SAM protein family and, often to an CC additional uncharacterized family. -- SN 1 ID Peptide maturation system acyl carrier-related protein DN Peptide maturation system acyl carrier-related protein RQ 0 EV IPR023972; TIGR04069; -- SN 2 ID Bacteriocin precursor, CLI_3235-class DN Bacteriocin precursor, CLI_3235-class RQ 1 EV IPR023968; TIGR04065; EV IPR023964; TIGR04067; -- SN 3 ID Radical SAM bacterocin maturase, CLI_3235 system DN Radical SAM bacterocin maturase, CLI_3235 system RQ 1 EV IPR024001; TIGR04068; -- SN 4 ID CLI_3235-class bacteriocin system protein DN CLI_3235-class bacteriocin system protein RQ 0 EV IPR023823; TIGR04066; // AC GenProp0948 DE RNA repair, Hen1/Pnkp system TP SYSTEM AU Haft DH TH 0 RN [1] RM 17986465 RT Characterization of the 2',3' cyclic phosphodiesterase activities of RT Clostridium thermocellum polynucleotide kinase-phosphatase and RT bacteriophage lambda phosphatase. RA Keppetipola N, Shuman S; RL Nucleic Acids Res. 2007;35:7721-7732. RN [2] RM 20007328 RT Bacterial Hen1 is a 3' terminal RNA ribose 2'-O-methyltransferase RT component of a bacterial RNA repair cassette. RA Jain R, Shuman S; RL RNA. 2010;16:316-323. CC This property describes the combination of an RNA modification enzyme CC (the methyltransferase Hen1) and an RNA repair enzyme (polynucleotide CC kinase-phosphatase) as found in Clostridium thermocellum, CC and in many other bacteria in a two-gene cassette. This pairing may CC allow RNA cleaved by ribotoxins to be repaired, and to be modified at CC the site of repair to prevent the same breakage from occurring again. -- SN 1 ID 3' terminal RNA ribose 2'-O-methyltransferase Hen1 DN 3' terminal RNA ribose 2'-O-methyltransferase Hen1 RQ 1 EV IPR024026; TIGR04074; TG GO:0042245; -- SN 2 ID Polynucleotide kinase-phosphatase DN Polynucleotide kinase-phosphatase RQ 1 EV IPR024028; TIGR04075; TG GO:0042245; // AC GenProp0950 DE dTDP-4-dehydro-6-deoxy-alpha-D-glucose biosynthesis from glucose-1-phosphate TP PATHWAY AU Haft DH, Richardson L TH 0 RN [1] RM 12773151 RT A structural perspective on the enzymes that convert dTDP-d-glucose RT into dTDP-l-rhamnose. RA Dong C, Beis K, Giraud MF, Blankenfeldt W, Allard S, Major LL, Kerr ID, RA Whitfield C, Naismith JH; RL Biochem Soc Trans. 2003;31:532-536. RN [2] RM 10802738 RT RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of RT epimerase. RA Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH; RL Nat Struct Biol. 2000;7:398-402. DC Streptomycin biosynthesis DR KEGG; map00521; DC dTDP-L-rhamnose biosynthesis I DR MetaCyc; DTDPRHAMSYN-PWY; DC 6-Deoxyhexose Biosynthesis DR IUBMB; polysacc; deoxyhex; CC dTDP-4-dehydro-6-deoxy-alpha-D-glucose is an intermediate in the CC biosynthesis of L-rhamnose and D-fucosamine derivatives. L-rhamnose is a CC common component of the bacterial capsule and/or cell wall, and is CC important in bacterial survival during infection. dTDP-L-rhamnose is the CC precursor of L-rhamnose[1,2]. dTDP-L-rhamnose is synthesized from CC glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a CC four-step enzymatic pathway. The four enzymes are: glucose-1-phosphate CC thymidyltransferase (also known as dTDP-glucose pyrophosphorylase, gene CC name rlmA or rfbA); dTDP-D-glucose 4,6-dehydratase (gene name rmlB or CC rfbB); dTDP-4-dehydrorhamnose 3,5-epimerase (also known as CC dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase, gene name rmlC or rfbC); CC and dTDP-4-dehydrorhamnose reductase (also known as CC dTDP-6-deoxy-L-lyxo-4-hexulose reductase (gene name rmlD or rfbD)[1,2]. CC This property refers to the first two steps of this pathway. -- SN 1 ID Glucose-1-phosphate thymidylyltransferase DN Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) RQ 1 EV IPR005907; TIGR01207; sufficient; EV IPR005908; TIGR01208; sufficient; -- SN 2 ID dTDP-glucose 4,6-dehydratase DN dTDP-glucose 4,6-dehydratase (EC 4.2.1.46) RQ 1 EV IPR005888; TIGR01181; sufficient; // AC GenProp0954 DE Radical SAM-cylized peptide, Pep1357C family TP SYSTEM AU Haft DH TH 0 RN [1] RM 17921293 RT Control of the transcription of a short gene encoding a cyclic peptide RT in Streptococcus thermophilus: a new quorum-sensing system? RA Ibrahim M, Guillot A, Wessner F, Algaron F, Besset C, Courtin P, Gardan RA R, Monnet V; RL J Bacteriol. 2007;189:8844-8854. CC Pep1357C from Streptococcus thermophilus is a secreted modified peptide CC whose 9-amino acid mature form AKGDGWKVM is cyclized between residues 2 CC (Lys) and 6 (Trp), probably via a dehydrogenation catalyzed by the CC adjacent radical SAM enzyme. Similar peptides with the same core CC sequence KGDGW and pairing with a radical SAM enzyme occur elsewhere, CC such as Lactococcus lactis subsp. cremoris MG1363. The Pep1357C system CC probably provides signaling rather than bacteriocin activity. -- SN 1 ID KxxxW-cyclizing radical SAM enzyme DN KxxxW-cyclizing radical SAM enzyme RQ 1 EV IPR024017; TIGR04080; -- SN 2 ID KxxxW-cyclized secreted peptide DN KxxxW-cyclized secreted peptide RQ 1 EV IPR023903; TIGR04079; // AC GenProp0955 DE Modified peptide/radical SAM maturase system, YydFG family TP SYSTEM AU Haft DH TH 0 RN [1] RM 17921301 RT The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces RT the LiaRS two-component system. RA Butcher BG, Lin YP, Helmann JD; RL J Bacteriol. 2007;189:8616-8625. CC The pairing of a precursor to a modified peptide with a cognate radical CC SAM maturase is a common theme in bacteriocin and peptide pheromone CC biosynthesis in bacteria. This system includes peptides related to YydF CC from Bacillus subtilis and radical SAM enzymes similar to YydG. -- SN 1 ID Exported signaling peptide, YydF/SAG_2028 family DN Exported signaling peptide, YydF/SAG_2028 family RQ 1 EV IPR023898; TIGR04077; -- SN 2 ID Peptide modification radical SAM enzyme, YydG family DN Peptide modification radical SAM enzyme, YydG family RQ 1 EV IPR023904; TIGR04078; // AC GenProp0956 DE Radical SAM maturase/selenobacteriocin system TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This property describes a peptide modification radical SAM family and CC its cognate target peptides, a number of which appear to be CC selenocysteine-containing peptides. Two homologous SECIS elements are CC found for GSU_1558, for example, by bSECISearch: CC UGAGGCAAGUCUUCCGGCGCCGGGAGCGCCAAGGAGAAG and CC UGAGGCGGAUCGUCCGGCGCCGGUGGCGCCGCAAAGAAG. -- SN 1 ID Peptide modification radical SAM enzyme, GSU_1560 family DN Peptide modification radical SAM enzyme, GSU_1560 family RQ 1 EV IPR023807; TIGR04082; -- SN 2 ID Radical SAM modification target peptide, GSU_1558 family DN Radical SAM modification target peptide, GSU_1558 family RQ 1 EV IPR023971; TIGR04081; // AC GenProp0957 DE Protein sorting system, SipW class TP SYSTEM AU Haft DH TH 0 RN [1] RM 9694797 RT Functional analysis of the secretory precursor processing machinery of RT Bacillus subtilis: identification of a eubacterial homolog of archaeal RT and eukaryotic signal peptidases. RA Tjalsma H, Bolhuis A, van Roosmalen ML, Wiegert T, Schumann W, RA Broekhuizen CP, Quax WJ, Venema G, Bron S, van Dijl JM; RL Genes Dev. 1998;12:2318-2331. RN [2] RM 10559173 RT Control of synthesis and secretion of the Bacillus subtilis protein RT YqxM. RA Stöver AG, Driks A; RL J Bacteriol. 1999;181:7065-7069. RN [3] RM 22328672 RT Identification of Bacillus subtilis SipW as a bifunctional signal RT peptidase that controls surface-adhered biofilm formation. RA Terra R, Stanley-Wall NR, Cao G, Lazazzera BA; RL J Bacteriol. 2012;194:2781-2790. CC SipW is a signal peptidase I variant class, found in Bacillus subtilis, CC Archaeoglobus fulgidus, and scattered other prokaryotic lineages. It CC appears to recognize a cognate signal sequence variant, many instances CC of which are detected by model TIGR04088. -- SN 1 ID Signal peptidase, SipW class DN Signal peptidase, SipW class RQ 1 EV IPR001733; TIGR02228; -- SN 2 ID SipW-sorted protein DN SipW-sorted protein RQ 1 EV IPR023833; TIGR04088; // AC GenProp0958 DE D-alanyl-lipoteichoic acid biosynthesis TP SYSTEM AU Haft DH TH 0 RN [1] RM 19324056 RT Crystal structure of Bacillus cereus D-alanyl carrier protein ligase RT (DltA) in complex with ATP. RA Osman KT, Du L, He Y, Luo Y; RL J Mol Biol. 2009;388:345-355. RN [2] RM 16885447 RT A functional dlt operon, encoding proteins required for incorporation RT of d-alanine in teichoic acids in gram-positive bacteria, confers RT resistance to cationic antimicrobial peptides in Streptococcus RT pneumoniae. RA Kovács M, Halfmann A, Fedtke I, Heintz M, Peschel A, Vollmer W, RA Hakenbeck R, Brückner R; RL J Bacteriol. 2006;188:5797-5805. CC The DltABCD operon, responsible for D-alanylation of LipoTeichoic acids CC (hence DLT) is near-universal in low-GC Gram-positive bacteria, CC although absent in Clostridium perfringens, Oceanobacillus iheyensis, CC etc. This Genome Property describes the DltABCD system, rather than LTA CC biosynthesis itself. Note that lipoteichoic acids (LTA, anionic CC polymers) are variable among species or strains, with backbones that CC often consist of polyglycerolphosphate (e.g. Staphylococcus aureus) but CC with additional modifications. LTA are covalently linked to membrane CC components, and differ from wall teichoic acids (WTA), such as the CC polyribitol phosphate WTAs in S. aureus and B. subtilis W23. -- SN 1 ID D-alanine-D-alanyl carrier protein ligase DN D-alanine-D-alanyl carrier protein ligase/DltA RQ 1 EV IPR010072; TIGR01734; TG GO:0070394; -- SN 2 ID D-alanyl-lipoteichoic acid biosynthesis protein DltB DN D-alanyl-lipoteichoic acid biosynthesis protein DltB RQ 1 EV IPR024024; TIGR04091; TG GO:0070394; -- SN 3 ID D-alanine-D-alanyl carrier protein DN D-alanine-D-alanyl carrier protein/DltC RQ 1 EV IPR003230; TIGR01688; TG GO:0070394; -- SN 4 ID D-alanyl-lipoteichoic acid biosynthesis protein DltD DN D-alanyl-lipoteichoic acid biosynthesis protein DltD RQ 1 EV IPR023896; TIGR04092; TG GO:0070394; // AC GenProp0961 DE Heme metabolism pair HutWX TP SYSTEM AU Haft DH TH 0 CC The hutW and hutX genes are found in Vibrio cholerae next to hutZ, CC which is essential for heme utilization. HutW is homologous to the heme CC carrier protein HemS, while HutW is homologous to (but does not CC complement) the heme biosynthesis protein HemN. The gene pair is CC occasionally fused, and may perform a salvage-like function, converting CC one form of heme into another. HutZ, which resembles the PPOX class CC heme oxidase HugZ, accompanies roughly half of the occurrences of HutW CC and HutX. -- SN 1 ID Heme utilization radical SAM enzyme HutW DN Heme utilization radical SAM enzyme HutW RQ 1 EV IPR026332; TIGR04107; TG GO:0042168; -- SN 2 ID Putative heme utilization carrier protein HutX DN Putative heme utilization carrier protein HutX RQ 1 EV IPR010413; TIGR04108; TG GO:0042168; -- SN 3 ID Heme utilization protein HutZ DN Heme utilization protein HutZ RQ 0 EV IPR014419; TIGR04110; TG GO:0042168; // AC GenProp0962 DE Methanobactin biosynthesis, Mb-OB3b family TP SYSTEM AU Haft DH TH 0 RN [1] RM 20961038 RT A comparison of methanobactins from Methylosinus trichosporium OB3b and RT Methylocystis strain Sb2 predicts methanobactins are synthesized from RT diverse peptide precursors modified to create a common core for binding RT and reducing copper ions. RA Krentz BD, Mulheron HJ, Semrau JD, Dispirito AA, Bandow NL, Haft DH, RA Vuilleumier S, Murrell JC, McEllistrem MT, Hartsel SC, Gallagher WH; RL Biochemistry. 2010;49:10117-10130. CC Methanobactins are siderophore-like copper chelators. The charter CC member for this Genome Property is Methylosinus trichosporium OB3b, in CC which the methanobactin is made from a 30-residue ribosomally CC translated precursor. The only other system known so far is in CC Azospirillum sp. B510. -- SN 1 ID Methanobactin precursor, Mb-OB3b family DN Methanobactin precursor, Mb-OB3b family RQ 1 EV IPR023963; TIGR04071; TG GO:0015677; -- SN 2 ID Methanobactin biosynthesis cassette protein MbnB DN Methanobactin biosynthesis cassette protein MbnB RQ 1 EV IPR026431; TIGR04159; TG GO:0015677; -- SN 3 ID Methanobactin biosynthesis cassette protein MbnC DN Methanobactin biosynthesis cassette protein MbnC RQ 1 EV IPR026434; TIGR04160; TG GO:0015677; // AC GenProp0967 DE Radical SAM maturase system, CXXX repeats type TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC The three components of this system are a peptide maturase class CC radical SAM enzyme, a conserved hypothetical protein that may be a CC chaperone or a bacteriocin immunity protein, and a peptide that CC contains low-complexity sequence in which every fourth residue is Cys. -- SN 1 ID CXXX repeat peptide modification system protein DN CXXX repeat peptide modification system protein RQ 1 EV IPR026413; TIGR04116; -- SN 2 ID CXXX repeat peptide maturase DN CXXX repeat peptide maturase RQ 1 EV IPR026401; TIGR04119; -- SN 3 ID CXXX repeats rSAM maturase target DN CXXX repeats rSAM maturase target RQ 0 EV IPR026393; TIGR04114; EV IPR026484; TIGR04117; EV IPR026424; TIGR04118; -- SN 4 ID Radical SAM peptide maturase, CXXXX repeats system DN Radical SAM peptide maturase, CXXXX repeats system RQ 1 EV IPR026412; TIGR04115; // AC GenProp0969 DE Biosynthesis of UDP-N-acetyl-D-mannosaminuronic acid (UDP-ManNAcA) TP METAPATH AU Haft DH TH 0 CC UDP-ManNAcA is a precursor in the biosynthesis of the entobacterial CC common antigen. -- SN 1 ID Source of UDP-ManNAc DN Source of UDP-ManNAc RQ 1 EV GenProp0975; -- SN 2 ID UDP-N-acetyl-mannosamine dehydrogenase DN UDP-N-acetyl-mannosamine dehydrogenase RQ 1 EV IPR017476; TIGR03026; // AC GenProp0970 DE Biosynthesis of Und-PP-GlcNAc TP METAPATH AU Haft DH TH 0 CC N-acetylglucosamine-1-pyrophospho-undecaprenol (Und-PP-GlcNAc) is CC synthesized by the WecA enzyme in E. coli from UDP-GlcNAc and CC undecaprenyl phosphate. -- SN 1 ID Source of UDP-GlcNAc DN Source of UDP-GlcNAc RQ 1 EV GenProp0750; -- SN 2 ID Source of undecaprenyl phosphate (Und-P) DN Source of undecaprenyl phosphate (Und-P) RQ 1 EV GenProp0971; -- SN 3 ID UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase DN UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase RQ 1 EV IPR012750; TIGR02380; // AC GenProp0971 DE Biosynthesis of undecaprenyl phosphate (Und-P) TP METAPATH AU Haft DH TH 0 CC Undecaprenyl phosphate (Und-P) is synthesized de novo from farnesyl CC diphosphate via eight successive additions of isopentenyl diphosphate CC followed by a final removal of one phosphate. Und-P is used as a CC carrier for polysaccharide units via a pyrophosphate linkage. Removal CC of the polysaccharide results in Und-PP, so the phosphatase is also CC used in the recycling back to Und-P. -- SN 1 ID Source of isopentenyl diphosphate (IPP) DN Source of isopentenyl diphosphate (IPP) RQ 1 EV GenProp0046; -- SN 2 ID Undecaprenyl-diphosphate phosphohydrolase DN Undecaprenyl-diphosphate phosphohydrolase RQ 1 EV IPR003824; TIGR00753; -- SN 3 ID Undecaprenyl-diphosphate synthase DN Undecaprenyl-diphosphate synthase RQ 1 EV IPR001441; TIGR00055; // AC GenProp0972 DE dTDP-4-acetamido-4,6-dideoxy-D-galactose (dTDP-Fuc4NAc) biosynthesis TP METAPATH AU Haft DH TH 0 CC A surface polysaccharide common to all Enterobacteria (the CC enterobacterial common antigen, or ECA) consists of a trisaccharide CC repeating unit: Fuc4NAc-ManNAcA-GlcNAc. Fuc4NAc is CC 4-acetamido-4,6-dideoxy-D-galactose. -- SN 1 ID TDP-D-fucosamine acetyltransferase, WecD, RffC DN TDP-D-fucosamine acetyltransferase, WecD, RffC RQ 1 EV IPR012752; TIGR02382; -- SN 2 ID TDP-4-keto-6-deoxy-D-glucose transaminase DN TDP-4-keto-6-deoxy-D-glucose transaminase RQ 1 EV IPR012749; TIGR02379; -- SN 3 ID Source of 4,6-dideoxy-4-oxo-dTDP-D-glucose DN Source of 4,6-dideoxy-4-oxo-dTDP-D-glucose RQ 1 EV GenProp0950; // AC GenProp0975 DE Biosynthesis of UDP-N-acetyl-D-mannosamine (UDP-ManNAc) TP METAPATH AU Haft DH TH 0 CC UDP-ManNAc is a donor of N-acetylmannose for polysaccharide CC biosynthesis, and a precursor of other sugars such as CC N-acetylmannosaminic acid, N-acetylfucosamine. The final enzyme, CC UDP-N-acetylglucosamine 2-epimerase carries a variety of gene symbols CC (WecB, gne, RffE, FnlC) depending on its context. -- SN 1 ID Source of UDP-N-acetyl glucosamine (UDP-GlcNAc) DN Source of UDP-N-acetyl glucosamine (UDP-GlcNAc) RQ 1 EV GenProp0750; -- SN 2 ID UDP-N-acetyl glucosamine-2-epimerase (5.1.3.14), WecB, GNE DN UDP-N-acetyl glucosamine-2-epimerase (5.1.3.14), WecB, GNE RQ 1 EV IPR029767; TIGR00236; // AC GenProp0977 DE DNA ligase/helicase system TP SYSTEM AU Haft DH TH 0 CC This set of four proteins occurs in about 12 % of prokaryotic reference CC genomes (mostly Proteobacteria) and consists of an ATP-dependent DNA CC ligase, a DEXH-box helicase, a putative exonuclease, and putative CC metallohydrolase. This system may play a role in DNA repair. -- SN 1 ID Metallophosphoesterase, DNA ligase-associated DN Metallophosphoesterase, DNA ligase-associated RQ 1 EV IPR026336; TIGR04123; -- SN 2 ID Exonuclease, DNA ligase-associated DN Exonuclease, DNA ligase-associated RQ 1 EV IPR026360; TIGR04122; -- SN 3 ID DEXH box helicase, DNA ligase-associated DN DEXH box helicase, DNA ligase-associated RQ 1 EV IPR026362; TIGR04121; -- SN 4 ID DNA ligase, PP_1105 family DN DNA ligase, PP_1105 family RQ 1 EV IPR026333; TIGR04120; // AC GenProp0978 DE Protein sorting system, PGF-CTERM/archaeosortase A TP SYSTEM AU Haft DH TH 0 CC This Genome Property is a strictly archaeal, presumed protein sorting CC system featuring a variant class of exosortase (TIGR04125) and up to CC fifteen target proteins per genome with a PGF-CTERM target sequence CC (TIGR04126). -- SN 1 ID PGF_CTERM archaeosortase target domain DN PGF_CTERM archaeosortase target domain RQ 1 EV IPR026371; TIGR04126; -- SN 2 ID Archaeosortase, PGF_CTERM-specific DN Archaeosortase, PGF_CTERM-specific RQ 1 EV IPR014522; TIGR04125; -- SN 3 ID Oligosaccharyl transferase, archaeosortase system-associated DN Oligosaccharyl transferase, archaeosortase system-associated RQ 1 EV IPR026410; TIGR04154; // AC GenProp0979 DE Protein sorting system, PEF-CTERM/archaeosortase C TP SYSTEM AU Haft DH TH 0 CC This Genome Property is a strictly archaeal presumed protein sorting CC system, featuring a variant class of exosortase (TIGR03762) and several CC target proteins per genome with the PEF-CTERM target sequence (TIGR03024). -- SN 1 ID PEF_CTERM archaeal exosortase target domain DN PEF_CTERM archaeal exosortase target domain RQ 1 EV IPR017474; TIGR03024; -- SN 2 ID Exosortase, archaeal PEF_CTERM-specific DN Exosortase, archaeal PEF_CTERM-specific RQ 1 EV IPR022504; TIGR03762; // AC GenProp0980 DE Protein sorting system, putative, exosortase F class TP SYSTEM AU Haft DH TH 0 CC This system occurs in the lineage Bacteriodetes, and contains a homolog CC to exosortase (EpsH). Like archaeal homologs, it is shorter by about 70 CC amino acids towards the N terminus, and it lacks an EpsI-like domain. CC Species with this system lack a classical PEP-CTERM, PEF-CTERM, or CC PGF-CTERM-like protein sorting C-terminal domain. -- SN 1 ID Exosortase-related protein-associated protein DN Exosortase-related protein-associated protein RQ 1 EV IPR026414; TIGR04127; -- SN 2 ID Exosortase-related protein, flavobacterial DN Exosortase-related protein, flavobacterial RQ 1 EV IPR026323; TIGR04128; // AC GenProp0981 DE Radical SAM/lipoprotein system TP SYSTEM AU Haft DH TH 0 CC This tandem two gene system appears restricted to the Bacteroidetes CC and Fibrobacteres lineages (Bacteroides sp., Porphyromonas endodontalis, CC Prevotella ruminicola, Fibrobacter succinogenes, Alistipes putredinis, CC etc). One member is a putative lipoprotein, the other a putative CC peptide/protein-modifying radical SAM enzyme. -- SN 1 ID Lipoprotein, rSAM/lipoprotein system DN Lipoprotein, rSAM/lipoprotein system RQ 1 EV IPR026403; TIGR04134; -- SN 2 ID Radical SAM protein, rSAM/lipoprotein system DN Radical SAM protein, rSAM/lipoprotein system RQ 1 EV IPR026404; TIGR04133; // AC GenProp0982 DE Radical SAM maturase system, FibroRumin system TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This rare system consists of a peptide-modifying radical SAM enzyme and CC its cysteine-rich targets. In this system, the targets are encoded by CC tandem gene pairs. The maturase is similar in sequence, and the targets CC in their cysteine richness, to the analogous components of the SCIFF CC (Six Cysteines in Forty-Five) system. This system is known so far in CC Fibrobacter succinogenes subsp. succinogenes S85 (targets missed in CC gene-calling) and in Ruminococcus albus 8. -- SN 1 ID Radical SAM peptide maturase, FibroRumin system DN Radical SAM peptide maturase, FibroRumin system RQ 1 EV IPR026426; TIGR04136; -- SN 2 ID Cys-rich radical SAM target, FibroRumin family DN Cys-rich radical SAM target, FibroRumin family RQ 1 EV IPR026425; TIGR04135; // AC GenProp0983 DE Protein sorting system, VPXXXP-CTERM/archaeosortase B TP SYSTEM AU Haft DH TH 0 CC This Genome Property is a strictly archaeal, narrowly distributed CC protein sorting system, featuring a variant class of exosortase CC (TIGR04144) and five to nine target proteins per genome with the CC VPXXXP-CTERM target sequence (TIGR04143). Target proteins tend to be CC repetitive and most show extensive mutual sequence homology. The first CC identified species with this system are Methanohalophilus mahii DSM CC 5219 and Methanohalobium evestigatum Z-7303. -- SN 1 ID VPXXXP-CTERM archaeal exosortase target domain DN VPXXXP-CTERM archaeal exosortase target domain RQ 1 EV IPR026428; TIGR04143; -- SN 2 ID Exosortase, archaeal VPXXXP-CTERM-specific DN Exosortase, archaeal VPXXXP-CTERM-specific RQ 1 EV IPR026430; TIGR04144; // AC GenProp0984 DE Radical SAM maturase system, GG-Bacteroidales group TP SYSTEM AU Haft DH TH 0 RN [1] RM 21478363 RT Biological systems discovery in silico: radical S-adenosylmethionine RT protein families and their target peptides for posttranslational RT modification. RA Haft DH, Basu MK; RL J Bacteriol. 2011;193:2745-2755. CC This Genome Property is one of many in which a ribosomally translated CC peptide is modified post-translationally. Many of the natural products CC generated are bacteriocins, although bacteriocin activity cannot be CC presumed. An odd feature of this system is the pairing of a radical SAM CC enzyme (TIGR04148) with a degenerate radical SAM (pseudo-SAM) protein CC (TIGR04150). Despite full-length homology in family TIGR04150, some CC members have but others lack the radical SAM signature 4Fe4S-binding CC site. However, all members are best conserved at the C terminus, where CC the signature motif for the SPASM (Subtilosin, PQQ, Anaearobic CC Sulfatase and Mycofactocin maturases) domain homology 4Fe4S binding CC site is invariant. This system occurs, so far, only in the Bacteroidales. -- SN 1 ID Glycosyltransferase, GG-Bacteroidales peptide system DN Glycosyltransferase, GG-Bacteroidales peptide system RQ 1 EV IPR026419; TIGR04157; -- SN 2 ID Peptide-modifying radical SAM enzyme, GG-Bacteroidales family DN Peptide-modifying radical SAM enzyme, GG-Bacteroidales family RQ 1 EV IPR026407; TIGR04148; -- SN 3 ID Natural product precursor, GG-Bacteroidales family DN Natural product precursor, GG-Bacteroidales family RQ 1 EV IPR026408; TIGR04149; -- SN 4 ID Pseudo-rSAM protein, GG-Bacteroidales system DN Pseudo-rSAM protein, GG-Bacteroidales system RQ 1 EV IPR026418; TIGR04150; // AC GenProp0985 DE Protein sorting system, VPDSG-CTERM/exosortase C TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a bacterial rare variant exosortase CC protein sorting system, with protein sorting motif VPDSG-CTERM CC (TIGR03778) and its cognate exosortase (TIGR04151). -- SN 1 ID VPDSG-CTERM protein sorting domain DN VPDSG-CTERM protein sorting domain RQ 1 EV IPR022288; TIGR03778; -- SN 2 ID Exosortase, VPDSG-CTERM-specific DN Exosortase, VPDSG-CTERM-specific RQ 1 EV IPR026488; TIGR04151; // AC GenProp0987 DE Protein sorting system, cyano-PEP-CTERM class TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a uniquely cyanobacterial subclass of CC the PEP-CTERM/exosortase system, restricted to but found in nearly CC every cyanobacterium outside of Prochlorococcus. The PEP-CTERM variant CC is somewhat longer at its C terminus, with much stronger conservation CC throughout the transmembrane region. At least one of two forms of CC cyanobacterial-restricted exosortase (cyanosortase) always CC occurs as well, occasionally adjacent to a PEP-CTERM protein. -- SN 1 ID Exosortase, cyanobacterial-specific DN Exosortase, cyanobacterial-specific RQ 1 EV IPR022505; TIGR03763; EV IPR026492; TIGR04156; -- SN 2 ID PEP-CTERM protein, cyanosortase-specific DN PEP-CTERM protein, cyanosortase-specific RQ 1 EV IPR026374; TIGR04155; -- SN 3 ID Cyanoexosortase accessory protein 1 DN Cyanoexosortase accessory protein 1 RQ 0 EV IPR026411; TIGR04153; EV IPR030917; TIGR04533; // AC GenProp0988 DE Elongation factor P beta-lysylation TP SYSTEM AU Haft DH TH 0 RN [1] RM 20070887 RT Predicting the pathway involved in post-translational modification of RT elongation factor P in a subset of bacterial species. RA Bailly M, de Crécy-Lagard V; RL Biol Direct. 2010;5:3. RN [2] RM 20729861 RT A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine RT residue in translation elongation factor P. RA Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S; RL Nat Struct Mol Biol. 2010;17:1136-1143. RN [3] RM 22128152 RT Post-translational modification by β-lysylation is required for RT activity of Escherichia coli elongation factor P (EF-P). RA Park JH, Johansson HE, Aoki H, Huang BX, Kim HY, Ganoza MC, Park MH; RL J Biol Chem. 2012;287:2579-2590. RN [4] RM 22706199 RT Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. RA Peil L, Starosta AL, Virumäe K, Atkinson GC, Tenson T, Remme J, Wilson RA DN; RL Nat Chem Biol. 2012;8:695-697. CC This system consists of a lysyl-tRNA ligase homolog and a lysine CC 2,3-aminomutase homolog frequently encoded next to elongation factor P CC in bacteria and responsible for post-translational modification. -- SN 1 ID Elongation Factor P Lys34 hydroxylase DN Elongation Factor P Lys34 hydroxylase RQ 0 EV IPR007411; PF04315; -- SN 2 ID EF-P lysine aminoacylase GenX DN EF-P lysine aminoacylase GenX RQ 1 EV IPR004525; TIGR00462; -- SN 3 ID EF-P lysine modification enzyme DN EF-P lysine modification enzyme RQ 1 EV IPR022462; TIGR03821; // AC GenProp0989 DE Protein sorting system, VPEID-CTERM/exosortase E TP SYSTEM AU Haft DH TH 0 CC This protein-sorting system occurs so far only in the alpha CC Proteobacteria. The system is largely dedicated, in the sense that the CC presumed substrate is usually one-per-genome and usually adjacent. CC Substrates contain the motif (V)PEID and are among the smallest of any CC proposed exosortase targets. The processing enzyme is an unusual fusion CC of an N-terminal exosortase region and a C-terminal region related to CC eukaryotic CAAX prenyl proteases and bacterial bacteriocin CC self-immunity proteins. -- SN 1 ID Exosortase/CAAX-like protease, VPEID-CTERM system DN Exosortase/CAAX-like protease, VPEID-CTERM system RQ 1 EV IPR026420; TIGR04162; -- SN 2 ID VPEID-CTERM protein sorting domain DN VPEID-CTERM protein sorting domain RQ 1 EV IPR026422; TIGR04161; // AC GenProp0991 DE ATP-grasp maturase system, microviridin/marinostatin class TP PATHWAY AU Haft DH TH 0 RN [1] RM 19035375 RT Post-translational modification in microviridin biosynthesis. RA Philmus B, Christiansen G, Yoshida WY, Hemscheidt TK; RL Chembiochem. 2008;9:3066-3073. CC Microviridins, marinostatins, and related peptide natural products CC become circularized into tricyclic depsipeptides, and serve as CC proteinase inhibitors. Characteristic proteins of their biosynthesis CC cassettes include a pair of closely related ATP-grasp proteins. -- SN 1 ID ATP-grasp family maturase 1 DN ATP-grasp family maturase 1 RQ 1 EV IPR026446; TIGR04185; -- SN 2 ID ATP-grasp family maturase 2 DN ATP-grasp family maturase 2 RQ 1 EV IPR026439; TIGR04184; -- SN 3 ID Microviridin/marinostatin family precursor DN Microviridin/marinostatin family precursor RQ 1 EV IPR022217; PF12559; // AC GenProp0992 DE Radical SAM maturase system, methanogen TP SYSTEM AU Haft DH TH 0 CC This system, which is restricted to a subset of archaea, always CC contains a radical SAM enzyme belonging to the peptide maturase CC subclass. A small protein encoded nearby in a couple of cases, CC is Cys-rich because of two CXXCG motifs, but that arrangement CC suggests ligand activity rather than post-translational CC modification. -- SN 1 ID Radical SAM probable peptide maturase DN Radical SAM probable peptide maturase RQ 1 EV IPR024018; TIGR04083; // AC GenProp0993 DE Protein sorting system, PIP-CTERM/archaeosortase D TP SYSTEM AU Haft DH TH 0 CC This Genome Property is a strictly archaeal dedicated protein sorting CC system, featuring a variant class of archaeosortase (TIGR04175) and CC always exactly one target protein, with target sequence PIP-CTERM CC (TIGR04173). In each cassette known so far, a short protein with a CC class III signal peptide sits between the two enzymes. -- SN 1 ID PIP-CTERM protein sorting domain DN PIP-CTERM protein sorting domain RQ 1 EV IPR026495; TIGR04173; -- SN 2 ID Archaeosortase D DN Archaeosortase D RQ 1 EV IPR026432; TIGR04175; -- SN 3 ID Class III signal peptide protein DN Class III signal peptide protein RQ 1 EV IPR026451; TIGR04205; // AC GenProp0996 DE Protein sorting system, IPTLxxWG-CTERM/exosortase H TP SYSTEM AU Haft DH TH 0 CC This system consists of a distinctive subfamily of exosortase-like CC proteins and their target sequences in bacteria. Target sequences have CC a signature motif approximated by IPTLxxWG. The processing enzyme is CC exosortase H. -- SN 1 ID Exosortase H DN Exosortase H RQ 1 EV IPR026441; TIGR04177; -- SN 2 ID IPTLxxWG-CTERM protein sorting domain DN IPTLxxWG-CTERM protein sorting domain RQ 1 EV IPR026442; TIGR04174; // AC GenProp0999 DE Por secretion system TP SYSTEM AU Haft DH TH 0 RN [1] RM 21731719 RT Por secretion system-dependent secretion and glycosylation of RT Porphyromonas gingivalis hemin-binding protein 35. RA Shoji M, Sato K, Yukitake H, Kondo Y, Narita Y, Kadowaki T, Naito M, RA Nakayama K; RL PLoS One. 2011;6:e21372. RN [2] RM 20971915 RT C-terminal domain residues important for secretion and attachment of RT RgpB in Porphyromonas gingivalis. RA Slakeski N, Seers CA, Ng K, Moore C, Cleal SM, Veith PD, Lo AW, RA Reynolds EC; RL J Bacteriol. 2011;193:132-142. RN [3] RM 19966289 RT A protein secretion system linked to bacteroidete gliding motility and RT pathogenesis. RA Sato K, Naito M, Yukitake H, Hirakawa H, Shoji M, McBride MJ, Rhodes RA RG, Nakayama K; RL Proc Natl Acad Sci U S A. 2010;107:276-281. CC This property describes large paralogous families of C-terminal domains CC shared by proteins destined for outer membrane locations. These occur CC in a range of species that include Porphyromonas gingivalis, Fibrobacter CC succinogenes, Flavobacterium johnsoniae, Cytophaga hutchinsonii, Gramella CC forsetii, Prevotella intermedia, and Salinibacter ruber. -- SN 1 ID Por secretion C-terminal signal DN Por secretion C-terminal signal RQ 1 EV IPR026444; TIGR04183; // AC GenProp1000 DE ATP-grasp maturase system, uncharacterized TP SYSTEM AU Haft DH TH 0 RN [1] RM 20023723 RT Amidoligases with ATP-grasp, glutamine synthetase-like and RT acetyltransferase-like domains: synthesis of novel metabolites and RT peptide modifications of proteins. RA Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L; RL Mol Biosyst. 2009;5:1636-1660. CC The microviridin family is an example of ribosomally produced, CC post-translationally modified peptides (RiPP) for which the peptide CC maturases come from the ATP-grasp ligase family. This Genome Property CC describes a cassette with a related ATP-grasp enzyme (TIGR04187), a CC putative target family, and a methyltransferase (TIGR04188). We CC propose the name TgmABC (Target/Grasp/Methyltransferase ABC) for the CC system. -- SN 1 ID ATP-grasp family maturase DN ATP-grasp family maturase RQ 1 EV IPR026449; TIGR04187; -- SN 2 ID Methyltransferase DN Methyltransferase RQ 1 EV IPR026448; TIGR04188; -- SN 3 ID Ribosomal peptide modification target DN Ribosomal peptide modification target RQ 1 EV IPR026496; TIGR04186; EV IPR025744; PF14404; // AC GenProp1002 DE Grasp-with-spasm peptide maturase system TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a Post-Ribosomal Natural Product CC Synthesis (PRNPS) system that features an ATP-GRASP domain protein and CC a SPASM domain protein. At least one associated leader peptide family CC is also defined. -- SN 1 ID Grasp-with-spasm ATP-GRASP maturase DN Grasp-with-spasm ATP-GRASP maturase RQ 1 EV IPR026455; TIGR04192; -- SN 2 ID Grasp-with-spasm leader peptide DN Grasp-with-spasm leader peptide RQ 0 EV IPR026498; TIGR04194; EV IPR026437; TIGR04139; -- SN 3 ID Grasp-with-spasm SPASM domain maturase DN Grasp-with-spasm SPASM domain maturase RQ 1 EV IPR026497; TIGR04193; // AC GenProp1003 DE Cysteine S-glycopeptide biosynthesis, sublancin family TP SYSTEM AU Haft DH TH 0 RN [1] RM 21196935 RT Sublancin is not a lantibiotic but an S-linked glycopeptide. RA Oman TJ, Boettcher JM, Wang H, Okalibe XN, van der Donk WA; RL Nat Chem Biol. 2011;7:78-80. CC Sublancin is an antibiotic bacterial peptide with a monosaccharide CC (glucose) added to a Cys side chain sulfur, in addition to having two CC disulfide bonds. This Genome Property represents components of the CC system, including the precursor and the S-glycosyltransferase. -- SN 1 ID S-glycopeptide, SunA family DN S-glycopeptide, SunA family RQ 1 EV IPR026479; TIGR04196; -- SN 2 ID Peptide cysteine S-glycosyltransferase, SunS family DN Peptide cysteine S-glycosyltransferase, SunS family RQ 1 EV IPR026499; TIGR04195; TG GO:0016144; // AC GenProp1004 DE Light-independent protochlorophyllide reductase TP SYSTEM AU Haft DH TH 0 CC Protochlorophyllide reductase is the final step in the biosynthesis of CC chlorophyllide a from protoporphyrin IX. This genome property CC represents the three-component, light-independent protochlorophyllide CC reductase. There is also a separate light-dependent protochlorophyllide CC reductase which is not covered by this property. -- SN 1 ID Protochlorophyllide reductase, ChlB DN Light-independent protochlorophyllide reductase subunit B (EC 1.3.7.7) RQ 1 EV IPR005969; TIGR01278; sufficient; -- SN 2 ID Protochlorophyllide reductase, iron protein subunit BchL DN Light-independent protochlorophyllide reductase iron-sulphur component/ChlL/BchL (EC 1.3.7.7) RQ 1 EV IPR005971; TIGR01281; sufficient; -- SN 3 ID Protochlorophyllide reductase, ChlN DN Light-independent protochlorophyllide reductase subunit N (EC 1.3.7.7) RQ 1 EV IPR005970; TIGR01279; sufficient; // AC GenProp1005 DE Protein sorting system, putative, exosortase J class TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a paralogous system from Acidobacterium CC sp. MP5ACTX8. One component is a novel exosortase subtype designated CC XrtJ, with a large unique C-terminal region. The other component is its CC putative target, consisting of an N-terminal signal sequence ending in CC a suggestive GC motif, then a PEP-CTERM-like motif PExP, then a CC C-terminal transmembrane domain ending in a basic cluster, all in ~ 62 CC residues. -- SN 1 ID Exosortase J DN Exosortase J RQ 1 EV IPR026478; TIGR04199; -- SN 2 ID TM-motif-TM protein, XrtJ-associated DN TM-motif-TM protein, XrtJ-associated RQ 1 EV IPR026477; TIGR04200; // AC GenProp1006 DE Orbivirus protein set TP SYSTEM AU Haft DH TH 0 RN [1] RM 20428242 RT Full genome characterisation of bluetongue virus serotype 6 from the RT Netherlands 2008 and comparison to other field and vaccine strains. RA Maan S, Maan NS, van Rijn PA, van Gennip RG, Sanders A, Wright IM, RA Batten C, Hoffmann B, Eschbaumer M, Oura CA, Potgieter AC, Nomikou K, RA Mertens PP; RL PLoS One. 2010;5:e10323. RN [2] RM 21808007 RT In vitro reconstitution of Bluetongue virus infectious cores. RA Lourenco S, Roy P; RL Proc Natl Acad Sci U S A. 2011;108:13746-13751. RN [3] RM 22022432 RT Detection of a fourth orbivirus non-structural protein. RA Belhouchet M, Mohd Jaafar F, Firth AE, Grimes JM, Mertens PP, Attoui H; RL PLoS One. 2011;6:e25697. CC This Genome Property collects HMMs that describe characteristic CC proteins from examples of orbivirus such as bluetongue virus (BTV). CC These viruses are dsRNA, segmented, and include a number of mammalian CC pathogens transmitted by arthropod vectors. Note that NS3A from BTV CC differs from NS3 by starting from an alternate initiator that makes it CC 13 amino acids shorter. -- SN 1 ID Tubule protein NS1 DN Tubule protein NS1 RQ 1 EV IPR002630; PF01718; -- SN 2 ID Inclusion body matrix protein NS2 DN Inclusion body matrix protein NS2 RQ 1 EV IPR007602; PF04514; -- SN 3 ID Nonstructural protein NS3/NS3A DN Nonstructural protein NS3/NS3A RQ 1 EV IPR002565; PF01616; -- SN 5 ID RNA-dependent RNA polymerase VP1 DN RNA-dependent RNA polymerase VP1 RQ 1 EV IPR008723; PF05788; -- SN 6 ID Outer capsid protein VP2 DN Outer capsid protein VP2 RQ 1 EV IPR001742; PF00898; -- SN 7 ID Inner capsid protein VP3 DN Inner capsid protein VP3 RQ 1 EV IPR002614; PF01700; -- SN 8 ID Capping/transmethylase enzyme VP4 DN Capping/transmethylase enzyme VP4 RQ 1 EV IPR007753; PF05059; -- SN 9 ID Outer capsid protein VP5 DN Outer capsid protein VP5 RQ 1 EV IPR000145; PF00901; -- SN 10 ID Helicase VP6 DN Helicase VP6 RQ 1 EV IPR001399; PF01516; -- SN 11 ID Inner capsid protein VP7 DN Inner capsid protein VP7 RQ 1 EV IPR001803; PF00897; // AC GenProp1007 DE Orthobunyavirus protein set TP SYSTEM AU Haft DH TH 0 CC This Genome Property collects HMMs that describe characteristic CC proteins from examples of bunyavirus such as Oropouche virus, a CC segmented, negative-strand ssRNA animal virus. Notable features include CC a polyprotein with glycoprotein G2, nonstructural protein NSm, and CC glycoprotein G1 encoded by the M segment, an RNA polymerase encoded on CC segment L, and overlapping reading frames on the S segment encoding CC nucleocapsid protein N and nonstructural protein NSs. -- SN 1 ID Glycoprotein G1 DN Glycoprotein G1 RQ 1 EV IPR005167; PF03557; -- SN 2 ID Glycoprotein G2 DN Glycoprotein G2 RQ 1 EV IPR005168; PF03563; -- SN 3 ID Bunyavirus nucleocapsid protein DN Bunyavirus nucleocapsid protein RQ 1 EV IPR001784; PF00952; -- SN 4 ID Non-structural protein NS-m DN Non-structural protein NS-m RQ 1 EV IPR026400; TIGR04210; -- SN 5 ID Non-structural protein NS-s DN Non-structural protein NS-s RQ 1 EV IPR000797; PF01104; -- SN 6 ID RNA-dependent RNA polymerase DN RNA-dependent RNA polymerase RQ 1 EV IPR007322; PF04196; // AC GenProp1009 DE Coronavirus protein set TP SYSTEM AU Haft DH TH 0 CC A coronavirus is an unsegmented ssRNA positive-strand enveloped virus CC with no DNA stage. A -1 frameshift can occur in production of the CC replicase polyprotein. -- SN 1 ID Nonstructural protein NS3/small envelope DN Nonstructural protein NS3/small envelope RQ 1 EV IPR003873; PF02723; -- SN 2 ID Coronavirus nonstructural protein NS1 DN Coronavirus nonstructural protein NS1 RQ 0 EV IPR009314; PF06145; -- SN 3 ID Replicase polyprotein NSP10 region DN Replicase polyprotein NSP10 region RQ 1 EV IPR018995; PF09401; -- SN 4 ID Coronavirus replicase polyprotein NSP11 region DN Coronavirus replicase polyprotein NSP11 region RQ 1 EV IPR009466; PF06471; -- SN 5 ID Replicase polyprotein NSP13 region DN Replicase polyprotein NSP13 region RQ 1 EV IPR009461; PF06460; -- SN 6 ID Coronavirus nonstructural protein NS2 DN Coronavirus nonstructural protein NS2 RQ 1 EV IPR006841; PF04753; -- SN 7 ID Main protease DN Main protease RQ 1 EV IPR008740; PF05409; -- SN 8 ID Replicase polyprotein NSP7 region DN Replicase polyprotein NSP7 region RQ 1 EV IPR014828; PF08716; -- SN 9 ID Replicase polyprotein NSP8 region DN Replicase polyprotein NSP8 region RQ 1 EV IPR014829; PF08717; -- SN 10 ID Replicase polyprotein NSP9 region DN Replicase polyprotein NSP9 region RQ 1 EV IPR014822; PF08710; -- SN 11 ID Papain-like protease DN Papain-like protease RQ 1 EV IPR014827; PF08715; -- SN 12 ID RNA-directed RNA Polymerase (N-terminal region) DN RNA-directed RNA Polymerase (N-terminal region) RQ 1 EV IPR009469; PF06478; -- SN 13 ID Coronavirus M matrix/glycoprotein DN Coronavirus M matrix/glycoprotein RQ 1 EV IPR002574; PF01635; -- SN 14 ID Corona nucleocapsid I protein DN Corona nucleocapsid I protein RQ 1 EV IPR004876; PF03187; -- SN 15 ID Coronavirus nucleocapsid protein DN Coronavirus nucleocapsid protein RQ 1 EV IPR001218; PF00937; -- SN 16 ID Coronavirus S1 glycoprotein DN Coronavirus S1 glycoprotein RQ 0 EV IPR002551; PF01600; -- SN 17 ID Coronavirus S2 glycoprotein DN Coronavirus S2 glycoprotein RQ 1 EV IPR002552; PF01601; // AC GenProp1010 DE Accessory Sec system, Actinobacterial type TP SYSTEM AU Haft DH TH 0 RN [1] RM 11717254 RT Two nonredundant SecA homologues function in mycobacteria. RA Braunstein M, Brown AM, Kurtz S, Jacobs WR; RL J Bacteriol. 2001;183:6979-6990. RN [2] RM 17496088 RT Identification of two Mycobacterium smegmatis lipoproteins exported by RT a SecA2-dependent pathway. RA Gibbons HS, Wolschendorf F, Abshire M, Niederweis M, Braunstein M; RL J Bacteriol. 2007;189:5090-5100. CC The gene symbol secA2 arose twice in the literature for accessory CC secretory systems acting in addition to the SecA (pre)protein CC translocase system. This genome property describes the form as it CC occurs in Mycobacterium tuberculosis and M. smegmatis. The two SecA2 CC families are both related to SecA but probably are not orthologous to CC each other. -- SN 1 ID Accessory Sec system translocase SecA2 DN Accessory Sec system translocase SecA2 RQ 1 EV IPR026389; TIGR04221; // AC GenProp1011 DE Quorum-sensing system, cyclic peptide-mediated TP SYSTEM AU Haft DH TH 0 RN [1] RM 16980448 RT Revised model for Enterococcus faecalis fsr quorum-sensing system: the RT small open reading frame fsrD encodes the gelatinase RT biosynthesis-activating pheromone propeptide corresponding to RT staphylococcal agrd. RA Nakayama J, Chen S, Oyama N, Nishiguchi K, Azab EA, Tanaka E, Kariyama RA R, Sonomoto K; RL J Bacteriol. 2006;188:8321-8326. CC The four characterized components of the staphylococcal agr system are a CC propeptide, a processing enzyme, a histidine kinase (AgrC), and a CC response regulator (AgrA). In the related Enterococcus faecalis fsr CC system, the propeptide occurs as an extension of the processing enzyme, CC may be autoprocessed from it, and may also be independently translated. -- SN 1 ID Processing enzyme DN Processing enzyme RQ 1 EV IPR006741; PF04647; -- SN 2 ID Autoinducing peptide DN Autoinducing peptide RQ 1 EV IPR009229; PF05931; // AC GenProp1012 DE Influenzae A virus protein set TP SYSTEM AU Haft DH TH 0 CC Segment 1 has PB2. Segment 2 has PB1 and PB1-F2 (overlapped). Segment 3 CC has PA. Segment 4 has hemagglutinin. Segment 5 has nucleocapsid. CC Segment 6 has neuraminidase. Segment 7 has M1 and M2. Segment 8 has NS2 CC and NS1. -- SN 1 ID Nonstructural protein PB1-F2 DN Nonstructural protein PB1-F2 RQ 1 EV IPR021045; PF11986; -- SN 2 ID Matrix protein 1 DN Matrix protein 1 RQ 1 EV IPR001561; PF00598; -- SN 3 ID Matrix protein 2 DN Matrix protein 2 RQ 1 EV IPR002089; PF00599; -- SN 4 ID Neuraminidase DN Neuraminidase RQ 1 EV IPR001860; PF00064; -- SN 5 ID Nucleocapsid DN Nucleocapsid RQ 1 EV IPR002141; PF00506; -- SN 6 ID Nonstructural protein 1 DN Nonstructural protein 1 RQ 1 EV IPR000256; PF00600; -- SN 7 ID Nuclear export protein DN Nuclear export protein RQ 1 EV IPR000968; PF00601; -- SN 8 ID RNA-dependent RNA polymerase subunit PA DN RNA-dependent RNA polymerase subunit PA RQ 1 EV IPR001009; PF00603; -- SN 9 ID RNA-dependent RNA polymerase subunit PB1 DN RNA-dependent RNA polymerase subunit PB1 RQ 1 EV IPR001407; PF00602; -- SN 10 ID Influenza RNA-dependent RNA polymerase subunit PB2 DN Influenza RNA-dependent RNA polymerase subunit PB2 RQ 1 EV IPR001591; PF00604; -- SN 11 ID Hemagglutinin DN Hemagglutinin RQ 1 EV IPR001364; PF00509; // AC GenProp1013 DE Influenzae B virus protein set TP SYSTEM AU Haft DH TH 0 CC Proteins of influenzae B differ somewhat from influenzae A. B-specific CC proteins include a different matrix protein 2 (PF04772), a different CC nonstructural protein 1 (PF02942), and NB glycoprotein (PF04159) which CC overlaps the neuraminidase coding region. -- SN 1 ID Matrix protein BM2 DN Matrix protein BM2 RQ 1 EV IPR006859; PF04772; -- SN 2 ID NB glycoprotein DN NB glycoprotein RQ 1 EV IPR007288; PF04159; -- SN 3 ID Nonstructural protein NS1 DN Nonstructural protein NS1 RQ 1 EV IPR004208; PF02942; // AC GenProp1016 DE Seadornavirus protein set TP SYSTEM AU Haft DH TH 0 RN [1] RM 10811934 RT Complete sequence determination and genetic analysis of Banna virus and RT Kadipiro virus: proposal for assignment to a new genus (Seadornavirus) RT within the family Reoviridae. RA Attoui H, Billoir F, Biagini P, de Micco P, de Lamballerie X; RL J Gen Virol. 2000;81:1507-1515. CC The seadornavirus group belongs to the parent group Reoviridae, and CC more specifically, subgroup B in the Coltivirus group. Examples include CC Banna virus, Kadipiro virus, and Liao ning virus. The VP-series names CC differ, so Banna virus designations will be used when a functional name CC cannot be assigned. These segmented RNA viruses have twelve segments CC with one recognized coding region on each. -- SN 1 ID RNA-dependent RNA polymerase DN RNA-dependent RNA polymerase RQ 1 EV IPR026381; TIGR04234; -- SN 2 ID Seadornavirus VP10 protein DN Seadornavirus VP10 protein RQ 1 EV IPR009930; PF07322; -- SN 3 ID Seadornavirus VP11 protein DN Seadornavirus VP11 protein RQ 1 EV IPR026378; TIGR04230; -- SN 4 ID Seadornavirus dsRNA-binding protein DN Seadornavirus dsRNA-binding protein RQ 1 EV IPR026388; TIGR04238; -- SN 5 ID Seadornavirus VP2 protein DN Seadornavirus VP2 protein RQ 1 EV IPR026384; TIGR04236; -- SN 6 ID Seadornavirus VP3 protein DN Seadornavirus VP3 protein RQ 1 EV IPR026379; TIGR04232; -- SN 7 ID Seadornavirus VP4 protein DN Seadornavirus VP4 protein RQ 1 EV IPR026383; TIGR04235; -- SN 8 ID Seadornavirus VP5 protein DN Seadornavirus VP5 protein RQ 1 EV IPR026373; TIGR04231; -- SN 9 ID Seadornavirus VP6 protein DN Seadornavirus VP6 protein RQ 1 EV IPR009982; PF07407; -- SN 10 ID Seadornavirus VP7 protein DN Seadornavirus VP7 protein RQ 1 EV IPR009973; PF07387; -- SN 11 ID Seadornavirus VP8 protein DN Seadornavirus VP8 protein RQ 1 EV IPR026380; TIGR04233; -- SN 12 ID Seadornavirus VP9 protein DN Seadornavirus VP9 protein RQ 1 EV IPR015072; PF08978; EV IPR015072; TIGR04237; // AC GenProp1017 DE GDP-D-mannose biosynthesis from b-D-fructose-6-phosphate TP PATHWAY AU Haft DH TH 0 CC GDP-D-mannose is used as a source of mannose when coupled with the gmm CC enzyme, as a source of GDP-4-keto-6-deoxymannose when coupled with the CC gmd enzyme (and then subsequently used to make fucose, perosamine and CC colicin and their derivatives). GDP-mannose may also be incorporated CC directly into polysaccharides such as the E. coli O8 and O9 antigens CC and the Klebsiella O5 antigen. The pathway consists of three acivities, CC an isomerase, a phosphomutase and a guanylyl transferase. The first and CC last steps are often catalyzed by a fusion protein (ManAC). -- SN 1 ID GDP-mannose mannosyl hydrolase DN GDP-mannose mannosyl hydrolase/gmm RQ 0 EV IPR000086; PF00293; -- SN 2 ID Mannose-6P-isomerase DN Mannose-6P-isomerase/manA RQ 1 EV IPR006375; TIGR01479; -- SN 3 ID Phosphomannomutase DN Phosphomannomutase/manB RQ 1 EV IPR005843; PF00408; EV IPR005844; PF02878; EV IPR005846; PF02880; EV IPR005845; PF02879; -- SN 4 ID Mannose-1P-guanylyltransferase DN Mannose-1P-guanylyltransferase/manC RQ 1 EV IPR006375; TIGR01479; // AC GenProp1026 DE Nodulation factor production TP SYSTEM AU Haft DH TH 0 RN [1] RM 8986807 RT The common nodABC genes of Rhizobium meliloti are host-range RT determinants. RA Roche P, Maillet F, Plazanet C, Debellé F, Ferro M, Truchet G, Promé RA JC, Dénarié J; RL Proc Natl Acad Sci U S A. 1996;93:15305-15310. RN [2] RM 8930915 RT The NodA proteins of Rhizobium meliloti and Rhizobium tropici specify RT the N-acylation of Nod factors by different fatty acids. RA Debellé F, Plazanet C, Roche P, Pujol C, Savagnac A, Rosenberg C, RA Promé JC, Dénarié J; RL Mol Microbiol. 1996;22:303-314. CC The gene trio nodABC, found in non-photosynthetic rhizobia such as CC Rhizobium meliloti that form root (not stem) nodules, produce the CC enzymes that create Nod factors. These mono-N-acylated CC chitooligosaccharide signals not only trigger the establishment of CC nitrogen-fixing root nodules, but also vary in ways that determine host CC range. -- SN 1 ID Nodulation N-acyltransferase NodA DN Nodulation N-acyltransferase NodA RQ 1 EV IPR003484; TIGR04245; -- SN 2 ID Chitooligosaccharide deacetylase NodB DN Chitooligosaccharide deacetylase NodB RQ 1 EV IPR026402; TIGR04243; -- SN 3 ID Chitooligosaccharide synthase NodC DN Chitooligosaccharide synthase NodC RQ 1 EV IPR026463; TIGR04242; // AC GenProp1032 DE dTDP-4-dehydro-L-rhamnose biosynthesis from dTDP-4-dehydro-6-deoxy-alpha-D-glucose TP METAPATH AU Haft DH, Richardson L TH 0 RN [1] RM 12773151 RT A structural perspective on the enzymes that convert dTDP-d-glucose RT into dTDP-l-rhamnose. RA Dong C, Beis K, Giraud MF, Blankenfeldt W, Allard S, Major LL, Kerr RA ID, Whitfield C, Naismith JH; RL Biochem Soc Trans. 2003;31:532-536. RN [2] RM 10802738 RT RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of RT epimerase. RA Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH; RL Nat Struct Biol. 2000;7:398-402. DC Streptomycin biosynthesis DR KEGG; map00521; DC dTDP-L-rhamnose biosynthesis I DR MetaCyc; DTDPRHAMSYN-PWY; CC L-rhamnose is a common component of the bacterial capsule and/or cell wall, CC and is important in bacterial survival during infection. dTDP-L-rhamnose is CC the precursor of L-rhamnose[1,2]. dTDP-L-rhamnose is synthesized from CC glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a four-step CC enzymatic pathway. The four enzymes are: glucose-1-phosphate CC thymidyltransferase (also known as dTDP-glucose pyrophosphorylase, gene CC name rlmA or rfbA); dTDP-D-glucose 4,6-dehydratase (gene name rmlB or CC rfbB); dTDP-4-dehydrorhamnose 3,5-epimerase (also known as CC dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase, gene name rmlC or rfbC); and CC dTDP-4-dehydrorhamnose reductase (also known as CC dTDP-6-deoxy-L-lyxo-4-hexulose reductase (gene name rmlD or rfbD)[1,2]. CC This property refers to the third step in this pathway, the conversion of CC dTDP-4-dehydro-6-deoxy-alpha-D-glucose to dTDP-4-dehydro-L-rhamnose. CC dTDP-4-dehydro-L-rhamnose is a precursor of both dTDP-L-rhamnose and CC dTDP-6-deoxy-L-talose. -- SN 1 ID Source of 4,6-dideoxy-4-oxo-dTDP-D-glucose RQ 1 EV GenProp0950; -- SN 2 ID dTDP-4-dehydrorhamnose 3,5-epimerase DN dTDP-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) RQ 1 EV IPR000888; TIGR01221; // AC GenProp1034 DE Decarboxylation/antiport proton-motive cycle: oxalate-formate TP METAPATH AU Haft DH TH 0 RN [1] RM 7823041 RT Bacterial anion exchange: reductionist and integrative approaches to RT membrane biology. RA Maloney PC, Yan RT, Abe K; RL J Exp Biol. 1994;196:471-482. RN [2] RM 2708365 RT Oxalate:formate exchange. The basis for energy coupling in Oxalobacter. RA Anantharam V, Allison MJ, Maloney PC; RL J Biol Chem. 1989;264:7244-7250. RN [3] RM 18359395 RT The roles and mechanisms of intestinal oxalate transport in oxalate RT homeostasis. RA Hatch M, Freel RW; RL Semin Nephrol. 2008;28:143-151. CC This Genome Property represents a proton-motive cycle. The cycle of CC decarboxylating oxalate, a dicarboxylic acid, to formate plus CO2, then CC exchanging the cytosolic formate for an extracellular oxalate, has the CC net effect of consuming one proton. This property has been studied CC extensively in Oxalobacter formigenes, which appears in the human CC microbiome and affects oxalate homeostasis. -- SN 1 ID Decarboxylation DN Decarboxylation RQ 1 EV GenProp0718; -- SN 2 ID Oxalate/formate antiporter DN Oxalate/formate antiporter RQ 1 EV IPR026355; TIGR04259; // AC GenProp1037 DE Radical SAM/SPASM system GRRM TP SYSTEM AU Haft DH TH 0 CC This system contains at least two proteins. One is a protein about 150 CC amino acids in length, with the last 60 highly repetitive and usually CC Gly-rich. In a number of genomes, the gene call was not made. The other CC is a radical SAM/SPASM domain protein that may be a protein maturase CC active on the amino acids in the repeat region of the Gly-rich protein. -- SN 1 ID RSAM-associated Gly-rich repeat protein DN RSAM-associated Gly-rich repeat protein RQ 1 EV IPR026356; TIGR04260; -- SN 2 ID Radical SAM/SPASM domain protein, GRRM system DN Radical SAM/SPASM domain protein, GRRM system RQ 1 EV IPR026357; TIGR04261; -- SN 3 ID Extracellular substrate-binding orphan protein DN Extracellular substrate-binding orphan protein RQ 0 EV IPR026358; TIGR04262; // AC GenProp1048 DE Quorum-sensing, biofilm formation, and developmental systems TP CATEGORY AU Haft DH TH 0 CC This category unites properties describing microbial processes that CC coordinate behavior between cells. These include quorum-sensing, CC biofilm formation, and various other signal-mediated interactions. -- SN 1 ID Exopolysaccharide biosynthesis, exosortase A-associated RQ 0 EV GenProp0652; -- SN 2 ID Exopolysaccharide biosynthesis, exosortase B-associated RQ 0 EV GenProp0655; -- SN 3 ID Quorum-sensing, autoinducer-2 system RQ 0 EV GenProp0757; -- SN 4 ID Quorum-sensing system, cyclic peptide-mediated RQ 0 EV GenProp1011; // AC GenProp1052 DE Geopeptide radical SAM/SPASM maturase system TP SYSTEM AU Haft DH TH 0 CC The core of this system is a putative peptide-modifying radical SAM CC family and its putative target, a short peptide with a Cys-Cys motif. -- SN 1 ID Geopeptide precursor DN Geopeptide precursor RQ 1 EV IPR026376; TIGR04229; -- SN 2 ID Geopeptide radical SAM maturase DN Geopeptide radical SAM maturase RQ 1 EV IPR026322; TIGR04280; // AC GenProp1053 DE RSAM/selenodomain system TP SYSTEM AU Haft DH TH 0 CC In this uncharacterized system, the radical SAM domain protein has a CC Cys-rich suffix domain. In at least eight reference genomes, one Cys CC is replaced by selenocysteine, suggesting enzymatic activity and a CC distinctive role. In a large number of genomes, the radical SAM enzyme CC is co-clustered with a member of family TIGR04169. -- SN 1 ID Phosphoesterase family protein DN Phosphoesterase family protein RQ 0 EV IPR027629; TIGR04168; -- SN 2 ID Putative glycosyltransferase, CofC-like DN Putative glycosyltransferase, CofC-like RQ 1 EV IPR018641; TIGR04282; -- SN 3 ID Putative glycosyltransferase, MftF-like DN Putative glycosyltransferase, MftF-like RQ 1 EV IPR026461; TIGR04283; -- SN 4 ID Alkylhydroperoxidase/carboxymuconolactone decarboxylase family protein DN Alkylhydroperoxidase/carboxymuconolactone decarboxylase family protein RQ 1 EV IPR026445; TIGR04169; -- SN 5 ID Radical SAM/selenodomain protein DN Radical SAM/selenodomain protein RQ 1 EV IPR026351; TIGR04167; // AC GenProp1054 DE Protein sorting system, MSEP-CTERM/exosortase K TP SYSTEM AU Haft DH TH 0 CC This system consists of a distinctive subfamily of exosortase-like CC proteins, XrtK, and its adjacent putative target protein. The CC C-terminal putative sorting sorting signal is MSEP-CTERM, found at the CC C terminus of proteins in family TIGR04286. -- SN 1 ID Exosortase K DN Exosortase K RQ 1 EV IPR027551; TIGR04287; -- SN 2 ID MSEP-CTERM protein DN MSEP-CTERM protein RQ 1 EV IPR027550; TIGR04286; // AC GenProp1055 DE Protein sorting system, PEFG-CTERM/thaumarchaeosortase TP SYSTEM AU Haft DH TH 0 CC Thaumarchaeosortase (archaeosortase G, ArtG) is a member of the CC exosortase/archaeosortase family of putative protein-processing CC enzymes. It is restricted to the Thaumarchaeota, a branch of the CC Archaea. Species with ArtG each have roughly ten sequences with a CC C-terminal putative protein-sorting domain, PEFG-CTERM. This system is CC unusual in that the Cys conserved in all other subfamilies described in CC the exosortase/archaeosortase family, and thought to be part of the CC active site, is replaced by Ser in ArtG. -- SN 1 ID PEFG-CTERM thaumarchaeosortase target domain DN PEFG-CTERM thaumarchaeosortase target domain RQ 1 EV IPR027560; TIGR04296; -- SN 2 ID Thaumarchaeosortase DN Thaumarchaeosortase RQ 1 EV IPR027561; TIGR04297; // AC GenProp1057 DE Radical SAM/SPASM system GeoRSP TP SYSTEM AU Haft DH TH 0 CC This Genome Property represents a functional cassette (with unknown CC boundaries) in several species of Geobacter, in genomic regions that CC include high-molecular-weight cytochrome c family proteins. The CC cassette has a PqqD family protein, a radical SAM/SPASM domain protein CC similar to PqqE, and an additional SPASM domain protein that appears CC also to have a degenerate radical SAM-like region. Unlike the CC SynChlorMet system, with similar components, no putative precursor CC peptide for ribosomal natural product formation has been found. -- SN 1 ID GeoRSP system PqqD family protein DN GeoRSP system PqqD family protein RQ 1 EV IPR027569; TIGR04302; -- SN 2 ID GeoRSP system SPASM domain protein DN GeoRSP system SPASM domain protein RQ 1 EV IPR027571; TIGR04304; -- SN 3 ID GeoRSP system radical SAM/SPASM protein DN GeoRSP system radical SAM/SPASM protein RQ 1 EV IPR027570; TIGR04303; // AC GenProp1058 DE 2,3-dihydroxybenzoate biosynthesis TP PATHWAY AU Haft DH TH 1 CC 2,3-dihydroxybenzoate is made in three steps from chorismate by the CC action of enzymes isochorismate synthase (EC 5.4.4.2), isochorismatase CC (EC 3.3.2.1), and 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase CC (EC 1.3.1.28). It can then be activated by (2,3-dihydroxybenzoyl)adenylate CC synthase (EC 2.7.7.58) to become a substrate for nonribosomal peptide CC synthases (NRPS) such as those that make catecholate siderophores. -- SN 1 ID 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase DN 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC 1.3.1.28) RQ 1 EV IPR003560; TIGR04316; -- SN 2 ID Isochorismatase DN Isochorismatase (EC 3.3.2.1) RQ 1 EV IPR000868; PF00857; -- SN 3 ID Isochorismate synthase DN Isochorismate synthase (EC 5.4.4.2) RQ 1 EV IPR004561; TIGR00543; // AC GenProp1060 DE tRNA N6-threonylcarbamoyladenosine modification TP SYSTEM AU Haft DH TH 0 RN [1] RM 21873492 RT Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, RT which are involved in a universal tRNA modification in Escherichia RT coli. RA Hashimoto C, Sakaguchi K, Taniguchi Y, Honda H, Oshima T, Ogasawara N, RA Kato J; RL J Bacteriol. 2011;193:6075-6079. RN [2] RM 22378793 RT Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA RT nucleoside. RA Deutsch C, El Yacoubi B, de Crécy-Lagard V, Iwata-Reuyl D; RL J Biol Chem. 2012;287:13666-13673. CC E. coli genes ygjD, yeaZ, yrdC (rimN) and yjeE encode proteins involved CC in a universal tRNA modification, N6-threonylcarbamoyladenosine. -- SN 1 ID YeaZ protein DN YeaZ protein RQ 1 EV IPR022496; TIGR03725; TG GO:0006400; -- SN 2 ID YgjD protein DN YgjD protein RQ 1 EV IPR022450; TIGR03723; TG GO:0006400; -- SN 3 ID YjeE protein DN YjeE protein RQ 1 EV IPR003442; TIGR00150; TG GO:0006400; -- SN 4 ID YrdC protein DN YrdC protein RQ 1 EV IPR006070; TIGR00057; TG GO:0006400; // AC GenProp1061 DE CRISPR system, PreFran subtype TP SYSTEM AU Haft DH TH 0 CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats. The repeats vary in size from 24 to 48 bp, CC interspaced by similarly sized non-repetitive sequences. These spacers CC often are derived from phage and other exogenous DNA, are transcribed CC into RNA, and confer resistance to those same phage. Several CC CRISPR-associated sequences (cas genes) are nearly as widespread as CC CRISPR itself and nearly always are found near repeat loci. Others CC represent minor cas genes that serve as markers for specific subtypes CC of CRISPR/cas system, each with characteristic cas gene makeup, repeat CC structure, and spacer length. The PreFran subtype is found in multiple CC reference genomes of Prevotella and Francisella, and found also in CC several additional species. It has a single long protein, Cpf1 (Cas CC protein 1 of PreFran subtype), in addition to Cas4, Cas1, and Cas2. The CC typical repeat has length 36. -- SN 1 ID Cas1, PreFran subtype DN Cas1, PreFran subtype RQ 1 EV IPR027617; TIGR04329; -- SN 2 ID Cas2 DN Cas2 RQ 1 EV IPR021127; TIGR01573; -- SN 3 ID Cas4, PreFran subtype DN Cas4, PreFran subtype RQ 1 EV IPR027616; TIGR04328; -- SN 4 ID CRISPR-associated protein Cpf1 DN CRISPR-associated protein Cpf1 RQ 1 EV IPR027620; TIGR04330; // AC GenProp1062 DE Radical SAM/SPASM system Clo7bot TP SYSTEM AU Haft DH TH 0 CC This property features a radical SAM/SPASM domain peptide maturase CC that, in multiple strains of Clostridium botulinum, is next to a tandem CC array of seven target peptides, all Cys-rich. This system also occurs CC in Clostridium sporogenes, and an array of six peptides occurs in CC Thermoanaerobacter italicus Ab9. Clostridium cellulovorans 743B has a CC matching radical SAM maturase, but a single weak candidate target CC sequence, MKFVKAPTKNISIIKCPYFCNTFFPILPPTF. -- SN 1 ID Clo7bot tandem target peptide DN Clo7bot tandem target peptide RQ 1 EV IPR027601; TIGR04333; -- SN 2 ID Radical SAM/SPASM domain Clo7bot peptide maturase DN Radical SAM/SPASM domain Clo7bot peptide maturase RQ 1 EV IPR027622; TIGR04334; // AC GenProp1063 DE Memo/AMMECR1/rSAM family trio system TP SYSTEM AU Haft DH TH 0 CC This broadly distributed and fairly common microbial three protein CC family system contains a radical SAM enzyme of unknown specificity, a CC branch of the AMMECR1 family, and a branch of the Memo (mediator of CC ErbB2-driven cell motility) family. The Memo-like component and CC AMMECR1-like component may be fused, or encoded by tandem genes if not CC fused, but this three-gene property has its genes encoded far from each CC other more often than is typical for most Genome Properties. -- SN 1 ID AmmeMemoRadiSam system protein A DN AmmeMemoRadiSam system protein A RQ 1 EV IPR027623; TIGR04335; -- SN 2 ID AmmeMemoRadiSam system protein B DN AmmeMemoRadiSam system protein B RQ 1 EV IPR002737; TIGR04336; -- SN 3 ID AmmeMemoRadiSam system radical SAM enzyme DN AmmeMemoRadiSam system radical SAM enzyme RQ 1 EV IPR027596; TIGR04337; // AC GenProp1064 DE Ovothiol biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 21247153 RT Identification and characterization of the first ovothiol biosynthetic RT enzyme. RA Braunshausen A, Seebeck FP; RL J Am Chem Soc. 2011;133:1757-1759. CC The first step in ovothiol A biosynthesis is conversion of cysteine and CC histidine to 5-histidylcysteine sulfoxide conjugate by CC 5-histidylcysteine sulfoxide synthase. The conjugate is trimmed by a CC currently unknown mechanism (perhaps different enzymes in different CC species) to 5-thiohistidine, and is N-methylated at the pi position of CC the imidazole ring. Many OvaA (5-histidylcysteine sulfoxide synthase) CC have an additional C-terminal methyltransferase domain likely to CC provide this methyltransferase activity. Ovothiols B and C differ from CC ovothiol A by having additional methylations of the histidine-derived CC amino group. -- SN 1 ID 4-mercaptohistidine N1-methyltransferase DN 4-mercaptohistidine N1-methyltransferase RQ 1 EV IPR027625; TIGR04345; -- SN 2 ID 5-histidylcysteine sulfoxide synthase DN 5-histidylcysteine sulfoxide synthase RQ 1 EV IPR027577; TIGR04344; // AC GenProp1065 DE Radical SAM/SPASM TIGR04347/TIGR04031 system TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a system with two known components, CC restricted so far to halophilic archaea. One is a radical SAM (or CC occasionally pseudo-SAM)/SPASM domain enzyme, family TIGR04347. The CC other, family TIGR04031, resembles the PaaH (or PaaB) subunit of the CC phenylacetate-CoA oxygenase complex. Unlike systems in which a radical CC SAM/SPASM enzyme acts on a peptide substrate, this system may instead CC act on a(n unknown) small molecule substrate. -- SN 1 ID RSAM-partnered protein, Htur_1727 family DN RSAM-partnered protein, Htur_1727 family RQ 1 EV IPR023976; TIGR04031; -- SN 2 ID Pseudo-rSAM protein/SPASM domain protein DN Pseudo-rSAM protein/SPASM domain protein RQ 1 EV IPR027626; TIGR04347; // AC GenProp1067 DE Defense systems TP CATEGORY AU Haft DH TH 0 CC This category includes restriction systems, CRISPR, abortive infection CC systems, and other defenses against invasive nucleic acids. -- SN 1 ID CRISPR systems RQ 0 EV GenProp1106; -- SN 2 ID Restriction enzyme system, type I RQ 0 EV GenProp0455; -- SN 3 ID DNA sulfur modification system dnd RQ 0 EV GenProp0701; -- SN 4 ID Abortive infection proteins RQ 0 EV GenProp1093; -- SN 5 ID Complement activation, common pathway 1 RQ 0 EV GenProp2007; // AC GenProp1069 DE FxLD lantipeptide system TP SYSTEM AU Haft DH TH 0 CC This Genome Property describes a putative lantipeptide-type CC Post-Ribosomal Natural Product (PRNP) system in which the putative CC precursor peptide is described by TIGRFAMs model TIGR04363. Genes CC always found in the vicinity include lanthionine synthetase and CC lantibiotic dehydratase proteins, as well a close homolog CC protein-L-isoaspartate(D-aspartate) O-methyltransferase, a repair CC enzyme for age-damaged proteins. -- SN 1 ID FxLD family lantipeptide DN FxLD family lantipeptide RQ 1 EV IPR027575; TIGR04363; -- SN 2 ID Lantibiotic dehydratase DN Lantibiotic dehydratase RQ 1 EV IPR006827; PF04738; -- SN 3 ID FxLD system methyltransferase DN FxLD system methyltransferase RQ 1 EV IPR027573; TIGR04364; -- SN 4 ID Lanthionine synthetase DN Lanthionine synthetase RQ 1 EV IPR007822; PF05147; // AC GenProp1070 DE Beta-glutamate biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 17222594 RT Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily RT of enzymes. RA Ruzicka FJ, Frey PA; RL Biochim Biophys Acta. 2007;1774:286-296. RN [2] RM 20511502 RT Evidence for widespread gene control function by the ydaO riboswitch RT candidate. RA Block KF, Hammond MC, Breaker RR; RL J Bacteriol. 2010;192:3983-3989. CC Beta-glutamate is an osmolyte produced in one step from glutamate by CC the action of glutamate 2,3-aminomutase. The eam gene, encoding CC glutamate 2,3-aminomutase, is often preceded by a ydaO (yuaA) family CC riboswitch, which appears to bind a metabolite that indicates cellular CC stress. -- SN 1 ID Glutamate 2,3-aminomutase DN Glutamate 2,3-aminomutase RQ 1 EV IPR030801; TIGR04368; // AC GenProp1071 DE Myo-inositol catabolism TP SYSTEM AU Haft DH TH 0 RN [1] RM 18310071 RT myo-Inositol catabolism in Bacillus subtilis. RA Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, RA Fujita Y; RL J Biol Chem. 2008;283:10415-10424. RN [2] RM 9805393 RT A model for the catabolism of rhizopine in Rhizobium leguminosarum RT involves a ferredoxin oxygenase complex and the inositol degradative RT pathway. RA Bahar M, de Majnik J, Wexler M, Fry J, Poole PS, Murphy PJ; RL Mol Plant Microbe Interact. 1998;11:1057-1068. -- SN 1 ID Inositol 2-dehydrogenase DN Inositol 2-dehydrogenase RQ 1 EV IPR030827; TIGR04380; -- SN 2 ID Myo-inosose-2 dehydratase DN Myo-inosose-2 dehydratase RQ 1 EV IPR030823; TIGR04379; -- SN 3 ID 3,5/4-trihydroxycyclohexa-1,2-dione hydrolase DN 3,5/4-trihydroxycyclohexa-1,2-dione hydrolase RQ 1 EV IPR030817; TIGR04377; -- SN 4 ID 5-deoxy-glucuronate isomerase DN 5-deoxy-glucuronate isomerase RQ 1 EV IPR024203; TIGR04378; -- SN 5 ID 5-dehydro-2-deoxygluconokinase DN 5-dehydro-2-deoxygluconokinase RQ 1 EV IPR030830; TIGR04382; -- SN 7 ID Malonate-semialdehyde dehydrogenase (acetylating) DN Malonate-semialdehyde dehydrogenase (acetylating) RQ 1 EV IPR010061; TIGR01722; // AC GenProp1072 DE Cyanase system TP SYSTEM AU Haft DH TH 0 RN [1] RM 8444806 RT A physiological role for cyanate-induced carbonic anhydrase in RT Escherichia coli. RA Guilloton MB, Lamblin AF, Kozliak EI, Gerami-Nejad M, Tu C, Silverman RA D, Anderson PM, Fuchs JA; RL J Bacteriol. 1993;175:1443-1451. CC The cyanase system in Escherichia coli is a divergon, with the CC transcriptional regulator CynR gene transcribed divergently from an CC operon consisting of a carbonic anhydrase, cyanase, and cyanate CC transporter. -- SN 1 ID Cyn operon transcriptional activator CynR DN Cyn operon transcriptional activator CynR RQ 0 EV IPR005119; PF03466; -- SN 2 ID Cyanase DN Cyanase RQ 1 EV IPR008076; TIGR00673; TG GO:0009440; -- SN 3 ID Carbonic anhydrase, cyanate-induced DN Carbonic anhydrase, cyanate-induced RQ 0 EV IPR001765; PF00484; TG GO:0009440; -- SN 4 ID Cyanate transporter DN Cyanate transporter RQ 0 EV IPR004747; TIGR00896; TG GO:0015704; // AC GenProp1074 DE Type V secretion TP SYSTEM AU Haft DH TH 0 RN [1] RM 22411980 RT Type V secretion: mechanism(s) of autotransport through the bacterial RT outer membrane. RA Leo JC, Grin I, Linke D; RL Philos Trans R Soc Lond B Biol Sci. 2012;367:1088-1101. CC Type V secretion systems (T5SS) are most commonly the classical CC monomeric autotransporters (type Va), in which a C-terminal outer CC membrane (OM) beta barrel domain functions as a translocator through CC the OM for an N-terminal passenger domain of the same polypeptide CC chain. Many type Va autotransporters cleave autocatalytically to CC release the passenger domain. In type Vb systems, called two-partner CC secretion systems, the passenger and translocator domains are in CC separate polypeptides. Additional variant forms Vc, Vd, and Ve have CC also been described. A special type of signal peptide (PF13018) tethers CC the nascent polypeptide chain to the Sec apparatus in some CC autotransporters to allow proper completion of C-terminal domain CC folding in the OM. -- SN 1 ID Type V secretion system signal peptide DN Type V secretion system signal peptide RQ 0 EV IPR024973; PF13018; TG GO:0046819; -- SN 2 ID T5SS outer membrane translocator DN T5SS outer membrane translocator RQ 1 EV IPR006315; TIGR01414; TG GO:0046819; EV IPR005565; PF03865; TG GO:0046819; // AC GenProp1075 DE Ferrous iron transport Feo system TP SYSTEM AU Haft DH TH 0 RN [1] RM 23104801 RT Solution structure of Escherichia coli FeoA and its potential role in RT bacterial ferrous iron transport. RA Lau CK, Ishida H, Liu Z, Vogel HJ; RL J Bacteriol. 2013;195:46-55. RN [2] RM 23024345 RT Crystal structure of the Klebsiella pneumoniae NFeoB/FeoC complex and RT roles of FeoC in regulation of Fe2+ transport by the bacterial Feo RT system. RA Hung KW, Tsai JY, Juan TH, Hsu YL, Hsiao CD, Huang TH; RL J Bacteriol. 2012;194:6518-6526. CC The proteins FeoA, FeoB, and FeoC are a bacterial ferrous iron CC transport system. No siderophores are involved. Ferrous iron (Fe(2+)) CC typically is present only during oxygen limitation. -- SN 1 ID Ferrous iron transport protein A DN Ferrous iron transport protein A RQ 1 EV IPR007167; PF04023; TG GO:0015684; -- SN 2 ID Ferrous iron transport protein B DN Ferrous iron transport protein B RQ 1 EV IPR003373; TIGR00437; TG GO:0015684; -- SN 3 ID Ferrous iron transport protein C DN Ferrous iron transport protein C RQ 0 EV IPR015102; PF09012; TG GO:1900390; // AC GenProp1076 DE Choline TMA-lyase system TP SYSTEM AU Haft DH TH 0 RN [1] RM 23151509 RT Microbial conversion of choline to trimethylamine requires a glycyl RT radical enzyme. RA Craciun S, Balskus EP; RL Proc Natl Acad Sci U S A. 2012;109:21307-21312. CC This system has two key enzymes for choline utilization. CutD is a CC radical SAM enzyme that performs a post-translational modification to CC activate the glycyl radical enzyme CutC. Bioinformatic, mutational, and CC chemical studies suggest CutC acts as a choline-TMA lyase, cleaving a CC C-N bond to turn choline into trimethylamine and acetaldehyde. -- SN 1 ID Choline TMA-lyase DN Choline TMA-lyase RQ 1 EV IPR030897; TIGR04394; TG GO:0042426; -- SN 2 ID Choline TMA-lyase-activating enzyme DN Choline TMA-lyase-activating enzyme RQ 1 EV IPR030905; TIGR04395; TG GO:0042426; // AC GenProp1077 DE tRNA(Pro) cmo5UGG modification TP SYSTEM AU Haft DH TH 0 RN [1] RM 15383682 RT The modified wobble nucleoside uridine-5-oxyacetic acid in RT tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. RA Nasvall SJ, Chen P, Bjork GR; RL RNA. 2004;10:1662-1673. CC The tRNA methyltransferases CmoA and CmoB, usually encoded by tandem CC genes, work together to complete a tRNA wobble position modification, CC uridine-5-oxyacetic acid (cmo5U). This modification was shown to allow CC a tRNA(Pro) to recognize all four proline codons. This system has a CC fairly narrow taxonomic range, including E. coli, in which cmoA and CC cmoB occur but are not essential. -- SN 1 ID tRNA (cmo5U34)-methyltransferase DN tRNA (cmo5U34)-methyltransferase RQ 1 EV IPR005271; TIGR00740; TG GO:0006400; -- SN 2 ID tRNA (mo5U34)-methyltransferase DN tRNA (mo5U34)-methyltransferase RQ 1 EV IPR010017; TIGR00452; TG GO:0006400; // AC GenProp1078 DE Sporulation killing factor system TP SYSTEM AU Haft DH TH 0 RN [1] RM 23282011 RT Two [4Fe-4S] clusters containing radical SAM enzyme SkfB catalyze RT thioether bond formation during the maturation of the sporulation RT killing factor. RA Flühe L, Burghaus O, Wieckowski BM, Giessen TW, Linne U, Marahiel MA; RL J Am Chem Soc. 2013;135:959-962. RN [2] RM 16816204 RT Phosphate starvation induces the sporulation killing factor of Bacillus RT subtilis. RA Allenby NE, Watts CA, Homuth G, Prágai Z, Wipat A, Ward AC, Harwood RA CR; RL J Bacteriol. 2006;188:5299-5303. CC This system is characterized in Bacillus subtilis 168, but occurs also CC in Bacillus sp. M 2-6 and Paenibacillus larvae subsp. larvae B-3650. CC Sporulation killing factor is a ribosomally translated, CC post-translationally modified sactipeptide, meaning it has a CC Sulfur-to-Alpha-Carbon covalent crosslink from a Cys residue, catalyzed CC by radical SAM enzyme. -- SN 1 ID Sporulation killing factor DN Sporulation killing factor RQ 1 EV IPR030919; TIGR04404; -- SN 2 ID Sporulation killing factor maturase DN Sporulation killing factor maturase RQ 1 EV IPR030915; TIGR04403; -- SN 3 ID Sporulation killing factor system SkfF protein DN Sporulation killing factor system SkfF protein RQ 1 EV IPR030920; TIGR04405; // AC GenProp1079 DE Lpt lipopolysaccharide export transenvelope protein complex TP SYSTEM AU Haft DH TH 0 RN [1] RM 23292770 RT The Escherichia coli Lpt transenvelope protein complex for RT lipopolysaccharide export is assembled via conserved structurally RT homologous domains. RA Villa R, Martorana AM, Okuda S, Gourlay LJ, Nardini M, Sperandeo P, RA Dehò G, Bolognesi M, Kahne D, Polissi A; RL J Bacteriol. 2013;195:1100-1108. RN [2] RM 21705335 RT The LptD chaperone LptE is not directly involved in lipopolysaccharide RT transport in Neisseria meningitidis. RA Bos MP, Tommassen J; RL J Biol Chem. 2011;286:28688-28696. CC Lipopolysaccharide transport (Lpt) as it occurs in E. coli requires a CC complex with seven essential genes. LptBCFG spans the inner membrane, CC with LptBFG being an ABC transporter. LptA is periplasmic, and LptDE is CC in the outer membrane. -- SN 1 ID LPS transport periplasmic protein LptA DN LPS transport periplasmic protein LptA RQ 1 EV IPR014340; TIGR03002; -- SN 2 ID LPS export ABC transporter ATP-binding protein DN LPS export ABC transporter ATP-binding protein/LptB RQ 1 EV IPR030921; TIGR04406; -- SN 3 ID Lipopolysaccharide export protein LptC DN Lipopolysaccharide export protein LptC RQ 1 EV IPR010664; PF06835; EV IPR026265; TIGR04409; -- SN 4 ID LPS assembly OM complex protein LptD DN LPS assembly OM complex protein LptD RQ 1 EV IPR007543; PF04453; -- SN 5 ID LPS assembly OM complex protein LptE DN LPS assembly OM complex protein LptE RQ 1 EV IPR007485; PF04390; -- SN 6 ID LPS export ABC permease LptF DN LPS export ABC permease LptF RQ 1 EV IPR030922; TIGR04407; -- SN 7 ID LPS export ABC permease LptG DN LPS export ABC permease LptG RQ 1 EV IPR030923; TIGR04408; // AC GenProp1080 DE Protein O-heptosyltransferase with autotransporter target TP SYSTEM AU Haft DH TH 0 RN [1] RM 22221153 RT N for AsN - O for strOcture? A strand-loop-strand motif for prokaryotic RT O-glycosylation. RA Otzen D; RL Mol Microbiol. 2012;83:879-883. CC Aah and TibC are protein O-heptosyltransferases that glycosylate CC certain repeat-rich proteins at multiple sites. Their targets are the CC autotransporter (T5SS) proteins AIDA (autotransporter adhesin involved CC in diffuse adherence) and TibA, respectively. Similar tandem gene pairs CC occur in Burkholderia vietnamiensis G4, Granulibacter bethesdensis CC CGDNIH1, Cronobacter sakazakii ATCC BAA-894, and Bradyrhizobium sp. CC ORS278. In Burkholderia mallei, the heptosyltransferase occurs next to CC BimA, an autotransporter virulence factor involved in actin-based CC motility, suggesting glycosylation, although BimA lacks the repeat CC structure recognized by model TIGR04415. -- SN 1 ID Autotransporter strand-loop-strand O-heptosyltransferase DN Autotransporter strand-loop-strand O-heptosyltransferase RQ 1 EV IPR030929; TIGR04414; -- SN 2 ID Autotransporter strand-loop-strand repeat DN Autotransporter strand-loop-strand repeat RQ 1 EV IPR030930; TIGR04415; // AC GenProp1081 DE Replication restart, PriA/PriB primosome pathway TP SYSTEM AU Haft DH TH 0 RN [1] RM 17588514 RT A hand-off mechanism for primosome assembly in replication restart. RA Lopper M, Boonsombat R, Sandler SJ, Keck JL; RL Mol Cell. 2007;26:781-793. RN [2] RM 21641914 RT Binding of two PriA-PriB complexes to the primosome assembly site RT initiates primosome formation. RA Szymanski MR, Jezewska MJ, Bujalowski W; RL J Mol Biol. 2011;411:123-142. CC The bacterial primosome, as in E. coli, restarts replication at sites CC away from oriC (where DnaA acts), the normal origin of replication. CC PriB is a member of the larger family of single-stranded DNA-binding CC (ssb) protein. It is nearly always located between the genes for CC ribosomal protein S6 and S18, but appears to be only a subset of such CC ssb family members. The ssb member from the same location in most CC genomes is longer, and more closely related to a paralog of E. coli CC PriB than to PriB itself. -- SN 2 ID Primosome helicase PriA DN Primosome helicase PriA RQ 1 EV IPR005259; TIGR00595; TG GO:0006269; -- SN 3 ID Primosome protein PriB DN Primosome protein PriB RQ 1 EV IPR023646; TIGR04418; TG GO:0006269; // AC GenProp1082 DE 16S rRNA C1402 m(4)Cm modification TP SYSTEM AU Haft DH TH 0 RN [1] RM 19965768 RT Fine-tuning of the ribosomal decoding center by conserved RT methyl-modifications in the Escherichia coli 16S rRNA. RA Kimura S, Suzuki T; RL Nucleic Acids Res. 2010;38:1341-1352. CC RsmH (previously MraW) and RsmI (previously YraL) together make a CC dimethyl modification to an invariant cytidine nucleotide found in the CC 16S rRNA of all bacteria (site in C1402 in E. coli). -- SN 1 ID 16S rRNA (cytosine(1402)-N(4))-methyltransferase DN 16S rRNA (cytosine(1402)-N(4))-methyltransferase RQ 1 EV IPR002903; TIGR00006; TG GO:0000154; -- SN 2 ID 16S rRNA (cytidine(1402)-2'-O)-methyltransferase DN 16S rRNA (cytidine(1402)-2'-O)-methyltransferase RQ 1 EV IPR008189; TIGR00096; TG GO:0000154; // AC GenProp1083 DE Cyanobactin-like ribosomal natural product biosynthesis TP SYSTEM AU Haft DH TH 0 CC Cyanobactins include patellamides, anacyclamides, piricyclamide. These CC typically are prenylated and macrocylized, and may contain additional CC heterocycle modifications. -- SN 1 ID Cyanobactin maturation protease, PatA/PatG family DN Cyanobactin maturation protease, PatA/PatG family RQ 1 EV IPR023830; TIGR03895; -- SN 2 ID Cyanobactin biosynthesis protein, PatB/AcyB/McaB family DN Cyanobactin biosynthesis protein, PatB/AcyB/McaB family RQ 1 EV IPR026473; TIGR04220; -- SN 3 ID Cyanobactin cluster PatC/TenC/TruC protein DN Cyanobactin cluster PatC/TenC/TruC protein RQ 1 EV IPR031035; TIGR04447; -- SN 4 ID Peptide O-prenyltransferase, LynF/TruF/PatF family DN Peptide O-prenyltransferase, LynF/TruF/PatF family RQ 1 EV IPR031037; TIGR04445; -- SN 5 ID Cyanobactin DN Cyanobactin RQ 1 EV IPR031036; TIGR04446; EV IPR022264; TIGR03678; // AC GenProp1084 DE Enduracididine biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 17005978 RT The enduracidin biosynthetic gene cluster from Streptomyces RT fungicidicus. RA Yin X, Zabriskie TM; RL Microbiology. 2006;152:2969-2983. RN [2] RM 23758195 RT Structural and functional characterization of MppR, an enduracididine RT biosynthetic enzyme from streptomyces hygroscopicus: functional RT diversity in the acetoacetate decarboxylase-like superfamily. RA Burroughs AM, Hoppe RW, Goebel NC, Sayyed BH, Voegtline TJ, Schwabacher RA AW, Zabriskie TM, Silvaggi NR; RL Biochemistry. 2013;52:4492-4506. CC Proteins MppR (homologous to acetoacetate decarboxylases), and MppP and CC MppQ (both pyridoxal phosphate enzymes related to aminotransferases) CC are responsible for the biosynthesis of enduracididine, a rare CC non-proteinogenic amino acid incorporated by some non-ribosomal peptide CC synthases (NRPS). -- SN 1 ID Enduracididine biosynthesis enzyme MppP DN Enduracididine biosynthesis enzyme MppP RQ 1 EV IPR031020; TIGR04462; TG GO:0042398; -- SN 2 ID Enduracididine biosynthesis enzyme MppQ DN Enduracididine biosynthesis enzyme MppQ RQ 1 EV IPR031021; TIGR04461; TG GO:0042398; -- SN 3 ID Enduracididine biosynthesis enzyme MppR DN Enduracididine biosynthesis enzyme MppR RQ 1 EV IPR031022; TIGR04460; TG GO:0042398; // AC GenProp1085 DE Pyranoside core peptidyl nucleoside antibiotic biosynthesis TP SYSTEM AU Haft DH TH 0 RN [1] RM 22753012 RT Analysis of the mildiomycin biosynthesis gene cluster in RT Streptoverticillum remofaciens ZJU5119 and characterization of MilC, a RT hydroxymethyl cytosyl-glucuronic acid synthase. RA Wu J, Li L, Deng Z, Zabriskie TM, He X; RL Chembiochem. 2012;13:1613-1621. RN [2] RM 23874663 RT Discovery and characterization of BlsE, a radical RT S-adenosyl-L-methionine decarboxylase involved in the blasticidin S RT biosynthetic pathway. RA Feng J, Wu J, Dai N, Lin S, Xu HH, Deng Z, He X; RL PLoS One. 2013;8:e68545. CC Blasticidin S and mildiomycin are examples of peptidyl nucleoside CC antibiotics with a pyranoside core moiety. The two key enzymes to make CC this moeity are cytosylglucuronate (or hydroxymethylcytosylglucuronate) CC synthase and cytosylglucuronate decarboxylase. The latter is a radical CC SAM enzyme. -- SN 1 ID Cytosylglucuronate synthase DN Cytosylglucuronate synthase RQ 1 EV IPR031016; TIGR04467; -- SN 2 ID Cytosylglucuronate decarboxylase DN Cytosylglucuronate decarboxylase RQ 1 EV IPR031014; TIGR04466; // AC GenProp1087 DE Protein sorting system, vault protein/exosortase N TP SYSTEM AU Haft DH TH 0 CC This dedicated protein-sorting system occurs so far only in the class CC Bacteriodetes or in the genus Leptospira. The two proteins are CC exosortase N and a member of the vault protein inter-alpha-trypsin CC inhibitor (VIT) family. The VIT family protein PEP-CTERM region usually CC begins VPEPxEWxL, but usually scores poorly to the generic PEP-CTERM CC model. -- SN 1 ID Exosortase N DN Exosortase N RQ 1 EV IPR031006; TIGR04476; -- SN 2 ID VIT domain PEP-CTERM protein DN VIT domain PEP-CTERM protein RQ 1 EV IPR031005; TIGR04477; // AC GenProp1088 DE Thiosulfate oxidation to sulfate TP SYSTEM AU Haft DH TH 0 RN [1] RM 21833341 RT Mechanisms and evolution of oxidative sulfur metabolism in green sulfur RT bacteria. RA Gregersen LH, Bryant DA, Frigaard NU; RL Front Microbiol. 2011;2:116. RN [2] RM 16995898 RT Thiosulphate oxidation in the phototrophic sulphur bacterium RT Allochromatium vinosum. RA Hensen D, Sperling D, Trüper HG, Brune DC, Dahl C; RL Mol Microbiol. 2006;62:794-810. RN [3] RM 19535341 RT Mechanism for the hydrolysis of a sulfur-sulfur bond based on the RT crystal structure of the thiosulfohydrolase SoxB. RA Sauvé V, Roversi P, Leath KJ, Garman EF, Antrobus R, Lea SM, Berks BC; RL J Biol Chem. 2009;284:21707-21718. CC The sulfate ion consists of one sulfur (S) and four bound oxygen (O). CC In thiosulfate, one O is replace by S. This property describes the CC oxidation of thiosulfate to sulfate. In most species, sulfur oxidation CC begins further upstream, with sulfide or elemental sulfur. Molecular CC markers of those processes are not included here. Key proteins in CC thiosulfate oxidation to sulfate include SoxA, SoxB, SoxX, SoxY, and CC SoxZ. SoxYZ is a heterodimer. SoxXA is a heterodimeric c-type CC cytochrome. SoxB is monomeric. -- SN 1 ID Sulfur oxidation c-type cytochrome SoxA DN Sulfur oxidation c-type cytochrome SoxA RQ 1 EV IPR025710; TIGR04484; -- SN 2 ID Sulfur oxidation protein SoxB DN Sulfur oxidation protein SoxB RQ 1 EV IPR030998; TIGR04486; -- SN 3 ID Sulfur oxidation c-type cytochrome SoxX DN Sulfur oxidation c-type cytochrome SoxX RQ 1 EV IPR030999; TIGR04485; -- SN 4 ID Sulfur oxidation protein SoxY DN Sulfur oxidation protein SoxY RQ 1 EV IPR016568; TIGR04488; -- SN 5 ID Sulfur oxidation protein SoxZ DN Sulfur oxidation protein SoxZ RQ 1 EV IPR030995; TIGR04490; // AC GenProp1089 DE B12-dependent trimeric diol/glycerol dehydratase TP SYSTEM AU Haft DH TH 0 RN [1] RM 10498708 RT The propanediol utilization (pdu) operon of Salmonella enterica serovar RT Typhimurium LT2 includes genes necessary for formation of polyhedral RT organelles involved in coenzyme B(12)-dependent 1, 2-propanediol RT degradation. RA Bobik TA, Havemann GD, Busch RJ, Williams DS, Aldrich HC; RL J Bacteriol. 1999;181:5967-5975. RN [2] RM 18469107 RT Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol RT dehydratase in metabolosomes and metabolizes 1,2-propanediol by RT disproportionation. RA Sriramulu DD, Liang M, Hernandez-Romero D, Raux-Deery E, Lünsdorf H, RA Parsons JB, Warren MJ, Prentice MB; RL J Bacteriol. 2008;190:4559-4567. RN [3] RM 21040475 RT Diol dehydratase-reactivating factor is a reactivase--evidence for RT multiple turnovers and subunit swapping with diol dehydratase. RA Mori K, Hosokawa Y, Yoshinaga T, Toraya T; RL FEBS J. 2010;277:4931-4943. CC This Genome Property describes a trimeric, B12-dependent enzyme in a CC polyhedral microcompartment, or metabolosome, related to (but distinct CC from) the RuBisCO-containing carboxysome. Described examples include CC the propanediol dehydratase PduCDE (Pdu means propane diol utilization) CC and the glycerol dehydratase (also called PduCDE) of Lactobacillus CC reuteri. The latter converts glycerol in one step to CC 3-hydroxypropionaldehyde, also called reuterin, a compound that confers CC probiotic effects. -- SN 1 ID Diol/glycerol dehydratase, large subunit DN Diol/glycerol dehydratase, large subunit/PduC RQ 1 EV IPR003206; PF02286; -- SN 2 ID Diol/glycerol dehydratase, medium subunit DN Diol/glycerol dehydratase, medium subunit/PduD RQ 1 EV IPR003208; PF02288; -- SN 3 ID Diol/glycerol dehydratase, small subunit DN Diol/glycerol dehydratase, small subunit/PduE RQ 1 EV IPR003207; PF02287; -- SN 4 ID Diol dehydratase reactivation protein PduG DN Diol dehydratase reactivation protein PduG/PduG RQ 1 EV IPR009191; TIGR04491; // AC GenProp1090 DE Radical SAM/SPASM maturase system XYE TP SYSTEM AU Haft DH TH 0 CC This system consists of XyeA as the precursor peptide for a peptide CC post-translational modification system, XyeB as the radical SAM/SPASM CC domain peptide maturase, and neighboring cleavage/export proteins. -- SN 1 ID XYE system RiPP precursor XyeA DN XYE system RiPP precursor XyeA RQ 1 EV IPR030990; TIGR04495; -- SN 2 ID XYE system radical SAM/SPASM maturase DN XYE system radical SAM/SPASM maturase RQ 1 EV IPR030989; TIGR04496; -- SN 3 ID XYE system cleavage/export protein DN XYE system cleavage/export protein RQ 0 EV IPR005074; PF03412; // AC GenProp1091 DE Toxin-antitoxin system, type I TP GUILD AU Haft DH TH 0 RN [1] RM 23324552 RT Bacterial type I toxin-antitoxin systems. RA Brantl S; RL RNA Biol. 2012;9:1488-1490. CC In a type I toxin-antitoxin system, the toxin is a small peptide and CC the antitoxin is an antisense RNA. This arrangement contrasts with type CC 2 systems, in which both toxin and antidote are small proteins. -- SN 2 ID Toxic peptide, type I toxin-antitoxin system DN Toxic peptide, type I toxin-antitoxin system RQ 1 EV IPR025211; TIGR04459; EV IPR025211; PF13939; EV IPR025253; PF13940; EV IPR025882; PF13955; EV IPR025881; PF13956; EV IPR014944; PF08845; // AC GenProp1092 DE Toxin-antitoxin system, type III TP GUILD AU Haft DH TH 0 RN [1] RM 23267117 RT Selectivity and self-assembly in the control of a bacterial toxin by an RT antitoxic noncoding RNA pseudoknot. RA Short FL, Pei XY, Blower TR, Ong SL, Fineran PC, Luisi BF, Salmond GP; RL Proc Natl Acad Sci U S A. 2013;110:e241-9. CC A type III toxin-antitoxin system consists of a toxic peptide and CC structural RNA antitoxin. -- SN 1 ID Toxin, type III toxin-antitoxin system DN Toxin, type III toxin-antitoxin system RQ 1 EV IPR025911; PF13958; // AC GenProp1093 DE Abortive infection proteins TP GUILD AU Haft DH TH 0 CC An abortive infection system is any system that interferes with the CC ability of a phage to replicate successfully after it has infected a CC prokaryotic cell. Mechanisms vary widely, and may include blockage of a CC specific step in phage replication, or else shutdown and/or death of CC the host cell. This Genome Property is designed as a guild for proteins CC that have been described in publications as abortive infection proteins CC and that do not belong to CRISPR or restriction enzyme systems. -- SN 1 ID Abortive infection protein DN Abortive infection protein RQ 1 EV IPR025911; PF13958; EV IPR030987; TIGR04498; EV IPR025935; PF14253; // AC GenProp1094 DE Energy-coupling factor transporters TP GUILD AU Haft DH TH 0 RN [1] RM 18931129 RT A novel class of modular transporters for vitamins in prokaryotes. RA Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, RA Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T; RL J Bacteriol. 2009;191:42-51. CC This Genome Property consists of a form of ATP-energized transport in CC which two subunits resemble ABC transporter ATP-binding subunits, but CC the other two are distinct. The T component marks the transporter CC class, and generally is encoded adjacent the ATP-binding subunits. The CC substrate capture component S spans the membrane multiple times, and CC somewhat more than half the time is encoded away from the other CC subunits. In these systems, a single T subunit may transfer energy to a CC number of different S subunits. -- SN 1 ID ECF transporter ATP-binding component 1 DN ECF transporter ATP-binding component 1 RQ 0 EV IPR030947; TIGR04520; -- SN 2 ID ECF transporter ATP-binding component 2 DN ECF transporter ATP-binding component 2 RQ 0 EV IPR030946; TIGR04521; -- SN 3 ID ECF transporter S component DN ECF transporter S component RQ 1 EV IPR003784; PF02632; EV IPR002751; PF01891; EV IPR009825; PF07155; EV IPR011733; PF09605; EV IPR010387; PF06177; EV IPR024529; PF12822; EV IPR012651; PF09515; EV IPR012651; TIGR02357; EV IPR012652; TIGR02359; EV IPR017195; PF09819; EV IPR023812; TIGR04002; EV IPR018024; TIGR00123; EV IPR030945; TIGR04522; -- SN 4 ID ECF transporter T component DN ECF transporter T component RQ 1 EV IPR003339; PF02361; // AC GenProp1095 DE Exodeoxyribonuclease VII TP SYSTEM AU Haft DH TH 0 RN [1] RM 22718974 RT Delineation of structural domains and identification of functionally RT important residues in DNA repair enzyme exonuclease VII. RA Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, RA Bujnicki JM; RL Nucleic Acids Res. 2012;40:8163-8174. RN [2] RM 18812402 RT Identification of two conserved aspartic acid residues required for DNA RT digestion by a novel thermophilic Exonuclease VII in Thermotoga RT maritima. RA Larrea AA, Pedroso IM, Malhotra A, Myers RS; RL Nucleic Acids Res. 2008;36:5992-6003. CC Exonuclease VII, consisting of a large subunit XseA and small subunit CC XseB, hydrolyzes single-stranded DNA. It acts in DNA mismatch repair CC and homologous recombination. -- SN 1 ID Exodeoxyribonuclease VII large subunit DN Exodeoxyribonuclease VII large subunit/XseA RQ 1 EV IPR003753; TIGR00237; -- SN 2 ID Exodeoxyribonuclease VII small subunit DN Exodeoxyribonuclease VII small subunit/XseB RQ 1 EV IPR003761; PF02609; EV IPR003761; TIGR01280; // AC GenProp1098 DE 3-methylarginine biosynthesis TP PATHWAY AU Haft DH TH 0 RN [1] RM 20190091 RT Identification of the biosynthetic gene cluster for 3-methylarginine, a RT toxin produced by Pseudomonas syringae pv. syringae 22d/93. RA Braun SD, Hofmann J, Wensing A, Ullrich MS, Weingart H, Völksch B, RA Spiteller D; RL Appl Environ Microbiol. 2010;76:2500-2508. RN [2] RM 24907335 RT Biosynthesis of the β-methylarginine residue of peptidyl nucleoside RT arginomycin in Streptomyces arginensis NRRL 15941. RA Feng J, Wu J, Gao J, Xia Z, Deng Z, He X; RL Appl Environ Microbiol. 2014;80:5021-5027. CC 3-methylarginine can be a natural product in its own right, or a CC precursor of another natural product, such as arginomycin. The CC aminotransferase catalyzes the first and third steps of the pathway, CC removing the alpha-amino group from arginine, later replacing it on the CC beta-methylated form. The second step is catalyzed by a CC C-methyltransferase that acts on 2-ketoarginine at the 3-position. -- SN 1 ID 2-ketoarginine methyltransferase DN 2-ketoarginine methyltransferase RQ 1 EV IPR030899; TIGR04543; -- SN 2 ID Aminotransferase, 3-methylarginine-biosynthetic DN Aminotransferase, 3-methylarginine-biosynthetic RQ 1 EV IPR030898; TIGR04544; // AC GenProp1099 DE 8-oxoguanine DNA repair TP SYSTEM AU Haft DH TH 0 RN [1] RM 11554297 RT Multiple DNA glycosylases for repair of 8-oxoguanine and their RT potential in vivo functions. RA Hazra TK, Hill JW, Izumi T, Mitra S; RL Prog Nucleic Acid Res Mol Biol. 2001;68:193-205. CC MutM excises 8-oxoguanine (8-oxoG) that has formed in DNA and that has CC not since replicated (meaning it should be paired with C). If CC replication allows 8-oxoG to mispair with A, MutY excises the A to allow CC replication repair to replace it with a C. Note that MutT performs a CC different process, hydrolyzing 8-oxo-dGTP to 8-oxo-dGMP to block its CC incorporation into DNA in the first place, and therefore does perform CC DNA repair per se. -- SN 1 ID DNA-formamidopyrimidine glycosylase DN DNA-formamidopyrimidine glycosylase/MutM RQ 1 EV IPR020629; TIGR00577; -- SN 2 ID A/G-specific adenine glycosylase DN A/G-specific adenine glycosylase/MutY RQ 1 EV IPR005760; TIGR01084; // AC GenProp1100 DE Mobile element associated three-Cys-motif pair TP SYSTEM AU Haft DH TH 0 CC This property describes gene pairs with a member of family PF07505 and CC a member of family TIGR04474. Both proteins appear to be enzymes, based CC on motif-like patterns of sequence conservation. Genomic contexts include CC phage contexts but other contexts as well, such as between recAX and CC miaB in Mycobacterium tuberculosis. -- SN 1 ID Three Cys motif protein DN Three Cys motif protein RQ 1 EV IPR011101; PF07505; -- SN 2 ID Three-Cys-motif partner protein DN Three-Cys-motif partner protein RQ 1 EV IPR031009; TIGR04474; // AC GenProp1101 DE Quinoprotein cytochrome relay system TP SYSTEM AU Haft DH TH 0 RN [1] RM 18174148 RT Identification of proteins involved in formaldehyde metabolism by RT Rhodobacter sphaeroides. RA Wilson SM, Gleisten MP, Donohue TJ; RL Microbiology. 2008;154:296-305. RN [2] RM 12686160 RT The role of the MxaD protein in the respiratory chain of RT Methylobacterium extorquens during growth on methanol. RA Toyama H, Inagaki H, Matsushita K, Anthony C, Adachi O; RL Biochim Biophys Acta. 2003;1647:372-375. RN [3] RM 19224199 RT Quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: the RT unusual disulfide ring formed by adjacent cysteine residues is RT essential for efficient electron transfer to cytochrome c550. RA Mennenga B, Kay CW, Görisch H; RL Arch Microbiol. 2009;191:361-367. CC This system features a putative carrier protein, TIGR04557, related to CC the SoxY and SoxZ carrier complex of the sulfate oxidation cycle, as CC well as PQQ-dependent enzymes that have a Cys-Cys motif, and CC specialized cytochromes involved in electron transport. Authentic SoxY CC is a carrier protein for sulfur oxidation, with a covalent attachment CC site near its C terminus, and a Cys residue in the context GGCGG or GGCG. CC The carrier Cys of SoxY is conserved in TIGR04557, but what might be CC attached in the latter is unknown. GenProp0895 (alcohol ABC transporter, CC PedABC-type) describes a four-gene operon closely tied to this system. -- SN 1 ID Probable periplasmic binding protein DN Probable periplasmic binding protein RQ 0 EV IPR022448; TIGR03871; -- SN 2 ID Relay cytochrome DN Relay cytochrome RQ 1 EV IPR022411; TIGR03874; EV IPR030991; TIGR04494; -- SN 3 ID PQQ-dependent dehydrogenase, CysCys motif family DN PQQ-dependent dehydrogenase, CysCys motif family RQ 1 EV IPR017512; TIGR03075; -- SN 4 ID SoxYZ-like carrier DN SoxYZ-like carrier RQ 1 EV IPR030831; TIGR04557; -- SN 5 ID Quinoprotein relay system zinc metallohydrolase DN Quinoprotein relay system zinc metallohydrolase RQ 1 EV IPR030811; TIGR04558; EV IPR030829; TIGR04559; // AC GenProp1102 DE Protein sorting system, CGP-CTERM/unknown of Thermococcaceae TP SYSTEM AU Haft DH TH 0 CC This C-terminal protein sorting signal domain CGP-CTERM (TIGR04288) is CC restricted to the the family Thermococcaceae (including Thermococcus, CC Pyrococcus, and Palaeococcus) within the Euryarchaeota. It may be CC universal in that family. The sorting family is unknown. By analogy to CC the sortase, exosortase/archaeosortase, and rhombosortase systems, it CC is predicted that some protein sorting and processing enzyme recognizes CC and cleaves the C-terminal region. The unknown putative sorting enzyme CC may act as a transpeptidase. -- SN 2 ID CGP-CTERM domain DN CGP-CTERM domain RQ 1 EV IPR027552; TIGR04288; -- SN 3 ID Cys-rich CGP-CTERM protein DN Cys-rich CGP-CTERM protein RQ 0 EV IPR027556; TIGR04292; // AC GenProp1103 DE Protein sorting system, Synergist-CTERM/unknown of Synergistetes TP SYSTEM AU Haft DH TH 0 CC This property describes a putative bacterial C-terminal protein-sorting CC system restricted to the Synergistetes, but not universal in that CC lineage. Model genomes from at least seven genera average ten proteins CC apiece with the Synergist-CTERM signal. Some protein-sorting signals CC have the signature motif separated from the transmembrane helix (TM) by CC a spacer region (e.g. LPXTG and MYXO-CTERM) while others are have it CC flush against the TM (PGF-CTERM, GlyGly-CTERM, and this one). The lack CC of spacer suggests that the unknown sorting enzyme is a multiple CC membrane-spanning protein, like archaeosortase and rhombosortase, CC rather than a predominantly hydrophilic enzyme like sortase, whose CC targets have a spacer. -- SN 2 ID Synergist_CTERM protein sorting domain DN Synergist_CTERM protein sorting domain RQ 1 EV IPR030821; TIGR04564; // AC GenProp1104 DE Acyl carrier protein phosphopantetheinylation TP SYSTEM AU Haft DH TH 0 CC This property consists of acyl carrier protein, as used in fatty acid CC biosynthesis, and the holo-[acyl-carrier-protein] synthase. -- SN 1 ID Acyl carrier protein DN Acyl carrier protein RQ 1 EV IPR003231; TIGR00517; -- SN 2 ID Holo-[acyl-carrier-protein] synthase DN Holo-[acyl-carrier-protein] synthase RQ 1 EV IPR002582; TIGR00516; // AC GenProp1106 DE CRISPR systems TP CATEGORY AU Haft DH, Richardson L TH 0 RN [1] RM 11952905 RT Identification of genes that are associated with DNA repeats in RT prokaryotes. RA Jansen R, Embden JD, Gaastra W, Schouls LM; RL Mol Microbiol. 2002;43:1565-1575. RN [2] RM 16292354 RT A guild of 45 CRISPR-associated (Cas) protein families and multiple RT CRISPR/Cas subtypes exist in prokaryotic genomes. RA Haft DH, Selengut J, Mongodin EF, Nelson KE; RL PLoS Comput Biol. 2005;1:e60. RN [3] RM 21552286 RT Evolution and classification of the CRISPR-Cas systems. RA Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, RA Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV; RL Nat Rev Microbiol. 2011;9:467-477. CC CRISPR repeats are by definition Clustered Regularly Interspaced Short CC Palindromic Repeats. CRISPR loci are described as having direct repeats, CC varying in size from 21 to 37 bp, interspaced by similarly sized CC non-repetitive sequences. Certain proteins, including Cas1 to Cas4, CC are found only in genomes with CRISPR repeats, and always near these CC repeats [1]. Haft, et al. described subtypes in which certain groups of CC subtype-specific genes are found in addition to characteristic sets of CC the more widely distributed Cas genes [2]. A further review of CRISPR CC families by Makarova, et al. describes broader categories of CRISPR CC systems, using a polythetic classification system [3]. -- SN 1 ID CRISPR region RQ 0 EV GenProp0021; -- SN 2 ID CRISPR system, I-F/Ypest subtype RQ 0 EV GenProp0310; -- SN 3 ID CRISPR system, I-C/Dvulg subtype RQ 0 EV GenProp0313; -- SN 4 ID CRISPR system, II/Nmeni subtype RQ 0 EV GenProp0314; -- SN 5 ID CRISPR system, I-E/Ecoli subtype RQ 0 EV GenProp0315; -- SN 6 ID CRISPR system, III-B/RAMP module subtype RQ 0 EV GenProp0316; -- SN 7 ID CRISPR system, I-B subtype, Tneap branch RQ 0 EV GenProp0317; -- SN 8 ID CRISPR system, III-A/Mtube subtype RQ 0 EV GenProp0318; -- SN 9 ID CRISPR system, I-A/Apern subtype RQ 0 EV GenProp0319; -- SN 10 ID CRISPR system, I-B subtype, Hmari branch RQ 0 EV GenProp0320; -- SN 11 ID CRISPR system, Dpsyc subtype RQ 0 EV GenProp0469; -- SN 12 ID CRISPR system, Aferr subtype RQ 0 EV GenProp0670; -- SN 13 ID CRISPR system, I-D/Cyano subtype RQ 0 EV GenProp0685; -- SN 14 ID CRISPR system, Pging subtype RQ 0 EV GenProp0768; -- SN 15 ID CRISPR system, Myxan subtype RQ 0 EV GenProp0922; -- SN 16 ID CRISPR system, PreFran subtype RQ 0 EV GenProp1061; // AC GenProp1107 DE Viral protein sets TP CATEGORY AU Richardson L TH 0 CC This category contains genome properties that describe characteristic sets CC of proteins found in specific classes of virus. -- SN 1 ID Orbivirus protein set RQ 0 EV GenProp1006; -- SN 2 ID Orthobunyavirus protein set RQ 0 EV GenProp1007; -- SN 3 ID Coronavirus protein set RQ 0 EV GenProp1009; -- SN 4 ID Influenzae A virus protein set RQ 0 EV GenProp1012; -- SN 5 ID Influenzae B virus protein set RQ 0 EV GenProp1013; -- SN 6 ID Seadornavirus protein set RQ 0 EV GenProp1016; // AC GenProp1108 DE Endopeptidase ClpXP complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22595189 RT ClpP: a structurally dynamic protease regulated by AAA+ proteins. RA Alexopoulos JA, Guarné A, Ortega J RL J Struct Biol. 2012;179:202-210 DR Complex Portal; CPX-3176; DR Complex Portal; CPX-3175; CC ATP-dependent serine protease which degrades intracellular unfolded or CC misfolded proteins. -- SN 1 ID ATP-dependent Clp protease proteolytic subunit RQ 1 EV IPR001907; MF_00444; sufficient; EV IPR001907; PR00127; sufficient; EV IPR001907; TIGR00493; sufficient; EV IPR001907; cd07017; sufficient; -- SN 2 ID ATP-dependent Clp protease ATP-binding subunit ClpX RQ 1 EV IPR004487; MF_00175; sufficient; EV IPR004487; PTHR11262; sufficient; EV IPR004487; TIGR00382; sufficient; // AC GenProp1109 DE UvrAB complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 2546148 RT The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC RT subunits in the incision complex. RA Orren DK, Sancar A RL Proc Natl Acad Sci U S A. 1989;86:5237-5241 DR Complex Portal; CPX-2151; CC Part of the UvrABC repair system that catalyzes the recognition and CC processing of DNA lesions. It scans the DNA for abnormalities. Upon CC binding of the UvrAB complex to a putative damaged site, the DNA wraps CC around one of the UvrB subunits. DNA wrapping is dependent on ATP CC binding by UvrB and probably causes local melting of the DNA helix, CC facilitating insertion of a UvrB beta-hairpin between the DNA strands. CC Then UvrB probes one DNA strand for the presence of a lesion. If a CC lesion is found the UvrA subunits dissociate and the UvrB-DNA CC preincision complex (CPX-2152) is formed. This complex is subsequently CC bound by UvrC (P0A8G0) and one of the UvrB monomers is released CC (CPX-2153). If no lesion is found, the DNA wraps around the other UvrB CC subunit that will check the other stand for damage. ATP hydrolysis by CC UvrB is UvrA-dependent and initiates dissociation of UvrB from the DNA, CC possibly because no lesion is found. The recruitment process of the CC UvrAB complex to the DNA remains unknown. A UvrA dimer exists in vitro, CC but it is uncertain if it also exists in vivo as UvrA is sequestered to CC the DNA by Mfd (CPX-2155). -- SN 1 ID UvrABC system protein B RQ 1 EV IPR004807; MF_00204; sufficient; EV IPR004807; PTHR24029; sufficient; EV IPR004807; TIGR00631; sufficient; -- SN 2 ID UvrABC system protein A RQ 1 EV IPR004602; MF_00205; sufficient; EV IPR004602; TIGR00630; sufficient; // AC GenProp1111 DE Acetyl-CoA carboxylase complex TP COMPLEX AU Complex Portal TH 3 RN [1] RM 22869039 RT Structure and function of biotin-dependent carboxylases. RA Tong L RL Cell Mol Life Sci. 2013;70:863-891 DR Complex Portal; CPX-3206; CC Biotin-dependent, multifunctional enzyme that catalyzes the first CC committed step in fatty acid synthesis. The overall reaction is the CC biotin-dependent carboxylation of acetyl-CoA to form malonyl-CoA. The CC first half-reaction catalyzed by biotin carboxylase, is an CC ATP-dependent carboxylation of biotin, which is covalently attached to CC biotin carboxyl carrier protein. The second half-reaction, catalyzed by CC carboxyl transferase, transfers the activated carboxyl group from CC carboxy-biotin to acetyl-CoA to form malonyl-CoA. -- SN 1 ID Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha RQ 1 EV IPR001095; MF_00823; sufficient; EV IPR001095; PF03255; sufficient; EV IPR001095; PR01069; sufficient; EV IPR001095; PTHR42853; sufficient; EV IPR001095; TIGR00513; sufficient; -- SN 2 ID Biotin carboxylase RQ 1 EV IPR004549; TIGR00514; sufficient; -- SN 3 ID Biotin carboxyl carrier protein of acetyl-CoA carboxylase RQ 1 EV IPR001249; PR01071; sufficient; EV IPR001249; TIGR00531; sufficient; -- SN 4 ID Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta RQ 1 EV IPR000438; MF_01395; sufficient; EV IPR000438; PR01070; sufficient; EV IPR000438; TIGR00515; sufficient; // AC GenProp1112 DE Respiratory chain complex II TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-1931; DR PDBe; 2ws3; DR PDBe; 2wu5; DR PDBe; 2wu2; DR PDBe; 2acz; DR PDBe; 2wdq; DR PDBe; 1nek; DR PDBe; 2wdr; DR PDBe; 2wp9; CC Key enzyme linking the Krebs cycle with the respiratory chain in CC aerobic respiration. Catalyzes the oxidation of succinate to fumarate CC and the reduction of quinone to quinol. Electrons flow from the CC FAD-bound succinate through the Fe-S clusters to a b556 heme. Electrons CC ultimately reduce quinone to quinol in the membrane bound part of the CC enzyme. Under most conditions the electrons are used to reduce oxygen, CC allowing ATP synthesis. Member of the Complex II family. The CC functionally inverse complex found in anaerobic respiration is the QFR CC complex (CPX-1967). -- SN 1 ID Succinate dehydrogenase cytochrome b556 subunit RQ 1 EV IPR014314; PIRSF000178; sufficient; EV IPR014314; TIGR02970; sufficient; -- SN 2 ID Succinate dehydrogenase iron-sulfur subunit RQ 1 EV IPR004489; TIGR00384; sufficient; -- SN 3 ID Succinate dehydrogenase hydrophobic membrane anchor subunit RQ 1 EV IPR014312; PIRSF000169; sufficient; EV IPR014312; PTHR38689; sufficient; EV IPR014312; TIGR02968; sufficient; -- SN 4 ID Succinate dehydrogenase flavoprotein subunit RQ 1 EV IPR011281; TIGR01816; sufficient; // AC GenProp1113 DE DnaA-Dps complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1948; CC Complex formation reduces replication initiation on oriC under CC oxidative stress conditions allowing DNA repair to proceed, prior to CC new rounds of replication. The incomplete blockage of replication CC initiation is thought to produce genetic variation in the bacterial CC population. -- SN 1 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; -- SN 2 ID DNA protection during starvation protein RQ 1 EV IPR002177; PIRSF005900; sufficient; EV IPR002177; PR01346; sufficient; EV IPR002177; PTHR42932; sufficient; EV IPR002177; cd01043; sufficient; // AC GenProp1114 DE ATP-dependent methionine-importing complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2114; DR PDBe; 3tuj; DR PDBe; 3tuz; DR PDBe; 3tui; CC An ABC transporter complex that transports extracellular methionine CC from the periplasm into the cytoplasm in an ATP-dependent manner. ATP CC hydrolysis at the dimerization interface of the MetN subunit opens up CC the dimerization interface of MetI and MetN allowing the methionine to CC travel through the plasma membrane. MetQ (P28635) is thought to be the CC periplasmic methionine-chaperon protein, although its interaction with CC methionine or MetI has yet to be demonstrated. -- SN 1 ID D-methionine transport system permease protein MetI RQ 1 EV IPR000515; PF00528; sufficient; EV IPR000515; PS50928; sufficient; EV IPR000515; cd06261; sufficient; -- SN 2 ID Methionine import ATP-binding protein MetN RQ 1 EV IPR026253; PTHR43166:SF18; sufficient; EV IPR026253; PTHR43166:SF3; sufficient; EV IPR026253; PTHR43166:SF5; sufficient; // AC GenProp1115 DE LptDE outer membrane translocon complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 26370939 RT Lipopolysaccharide transport to the cell surface: periplasmic transport RT and assembly into the outer membrane. RA May JM, Sherman DJ, Simpson BW, Ruiz N, Kahne D RL Philos Trans R Soc Lond B Biol Sci. 2015;370:- DR Complex Portal; CPX-1093; CC A translocon complex responsible for inserting lipopolysaccharide (LPS) CC into the outer membrane of the bacteria to maintain the asymmetric CC bilayer, which consists of phospholipids in the inner leaflet and LPS CC in the outer. -- SN 1 ID LPS-assembly lipoprotein LptE RQ 1 EV IPR007485; MF_01186; sufficient; EV IPR007485; PF04390; sufficient; EV IPR007485; PTHR38098; sufficient; -- SN 2 ID LPS-assembly protein LptD RQ 1 EV IPR020889; MF_01411; sufficient; // AC GenProp1116 DE Bam complex TP COMPLEX AU Complex Portal TH 4 RN [1] RM 21586578 RT Structural basis of outer membrane protein biogenesis in bacteria. RA Albrecht R, Zeth K RL J Biol Chem. 2011;286:27792-27803 DR Complex Portal; CPX-1923; DR PDBe; 5d0q; CC Outer membrane protein assembly complex involved in assembly and CC insertion of beta-barrel proteins into the outer membrane. -- SN 1 ID Outer membrane protein assembly factor BamD RQ 1 EV IPR017689; MF_00922; sufficient; EV IPR017689; PTHR37423; sufficient; EV IPR017689; TIGR03302; sufficient; EV IPR017689; cd15830; sufficient; -- SN 2 ID Outer membrane protein assembly factor BamC RQ 1 EV IPR014524; MF_00924; sufficient; EV IPR014524; PIRSF026343; sufficient; -- SN 3 ID Outer membrane protein assembly factor BamA RQ 1 EV IPR023707; MF_01430; sufficient; EV IPR023707; PIRSF006076; sufficient; EV IPR023707; PTHR12815:SF23; sufficient; EV IPR023707; TIGR03303; sufficient; -- SN 4 ID Outer membrane protein assembly factor BamE RQ 1 EV IPR026592; MF_00925; sufficient; EV IPR026592; PTHR37482; sufficient; -- SN 5 ID Outer membrane protein assembly factor BamB RQ 1 EV IPR017687; MF_00923; sufficient; EV IPR017687; TIGR03300; sufficient; // AC GenProp1117 DE DNA polymerase III clamp loader chi-psi subcomplex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 20413500 RT Stoichiometry and architecture of active DNA replication machinery in RT Escherichia coli. RA Reyes-Lamothe R, Sherratt DJ, Leake MC RL Science. 2010;328:498-501 RN [2] RM 21675919 RT DNA replicases from a bacterial perspective. RA McHenry CS RL Annu Rev Biochem. 2011;80:403-436 DR Complex Portal; CPX-1964; DR PDBe; 1em8; CC Required for replicative synthesis, forming a link between the DNA CC polymerase III clamp loader complex (CPX-1926) and the DNA binding CC protein tetramer SSB (CPX-1928). This aids in the tethering of the DNA CC polymerase III holoenzyme to single-stranded DNA. A further 3 CC heterodimers co-localise at the replisome and are thought to interact CC with other SSB protomers. It is possible that multimers of the gamma CC subunit (P06710-2) are linked to the free end of these psi protomers. CC The function of these subcomplexes is as yet unknown. -- SN 1 ID DNA polymerase III subunit psi RQ 1 EV IPR004615; PD032475; sufficient; EV IPR004615; PF03603; sufficient; EV IPR004615; PIRSF029225; sufficient; -- SN 2 ID DNA polymerase III subunit chi RQ 1 EV IPR007459; PF04364; sufficient; EV IPR007459; PTHR38767; sufficient; // AC GenProp1118 DE DnaB-DnaC complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 21856207 RT Replication initiation at the Escherichia coli chromosomal origin. RA Kaguni JM RL Curr Opin Chem Biol. 2011;15:606-613 DR Complex Portal; CPX-1934; CC Facilitates replication initiation following recruitment to each strand CC of the replication origin oriC by DnaA. DnaB is complexed with ATP CC whose hydrolysis facilitates translocation and unwinding. This process CC is inhibited by DnaC which needs to be displaced by the binding of CC primase DnaG to DnaB before DnaB can initiate its helicase CC function. DnaC is a weak ATPase and binds weakly to ssDNA. It acts as a CC regulator of DnaB activity. -- SN 1 ID DNA replication protein DnaC RQ 1 EV IPR028350; PIRSF003073; sufficient; -- SN 2 ID Replicative DNA helicase (DnaB) RQ 1 EV IPR007692; TIGR00665; sufficient; // AC GenProp1119 DE p-aminobenzoyl-glutamate hydrolase TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-28; CC Catalyzes the cleavage of the folate breakdown product CC p-aminobenzoyl-glutamate (PABA-GLU) to form p-aminobenzoate (PABA) and CC glutamate. Reduced derivatives of folic acid are required for CC biosynthesis of DNA, RNA, amino acids, and other important cellular CC components. -- SN 1 ID p-aminobenzoyl-glutamate hydrolase subunit A RQ 1 EV IPR033845; cd05665; sufficient; -- SN 2 ID p-aminobenzoyl-glutamate hydrolase subunit B RQ 1 EV IPR017145; PIRSF037227; sufficient; EV IPR017145; cd05673; sufficient; // AC GenProp1120 DE HipBA toxin-antitoxin complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 25056321 RT The bacterial antitoxin HipB establishes a ternary complex with RT operator DNA and phosphorylated toxin HipA to regulate bacterial RT persistence. RA Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B, Devreese B, RA Savvides SN RL Nucleic Acids Res. 2014;42:10134-10147 RN [2] RM 19150849 RT Molecular mechanisms of HipA-mediated multidrug tolerance and its RT neutralization by HipB. RA Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG RL Science. 2009;323:396-401 RN [3] RM 26222023 RT HipBA-promoter structures reveal the basis of heritable multidrug RT tolerance. RA Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulić M, Lewis RA K, Brennan RG RL Nature. 2015;524:59-64 RN [4] RM 1715862 RT Structure and organization of hip, an operon that affects lethality due RT to inhibition of peptidoglycan or DNA synthesis. RA Black DS, Kelly AJ, Mardis MJ, Moyed HS RL J Bacteriol. 1991;173:5732-5739 DR Complex Portal; CPX-180; DR PDBe; 3dnv; DR PDBe; 4yg7; DR PDBe; 3hzi; CC Toxin-antitoxin (TA) complex. TA systems act as effectors of dormancy CC and persistence and are composed of a toxin, which causes growth arrest CC by interfering with a vital cellular process, and a cognate antitoxin, CC which neutralizes the toxin activity during normal growth conditions. CC Under conditions of stress the antitoxins are selectively degraded, CC leaving the toxins to exert their toxic effects, leading to growth CC arrest and dormancy. Type II TA complexes are small protein-protein CC pairs; under growth conditions, the toxin is bound to the antitoxin, CC which inhibits its activity. Both the antitoxin and, in most cases, the CC TA complex bind the TA promoter to repress transcription. Under stress CC conditions, cellular proteases such as Lon (P0A9M0) and ClpXP CC (CPX-3176) are activated that preferentially cleave the antitoxins, CC freeing the toxins to inhibit growth by inhibiting translation or CC replication, enabling cells to enter a metabolically dormant state CC until the stress is removed. Complex formation prevents the protein CC kinase HipA acting as a persistence factor, inducing multi-drug CC tolerance by triggering growth arrest. HipA activity is inhibited upon CC binding to HipB through sequestration to the nucleoid and binding to CC DNA. HipB and HipAB act as transcriptional autoregulators of the CC hipBA operon. -- SN 1 ID Antitoxin HipB RQ 1 EV IPR001387; PF01381; sufficient; EV IPR001387; PF12844; sufficient; EV IPR001387; PF13443; sufficient; EV IPR001387; PS50943; sufficient; EV IPR001387; SM00530; sufficient; EV IPR001387; cd00093; sufficient; -- SN 2 ID Serine/threonine-protein kinase toxin HipA RQ 1 EV IPR017508; PF13657; sufficient; EV IPR017508; TIGR03071; sufficient; // AC GenProp1121 DE ModE complex TP COMPLEX AU Complex Portal TH 0 DR Complex Portal; CPX-2115; DR PDBe; 1h9r; DR PDBe; 1o7l; CC Transcriptional regulator involved in various aspects of molybdenum CC metabolism by both limiting molybdate uptake by repressing the CC molybdate transporter operon modABCD, and enhancing the transcription CC of molybdenum-dependent, and of molybdenum cofactor biosynthesis CC enzymes. It is activated by the binding of 2 molecules of molybdate to CC the dimerization interface. Upon binding of molybdate, the conformation CC of the dimer changes, probably enhancing the DNA affinity of the CC complex. It recognizes an 8-base inverted repeat 5'-TAACGTTA-3' flanked CC by two CAT boxes upstream of the modABCD operon. ModE also interacts CC with tungstate. -- SN 1 ID Transcriptional regulator ModE RQ 1 EV IPR016462; PIRSF005763; sufficient; // AC GenProp1122 DE Nitrate reductase A complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-1974; DR PDBe; 3egw; DR PDBe; 1siw; DR PDBe; 3ir7; DR PDBe; 1y5l; DR PDBe; 1y5i; DR PDBe; 1y5n; DR PDBe; 1y4z; DR PDBe; 3ir6; DR PDBe; 3ir5; CC Involved in electron transport during anaerobic respiration: electrons CC are passed from the formate dehydrogenase-N (Fdh-N) complex (CPX-1975) CC to nitrate reductase (NarGHI) complex via a quinone-quinol redox CC reaction. Within NarGHI, the distal heme molecule of NarI receives CC electrons from quinol (hydroquinone), passes them on to the proximal CC heme which passes it down a Fe-S cluster chain to the molybdopterin CC cofactor Mo-bisMGD where they reduce nitrate to nitrite. The CC collaboration of these two complexes contributes to the proton motive CC force: electrons are ultimately donated to Fdh-N by formate in the CC periplasm, transported to the cytoplasm and accepted by nitrate. CC Hydrogen ions are transported in the opposite direction: Quinone is CC reduced to quinol by cytoplasmic protons which are in turn released CC into the periplasm when quinol is oxidized to quinone. -- SN 1 ID Respiratory nitrate reductase 1 beta chain RQ 1 EV IPR006547; TIGR01660; sufficient; EV IPR006547; cd10557; sufficient; -- SN 2 ID Respiratory nitrate reductase 1 alpha chain RQ 1 EV IPR006468; TIGR01580; sufficient; -- SN 3 ID Respiratory nitrate reductase 1 gamma chain RQ 1 EV IPR003816; TIGR00351; sufficient; // AC GenProp1123 DE DnaB-DnaG complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 17947583 RT Structure of hexameric DnaB helicase and its complex with a domain of RT DnaG primase. RA Bailey S, Eliason WK, Steitz TA RL Science. 2007;318:459-463 RN [2] RM 6323419 RT Structural and functional studies of the dnaB protein using limited RT proteolysis. Characterization of domains for DNA-dependent ATP RT hydrolysis and for protein association in the primosome. RA Nakayama N, Arai N, Kaziro Y, Arai K RL J Biol Chem. 1984;259:88-96 RN [3] RM 8702920 RT The extreme C terminus of primase is required for interaction with DnaB RT at the replication fork. RA Tougu K, Marians KJ RL J Biol Chem. 1996;271:21391-21397 RN [4] RM 21856207 RT Replication initiation at the Escherichia coli chromosomal origin. RA Kaguni JM RL Curr Opin Chem Biol. 2011;15:606-613 DR Complex Portal; CPX-1933; CC Involved in the synthesis of RNA primer sequences used in DNA CC replication. DnaG binding to DnaB displaces DnaC from DnaB (CPX-1934), CC activates the helicase and transposition activity of DnaB and thereby CC moves replication from the initiation to the priming phase. The CC interaction of the DnaB helicase and DnaG primase at the replication CC fork stimulates each others activities: As the helicase unwinds the CC parental DNA, the primase synthesises Okasaki RNA primers. Finally, CC DNA Polymerase III holoenzyme docks onto the primer-ssDNA duplex and CC initiates DNA synthesis. -- SN 1 ID DNA primase (DnaG) RQ 1 EV IPR030846; MF_00974; sufficient; EV IPR030846; PIRSF002811; sufficient; -- SN 2 ID Replicative DNA helicase (DnaB) RQ 1 EV IPR007692; TIGR00665; sufficient; // AC GenProp1124 DE UgpAEC-UgpB complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-2150; CC Binds glycerol-3-phosphate (G3P) and glycerol-3-phosphocholine (GPC) CC and functions as an ATPase. It is thought to facilitate G3P transport CC into the cell. Genetic studies have shown that excess phosphate in the CC cell can inhibit the Ugp transporter but this observation has not been CC replicated in vitro. -- SN 1 ID sn-glycerol-3-phosphate-binding periplasmic protein UgpB RQ 1 EV IPR006059; PF01547; sufficient; EV IPR006059; PF13416; sufficient; -- SN 2 ID sn-glycerol-3-phosphate transport system permease protein UgpE RQ 1 EV IPR030165; PTHR43744:SF8; sufficient; -- SN 3 ID sn-glycerol-3-phosphate transport system permease protein UgpA RQ 1 EV IPR000515; PF00528; sufficient; EV IPR000515; PS50928; sufficient; EV IPR000515; cd06261; sufficient; -- SN 4 ID sn-glycerol-3-phosphate import ATP-binding protein UgpC RQ 1 EV IPR017922; PS51315; sufficient; // AC GenProp1125 DE DinJ-YafQ toxin-antitoxin complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 24898247 RT Mechanisms of toxin inhibition and transcriptional repression by RT Escherichia coli DinJ-YafQ. RA Ruangprasert A, Maehigashi T, Miles SJ, Giridharan N, Liu JX, Dunham CM RL J Biol Chem. 2014;289:20559-20569 RN [2] RM 26991085 RT Toxin-antitoxin systems in bacterial growth arrest and persistence. RA Page R, Peti W RL Nat Chem Biol. 2016;12:208-214 DR Complex Portal; CPX-1079; CC Toxin-antitoxin (TA) system that appears to be a principal mediator of CC cell death in biofilm formations. TA systems act as effectors of CC dormancy and persistence and are composed of a toxin, which causes CC growth arrest by interfering with a vital cellular process, and a CC cognate antitoxin, which neutralizes the toxin activity during normal CC growth conditions. Under conditions of stress the antitoxins are CC selectively degraded, leaving the toxins to exert their toxic effects, CC leading to growth arrest and dormancy. Type II TA complexes are small CC protein-protein pairs; under growth conditions, the toxin is bound to CC the antitoxin, which inhibits its activity. Both the antitoxin and, in CC most cases, the TA complex bind the TA promoter to repress CC transcription. Under stress conditions, cellular proteases such as Lon CC (P0A9M0) and ClpXP (CPX-3176) are activated that preferentially cleave CC the antitoxins, freeing the toxins to inhibit growth by inhibiting CC translation or replication, enabling cells to enter a metabolically CC dormant state until the stress is removed. The toxin YafQ degrades mRNA CC at adenosine-rich codons, most likely while it is bound to the CC ribosome. The binding of DinJ occludes the active site of YafQ and a CC single YafQ-(DinJ)2-YafQ complex bound to one inverted repeat in one of CC two palindromic operator regions in the dinJ promoter represses CC transcription. -- SN 1 ID Antitoxin DinJ RQ 1 EV IPR026262; PIRSF003108; sufficient; -- SN 2 ID mRNA interferase toxin YafQ RQ 1 EV IPR004386; PF15738; sufficient; EV IPR004386; PIRSF006156; sufficient; EV IPR004386; PTHR40588; sufficient; EV IPR004386; TIGR00053; sufficient; // AC GenProp1126 DE ProVWX complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-2126; CC Belongs to the family of ATP-binding cassette (ABC) transporter CC proteins complexes. It is capable of translocating a wide variety of CC solutes (e.g. glycine betaine) across the plasma membrane. The proVWX CC operon is activated under osmotic stress conditions. -- SN 1 ID Glycine betaine/proline betaine transport system ATP-binding protein ProV RQ 1 EV IPR005892; TIGR01186; sufficient; -- SN 2 ID Glycine betaine/proline betaine transport system permease protein ProW RQ 1 EV IPR000515; PF00528; sufficient; EV IPR000515; PS50928; sufficient; EV IPR000515; cd06261; sufficient; -- SN 3 ID Glycine betaine/proline betaine-binding periplasmic protein RQ 1 EV IPR007210; PF04069; sufficient; // AC GenProp1127 DE ThiG-ThiH thiazole phosphate synthase complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2135; CC Role in thiamine biosynthesis, catalysing the synthesis of the thiazole CC phosphate moiety of thiamine. ThiG-ThiH is found downstream of the CC activities of IscS, the ThiS-ThiF complex (CPX-2134) and ThiI, and CC requires the activity of 1-deoxy-D-xylulose 5-phosphate (DXP). The ThiH CC subunit binds a 4Fe-4S cluster that is coordinated by 3 cysteines CC (Cys-X-X-X-Cys-X-X-Cys) and an exchangeable S-adenosyl-L-methionine CC molecule. Sulfur is donated by the ThiS-ThiF complex. -- SN 1 ID Thiazole synthase (ThiG) RQ 1 EV IPR008867; MF_00443; sufficient; EV IPR008867; PTHR34266; sufficient; EV IPR008867; cd04728; sufficient; -- SN 2 ID 2-iminoacetate synthase (ThiH) RQ 1 EV IPR012726; PTHR43583:SF1; sufficient; EV IPR012726; SFLDF00301; sufficient; EV IPR012726; TIGR02351; sufficient; // AC GenProp1129 DE Carbamoyl phosphate synthetase complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1937; DR PDBe; 1A9X; DR PDBe; 1BXR; DR PDBe; 1CE8; CC Plays a key role in both pyrimidine and arginine biosynthesis by CC catalyzing the production of carbamoyl phosphate from one molecule of CC bicarbonate, two molecules of MgATP, and one molecule of glutamine. CC Consists of two polypeptide chains referred to as the small and large CC subunits, which contain a total of three separate active sites that are CC connected by an intramolecular tunnel. The small subunit harbors one of CC these active sites and is responsible for the hydrolysis of glutamine CC to glutamate and ammonia. The large subunit binds the two required CC molecules of MgATP and is involved in assembling the final product. CC Compounds such as L-ornithine, UMP, and IMP allosterically regulate the CC enzyme. -- SN 1 ID Carbamoyl-phosphate synthase small chain RQ 1 EV IPR006274; MF_01209; sufficient; EV IPR006274; TIGR01368; sufficient; -- SN 2 ID Carbamoyl-phosphate synthase large chain RQ 1 EV IPR006275; MF_01210_A; sufficient; EV IPR006275; MF_01210_B; sufficient; EV IPR006275; TIGR01369; sufficient; // AC GenProp1130 DE DnaB-DnaC-DnaT-PriA-PriB complex TP COMPLEX AU Complex Portal TH 4 DR Complex Portal; CPX-1951; CC An intermediate but essential pre-primosome complex formed during CC re-initiation of replication. It is formed by the interaction of the CC helicase loading complex DnaB-DnaC with replication restart proteins CC after a stalled replication fork has been repaired. -- SN 1 ID Replicative DNA helicase RQ 1 EV IPR007692; TIGR00665; sufficient; -- SN 2 ID Primosomal protein 1 RQ 1 EV IPR020917; MF_01061; sufficient; -- SN 3 ID DNA replication protein DnaC RQ 1 EV IPR028350; PIRSF003073; sufficient; -- SN 4 ID Primosomal protein N' RQ 1 EV IPR005259; MF_00983; sufficient; EV IPR005259; TIGR00595; sufficient; -- SN 5 ID Primosomal replication protein N RQ 1 EV IPR023646; MF_00720; sufficient; EV IPR023646; PIRSF003135; sufficient; EV IPR023646; TIGR04418; sufficient; // AC GenProp1131 DE Glutathione-regulated potassium-efflux system KefB-KefG complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-3090; CC Potassium efflux pore which protects the bacteria from the toxic CC effects of electrophilic compounds that react with nucleophiles found CC in the bases of DNA and the side chains of proteins, especially CC cysteine. Potassium efflux via KefB is accompanied by H+ and Na+ influx CC and hence causes acidification of the cytoplasm. KefB is activated by CC glutathione adducts and inactivated by glutathione which bind to the CC cytosolic regulatory K+ transport and nucleotide binding domain of CC KefB. -- SN 1 ID Glutathione-regulated potassium-efflux system ancillary protein KefG RQ 1 EV IPR023947; MF_01415; sufficient; -- SN 2 ID Glutathione-regulated potassium-efflux system protein KefB RQ 1 EV IPR020884; MF_01412; sufficient; // AC GenProp1132 DE Holo-translocon SecYEG-SecDF-YajC-YidC complex TP COMPLEX AU Complex Portal TH 6 RN [1] RM 27924919 RT A central cavity within the holo-translocon suggests a mechanism for RT membrane protein insertion. RA Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, RA Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, RA Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C RL Sci Rep. 2016;6:38399 DR Complex Portal; CPX-1095; DR PDBe; 2akh; DR PDBe; 2aki; CC Functions in both protein secretion to the trans side of the plasma CC membrane and insertion of membrane proteins into the lipid bilayer. The CC HTL complex is more proficient in cotranslational membrane protein CC insertion compared with SecYEG (CPX-1096) alone, and the CC post-translational secretion of a beta-barreled outer-membrane protein CC driven by secA and ATP becomes much more dependent on the proton-motive CC force than is the case for SecYEG. The YidC periplasmic and SecD CC periplasmic region P1-head domains are positioned to interact with CC translocation substrates preventing backsliding of the polypeptide CC through the translocation channel. -- SN 1 ID Protein translocase subunit SecD RQ 1 EV IPR005791; MF_01463_B; sufficient; EV IPR005791; TIGR01129; sufficient; -- SN 2 ID Sec translocon accessory complex subunit YajC RQ 1 EV IPR003849; PF02699; sufficient; EV IPR003849; PR01853; sufficient; EV IPR003849; PTHR33909; sufficient; EV IPR003849; SM01323; sufficient; EV IPR003849; TIGR00739; sufficient; -- SN 3 ID Protein translocase subunit SecF RQ 1 EV IPR005665; MF_01464_B; sufficient; EV IPR005665; TIGR00966; sufficient; -- SN 4 ID Protein translocase subunit SecY RQ 1 EV IPR026593; MF_01465; sufficient; -- SN 5 ID Protein translocase subunit SecE RQ 1 EV IPR005807; PR01650; sufficient; EV IPR005807; PTHR33910; sufficient; EV IPR005807; TIGR00964; sufficient; -- SN 6 ID Membrane protein insertase YidC RQ 1 EV IPR019998; MF_01810; sufficient; -- SN 7 ID Protein-export membrane protein SecG RQ 1 EV IPR004692; PF03840; sufficient; EV IPR004692; PR01651; sufficient; EV IPR004692; PTHR34182; sufficient; EV IPR004692; TIGR00810; sufficient; // AC GenProp1133 DE YoeB-YefM toxin-antitoxin complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 16109374 RT Conformational change in the catalytic site of the ribonuclease YoeB RT toxin by YefM antitoxin. RA Kamada K, Hanaoka F RL Mol Cell. 2005;19:497-509 RN [2] RM 24561554 RT The binary protein-protein interaction landscape of Escherichia coli. RA Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, RA Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty RA S, Emili A, Babu M, Aloy P, Pieper R, Uetz P RL Nat Biotechnol. 2014;32:285-290 DR Complex Portal; CPX-1087; CC Toxin-antitoxin (TA) complex. Antitoxin YefM binding to toxin YoeB CC suppresses YoeB toxicity and represses its own transcription by binding CC to the yefM-yoeB operon. On its own, YoeB has translation-dependent CC mRNA degradation activity and preferentially cleaves at 3' ends of CC purine-rich ribonucleotides. -- SN 1 ID Toxin YoeB RQ 1 EV IPR009614; PF06769; sufficient; EV IPR009614; PTHR38039; sufficient; EV IPR009614; TIGR02116; sufficient; -- SN 2 ID Antitoxin YefM RQ 1 EV IPR006442; PF02604; sufficient; // AC GenProp1134 DE TusBCDE complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-2144; DR PDBe; 2d1p; CC Involved in the sulfur-relay system required for 2-thiolation of CC 5-methylaminomethyl-2-thiouridine (mnm5s2U) at tRNA wobble positions. CC It transfers sulfur (most likely in persulfide form) from TusA (P0A890) CC to the TusE-MnmA complex (CPX-2145) via Cys78-TusD and CC Cys108-TusE. Although TusBCD complex has been crystallised it has not CC yet been shown experimentally that it exists in vivo without subunit CC TusE attached. -- SN 1 ID Sulfurtransferase TusE RQ 1 EV IPR007453; PF04358; sufficient; EV IPR007453; PIRSF006223; sufficient; EV IPR007453; PTHR37010; sufficient; EV IPR007453; TIGR03342; sufficient; -- SN 2 ID Sulfurtransferase TusD RQ 1 EV IPR017463; MF_00390; sufficient; EV IPR017463; TIGR03012; sufficient; -- SN 3 ID Protein TusC RQ 1 EV IPR037450; MF_00389; sufficient; -- SN 4 ID Protein TusB RQ 1 EV IPR023526; MF_01564; sufficient; // AC GenProp1135 DE Formate dehydrogenase N complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-1975; DR PDBe; 1kqg; CC Involved in electron transport during anaerobic respiration: electrons CC are passed from formate dehydrogenase-N (Fdh-N) complex to nitrate CC reductase (NarGHI, CPX-1974) complex via a quinone-quinol CC (hydroquinone) redox reaction. The molybdopterin cofactor Mo-bisMGD CC receives electrons from formate, passes them down a Fe-S cluster chain CC to the periplasmic heme, from there to the cytoplasmic heme from where CC it is transferred to quinone on FdnH. Quinol transports the electrons CC to the NarGHI complex. The collaboration of these two complexes CC contributes to the proton motive force: electrons are ultimately CC donated to Fdh-N by formate in the periplasm, transported to the CC cytoplasm and accepted by nitrate. Hydrogen ions are transported in the CC opposite direction: Quinone is reduced to quinol by cytoplasmic protons CC which are in turn released into the periplasm when quinol is oxidized CC to quinone. -- SN 1 ID Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit RQ 1 EV IPR006471; TIGR01583; sufficient; -- SN 2 ID Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit RQ 1 EV IPR014603; PIRSF036298; sufficient; -- SN 3 ID Formate dehydrogenase, nitrate-inducible, major subunit RQ 1 EV IPR006443; TIGR01553; sufficient; // AC GenProp1136 DE Twin-arginine translocation complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-3445; CC Proton motive force dependent transporter of folded precursor proteins CC containing a SRRxFLK (TAT) sequence motif in the N-terminal part of CC their signal sequences across the cytoplasmic membrane. -- SN 1 ID Sec-independent protein translocase protein TatE RQ 1 EV IPR024905; MF_00903; sufficient; -- SN 2 ID Sec-independent protein translocase protein TatB RQ 1 EV IPR018448; MF_00237; sufficient; EV IPR018448; TIGR01410; sufficient; -- SN 3 ID Sec-independent protein translocase protein TatC RQ 1 EV IPR002033; MF_00902; sufficient; EV IPR002033; PF00902; sufficient; EV IPR002033; PR01840; sufficient; EV IPR002033; PTHR30371; sufficient; EV IPR002033; TIGR00945; sufficient; -- SN 4 ID Sec-independent protein translocase protein TatA RQ 1 EV IPR006312; MF_00236; sufficient; EV IPR006312; TIGR01411; sufficient; // AC GenProp1137 DE Endopeptidase ClpAP complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22595189 RT ClpP: a structurally dynamic protease regulated by AAA+ proteins. RA Alexopoulos JA, Guarné A, Ortega J RL J Struct Biol. 2012;179:202-210 DR Complex Portal; CPX-3175; CC ATP-dependent serine protease which degrades intracellular unfolded or CC misfolded proteins. -- SN 1 ID ATP-dependent Clp protease proteolytic subunit RQ 1 EV IPR001907; MF_00444; sufficient; EV IPR001907; PR00127; sufficient; EV IPR001907; TIGR00493; sufficient; EV IPR001907; cd07017; sufficient; -- SN 2 ID ATP-dependent Clp protease ATP-binding subunit ClpA RQ 1 EV IPR013461; TIGR02639; sufficient; // AC GenProp1138 DE Molybdopterin synthase TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1970; DR PDBe; 1fm0; DR PDBe; 3bii; DR PDBe; 1nvi; DR PDBe; 1fma; CC Involved in molybdopterin cofactor (Moco) biosynthesis under anaerobic CC conditions converting molybdopterin precursor Z to molybdopterin. This CC requires the incorporation of two sulfur atoms into precursor Z to CC generate a dithiolene group. The sulfur is provided by MoaD. This CC process is evolutionarily conserved and is equivalent to REACT_25073.1 -- SN 1 ID Molybdopterin synthase catalytic subunit (MoaE) RQ 1 EV IPR003448; PF02391; sufficient; EV IPR003448; cd00756; sufficient; -- SN 2 ID Molybdopterin synthase sulfur carrier subunit (MoaD) RQ 1 EV IPR010034; TIGR01682; sufficient; // AC GenProp1139 DE Chemotaxis phosphorelay complex CheY-CheZ TP COMPLEX AU Complex Portal TH 1 RN [1] RM 12080332 RT Structure and catalytic mechanism of the E. coli chemotaxis phosphatase RT CheZ. RA Zhao R, Collins EJ, Bourret RB, Silversmith RE RL Nat Struct Biol. 2002;9:570-575 DR Complex Portal; CPX-1088; DR PDBe; 1kmi; CC Plays a role in chemotaxis, the movement toward or away from chemicals. CC The flagellar motor of bacteria is a rotary device energized by the CC membrane ion gradient and the complex is required for the rotation and CC directional switching of the flagellum and also functions in flagellar CC assembly. Motor torque is produced at the top of the switch complex, CC where the FliG C-terminal domain bears several conserved charged CC residues that interact with charged groups of the stator protein MotA CC (P09348). The directionality of the rotation is determined by binding CC of CheY-P to the lower part of the C-ring which switches the CC directionality from counter-clockwise to clockwise. The CheY-CheZ CC complex enhances the dephosphorylation rate of P-CheY. This CC dephosphorylation reduces the binding of CheY to the switch and ensures CC rapid locomotor responses to changes in the supply of signaling CC phosphoryl groups to CheY, thus enabling a continuous response to CC environmental changes. -- SN 1 ID Protein phosphatase CheZ RQ 1 EV IPR007439; PF04344; sufficient; EV IPR007439; PIRSF002884; sufficient; -- SN 2 ID Chemotaxis protein CheY RQ 1 EV IPR001789; PF00072; sufficient; EV IPR001789; PS50110; sufficient; EV IPR001789; SM00448; sufficient; EV IPR001789; cd00156; sufficient; // AC GenProp1140 DE IHF complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1957; DR PDBe; 1OWF; DR PDBe; 1OWG; DR PDBe; 2ht0; DR PDBe; 1ihf; CC Histone-like, specific DNA-binding complex that functions in genetic CC recombination as well as in transcriptional and translational control. CC DNA-binding is both topology- or structural-dependent, and CC sequence-specific. -- SN 1 ID Integration host factor subunit beta RQ 1 EV IPR005685; MF_00381; sufficient; EV IPR005685; TIGR00988; sufficient; -- SN 2 ID Integration host factor subunit alpha RQ 1 EV IPR005684; MF_00380; sufficient; EV IPR005684; TIGR00987; sufficient; EV IPR005684; cd13835; sufficient; // AC GenProp1141 DE Cytochrome bd-I ubiquinol oxidase complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-268; CC A protein complex integral to the bacterial electron transport chain. CC Electrons are donated by the oxidation of ubiquinol to ubiquinone and CC used to reduce molecular oxygen, generating a proton motive force using CC protons and electrons from opposite sides of the membrane to generate CC water. -- SN 1 ID Cytochrome bd-I ubiquinol oxidase subunit X RQ 1 EV IPR011724; TIGR02106; sufficient; -- SN 2 ID Cytochrome bd-I ubiquinol oxidase subunit 1 RQ 1 EV IPR002585; PF01654; sufficient; EV IPR002585; PIRSF006446; sufficient; EV IPR002585; PTHR30365; sufficient; -- SN 3 ID Cytochrome bd-I ubiquinol oxidase subunit 2 RQ 1 EV IPR003317; PF02322; sufficient; EV IPR003317; PIRSF000267; sufficient; EV IPR003317; PTHR43141; sufficient; EV IPR003317; TIGR00203; sufficient; // AC GenProp1142 DE FtsQBL complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 22888013 RT Bacterial cytokinesis: From Z ring to divisome. RA Lutkenhaus J, Pichoff S, Du S RL Cytoskeleton (Hoboken). 2012;69:778-790 DR Complex Portal; CPX-3099; CC Sub-complex of the divisome, required for cell division. FtsQBL appears CC to form independently of the divisome and is hypothesized to link CC cytoplasmic to periplasmic events during cell division through a CC multitude of transient interactions. -- SN 1 ID Cell division protein FtsL RQ 1 EV IPR011922; MF_00910; sufficient; EV IPR011922; PF04999; sufficient; EV IPR011922; PTHR37479; sufficient; EV IPR011922; TIGR02209; sufficient; -- SN 2 ID Cell division protein FtsB RQ 1 EV IPR023081; MF_00599; sufficient; EV IPR023081; PTHR37485; sufficient; -- SN 3 ID Cell division protein FtsQ RQ 1 EV IPR026579; MF_00911; sufficient; EV IPR026579; PTHR35851; sufficient; // AC GenProp1143 DE Plasma membrane fumarate reductase complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-1967; CC Catalyzes the terminal step of anaerobic respiration. Electrons are CC donated to membrane-bound subunits FrdC and FrdD by 2 quinol CC (hydroquinone) molecules and transferred to a flavin adenine nucleotide CC (FAD, covalently-bound to subunit FrdA) through three distinct Fe-S CC clusters (within subunit FrdB). Ultimately, the electrons are used to CC reduce FAD-bound fumarate to succinate. Electrons can also be CC transported in the opposite direction where they are donated by CC succinate and ultimately reduce quinone to quinol. Member of the Complex CC II family. The functionally inverse complex found in aerobic CC respiration is the SQR complex (CPX-1931). -- SN 1 ID Fumarate reductase flavoprotein subunit RQ 1 EV IPR005884; TIGR01176; sufficient; -- SN 2 ID Fumarate reductase iron-sulfur subunit RQ 1 EV IPR004489; TIGR00384; sufficient; -- SN 3 ID Fumarate reductase subunit D RQ 1 EV IPR003418; MF_00709; sufficient; EV IPR003418; PD015693; sufficient; EV IPR003418; PF02313; sufficient; EV IPR003418; PIRSF000179; sufficient; EV IPR003418; cd00547; sufficient; -- SN 4 ID Fumarate reductase subunit C RQ 1 EV IPR003510; MF_00708; sufficient; EV IPR003510; PD015900; sufficient; EV IPR003510; PF02300; sufficient; EV IPR003510; PIRSF000180; sufficient; EV IPR003510; cd00546; sufficient; // AC GenProp1144 DE IscS-ThiL complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 20404999 RT Structural basis for Fe-S cluster assembly and tRNA thiolation mediated RT by IscS protein-protein interactions. RA Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte RA A, Armengod ME, Cygler M RL PLoS Biol. 2010;8:e1000354 RN [2] RM 16387657 RT Mechanistic insights into sulfur relay by multiple sulfur mediators RT involved in thiouridine biosynthesis at tRNA wobble positions. RA Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T RL Mol Cell. 2006;21:97-108 DR Complex Portal; CPX-2140; CC IscS desulfurases L-cysteine and transfers the sulfur moiety to Cys456 CC on ThiI in a transpersulfidation reaction. Downstream, ThiL is involved CC in thiamine-pyrophosphate biosynthesis, the active form of vitamin B1. -- SN 1 ID Thiamine-monophosphate kinase RQ 1 EV IPR006283; MF_02128; sufficient; EV IPR006283; PIRSF005303; sufficient; EV IPR006283; PTHR30270; sufficient; EV IPR006283; TIGR01379; sufficient; EV IPR006283; cd02194; sufficient; -- SN 2 ID Cysteine desulfurase IscS RQ 1 EV IPR010240; MF_00331; sufficient; EV IPR010240; PTHR11601:SF34; sufficient; EV IPR010240; TIGR02006; sufficient; // AC GenProp1146 DE Dha Kinase TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-2634; DR PDBe; 3pnl; CC Catalyses the phosphorylation of dihydroxyacetone (Dha) using CC phosphoenolpyruvate (PEP) as a phosphoryl donor. Dihydroxyacetone CC phosphate (Dha-P) is an intermediate for the synthesis of pyruvate. The CC E1 domain of DhaM catalyses the phosphoryl transfer from PEP to the CC small (9 kDa) soluble HPr (histidine-containing phosphoryl carrier CC protein) domain. Phosphorylated DhaM binds to ADP-bound DhaL and CC transiently phosphorylates the ADP. ATP-loaded DhaL associates with CC DhaK containing the Dha substrate covalently bound to His-218 through a CC hemiaminal bond. Coenzyme, ATP-bound DhaL transfers a phosphate to Dha CC yielding Dha-P. -- SN 1 ID PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL RQ 1 EV IPR012737; TIGR02365; sufficient; -- SN 2 ID PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK RQ 1 EV IPR012736; TIGR02363; sufficient; -- SN 3 ID Protein-lysine deacetylase RQ 1 EV IPR012844; TIGR02364; sufficient; // AC GenProp1147 DE Chemotaxis phosphorelay complex CheA-CheY TP COMPLEX AU Complex Portal TH 1 RN [1] RM 9437425 RT Structure of the CheY-binding domain of histidine kinase CheA in RT complex with CheY. RA Welch M, Chinardet N, Mourey L, Birck C, Samama JP RL Nat Struct Biol. 1998;5:25-29 DR Complex Portal; CPX-1077; DR PDBe; 1eay; DR PDBe; 1ffg; DR PDBe; 1ffs; DR PDBe; 1ffw; CC Plays a role in chemotaxis, the movement toward or away from chemicals. CC The complex is formed to activate CheY protein that then induces the CC change of the flagellar rotors from counterclocwise to clockwise CC rotation. CheA interacts with transmembrane chemoreceptors to generate CC stimulus signals via autophosphorylion of CheA which then serves as a CC phosphodonor for CheY. The P-CheY generated by this interaction binds CC to FliM (P06974), the switch component of the flagellar motor. -- SN 1 ID Chemotaxis protein CheA RQ 1 EV IPR004105; PF02895; sufficient; EV IPR004105; SM01231; sufficient; -- SN 2 ID Chemotaxis protein CheY RQ 1 EV IPR001789; PF00072; sufficient; EV IPR001789; PS50110; sufficient; EV IPR001789; SM00448; sufficient; EV IPR001789; cd00156; sufficient; // AC GenProp1148 DE DMSO reductase complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-320; CC Terminal reductase required for the reduction of dimethyl sulfoxide CC (DMSO) to dimethyl sulfide (DMS) and that of a broad array of S- and CC N-oxide compounds during anaerobic growth. Induced in the presence of CC fumarate. The expression of the enzyme is dependent on molybdenum. -- SN 1 ID Dimethyl sulfoxide reductase DmsA RQ 1 EV IPR011888; TIGR02166; sufficient; -- SN 2 ID Anaerobic dimethyl sulfoxide reductase chain B RQ 1 EV IPR014297; TIGR02951; sufficient; -- SN 3 ID Anaerobic dimethyl sulfoxide reductase chain C RQ 1 EV IPR007059; PF04976; sufficient; EV IPR007059; PTHR38095; sufficient; // AC GenProp1149 DE Topoisomerase IV TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1104; CC Type II DNA topoisomerase responsible for relaxing supercoiled DNA by CC introducing a double-stranded break in DNA and passing a second duplex CC segment of DNA through the break before resealing it. Acts on CC topologically different substrates including (+) and negative (-) CC supercoiled DNA and knotted and catenated DNA. Decatenates newly CC replicated DNA, removing the majority of links behind the replication CC forks. -- SN 1 ID DNA topoisomerase 4 subunit B RQ 1 EV IPR005737; MF_00938; sufficient; EV IPR005737; PR01098; sufficient; EV IPR005737; PTHR10169:SF45; sufficient; EV IPR005737; TIGR01055; sufficient; -- SN 2 ID DNA topoisomerase 4 subunit A RQ 1 EV IPR005742; MF_00936; sufficient; // AC GenProp1150 DE Cobalamin transport complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-2105; DR PDBe; 2qi9; DR PDBe; 4fi3; CC Type II ABC importer catalysing the ATP-dependent uptake of cobalamin CC (vitamin B12) from the periplasm across the plasma membrane into the CC cytoplasm. -- SN 1 ID Vitamin B12 import system permease protein BtuC RQ 1 EV IPR023691; MF_01004; sufficient; -- SN 2 ID Vitamin B12 import ATP-binding protein BtuD RQ 1 EV IPR023693; MF_01005; sufficient; -- SN 3 ID Vitamin B12-binding protein RQ 1 EV IPR023544; MF_01000; sufficient; // AC GenProp1151 DE MacAB-TolC complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 20307498 RT The tip region of the MacA alpha-hairpin is important for the binding RT to TolC to the Escherichia coli MacAB-TolC pump. RA Xu Y, Sim SH, Song S, Piao S, Kim HM, Jin XL, Lee K, Ha NC RL Biochem Biophys Res Commun. 2010;394:962-965 DR Complex Portal; CPX-2107; DR PDBe; 5nik; DR PDBe; 5nil; DR PDBe; 3fpp; DR PDBe; 1ek9; CC Tripartite, ATP-dependent efflux pump spanning the entire cell membrane CC system. Confers resistance to antibiotics and other toxins CC (specifically macrolide compounds containing 14- and 15-membered CC lactones) by transporting them out of the bacterial cell. MacB is the CC dimeric, non-canonical ATP-binding cassette (ABC) transporter subunit CC containing 4 transmembrane domains which span the entire inner CC membrane, an N-terminal nucleotide binding domain, and a central CC hydrophilic periplasmic domain. It binds to the periplasmic membrane CC fusion protein MacA. Whether it also binds directly to TolC is unclear CC (EBI-6305934 shows a very weak reaction). MacA is hexameric and binds CC directly to MacB and TolC facilitating direct channelling of toxins out CC of the cell. It consists of an alpha-helical, TolC-binding barrel CC domain, an intermediate lipyl domain, and a beta-barrel domain which is CC the likely MacB binding domain. It may also have a plasma membrane CC binding domain (through its N and C termini), but does not bind CC directly to the outer membrane. It appears to enhance the ATPase CC activity of MacB. TolC is trimeric and has two major domains, a CC transmembrane beta-barrel spanning the entire outer membrane, and an CC alpha-helical periplasmic barrel domain through which it binds to CC MacA. MacA and TolC appear to interact allosterically in a tip-to-tip CC fashion through the 'cogwheel' alpha-hairpin tip regions of both CC complexes. -- SN 1 ID Macrolide export ATP-binding/permease protein MacB RQ 1 EV IPR025857; PF12704; sufficient; -- SN 2 ID Macrolide export protein MacA RQ 1 EV IPR030190; PTHR30572:SF10; sufficient; -- SN 3 ID Outer membrane protein TolC RQ 1 EV IPR010130; TIGR01844; sufficient; // AC GenProp1152 DE DnaA-DnaB complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 21856207 RT Replication initiation at the Escherichia coli chromosomal origin. RA Kaguni JM RL Curr Opin Chem Biol. 2011;15:606-613 DR Complex Portal; CPX-1935; CC DnaA forms homo-oligomers (CPX-1943) on specific regions of the CC replication origin oriC and initiates unwinding of a 13 nt region when CC complexed with ATP. DnaA loads one DnaB-DnaC complex (CPX-1934) on the CC top strand near the left border of oriC and a second DnaB-DnaC complex CC on the lower strand next to DnaA box R1. After DnaB loads at oriC, DnaC CC must dissociate so that DnaB can unwind the parental duplex DNA. DnaA CC P46 is an essential residue for the binding to DnaB. -- SN 1 ID Replicative DNA helicase RQ 1 EV IPR007692; TIGR00665; sufficient; -- SN 2 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; // AC GenProp1153 DE TRCF-UvrA complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2155; CC An SF2 ATPase that orchestrates a preferential pathway for nucleotide CC excision repair (NER) called transcription-coupled repair (TCR) by CC specific recognition of the transcription and NER assemblies. First, CC TRCF relieves transcription-dependent NER inhibition due to occlusion CC of the DNA lesion by RNAP. TRCF approaches the stalled RNAP from behind CC and induces its forward translocation and subsequent release by CC stepping on dsDNA using ATP hydrolysis. The consequent collapse of the CC upstream end of the transcription bubble leads to a massive CC destabilization of the otherwise stable ternary elongation complex, CC consisting of the open DNA transcription fork and the newly-synthesised CC RNA, and transcription termination. Second, TRCF recruits the UvrABC CC repair system (CPX-2151, CPX-2152, CPX-2153) to the unmasked lesion by CC binding to UvrA, a subunit of the UvrAB complex (CPX-2151). UvrA CC binding to TRCF and UvrB are probably mutually exclusive owing to the CC conserved interface on UvrA. Formation of the TRCF-UvrA complex CC initiates a cascade of events resulting in lesion excision and gap CC filling. TRCF also has roles beyond TCR - in the rescue of replication CC forks stalled by head-on collisions with RNAPs, in the development of CC antibiotic resistance, recombination, and transcriptional regulation. -- SN 1 ID UvrABC system protein A RQ 1 EV IPR004602; MF_00205; sufficient; EV IPR004602; TIGR00630; sufficient; -- SN 2 ID Transcription-repair-coupling factor RQ 1 EV IPR004576; MF_00969; sufficient; EV IPR004576; TIGR00580; sufficient; // AC GenProp1154 DE FtsBL complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22888013 RT Bacterial cytokinesis: From Z ring to divisome. RA Lutkenhaus J, Pichoff S, Du S RL Cytoskeleton (Hoboken). 2012;69:778-790 DR Complex Portal; CPX-3299; CC Hypothesized to be structural proteins that contribute to the CC stabilization of the Z-ring. May be a multi-valent tethering structural CC element of the divisome. -- SN 1 ID Cell division protein FtsL RQ 1 EV IPR011922; MF_00910; sufficient; EV IPR011922; PF04999; sufficient; EV IPR011922; PTHR37479; sufficient; EV IPR011922; TIGR02209; sufficient; -- SN 2 ID Cell division protein FtsB RQ 1 EV IPR023081; MF_00599; sufficient; EV IPR023081; PTHR37485; sufficient; // AC GenProp1155 DE DNA polymerase III proofreading complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 14630952 RT A peptide switch regulates DNA polymerase processivity. RA López de Saro FJ, Georgescu RE, O'Donnell M RL Proc Natl Acad Sci U S A. 2003;100:14689-14694 RN [2] RM 20413500 RT Stoichiometry and architecture of active DNA replication machinery in RT Escherichia coli. RA Reyes-Lamothe R, Sherratt DJ, Leake MC RL Science. 2010;328:498-501 RN [3] RM 21675919 RT DNA replicases from a bacterial perspective. RA McHenry CS RL Annu Rev Biochem. 2011;80:403-436 DR Complex Portal; CPX-1925; CC Functions as the leading- and lagging-strand replicase in DNA CC replication. Pol III alone exhibits a very low processivity, additional CC interactions stabilize the interaction of Pol III with the replication CC fork and increase its processivity. The polymerase subunit of the DNA CC polymerase III holoenzyme (CPX-1924) contains three participants: the CC polymerase subunit alpha and the two proofreading subunits, epsilon and CC theta. While two polymerase subcomplexes elongate the leading and CC lagging strands the function of the third polymerase subcomplex - bound CC to the third tau subunit of the clamp loading complex (CPX-1926) - is CC as of yet unknown. The beta and tau subunits of the Pol III holoenzyme CC appear to be competing for the same binding site on alpha. This CC competition allows for the clamp loader (CPX-1926) to disengage from CC the polymerase unit and facilitate binding of alpha to the sliding CC clamp (CPX-1927) to commence strand elongation. At the end of CC replication the tau subunit re-connects with alpha, displacing the CC polymerase subcomplex from the newly-synthesised double-stranded DNA. -- SN 1 ID DNA polymerase III subunit theta RQ 1 EV IPR009052; PD057609; sufficient; EV IPR009052; PF06440; sufficient; -- SN 2 ID DNA polymerase III subunit alpha RQ 1 EV IPR004805; PTHR32294; sufficient; EV IPR004805; TIGR00594; sufficient; -- SN 3 ID DNA polymerase III subunit epsilon RQ 1 EV IPR006309; TIGR01406; sufficient; EV IPR006309; cd06131; sufficient; // AC GenProp1156 DE BtuCD complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2106; CC Core subunit of the cobalamin transport complex containing the CC transmembrane homodimer BtuC and the cytoplasmic ATPase homodimer CC BtuD. Requires the binding of cobalamin (vitamin B12)-bound subunit BtuF CC to bind to the periplasmic site of the transmembrane subunit in order CC to transport cobalamin through the periplasmic membrane. -- SN 1 ID Vitamin B12 import ATP-binding protein BtuD RQ 1 EV IPR023693; MF_01005; sufficient; -- SN 2 ID Vitamin B12 import system permease protein BtuC RQ 1 EV IPR023691; MF_01004; sufficient; // AC GenProp1157 DE Vitamin B12 outer membrane transporter complex TP COMPLEX AU Complex Portal TH 3 RN [1] RM 16741124 RT Outer membrane active transport: structure of the BtuB:TonB complex. RA Shultis DD, Purdy MD, Banchs CN, Wiener MC RL Science. 2006;312:1396-1399 DR Complex Portal; CPX-1083; DR PDBe; 2gsk; DR PDBe; 5sv1; CC A member of the TonB-dependent transporter family (TBDTs) which binds CC and then transports cobalamine (vitamin B12) across the outer membrane. CC TBDTs are energy-dependent gated channels that usually transport large CC metal complexes which cannot fit through porins, and are too scarce to CC enter by mass-action-driven transport. Energy-dependent uptake through CC TBDTs requires interaction with TonB in complex with ExbB and ExbD in CC the inner membrane, ExbBD. TonB undergoes rapid energized movement CC driven by ExbBD which harvests the electrochemical force from the CC proton gradient across the inner membrane and converts it into rotational CC motion. Hence, TonB may pull or twist the N-termini of TBDTs to promote CC transport of substrates into the periplasm. ATP-binding-cassette (ABC) CC transporters subsequently move the cyanocobalamine through the periplasm CC and inner membrane. -- SN 1 ID Biopolymer transport protein ExbD RQ 1 EV IPR014170; TIGR02803; sufficient; EV IPR014171; TIGR02804; sufficient; -- SN 2 ID Vitamin B12 transporter BtuB RQ 1 EV IPR010101; MF_01531; sufficient; EV IPR010101; TIGR01779; sufficient; -- SN 3 ID Biopolymer transport protein ExbB RQ 1 EV IPR014164; TIGR02797; sufficient; EV IPR014172; TIGR02805; sufficient; -- SN 4 ID Protein TonB RQ 1 EV IPR003538; PR01374; sufficient; // AC GenProp1158 DE Molybdopterin-synthase adenylyltransferase complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1968; DR PDBe; 1jw9; DR PDBe; 1jwb; CC Involved in molybdopterin cofactor (Moco) biosynthesis under anaerobic CC conditions. MoeB catalyses the adenylation of MoaD by ATP, a CC requirement for MoaD's activity in MPT synthase (CPX-1970). Receives CC sulfur moiety from IscS (P0a6b7). This process is evolutionarily conserved CC and is equivalent to REACT_25073.1 -- SN 1 ID Molybdopterin-synthase adenylyltransferase RQ 1 EV IPR012730; TIGR02355; sufficient; -- SN 2 ID Molybdopterin synthase sulfur carrier subunit RQ 1 EV IPR010034; TIGR01682; sufficient; // AC GenProp1159 DE Enzyme IIA-maltose transporter complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-1978; CC Binding of enzyme IIA (EIIA-Glc), a component of the glucose-specific CC phosphotransferase system, inhibits maltose transport from the CC periplasm to the cytoplasm. Two molecules of EIIA-Glc each bind CC allosterically to both subunits of MalK thereby fastening the maltose CC transporter in the open, inward-facing conformation which prevents the CC binding of maltose-loaded maltose binding protein MBP (MalE) CC (CPX-1932). Only the non-phosphorylated form of enzyme IIA functions CC as a maltose uptake inhibitor. -- SN 1 ID Maltose transport system permease protein MalF RQ 1 EV IPR030156; PTHR30193:SF22; sufficient; -- SN 2 ID Maltose transport system permease protein MalG RQ 1 EV IPR000515; PF00528; sufficient; EV IPR000515; PS50928; sufficient; EV IPR000515; cd06261; sufficient; -- SN 3 ID PTS system glucose-specific EIIA component RQ 1 EV IPR001127; PF00358; sufficient; EV IPR001127; PS00371; sufficient; EV IPR001127; PS51093; sufficient; EV IPR001127; TIGR00830; sufficient; -- SN 4 ID Maltose/maltodextrin import ATP-binding protein MalK RQ 1 EV IPR015855; PS51245; sufficient; // AC GenProp1160 DE Glutathione-regulated potassium-efflux system KefC-KefF complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2543; DR PDBe; 3eyw; DR PDBe; 3l9w; CC Potassium efflux pore which protects the bacteria from the toxic CC effects of electrophilic compounds which react with nucleophiles found CC in the bases of DNA and the side chains of proteins, especially CC cysteine. Potassium efflux via KefC is accompanied by H+ and Na+ influx CC and hence causes acidification of the cytoplasm. KefC is activated by CC glutathione adducts and inactivated by glutathione which bind to the CC cytosolic regulatory K+ transport and nucleotide binding domain of CC KefC. -- SN 1 ID Glutathione-regulated potassium-efflux system ancillary protein KefF RQ 1 EV IPR023948; MF_01414; sufficient; EV IPR023948; PTHR10204:SF41; sufficient; -- SN 2 ID Glutathione-regulated potassium-efflux system protein KefC RQ 1 EV IPR023941; MF_01413; sufficient; EV IPR023941; PTHR16254:SF28; sufficient; // AC GenProp1161 DE TusE-MnmA complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2145; CC Involved in the sulfur-relay system required for 2-thiolation of CC 5-methylaminomethyl-2-thiouridine (mnm5s2U) at tRNA wobble positions. CC The TusE subunit transfers sulfur (most likely bound to Cys108 as CC persulfide) from the TusBCDE complex (CPX-2144) to the tRNA. -- SN 1 ID Sulfurtransferase TusE RQ 1 EV IPR007453; PF04358; sufficient; EV IPR007453; PIRSF006223; sufficient; EV IPR007453; PTHR37010; sufficient; EV IPR007453; TIGR03342; sufficient; -- SN 2 ID tRNA-specific 2-thiouridylase MnmA RQ 1 EV IPR004506; MF_00144; sufficient; EV IPR004506; PTHR11933; sufficient; EV IPR004506; TIGR00420; sufficient; EV IPR004506; cd01998; sufficient; // AC GenProp1162 DE Hda-beta clamp complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1954; CC Part of the replication initiation inhibiting machinery. The CC interaction of Hda with the beta clamp of the DNA polymerase III CC holoenzyme activates the ATPase activity of DnaA, transforming DnaA-ATP CC to DnaA-ADP and thereby inhibiting further initiation of replication CC events. -- SN 1 ID DnaA regulatory inactivator Hda RQ 1 EV IPR017788; TIGR03420; sufficient; -- SN 2 ID Beta sliding clamp RQ 1 EV IPR001001; PIRSF000804; sufficient; EV IPR001001; PTHR30478; sufficient; EV IPR001001; SM00480; sufficient; EV IPR001001; TIGR00663; sufficient; EV IPR001001; cd00140; sufficient; // AC GenProp1163 DE IscS-IscU complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22203963 RT Disordered form of the scaffold protein IscU is the substrate for RT iron-sulfur cluster assembly on cysteine desulfurase. RA Kim JH, Tonelli M, Markley JL RL Proc Natl Acad Sci U S A. 2012;109:454-459 RN [2] RM 20404999 RT Structural basis for Fe-S cluster assembly and tRNA thiolation mediated RT by IscS protein-protein interactions. RA Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte RA A, Armengod ME, Cygler M RL PLoS Biol. 2010;8:e1000354 RN [3] RM 16387657 RT Mechanistic insights into sulfur relay by multiple sulfur mediators RT involved in thiouridine biosynthesis at tRNA wobble positions. RA Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T RL Mol Cell. 2006;21:97-108 DR Complex Portal; CPX-2141; CC Involved in the sulfur transfer during iron-sulfur cluster assembly and CC in the modification of tRNA wobble positions. IscS desulfurases CC L-cysteine and transfers sulfur on IscU while the latter is in the CC D-state, a partly disordered state that contains an ordered domain that CC stabilizes two cis peptidyl-prolyl peptide bonds. After Fe-S cluster CC formation on IscU, IscU converts to the S-state, which has a lower CC affinity for IscS and minimizes product inhibition. -- SN 1 ID Cysteine desulfurase IscS RQ 1 EV IPR010240; MF_00331; sufficient; EV IPR010240; PTHR11601:SF34; sufficient; EV IPR010240; TIGR02006; sufficient; -- SN 2 ID Iron-sulfur cluster assembly scaffold protein IscU RQ 1 EV IPR011339; TIGR01999; sufficient; // AC GenProp1164 DE Cytochrome o ubiquinol oxidase complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-2102; DR PDBe; 1fft; CC A protein complex integral to the bacterial electron transport chain. CC Electrons are donated by the oxidation of ubiquinol to ubiquinone, CC transferred to a slow-spinning heme b and subsequently accepted by a CC binuclear centre consisting of a heme o3 and a copper ion. In the CC process, the ubiquinol oxidase functions as a proton pump creating a CC transmembrane electrochemical gradient as 4 hydrogen ions are pumped CC through the membrane into the periplasmic space while 1/2 O2 molecule CC is oxidized to water. The electron transport happens exclusively in CC subunit I (cyoB). Ubiquinol oxidase is the final electron acceptor in CC the bacterial respiratory chain and thought to possess one of the most CC important functions in the cellular system due to its anti-oxidant CC properties. -- SN 1 ID Cytochrome bo(3) ubiquinol oxidase subunit 2 RQ 1 EV IPR006333; PIRSF000292; sufficient; EV IPR006333; TIGR01433; sufficient; -- SN 2 ID Cytochrome bo(3) ubiquinol oxidase subunit 4 RQ 1 EV IPR014210; TIGR02847; sufficient; -- SN 3 ID Cytochrome bo(3) ubiquinol oxidase subunit 1 RQ 1 EV IPR014207; TIGR02843; sufficient; -- SN 4 ID Cytochrome bo(3) ubiquinol oxidase subunit 3 RQ 1 EV IPR014206; TIGR02842; sufficient; // AC GenProp1165 DE PhnGHIJKL complex TP COMPLEX AU Complex Portal TH 5 RN [1] RM 21705661 RT Five phosphonate operon gene products as components of a multi-subunit RT complex of the carbon-phosphorus lyase pathway. RA Jochimsen B, Lolle S, McSorley FR, Nabi M, Stougaard J, Zechel DL, RA Hove-Jensen B RL Proc Natl Acad Sci U S A. 2011;108:11393-11398 RN [2] RM 22089136 RT Intermediates in the transformation of phosphonates to phosphate by RT bacteria. RA Kamat SS, Williams HJ, Raushel FM RL Nature. 2011;480:570-573 RN [3] RM 23830682 RT The enzymatic conversion of phosphonates to phosphate by bacteria. RA Kamat SS, Raushel FM RL Curr Opin Chem Biol. 2013;17:589-596 DR Complex Portal; CPX-1929; CC Formed from components of the phn operon in gram-negative bacteria that CC facilitates the internalization and degradation of organophosphonates. CC Carbon-phosphorous lyase (CP lyase) and alpha-D-ribose CC 1-methylphosphonate 5-triphosphate synthase activites have been CC attributed to at least the PhnG, PhnH, PhnI, PhnJ, PhnK and PhnL CC components of the Phn operon. It is unclear which of the subunits are CC absolutely necessary for each activity. PhnG, PhnH, PhnI and PhnL have CC alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity and CC PhnJ has alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase CC activity in vitro. However, PhnJ can only be isolated in a complex of CC at least PhnG, PhnH, PhnI, PhnJ and PhnK but this complex is CC catalytically inactive, possibly because it lacks PhnL. -- SN 1 ID Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase RQ 1 EV IPR010306; PF06007; sufficient; EV IPR010306; PIRSF011468; sufficient; EV IPR010306; SFLDF00379; sufficient; -- SN 2 ID Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG RQ 1 EV IPR009609; PF06754; sufficient; EV IPR009609; TIGR03293; sufficient; -- SN 3 ID Putative phosphonates utilization ATP-binding protein PhnK RQ 1 EV IPR012700; PIRSF037116; sufficient; EV IPR012700; TIGR02323; sufficient; -- SN 4 ID Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL RQ 1 EV IPR012701; TIGR02324; sufficient; -- SN 5 ID Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH RQ 1 EV IPR008772; PF05845; sufficient; EV IPR008772; PIRSF020680; sufficient; EV IPR008772; TIGR03292; sufficient; -- SN 6 ID Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI RQ 1 EV IPR008773; PF05861; sufficient; EV IPR008773; PIRSF007313; sufficient; // AC GenProp1166 DE Degradosome TP COMPLEX AU Complex Portal TH 3 RN [1] RM 21805185 RT Current perspectives of the Escherichia coli RNA degradosome. RA Burger A, Whiteley C, Boshoff A RL Biotechnol Lett. 2011;33:2337-2350 DR Complex Portal; CPX-403; CC Key role in mRNA degradation and RNA processing. RNA binds to RnaE, CC RhlB helicase is necessary to unwind the RNA secondary structures and, CC once unwound, the 3'-5' decay of the transcripts is ensued by CC phosphate-dependent PNPase. RNase E bound-enolase may connect cellular CC metabolic status with post-transcriptional gene regulation and link RNA CC degradation to glycolytic processes. A dynamic set of minor components CC of this complex may regulate its function and compartmentalization. -- SN 1 ID Ribonuclease E RQ 1 EV IPR028878; MF_00970; sufficient; -- SN 2 ID Enolase RQ 1 EV IPR000941; cd03313; sufficient; -- SN 3 ID Polyribonucleotide nucleotidyltransferase RQ 1 EV IPR012162; TIGR03591; sufficient; -- SN 4 ID ATP-dependent RNA helicase RhlB RQ 1 EV IPR023554; MF_00661; sufficient; // AC GenProp1167 DE Ethanolamine ammonia-lyase complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2313; DR PDBe; 3abo; DR PDBe; 3abs; DR PDBe; 3abq; CC Catalyzes the adenosylcobalamin (coenzyme B12)-dependent conversion of CC ethanolamine to acetaldehyde and ammonia and enabling growth on CC ethanolamine. The complex acts on both enantiomers of ethanolamine. -- SN 1 ID Ethanolamine ammonia-lyase light chain RQ 1 EV IPR009246; MF_00601; sufficient; EV IPR009246; PF05985; sufficient; EV IPR009246; PIRSF018982; sufficient; EV IPR009246; PTHR39330; sufficient; -- SN 2 ID Ethanolamine ammonia-lyase heavy chain RQ 1 EV IPR010628; PF06751; sufficient; EV IPR010628; PIRSF018788; sufficient; EV IPR010628; PTHR39329; sufficient; // AC GenProp1168 DE Cus cation efflux complex TP COMPLEX AU Complex Portal TH 3 RN [1] RM 23122209 RT Evolution and diversity of periplasmic proteins involved in copper RT homeostasis in gamma proteobacteria. RA Hernández-Montes G, Argüello JM, Valderrama B RL BMC Microbiol. 2012;12:249 DR Complex Portal; CPX-2254; DR PDBe; 3ne5; CC Transmembrane complex that mediates resistance to copper and silver by CC cation efflux directly from the cell using the proton-motive force. CC Spans the inner membrane, periplasm, and outer membrane. CusF delivers CC metal ions to the CusCBA tripartite efflux system in the periplasm, CC CusB then appears to deliver the bound metal ion from CusB to the CC three-methionine cluster (Met-573, Met-623 and Met-672) inside the CC periplasmic cleft of CusA from where it is passed into the central CC funnel of CusA and eventually the CusC channel for final extrusion. CC Primarily activated under anaerobic conditions by CusR (P0ACZ8) and CC CusS (P77485) but also expressed under extreme copper stress, in CC aerobic growth. -- SN 1 ID Cation efflux system protein CusF RQ 1 EV IPR021647; PF11604; sufficient; -- SN 2 ID Cation efflux system protein CusA RQ 1 EV IPR004763; TIGR00914; sufficient; -- SN 3 ID Cation efflux system protein CusC RQ 1 EV IPR010131; TIGR01845; sufficient; -- SN 4 ID Cation efflux system protein CusB RQ 1 EV IPR006143; PF00529; sufficient; EV IPR006143; TIGR01730; sufficient; // AC GenProp1171 DE YgjD-YeaZ-YjeE complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 23242255 RT A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed RT tRNA hypermodification. RA Miyauchi K, Kimura S, Suzuki T RL Nat Chem Biol. 2013;9:105-111 RN [2] RM 25578970 RT The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required RT for the biosynthesis of tRNA t6A in Escherichia coli. RA Zhang W, Collinet B, Perrochia L, Durand D, van Tilbeurgh H RL Nucleic Acids Res. 2015;43:1804-1817 DR Complex Portal; CPX-1094; DR PDBe; 4wq4; DR PDBe; 4ydu; DR PDBe; 4wq5; CC Catalyses the transfer of the threonylcarbamoyl-moiety of CC threonylcarbamoyladenylate onto A37 of substrate tRNA in the cytoplasm, CC or more probably in E.coli, the formation of 'cyclic t6A' (ct6A), which CC is a cyclized active ester with an oxazolone ring. The CC N6-threonylcarbamoyladenosine (t6A) modification is present at position CC 37 of tRNAs that recognize ANN-codons, with N being any nucleotide, CC enhancing the codon-anti-codon interaction and is required for CC recognition of the AUG start codon. The modification is thus important CC for maintaining translational fidelity. A stable YgjD-YeaZ heterodimer CC first forms, which has an atypical ADP-binding site at the YgjD-YeaZ CC interface that may also be the binding site for YjeE as the ternary CC complex only forms in the presence of ATP. An additional YrdC protein CC is necessary for T6a activity. -- SN 1 ID tRNA threonylcarbamoyladenosine biosynthesis protein TsaB (YeaZ) RQ 1 EV IPR022496; PTHR11735:SF11; sufficient; EV IPR022496; TIGR03725; sufficient; -- SN 2 ID tRNA threonylcarbamoyladenosine biosynthesis protein TsaE (YgjE) RQ 1 EV IPR003442; PF02367; sufficient; EV IPR003442; TIGR00150; sufficient; -- SN 3 ID tRNA N6-adenosine threonylcarbamoyltransferase (TsaD/YgjD) RQ 1 EV IPR022450; MF_01445; sufficient; EV IPR022450; PTHR11735:SF6; sufficient; EV IPR022450; TIGR03723; sufficient; // AC GenProp1172 DE Aspartate carbamoyltransferase complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22011033 RT Structure and mechanisms of Escherichia coli aspartate RT transcarbamoylase. RA Lipscomb WN, Kantrowitz ER RL Acc Chem Res. 2012;45:444-453 DR Complex Portal; CPX-3091; DR PDBe; 1EZZ; DR PDBe; 1SKU; DR PDBe; 1TUG; DR PDBe; 1TTH; DR PDBe; 1F1B; DR PDBe; 1I5O; DR PDBe; 1Q95; DR PDBe; 1R0B; DR PDBe; 1R0C; DR PDBe; 1TU0; CC Catalyzes the committed step in pyrimidine nucleotide biosynthesis and CC allosterically regulates the pathway. The enzyme is activated by ATP, CC inhibited by CTP and can be further inhibited by UTP, although UTP CC alone has little effect on activity. The catalytic mechanism is CC ordered, carbamoyl phosphate binds before aspartate and carbamoyl CC aspartate leaves before phosphate. -- SN 1 ID Aspartate carbamoyltransferase regulatory chain RQ 1 EV IPR002801; MF_00002; sufficient; EV IPR002801; PTHR35805; sufficient; EV IPR002801; TIGR00240; sufficient; -- SN 2 ID Aspartate carbamoyltransferase catalytic subunit RQ 1 EV IPR002082; MF_00001; sufficient; EV IPR002082; PR00101; sufficient; EV IPR002082; PTHR11405:SF16; sufficient; EV IPR002082; TIGR00670; sufficient; // AC GenProp1173 DE HslUV protease complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2104; DR PDBe; 1hqy; DR PDBe; 1ht1; DR PDBe; 1e94; DR PDBe; 1g4a; DR PDBe; 1g4b; DR PDBe; 1ht2; DR PDBe; 1g3i; CC A proteasome-like degradation complex with two functional subunits: the CC HslU hexamer forms the ATPase subunit which has chaperone activity and CC the HslV duodecamer forms the protease subunit. The binding of ATP and CC its subsequent hydrolysis by HslU are essential for unfolding of CC protein substrates subsequently hydrolyzed by HslV. HslU recognizes the CC N-terminal part of its protein substrates and unfolds these before they CC are guided to HslV for hydrolysis. ATP hydrolysis causes a CC conformational change in the HslU subunit 'closing' the central pore CC and 'un-docking' the ATPase unit from the protease by way of flicking CC the HslU C terminus from the HslV-HslV interface into the HslU-HslU CC interface. The complex has been shown to be involved in the specific CC degradation of heat shock induced transcription factors such as RpoH CC and SulA. In addition, small hydrophobic peptides are also hydrolyzed CC by HslV. HslV has weak protease activity even in the absence of HslU, CC but this activity is induced more than 100-fold in the presence of CC HslU. Owing to the size of the central pore of both subunits HslV is CC not believed to degrade folded proteins. -- SN 1 ID ATP-dependent protease ATPase subunit HslU RQ 1 EV IPR004491; MF_00249; sufficient; EV IPR004491; PTHR43815; sufficient; EV IPR004491; TIGR00390; sufficient; -- SN 2 ID ATP-dependent protease subunit HslV RQ 1 EV IPR022281; MF_00248; sufficient; EV IPR022281; PIRSF039093; sufficient; EV IPR022281; PTHR32194; sufficient; EV IPR022281; TIGR03692; sufficient; EV IPR022281; cd01913; sufficient; // AC GenProp1174 DE CdsA-CdsE complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 20054882 RT The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting RT Suf components and participates to a new sulphur transfer pathway by RT recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. RA Trotter V, Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, RA Barras F RL Mol Microbiol. 2009;74:1527-1542 RN [2] RM 15901727 RT Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting RT Fe-S cluster biogenesis in Escherichia coli. RA Loiseau L, Ollagnier-de Choudens S, Lascoux D, Forest E, Fontecave M, RA Barras F RL J Biol Chem. 2005;280:26760-26769 DR Complex Portal; CPX-2138; DR PDBe; 4lw4; CC Acts as a L-cysteine desulfurase and sufurtransferase. CsdA CC desulfurases L-cysteine to produce L-alanine atomic sulfur (in the form CC of a persulfide). It transfers the sulfur to CsdE which increases the CC cysteine desulfurase activity of CsdA. CsdE accepts the sulfur on CC Cys61. While the CsdE dimer can be isolated in vitro it is uncertain CC whether it also exists on its own in vivo. -- SN 1 ID Sulfur acceptor protein CsdE RQ 1 EV IPR017763; TIGR03391; sufficient; -- SN 2 ID Cysteine desulfurase CsdA RQ 1 EV IPR022471; TIGR03392; sufficient; // AC GenProp1175 DE ThiF-ThiS complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2134; CC Catalyses the initial steps of thiamine (vitamin B1) pyrophosphate CC synthesis by donating the sulfur for the synthesis of the intermediate CC thiazole phosphate moiety. This step is ATP-dependent as ThiS is CC temporarity adenylated by ThiF. A further persulfate group is donated CC to the intermediate products by ThiI (P77718). -- SN 1 ID Sulfur carrier protein ThiS adenylyltransferase (ThiF) RQ 1 EV IPR012731; TIGR02356; sufficient; -- SN 2 ID Sulfur carrier protein ThiS RQ 1 EV IPR010035; PTHR34472; sufficient; EV IPR010035; TIGR01683; sufficient; // AC GenProp1176 DE Protein-conducting channel SecYEG complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 16292303 RT Structure of the E. coli protein-conducting channel bound to a RT translating ribosome. RA Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, RA Frank J RL Nature. 2005;438:318-324 DR Complex Portal; CPX-1096; DR PDBe; 2aki; CC Functions in both protein secretion to the trans side of the plasma CC membrane and insertion of membrane proteins into the lipid bilayer. CC Associates with the motor ATPase SecA, which drives post-translational CC translocation of pre-proteins across the membrane.Membrane proteins are CC targeted to the membrane co-translationally by the signal recognition CC particle (SRP) associating with its receptor at the cytosolic surface. CC The ribosome nascent chain complex is then passed onto the dimeric CC SecYEG complex and the nascent membrane protein is threaded through the CC protein channel and into the bilayer via a lateral gate. Also forms a CC holo-translocon super-complex comprising of the SecYEG core complex, CC the accessory sub-complex SecDF-YajC and YidC. -- SN 1 ID Protein translocase subunit SecY RQ 1 EV IPR026593; MF_01465; sufficient; -- SN 2 ID Protein translocase subunit SecE RQ 1 EV IPR005807; PR01650; sufficient; EV IPR005807; PTHR33910; sufficient; EV IPR005807; TIGR00964; sufficient; -- SN 3 ID Protein-export membrane protein SecG RQ 1 EV IPR004692; PF03840; sufficient; EV IPR004692; PR01651; sufficient; EV IPR004692; PTHR34182; sufficient; EV IPR004692; TIGR00810; sufficient; // AC GenProp1178 DE GyrA-GyrB complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 20675723 RT A domain insertion in Escherichia coli GyrB adopts a novel fold that RT plays a critical role in gyrase function. RA Schoeffler AJ, May AP, Berger JM RL Nucleic Acids Res. 2010;38:7830-7844 DR Complex Portal; CPX-2177; CC A DNA gyrase of type IIA topoisomerase that negatively supercoils CC closed circular double-stranded DNA in an ATP-dependent manner and also CC catalyzes the interconversion of other topological isomers of CC double-stranded DNA rings, including catenanes and knotted rings. It CC cleaves both strands and facilitates DNA melting at oriC in order for CC replication initiation to take place. Gyrase also removes the CC left-handed positive supercoiling generated in front of moving CC replication forks. It is vital in all bacteria but not found in CC eukaryotes except some plant organelles. Structure-guided deletion of a CC 170-amino acid insertion (Thr565 - Arg731) in GyrB greatly reduces the CC DNA binding, supercoiling and DNA-stimulated ATPase activities of CC gyrase. -- SN 1 ID DNA gyrase subunit B RQ 1 EV IPR011557; MF_01898; sufficient; EV IPR011557; TIGR01059; sufficient; -- SN 2 ID DNA gyrase subunit A RQ 1 EV IPR005743; MF_01897; sufficient; // AC GenProp1179 DE Cascade complex TP COMPLEX AU Complex Portal TH 4 RN [1] RM 26863189 RT Structural basis for promiscuous PAM recognition in type I-E Cascade RT from E. coli. RA Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, RA Wiedenheft B, Ke A RL Nature. 2016;530:499-503 RN [2] RM 25118175 RT Crystal structure of the RNA-guided immune surveillance Cascade complex RT in Escherichia coli. RA Zhao H, Sheng G, Wang J, Wang M, Bunkoczi G, Gong W, Wei Z, Wang Y RL Nature. 2014;515:147-150 RN [3] RM 27672148 RT CRISPR-Cas: biology, mechanisms and relevance. RA Hille F, Charpentier E RL Philos Trans R Soc Lond B Biol Sci. 2016;371:- DR Complex Portal; CPX-1005; DR PDBe; 5h9f; DR PDBe; 5cd4; DR PDBe; 5h9e; DR PDBe; 4tvw; DR PDBe; 4qyz; CC CRISPR (clustered regularly interspaced short palindromic repeat), is CC an adaptive immune system that provides protection against mobile CC genetic elements (viruses, transposable elements and conjugative CC plasmids). The system memorizes previous infections by integrating CC short sequences of invading genomes (spacers) into the CRISPR locus. CC The spacers, interspaced with repeats, are expressed as small guide CC CRISPR RNAs (crRNAs) that are employed by Cas proteins to target CC invaders sequence-specifically upon a reoccurring infection. Upon viral CC invasion, the Cascade complex binds double-stranded DNA exhibiting CC sequence complementary to the crRNA spacer sequence, while displacing CC the non-target strand to form an R-loop, and then recruits the nuclease CC Cas3/ygcB (P38036) for target degradation. -- SN 1 ID CRISPR system Cascade subunit CasB RQ 1 EV IPR013382; PF09485; sufficient; EV IPR013382; TIGR02548; sufficient; EV IPR013382; cd09670; sufficient; -- SN 2 ID CRISPR system Cascade subunit CasC RQ 1 EV IPR010148; PF09344; sufficient; EV IPR010148; TIGR01869; sufficient; EV IPR010148; cd09646; sufficient; -- SN 3 ID CRISPR system Cascade subunit CasE RQ 1 EV IPR010179; PF08798; sufficient; EV IPR010179; SM01101; sufficient; EV IPR010179; TIGR01907; sufficient; -- SN 4 ID CRISPR system Cascade subunit CasA RQ 1 EV IPR013381; PF09481; sufficient; EV IPR013381; TIGR02547; sufficient; EV IPR013381; cd09669; sufficient; -- SN 5 ID CRISPR system Cascade subunit CasD RQ 1 EV IPR010147; TIGR01868; sufficient; // AC GenProp1180 DE MukBEF condensin complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 26686641 RT The Localization and Action of Topoisomerase IV in Escherichia coli RT Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF. RA Zawadzki P, Stracy M, Ginda K, Zawadzka K, Lesterlin C, Kapanidis AN, RA Sherratt DJ RL Cell Rep. 2015;13:2587-2596 RN [2] RM 24097060 RT Structural basis for the MukB-topoisomerase IV interaction and its RT functional implications in vivo. RA Vos SM, Stewart NK, Oakley MG, Berger JM RL EMBO J. 2013;32:2950-2962 DR Complex Portal; CPX-1090; DR PDBe; 3euh; CC Key mediator of chromosome condensation, ensuring chromosomes are CC efficiently separated during replication and are faithfully segregated CC into daughter cells. A direct interaction between ParC of Topoisomerase CC IV (CPX-1104) and MukB leads to a fraction of TopoIV molecules being CC bound to MukBEF clusters. Involved in chromosome condensation and CC segregation. MukB can stimulate the ability of topoisomerase IV to CC relax negatively supercoiled DNA. -- SN 1 ID Chromosome partition protein MukE RQ 1 EV IPR007385; MF_01802; sufficient; EV IPR007385; PF04288; sufficient; -- SN 2 ID Chromosome partition protein MukF RQ 1 EV IPR005582; MF_01803; sufficient; EV IPR005582; PIRSF018282; sufficient; -- SN 3 ID Chromosome partition protein MukB RQ 1 EV IPR012090; MF_01800; sufficient; EV IPR012090; PIRSF005246; sufficient; // AC GenProp1181 DE GroEL-GroES complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2113; DR PDBe; 1PCQ; CC Member of the chaperonin class of molecular chaperones required for the CC ATP-driven assisted folding of many proteins. Direct contact between CC substrate proteins and the C-terminal tails of the GroEL subunits helps CC prevent premature substrate protein escape during encapsulation. CC Encapsulation seals the GroEL cavity and results in the release of the CC substrate protein into an enlarged GroEL-GroES chamber. Protein folding CC is initiated by a conformational shift within the GroEL-GroES complex. CC Hydrolysis of ATP and binding of a new substrate protein to the CC opposite cavity sends an allosteric signal causing GroES and the CC encapsulated protein to be released into the cytosol. -- SN 1 ID 60 kDa chaperonin (GroEL) RQ 1 EV IPR001844; MF_00600; sufficient; EV IPR001844; PR00298; sufficient; EV IPR001844; TIGR02348; sufficient; EV IPR001844; cd03344; sufficient; -- SN 2 ID 10 kDa chaperonin (GroES) RQ 1 EV IPR020818; MF_00580; sufficient; EV IPR020818; PF00166; sufficient; EV IPR020818; PR00297; sufficient; EV IPR020818; PTHR10772; sufficient; EV IPR020818; SM00883; sufficient; EV IPR020818; cd00320; sufficient; // AC GenProp1182 DE H-NS-Hha complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1979; CC Functions as transcription factor that negatively regulates a range of CC genes in the Enterobacteriaceae. -- SN 1 ID DNA-binding protein H-NS RQ 1 EV IPR001801; PF00816; sufficient; EV IPR001801; PIRSF002096; sufficient; -- SN 2 ID Hemolysin expression-modulating protein Hha RQ 1 EV IPR007985; PF05321; sufficient; // AC GenProp1183 DE Flagellar Motor Switch Complex, CCW variant TP COMPLEX AU Complex Portal TH 2 RN [1] RM 24697492 RT Molecular architecture of the bacterial flagellar motor in cells. RA Zhao X, Norris SJ, Liu J RL Biochemistry. 2014;53:4323-4333 RN [2] RM 21673656 RT Architecture of the flagellar rotor. RA Paul K, Gonzalez-Bonet G, Bilwes AM, Crane BR, Blair D RL EMBO J. 2011;30:2962-2971 DR Complex Portal; CPX-1085; CC Plays a role in chemotaxis, the movement toward or away from chemicals. CC The flagellar motor of bacteria is a rotary device energized by the CC membrane ion gradient and the complex is required for the rotation and CC directional switching of the flagellum and also functions in flagellar CC assembly. Motor torque is produced at the top of the switch complex, CC where the FliG C-terminal domain bears several conserved charged CC residues that interact with charged groups of the stator protein MotA CC (P09348). The conformation of this complex is such that the flagellum CC rotates in a counter-clockwise (CCW) direction. -- SN 1 ID Flagellar motor switch protein FliG RQ 1 EV IPR000090; PIRSF003161; sufficient; EV IPR000090; PR00954; sufficient; EV IPR000090; PTHR30534; sufficient; EV IPR000090; TIGR00207; sufficient; -- SN 2 ID Flagellar motor switch protein FliN RQ 1 EV IPR012826; TIGR02480; sufficient; -- SN 3 ID Flagellar motor switch protein FliM RQ 1 EV IPR001689; PF02154; sufficient; EV IPR001689; PIRSF002888; sufficient; EV IPR001689; PR00955; sufficient; EV IPR001689; TIGR01397; sufficient; // AC GenProp1184 DE Sigma-E factor negative regulation complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 23687042 RT Dual molecular signals mediate the bacterial response to outer-membrane RT stress. RA Lima S, Guo MS, Chaba R, Gross CA, Sauer RT RL Science. 2013;340:837-841 DR Complex Portal; CPX-2532; CC Inactive form of the sigma-E transcription factor. Sigma-E-mediated CC envelope stress response is the major pathway to ensure homeostasis in CC the envelope compartment of the cell. In response to stress, outer CC membrane proteins accumulate in the periplasm and activate cleavage of CC RseA periplasmic domain by DegS (P0AEE3), triggering a proteolytic CC cascade that frees sigma-E to activate gene expression. RseB binding to CC RseA prevents activated DegS from cleaving RseA. -- SN 1 ID Sigma-E factor regulatory protein RseB RQ 1 EV IPR005588; PIRSF005427; sufficient; EV IPR005588; PTHR38782; sufficient; -- SN 2 ID ECF RNA polymerase sigma-E factor RQ 1 EV IPR014286; TIGR02939; sufficient; -- SN 3 ID Anti-sigma-E factor RseA RQ 1 EV IPR026279; PIRSF016938; sufficient; // AC GenProp1186 DE DnaA-Hda complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1945; CC Role in chromosonal replication. DnaA-ATP-hydrolysis at oriC results in CC replication initiation. Hda protein binds to inactive DnaA-ADP thereby CC inhibiting multiple events of replication initiation in one replication CC cycle. Although Hda can bind DnaA-ATP it has a far greater affinity for CC DnaA-ADP. This prevents the DnaA from swapping ADP for ATP prior to the CC completion of the current replication cycle. -- SN 1 ID DnaA regulatory inactivator Hda RQ 1 EV IPR017788; TIGR03420; sufficient; -- SN 2 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; // AC GenProp1187 DE DnaB-DnaC-DnaT-PriA-PriC complex TP COMPLEX AU Complex Portal TH 4 DR Complex Portal; CPX-1952; CC An intermediate but essential pre-primosome complex formed during CC re-initiation of replication. It is formed by the interaction of the CC helicase loading complex DnaB-DnaC with replication restart proteins CC after a stalled replication folk has been repaired. -- SN 1 ID Replicative DNA helicase (DnaB) RQ 1 EV IPR007692; TIGR00665; sufficient; -- SN 2 ID Primosomal protein 1 RQ 1 EV IPR020917; MF_01061; sufficient; -- SN 3 ID Primosomal replication protein N'' (PriC) RQ 1 EV IPR010890; PF07445; sufficient; -- SN 4 ID DNA replication protein DnaC RQ 1 EV IPR028350; PIRSF003073; sufficient; -- SN 5 ID Primosomal protein N' (PriA) RQ 1 EV IPR005259; MF_00983; sufficient; EV IPR005259; TIGR00595; sufficient; // AC GenProp1188 DE Exodeoxyribonuclease V complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 15538360 RT Crystal structure of RecBCD enzyme reveals a machine for processing DNA RT breaks. RA Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB RL Nature. 2004;432:187-193 DR Complex Portal; CPX-2197; DR PDBe; 3k70; CC An exonuclease complex essential in DNA double-strand break repair by CC homologous recombination. It catalyzes the unwinding of double-stranded CC DNA at DNA damage sites and cleaves the resulting single-stranded DNA CC (through RecB activity). This process is ATP-hydrolysis-dependent which CC is provided by the ATPase activity of RecD. The two helicases act with CC opposite polarity: RecB is an SF1A enzyme with a 3'–5' polarity and CC RecD an SF1B enzyme with a 5'–3' polarity. They cooperate to unwind CC DNA in a highly processive manner where the DNA gets unwound in the CC RecB-RecC interface with the 5'ssDNA single-strand fed into the RecD CC subunit and the 3'ssDNA remaining in the RecB-RecC dimer. The nuclease CC activity of the RecB subunit might be regulated by the RecD protein. A CC mutant lacking the the N-terminal 1B domain of RecD loses its helicase CC function completely. -- SN 1 ID RecBCD enzyme subunit RecC RQ 1 EV IPR006697; MF_01486; sufficient; EV IPR006697; PIRSF000980; sufficient; EV IPR006697; TIGR01450; sufficient; -- SN 2 ID RecBCD enzyme subunit RecD RQ 1 EV IPR006344; MF_01487; sufficient; EV IPR006344; TIGR01447; sufficient; -- SN 3 ID RecBCD enzyme subunit RecB RQ 1 EV IPR004586; MF_01485; sufficient; EV IPR004586; PTHR11070:SF23; sufficient; EV IPR004586; TIGR00609; sufficient; // AC GenProp1189 DE MqsRA toxin-antitoxin complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 26991085 RT Toxin-antitoxin systems in bacterial growth arrest and persistence. RA Page R, Peti W RL Nat Chem Biol. 2016;12:208-214 RN [2] RM 20041169 RT Three dimensional structure of the MqsR:MqsA complex: a novel TA pair RT comprised of a toxin homologous to RelE and an antitoxin with unique RT properties. RA Brown BL, Grigoriu S, Kim Y, Arruda JM, Davenport A, Wood TK, Peti W, RA Page R RL PLoS Pathog. 2009;5:e1000706 DR Complex Portal; CPX-1084; DR PDBe; 3gn5; DR PDBe; 3fmy; DR PDBe; 3o9x; CC Type II toxin-antitoxin (TA) module consisting of MqsR toxins bound to CC MqsA antitoxin dimer. TA systems act as effectors of dormancy and CC persistence and are composed of a toxin, which causes growth arrest by CC interfering with a vital cellular process, and a cognate antitoxin, CC which neutralizes the toxin activity during normal growth conditions. CC Under conditions of stress the antitoxins are selectively degraded, CC leaving the toxins to exert their toxic effects, leading to growth CC arrest and dormancy. Type II TA complexes are small protein-protein CC pairs; under growth conditions, the toxin is bound to the antitoxin, CC which inhibits its activity. Both the antitoxin and, in most cases, the CC TA complex bind the TA promoter to repress transcription. Under stress CC conditions, cellular proteases such as Lon (P0A9M0) and ClpXP CC (CPX-3176) are activated that preferentially cleave the antitoxins, CC freeing the toxins to inhibit growth by inhibiting translation or CC replication, enabling cells to enter a metabolically dormant state CC until the stress is removed. MqsR toxin is the most up-regulated gene CC in the persister phenotype of cells. When active, MqsA binds its CC promoter with extremely tight affinity, however this is destabilized by CC TA complex formation as the binding sites of MqsR and MqsA on DNA CC overlap and their binding is mutually exclusive. Plays a role in CC biofilm formation. -- SN 1 ID Antitoxin MqsA RQ 1 EV IPR022452; TIGR03830; sufficient; -- SN 2 ID mRNA interferase toxin MqsR RQ 1 EV IPR031451; PF15723; sufficient; EV IPR031451; cd12869; sufficient; // AC GenProp1190 DE UvrBC complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-2153; CC The UvrBC excinuclease repair complex is part of the UvrABC repair CC system that catalyzes the recognition and processing of DNA lesions. It CC scans the DNA for abnormalities. Upon binding of the UvrAB complex CC (CPX-2151) to a putative damaged site, the DNA wraps around one of the CC UvrB subunits. DNA wrapping is dependent on ATP binding by UvrB and CC probably causes local melting of the DNA helix, facilitating insertion CC of a UvrB beta-hairpin between the DNA strands. Then UvrB probes one CC DNA strand for the presence of a lesion. If a lesion is found the UvrA CC subunits dissociate and the UvrB-DNA preincision complex (CPX-2152) is CC formed. This complex is subsequently bound by UvrC and one of the UvrB CC monomers is released. UvrC incises both the 5' and 3' sides of the CC lesion. The N-terminal half is responsible for the 3' incision and the CC C-terminal half is responsible for the 5' incision. -- SN 1 ID UvrABC system protein C RQ 1 EV IPR004791; MF_00203; sufficient; EV IPR004791; TIGR00194; sufficient; -- SN 2 ID UvrABC system protein B RQ 1 EV IPR004807; MF_00204; sufficient; EV IPR004807; PTHR24029; sufficient; EV IPR004807; TIGR00631; sufficient; // AC GenProp1191 DE Ribonucleoside-diphosphate reductase complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22160671 RT Structural interconversions modulate activity of Escherichia coli RT ribonucleotide reductase. RA Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, RA Stubbe J, Drennan CL RL Proc Natl Acad Sci U S A. 2011;108:21046-21051 DR Complex Portal; CPX-1075; DR PDBe; 5cnv; DR PDBe; 1r1r; DR PDBe; 2r1r; DR PDBe; 4r1r; DR PDBe; 3uus; DR PDBe; 2x0x; DR PDBe; 6r1r; DR PDBe; 7r1r; DR PDBe; 4erp; DR PDBe; 4erm; DR PDBe; 5cnu; DR PDBe; 5cns; DR PDBe; 5cnt; DR PDBe; 2xaw; DR PDBe; 3r1r; DR PDBe; 2xax; DR PDBe; 1piz; DR PDBe; 1pj0; DR PDBe; 1pj1; DR PDBe; 1yfd; DR PDBe; 5ci2; DR PDBe; 2xap; DR PDBe; 2xay; DR PDBe; 2xo4; DR PDBe; 2xaz; DR PDBe; 2xo5; DR PDBe; 2xak; DR PDBe; 2xav; DR PDBe; 5r1r; DR PDBe; 1av8; DR PDBe; 1biq; DR PDBe; 1jpr; DR PDBe; 1jqc; DR PDBe; 1mrr; DR PDBe; 1mxr; DR PDBe; 1pfr; DR PDBe; 1pim; DR PDBe; 1piu; DR PDBe; 1piy; DR PDBe; 1pm2; DR PDBe; 1r65; DR PDBe; 1rib; DR PDBe; 1rnr; DR PDBe; 1rsr; DR PDBe; 1rsv; DR PDBe; 1xik; DR PDBe; 2alx; DR PDBe; 2av8; DR PDBe; 2xof; DR PDBe; 5ci3; CC Catalyzes the reduction of ribonucleotides to the corresponding CC deoxyribonucleotides, an essential step in the de novo synthesis of CC monomeric precursors for DNA replication and repair. The binding of CC effector dATP alters the active site to select for pyrimidines over CC purines, whereas effectors dGTP and TTP select for substrates ADP and CC GDP, respectively. -- SN 1 ID Ribonucleoside-diphosphate reductase 1 subunit beta RQ 1 EV IPR033909; cd01049; sufficient; -- SN 2 ID Ribonucleoside-diphosphate reductase 1 subunit alpha RQ 1 EV IPR013346; TIGR02506; sufficient; // AC GenProp1192 DE SufBCD complex TP COMPLEX AU Complex Portal TH 2 RN [1] RM 20857974 RT SufD and SufC ATPase activity are required for iron acquisition during RT in vivo Fe-S cluster formation on SufB. RA Saini A, Mapolelo DT, Chahal HK, Johnson MK, Outten FW RL Biochemistry. 2010;49:9402-9412 RN [2] RM 12941942 RT The SufE protein and the SufBCD complex enhance SufS cysteine RT desulfurase activity as part of a sulfur transfer pathway for Fe-S RT cluster assembly in Escherichia coli. RA Outten FW, Wood MJ, Munoz FM, Storz G RL J Biol Chem. 2003;278:45713-45719 DR Complex Portal; CPX-2123; CC Scaffold complex that assembles an Fe-S cluster. The SufB protomer of CC the SufBCD complex accepts the atomic sulfur from the sulfur transfer CC protein SufE (CPX-2125 [SufE dimer], EBI-8844754 [transfer CC interaction]) and incorporates it into an [4Fe-4S] cluster in an as yet CC undiscovered manner. SufBCD further transfers the Fe-S cluster to the CC carrier protein SufA (CPX-2142 [dimer], EBI-8805910 [transfer CC interaction]). SufBCD is a component of the sufABCDSE operon, which is CC activated and required under specific conditions such as oxidative CC stress and iron limitation. The SufBCD complex is a putative ATP-binding CC cassette (ABC) transporter complex, inferred by its structural CC similarity with other ABC transporters. SufC has been shown to be an CC ATPase whose activity is enhanced by the presence of SufB and SufD [1]. CC The precise function of FADH2 is not yet clear. Under aerobic conditions CC FADH2 is oxidised to FAD and dissociates from SufBCD. -- SN 1 ID Probable ATP-dependent transporter SufC RQ 1 EV IPR010230; PTHR43204:SF1; sufficient; EV IPR010230; TIGR01978; sufficient; EV IPR010230; cd03217; sufficient; -- SN 2 ID FeS cluster assembly protein SufB RQ 1 EV IPR010231; TIGR01980; sufficient; -- SN 3 ID FeS cluster assembly protein SufD RQ 1 EV IPR011542; PTHR43575; sufficient; EV IPR011542; TIGR01981; sufficient; // AC GenProp1193 DE RelBE toxin-antitoxin complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 22981948 RT The crystal structure of the intact E. coli RelBE toxin-antitoxin RT complex provides the structural basis for conditional cooperativity. RA Bøggild A, Sofos N, Andersen KR, Feddersen A, Easter AD, Passmore LA, RA Brodersen DE RL Structure. 2012;20:1641-1648 RN [2] RM 26991085 RT Toxin-antitoxin systems in bacterial growth arrest and persistence. RA Page R, Peti W RL Nat Chem Biol. 2016;12:208-214 DR Complex Portal; CPX-1081; DR PDBe; 2kc8; DR PDBe; 2k29; CC Type II toxin-antitoxin (TA) module consisting of relA toxin and relB CC antitoxin. TA systems act as effectors of dormancy and persistence and CC are composed of a toxin, which causes growth arrest by interfering with CC a vital cellular process, and a cognate antitoxin, which neutralizes CC the toxin activity during normal growth conditions. Under conditions CC of stress the antitoxins are selectively degraded, leaving the toxins CC to exert their toxic effects, leading to growth arrest and dormancy. CC Type II TA complexes are small protein-protein pairs; under growth CC conditions, the toxin is bound to the antitoxin, which inhibits its CC activity. Both the antitoxin and, in most cases, the TA complex bind CC the TA promoter to repress transcription. Under stress conditions, CC cellular proteases such as Lon (P0A9M0) and ClpXP (CPX-3176) are CC activated that preferentially cleave the antitoxins, freeing the toxins CC to inhibit growth by inhibiting translation or replication, enabling CC cells to enter a metabolically dormant state until the stress is CC removed. Free RelE toxin is capable of cleaving mRNA during translation CC at the ribosomal A site, thus inhibiting translation during amino acid CC starvation (the stringent response). The antitoxin, RelB, both binds CC and inhibits RelE by inducing conformational changes in the RelE active CC site, and regulates transcription through operator binding and CC conditional cooperativity controlled by RelE. During nutritional CC stress, the labile RelB is degraded by Lon, releasing RelE. -- SN 1 ID mRNA interferase toxin RelE RQ 1 EV IPR007712; PF05016; sufficient; EV IPR007712; TIGR02385; sufficient; -- SN 2 ID Antitoxin RelB RQ 1 EV IPR007337; PF04221; sufficient; EV IPR007337; PTHR38781; sufficient; EV IPR007337; TIGR02384; sufficient; // AC GenProp1194 DE Flagellar Motor Switch Complex, CW variant TP COMPLEX AU Complex Portal TH 3 RN [1] RM 24697492 RT Molecular architecture of the bacterial flagellar motor in cells. RA Zhao X, Norris SJ, Liu J RL Biochemistry. 2014;53:4323-4333 RN [2] RM 15351654 RT Structure of the constitutively active double mutant CheYD13K Y106W RT alone and in complex with a FliM peptide. RA Dyer CM, Quillin ML, Campos A, Lu J, McEvoy MM, Hausrath AC, Westbrook RA EM, Matsumura P, Matthews BW, Dahlquist FW RL J Mol Biol. 2004;342:1325-1335 DR Complex Portal; CPX-1082; DR PDBe; 2b1j; DR PDBe; 1f4v; DR PDBe; 1u8t; CC Plays a role in chemotaxis, the movement toward or away from chemicals. CC The flagellar motor of bacteria is a rotary device energized by the CC membrane ion gradient and the complex is required for the rotation and CC directional switching of the flagellum and also functions in flagellar CC assembly. Motor torque is produced at the top of the switch complex, CC where the FliG C-terminal domain bears several conserved charged CC residues that interact with charged groups of the stator protein MotA CC (P09348). The conformation of this complex is such that the flagellum CC rotates in a clockwise (CW) direction, induced by binding of CheY-P to CC the lower part of the C-ring. CheY-P interacts initially with the CC N-terminal segment of FliM, which is flexible enough to allow CC subsequent binding to a site on FliN. Coupled conformational CC transitions in FliM trigger large displacements of a distant CC alpha-helix in FliG, involved in stator contacts, inducing the change CC of the flagellar rotors from counterclocwise (smooth-swimming CC phenotype) to clockwise rotation (tumbly phenotype). -- SN 1 ID Flagellar motor switch protein FliN RQ 1 EV IPR012826; TIGR02480; sufficient; -- SN 2 ID Chemotaxis protein CheY RQ 1 EV IPR001789; PF00072; sufficient; EV IPR001789; PS50110; sufficient; EV IPR001789; SM00448; sufficient; EV IPR001789; cd00156; sufficient; -- SN 3 ID Flagellar motor switch protein FliG RQ 1 EV IPR000090; PIRSF003161; sufficient; EV IPR000090; PR00954; sufficient; EV IPR000090; PTHR30534; sufficient; EV IPR000090; TIGR00207; sufficient; -- SN 4 ID Flagellar motor switch protein FliM RQ 1 EV IPR001689; PF02154; sufficient; EV IPR001689; PIRSF002888; sufficient; EV IPR001689; PR00955; sufficient; EV IPR001689; TIGR01397; sufficient; // AC GenProp1195 DE DnaA-L2 TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1944; CC Contributes to the regulation of replication initiation preventing CC multiple replication origins during one replication cycle: L2 interacts CC with N-terminal domain of DnaA inhibiting DnaA multimerization and CC therefore inhibiting further replication initiation. -- SN 1 ID 50S ribosomal protein L2 RQ 1 EV IPR002171; PIRSF002158; sufficient; EV IPR002171; PTHR13691; sufficient; EV IPR002171; SM01383; sufficient; -- SN 2 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; // AC GenProp1196 DE Cas1-Cas2 complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 27672148 RT CRISPR-Cas: biology, mechanisms and relevance. RA Hille F, Charpentier E RL Philos Trans R Soc Lond B Biol Sci. 2016;371:- RN [2] RM 26503043 RT Foreign DNA capture during CRISPR-Cas adaptive immunity. RA Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA RL Nature. 2015;527:535-538 RN [3] RM 26478180 RT Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in RT CRISPR-Cas Systems. RA Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y RL Cell. 2015;163:840-853 DR Complex Portal; CPX-996; DR PDBe; 5dqt; DR PDBe; 4p6i; DR PDBe; 4qdl; DR PDBe; 5dlj; DR PDBe; 5dqz; DR PDBe; 5ds4; DR PDBe; 5ds5; DR PDBe; 5ds6; DR PDBe; 5dqu; CC CRISPR (clustered regularly interspaced short palindromic repeat), is CC an adaptive immune system that provides protection against mobile CC genetic elements (viruses, transposable elements and conjugative CC plasmids). The system memorizes previous infections by integrating CC short sequences of invading genomes (spacers) into the CRISPR locus. CC The spacers, interspaced with repeats, are expressed as small guide CC CRISPR RNAs (crRNAs) that are employed by Cas proteins to target CC invaders, sequence-specifically, upon a recurring infection. The CC Cas1-Cas2 complex is essential for the incorporation of 33-bp long CC sequence-variable foreign DNA protospacers into the host CRISPR locus. CC CRISPR transcripts generated from the loci assemble with Cas proteins CC to detect and cleave foreign nucleic acids bearing sequence CC complementarity to the spacer segment. Cas1 is the probable nuclease CC that catalyzes the integration reaction, whilst Cas2 may provide a CC structural scaffold and stimulate the catalytic activity of Cas1. -- SN 1 ID CRISPR-associated endoribonuclease Cas2 RQ 1 EV IPR010152; PF09707; sufficient; EV IPR010152; TIGR01873; sufficient; -- SN 2 ID CRISPR-associated endonuclease Cas1 RQ 1 EV IPR002729; MF_01470; sufficient; EV IPR002729; PF01867; sufficient; EV IPR002729; TIGR00287; sufficient; // AC GenProp1197 DE IscS-TusA complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 16387657 RT Mechanistic insights into sulfur relay by multiple sulfur mediators RT involved in thiouridine biosynthesis at tRNA wobble positions. RA Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T RL Mol Cell. 2006;21:97-108 RN [2] RM 20404999 RT Structural basis for Fe-S cluster assembly and tRNA thiolation mediated RT by IscS protein-protein interactions. RA Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte RA A, Armengod ME, Cygler M RL PLoS Biol. 2010;8:e1000354 DR Complex Portal; CPX-2139; DR PDBe; 3lvj; CC Involved in the sulfur-relay system required for 2-thiolation of CC 5-methylaminomethyl-2-thiouridine (mnm5s2U) at tRNA wobble positions. CC TusA stimulates IscS activity while IscS transfers sulfur on CC Cys19-TusA in a transpersulfidation reaction. In turn, TusA transfers CC the sulfur to TusD in the TusA-TusBCD-TusE-MnmA pathway. -- SN 1 ID Cysteine desulfurase IscS RQ 1 EV IPR010240; MF_00331; sufficient; EV IPR010240; PTHR11601:SF34; sufficient; EV IPR010240; TIGR02006; sufficient; -- SN 2 ID Sulfur carrier protein TusA RQ 1 EV IPR022931; MF_00413; sufficient; EV IPR022931; cd03423; sufficient; // AC GenProp1198 DE Respiratory chain complex I TP COMPLEX AU Complex Portal TH 12 DR Complex Portal; CPX-243; CC Catalyses the first step of electron transport by the oxidation of CC NADH, thus providing two electrons for the reduction of ubiquinone. CC Electron transfer is coupled with the translocation of protons across CC the membrane, generating a proton motive force. Preferred NADH CC dehydrogenase under anaerobic conditions. -- SN 1 ID NADH-quinone oxidoreductase subunit L RQ 1 EV IPR003945; TIGR01974; sufficient; -- SN 2 ID NADH-quinone oxidoreductase subunit H RQ 1 EV IPR001694; MF_01350; sufficient; EV IPR001694; PF00146; sufficient; EV IPR001694; PTHR11432; sufficient; -- SN 3 ID NADH-quinone oxidoreductase subunit K RQ 1 EV IPR001133; MF_01456; sufficient; EV IPR001133; PTHR11434; sufficient; -- SN 4 ID NADH-quinone oxidoreductase subunit M RQ 1 EV IPR010227; TIGR01972; sufficient; -- SN 5 ID NADH-quinone oxidoreductase subunit E RQ 1 EV IPR002023; PIRSF000216; sufficient; EV IPR002023; PS01099; sufficient; EV IPR002023; PTHR10371; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR002023; cd03064; sufficient; -- SN 6 ID NADH-quinone oxidoreductase subunit A RQ 1 EV IPR000440; PF00507; sufficient; EV IPR000440; PTHR11058; sufficient; -- SN 7 ID NADH-quinone oxidoreductase subunit B RQ 1 EV IPR006138; MF_01356; sufficient; EV IPR006138; PS01150; sufficient; EV IPR006138; TIGR01957; sufficient; -- SN 8 ID NADH-quinone oxidoreductase subunit F RQ 1 EV IPR011537; TIGR01959; sufficient; -- SN 9 ID NADH-quinone oxidoreductase subunit J RQ 1 EV IPR001457; PF00499; sufficient; -- SN 10 ID NADH-quinone oxidoreductase subunit I RQ 1 EV IPR010226; MF_01351; sufficient; EV IPR010226; TIGR01971; sufficient; -- SN 11 ID NADH-quinone oxidoreductase subunit G RQ 1 EV IPR010228; TIGR01973; sufficient; -- SN 12 ID NADH-quinone oxidoreductase subunit C/D RQ 1 EV IPR023062; MF_01359; sufficient; -- SN 13 ID NADH-quinone oxidoreductase subunit N RQ 1 EV IPR010096; MF_00445; sufficient; EV IPR010096; TIGR01770; sufficient; // AC GenProp1199 DE MdtBC complex TP COMPLEX AU Complex Portal TH 1 RN [1] RM 12107133 RT The putative response regulator BaeR stimulates multidrug resistance of RT Escherichia coli via a novel multidrug exporter system, MdtABC. RA Nagakubo S, Nishino K, Hirata T, Yamaguchi A RL J Bacteriol. 2002;184:4161-4167 DR Complex Portal; CPX-2119; CC Involved in the resistance of gram negative bacteria to novobiocin, CC deoxycholate and beta-lactams. MdtB and MdtC are transmembrane proteins CC facilitating drug export while MdtA is the (cytoplasmic?) membrane CC fusion protein associated with MdtBC (no binding data available yet). CC MdtABC requires TolC (P02930), an outer membrane 'channel-tunnel' CC trimer, for its function. The composition of the MdtABC CC holo-transporter may be variably composed of the MdtA, MdtB and MdtC CC subunits, however, either MdtB or MdtC must the present. The mdtABC CC operon is transcriptionally activated by BaeR (P69228). -- SN 1 ID Multidrug resistance protein MdtB RQ 1 EV IPR022831; MF_01423; sufficient; -- SN 2 ID Multidrug resistance protein MdtC RQ 1 EV IPR023931; MF_01424; sufficient; // AC GenProp1200 DE DnaA-DnaB-DnaC complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-1950; CC An intermediate but essential pre-primosome complex formed by the CC interaction of the helicase loading complex DnaB-DnaC (CPX-1934) with CC the DNA replication initiation protein DnaA at the origin of CC replication, oriC. DnaA loads one DnaB-DnaC complex on the top strand CC near the left border of oriC and a second DnaB-DnaC complex on the CC lower strand next to DnaA box R1. DnaA P46 is an essential residue for CC the binding to DnaB. -- SN 1 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; -- SN 2 ID Replicative DNA helicase RQ 1 EV IPR007692; TIGR00665; sufficient; -- SN 3 ID DNA replication protein DnaC RQ 1 EV IPR028350; PIRSF003073; sufficient; // AC GenProp1201 DE Succinyl-CoA synthetase TP COMPLEX AU Complex Portal TH 1 RN [1] RM 9917402 RT A detailed structural description of Escherichia coli succinyl-CoA RT synthetase. RA Fraser ME, James MN, Bridger WA, Wolodko WT RL J Mol Biol. 1999;285:1633-1653 RN [2] RM 10625475 RT ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed RT by x-ray crystallography. RA Joyce MA, Fraser ME, James MN, Bridger WA, Wolodko WT RL Biochemistry. 2000;39:17-25 DR Complex Portal; CPX-1092; DR PDBe; 1scu; DR PDBe; 1jll; DR PDBe; 1jkj; DR PDBe; 2nua; DR PDBe; 2nu6; DR PDBe; 2nu8; DR PDBe; 2nu7; DR PDBe; 2nu9; DR PDBe; 2scu; DR PDBe; 1cqi; CC Succinyl-CoA synthetase functions in the citric acid cycle (TCA), CC coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP CC or GTP and thus represents the only step of substrate-level CC phosphorylation in the TCA. It catalyzes the reversible interchange of CC purine nucleoside diphosphate, succinyl-CoA and phosphate with purine CC nucleoside triphosphate, succinate, and CoA via a phosphorylated CC histidine intermediate. -- SN 1 ID Succinate--CoA ligase [ADP-forming] subunit alpha RQ 1 EV IPR005810; MF_01988; sufficient; EV IPR005810; PIRSF001553; sufficient; EV IPR005810; TIGR01019; sufficient; -- SN 2 ID Succinate--CoA ligase [ADP-forming] subunit beta RQ 1 EV IPR005809; MF_00558; sufficient; EV IPR005809; PIRSF001554; sufficient; EV IPR005809; PTHR11815; sufficient; EV IPR005809; TIGR01016; sufficient; // AC GenProp1202 DE Cytochrome bd-II ubiquinol oxidase complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-269; CC A protein complex integral to the bacterial electron transport chain. CC Electrons are donated by the oxidation of ubiquinol to ubiquinone and CC used to reduce molecular oxygen, generating a proton motive force using CC protons and electrons from opposite sides of the membrane to generate CC water. This complex appears to be expressed under micro-aerobic CC conditions or under conditions of phosphate starvation. -- SN 1 ID Cytochrome bd-II ubiquinol oxidase subunit 1 RQ 1 EV IPR002585; PF01654; sufficient; EV IPR002585; PIRSF006446; sufficient; EV IPR002585; PTHR30365; sufficient; -- SN 2 ID Cytochrome bd-II ubiquinol oxidase subunit 2 RQ 1 EV IPR003317; PF02322; sufficient; EV IPR003317; PIRSF000267; sufficient; EV IPR003317; PTHR43141; sufficient; EV IPR003317; TIGR00203; sufficient; // AC GenProp1204 DE Maltose transport complex TP COMPLEX AU Complex Portal TH 3 RN [1] RM 18033289 RT Crystal structure of a catalytic intermediate of the maltose RT transporter. RA Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J RL Nature. 2007;450:515-521 DR Complex Portal; CPX-1932; DR PDBe; 3puy; CC Transports maltose from the periplasmic space into the cytoplasm CC through an ATP-dependent transmembrane channel. Maltose binds to malE CC which attaches to the malFG dimer. Upon release of the maltose into the CC transmembrane channel, the malK2 dimer binds ATP the hydrolysis of CC which triggers the release of maltose into the cytoplasm. -- SN 1 ID Maltose transport system permease protein MalF RQ 1 EV IPR030156; PTHR30193:SF22; sufficient; -- SN 2 ID Maltose transport system permease protein MalG RQ 1 EV IPR000515; PF00528; sufficient; EV IPR000515; PS50928; sufficient; EV IPR000515; cd06261; sufficient; -- SN 3 ID Maltose-binding periplasmic protein RQ 1 EV IPR006060; PR00181; sufficient; -- SN 4 ID Maltose/maltodextrin import ATP-binding protein MalK RQ 1 EV IPR015855; PS51245; sufficient; // AC GenProp1205 DE Trimethylamine-N-oxide reductase TorAC complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-319; CC Reduces trimethylamine-N-oxide (TMAO) to trimethylamine, enabling its CC use under anaerobic conditions as an electron acceptor for the CC oxidation of organic substrates and the production of energy. TorAC is CC also present under aerobic conditions, when production of alkaline CC trimethylamine may balance the acidification of the cell caused by CC generation of acetic acid caused by glycerol utilization. -- SN 1 ID Trimethylamine-N-oxide reductase 1 (TorA) RQ 1 EV IPR011887; TIGR02164; sufficient; -- SN 2 ID Cytochrome c-type protein TorC RQ 1 EV IPR009154; PIRSF000014; sufficient; EV IPR009154; TIGR02162; sufficient; // AC GenProp1206 DE H-NS-Cnu complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1980; CC Functions as transcription factor that negatively regulates a range of CC bacterial genes. -- SN 1 ID DNA-binding protein H-NS RQ 1 EV IPR001801; PF00816; sufficient; EV IPR001801; PIRSF002096; sufficient; -- SN 2 ID OriC-binding nucleoid-associated protein RQ 1 EV IPR007985; PF05321; sufficient; // AC GenProp1207 DE DnaA-HU complex variant 1 TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1962; CC HU dimers (alpha homodimers as well as alpha-beta dimers [CPX-1958]) CC are essential proteins during the DnaA-dependent initiation of CC replication. They facilitate DnaA oligomerization and proper timing of CC initiation of replication. -- SN 1 ID DNA-binding protein HU-alpha RQ 1 EV IPR000119; PF00216; sufficient; EV IPR000119; PR01727; sufficient; EV IPR000119; PTHR33175; sufficient; EV IPR000119; SM00411; sufficient; -- SN 2 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; // AC GenProp1208 DE DnaB-DnaC-Rep-PriC complex TP COMPLEX AU Complex Portal TH 3 DR Complex Portal; CPX-1953; CC An intermediate but essential pre-primosome complex formed during CC re-initiation of replication. It is formed by the interaction of the CC helicase loading complex DnaB-DnaC with replication restart proteins CC after a stalled replication folk has been repaired. -- SN 1 ID Primosomal replication protein N'' (PriC) RQ 1 EV IPR010890; PF07445; sufficient; -- SN 2 ID ATP-dependent DNA helicase Rep RQ 1 EV IPR005752; MF_01920; sufficient; EV IPR005752; TIGR01074; sufficient; -- SN 3 ID Replicative DNA helicase (DnaB) RQ 1 EV IPR007692; TIGR00665; sufficient; -- SN 4 ID DNA replication protein DnaC RQ 1 EV IPR028350; PIRSF003073; sufficient; // AC GenProp1209 DE Hydrogenase-1 complex TP COMPLEX AU Complex Portal TH 2 DR Complex Portal; CPX-281; DR PDBe; 3uqy; DR PDBe; 3use; DR PDBe; 4ue3; DR PDBe; 3usc; DR PDBe; 5adu; DR PDBe; 5a4m; DR PDBe; 5a4f; DR PDBe; 5a4i; CC Catalyzes the reversible oxidation of hydrogen (H2) to protons and CC electrons. Maximally produced during fermentation and under various CC types of stress such as carbon and phosphate starvation, osmotic up CC shift, and stationary phase conditions. Hydrogenase-1 is oxygen CC tolerant and contains the special proximal (relative to the active CC site) [Fe4S3] cluster that can rapidly undergo two successive CC one-electron oxidations within a narrow potential range. The additional CC two electrons required to reduce the attacking O2 to two water CC molecules, can originate from either the two-electron oxidation of CC Ni(I) to Ni(III), or the one-electron oxidation of Ni(II) to Ni(III) at CC the active site, the latter coupled to the one-electron oxidation of CC the [Fe4S4] medial cluster. -- SN 1 ID Hydrogenase-1 large chain RQ 1 EV IPR001501; PF00374; sufficient; -- SN 2 ID Hydrogenase-1 small chain RQ 1 EV IPR001821; PIRSF000310; sufficient; EV IPR001821; PTHR30013; sufficient; EV IPR001821; TIGR00391; sufficient; -- SN 3 ID Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit RQ 1 EV IPR000516; PR00161; sufficient; EV IPR000516; PS00882; sufficient; EV IPR000516; PS00883; sufficient; EV IPR000516; TIGR02125; sufficient; // AC GenProp1210 DE DnaA-DiaA complex TP COMPLEX AU Complex Portal TH 1 DR Complex Portal; CPX-1963; CC Required for the timely initiation of chromosomal replication. DiaA CC stimulates DnaA oligomerization (CPX-1943), DnaA-ATP binding to the CC origin of replication, oriC and unwinding of DNA at oriC by DnaA. CC Formation of DiaA tetramers (CPX-1938) is essential for properly timed CC replication initiation. Each DiaA protomer binds to a DnaA molecule but CC only a selection of DnaA molecules have to be bound for proper CC replication initiation to occur. DiaA-DnaA dissociation facilitates CC DnaA-DnaB binding (CPX-1935). -- SN 1 ID Chromosomal replication initiator protein DnaA RQ 1 EV IPR001957; MF_00377; sufficient; EV IPR001957; PTHR30050:SF2; sufficient; EV IPR001957; TIGR00362; sufficient; -- SN 2 ID DnaA initiator-associating protein DiaA RQ 1 EV IPR023070; MF_01157; sufficient; // AC GenProp1211 DE Regulatory systems TP CATEGORY AU Richardson L TH 0 CC Properties that describe systems involved in the regulation of CC various processes. -- SN 1 ID Gene regulatory systems RQ 0 EV GenProp0551; // AC GenProp1212 DE Regulation of biological processes TP CATEGORY AU Richardson L TH 0 CC Properties that describe systems involved in the regulation of CC various biological processes, incluing both positive and negative CC regulation. -- SN 1 ID Chemotaxis phosphorelay complex CheY-CheZ RQ 0 EV GenProp1139; -- SN 2 ID Trimethylamine-N-oxide reductase TorAC complex RQ 0 EV GenProp1205; -- SN 3 ID DnaA-DiaA complex RQ 0 EV GenProp1210; -- SN 4 ID DnaA-Dps complex RQ 0 EV GenProp1113; -- SN 5 ID DinJ-YafQ toxin-antitoxin complex RQ 0 EV GenProp1125; -- SN 6 ID Enzyme IIA-maltose transporter complex RQ 0 EV GenProp1159; -- SN 7 ID Hda-beta clamp complex RQ 0 EV GenProp1162; -- SN 8 ID Sigma-E factor negative regulation complex RQ 0 EV GenProp1184; -- SN 9 ID DnaA-Hda complex RQ 0 EV GenProp1186; -- SN 10 ID DnaA-L2 RQ 0 EV GenProp1195; // AC GenProp1213 DE Response to stimulus TP CATEGORY AU Richardson L TH 0 CC Properties that describe systems involved in the response to CC various stimuli. -- SN 1 ID Response to external environment RQ 0 EV GenProp0864; // AC GenProp1214 DE Transcription TP CATEGORY AU Richardson L TH 0 CC This category covers properties that are involved in the transcription CC of genetic information. This includes initiation, regulation, and CC termination of transcription. -- SN 1 ID ModE complex RQ 0 EV GenProp1121; -- SN 2 ID H-NS-Hha complex RQ 0 EV GenProp1182; -- SN 3 ID H-NS-Cnu complex RQ 0 EV GenProp1206; -- SN 5 ID IHF complex RQ 0 EV GenProp1140; // AC GenProp1215 DE Siroheme biosynthesis TP PATHWAY AU Fulcher C, Caspi R TH 2 DC Siroheme biosynthesis DR MetaCyc; PWY-5194; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Precorrin-2 dehydrogenase DN Precorrin-2 dehydrogenase (EC 1.3.1.76) RQ 1 EV IPR000878; PF00590; sufficient; EV IPR006366; TIGR01469; sufficient; EV IPR006367; PF13241; sufficient; EV IPR006367; TIGR01470; sufficient; EV IPR019478; PF10414; sufficient; EV IPR028281; PF14824; sufficient; EV IPR028162; PF14823; sufficient; -- SN 2 ID Precorrin-1 C-methyltransferase DN Precorrin-1 C-methyltransferase RQ 1 EV IPR000878; PF00590; sufficient; EV IPR006366; TIGR01469; sufficient; EV IPR006367; PF13241; sufficient; EV IPR006367; TIGR01470; sufficient; EV IPR019478; PF10414; sufficient; EV IPR028281; PF14824; sufficient; -- SN 3 ID Sirohydrochlorin ferrochelatase DN Sirohydrochlorin ferrochelatase (EC 4.99.1.4) RQ 1 EV IPR000878; PF00590; sufficient; EV IPR006366; TIGR01469; sufficient; EV IPR006367; PF13241; sufficient; EV IPR006367; TIGR01470; sufficient; EV IPR019478; PF10414; sufficient; EV IPR028281; PF14824; sufficient; EV IPR028162; PF14823; sufficient; -- SN 4 ID Uroporphyrinogen-III (C2)-methyltransferase DN Uroporphyrinogen-III (C2)-methyltransferase RQ 1 EV IPR000878; PF00590; sufficient; EV IPR006366; TIGR01469; sufficient; EV IPR006367; PF13241; sufficient; EV IPR006367; TIGR01470; sufficient; EV IPR019478; PF10414; sufficient; EV IPR028281; PF14824; sufficient; // AC GenProp1216 DE Tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate TP PATHWAY AU Caspi R TH 0 DC Tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate DR MetaCyc; PWY-6613; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoribosylglycinamide formyltransferase DN Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) RQ 1 EV IPR004607; TIGR00639; sufficient; EV IPR000115; TIGR00877; sufficient; EV IPR004733; TIGR00878; sufficient; -- SN 2 ID Methenyltetrahydrofolate cyclohydrolase DN Methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9) RQ 1 EV IPR000559; PF01268; sufficient; // AC GenProp1217 DE Superpathway of steroid hormone biosynthesis TP PATHWAY AU Caspi R TH 8 DC Superpathway of steroid hormone biosynthesis DR MetaCyc; PWY-7305; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Androstenedione reductase DN Androstenedione reductase (EC 1.1.1.64) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID 20-Alpha-22-beta-dihydroxycholesterol side-chain lyase DN 20-Alpha-22-beta-dihydroxycholesterol side-chain lyase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID Pregnenolone 17-alpha-hydroxylase DN Pregnenolone 17-alpha-hydroxylase (EC 1.14.14.19) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 4 ID Androstenedione 19-hydroxylase DN Androstenedione 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 5 ID Testosterone 19-hydroxylase DN Testosterone 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 6 ID Pregnenolone dehydrogenase DN Pregnenolone dehydrogenase (EC 1.1.1.145) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 7 ID Preg-5-en-3,20-dione isomerase DN Preg-5-en-3,20-dione isomerase (EC 5.3.3.1) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 8 ID Progesterone 17-hydroxylase DN Progesterone 17-hydroxylase (EC 1.14.14.19) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 9 ID Progesterone 21-hydroxylase DN Progesterone 21-hydroxylase (EC 1.14.13) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 10 ID Androstenedione isomerase DN Androstenedione isomerase (EC 5.3.3.1) RQ 1 EV IPR002225; PF01073; sufficient; // AC GenProp1218 DE Hydroxymethylpyrimidine salvage TP PATHWAY AU Caspi R TH 0 DC Hydroxymethylpyrimidine salvage DR MetaCyc; PWY-6910; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Amino-2-methyl-5-hydroxymethylpyrimidine kinase DN 4-Amino-2-methyl-5-hydroxymethylpyrimidine kinase (EC 2.7.1.49) RQ 1 EV IPR027574; TIGR04306; sufficient; EV IPR004625; TIGR00687; sufficient; -- SN 2 ID Phosphomethylpyrimidine kinase DN Phosphomethylpyrimidine kinase (EC 2.7.4.7) RQ 1 EV IPR027574; TIGR04306; sufficient; // AC GenProp1219 DE Thiamine salvage I TP PATHWAY AU Caspi R TH 0 DC Thiamine salvage I DR MetaCyc; PWY-6896; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Thiamine-monophosphate kinase DN Thiamine-monophosphate kinase (EC 2.7.4.16) RQ 1 EV IPR006283; TIGR01379; sufficient; -- SN 2 ID Thiamine kinase DN Thiamine kinase (EC 2.7.1.89) RQ 1 EV IPR014093; TIGR02721; sufficient; // AC GenProp1220 DE Fatty acid biosynthesis initiation II TP PATHWAY AU Caspi R TH 0 DC Fatty acid biosynthesis initiation II DR MetaCyc; PWY-5966; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetoacetyl-[acp] synthase DN Acetoacetyl-[acp] synthase (EC 2.3.1.179) RQ 1 EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR001031; PF00975; sufficient; EV IPR009081; PF00550; sufficient; EV IPR013149; PF00107; sufficient; EV IPR013217; PF08242; sufficient; EV IPR013968; PF08659; sufficient; EV IPR014043; PF00698; sufficient; EV IPR020807; PF14765; sufficient; EV IPR032821; PF16197; sufficient; EV IPR004568; TIGR00556; sufficient; EV IPR008278; PF01648; sufficient; -- SN 2 ID Acetyl-CoA:ACP transacylase DN Acetyl-CoA:ACP transacylase (EC 2.3.1.86) RQ 1 EV IPR004655; TIGR00747; sufficient; // AC GenProp1221 DE Pyrimidine deoxyribonucleosides salvage TP PATHWAY AU Caspi R, Ingraham J, Arnaud M TH 3 DC Pyrimidine deoxyribonucleosides salvage DR MetaCyc; PWY-7199; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Deoxycytidine deaminase DN Deoxycytidine deaminase (EC 3.5.4.5) RQ 1 EV IPR006263; TIGR01355; sufficient; EV IPR006262; TIGR01354; sufficient; -- SN 2 ID 2'-Deoxycytidine kinase DN 2'-Deoxycytidine kinase (EC 2.7.1.74) RQ 1 EV IPR031314; PF01712; sufficient; -- SN 3 ID 2'-Deoxyuridine kinase DN 2'-Deoxyuridine kinase (EC 2.7.1.145) RQ 1 EV IPR001267; PF00265; sufficient; -- SN 4 ID Thymidine kinase DN Thymidine kinase (EC 2.7.1.21) RQ 1 EV IPR001267; PF00265; sufficient; -- SN 5 ID Thymidylate synthase DN Thymidylate synthase (EC 2.1.1.45) RQ 1 EV IPR000398; TIGR03284; sufficient; // AC GenProp1222 DE UDP-N-acetyl-D-glucosamine biosynthesis II TP PATHWAY AU Fulcher C, Ying H TH 2 DC UDP-N-acetyl-D-glucosamine biosynthesis II DR MetaCyc; UDPNACETYLGALSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucosamine-6-phosphate acetyltransferase DN Glucosamine-6-phosphate acetyltransferase (EC 2.3.1.4) RQ 1 EV IPR000182; PF00583; sufficient; -- SN 2 ID Glutamine:fructose-6-phosphate amidotransferase DN Glutamine:fructose-6-phosphate amidotransferase (EC 2.6.1.16) RQ 1 EV IPR005855; TIGR01135; sufficient; -- SN 3 ID UDP-N-acetylglucosamine pyrophosphorylase DN UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) RQ 1 EV IPR002618; PF01704; sufficient; -- SN 4 ID Phosphoacetylglucosamine mutase DN Phosphoacetylglucosamine mutase (EC 5.4.2.3) RQ 1 EV IPR005843; PF00408; sufficient; EV IPR005844; PF02878; sufficient; // AC GenProp1223 DE L-threonine degradation V TP PATHWAY AU Weerasinghe D TH 0 DC L-threonine degradation V DR MetaCyc; PWY66-428; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Oxobutanoate dehydrogenase DN 2-Oxobutanoate dehydrogenase (EC 1.2.1.M8) RQ 1 EV IPR006258; TIGR01350; sufficient; -- SN 2 ID L-threonine deaminase DN L-threonine deaminase (EC 4.3.1.19) RQ 1 EV IPR001926; PF00291; sufficient; // AC GenProp1224 DE Lipoate salvage I TP PATHWAY AU Caspi R, Arnaud M TH 0 DC Lipoate salvage I DR MetaCyc; PWY0-522; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lipoate-ATP adenylate transferase DN Lipoate-ATP adenylate transferase RQ 1 EV IPR004562; TIGR00545; sufficient; -- SN 2 ID Lipoate-protein ligase DN Lipoate-protein ligase RQ 1 EV IPR004562; TIGR00545; sufficient; // AC GenProp1225 DE D-galactarate degradation I TP PATHWAY AU Keseler I, Riley M TH 2 DC D-galactarate degradation I DR MetaCyc; GALACTARDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-galactarate dehydratase DN D-galactarate dehydratase (EC 4.2.1.42) RQ 1 EV IPR017654; TIGR03248; sufficient; -- SN 2 ID Glycerate 2-kinase DN Glycerate 2-kinase (EC 2.7.1.165) RQ 1 EV IPR004381; PF02595; sufficient; EV IPR004381; TIGR00045; sufficient; -- SN 3 ID Alpha-dehydro-beta-deoxy-D-glucarate aldolase DN Alpha-dehydro-beta-deoxy-D-glucarate aldolase (EC 4.1.2.20) RQ 1 EV IPR017648; TIGR03239; sufficient; -- SN 4 ID Tartronate semialdehyde reductase DN Tartronate semialdehyde reductase (EC 1.1.1.60) RQ 1 EV IPR006398; TIGR01505; sufficient; // AC GenProp1226 DE Pyruvate fermentation to ethanol II TP PATHWAY AU Caspi R TH 0 DC Pyruvate fermentation to ethanol II DR MetaCyc; PWY-5486; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; EV IPR015590; PF00171; sufficient; -- SN 2 ID Pyruvate decarboxylase DN Pyruvate decarboxylase (EC 4.1.1.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; // AC GenProp1227 DE Guanosine deoxyribonucleotides de novo biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Guanosine deoxyribonucleotides de novo biosynthesis I DR MetaCyc; PWY-7226; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID DGDP kinase DN DGDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 2 ID GDP reductase DN GDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; // AC GenProp1228 DE L-idonate degradation TP PATHWAY AU Keseler I, Pellegrini-Toole A TH 1 DC L-idonate degradation DR MetaCyc; IDNCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-idonate 5-dehydrogenase DN L-idonate 5-dehydrogenase (EC 1.1.1.264) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; -- SN 2 ID 5-Keto-D-gluconate 5-reductase DN 5-Keto-D-gluconate 5-reductase (EC 1.1.1.69) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 3 ID Gluconate kinase DN Gluconate kinase (EC 2.7.1.12) RQ 1 EV IPR006001; TIGR01313; sufficient; EV IPR031322; PF01202; sufficient; // AC GenProp1229 DE D-myo-inositol (1,3,4)-trisphosphate biosynthesis TP PATHWAY AU Caspi R TH 1 DC D-myo-inositol (1,3,4)-trisphosphate biosynthesis DR MetaCyc; PWY-6364; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol-1,4,5-trisphosphate 3-kinase DN Inositol-1,4,5-trisphosphate 3-kinase (EC 2.7.1.127) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 2 ID Inositol-1,3,4,5-tetrakisphosphate 3-phosphatase DN Inositol-1,3,4,5-tetrakisphosphate 3-phosphatase (EC 3.1.3.62) RQ 1 EV IPR000560; PF00328; sufficient; -- SN 3 ID Inositol-1,3,4,5-tetrakisphosphate 5-phosphatase DN Inositol-1,3,4,5-tetrakisphosphate 5-phosphatase (EC 3.1.3.56) RQ 1 EV IPR005135; PF03372; sufficient; EV IPR000198; PF00620; sufficient; EV IPR031995; PF16726; sufficient; EV IPR031896; PF16776; sufficient; EV IPR002013; PF02383; sufficient; EV IPR015047; PF08952; sufficient; EV IPR000980; PF00017; sufficient; EV IPR001660; PF00536; sufficient; // AC GenProp1230 DE Aerobic respiration III (alternative oxidase pathway) TP PATHWAY AU N/A TH 0 DC Aerobic respiration III (alternative oxidase pathway) DR MetaCyc; PWY-4302; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID NADH dehydrogenase DN NADH dehydrogenase (EC 1.6.5.3) RQ 1 EV IPR010226; TIGR01971; sufficient; EV IPR008698; PF05676; sufficient; EV IPR009346; PF06212; sufficient; EV IPR019329; PF10183; sufficient; EV IPR019342; PF10200; sufficient; EV IPR007763; PF05071; sufficient; EV IPR017384; PF15879; sufficient; EV IPR010029; TIGR01676; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR006806; PF04716; sufficient; EV IPR006885; PF04800; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR001694; PF00146; sufficient; -- SN 2 ID Ubiquinol:oxygen oxidoreductase DN Ubiquinol:oxygen oxidoreductase (EC 1.10.3.11) RQ 1 EV IPR002680; PF01786; sufficient; // AC GenProp1231 DE 2-Hydroxypenta-2,4-dienoate degradation TP PATHWAY AU Caspi R TH 1 DC 2-Hydroxypenta-2,4-dienoate degradation DR MetaCyc; PWY-5162; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Oxopent-4-enoate hydratase DN 2-Oxopent-4-enoate hydratase (EC 4.2.1.80) RQ 1 EV IPR011234; PF01557; sufficient; -- SN 2 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR003361; TIGR03215; sufficient; -- SN 3 ID 4-Hydroxy-2-oxovalerate aldolase DN 4-Hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) RQ 1 EV IPR017629; TIGR03217; sufficient; // AC GenProp1233 DE L-glutamate degradation II TP PATHWAY AU Fulcher C, Caspi R TH 0 DC L-glutamate degradation II DR MetaCyc; GLUTDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID Aspartate ammonia-lyase DN Aspartate ammonia-lyase (EC 4.3.1.1) RQ 1 EV IPR004708; TIGR00839; sufficient; // AC GenProp1234 DE Superpathway of L-tyrosine biosynthesis TP PATHWAY AU Caspi R TH 0 DC Superpathway of L-tyrosine biosynthesis DR MetaCyc; PWY-6630; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; PF01264; sufficient; EV IPR000453; TIGR00033; sufficient; -- SN 2 ID Chorismate mutase DN Chorismate mutase (EC 5.4.99.5) RQ 1 EV IPR003099; PF02153; sufficient; EV IPR011277; TIGR01799; sufficient; EV IPR001086; PF00800; sufficient; EV IPR010952; TIGR01797; sufficient; // AC GenProp1235 DE Adenine and adenosine salvage III TP PATHWAY AU Caspi R TH 2 DC Adenine and adenosine salvage III DR MetaCyc; PWY-6609; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine deaminase DN Adenosine deaminase (EC 3.5.4.4) RQ 1 EV IPR006330; TIGR01430; sufficient; -- SN 2 ID Adenosine phosphorylase DN Adenosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; EV IPR009664; PF06865; sufficient; -- SN 3 ID Hypoxanthine phosphoribosyltransferase DN Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) RQ 1 EV IPR005904; TIGR01203; sufficient; -- SN 4 ID Inosine phosphorylase DN Inosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR009664; PF06865; sufficient; EV IPR004402; TIGR00107; sufficient; // AC GenProp1236 DE Retinoate biosynthesis II TP PATHWAY AU Caspi R TH 1 DC Retinoate biosynthesis II DR MetaCyc; PWY-6875; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Retinal oxidase DN Retinal oxidase (EC 1.17.1) RQ 1 EV IPR000674; PF01315; sufficient; EV IPR001041; PF00111; sufficient; EV IPR002346; PF00941; sufficient; EV IPR002888; PF01799; sufficient; EV IPR005107; PF03450; sufficient; EV IPR008274; PF02738; sufficient; EV IPR014307; TIGR02963; sufficient; -- SN 2 ID Cellular retinol-binding protein DN Cellular retinol-binding protein RQ 1 EV IPR000566; PF00061; sufficient; -- SN 3 ID Plasma retinol-binding protein DN Plasma retinol-binding protein RQ 1 EV IPR000566; PF00061; sufficient; // AC GenProp1237 DE Lipoate biosynthesis and incorporation I TP PATHWAY AU Caspi R, Arnaud M TH 0 DC Lipoate biosynthesis and incorporation I DR MetaCyc; PWY0-501; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID LIPoyl ligase 2 DN LIPoyl ligase 2 (EC 2.3.1.181) RQ 1 EV IPR000544; TIGR00214; sufficient; -- SN 2 ID Lipoyl synthase DN Lipoyl synthase (EC 2.8.1.8) RQ 1 EV IPR003698; TIGR00510; sufficient; // AC GenProp1238 DE L-cysteine biosynthesis IV (fungi) TP PATHWAY AU Caspi R TH 0 DC L-cysteine biosynthesis IV (fungi) DR MetaCyc; PWY-6293; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID O-acetylhomoserine sulfhydrylase DN O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) RQ 1 EV IPR000277; PF01053; sufficient; EV IPR006235; TIGR01326; sufficient; -- SN 2 ID Cystathionine beta-synthase DN Cystathionine beta-synthase (EC 4.2.1.22) RQ 1 EV IPR005857; TIGR01137; sufficient; // AC GenProp1239 DE ADP-L-glycero-beta-D-manno-heptose biosynthesis TP PATHWAY AU Keseler I TH 3 DC ADP-L-glycero-beta-D-manno-heptose biosynthesis DR MetaCyc; PWY0-1241; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ADP-L-glycero-D-mannoheptose 6-epimerase DN ADP-L-glycero-D-mannoheptose 6-epimerase (EC 5.1.3.20) RQ 1 EV IPR011912; TIGR02197; sufficient; -- SN 2 ID D-sedoheptulose 7-phosphate isomerase DN D-sedoheptulose 7-phosphate isomerase (EC 5.3.1.28) RQ 1 EV IPR004515; TIGR00441; sufficient; -- SN 3 ID Heptose 7-phosphate kinase DN Heptose 7-phosphate kinase (EC 2.7.1.167) RQ 1 EV IPR004821; PF01467; sufficient; EV IPR004821; TIGR00125; sufficient; EV IPR011611; PF00294; sufficient; EV IPR011913; TIGR02198; sufficient; EV IPR011914; TIGR02199; sufficient; -- SN 4 ID Heptose 1-phosphate adenyltransferase DN Heptose 1-phosphate adenyltransferase (EC 2.7.7.70) RQ 1 EV IPR004821; PF01467; sufficient; EV IPR004821; TIGR00125; sufficient; EV IPR011611; PF00294; sufficient; EV IPR011913; TIGR02198; sufficient; EV IPR011914; TIGR02199; sufficient; -- SN 5 ID D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase DN D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase (EC 3.1.3.82) RQ 1 EV IPR004446; TIGR00213; sufficient; // AC GenProp1240 DE Ketolysis TP PATHWAY AU Trupp M TH 1 DC Ketolysis DR MetaCyc; PWY66-368; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Hydroxybutyrate dehydrogenase DN 3-Hydroxybutyrate dehydrogenase (EC 1.1.1.30) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID Acetoacetyl-CoA thiolase DN Acetoacetyl-CoA thiolase (EC 2.3.1.9) RQ 1 EV IPR002155; TIGR01930; sufficient; -- SN 3 ID Acetoacetate CoA-transferase DN Acetoacetate CoA-transferase (EC 2.8.3.5) RQ 1 EV IPR004165; PF01144; sufficient; // AC GenProp1241 DE Wybutosine biosynthesis TP PATHWAY AU Caspi R TH 1 DC Wybutosine biosynthesis DR MetaCyc; PWY-7283; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID tRNA(Phe) 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase DN tRNA(Phe) 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase (EC 2.1.1.282) RQ 1 EV IPR003827; PF02676; sufficient; -- SN 2 ID 7-(3-Amino-3-methylcarboxypropyl)-wyosine carboxycarbonylase DN 7-(3-Amino-3-methylcarboxypropyl)-wyosine carboxycarbonylase (EC 2.3.1.231) RQ 1 EV IPR007213; PF04072; sufficient; -- SN 3 ID 7-(3-Amino-3-carboxypropyl)-wyosine methyltransferase DN 7-(3-Amino-3-carboxypropyl)-wyosine methyltransferase (EC 2.1.1.290) RQ 1 EV IPR007213; PF04072; sufficient; // AC GenProp1242 DE Muropeptide degradation TP PATHWAY AU Keseler I TH 2 DC Muropeptide degradation DR MetaCyc; PWY0-1546; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Muramoyltetrapeptide carboxypeptidase DN Muramoyltetrapeptide carboxypeptidase (EC 3.4.17.13) RQ 1 EV IPR003507; PF02016; sufficient; -- SN 2 ID L-Ala-D/L-Glu epimerase DN L-Ala-D/L-Glu epimerase (EC 5.1.1.20) RQ 1 EV IPR013341; PF02746; sufficient; EV IPR029065; PF13378; sufficient; -- SN 3 ID Alanylglutamate dipeptidase DN Alanylglutamate dipeptidase (EC 3.4.13.18) RQ 1 EV IPR001160; TIGR01893; sufficient; EV IPR002933; PF01546; sufficient; -- SN 4 ID Murein tripeptide amidase DN Murein tripeptide amidase RQ 1 EV IPR000834; PF00246; sufficient; // AC GenProp1243 DE Salicylate biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Salicylate biosynthesis I DR MetaCyc; PWY-6406; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Isochorismate synthase DN Isochorismate synthase (EC 5.4.4.2) RQ 1 EV IPR004561; TIGR00543; sufficient; -- SN 2 ID Isochorismate pyruvate lyase DN Isochorismate pyruvate lyase (EC 4.2.99.21) RQ 1 EV IPR008241; TIGR01803; sufficient; // AC GenProp1244 DE Myo-inositol biosynthesis TP PATHWAY AU Caspi R TH 0 DC Myo-inositol biosynthesis DR MetaCyc; PWY-2301; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol-1-phosphate synthase DN Inositol-1-phosphate synthase (EC 5.5.1.4) RQ 1 EV IPR017815; TIGR03450; sufficient; -- SN 2 ID Myo-inositol-3-phosphate monophosphatase DN Myo-inositol-3-phosphate monophosphatase (EC 3.1.3.25) RQ 1 EV IPR000760; PF00459; sufficient; EV IPR011809; TIGR02067; sufficient; // AC GenProp1245 DE L-tyrosine degradation III TP PATHWAY AU Caspi R, Krieger C TH 2 DC L-tyrosine degradation III DR MetaCyc; PWY3O-4108; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Hydroxyphenylpyruvate carboxy-lyase DN 4-Hydroxyphenylpyruvate carboxy-lyase (EC 4.1.1.80) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID Tyrosol:NAD+oxidoreductase DN Tyrosol:NAD+oxidoreductase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; -- SN 3 ID L-tyrosine:pyruvate aminotransferase DN L-tyrosine:pyruvate aminotransferase (EC 2.6.1.58) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 4 ID L-tyrosine:2-oxoglutarate aminotransferase DN L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) RQ 1 EV IPR004839; PF00155; sufficient; // AC GenProp1246 DE Zymosterol biosynthesis TP PATHWAY AU Caspi R TH 10 DC Zymosterol biosynthesis DR MetaCyc; PWY-6074; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lanosterol 14a-demethylase DN Lanosterol 14a-demethylase (EC 1.14.13.70) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID 14-Demethyllanosterol Delta14 reductase DN 14-Demethyllanosterol Delta14 reductase (EC 1.3.1.70) RQ 1 EV IPR001171; PF01222; sufficient; -- SN 3 ID 4,4-Dimethylzymosterol 4-hydroxylase DN 4,4-Dimethylzymosterol 4-hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 4 ID 4-Alpha-hydroxymethyl-4-beta-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol dehydrogenase DN 4-Alpha-hydroxymethyl-4-beta-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol dehydrogenase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 5 ID 4-Alpha-formyl-4-beta-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol 4-hydroxylase DN 4-Alpha-formyl-4-beta-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol 4-hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 6 ID 3-beta-hydroxysteroid dehydrogenase/C4-decarboxylase DN 3-beta-hydroxysteroid dehydrogenase/C4-decarboxylase (EC 1.1.1.170) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 7 ID 4-Alpha-methylzymosterol 3-dehydrogenase DN 4-Alpha-methylzymosterol 3-dehydrogenase (EC 1.1.1.270) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 8 ID 4-Alpha-methyl-zymosterol 4-hydroxylase DN 4-Alpha-methyl-zymosterol 4-hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 9 ID 4-Alpha-hydroxymethyl-5-alpha-cholesta-8,24-dien-3-beta-ol dehydrogenase DN 4-Alpha-hydroxymethyl-5-alpha-cholesta-8,24-dien-3-beta-ol dehydrogenase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 10 ID 4-Alpha-formyl-5-alpha-cholesta-8,24-dien-3-beta-ol 4-hydroxylase DN 4-Alpha-formyl-5-alpha-cholesta-8,24-dien-3-beta-ol 4-hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 11 ID 4-Alpha-carboxy-5-alpha-cholesta-8,24-dien-3-beta-ol:NAD(P)+ 3-oxidoreductase (decarboxylating) DN 4-Alpha-carboxy-5-alpha-cholesta-8,24-dien-3-beta-ol:NAD(P)+ 3-oxidoreductase (decarboxylating) (EC 1.1.1.170) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 12 ID Zymosterol 3-dehydrogenase DN Zymosterol 3-dehydrogenase (EC 1.1.1.270) RQ 1 EV IPR002347; PF00106; sufficient; // AC GenProp1247 DE Glycogen biosynthesis I (from ADP-D-Glucose) TP PATHWAY AU Caspi R, Keseler I, Riley M TH 2 DC Glycogen biosynthesis I (from ADP-D-Glucose) DR MetaCyc; GLYCOGENSYNTH-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ADP-glucose pyrophosphorylase DN ADP-glucose pyrophosphorylase (EC 2.7.7.27) RQ 1 EV IPR011831; TIGR02091; sufficient; -- SN 2 ID 1,4-Alpha-glucan branching enzyme DN 1,4-Alpha-glucan branching enzyme (EC 2.4.1.18) RQ 1 EV IPR006407; TIGR01515; sufficient; -- SN 3 ID Starch synthase DN Starch synthase (EC 2.4.1.21) RQ 1 EV IPR011835; TIGR02095; sufficient; -- SN 4 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005852; TIGR01132; sufficient; // AC GenProp1248 DE Fructose 2,6-bisphosphate biosynthesis TP PATHWAY AU Weerasinghe D TH 0 DC Fructose 2,6-bisphosphate biosynthesis DR MetaCyc; PWY66-423; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Fructose-2,6-bisphosphatase DN Fructose-2,6-bisphosphatase (EC 3.1.3.46) RQ 1 EV IPR013078; PF00300; sufficient; -- SN 2 ID Fructose-6P, 2 kinase DN Fructose-6P, 2 kinase (EC 2.7.1.105) RQ 1 EV IPR013078; PF00300; sufficient; // AC GenProp1249 DE 1D-myo-inositol hexakisphosphate biosynthesis I (from Ins(1,4,5)P3) TP PATHWAY AU Caspi R TH 3 DC 1D-myo-inositol hexakisphosphate biosynthesis I (from Ins(1,4,5)P3) DR MetaCyc; PWY-6361; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol-1,4,5-trisphosphate 3-kinase DN Inositol-1,4,5-trisphosphate 3-kinase (EC 2.7.1.127) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 2 ID Myo-inositol-1,4,5-trisphosphate 6-kinase DN Myo-inositol-1,4,5-trisphosphate 6-kinase (EC 2.7.1.151) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 3 ID Myo-inositol-1,4,5,6-tetrakrisphosphate 3-kinase DN Myo-inositol-1,4,5,6-tetrakrisphosphate 3-kinase (EC 2.7.1.151) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 4 ID Ins(1,3,4,5,6)P5 2-kinase DN Ins(1,3,4,5,6)P5 2-kinase (EC 2.7.1.158) RQ 1 EV IPR009286; PF06090; sufficient; -- SN 5 ID Myo-inositol-1,3,4,5-tetrakisphosphate 6-kinase DN Myo-inositol-1,3,4,5-tetrakisphosphate 6-kinase (EC 2.7.1.151) RQ 1 EV IPR005522; PF03770; sufficient; // AC GenProp1250 DE Aspartate superpathway TP PATHWAY AU Caspi R TH 4 DC Aspartate superpathway DR MetaCyc; PWY0-781; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID Aspartate kinase DN Aspartate kinase (EC 2.7.2.4) RQ 1 EV IPR005260; TIGR00656; sufficient; -- SN 3 ID Cobalamin-independent homocysteine transmethylase DN Cobalamin-independent homocysteine transmethylase (EC 2.1.1.14) RQ 1 EV IPR006276; TIGR01371; sufficient; -- SN 4 ID Methionine synthase DN Methionine synthase (EC 2.1.1.13) RQ 1 EV IPR011822; TIGR02082; sufficient; -- SN 5 ID L-aspartate oxidase DN L-aspartate oxidase (EC 1.4.3.16) RQ 1 EV IPR005288; TIGR00551; sufficient; -- SN 6 ID Methionine adenosyltransferase DN Methionine adenosyltransferase (EC 2.5.1.6) RQ 1 EV IPR002133; TIGR01034; sufficient; // AC GenProp1251 DE L-tyrosine biosynthesis I TP PATHWAY AU Fulcher C, Ingraham J, Riley M TH 1 DC L-tyrosine biosynthesis I DR MetaCyc; TYRSYN; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Chorismate mutase DN Chorismate mutase (EC 5.4.99.5) RQ 1 EV IPR003099; PF02153; sufficient; EV IPR011277; TIGR01799; sufficient; EV IPR001086; PF00800; sufficient; EV IPR010952; TIGR01797; sufficient; -- SN 2 ID Prephenate dehydrogenase DN Prephenate dehydrogenase (EC 1.3.1.12) RQ 1 EV IPR003099; PF02153; sufficient; EV IPR011277; TIGR01799; sufficient; -- SN 3 ID L-tyrosine:2-oxoglutarate aminotransferase DN L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) RQ 1 EV IPR004839; PF00155; sufficient; // AC GenProp1252 DE Cardiolipin biosynthesis III TP PATHWAY AU Keseler I TH 1 DC Cardiolipin biosynthesis III DR MetaCyc; PWY0-1545; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylglycerolphosphate phosphatase DN Phosphatidylglycerolphosphate phosphatase (EC 3.1.3.27) RQ 1 EV IPR006435; TIGR01545; sufficient; -- SN 2 ID Phosphatidylglycerolphosphate synthase DN Phosphatidylglycerolphosphate synthase (EC 2.7.8.5) RQ 1 EV IPR000462; PF01066; sufficient; EV IPR004570; TIGR00560; sufficient; -- SN 3 ID Cardiolipin synthase DN Cardiolipin synthase RQ 1 EV IPR025202; PF13091; sufficient; // AC GenProp1253 DE Superpathway of arginine and polyamine biosynthesis TP PATHWAY AU N/A TH 0 DC Superpathway of arginine and polyamine biosynthesis DR MetaCyc; ARG+POLYAMINE-SYN; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arginine decarboxylase DN Arginine decarboxylase (EC 4.1.1.19) RQ 1 EV IPR002985; TIGR01273; sufficient; -- SN 2 ID Argininosuccinase DN Argininosuccinase (EC 4.3.2.1) RQ 1 EV IPR009049; TIGR00838; sufficient; // AC GenProp1254 DE NADH to hydrogen peroxide electron transfer TP PATHWAY AU Mackie A TH 0 DC NADH to hydrogen peroxide electron transfer DR MetaCyc; PWY0-1590; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytochrome c peroxidase DN Cytochrome c peroxidase (EC 1.11.1) RQ 1 EV IPR004852; PF03150; sufficient; EV IPR009056; PF00034; sufficient; EV IPR025992; PF14376; sufficient; -- SN 2 ID NADH:menaquinone oxidoreductase (H+-transporting) DN NADH:menaquinone oxidoreductase (H+-transporting) (EC 1.6.5) RQ 1 EV IPR000440; PF00507; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR001694; PF00146; sufficient; EV IPR010226; TIGR01971; sufficient; EV IPR001457; PF00499; sufficient; EV IPR001133; PF00420; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR010227; TIGR01972; sufficient; EV IPR010096; TIGR01770; sufficient; // AC GenProp1255 DE Adenosine nucleotides degradation II TP PATHWAY AU Arnaud M TH 3 DC Adenosine nucleotides degradation II DR MetaCyc; SALVADEHYPOX-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine deaminase DN Adenosine deaminase (EC 3.5.4.4) RQ 1 EV IPR006330; TIGR01430; sufficient; -- SN 2 ID 5'-AMP nucleotidase DN 5'-AMP nucleotidase (EC 3.1.3.5) RQ 1 EV IPR010394; PF06189; sufficient; EV IPR001952; PF00245; sufficient; -- SN 3 ID Inosine phosphorylase DN Inosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR009664; PF06865; sufficient; EV IPR004402; TIGR00107; sufficient; -- SN 4 ID Hypoxanthine dehydrogenase DN Hypoxanthine dehydrogenase (EC 1.17.1.4) RQ 1 EV IPR000674; PF01315; sufficient; EV IPR001041; PF00111; sufficient; EV IPR002346; PF00941; sufficient; EV IPR002888; PF01799; sufficient; EV IPR005107; PF03450; sufficient; EV IPR008274; PF02738; sufficient; EV IPR014307; TIGR02963; sufficient; -- SN 5 ID Xanthine:NAD+ oxidoreductase DN Xanthine:NAD+ oxidoreductase (EC 1.17.1.4) RQ 1 EV IPR000674; PF01315; sufficient; EV IPR001041; PF00111; sufficient; EV IPR002346; PF00941; sufficient; EV IPR002888; PF01799; sufficient; EV IPR005107; PF03450; sufficient; EV IPR008274; PF02738; sufficient; EV IPR014307; TIGR02963; sufficient; // AC GenProp1256 DE Pyruvate to cytochrome bo oxidase electron transfer TP PATHWAY AU Mackie A TH 0 DC Pyruvate to cytochrome bo oxidase electron transfer DR MetaCyc; PWY-7544; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pyruvate oxidase DN Pyruvate oxidase (EC 1.2.5.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; // AC GenProp1257 DE Allantoin degradation to glyoxylate I TP PATHWAY AU Caspi R TH 0 DC Allantoin degradation to glyoxylate I DR MetaCyc; PWY-5694; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Allantoicase DN Allantoicase (EC 3.5.3.4) RQ 1 EV IPR005164; TIGR02961; sufficient; -- SN 2 ID Ureidoglycolate urea-lyase DN Ureidoglycolate urea-lyase (EC 4.3.2.3) RQ 1 EV IPR007247; PF04115; sufficient; // AC GenProp1258 DE Superpathway of S-adenosyl-L-methionine biosynthesis TP PATHWAY AU Caspi R TH 1 DC Superpathway of S-adenosyl-L-methionine biosynthesis DR MetaCyc; MET-SAM-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cobalamin-independent homocysteine transmethylase DN Cobalamin-independent homocysteine transmethylase (EC 2.1.1.14) RQ 1 EV IPR006276; TIGR01371; sufficient; -- SN 2 ID Methionine synthase DN Methionine synthase (EC 2.1.1.13) RQ 1 EV IPR011822; TIGR02082; sufficient; -- SN 3 ID Methionine adenosyltransferase DN Methionine adenosyltransferase (EC 2.5.1.6) RQ 1 EV IPR002133; TIGR01034; sufficient; // AC GenProp1259 DE Glycogen degradation II TP PATHWAY AU Caspi R TH 4 DC Glycogen degradation II DR MetaCyc; PWY-5941; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Amylo-alpha-1,6-glucosidase DN Amylo-alpha-1,6-glucosidase (EC 3.2.1.33) RQ 1 EV IPR006421; TIGR01531; sufficient; -- SN 2 ID Glycogen phosphorylase DN Glycogen phosphorylase (EC 2.4.1.1) RQ 1 EV IPR000811; PF00343; sufficient; EV IPR011833; TIGR02093; sufficient; -- SN 3 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005843; PF00408; sufficient; EV IPR005844; PF02878; sufficient; EV IPR005845; PF02879; sufficient; EV IPR005846; PF02880; sufficient; -- SN 4 ID 4-Alpha-glucanotransferase DN 4-Alpha-glucanotransferase (EC 2.4.1.25) RQ 1 EV IPR006421; TIGR01531; sufficient; -- SN 5 ID Glucan 1,4-alpha-glucosidase DN Glucan 1,4-alpha-glucosidase (EC 3.2.1.3) RQ 1 EV IPR011613; PF00723; sufficient; -- SN 6 ID Glycogen phosphorylase DN Glycogen phosphorylase (EC 2.4.1.1) RQ 1 EV IPR000811; PF00343; sufficient; EV IPR011833; TIGR02093; sufficient; // AC GenProp1260 DE UDP-alpha-D-xylose biosynthesis TP PATHWAY AU N/A TH 0 DC UDP-alpha-D-xylose biosynthesis DR MetaCyc; PWY-4821; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-glucuronate decarboxylase DN UDP-glucuronate decarboxylase (EC 4.1.1.35) RQ 1 EV IPR016040; PF16363; sufficient; EV IPR001509; PF01370; sufficient; -- SN 2 ID UDP-glucose dehydrogenase DN UDP-glucose dehydrogenase (EC 1.1.1.22) RQ 1 EV IPR017476; TIGR03026; sufficient; // AC GenProp1261 DE Cytokinins 7-N-glucoside biosynthesis TP PATHWAY AU N/A TH 0 DC Cytokinins 7-N-glucoside biosynthesis DR MetaCyc; PWY-2881; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-glucose:trans-zeatin 7-N-glucosyltransferase DN UDP-glucose:trans-zeatin 7-N-glucosyltransferase (EC 2.4.1) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 2 ID UDP-glucose:cis-zeatin 7-N-glucosyltransferase DN UDP-glucose:cis-zeatin 7-N-glucosyltransferase (EC 2.4.1) RQ 1 EV IPR002213; PF00201; sufficient; // AC GenProp1262 DE UTP and CTP de novo biosynthesis TP PATHWAY AU Caspi R TH 1 DC UTP and CTP de novo biosynthesis DR MetaCyc; PWY-7176; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID CTP synthetase DN CTP synthetase (EC 6.3.4.2) RQ 1 EV IPR004468; TIGR00337; sufficient; -- SN 2 ID UMP kinase DN UMP kinase (EC 2.7.4.14) RQ 1 EV IPR006266; TIGR01359; sufficient; EV IPR015963; TIGR02075; sufficient; -- SN 3 ID UDP kinase DN UDP kinase (EC 2.7.4.6) RQ 1 EV IPR006259; TIGR01351; sufficient; EV IPR001564; PF00334; sufficient; // AC GenProp1263 DE Methylglyoxal degradation III TP PATHWAY AU Caspi R TH 0 DC Methylglyoxal degradation III DR MetaCyc; PWY-5453; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-1,2-propanediol dehydrogenase DN L-1,2-propanediol dehydrogenase RQ 1 EV IPR023210; PF00248; sufficient; EV IPR001670; PF00465; sufficient; -- SN 2 ID Methylglyoxal reductase DN Methylglyoxal reductase (EC 1.1.1) RQ 1 EV IPR023210; PF00248; sufficient; EV IPR001670; PF00465; sufficient; // AC GenProp1264 DE Superpathway of pyrimidine deoxyribonucleoside salvage TP PATHWAY AU Caspi R TH 3 DC Superpathway of pyrimidine deoxyribonucleoside salvage DR MetaCyc; PWY-7200; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2'-Deoxycytidine kinase DN 2'-Deoxycytidine kinase (EC 2.7.1.74) RQ 1 EV IPR031314; PF01712; sufficient; -- SN 2 ID Thymidylate kinase DN Thymidylate kinase (EC 2.7.4.12) RQ 1 EV IPR018094; TIGR00041; sufficient; -- SN 3 ID DCMP kinase DN DCMP kinase (EC 2.7.4.25) RQ 1 EV IPR006266; TIGR01359; sufficient; -- SN 4 ID Thymidine kinase DN Thymidine kinase (EC 2.7.1.21) RQ 1 EV IPR001267; PF00265; sufficient; -- SN 5 ID Thymidylate synthase DN Thymidylate synthase (EC 2.1.1.45) RQ 1 EV IPR003745; PF02593; sufficient; EV IPR000398; TIGR03284; sufficient; // AC GenProp1265 DE Glyoxylate cycle TP PATHWAY AU Caspi R TH 4 DC Glyoxylate cycle DR MetaCyc; GLYOXYLATE-BYPASS; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aconitase DN Aconitase RQ 1 EV IPR006249; TIGR01341; sufficient; EV IPR004406; TIGR00117; sufficient; -- SN 2 ID Cis-aconitate hydratase DN Cis-aconitate hydratase RQ 1 EV IPR006249; TIGR01341; sufficient; EV IPR004406; TIGR00117; sufficient; -- SN 3 ID Citrate synthase DN Citrate synthase (EC 2.3.3.1) RQ 1 EV IPR002020; PF00285; sufficient; EV IPR010953; TIGR01798; sufficient; -- SN 4 ID Isocitrate lyase DN Isocitrate lyase (EC 4.1.3.1) RQ 1 EV IPR006254; PF00463; sufficient; EV IPR006254; TIGR01346; sufficient; -- SN 5 ID Malate dehydrogenase (NAD) DN Malate dehydrogenase (NAD) (EC 1.1.1.37) RQ 1 EV IPR010097; TIGR01772; sufficient; -- SN 6 ID Malate synthase DN Malate synthase (EC 2.3.3.9) RQ 1 EV IPR001465; PF01274; sufficient; EV IPR006252; TIGR01344; sufficient; // AC GenProp1266 DE Superpathway of thiamine diphosphate biosynthesis II TP PATHWAY AU Caspi R TH 1 DC Superpathway of thiamine diphosphate biosynthesis II DR MetaCyc; PWY-6895; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphomethylpyrimidine kinase DN Phosphomethylpyrimidine kinase (EC 2.7.4.7) RQ 1 EV IPR004399; TIGR00097; sufficient; EV IPR013749; PF08543; sufficient; -- SN 2 ID Thiazole tautomerase DN Thiazole tautomerase (EC 5.3.99.10) RQ 1 EV IPR003733; PF02581; sufficient; -- SN 3 ID Thiamine phosphate synthase DN Thiamine phosphate synthase (EC 2.5.1.3) RQ 1 EV IPR003733; PF02581; sufficient; EV IPR003733; TIGR00693; sufficient; // AC GenProp1267 DE Mixed acid fermentation TP PATHWAY AU Riley M, Ingraham J TH 14 DC Mixed acid fermentation DR MetaCyc; FERMENTATION-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR001670; PF00465; sufficient; EV IPR015590; PF00171; sufficient; -- SN 2 ID Acetate kinase DN Acetate kinase (EC 2.7.2.1) RQ 1 EV IPR000890; PF00871; sufficient; EV IPR004372; TIGR00016; sufficient; -- SN 3 ID Aconitase DN Aconitase RQ 1 EV IPR004406; TIGR00117; sufficient; -- SN 4 ID Cis-aconitate hydratase DN Cis-aconitate hydratase RQ 1 EV IPR004406; TIGR00117; sufficient; -- SN 5 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; EV IPR015590; PF00171; sufficient; -- SN 6 ID Citrate synthase DN Citrate synthase (EC 2.3.3.1) RQ 1 EV IPR002020; PF00285; sufficient; EV IPR010953; TIGR01798; sufficient; -- SN 7 ID D-lactate dehydrogenase DN D-lactate dehydrogenase (EC 1.1.1.28) RQ 1 EV IPR006139; PF00389; sufficient; EV IPR006140; PF02826; sufficient; -- SN 8 ID Formate hydrogenlyase complex DN Formate hydrogenlyase complex RQ 1 EV IPR006478; TIGR01591; sufficient; EV IPR001694; PF00146; sufficient; -- SN 9 ID Fumarase B DN Fumarase B (EC 4.2.1.2) RQ 1 EV IPR024493; PF10965; sufficient; EV IPR007761; PF05068; sufficient; EV IPR005677; TIGR00979; sufficient; -- SN 10 ID NADP+-dependent isocitrate dehydrogenase DN NADP+-dependent isocitrate dehydrogenase (EC 1.1.1.42) RQ 1 EV IPR004439; TIGR00183; sufficient; -- SN 11 ID Malate dehydrogenase (NAD) DN Malate dehydrogenase (NAD) (EC 1.1.1.37) RQ 1 EV IPR010097; TIGR01772; sufficient; -- SN 12 ID Phosphoenolpyruvate carboxylase DN Phosphoenolpyruvate carboxylase (EC 4.1.1.31) RQ 1 EV IPR021135; PF00311; sufficient; -- SN 13 ID Pyruvate kinase DN Pyruvate kinase (EC 2.7.1.40) RQ 1 EV IPR001697; TIGR01064; sufficient; -- SN 14 ID Phosphotransacetylase DN Phosphotransacetylase (EC 2.3.1.8) RQ 1 EV IPR002505; PF01515; sufficient; EV IPR004614; TIGR00651; sufficient; EV IPR010766; PF07085; sufficient; -- SN 15 ID Pyruvate formate lyase DN Pyruvate formate lyase (EC 2.3.1.54) RQ 1 EV IPR005949; TIGR01255; sufficient; -- SN 16 ID Fumarate reductase DN Fumarate reductase (EC 1.3.5.4) RQ 1 EV IPR004489; TIGR00384; sufficient; EV IPR005884; TIGR01176; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR003510; PF02300; sufficient; EV IPR003418; PF02313; sufficient; // AC GenProp1268 DE Adenine salvage TP PATHWAY AU Caspi R TH 1 DC Adenine salvage DR MetaCyc; PWY-6610; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenine deaminase DN Adenine deaminase (EC 3.5.4.2) RQ 1 EV IPR006679; TIGR01178; sufficient; -- SN 2 ID Adenine phosphoribosyltransferase DN Adenine phosphoribosyltransferase (EC 2.4.2.7) RQ 1 EV IPR005764; TIGR01090; sufficient; -- SN 3 ID Hypoxanthine phosphoribosyltransferase DN Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) RQ 1 EV IPR000836; PF00156; sufficient; // AC GenProp1269 DE Pyruvate to cytochrome bd oxidase electron transfer TP PATHWAY AU Mackie A TH 0 DC Pyruvate to cytochrome bd oxidase electron transfer DR MetaCyc; PWY-7545; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pyruvate oxidase DN Pyruvate oxidase (EC 1.2.5.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID Cytochrome bd-I ubiquinol oxidase DN Cytochrome bd-I ubiquinol oxidase (EC 1.10.3.14) RQ 1 EV IPR002585; PF01654; sufficient; EV IPR003317; PF02322; sufficient; EV IPR003317; TIGR00203; sufficient; EV IPR011724; TIGR02106; sufficient; EV IPR012994; PF08173; sufficient; // AC GenProp1270 DE Enterobacterial common antigen biosynthesis TP PATHWAY AU N/A TH 3 DC Enterobacterial common antigen biosynthesis DR MetaCyc; ECASYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Acetamido-4,6-dideoxy-D-galactose transferase DN 4-Acetamido-4,6-dideoxy-D-galactose transferase (EC 2.4.1.325) RQ 1 EV IPR009993; PF07429; sufficient; -- SN 2 ID UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase DN UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.33) RQ 1 EV IPR000715; PF00953; sufficient; EV IPR012750; TIGR02380; sufficient; -- SN 3 ID DTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase DN DTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase (EC 2.3.1.210) RQ 1 EV IPR012752; TIGR02382; sufficient; -- SN 4 ID UDP-N-acetyl-D-mannosaminuronic acid transferase DN UDP-N-acetyl-D-mannosaminuronic acid transferase (EC 2.4.1.180) RQ 1 EV IPR004629; PF03808; sufficient; EV IPR004629; TIGR00696; sufficient; -- SN 5 ID UDP-N-acetyl-D-mannosamine dehydrogenase DN UDP-N-acetyl-D-mannosamine dehydrogenase (EC 1.1.1.336) RQ 1 EV IPR017476; TIGR03026; sufficient; // AC GenProp1271 DE Myo-, chiro- and scyllo-inositol degradation TP PATHWAY AU Caspi R TH 3 DC Myo-, chiro- and scyllo-inositol degradation DR MetaCyc; PWY-7237; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Myo-inositol 2-dehydrogenase DN Myo-inositol 2-dehydrogenase (EC 1.1.1.18) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR004104; PF02894; sufficient; -- SN 2 ID Scyllo-inosose dehydratase DN Scyllo-inosose dehydratase (EC 4.2.1.44) RQ 1 EV IPR030823; TIGR04379; sufficient; -- SN 3 ID Scyllo-inositol 2-dehydrogenase DN Scyllo-inositol 2-dehydrogenase (EC 1.1.1.370) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR004104; PF02894; sufficient; -- SN 4 ID 1D-chiro-inositol 1-dehydrogenase DN 1D-chiro-inositol 1-dehydrogenase (EC 1.1.1.369) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR004104; PF02894; sufficient; -- SN 5 ID Scyllo-inosose epimerase/isomerase DN Scyllo-inosose epimerase/isomerase (EC 5.3.99.11) RQ 1 EV IPR013022; PF01261; sufficient; // AC GenProp1272 DE Spermine and spermidine degradation III TP PATHWAY AU Zhang P TH 0 DC Spermine and spermidine degradation III DR MetaCyc; PWY-6441; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Spermidine oxidase DN Spermidine oxidase (EC 1.5.3.17) RQ 1 EV IPR002937; PF01593; sufficient; -- SN 2 ID Spermine oxidase DN Spermine oxidase (EC 1.5.3.16) RQ 1 EV IPR002937; PF01593; sufficient; // AC GenProp1273 DE Thymine degradation TP PATHWAY AU Caspi R TH 1 DC Thymine degradation DR MetaCyc; PWY-6430; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dihydrothymine dehydrogenase DN Dihydrothymine dehydrogenase (EC 1.3.1.2) RQ 1 EV IPR005720; PF01180; sufficient; EV IPR005720; TIGR01037; sufficient; EV IPR023753; PF07992; sufficient; EV IPR028261; PF14691; sufficient; -- SN 2 ID 3-Ureido-isobutyrate amidohydrolase DN 3-Ureido-isobutyrate amidohydrolase (EC 3.5.1.6) RQ 1 EV IPR003010; PF00795; sufficient; -- SN 3 ID Dihydrothyminidase DN Dihydrothyminidase (EC 3.5.2.2) RQ 1 EV IPR011778; TIGR02033; sufficient; // AC GenProp1274 DE D-serine metabolism TP PATHWAY AU Pujar A TH 0 DC D-serine metabolism DR MetaCyc; PWY-6196; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Serine racemase DN Serine racemase (EC 5.1.1.18) RQ 1 EV IPR001926; PF00291; sufficient; -- SN 2 ID D-serine ammonia-lyase (pyruvate-forming) DN D-serine ammonia-lyase (pyruvate-forming) RQ 1 EV IPR001926; PF00291; sufficient; // AC GenProp1275 DE Glycine cleavage TP PATHWAY AU Fulcher C, Caspi R, Riley M TH 1 DC Glycine cleavage DR MetaCyc; GLYCLEAV-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycine dehydrogenase DN Glycine dehydrogenase (EC 1.4.4.2) RQ 1 EV IPR003437; TIGR00461; sufficient; -- SN 2 ID Aminomethyltransferase DN Aminomethyltransferase (EC 2.1.2.10) RQ 1 EV IPR006223; TIGR00528; sufficient; -- SN 3 ID Dihydrolipoyl dehydrogenase DN Dihydrolipoyl dehydrogenase (EC 1.8.1.4) RQ 1 EV IPR006258; TIGR01350; sufficient; // AC GenProp1276 DE Putrescine degradation V TP PATHWAY AU Caspi R TH 0 DC Putrescine degradation V DR MetaCyc; PWY-3; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Aminobutyraldehyde dehydrogenase DN 4-Aminobutyraldehyde dehydrogenase (EC 1.2.1.19) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID Polyamine aminotransferase DN Polyamine aminotransferase (EC 2.6.1.113) RQ 1 EV IPR005814; PF00202; sufficient; // AC GenProp1277 DE Sphingosine and sphingosine-1-phosphate metabolism TP PATHWAY AU Evsikov A TH 3 DC Sphingosine and sphingosine-1-phosphate metabolism DR MetaCyc; PWY3DJ-11470; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Alkenal reductase DN 2-Alkenal reductase (EC 1.3.1.27) RQ 1 EV IPR014190; TIGR02825; sufficient; -- SN 2 ID N-acylsphingosine amidohydrolase (alkaline ceramidase) DN N-acylsphingosine amidohydrolase (alkaline ceramidase) (EC 3.5.1.23) RQ 1 EV IPR008901; PF05875; sufficient; -- SN 3 ID Sphingosine phosphate lyase DN Sphingosine phosphate lyase (EC 4.3.2) RQ 1 EV IPR002129; PF00282; sufficient; -- SN 4 ID Sphingosine kinase DN Sphingosine kinase (EC 2.7.1.91) RQ 1 EV IPR001206; PF00781; sufficient; -- SN 5 ID Sphingosine-1-phosphate phosphatase DN Sphingosine-1-phosphate phosphatase RQ 1 EV IPR000326; PF01569; sufficient; // AC GenProp1278 DE Purine ribonucleosides degradation TP PATHWAY AU Ingraham J TH 4 DC Purine ribonucleosides degradation DR MetaCyc; PWY0-1296; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine deaminase DN Adenosine deaminase (EC 3.5.4.4) RQ 1 EV IPR006330; TIGR01430; sufficient; -- SN 2 ID Adenosine phosphorylase DN Adenosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; EV IPR009664; PF06865; sufficient; -- SN 3 ID Inosine phosphorylase DN Inosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR009664; PF06865; sufficient; EV IPR004402; TIGR00107; sufficient; -- SN 4 ID Phosphodeoxyribomutase DN Phosphodeoxyribomutase (EC 5.4.2.7) RQ 1 EV IPR010045; TIGR01696; sufficient; -- SN 5 ID Guanosine phosphorylase DN Guanosine phosphorylase (EC 2.4.2.15) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR004402; TIGR00107; sufficient; -- SN 6 ID Xanthosine phosphorylase DN Xanthosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR009664; PF06865; sufficient; EV IPR010943; TIGR01699; sufficient; // AC GenProp1279 DE Superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation TP PATHWAY AU Caspi R TH 5 DC Superpathway of L-arginine, putrescine, and 4-aminobutanoate DC degradation DR MetaCyc; ARGDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Agmatinase DN Agmatinase (EC 3.5.3.11) RQ 1 EV IPR005925; TIGR01230; sufficient; EV IPR006035; PF00491; sufficient; -- SN 2 ID 4-Aminobutyraldehyde dehydrogenase DN 4-Aminobutyraldehyde dehydrogenase (EC 1.2.1.19) RQ 1 EV IPR017749; TIGR03374; sufficient; -- SN 3 ID Arginine decarboxylase DN Arginine decarboxylase (EC 4.1.1.19) RQ 1 EV IPR000310; PF01276; sufficient; EV IPR005308; PF03709; sufficient; EV IPR008286; PF03711; sufficient; -- SN 4 ID 4-Aminobutyrate aminotransferase DN 4-Aminobutyrate aminotransferase (EC 2.6.1.19) RQ 1 EV IPR004632; TIGR00700; sufficient; EV IPR005814; PF00202; sufficient; -- SN 5 ID Putrescine aminotransferase DN Putrescine aminotransferase RQ 1 EV IPR005814; PF00202; sufficient; EV IPR017747; TIGR03372; sufficient; -- SN 6 ID Glutamate-putrescine ligase DN Glutamate-putrescine ligase (EC 6.3.1.11) RQ 1 EV IPR008146; PF00120; sufficient; -- SN 7 ID Gamma-glutamyl-gamma-aminobutyrate hydrolase DN Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) RQ 1 EV IPR011697; PF07722; sufficient; // AC GenProp1280 DE L-arginine degradation II (AST pathway) TP PATHWAY AU Caspi R, Ingraham J TH 3 DC L-arginine degradation II (AST pathway) DR MetaCyc; AST-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arginine succinyltransferase DN Arginine succinyltransferase (EC 2.3.1.109) RQ 1 EV IPR007041; PF04958; sufficient; EV IPR007041; TIGR03243; sufficient; EV IPR017650; TIGR03244; sufficient; EV IPR017651; TIGR03245; sufficient; -- SN 2 ID N-succinylarginine dihydrolase DN N-succinylarginine dihydrolase (EC 3.5.3.23) RQ 1 EV IPR007079; PF04996; sufficient; EV IPR007079; TIGR03241; sufficient; -- SN 3 ID Succinylglutamate semialdehyde dehydrogenase DN Succinylglutamate semialdehyde dehydrogenase (EC 1.2.1.71) RQ 1 EV IPR017649; TIGR03240; sufficient; -- SN 4 ID Succinylglutamate desuccinylase DN Succinylglutamate desuccinylase (EC 3.5.1.96) RQ 1 EV IPR007036; PF04952; sufficient; EV IPR016681; TIGR03242; sufficient; -- SN 5 ID Succinylornithine transaminase DN Succinylornithine transaminase (EC 2.6.1.81) RQ 1 EV IPR004636; TIGR00707; sufficient; EV IPR005814; PF00202; sufficient; EV IPR017652; TIGR03246; sufficient; // AC GenProp1281 DE Hydrogen sulfide biosynthesis I TP PATHWAY AU Keseler I TH 0 DC Hydrogen sulfide biosynthesis I DR MetaCyc; PWY0-1534; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cysteine aminotransferase DN Cysteine aminotransferase (EC 2.6.1.3) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID 3-Mercaptopyruvate sulfurtransferase DN 3-Mercaptopyruvate sulfurtransferase (EC 4.4.1) RQ 1 EV IPR001763; PF00581; sufficient; // AC GenProp1282 DE L-arginine degradation III (arginine decarboxylase/agmatinase pathway) TP PATHWAY AU Caspi R, Arnaud M TH 0 DC L-arginine degradation III (arginine decarboxylase/agmatinase pathway) DR MetaCyc; PWY0-823; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Agmatinase DN Agmatinase (EC 3.5.3.11) RQ 1 EV IPR005925; TIGR01230; sufficient; EV IPR006035; PF00491; sufficient; -- SN 2 ID Arginine decarboxylase DN Arginine decarboxylase (EC 4.1.1.19) RQ 1 EV IPR002985; TIGR01273; sufficient; // AC GenProp1283 DE Sulfate reduction I (assimilatory) TP PATHWAY AU Riley M, Caspi R TH 1 DC Sulfate reduction I (assimilatory) DR MetaCyc; SO4ASSIM-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoadenosine phosphosulfate reductase DN Phosphoadenosine phosphosulfate reductase (EC 1.8.4.8) RQ 1 EV IPR004511; TIGR00434; sufficient; EV IPR011800; TIGR02057; sufficient; -- SN 2 ID Adenylyl-sulfate kinase DN Adenylyl-sulfate kinase (EC 2.7.1.25) RQ 1 EV IPR002891; TIGR00455; sufficient; -- SN 3 ID Assimilatory sulfite reductase (NADPH) DN Assimilatory sulfite reductase (NADPH) (EC 1.8.1.2) RQ 1 EV IPR010199; TIGR01931; sufficient; EV IPR011786; TIGR02041; sufficient; // AC GenProp1284 DE 5-Aminoimidazole ribonucleotide biosynthesis I TP PATHWAY AU Caspi R TH 3 DC 5-Aminoimidazole ribonucleotide biosynthesis I DR MetaCyc; PWY-6121; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoribosylformylglycinamide cyclo-ligase DN Phosphoribosylformylglycinamide cyclo-ligase (EC 6.3.3.1) RQ 1 EV IPR004733; TIGR00878; sufficient; EV IPR000115; TIGR00877; sufficient; EV IPR004607; TIGR00639; sufficient; -- SN 2 ID Phosphoribosylformylglycinamidine synthetase DN Phosphoribosylformylglycinamidine synthetase (EC 6.3.5.3) RQ 1 EV IPR010073; TIGR01735; sufficient; -- SN 3 ID Phosphoribosylglycinamide formyltransferase DN Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) RQ 1 EV IPR004607; TIGR00639; sufficient; EV IPR000115; TIGR00877; sufficient; EV IPR004733; TIGR00878; sufficient; -- SN 4 ID Phosphoribosylamine-glycine ligase DN Phosphoribosylamine-glycine ligase (EC 6.3.4.13) RQ 1 EV IPR000115; TIGR00877; sufficient; EV IPR004733; TIGR00878; sufficient; EV IPR004607; TIGR00639; sufficient; -- SN 5 ID Phosphoribosylpyrophosphate amidotransferase DN Phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) RQ 1 EV IPR005854; TIGR01134; sufficient; // AC GenProp1286 DE Myo-inositol degradation I TP PATHWAY AU Caspi R, Pellegrini-Toole A TH 5 DC Myo-inositol degradation I DR MetaCyc; P562-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Deoxy-5-keto-D-gluconate 6-phosphate aldolase DN 2-Deoxy-5-keto-D-gluconate 6-phosphate aldolase (EC 4.1.2.29) RQ 1 EV IPR000771; PF01116; sufficient; EV IPR000771; TIGR00167; sufficient; EV IPR011289; TIGR01859; sufficient; -- SN 2 ID 5-Dehydro-2-deoxy-D-gluconate kinase DN 5-Dehydro-2-deoxy-D-gluconate kinase (EC 2.7.1.92) RQ 1 EV IPR030830; TIGR04382; sufficient; -- SN 3 ID Myo-inositol 2-dehydrogenase DN Myo-inositol 2-dehydrogenase (EC 1.1.1.18) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR004104; PF02894; sufficient; -- SN 4 ID Scyllo-inosose dehydratase DN Scyllo-inosose dehydratase (EC 4.2.1.44) RQ 1 EV IPR030823; TIGR04379; sufficient; -- SN 5 ID 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase DN 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase (EC 3.7.1.22) RQ 1 EV IPR030817; TIGR04377; sufficient; -- SN 6 ID 5-Deoxy-D-glucuronate isomerase DN 5-Deoxy-D-glucuronate isomerase (EC 5.3.1.30) RQ 1 EV IPR021120; PF04962; sufficient; EV IPR024203; TIGR04378; sufficient; -- SN 7 ID Malonate semialdehyde dehydrogenase DN Malonate semialdehyde dehydrogenase (EC 1.2.1.18) RQ 1 EV IPR010061; TIGR01722; sufficient; // AC GenProp1287 DE 3-Phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation to 2-hydroxypentadienoate TP PATHWAY AU Riley M TH 3 DC 2-hydroxypentadienoate DR MetaCyc; HCAMHPDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2,3-Dihydroxyphenylpropionate 1,2-dioxygenase DN 2,3-Dihydroxyphenylpropionate 1,2-dioxygenase (EC 1.13.11.16) RQ 1 EV IPR004183; PF02900; sufficient; -- SN 2 ID 3-Phenylpropionate dioxygenase DN 3-Phenylpropionate dioxygenase (EC 1.14.12.19) RQ 1 EV IPR000391; PF00866; sufficient; -- SN 3 ID 2-Hydroxy-6-ketonona-2,4-dienedioate hydrolase DN 2-Hydroxy-6-ketonona-2,4-dienedioate hydrolase (EC 3.7.1.14) RQ 1 EV IPR000073; PF12697; sufficient; -- SN 4 ID 3-(3-Hydroxyphenyl)propanoate hydroxylase DN 3-(3-Hydroxyphenyl)propanoate hydroxylase (EC 1.14.13.127) RQ 1 EV IPR002938; PF01494; sufficient; -- SN 5 ID 2,3-Dihydroxy-2,3-dihydrophenylpropionate dehydrogenase DN 2,3-Dihydroxy-2,3-dihydrophenylpropionate dehydrogenase (EC 1.3.1.87) RQ 1 EV IPR002347; PF00106; sufficient; // AC GenProp1288 DE GABA shunt TP PATHWAY AU Weerasinghe D, Caspi R, Ying H TH 2 DC GABA shunt DR MetaCyc; GLUDEG-I-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Aminobutyrate aminotransferase DN 4-Aminobutyrate aminotransferase (EC 2.6.1.19) RQ 1 EV IPR004631; TIGR00699; sufficient; EV IPR005814; PF00202; sufficient; -- SN 2 ID Glutamate dehydrogenase DN Glutamate dehydrogenase (EC 1.4.1.3) RQ 1 EV IPR006096; PF00208; sufficient; EV IPR006097; PF02812; sufficient; -- SN 3 ID Glutamate decarboxylase B DN Glutamate decarboxylase B (EC 4.1.1.15) RQ 1 EV IPR002129; PF00282; sufficient; -- SN 4 ID Succinate-semialdehyde dehydrogenase (NAD+) DN Succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) RQ 1 EV IPR010102; TIGR01780; sufficient; // AC GenProp1289 DE Thiamine salvage II TP PATHWAY AU Caspi R TH 2 DC Thiamine salvage II DR MetaCyc; PWY-6897; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphomethylpyrimidine kinase DN Phosphomethylpyrimidine kinase (EC 2.7.4.7) RQ 1 EV IPR004399; TIGR00097; sufficient; EV IPR013749; PF08543; sufficient; -- SN 2 ID Thiamine-monophosphate kinase DN Thiamine-monophosphate kinase (EC 2.7.4.16) RQ 1 EV IPR006283; TIGR01379; sufficient; -- SN 3 ID Thiamine monophosphate pyrophosphorylase DN Thiamine monophosphate pyrophosphorylase (EC 2.5.1.3) RQ 1 EV IPR003733; PF02581; sufficient; EV IPR003733; TIGR00693; sufficient; -- SN 4 ID Hydroxyethylthiazole kinase DN Hydroxyethylthiazole kinase (EC 2.7.1.50) RQ 1 EV IPR000417; PF02110; sufficient; EV IPR000417; TIGR00694; sufficient; // AC GenProp1290 DE Lipid IVA biosynthesis TP PATHWAY AU Riley M TH 4 DC Lipid IVA biosynthesis DR MetaCyc; NAGLIPASYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lipid A disaccharide synthase DN Lipid A disaccharide synthase (EC 2.4.1.182) RQ 1 EV IPR003835; PF02684; sufficient; EV IPR003835; TIGR00215; sufficient; -- SN 2 ID UDP-2,3-diacylglucosamine diphosphatase DN UDP-2,3-diacylglucosamine diphosphatase (EC 3.6.1.54) RQ 1 EV IPR010138; TIGR01854; sufficient; -- SN 3 ID Tetraacyldisaccharide 4'-kinase DN Tetraacyldisaccharide 4'-kinase (EC 2.7.1.130) RQ 1 EV IPR003758; PF02606; sufficient; EV IPR003758; TIGR00682; sufficient; -- SN 4 ID UDP-3-O-acyl-N-acetylglucosamine deacetylase DN UDP-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) RQ 1 EV IPR004463; PF03331; sufficient; EV IPR004463; TIGR00325; sufficient; -- SN 5 ID UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase DN UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase (EC 2.3.1.191) RQ 1 EV IPR007691; TIGR01853; sufficient; -- SN 6 ID UDP-N-acetylglucosamine acyltransferase DN UDP-N-acetylglucosamine acyltransferase (EC 2.3.1.129) RQ 1 EV IPR010137; TIGR01852; sufficient; // AC GenProp1291 DE Superpathway of chorismate metabolism TP PATHWAY AU N/A TH 5 DC Superpathway of chorismate metabolism DR MetaCyc; ALL-CHORISMATE-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID S-adenosylmethionine:2-demethylquinol-8 methyltransferase DN S-adenosylmethionine:2-demethylquinol-8 methyltransferase (EC 2.1.1.163) RQ 1 EV IPR004033; PF01209; sufficient; EV IPR004033; TIGR01934; sufficient; -- SN 2 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; PF01264; sufficient; EV IPR000453; TIGR00033; sufficient; -- SN 3 ID Chorismate lyase DN Chorismate lyase (EC 4.1.3.40) RQ 1 EV IPR007440; PF04345; sufficient; -- SN 4 ID 1,4-Dihydroxy-2-naphthoate octaprenyltransferase DN 1,4-Dihydroxy-2-naphthoate octaprenyltransferase (EC 2.5.1.74) RQ 1 EV IPR000537; PF01040; sufficient; -- SN 5 ID Isochorismate synthase DN Isochorismate synthase (EC 5.4.4.2) RQ 1 EV IPR004561; TIGR00543; sufficient; -- SN 6 ID Aminodeoxychorismate synthase DN Aminodeoxychorismate synthase (EC 2.6.1.85) RQ 1 EV IPR005802; TIGR00553; sufficient; -- SN 7 ID 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase DN 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase (EC 3.1.2.28) RQ 1 EV IPR003736; TIGR00369; sufficient; EV IPR006683; PF03061; sufficient; // AC GenProp1292 DE L-tryptophan degradation VIII (to tryptophol) TP PATHWAY AU Caspi R TH 2 DC L-tryptophan degradation VIII (to tryptophol) DR MetaCyc; PWY-5081; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Indole-3-ethanol dehydrogenase DN Indole-3-ethanol dehydrogenase (EC 1.1.1.190) RQ 1 EV IPR014183; TIGR02818; sufficient; -- SN 2 ID L-tryptophan:phenylpyruvate aminotransferas DN L-tryptophan:phenylpyruvate aminotransferas (EC 2.6.1.28) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 3 ID Indole-3-pyruvate carboxy-lyase DN Indole-3-pyruvate carboxy-lyase (EC 4.1.1.74) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 4 ID L-tryptophan transaminase DN L-tryptophan transaminase (EC 2.6.1.27) RQ 1 EV IPR004839; PF00155; sufficient; // AC GenProp1293 DE Chitobiose degradation TP PATHWAY AU Keseler I, Johnson A TH 0 DC Chitobiose degradation DR MetaCyc; PWY0-1309; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Chitin disaccharide deacetylase DN Chitin disaccharide deacetylase (EC 3.5.1.105) RQ 1 EV IPR006879; PF04794; sufficient; -- SN 2 ID Monoacetylchitobiose-6-phosphate hydrolase DN Monoacetylchitobiose-6-phosphate hydrolase (EC 3.2.1.86) RQ 1 EV IPR001088; PF02056; sufficient; // AC GenProp1294 DE Pentose phosphate pathway (non-oxidative branch) TP PATHWAY AU Riley M, Ingraham J TH 3 DC Pentose phosphate pathway (non-oxidative branch) DR MetaCyc; NONOXIPENT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Transketolase DN Transketolase (EC 2.2.1.1) RQ 1 EV IPR005478; TIGR00232; sufficient; -- SN 2 ID Transketolase DN Transketolase (EC 2.2.1.1) RQ 1 EV IPR005478; TIGR00232; sufficient; -- SN 3 ID Ribose-5-phosphate isomerase A DN Ribose-5-phosphate isomerase A (EC 5.3.1.6) RQ 1 EV IPR004788; PF06026; sufficient; EV IPR004788; TIGR00021; sufficient; EV IPR003500; PF02502; sufficient; EV IPR003500; TIGR00689; sufficient; EV IPR004785; TIGR01120; sufficient; -- SN 4 ID Ribulose-phosphate 3-epimerase DN Ribulose-phosphate 3-epimerase (EC 5.1.3.1) RQ 1 EV IPR000056; PF00834; sufficient; EV IPR000056; TIGR01163; sufficient; -- SN 5 ID Transaldolase DN Transaldolase (EC 2.2.1.2) RQ 1 EV IPR001585; PF00923; sufficient; EV IPR004730; TIGR00874; sufficient; // AC GenProp1295 DE Methylerythritol phosphate pathway I TP PATHWAY AU Weerasinghe D, Pellegrini-Toole A, Shearer A TH 7 DC Methylerythritol phosphate pathway I DR MetaCyc; NONMEVIPP-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase DN 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase (EC 2.7.1.148) RQ 1 EV IPR004424; TIGR00154; sufficient; -- SN 2 ID 4-Diphosphocytidyl-2C-methyl-D-erythritol synthase DN 4-Diphosphocytidyl-2C-methyl-D-erythritol synthase (EC 2.7.7.60) RQ 1 EV IPR001228; PF01128; sufficient; EV IPR001228; TIGR00453; sufficient; -- SN 3 ID 1-Deoxy-D-xylulose 5-phosphate reductoisomerase DN 1-Deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) RQ 1 EV IPR003821; TIGR00243; sufficient; -- SN 4 ID 1-Deoxy-D-xylulose 5-phosphate synthase DN 1-Deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7) RQ 1 EV IPR005477; PF13292; sufficient; EV IPR005477; TIGR00204; sufficient; -- SN 5 ID Isopentenyl pyrophosphate isomerase DN Isopentenyl pyrophosphate isomerase (EC 5.3.3.2) RQ 1 EV IPR011876; TIGR02150; sufficient; -- SN 6 ID Isopentenyl-diphosphate:NAD(P)+ oxidoreductase DN Isopentenyl-diphosphate:NAD(P)+ oxidoreductase (EC 1.17.7.4) RQ 1 EV IPR003451; PF02401; sufficient; EV IPR003451; TIGR00216; sufficient; -- SN 7 ID 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase DN 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (EC 1.17.7.3) RQ 1 EV IPR004588; PF04551; sufficient; EV IPR004588; TIGR00612; sufficient; -- SN 8 ID 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase DN 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) RQ 1 EV IPR003526; PF02542; sufficient; EV IPR003526; TIGR00151; sufficient; -- SN 9 ID Dimethylallyl-diphosphate:NAD(P)+ oxidoreductase DN Dimethylallyl-diphosphate:NAD(P)+ oxidoreductase (EC 1.17.7.4) RQ 1 EV IPR003451; PF02401; sufficient; EV IPR003451; TIGR00216; sufficient; // AC GenProp1296 DE NAD biosynthesis III TP PATHWAY AU Caspi R TH 0 DC NAD biosynthesis III DR MetaCyc; NAD-BIOSYNTHESIS-III; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Nicotinamide phosphoribosyltransferase DN Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) RQ 1 EV IPR007229; PF04095; sufficient; -- SN 2 ID Nicotinamide mononucleotide adenylyltransferase DN Nicotinamide mononucleotide adenylyltransferase (EC 2.7.7.1) RQ 1 EV IPR000086; PF00293; sufficient; EV IPR004821; PF01467; sufficient; EV IPR004821; TIGR00125; sufficient; // AC GenProp1297 DE Superpathway of glycol metabolism and degradation TP PATHWAY AU Weerasinghe D TH 0 DC Superpathway of glycol metabolism and degradation DR MetaCyc; GLYCOL-GLYOXDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycolaldehyde dehydrogenase DN Glycolaldehyde dehydrogenase (EC 1.2.1.21) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID Glycolate oxidase DN Glycolate oxidase (EC 1.1.99.14) RQ 1 EV IPR004490; TIGR00387; sufficient; // AC GenProp1298 DE Lipoate biosynthesis and incorporation II TP PATHWAY AU Caspi R TH 0 DC Lipoate biosynthesis and incorporation II DR MetaCyc; PWY0-1275; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lipoate-protein ligase DN Lipoate-protein ligase (EC 6.3.1.20) RQ 1 EV IPR004562; TIGR00545; sufficient; -- SN 2 ID Lipoyl synthase DN Lipoyl synthase (EC 2.8.1.8) RQ 1 EV IPR003698; TIGR00510; sufficient; // AC GenProp1299 DE 2-O-alpha-mannosyl-D-glycerate degradation TP PATHWAY AU Johnson A TH 0 DC 2-O-alpha-mannosyl-D-glycerate degradation DR MetaCyc; PWY0-1300; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerate 2-kinase DN Glycerate 2-kinase (EC 2.7.1.165) RQ 1 EV IPR004381; PF02595; sufficient; EV IPR004381; TIGR00045; sufficient; -- SN 2 ID 2-O-(6-phospho-alpha-mannosyl)-D-glycerate hydrolase DN 2-O-(6-phospho-alpha-mannosyl)-D-glycerate hydrolase (EC 3.2.1) RQ 1 EV IPR000602; PF01074; sufficient; EV IPR011682; PF07748; sufficient; EV IPR015341; PF09261; sufficient; // AC GenProp1300 DE Urea cycle TP PATHWAY AU Caspi R TH 3 DC Urea cycle DR MetaCyc; PWY-4984; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arginase DN Arginase (EC 3.5.3.1) RQ 1 EV IPR006035; PF00491; sufficient; EV IPR014033; TIGR01229; sufficient; -- SN 2 ID Argininosuccinase DN Argininosuccinase (EC 4.3.2.1) RQ 1 EV IPR009049; TIGR00838; sufficient; -- SN 3 ID Argininosuccinate synthase DN Argininosuccinate synthase (EC 6.3.4.5) RQ 1 EV IPR001518; PF00764; sufficient; EV IPR001518; TIGR00032; sufficient; -- SN 4 ID Ornithine carbamoyltransferase DN Ornithine carbamoyltransferase (EC 2.1.3.3) RQ 1 EV IPR002292; TIGR00658; sufficient; -- SN 5 ID Ammonia-dependent carbamoyl-phosphate synthase DN Ammonia-dependent carbamoyl-phosphate synthase (EC 6.3.4.16) RQ 1 EV IPR006274; TIGR01368; sufficient; EV IPR006275; TIGR01369; sufficient; // AC GenProp1301 DE Superpathway of sulfate assimilation and cysteine biosynthesis TP PATHWAY AU N/A TH 2 DC Superpathway of sulfate assimilation and cysteine biosynthesis DR MetaCyc; SULFATE-CYS-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cysteine synthase DN Cysteine synthase (EC 2.5.1.47) RQ 1 EV IPR005856; TIGR01136; sufficient; EV IPR005859; TIGR01139; sufficient; EV IPR005858; TIGR01138; sufficient; -- SN 2 ID L-3-phosphoserine phosphatase DN L-3-phosphoserine phosphatase (EC 3.1.3.3) RQ 1 EV IPR005519; PF03767; sufficient; EV IPR010025; TIGR01672; sufficient; -- SN 3 ID Serine O-acetyltransferase DN Serine O-acetyltransferase (EC 2.3.1.30) RQ 1 EV IPR005881; TIGR01172; sufficient; -- SN 4 ID Assimilatory sulfite reductase (NADPH) DN Assimilatory sulfite reductase (NADPH) (EC 1.8.1.2) RQ 1 EV IPR010199; TIGR01931; sufficient; EV IPR011786; TIGR02041; sufficient; // AC GenProp1302 DE Galactolipid biosynthesis I TP PATHWAY AU Caspi R, Zhang P TH 3 DC Galactolipid biosynthesis I DR MetaCyc; PWY-401; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-galactose:DAG galactosyltransferase DN UDP-galactose:DAG galactosyltransferase (EC 2.4.1.46) RQ 1 EV IPR007235; PF04101; sufficient; EV IPR009695; PF06925; sufficient; -- SN 2 ID UDP-galactose:MGDG galactosyltransferase DN UDP-galactose:MGDG galactosyltransferase (EC 2.4.1.241) RQ 1 EV IPR001296; PF00534; sufficient; -- SN 3 ID beta-monogalactosyldiacylglycerol galactosyltransferase DN beta-monogalactosyldiacylglycerol galactosyltransferase (EC 2.4.1.184) RQ 1 EV IPR001360; PF00232; sufficient; -- SN 4 ID beta,beta,beta-trigalactosyldiacylglycerol galactosyltransferase DN beta,beta,beta-trigalactosyldiacylglycerol galactosyltransferase (EC 2.4.1.184) RQ 1 EV IPR001360; PF00232; sufficient; -- SN 5 ID beta,beta-digalactosyldiacylglycerol galactosyltransferase DN beta,beta-digalactosyldiacylglycerol galactosyltransferase (EC 2.4.1.184) RQ 1 EV IPR001360; PF00232; sufficient; // AC GenProp1303 DE N-acetylglucosamine degradation I TP PATHWAY AU Riley M, Keseler I, Ingraham J TH 0 DC N-acetylglucosamine degradation I DR MetaCyc; GLUAMCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucosamine 6-phosphate isomerase DN Glucosamine 6-phosphate isomerase (EC 3.5.99.6) RQ 1 EV IPR004547; TIGR00502; sufficient; -- SN 2 ID N-acetylglucosamine-6-phosphate deacetylase DN N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) RQ 1 EV IPR003764; TIGR00221; sufficient; // AC GenProp1304 DE Globo-series glycosphingolipids biosynthesis TP PATHWAY AU Caspi R TH 6 DC Globo-series glycosphingolipids biosynthesis DR MetaCyc; PWY-7838; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lactosylceramide 4-alpha-galactosyltransferase DN Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) RQ 1 EV IPR007652; PF04572; sufficient; -- SN 2 ID Globotriaosylceramide 3-beta-N-acetylgalactosaminyltransferase DN Globotriaosylceramide 3-beta-N-acetylgalactosaminyltransferase (EC 2.4.1.79) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 3 ID Globoside alpha-1,3-N-acetylgalactosaminyltransferase DN Globoside alpha-1,3-N-acetylgalactosaminyltransferase (EC 2.4.1.88) RQ 1 EV IPR005076; PF03414; sufficient; -- SN 4 ID Ceramide glucosyltransferase DN Ceramide glucosyltransferase (EC 2.4.1.80) RQ 1 EV IPR025993; PF13506; sufficient; -- SN 5 ID Glucosylceramide beta-1,4-galactosyltransferase DN Glucosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.274) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 6 ID Globotetraosylceramide beta-1,3-galactosyltransferase DN Globotetraosylceramide beta-1,3-galactosyltransferase (EC 2.4.1) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 7 ID SSEA-3 alpha-2,3-sialyltransferase DN SSEA-3 alpha-2,3-sialyltransferase (EC 2.4.99.4) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 8 ID SSEA-3 alpha-2-fucosyltransferase DN SSEA-3 alpha-2-fucosyltransferase (EC 2.4.1) RQ 1 EV IPR002516; PF01531; sufficient; // AC GenProp1305 DE NAD phosphorylation and transhydrogenation TP PATHWAY AU Weerasinghe D, Riley M TH 0 DC NAD phosphorylation and transhydrogenation DR MetaCyc; NADPHOS-DEPHOS-PWY-1; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID NAD kinase DN NAD kinase (EC 2.7.1.23) RQ 1 EV IPR002504; PF01513; sufficient; -- SN 2 ID NAD(P) transhydrogenase DN NAD(P) transhydrogenase (EC 1.6.1.5) RQ 1 EV IPR012136; PF02233; sufficient; EV IPR026255; TIGR00561; sufficient; // AC GenProp1306 DE Glycolysis I (from glucose 6-phosphate) TP PATHWAY AU Ingraham J TH 10 DC Glycolysis I (from glucose 6-phosphate) DR MetaCyc; GLYCOLYSIS; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Enolase DN Enolase (EC 4.2.1.11) RQ 1 EV IPR000941; TIGR01060; sufficient; -- SN 2 ID 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) RQ 1 EV IPR005995; TIGR01307; sufficient; -- SN 3 ID 6-Phosphofructokinase DN 6-Phosphofructokinase (EC 2.7.1.11) RQ 1 EV IPR012828; TIGR02482; sufficient; EV IPR017583; TIGR03168; sufficient; -- SN 4 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase (EC 4.1.2.13) RQ 1 EV IPR002915; PF01791; sufficient; EV IPR000771; PF01116; sufficient; EV IPR000771; TIGR00167; sufficient; EV IPR006411; TIGR01520; sufficient; -- SN 5 ID Fructose 1,6-bisphosphatase DN Fructose 1,6-bisphosphatase (EC 3.1.3.11) RQ 1 EV IPR004464; PF03320; sufficient; EV IPR004464; TIGR00330; sufficient; EV IPR000150; TIGR00099; sufficient; EV IPR006379; TIGR01484; sufficient; -- SN 6 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 7 ID Pyruvate kinase DN Pyruvate kinase (EC 2.7.1.40) RQ 1 EV IPR001697; TIGR01064; sufficient; -- SN 8 ID Phosphoenolpyruvate synthetase DN Phosphoenolpyruvate synthetase (EC 2.7.9.2) RQ 1 EV IPR006319; TIGR01418; sufficient; -- SN 9 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; -- SN 10 ID Phosphoglycerate kinase DN Phosphoglycerate kinase (EC 2.7.2.3) RQ 1 EV IPR001576; PF00162; sufficient; -- SN 11 ID 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.11) RQ 1 EV IPR005952; TIGR01258; sufficient; EV IPR013078; PF00300; sufficient; -- SN 12 ID Triose-phosphate isomerase DN Triose-phosphate isomerase (EC 5.3.1.1) RQ 1 EV IPR000652; PF00121; sufficient; EV IPR000652; TIGR00419; sufficient; // AC GenProp1307 DE Superpathway of pyrimidine nucleobases salvage TP PATHWAY AU Caspi R TH 0 DC Superpathway of pyrimidine nucleobases salvage DR MetaCyc; PWY-7208; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UMP kinase DN UMP kinase (EC 2.7.4.14) RQ 1 EV IPR006266; TIGR01359; sufficient; EV IPR015963; TIGR02075; sufficient; -- SN 2 ID Uracil phosphoribosyltransferase DN Uracil phosphoribosyltransferase (EC 2.4.2.9) RQ 1 EV IPR005765; TIGR01091; sufficient; // AC GenProp1308 DE Fatty acid beta-oxidation VI (peroxisome) TP PATHWAY AU Fulcher C TH 5 DC Fatty acid beta-oxidation VI (peroxisome) DR MetaCyc; PWY66-391; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2,3,4-Saturated fatty acyl-CoA synthetase DN 2,3,4-Saturated fatty acyl-CoA synthetase (EC 6.2.1.3) RQ 1 EV IPR000873; PF00501; sufficient; EV IPR025110; PF13193; sufficient; -- SN 2 ID Enoyl-CoA hydratase DN Enoyl-CoA hydratase (EC 4.2.1.17) RQ 1 EV IPR001753; PF00378; sufficient; -- SN 3 ID 3-Ketoacyl-CoA thiolase DN 3-Ketoacyl-CoA thiolase (EC 2.3.1.16) RQ 1 EV IPR002155; TIGR01930; sufficient; -- SN 4 ID 3-Hydroxyacyl-CoA dehydrogenase DN 3-Hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) RQ 1 EV IPR001753; PF00378; sufficient; -- SN 5 ID Acyl-CoA oxidase DN Acyl-CoA oxidase (EC 1.3.3.6) RQ 1 EV IPR002655; PF01756; sufficient; EV IPR006091; PF02770; sufficient; EV IPR029320; PF14749; sufficient; -- SN 6 ID (R)-specific enoyl-CoA hydratase DN (R)-specific enoyl-CoA hydratase (EC 4.2.1.119) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 7 ID 3-Hydroxyacyl-CoA dehydrogenase DN 3-Hydroxyacyl-CoA dehydrogenase (EC 1.1.1.M19) RQ 1 EV IPR002347; PF00106; sufficient; // AC GenProp1309 DE Superpathway of L-phenylalanine biosynthesis TP PATHWAY AU Caspi R TH 0 DC Superpathway of L-phenylalanine biosynthesis DR MetaCyc; PWY-6628; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; PF01264; sufficient; EV IPR000453; TIGR00033; sufficient; -- SN 2 ID Chorismate mutase DN Chorismate mutase (EC 5.4.99.5) RQ 1 EV IPR003099; PF02153; sufficient; EV IPR011277; TIGR01799; sufficient; EV IPR001086; PF00800; sufficient; EV IPR010952; TIGR01797; sufficient; // AC GenProp1310 DE D-galactose degradation I (Leloir pathway) TP PATHWAY AU Caspi R TH 3 DC D-galactose degradation I (Leloir pathway) DR MetaCyc; PWY-6317; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Mutarotase DN Mutarotase (EC 5.1.3.3) RQ 1 EV IPR008183; PF01263; sufficient; EV IPR013458; TIGR02636; sufficient; -- SN 2 ID Galactokinase DN Galactokinase (EC 2.7.1.6) RQ 1 EV IPR000705; TIGR00131; sufficient; -- SN 3 ID Galactose-1-phosphate uridylyltransferase DN Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) RQ 1 EV IPR001937; TIGR00209; sufficient; -- SN 4 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005852; TIGR01132; sufficient; -- SN 5 ID UDP-galactose 4-epimerase DN UDP-galactose 4-epimerase (EC 5.1.3.2) RQ 1 EV IPR005886; TIGR01179; sufficient; // AC GenProp1311 DE Protein NEDDylation TP PATHWAY AU Caspi R TH 1 DC Protein NEDDylation DR MetaCyc; PWY-7899; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID E3 NEDD8 transferase DN E3 NEDD8 transferase (EC 2.3.2.32) RQ 1 EV IPR005176; PF03556; sufficient; EV IPR001373; PF00888; sufficient; EV IPR019559; PF10557; sufficient; EV IPR024766; PF12678; sufficient; -- SN 2 ID E2 NEDD8-conjugating enzyme DN E2 NEDD8-conjugating enzyme RQ 1 EV IPR000608; PF00179; sufficient; -- SN 3 ID E1 NEDD8-activating enzyme DN E1 NEDD8-activating enzyme RQ 1 EV IPR000594; PF00899; sufficient; EV IPR014929; PF08825; sufficient; // AC GenProp1312 DE Aminopropanol phosphate biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Aminopropanol phosphate biosynthesis I DR MetaCyc; PWY-5443; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Threonine-phosphate decarboxylase DN Threonine-phosphate decarboxylase (EC 4.1.1.81) RQ 1 EV IPR005860; TIGR01140; sufficient; -- SN 2 ID L-threonine kinase DN L-threonine kinase (EC 2.7.1.177) RQ 1 EV IPR006204; PF00288; sufficient; // AC GenProp1313 DE tRNA-uridine 2-thiolation (mammalian mitochondria) TP PATHWAY AU Caspi R TH 2 DC tRNA-uridine 2-thiolation (mammalian mitochondria) DR MetaCyc; PWY-7889; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID tRNA 2-thiouridylase DN tRNA 2-thiouridylase (EC 2.8.1.14) RQ 1 EV IPR004506; TIGR00420; sufficient; -- SN 2 ID 5-Taurinomethyluridine-[tRNA] synthase DN 5-Taurinomethyluridine-[tRNA] synthase RQ 1 EV IPR002218; PF01134; sufficient; -- SN 3 ID Cysteine desulfurase:TUM1 sulfurtransferase DN Cysteine desulfurase:TUM1 sulfurtransferase (EC 2.8.1) RQ 1 EV IPR001763; PF00581; sufficient; -- SN 4 ID Cysteine desulfurase DN Cysteine desulfurase RQ 1 EV IPR010240; TIGR02006; sufficient; // AC GenProp1315 DE Fatty acid biosynthesis initiation III TP PATHWAY AU Caspi R TH 0 DC Fatty acid biosynthesis initiation III DR MetaCyc; PWY-5965; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetoacetyl-[acp] synthase DN Acetoacetyl-[acp] synthase (EC 2.3.1.179) RQ 1 EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; -- SN 2 ID Malonyl-ACP decarboxylase DN Malonyl-ACP decarboxylase (EC 2.3.1) RQ 1 EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; // AC GenProp1316 DE Phosphatidate biosynthesis (yeast) TP PATHWAY AU Foerster H TH 3 DC Phosphatidate biosynthesis (yeast) DR MetaCyc; PWY-7411; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol-3-phosphate dehydrogenase DN Glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) RQ 1 EV IPR017751; TIGR03376; sufficient; -- SN 2 ID Oleoyl-CoA:lysophosphatidate acyltransferase DN Oleoyl-CoA:lysophosphatidate acyltransferase (EC 2.3.1.51) RQ 1 EV IPR021771; PF11815; sufficient; EV IPR004299; PF03062; sufficient; -- SN 3 ID Dihydroxyacetone phosphate acyltransferase DN Dihydroxyacetone phosphate acyltransferase (EC 2.3.1.42) RQ 1 EV IPR002123; PF01553; sufficient; -- SN 4 ID Glycerol-3-phosphate O-acyltransferase DN Glycerol-3-phosphate O-acyltransferase (EC 2.3.1.15) RQ 1 EV IPR002123; PF01553; sufficient; -- SN 5 ID 1-Acyl dihydroxyacetone phosphate reductase DN 1-Acyl dihydroxyacetone phosphate reductase (EC 1.1.1.101) RQ 1 EV IPR002347; PF00106; sufficient; // AC GenProp1317 DE Protein Pupylation and dePupylation TP PATHWAY AU Caspi R TH 1 DC Protein Pupylation and dePupylation DR MetaCyc; PWY-7893; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pup deamidase DN Pup deamidase (EC 3.5.1.119) RQ 1 EV IPR004347; PF03136; sufficient; EV IPR022366; TIGR03688; sufficient; -- SN 2 ID Prokaryotic ubiquitin-like protein ligase DN Prokaryotic ubiquitin-like protein ligase (EC 6.3.1.19) RQ 1 EV IPR004347; PF03136; sufficient; EV IPR022279; TIGR03686; sufficient; -- SN 3 ID N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine hydrolase DN N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine hydrolase (EC 3.4.11.M1) RQ 1 EV IPR004347; PF03136; sufficient; EV IPR022366; TIGR03688; sufficient; // AC GenProp1318 DE Superpathway of pyrimidine ribonucleotides de novo biosynthesis TP PATHWAY AU Caspi R, Arnaud M TH 0 DC Superpathway of pyrimidine ribonucleotides de novo biosynthesis DR MetaCyc; PWY0-162; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Orotidine 5'-phosphate decarboxylase DN Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) RQ 1 EV IPR014732; TIGR01740; sufficient; -- SN 2 ID UMP kinase DN UMP kinase (EC 2.7.4.14) RQ 1 EV IPR006266; TIGR01359; sufficient; EV IPR015963; TIGR02075; sufficient; // AC GenProp1320 DE Nitric oxide biosynthesis II (mammals) TP PATHWAY AU Caspi R TH 1 DC Nitric oxide biosynthesis II (mammals) DR MetaCyc; PWY-4983; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Argininosuccinase DN Argininosuccinase (EC 4.3.2.1) RQ 1 EV IPR009049; TIGR00838; sufficient; -- SN 2 ID Argininosuccinate synthase DN Argininosuccinate synthase (EC 6.3.4.5) RQ 1 EV IPR001518; PF00764; sufficient; EV IPR001518; TIGR00032; sufficient; -- SN 3 ID Nitric-oxide synthase DN Nitric-oxide synthase (EC 1.14.13.39) RQ 1 EV IPR001433; PF00175; sufficient; EV IPR001478; PF00595; sufficient; EV IPR003097; PF00667; sufficient; EV IPR004030; PF02898; sufficient; EV IPR008254; PF00258; sufficient; // AC GenProp1321 DE Retinoate biosynthesis I TP PATHWAY AU Caspi R TH 2 DC Retinoate biosynthesis I DR MetaCyc; PWY-6872; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cellular retinol-binding protein DN Cellular retinol-binding protein RQ 1 EV IPR000566; PF00061; sufficient; -- SN 2 ID Plasma retinol-binding protein DN Plasma retinol-binding protein RQ 1 EV IPR000566; PF00061; sufficient; -- SN 3 ID All-trans-retinol dehydrogenase DN All-trans-retinol dehydrogenase (EC 1.1.1.105) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 4 ID All-trans-retinal dehydrogenase DN All-trans-retinal dehydrogenase (EC 1.2.1.36) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1322 DE Superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) TP PATHWAY AU Caspi R, Tissier C TH 0 DC Superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) DR MetaCyc; PWY-5121; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Geranylgeranyl diphosphate synthase DN Geranylgeranyl diphosphate synthase (EC 2.5.1.29) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; // AC GenProp1323 DE Purine deoxyribonucleosides degradation I TP PATHWAY AU Caspi R TH 2 DC Purine deoxyribonucleosides degradation I DR MetaCyc; PWY-7179; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine deaminase DN Adenosine deaminase (EC 3.5.4.4) RQ 1 EV IPR006330; TIGR01430; sufficient; -- SN 2 ID Deoxyadenosine phosphorylase DN Deoxyadenosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; -- SN 3 ID Deoxyguanosine phosphorylase DN Deoxyguanosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; -- SN 4 ID Deoxyinosine phosphorylase DN Deoxyinosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; // AC GenProp1324 DE Glycerol degradation V TP PATHWAY AU Keseler I, Riley M TH 0 DC Glycerol degradation V DR MetaCyc; GLYCEROLMETAB-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dihydroxyacetone kinase DN Dihydroxyacetone kinase (EC 2.7.1.121) RQ 1 EV IPR000032; PF00381; sufficient; EV IPR000032; TIGR01003; sufficient; EV IPR004701; PF03610; sufficient; EV IPR008279; PF00391; sufficient; EV IPR008731; PF05524; sufficient; EV IPR012844; TIGR02364; sufficient; EV IPR004006; PF02733; sufficient; EV IPR012736; TIGR02363; sufficient; EV IPR004007; PF02734; sufficient; EV IPR012737; TIGR02365; sufficient; -- SN 2 ID Glycerol dehydrogenase DN Glycerol dehydrogenase (EC 1.1.1.6) RQ 1 EV IPR001670; PF00465; sufficient; // AC GenProp1325 DE Superpathway of (Kdo)2-lipid A biosynthesis TP PATHWAY AU N/A TH 6 DC Superpathway of (Kdo)2-lipid A biosynthesis DR MetaCyc; KDO-NAGLIPASYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Deoxy-manno-octulosonate cytidylyltransferase DN 3-Deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) RQ 1 EV IPR003329; PF02348; sufficient; EV IPR004528; TIGR00466; sufficient; -- SN 2 ID Lipid IVA (2-6) 3-deoxy-D-manno-octulosonic acid transferase DN Lipid IVA (2-6) 3-deoxy-D-manno-octulosonic acid transferase (EC 2.4.99.12) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR007507; PF04413; sufficient; -- SN 3 ID KDO transferase DN KDO transferase (EC 2.4.99.13) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR007507; PF04413; sufficient; -- SN 4 ID Lauroyl acyltransferase DN Lauroyl acyltransferase (EC 2.3.1.241) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011920; TIGR02207; sufficient; -- SN 5 ID Myristoyl-acyl carrier protein-dependent acyltransferase DN Myristoyl-acyl carrier protein-dependent acyltransferase (EC 2.3.1.243) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011921; TIGR02208; sufficient; -- SN 6 ID Myristoyl-acyl carrier protein-dependent acyltransferase DN Myristoyl-acyl carrier protein-dependent acyltransferase (EC 2.3.1) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011921; TIGR02208; sufficient; -- SN 7 ID Palmitoleoyl acyltransferase DN Palmitoleoyl acyltransferase (EC 2.3.1.242) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011920; TIGR02207; sufficient; -- SN 8 ID Tetraacyldisaccharide 4'-kinase DN Tetraacyldisaccharide 4'-kinase (EC 2.7.1.130) RQ 1 EV IPR003758; PF02606; sufficient; EV IPR003758; TIGR00682; sufficient; // AC GenProp1326 DE Allantoin degradation to ureidoglycolate II (ammonia producing) TP PATHWAY AU Caspi R, Keseler I TH 1 DC Allantoin degradation to ureidoglycolate II (ammonia producing) DR MetaCyc; PWY-5698; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Allantoate amidohydrolase DN Allantoate amidohydrolase (EC 3.5.3.9) RQ 1 EV IPR002933; PF01546; sufficient; EV IPR010158; TIGR01879; sufficient; EV IPR017591; TIGR03176; sufficient; -- SN 2 ID Allantoinase DN Allantoinase (EC 3.5.2.5) RQ 1 EV IPR017593; TIGR03178; sufficient; -- SN 3 ID Ureidoglycine aminohydrolase DN Ureidoglycine aminohydrolase (EC 3.5.3.26) RQ 1 EV IPR017627; TIGR03214; sufficient; // AC GenProp1327 DE Lipoprotein posttranslational modification TP PATHWAY AU Caspi R TH 2 DC Lipoprotein posttranslational modification DR MetaCyc; PWY-7884; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Prolipoprotein signal peptidase DN Prolipoprotein signal peptidase (EC 3.4.23.36) RQ 1 EV IPR001872; PF01252; sufficient; EV IPR001872; TIGR00077; sufficient; -- SN 2 ID Apolipoprotein N-acyltransferase DN Apolipoprotein N-acyltransferase RQ 1 EV IPR004563; TIGR00546; sufficient; -- SN 3 ID Phosphatidylglycerol-prolipoprotein diacylglyceryl transferase DN Phosphatidylglycerol-prolipoprotein diacylglyceryl transferase RQ 1 EV IPR001640; PF01790; sufficient; EV IPR001640; TIGR00544; sufficient; -- SN 4 ID Lipoprotein signal peptide peptidase DN Lipoprotein signal peptide peptidase (EC 3.4.21) RQ 1 EV IPR004634; TIGR00705; sufficient; EV IPR004387; TIGR00054; sufficient; // AC GenProp1328 DE L-isoleucine degradation II TP PATHWAY AU Caspi R TH 1 DC L-isoleucine degradation II DR MetaCyc; PWY-5078; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Keto-methylvalerate decarboxylase DN 2-Keto-methylvalerate decarboxylase (EC 4.1.1.72) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID L-isoleucine:2-oxoglutarate aminotransferase DN L-isoleucine:2-oxoglutarate aminotransferase (EC 2.6.1.42) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005786; TIGR01123; sufficient; -- SN 3 ID 2-Methylbutanol dehydrogenase DN 2-Methylbutanol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR014183; TIGR02818; sufficient; // AC GenProp1329 DE Nitrate reduction III (dissimilatory) TP PATHWAY AU Mackie A, Nolan L, Krummenacker M TH 0 DC Nitrate reduction III (dissimilatory) DR MetaCyc; PWY0-1321; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Formate dehydrogenase (menaquinone) DN Formate dehydrogenase (menaquinone) (EC 1.17.5.3) RQ 1 EV IPR006443; TIGR01553; sufficient; EV IPR006470; TIGR01582; sufficient; EV IPR006471; TIGR01583; sufficient; -- SN 2 ID Menaquinol:nitrate oxidoreductase DN Menaquinol:nitrate oxidoreductase (EC 1.7.5.1) RQ 1 EV IPR006468; TIGR01580; sufficient; EV IPR006547; TIGR01660; sufficient; EV IPR003816; TIGR00351; sufficient; // AC GenProp1330 DE UDP-beta-L-arabinose biosynthesis II (from beta-L-arabinose) TP PATHWAY AU N/A TH 0 DC UDP-beta-L-arabinose biosynthesis II (from beta-L-arabinose) DR MetaCyc; PWY-82; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arabinose kinase DN Arabinose kinase (EC 2.7.1.46) RQ 1 EV IPR006204; PF00288; sufficient; EV IPR019539; PF10509; sufficient; -- SN 2 ID UDP-L-arabinose pyrophosphorylase DN UDP-L-arabinose pyrophosphorylase (EC 2.7.7.37) RQ 1 EV IPR002618; PF01704; sufficient; // AC GenProp1331 DE Pyocyanin biosynthesis TP PATHWAY AU Fulcher C TH 0 DC Pyocyanin biosynthesis DR MetaCyc; PWY-6666; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 5-Methyl-phenazine-1-carboxylate N-methyltransferase DN 5-Methyl-phenazine-1-carboxylate N-methyltransferase (EC 2.1.1.327) RQ 1 EV IPR001077; PF00891; sufficient; EV IPR031725; PF16864; sufficient; -- SN 2 ID 5-Methylphenazine-1-carboxylate 1-monooxygenase DN 5-Methylphenazine-1-carboxylate 1-monooxygenase (EC 1.14.13.218) RQ 1 EV IPR002938; PF01494; sufficient; // AC GenProp1332 DE Superpathway of tetrahydrofolate biosynthesis TP PATHWAY AU Caspi R TH 1 DC Superpathway of tetrahydrofolate biosynthesis DR MetaCyc; PWY-6612; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aminodeoxychorismate lyase DN Aminodeoxychorismate lyase (EC 4.1.3.38) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR017824; TIGR03461; sufficient; -- SN 2 ID 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase DN 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (EC 2.7.6.3) RQ 1 EV IPR000550; PF01288; sufficient; EV IPR000550; TIGR01498; sufficient; -- SN 3 ID Dihydropteroate synthase DN Dihydropteroate synthase (EC 2.5.1.15) RQ 1 EV IPR000489; PF00809; sufficient; EV IPR006390; TIGR01496; sufficient; // AC GenProp1333 DE Superpathway of L-alanine biosynthesis TP PATHWAY AU N/A TH 2 DC Superpathway of L-alanine biosynthesis DR MetaCyc; PWY0-1061; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-alanine:2-oxoglutarate aminotransferase DN L-alanine:2-oxoglutarate aminotransferase (EC 2.6.1.2) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID Alanine racemase DN Alanine racemase (EC 5.1.1.1) RQ 1 EV IPR000821; TIGR00492; sufficient; -- SN 3 ID Cysteine desulfurase DN Cysteine desulfurase (EC 2.8.1.7) RQ 1 EV IPR010240; TIGR02006; sufficient; EV IPR010970; TIGR01979; sufficient; -- SN 4 ID Cysteine desulfurase DN Cysteine desulfurase RQ 1 EV IPR010240; TIGR02006; sufficient; // AC GenProp1334 DE L-leucine degradation III TP PATHWAY AU Caspi R TH 1 DC L-leucine degradation III DR MetaCyc; PWY-5076; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Leucine transaminase DN Leucine transaminase (EC 2.6.1.42) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005786; TIGR01123; sufficient; -- SN 2 ID 4-Methyl-2-oxopentanoate decarboxylase DN 4-Methyl-2-oxopentanoate decarboxylase (EC 4.1.1.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 3 ID 3-Methlbutanol dehydrogenase DN 3-Methlbutanol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR014183; TIGR02818; sufficient; // AC GenProp1335 DE Ceramide degradation TP PATHWAY AU Zhang P TH 1 DC Ceramide degradation DR MetaCyc; PWY-6483; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ceramidase DN Ceramidase (EC 3.5.1.23) RQ 1 EV IPR031329; PF04734; sufficient; EV IPR031331; PF17048; sufficient; -- SN 2 ID Sphingoid base kinase DN Sphingoid base kinase (EC 2.7.1.91) RQ 1 EV IPR001206; PF00781; sufficient; -- SN 3 ID Sphingoid 1-phosphate lyase DN Sphingoid 1-phosphate lyase RQ 1 EV IPR002129; PF00282; sufficient; // AC GenProp1336 DE 2,3-Dihydroxybenzoate biosynthesis TP PATHWAY AU Keseler I, Caspi R TH 1 DC 2,3-Dihydroxybenzoate biosynthesis DR MetaCyc; PWY-5901; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2,3-Dihydro-2,3-dihydroxybenzoate dehydrogenase DN 2,3-Dihydro-2,3-dihydroxybenzoate dehydrogenase (EC 1.3.1.28) RQ 1 EV IPR003560; TIGR04316; sufficient; EV IPR002347; PF00106; sufficient; -- SN 2 ID Vibriobactin-specific isochorismatase DN Vibriobactin-specific isochorismatase (EC 3.3.2.1) RQ 1 EV IPR000868; PF00857; sufficient; EV IPR009081; PF00550; sufficient; -- SN 3 ID Isochorismate synthase DN Isochorismate synthase (EC 5.4.4.2) RQ 1 EV IPR004561; TIGR00543; sufficient; // AC GenProp1337 DE Vitamin E biosynthesis (tocopherols) TP PATHWAY AU Zhang P TH 5 DC Vitamin E biosynthesis (tocopherols) DR MetaCyc; PWY-1422; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Hydroxyphenylpyruvate dioxygenase DN 4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) RQ 1 EV IPR005956; TIGR01263; sufficient; -- SN 2 ID Homogentisate phytyltransferase DN Homogentisate phytyltransferase (EC 2.5.1.115) RQ 1 EV IPR000537; PF01040; sufficient; -- SN 3 ID 2-Methyl-6-phytyl-1,4-benzoquinol methyltransferase DN 2-Methyl-6-phytyl-1,4-benzoquinol methyltransferase (EC 2.1.1.295) RQ 1 EV IPR013216; PF08241; sufficient; -- SN 4 ID 2,3-Dimethyl-6-phytyl-1,4-benzoquinone cyclase DN 2,3-Dimethyl-6-phytyl-1,4-benzoquinone cyclase (EC 5.5.1.24) RQ 1 EV IPR025893; PF14249; sufficient; -- SN 5 ID 2-Methyl-6-phytyl-1,4-benzoquinone cyclase DN 2-Methyl-6-phytyl-1,4-benzoquinone cyclase (EC 5.5.1.24) RQ 1 EV IPR025893; PF14249; sufficient; -- SN 6 ID Delta-tocopherol methyltransferase DN Delta-tocopherol methyltransferase (EC 2.1.1.95) RQ 1 EV IPR013216; PF08241; sufficient; -- SN 7 ID Gamma-tocopherol methyltransferase DN Gamma-tocopherol methyltransferase (EC 2.1.1.95) RQ 1 EV IPR013216; PF08241; sufficient; // AC GenProp1338 DE Estradiol biosynthesis I (via estrone) TP PATHWAY AU Trupp M TH 2 DC Estradiol biosynthesis I (via estrone) DR MetaCyc; PWY66-380; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Estradiol-17-beta dehydrogenase / estrone reductase DN Estradiol-17-beta dehydrogenase / estrone reductase (EC 1.1.1.62) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID Androstenedione 19-hydroxylase DN Androstenedione 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID 19-Hydroxyandrostendione 19-dehydrogenase DN 19-Hydroxyandrostendione 19-dehydrogenase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 4 ID 19-Oxoandrostenedione 2-betahydroxylase DN 19-Oxoandrostenedione 2-betahydroxylase RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1339 DE Alpha-linolenate biosynthesis I (plants and red algae) TP PATHWAY AU Caspi R TH 0 DC Alpha-linolenate biosynthesis I (plants and red algae) DR MetaCyc; PWY-5997; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Linolenoyl-lipid 15-desaturase DN Linolenoyl-lipid 15-desaturase (EC 1.14.19.25) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 2 ID Linolenoyl-lipid 15-desaturase DN Linolenoyl-lipid 15-desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; // AC GenProp1340 DE 5-(Carboxymethoxy)uridine biosynthesis TP PATHWAY AU Keseler I TH 0 DC 5-(Carboxymethoxy)uridine biosynthesis DR MetaCyc; PWY0-1554; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Carboxy-S-adenosyl-L-methionine synthase DN Carboxy-S-adenosyl-L-methionine synthase RQ 1 EV IPR005271; TIGR00740; sufficient; -- SN 2 ID tRNA U34 carboxymethyltransferase DN tRNA U34 carboxymethyltransferase RQ 1 EV IPR010017; TIGR00452; sufficient; EV IPR027555; PF08003; sufficient; // AC GenProp1341 DE NADH to trimethylamine N-oxide electron transfer TP PATHWAY AU Mackie A, Nolan L TH 0 DC NADH to trimethylamine N-oxide electron transfer DR MetaCyc; PWY0-1347; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Trimethylamine-N-oxide reductase (menaquinone) DN Trimethylamine-N-oxide reductase (menaquinone) (EC 1.7.2.3) RQ 1 EV IPR009154; TIGR02162; sufficient; EV IPR006658; TIGR00509; sufficient; EV IPR011887; TIGR02164; sufficient; -- SN 2 ID NADH:menaquinone oxidoreductase (H+-transporting) DN NADH:menaquinone oxidoreductase (H+-transporting) (EC 1.6.5) RQ 1 EV IPR000440; PF00507; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR001694; PF00146; sufficient; EV IPR010226; TIGR01971; sufficient; EV IPR001457; PF00499; sufficient; EV IPR001133; PF00420; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR010227; TIGR01972; sufficient; EV IPR010096; TIGR01770; sufficient; // AC GenProp1342 DE Pyruvate fermentation to isobutanol (engineered) TP PATHWAY AU Caspi R TH 3 DC Pyruvate fermentation to isobutanol (engineered) DR MetaCyc; PWY-7111; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID (R)-2,3-dihydroxy-3-methylbutanoate isomeroreductase DN (R)-2,3-dihydroxy-3-methylbutanoate isomeroreductase (EC 1.1.1.86) RQ 1 EV IPR013023; TIGR00465; sufficient; -- SN 2 ID (S)-2-acetolactate synthase DN (S)-2-acetolactate synthase (EC 2.2.1.6) RQ 1 EV IPR012846; TIGR00118; sufficient; EV IPR004789; TIGR00119; sufficient; -- SN 3 ID 2,3-Dihydroxy-isovalerate dehydratase DN 2,3-Dihydroxy-isovalerate dehydratase (EC 4.2.1.9) RQ 1 EV IPR000581; PF00920; sufficient; EV IPR004404; TIGR00110; sufficient; -- SN 4 ID 2-Oxoisovalerate carboxy-lyase DN 2-Oxoisovalerate carboxy-lyase (EC 4.1.1.72) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 5 ID Isobutanol dehydrogenase DN Isobutanol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; // AC GenProp1343 DE Guanosine deoxyribonucleotides de novo biosynthesis II TP PATHWAY AU Caspi R TH 2 DC Guanosine deoxyribonucleotides de novo biosynthesis II DR MetaCyc; PWY-7222; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID DGDP kinase DN DGDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 2 ID GDP reductase DN GDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 3 ID GTP reductase DN GTP reductase (EC 1.1.98.6) RQ 1 EV IPR012833; PF13597; sufficient; EV IPR012833; TIGR02487; sufficient; -- SN 4 ID 2'-Deoxyguanosine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase DN 2'-Deoxyguanosine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase (EC 1.17.4.1) RQ 1 EV IPR026459; TIGR04170; sufficient; EV IPR000358; PF00268; sufficient; EV IPR026494; TIGR04171; sufficient; // AC GenProp1344 DE Gluconeogenesis I TP PATHWAY AU Riley M TH 11 DC Gluconeogenesis I DR MetaCyc; GLUCONEO-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Malic enzyme (NAD) DN Malic enzyme (NAD) (EC 1.1.1.39) RQ 1 EV IPR012301; PF00390; sufficient; EV IPR012302; PF03949; sufficient; -- SN 2 ID Enolase DN Enolase (EC 4.2.1.11) RQ 1 EV IPR000941; TIGR01060; sufficient; -- SN 3 ID 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) RQ 1 EV IPR005995; TIGR01307; sufficient; -- SN 4 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase (EC 4.1.2.13) RQ 1 EV IPR002915; PF01791; sufficient; EV IPR000771; PF01116; sufficient; EV IPR000771; TIGR00167; sufficient; EV IPR006411; TIGR01520; sufficient; -- SN 5 ID Fructose 1,6-bisphosphatase DN Fructose 1,6-bisphosphatase (EC 3.1.3.11) RQ 1 EV IPR004464; PF03320; sufficient; EV IPR004464; TIGR00330; sufficient; EV IPR000150; TIGR00099; sufficient; EV IPR006379; TIGR01484; sufficient; -- SN 6 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 7 ID Malate dehydrogenase (NAD) DN Malate dehydrogenase (NAD) (EC 1.1.1.37) RQ 1 EV IPR010097; TIGR01772; sufficient; -- SN 8 ID Malate dehydrogenase DN Malate dehydrogenase (EC 1.1.1.40) RQ 1 EV IPR002505; PF01515; sufficient; EV IPR012301; PF00390; sufficient; EV IPR012302; PF03949; sufficient; -- SN 9 ID Phosphoenolpyruvate carboxykinase (ATP) DN Phosphoenolpyruvate carboxykinase (ATP) (EC 4.1.1.49) RQ 1 EV IPR001272; PF01293; sufficient; EV IPR001272; TIGR00224; sufficient; -- SN 10 ID Phosphoenolpyruvate synthetase DN Phosphoenolpyruvate synthetase (EC 2.7.9.2) RQ 1 EV IPR006319; TIGR01418; sufficient; -- SN 11 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; -- SN 12 ID Phosphoglycerate kinase DN Phosphoglycerate kinase (EC 2.7.2.3) RQ 1 EV IPR001576; PF00162; sufficient; -- SN 13 ID Triose-phosphate isomerase DN Triose-phosphate isomerase (EC 5.3.1.1) RQ 1 EV IPR000652; PF00121; sufficient; EV IPR000652; TIGR00419; sufficient; // AC GenProp1345 DE Acetate formation from acetyl-CoA I TP PATHWAY AU Caspi R TH 0 DC Acetate formation from acetyl-CoA I DR MetaCyc; PWY0-1312; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetate kinase DN Acetate kinase (EC 2.7.2.1) RQ 1 EV IPR000890; PF00871; sufficient; EV IPR004372; TIGR00016; sufficient; -- SN 2 ID Phosphotransacetylase DN Phosphotransacetylase (EC 2.3.1.8) RQ 1 EV IPR002505; PF01515; sufficient; EV IPR004614; TIGR00651; sufficient; EV IPR010766; PF07085; sufficient; // AC GenProp1346 DE Glutathione degradation (DUG pathway - yeast) TP PATHWAY AU Foerster H TH 0 DC Glutathione degradation (DUG pathway - yeast) DR MetaCyc; PWY-7559; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutathione hydrolase DN Glutathione hydrolase (EC 3.4.19.13) RQ 1 EV IPR002933; PF01546; sufficient; EV IPR026869; PF13230; sufficient; EV IPR000101; PF01019; sufficient; EV IPR000101; TIGR00066; sufficient; -- SN 2 ID Cysteinylglycine dipeptidase DN Cysteinylglycine dipeptidase (EC 3.4.13.18) RQ 1 EV IPR002933; PF01546; sufficient; // AC GenProp1347 DE UDP-alpha-D-glucuronate biosynthesis (from myo-inositol) TP PATHWAY AU N/A TH 1 DC UDP-alpha-D-glucuronate biosynthesis (from myo-inositol) DR MetaCyc; PWY-4841; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-D-glucuronate pyrophosphorylase DN UDP-D-glucuronate pyrophosphorylase (EC 2.7.7.44) RQ 1 EV IPR002618; PF01704; sufficient; -- SN 2 ID Glucuronokinase DN Glucuronokinase (EC 2.7.1.43) RQ 1 EV IPR006204; PF00288; sufficient; -- SN 3 ID Myo-inositol oxygenase DN Myo-inositol oxygenase (EC 1.13.99.1) RQ 1 EV IPR007828; PF05153; sufficient; // AC GenProp1348 DE 2-Oxoglutarate decarboxylation to succinyl-CoA TP PATHWAY AU Caspi R TH 1 DC 2-Oxoglutarate decarboxylation to succinyl-CoA DR MetaCyc; PWY-5084; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Oxoglutarate decarboxylase DN 2-Oxoglutarate decarboxylase (EC 1.2.4.2) RQ 1 EV IPR011603; TIGR00239; sufficient; -- SN 2 ID Dihydrolipoyl dehydrogenase DN Dihydrolipoyl dehydrogenase (EC 1.8.1.4) RQ 1 EV IPR006258; TIGR01350; sufficient; -- SN 3 ID Dihydrolipoyltranssuccinylase DN Dihydrolipoyltranssuccinylase (EC 2.3.1.61) RQ 1 EV IPR006255; TIGR01347; sufficient; // AC GenProp1349 DE Superpathway of adenosylcobalamin salvage from cobinamide I TP PATHWAY AU Riley M TH 3 DC Superpathway of adenosylcobalamin salvage from cobinamide I DR MetaCyc; COBALSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cobalamin 5'-phosphate synthase DN Cobalamin 5'-phosphate synthase (EC 2.7.8.26) RQ 1 EV IPR003805; PF02654; sufficient; EV IPR003805; TIGR00317; sufficient; -- SN 2 ID ATP:adenosylcobinamide phosphotransferase DN ATP:adenosylcobinamide phosphotransferase (EC 2.7.1.156) RQ 1 EV IPR003203; PF02283; sufficient; -- SN 3 ID GTP:adenosylcobinamide-phosphate guanylyltransferase DN GTP:adenosylcobinamide-phosphate guanylyltransferase (EC 2.7.7.62) RQ 1 EV IPR003203; PF02283; sufficient; -- SN 4 ID Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase DN Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) RQ 1 EV IPR017846; TIGR03160; sufficient; -- SN 5 ID Adenosylcobalamin 5'-phosphate phosphatase DN Adenosylcobalamin 5'-phosphate phosphatase (EC 3.1.3.73) RQ 1 EV IPR013078; PF00300; sufficient; EV IPR017578; TIGR03162; sufficient; // AC GenProp1351 DE Phosphatidylcholine biosynthesis I TP PATHWAY AU Caspi R, Fulcher C, Hong E TH 1 DC Phosphatidylcholine biosynthesis I DR MetaCyc; PWY3O-450; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID CTP:phosphocholine cytidylyltransferase DN CTP:phosphocholine cytidylyltransferase (EC 2.7.7.15) RQ 1 EV IPR004821; PF01467; sufficient; EV IPR004821; TIGR00125; sufficient; -- SN 2 ID Choline kinase DN Choline kinase (EC 2.7.1.32) RQ 1 EV IPR007521; PF04428; sufficient; -- SN 3 ID Diacylglycerol cholinephosphotransferase DN Diacylglycerol cholinephosphotransferase (EC 2.7.8.2) RQ 1 EV IPR000462; PF01066; sufficient; // AC GenProp1352 DE Phosphatidylcholine resynthesis via glycerophosphocholine TP PATHWAY AU Foerster H TH 1 DC Phosphatidylcholine resynthesis via glycerophosphocholine DR MetaCyc; PWY-7367; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerophosphocholine phosphodiesterase DN Glycerophosphocholine phosphodiesterase (EC 3.1.4.2) RQ 1 EV IPR004331; PF03105; sufficient; EV IPR020683; PF12796; sufficient; EV IPR030395; PF03009; sufficient; -- SN 2 ID Phosphatidylcholine phospholipase DN Phosphatidylcholine phospholipase (EC 3.1.1) RQ 1 EV IPR000595; PF00027; sufficient; EV IPR002641; PF01734; sufficient; -- SN 3 ID Diacylglycerol cholinephosphotransferase DN Diacylglycerol cholinephosphotransferase (EC 2.7.8.2) RQ 1 EV IPR000462; PF01066; sufficient; // AC GenProp1353 DE Superpathway of photosynthetic hydrogen production TP PATHWAY AU Caspi R TH 2 DC Superpathway of photosynthetic hydrogen production DR MetaCyc; PWY-7731; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Hydrogenase DN Hydrogenase (EC 1.12.7.2) RQ 1 EV IPR003149; PF02256; sufficient; EV IPR004108; PF02906; sufficient; -- SN 2 ID Plastoquinol-plastocyanin reductase DN Plastoquinol-plastocyanin reductase (EC 1.10.9.1) RQ 1 EV IPR005497; PF03742; sufficient; EV IPR002325; PF01333; sufficient; EV IPR005870; TIGR01156; sufficient; EV IPR003683; PF02529; sufficient; EV IPR007802; PF05115; sufficient; -- SN 3 ID NAD(P)H dehydrogenase (plastoquinone) DN NAD(P)H dehydrogenase (plastoquinone) (EC 1.6.5.2) RQ 1 EV IPR002048; PF13202; sufficient; EV IPR023753; PF07992; sufficient; -- SN 4 ID Photosystem I DN Photosystem I (EC 1.97.1.12) RQ 1 EV IPR001302; PF00796; sufficient; EV IPR001302; TIGR03052; sufficient; EV IPR008796; PF05479; sufficient; EV IPR017498; TIGR03059; sufficient; EV IPR001280; PF00223; sufficient; EV IPR006243; TIGR01335; sufficient; EV IPR006244; TIGR01336; sufficient; EV IPR002615; PF01701; sufficient; EV IPR017491; TIGR03048; sufficient; // AC GenProp1354 DE mRNA capping I TP PATHWAY AU Caspi R TH 1 DC mRNA capping I DR MetaCyc; PWY-7375; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Guanine-N7 methyltransferase DN Guanine-N7 methyltransferase (EC 2.1.1.56) RQ 1 EV IPR004971; PF03291; sufficient; -- SN 2 ID mRNA guanylyltransferase DN mRNA guanylyltransferase (EC 2.7.7.50) RQ 1 EV IPR001339; PF01331; sufficient; EV IPR013846; PF03919; sufficient; EV IPR000340; PF00782; sufficient; -- SN 3 ID mRNA 5'-triphosphate phosphatase DN mRNA 5'-triphosphate phosphatase (EC 3.1.3.33) RQ 1 EV IPR004206; PF02940; sufficient; EV IPR000340; PF00782; sufficient; EV IPR001339; PF01331; sufficient; EV IPR013846; PF03919; sufficient; // AC GenProp1355 DE Chlorophyll a biosynthesis II TP PATHWAY AU N/A TH 3 DC Chlorophyll a biosynthesis II DR MetaCyc; PWY-5064; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3,8-Divinyl-chlorophyllide 8-vinyl reductase DN 3,8-Divinyl-chlorophyllide 8-vinyl reductase (EC 1.3.1.75) RQ 1 EV IPR016040; PF13460; sufficient; -- SN 2 ID Chlorophyllide-a:geranyl-geranyl diphosphate geranyl-geranyl transferase DN Chlorophyllide-a:geranyl-geranyl diphosphate geranyl-geranyl transferase (EC 2.5.1.62) RQ 1 EV IPR000537; PF01040; sufficient; EV IPR006372; TIGR01476; sufficient; EV IPR011799; TIGR02056; sufficient; -- SN 3 ID Geranylgeranyl-chlorophyll a reductase DN Geranylgeranyl-chlorophyll a reductase RQ 1 EV IPR010253; TIGR02023; sufficient; EV IPR011774; TIGR02028; sufficient; EV IPR011777; TIGR02032; sufficient; -- SN 4 ID Dihydrogeranylgeranyl-chlorophyll a reductase DN Dihydrogeranylgeranyl-chlorophyll a reductase RQ 1 EV IPR010253; TIGR02023; sufficient; EV IPR011774; TIGR02028; sufficient; EV IPR011777; TIGR02032; sufficient; -- SN 5 ID Tetrahydrogeranylgeranyl-chlorophyll a reductase DN Tetrahydrogeranylgeranyl-chlorophyll a reductase RQ 1 EV IPR010253; TIGR02023; sufficient; EV IPR011774; TIGR02028; sufficient; EV IPR011777; TIGR02032; sufficient; // AC GenProp1356 DE N10-formyl-tetrahydrofolate biosynthesis TP PATHWAY AU Sarker M, Riley M TH 7 DC N10-formyl-tetrahydrofolate biosynthesis DR MetaCyc; 1CMET2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 5,10-Methylenetetrahydrofolate reductase DN 5,10-Methylenetetrahydrofolate reductase (EC 1.5.1.20) RQ 1 EV IPR003171; PF02219; sufficient; EV IPR004620; TIGR00676; sufficient; -- SN 2 ID 5-Formyltetrahydrofolate cyclo-ligase DN 5-Formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) RQ 1 EV IPR002698; PF01812; sufficient; EV IPR002698; TIGR02727; sufficient; -- SN 3 ID Dihydrofolate reductase DN Dihydrofolate reductase (EC 1.5.1.3) RQ 1 EV IPR001796; PF00186; sufficient; -- SN 4 ID Glycine decarboxylase DN Glycine decarboxylase RQ 1 EV IPR006258; TIGR01350; sufficient; EV IPR003437; TIGR00461; sufficient; EV IPR006223; TIGR00528; sufficient; EV IPR002930; PF01597; sufficient; EV IPR017453; TIGR00527; sufficient; -- SN 5 ID 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase DN 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase (EC 2.1.2.1) RQ 1 EV IPR001085; PF00464; sufficient; -- SN 6 ID Methionine synthase DN Methionine synthase (EC 2.1.1.13) RQ 1 EV IPR011822; TIGR02082; sufficient; -- SN 7 ID Methenyltetrahydrofolate cyclohydrolase DN Methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9) RQ 1 EV IPR020630; PF00763; sufficient; EV IPR020631; PF02882; sufficient; -- SN 8 ID Methylenetetrahydrofolate dehydrogenase DN Methylenetetrahydrofolate dehydrogenase (EC 1.5.1.5) RQ 1 EV IPR020630; PF00763; sufficient; EV IPR020631; PF02882; sufficient; -- SN 9 ID Thymidylate synthase DN Thymidylate synthase (EC 2.1.1.45) RQ 1 EV IPR000398; TIGR03284; sufficient; // AC GenProp1357 DE L-citrulline degradation TP PATHWAY AU Foerster H, Caspi R, Ying H TH 0 DC L-citrulline degradation DR MetaCyc; CITRULLINE-DEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Carbamate kinase DN Carbamate kinase (EC 2.7.2.2) RQ 1 EV IPR003964; TIGR00746; sufficient; -- SN 2 ID Ornithine carbamoyltransferase DN Ornithine carbamoyltransferase (EC 2.1.3.3) RQ 1 EV IPR002292; TIGR00658; sufficient; // AC GenProp1358 DE Superpathway of L-threonine biosynthesis TP PATHWAY AU Caspi R, Riley M TH 2 DC Superpathway of L-threonine biosynthesis DR MetaCyc; THRESYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID Aspartate kinase DN Aspartate kinase (EC 2.7.2.4) RQ 1 EV IPR005260; TIGR00656; sufficient; -- SN 3 ID Homoserine dehydrogenase DN Homoserine dehydrogenase (EC 1.1.1.3) RQ 1 EV IPR001048; PF00696; sufficient; EV IPR001341; TIGR00657; sufficient; EV IPR001342; PF00742; sufficient; EV IPR002912; PF01842; sufficient; EV IPR005106; PF03447; sufficient; EV IPR027795; PF13840; sufficient; -- SN 4 ID Homoserine kinase DN Homoserine kinase (EC 2.7.1.39) RQ 1 EV IPR000870; TIGR00191; sufficient; // AC GenProp1359 DE Glutathione biosynthesis TP PATHWAY AU Keseler I, Riley M, Foerster H TH 0 DC Glutathione biosynthesis DR MetaCyc; GLUTATHIONESYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutathione synthetase DN Glutathione synthetase (EC 6.3.2.3) RQ 1 EV IPR005615; PF03917; sufficient; EV IPR005615; TIGR01986; sufficient; EV IPR006284; TIGR01380; sufficient; -- SN 2 ID Glutamate-cysteine ligase DN Glutamate-cysteine ligase (EC 6.3.2.2) RQ 1 EV IPR004308; PF03074; sufficient; EV IPR006336; PF04107; sufficient; EV IPR011556; TIGR01436; sufficient; EV IPR006334; TIGR01434; sufficient; // AC GenProp1360 DE tRNA processing TP PATHWAY AU Shearer A TH 8 DC tRNA processing DR MetaCyc; PWY0-1479; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ribonuclease DN Ribonuclease (EC 3.1.26.5) RQ 1 EV IPR000100; PF00825; sufficient; EV IPR000100; TIGR00188; sufficient; -- SN 2 ID RNase BN ribonuclease DN RNase BN ribonuclease (EC 3.1.13.1) RQ 1 EV IPR013469; TIGR02649; sufficient; EV IPR013471; TIGR02651; sufficient; -- SN 3 ID Ribonuclease DN Ribonuclease (EC 3.1.26.12) RQ 1 EV IPR004659; TIGR00757; sufficient; EV IPR019307; PF10150; sufficient; -- SN 4 ID Exoribonuclease DN Exoribonuclease (EC 3.1.13.1) RQ 1 EV IPR012162; TIGR03591; sufficient; EV IPR004476; TIGR00358; sufficient; EV IPR011804; TIGR02062; sufficient; -- SN 5 ID Ribonuclease DN Ribonuclease (EC 3.1.26.5) RQ 1 EV IPR000100; PF00825; sufficient; EV IPR000100; TIGR00188; sufficient; -- SN 6 ID Phosphate-dependent exonuclease DN Phosphate-dependent exonuclease (EC 2.7.7.56) RQ 1 EV IPR002381; TIGR01966; sufficient; -- SN 7 ID Phosphate-dependent exonuclease DN Phosphate-dependent exonuclease (EC 2.7.7.56) RQ 1 EV IPR002381; TIGR01966; sufficient; -- SN 8 ID RNase T exonuclease DN RNase T exonuclease (EC 3.1.13.5) RQ 1 EV IPR005987; TIGR01298; sufficient; EV IPR006292; TIGR01388; sufficient; -- SN 9 ID RNase D exonuclease DN RNase D exonuclease (EC 3.1.13.5) RQ 1 EV IPR005987; TIGR01298; sufficient; EV IPR006292; TIGR01388; sufficient; -- SN 10 ID Ribonuclease DN Ribonuclease (EC 3.1.26.12) RQ 1 EV IPR004659; TIGR00757; sufficient; EV IPR019307; PF10150; sufficient; // AC GenProp1361 DE Pyrimidine nucleobases salvage II TP PATHWAY AU Caspi R TH 0 DC Pyrimidine nucleobases salvage II DR MetaCyc; PWY-7194; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytosine deaminase DN Cytosine deaminase (EC 3.5.4.1) RQ 1 EV IPR013108; PF07969; sufficient; EV IPR002125; PF00383; sufficient; -- SN 2 ID Uracil phosphoribosyltransferase DN Uracil phosphoribosyltransferase (EC 2.4.2.9) RQ 1 EV IPR005765; TIGR01091; sufficient; // AC GenProp1362 DE Putrescine degradation I TP PATHWAY AU Caspi R, Riley M TH 0 DC Putrescine degradation I DR MetaCyc; PUTDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Aminobutyraldehyde dehydrogenase DN 4-Aminobutyraldehyde dehydrogenase (EC 1.2.1.19) RQ 1 EV IPR017749; TIGR03374; sufficient; -- SN 2 ID Putrescine aminotransferase DN Putrescine aminotransferase RQ 1 EV IPR005814; PF00202; sufficient; EV IPR017747; TIGR03372; sufficient; // AC GenProp1363 DE Sphingolipid recycling and degradation (yeast) TP PATHWAY AU Caspi R TH 9 DC Sphingolipid recycling and degradation (yeast) DR MetaCyc; PWY-7119; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phytoceramidase DN Phytoceramidase (EC 3.5.1.23) RQ 1 EV IPR008901; PF05875; sufficient; -- SN 2 ID Dihydrosphingosine phosphatase DN Dihydrosphingosine phosphatase (EC 3.1.3) RQ 1 EV IPR000326; PF01569; sufficient; -- SN 3 ID Phytosphingosine 1-phosphate aldolase DN Phytosphingosine 1-phosphate aldolase (EC 4.1.2.27) RQ 1 EV IPR002129; PF00282; sufficient; -- SN 4 ID Inositol-phospho-alpha hydroxyphytoceramide phospholipase DN Inositol-phospho-alpha hydroxyphytoceramide phospholipase (EC 3.1.4.-) RQ 1 EV IPR005135; PF03372; sufficient; -- SN 5 ID Mannosyl-inositol-phospho-alpha hydroxyphytoceramide phospholipase DN Mannosyl-inositol-phospho-alpha hydroxyphytoceramide phospholipase (EC 3.1.4.-) RQ 1 EV IPR005135; PF03372; sufficient; -- SN 6 ID Mannosyl-diphosphoinositol-ceramide phospholipase DN Mannosyl-diphosphoinositol-ceramide phospholipase (EC 3.1.4.-) RQ 1 EV IPR005135; PF03372; sufficient; -- SN 7 ID Dihydroceramidase DN Dihydroceramidase (EC 3.5.1.23) RQ 1 EV IPR008901; PF05875; sufficient; -- SN 8 ID Phytosphingosine kinase DN Phytosphingosine kinase (EC 2.7.1.91) RQ 1 EV IPR001206; PF00781; sufficient; -- SN 9 ID Sphingoid base phosphate phosphatase DN Sphingoid base phosphate phosphatase (EC 3.1.3) RQ 1 EV IPR000326; PF01569; sufficient; -- SN 10 ID Dihydrosphingosine phosphate lyase DN Dihydrosphingosine phosphate lyase (EC 4.1.2.27) RQ 1 EV IPR002129; PF00282; sufficient; -- SN 11 ID Sphinganine kinase DN Sphinganine kinase (EC 2.7.1.91) RQ 1 EV IPR001206; PF00781; sufficient; // AC GenProp1364 DE Hentriaconta-3,6,9,12,15,19,22,25,28-nonaene biosynthesis TP PATHWAY AU Caspi R TH 2 DC Hentriaconta-3,6,9,12,15,19,22,25,28-nonaene biosynthesis DR MetaCyc; PWY-7027; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Hentriaconta-3,6,9,12,19,22,25,28-octaene-16-one-15-oyl-CoA hydrolase DN Hentriaconta-3,6,9,12,19,22,25,28-octaene-16-one-15-oyl-CoA hydrolase (EC 2.3.3.20) RQ 1 EV IPR013747; PF08541; sufficient; EV IPR020616; PF00108; sufficient; -- SN 2 ID Hentriaconta-3,6,9,12,19,22,25,28-octaene-16-one-15-oate reductase DN Hentriaconta-3,6,9,12,19,22,25,28-octaene-16-one-15-oate reductase (EC 1.1.1.412) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 3 ID 3-[(3Z,6Z,9Z,12Z)-pentadeca-3,6,9,12-tetraen-1-yl]-4-[(2Z,5Z,8Z,11Z)-tetradeca-2,5,8,11-tetraen-1-yl]oxetan-2-one synthetase DN 3-[(3Z,6Z,9Z,12Z)-pentadeca-3,6,9,12-tetraen-1-yl]-4-[(2Z,5Z,8Z,11Z)-tetradeca-2,5,8,11-tetraen-1-yl]oxetan-2-one synthetase (EC 6.1.3.1) RQ 1 EV IPR000873; PF00501; sufficient; -- SN 4 ID 3-[(3Z,6Z,9Z,12Z)-pentadeca-3,6,9,12-tetraen-1-yl]-4-[(2Z,5Z,8Z,11Z)-tetradeca-2,5,8,11-tetraen-1-yl]oxetan-2-one decarboxylase DN 3-[(3Z,6Z,9Z,12Z)-pentadeca-3,6,9,12-tetraen-1-yl]-4-[(2Z,5Z,8Z,11Z)-tetradeca-2,5,8,11-tetraen-1-yl]oxetan-2-one decarboxylase RQ 1 EV IPR000073; PF00561; sufficient; // AC GenProp1365 DE L-asparagine degradation III (mammalian) TP PATHWAY AU Weerasinghe D, Fulcher C TH 1 DC L-asparagine degradation III (mammalian) DR MetaCyc; ASPARAGINE-DEG1-PWY-1; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-asparaginase DN L-asparaginase (EC 3.5.1.26) RQ 1 EV IPR000246; PF01112; sufficient; -- SN 2 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 3 ID L-asparaginase DN L-asparaginase (EC 3.5.1.1) RQ 1 EV IPR000246; PF01112; sufficient; EV IPR006033; TIGR00519; sufficient; // AC GenProp1366 DE 2-Methyladeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP TP PATHWAY AU Caspi R TH 1 DC 2-Methyladeninyl adenosylcobamide biosynthesis from DC adenosylcobinamide-GDP DR MetaCyc; PWY-7965; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Nicotinate-nucleotide-2-methyladenine phosphoribosyltransferase DN Nicotinate-nucleotide-2-methyladenine phosphoribosyltransferase (EC 2.4.2.21) RQ 1 EV IPR017846; TIGR03160; sufficient; -- SN 2 ID Adenosylcobinamide-GDP 2-methyladenine ribotide phosphate transferase DN Adenosylcobinamide-GDP 2-methyladenine ribotide phosphate transferase (EC 2.7.8.26) RQ 1 EV IPR003805; PF02654; sufficient; EV IPR003805; TIGR00317; sufficient; -- SN 3 ID Co alpha-[a-(2-methyladen-9-yl)]-Co beta-adenosylcobamide 5'-phosphate phosphatase DN Co alpha-[a-(2-methyladen-9-yl)]-Co beta-adenosylcobamide 5'-phosphate phosphatase (EC 3.1.3.73) RQ 1 EV IPR013078; PF00300; sufficient; EV IPR017578; TIGR03162; sufficient; // AC GenProp1367 DE D-lactate to cytochrome bo oxidase electron transfer TP PATHWAY AU Mackie A TH 0 DC D-lactate to cytochrome bo oxidase electron transfer DR MetaCyc; PWY0-1565; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-lactate dehydrogenase DN D-lactate dehydrogenase (EC 1.1.5.12) RQ 1 EV IPR006094; PF01565; sufficient; EV IPR015409; PF09330; sufficient; -- SN 2 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; // AC GenProp1368 DE L-arabinose degradation I TP PATHWAY AU Riley M, Ingraham J TH 1 DC L-arabinose degradation I DR MetaCyc; ARABCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-arabinose isomerase DN L-arabinose isomerase (EC 5.3.1.4) RQ 1 EV IPR003762; PF02610; sufficient; -- SN 2 ID L-ribulose-5-phosphate 4-epimerase DN L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) RQ 1 EV IPR004661; TIGR00760; sufficient; -- SN 3 ID Ribulokinase DN Ribulokinase (EC 2.7.1.16) RQ 1 EV IPR005929; TIGR01234; sufficient; // AC GenProp1369 DE Superpathway of pyrimidine ribonucleosides salvage TP PATHWAY AU Caspi R TH 4 DC Superpathway of pyrimidine ribonucleosides salvage DR MetaCyc; PWY-7196; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytidine kinase DN Cytidine kinase (EC 2.7.1.213) RQ 1 EV IPR000764; TIGR00235; sufficient; -- SN 2 ID CMP kinase DN CMP kinase (EC 2.7.4.25) RQ 1 EV IPR003136; TIGR00017; sufficient; EV IPR006266; TIGR01359; sufficient; -- SN 3 ID UMP kinase DN UMP kinase (EC 2.7.4.14) RQ 1 EV IPR006266; TIGR01359; sufficient; EV IPR015963; TIGR02075; sufficient; -- SN 4 ID Uracil phosphoribosyltransferase DN Uracil phosphoribosyltransferase (EC 2.4.2.9) RQ 1 EV IPR005765; TIGR01091; sufficient; -- SN 5 ID Uridine nucleosidase DN Uridine nucleosidase (EC 3.2.2.3) RQ 1 EV IPR001910; PF01156; sufficient; -- SN 6 ID Uridine kinase DN Uridine kinase (EC 2.7.1.48) RQ 1 EV IPR000764; TIGR00235; sufficient; // AC GenProp1370 DE Ethylene glycol degradation TP PATHWAY AU Ingraham J TH 0 DC Ethylene glycol degradation DR MetaCyc; PWY0-1280; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycolaldehyde dehydrogenase DN Glycolaldehyde dehydrogenase (EC 1.2.1.21) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID Glycolaldehyde reductase DN Glycolaldehyde reductase (EC 1.1.1.77) RQ 1 EV IPR013460; TIGR02638; sufficient; // AC GenProp1371 DE Uracil degradation I (reductive) TP PATHWAY AU Caspi R, Tissier C TH 1 DC Uracil degradation I (reductive) DR MetaCyc; PWY-3982; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dihydropyrimidine dehydrogenase (NADP+) DN Dihydropyrimidine dehydrogenase (NADP+) (EC 1.3.1.2) RQ 1 EV IPR005720; PF01180; sufficient; EV IPR005720; TIGR01037; sufficient; EV IPR023753; PF07992; sufficient; EV IPR028261; PF14691; sufficient; -- SN 2 ID Beta-ureidopropionase DN Beta-ureidopropionase (EC 3.5.1.6) RQ 1 EV IPR003010; PF00795; sufficient; -- SN 3 ID Dihydrouracil amidohydrolase DN Dihydrouracil amidohydrolase (EC 3.5.2.2) RQ 1 EV IPR011778; TIGR02033; sufficient; // AC GenProp1372 DE Adenosine ribonucleotides de novo biosynthesis TP PATHWAY AU Caspi R TH 1 DC Adenosine ribonucleotides de novo biosynthesis DR MetaCyc; PWY-7219; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID AMP kinase DN AMP kinase (EC 2.7.4.3) RQ 1 EV IPR006259; TIGR01351; sufficient; EV IPR006267; TIGR01360; sufficient; -- SN 2 ID Adenylosuccinate synthase DN Adenylosuccinate synthase (EC 6.3.4.4) RQ 1 EV IPR001114; PF00709; sufficient; EV IPR001114; TIGR00184; sufficient; -- SN 3 ID Adenylosuccinate lyase DN Adenylosuccinate lyase (EC 4.3.2.2) RQ 1 EV IPR004769; TIGR00928; sufficient; // AC GenProp1373 DE NADH to cytochrome bd oxidase electron transfer II TP PATHWAY AU Mackie A TH 0 DC NADH to cytochrome bd oxidase electron transfer II DR MetaCyc; PWY0-1568; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytochrome bd-I ubiquinol oxidase DN Cytochrome bd-I ubiquinol oxidase (EC 1.10.3.14) RQ 1 EV IPR002585; PF01654; sufficient; EV IPR003317; PF02322; sufficient; EV IPR003317; TIGR00203; sufficient; EV IPR011724; TIGR02106; sufficient; EV IPR012994; PF08173; sufficient; -- SN 2 ID NADH:ubiquinone oxidoreductase 1 (external) DN NADH:ubiquinone oxidoreductase 1 (external) (EC 1.6.5.9) RQ 1 EV IPR023753; PF07992; sufficient; // AC GenProp1374 DE Glycolate and glyoxylate degradation I TP PATHWAY AU Keseler I, Riley M, Ingraham J TH 2 DC Glycolate and glyoxylate degradation I DR MetaCyc; GLYCOLATEMET-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerate 2-kinase DN Glycerate 2-kinase (EC 2.7.1.165) RQ 1 EV IPR004381; PF02595; sufficient; EV IPR004381; TIGR00045; sufficient; -- SN 2 ID Glycolate oxidase DN Glycolate oxidase (EC 1.1.99.14) RQ 1 EV IPR004490; TIGR00387; sufficient; -- SN 3 ID Glyoxylate carboligase DN Glyoxylate carboligase (EC 4.1.1.47) RQ 1 EV IPR006397; TIGR01504; sufficient; -- SN 4 ID Tartronate semialdehyde reductase DN Tartronate semialdehyde reductase (EC 1.1.1) RQ 1 EV IPR006398; TIGR01505; sufficient; // AC GenProp1375 DE L-tyrosine degradation I TP PATHWAY AU Fulcher C TH 3 DC L-tyrosine degradation I DR MetaCyc; TYRFUMCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Hydroxyphenylpyruvate dioxygenase DN 4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) RQ 1 EV IPR005956; TIGR01263; sufficient; -- SN 2 ID Fumarylacetoacetate hydrolase DN Fumarylacetoacetate hydrolase (EC 3.7.1.2) RQ 1 EV IPR005959; TIGR01266; sufficient; -- SN 3 ID Homogentisate oxygenase DN Homogentisate oxygenase (EC 1.13.11.5) RQ 1 EV IPR005708; PF04209; sufficient; EV IPR005708; TIGR01015; sufficient; -- SN 4 ID Maleylacetoacetate isomerase DN Maleylacetoacetate isomerase (EC 5.2.1.2) RQ 1 EV IPR005955; TIGR01262; sufficient; -- SN 5 ID L-tyrosine:2-oxoglutarate aminotransferase DN L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) RQ 1 EV IPR005957; TIGR01264; sufficient; EV IPR005958; TIGR01265; sufficient; // AC GenProp1376 DE Very long chain fatty acid biosynthesis II TP PATHWAY AU Caspi R TH 14 DC Very long chain fatty acid biosynthesis II DR MetaCyc; PWY-7036; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Oxo-arachidoyl-CoA synthase DN 3-Oxo-arachidoyl-CoA synthase (EC 2.3.1.199) RQ 1 EV IPR002076; PF01151; sufficient; -- SN 2 ID 3-Oxo-behenoyl-CoA synthase DN 3-Oxo-behenoyl-CoA synthase (EC 2.3.1.199) RQ 1 EV IPR002076; PF01151; sufficient; -- SN 3 ID 3-Oxo-cerotoyl-CoA synthase DN 3-Oxo-cerotoyl-CoA synthase (EC 2.3.1.199) RQ 1 EV IPR002076; PF01151; sufficient; -- SN 4 ID 3-Oxo-lignoceronyl-CoA synthase DN 3-Oxo-lignoceronyl-CoA synthase (EC 2.3.1.199) RQ 1 EV IPR002076; PF01151; sufficient; -- SN 5 ID 3-Oxo-arachidoyl-CoA reductase DN 3-Oxo-arachidoyl-CoA reductase (EC 1.1.1.330) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 6 ID 3-Oxo-behenoyl-CoA reductase DN 3-Oxo-behenoyl-CoA reductase (EC 1.1.1.330) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 7 ID 3-Oxo-lignoceroyl-CoA reductase DN 3-Oxo-lignoceroyl-CoA reductase (EC 1.1.1.330) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 8 ID 3-Oxo-cerotoyl-CoA reductase DN 3-Oxo-cerotoyl-CoA reductase (EC 1.1.1.330) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 9 ID 3-Hydroxy-arachidoyl-CoA dehydratase DN 3-Hydroxy-arachidoyl-CoA dehydratase (EC 4.2.1.134) RQ 1 EV IPR007482; PF04387; sufficient; -- SN 10 ID 3-Hydroxy-behenoyl-CoA dehydratase DN 3-Hydroxy-behenoyl-CoA dehydratase (EC 4.2.1.134) RQ 1 EV IPR007482; PF04387; sufficient; -- SN 11 ID 3-Hydroxy-lignoceroyl-CoA dehydratase DN 3-Hydroxy-lignoceroyl-CoA dehydratase (EC 4.2.1.134) RQ 1 EV IPR007482; PF04387; sufficient; -- SN 12 ID 3-Hydroxy-cerotoyl-CoA dehydratase DN 3-Hydroxy-cerotoyl-CoA dehydratase (EC 4.2.1.134) RQ 1 EV IPR007482; PF04387; sufficient; -- SN 13 ID Trans-arachidon-2-enoyl-CoA reductase DN Trans-arachidon-2-enoyl-CoA reductase (EC 1.3.1.93) RQ 1 EV IPR001104; PF02544; sufficient; -- SN 14 ID Trans-docosan-2-enoyl-CoA reductase DN Trans-docosan-2-enoyl-CoA reductase (EC 1.3.1.93) RQ 1 EV IPR001104; PF02544; sufficient; -- SN 15 ID Trans-lignocero-2-enoyl-CoA reductase DN Trans-lignocero-2-enoyl-CoA reductase (EC 1.3.1.93) RQ 1 EV IPR001104; PF02544; sufficient; -- SN 16 ID Trans-cerot-2-enoyl-CoA reductase DN Trans-cerot-2-enoyl-CoA reductase (EC 1.3.1.93) RQ 1 EV IPR001104; PF02544; sufficient; // AC GenProp1377 DE Biotin biosynthesis from 8-amino-7-oxononanoate I TP PATHWAY AU Keseler I, Caspi R, Riley M TH 1 DC Biotin biosynthesis from 8-amino-7-oxononanoate I DR MetaCyc; PWY0-1507; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Biotin synthase DN Biotin synthase (EC 2.8.1.6) RQ 1 EV IPR002684; TIGR00433; sufficient; -- SN 2 ID 7,8-Diaminopelargonic acid aminotransferase DN 7,8-Diaminopelargonic acid aminotransferase (EC 2.6.1.62) RQ 1 EV IPR005814; PF00202; sufficient; EV IPR005815; TIGR00508; sufficient; -- SN 3 ID Dethiobiotin synthetase DN Dethiobiotin synthetase (EC 6.3.3.3) RQ 1 EV IPR004472; TIGR00347; sufficient; // AC GenProp1378 DE Adeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP TP PATHWAY AU Caspi R TH 1 DC Adeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP DR MetaCyc; PWY-7964; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Nicotinate-nucleotide-adenine phosphoribosyltransferase DN Nicotinate-nucleotide-adenine phosphoribosyltransferase (EC 2.4.2.21) RQ 1 EV IPR017846; TIGR03160; sufficient; -- SN 2 ID Adenosylcobinamide-GDP adenine ribotide phosphate transferase DN Adenosylcobinamide-GDP adenine ribotide phosphate transferase (EC 2.7.8.26) RQ 1 EV IPR003805; PF02654; sufficient; EV IPR003805; TIGR00317; sufficient; -- SN 3 ID Co alpha-[a-(aden-9-yl)]-Co beta-adenosylcobamide 5'-phosphate phosphatase DN Co alpha-[a-(aden-9-yl)]-Co beta-adenosylcobamide 5'-phosphate phosphatase (EC 3.1.3.73) RQ 1 EV IPR013078; PF00300; sufficient; EV IPR017578; TIGR03162; sufficient; // AC GenProp1379 DE Ethanol degradation IV TP PATHWAY AU N/A TH 1 DC Ethanol degradation IV DR MetaCyc; PWY66-162; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetyl CoA synthetase DN Acetyl CoA synthetase (EC 6.2.1.1) RQ 1 EV IPR011904; TIGR02188; sufficient; -- SN 2 ID Ethanol peroxidase DN Ethanol peroxidase (EC 1.11.1.6) RQ 1 EV IPR010582; PF06628; sufficient; EV IPR011614; PF00199; sufficient; -- SN 3 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.3) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1380 DE Superpathway of pyrimidine ribonucleosides degradation TP PATHWAY AU Caspi R TH 0 DC Superpathway of pyrimidine ribonucleosides degradation DR MetaCyc; PWY-7209; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dihydropyrimidine dehydrogenase (NADP+) DN Dihydropyrimidine dehydrogenase (NADP+) (EC 1.3.1.2) RQ 1 EV IPR005720; PF01180; sufficient; EV IPR005720; TIGR01037; sufficient; EV IPR023753; PF07992; sufficient; EV IPR028261; PF14691; sufficient; -- SN 2 ID Uridine phosphorylase DN Uridine phosphorylase (EC 2.4.2.3) RQ 1 EV IPR010059; TIGR01719; sufficient; // AC GenProp1381 DE Methylphosphonate degradation I TP PATHWAY AU Caspi R, Keseler I TH 2 DC Methylphosphonate degradation I DR MetaCyc; PWY0-1533; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoribosyl 1,2-cyclic phosphodiesterase DN Phosphoribosyl 1,2-cyclic phosphodiesterase (EC 3.1.4.55) RQ 1 EV IPR017693; TIGR03307; sufficient; -- SN 2 ID alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase DN alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase (EC 2.7.8.37) RQ 1 EV IPR009609; PF06754; sufficient; EV IPR009609; TIGR03293; sufficient; EV IPR008772; PF05845; sufficient; EV IPR008772; TIGR03292; sufficient; EV IPR008773; PF05861; sufficient; EV IPR012701; TIGR02324; sufficient; -- SN 3 ID alpha-D-ribose-1-methylphosphonate-5-triphosphate diphosphatase DN alpha-D-ribose-1-methylphosphonate-5-triphosphate diphosphatase (EC 3.6.1.63) RQ 1 EV IPR012696; TIGR02318; sufficient; -- SN 4 ID Carbon-phosphorous lyase DN Carbon-phosphorous lyase (EC 4.7.1.1) RQ 1 EV IPR010306; PF06007; sufficient; // AC GenProp1382 DE Phytyl diphosphate biosynthesis TP PATHWAY AU Foerster H, Caspi R TH 1 DC Phytyl diphosphate biosynthesis DR MetaCyc; PWY-5063; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID All-trans-geranyl-geranyl diphosphate reductase DN All-trans-geranyl-geranyl diphosphate reductase RQ 1 EV IPR010253; TIGR02023; sufficient; EV IPR011774; TIGR02028; sufficient; EV IPR011777; TIGR02032; sufficient; -- SN 2 ID Dihydrogeranylgeranyl diphosphate reductase DN Dihydrogeranylgeranyl diphosphate reductase RQ 1 EV IPR010253; TIGR02023; sufficient; EV IPR011774; TIGR02028; sufficient; EV IPR011777; TIGR02032; sufficient; -- SN 3 ID Tetrahydrogeranylgeranyl-PP reductase DN Tetrahydrogeranylgeranyl-PP reductase RQ 1 EV IPR010253; TIGR02023; sufficient; EV IPR011774; TIGR02028; sufficient; EV IPR011777; TIGR02032; sufficient; // AC GenProp1383 DE Glutaminyl-tRNAgln biosynthesis via transamidation TP PATHWAY AU Fulcher C TH 0 DC Glutaminyl-tRNAgln biosynthesis via transamidation DR MetaCyc; PWY-5921; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartyl-tRNAAsn amidotransferase DN Aspartyl-tRNAAsn amidotransferase (EC 6.3.5.7) RQ 1 EV IPR004412; TIGR00132; sufficient; EV IPR004413; TIGR00133; sufficient; EV IPR003837; PF02686; sufficient; EV IPR003837; TIGR00135; sufficient; -- SN 2 ID Glutamyl-tRNAGln synthetase DN Glutamyl-tRNAGln synthetase (EC 6.1.1.24) RQ 1 EV IPR004527; TIGR00464; sufficient; // AC GenProp1384 DE Pyrimidine ribonucleosides salvage I TP PATHWAY AU Caspi R TH 1 DC Pyrimidine ribonucleosides salvage I DR MetaCyc; PWY-7193; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytidine deaminase DN Cytidine deaminase (EC 3.5.4.5) RQ 1 EV IPR006263; TIGR01355; sufficient; EV IPR006262; TIGR01354; sufficient; -- SN 2 ID Cytidine kinase DN Cytidine kinase (EC 2.7.1.213) RQ 1 EV IPR000764; TIGR00235; sufficient; -- SN 3 ID Uridine kinase DN Uridine kinase (EC 2.7.1.48) RQ 1 EV IPR000764; TIGR00235; sufficient; // AC GenProp1385 DE Progesterone biosynthesis TP PATHWAY AU Caspi R TH 0 DC Progesterone biosynthesis DR MetaCyc; PWY-7299; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pregnenolone dehydrogenase DN Pregnenolone dehydrogenase (EC 1.1.1.145) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 2 ID Preg-5-en-3,20-dione isomerase DN Preg-5-en-3,20-dione isomerase (EC 5.3.3.1) RQ 1 EV IPR002225; PF01073; sufficient; // AC GenProp1386 DE Superpathway of L-serine and glycine biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Superpathway of L-serine and glycine biosynthesis I DR MetaCyc; SER-GLYSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase DN 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase (EC 2.1.2.1) RQ 1 EV IPR001085; PF00464; sufficient; -- SN 2 ID L-3-phosphoserine phosphatase DN L-3-phosphoserine phosphatase (EC 3.1.3.3) RQ 1 EV IPR006383; TIGR01488; sufficient; // AC GenProp1387 DE Superpathway of beta-D-glucuronosides degradation TP PATHWAY AU Caspi R, Keseler I, Riley M TH 0 DC Superpathway of beta-D-glucuronosides degradation DR MetaCyc; GLUCUROCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-glucuronate isomerase DN D-glucuronate isomerase (EC 5.3.1.12) RQ 1 EV IPR003766; PF02614; sufficient; -- SN 2 ID D-mannonate dehydrogenase DN D-mannonate dehydrogenase (EC 1.1.1.57) RQ 1 EV IPR013118; PF08125; sufficient; EV IPR013131; PF01232; sufficient; // AC GenProp1388 DE Pterostilbene biosynthesis TP PATHWAY AU Pujar A TH 0 DC Pterostilbene biosynthesis DR MetaCyc; PWY-6665; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Resveratrol O-methyltransferase DN Resveratrol O-methyltransferase RQ 1 EV IPR001077; PF00891; sufficient; EV IPR012967; PF08100; sufficient; -- SN 2 ID 3-Methoxy-4',5-dihydroxy-trans-stilbene methyltransferase DN 3-Methoxy-4',5-dihydroxy-trans-stilbene methyltransferase RQ 1 EV IPR001077; PF00891; sufficient; EV IPR012967; PF08100; sufficient; // AC GenProp1389 DE Superpathway of guanosine nucleotides de novo biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Superpathway of guanosine nucleotides de novo biosynthesis I DR MetaCyc; PWY-7228; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GDP reductase DN GDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 2 ID Guanylate kinase DN Guanylate kinase (EC 2.7.4.8) RQ 1 EV IPR017665; TIGR03263; sufficient; // AC GenProp1390 DE Choline degradation I TP PATHWAY AU Caspi R, Ying H TH 0 DC Choline degradation I DR MetaCyc; CHOLINE-BETAINE-ANA-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Betaine aldehyde dehydrogenase DN Betaine aldehyde dehydrogenase (EC 1.2.1.8) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID Choline dehydrogenase DN Choline dehydrogenase (EC 1.1.99.1) RQ 1 EV IPR011533; TIGR01810; sufficient; // AC GenProp1391 DE Glycerol-3-phosphate to fumarate electron transfer TP PATHWAY AU Mackie A TH 0 DC Glycerol-3-phosphate to fumarate electron transfer DR MetaCyc; PWY0-1582; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Fumarate reductase DN Fumarate reductase (EC 1.3.5.4) RQ 1 EV IPR004489; TIGR00384; sufficient; EV IPR005884; TIGR01176; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR003510; PF02300; sufficient; EV IPR003418; PF02313; sufficient; -- SN 2 ID Glycerol-3-phosphate dehydrogenase, anaerobic DN Glycerol-3-phosphate dehydrogenase, anaerobic (EC 1.1.5.3) RQ 1 EV IPR017752; TIGR03377; sufficient; EV IPR009158; TIGR03378; sufficient; EV IPR017753; TIGR03379; sufficient; // AC GenProp1392 DE Sulfate reduction II (assimilatory) TP PATHWAY AU Caspi R, Irina Iourovitski I TH 1 DC Sulfate reduction II (assimilatory) DR MetaCyc; SULFMETII-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID APS reductase DN APS reductase (EC 1.8.4.9) RQ 1 EV IPR004508; TIGR00424; sufficient; -- SN 2 ID Sulfate adenylyltransferase DN Sulfate adenylyltransferase (EC 2.7.7.4) RQ 1 EV IPR002650; TIGR00339; sufficient; EV IPR024951; PF01747; sufficient; EV IPR025980; PF14306; sufficient; -- SN 3 ID Octaheme sulfite reductase DN Octaheme sulfite reductase (EC 1.8.7.1) RQ 1 EV IPR011787; TIGR02042; sufficient; // AC GenProp1393 DE Allantoin degradation to glyoxylate II TP PATHWAY AU Caspi R TH 1 DC Allantoin degradation to glyoxylate II DR MetaCyc; PWY-5692; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Allantoate amidohydrolase DN Allantoate amidohydrolase (EC 3.5.3.9) RQ 1 EV IPR002933; PF01546; sufficient; EV IPR010158; TIGR01879; sufficient; -- SN 2 ID Ureidoglycolate amidohydrolase DN Ureidoglycolate amidohydrolase (EC 3.5.1.116) RQ 1 EV IPR002933; PF01546; sufficient; EV IPR010158; TIGR01879; sufficient; -- SN 3 ID Ureidoglycine aminohydrolase DN Ureidoglycine aminohydrolase (EC 3.5.3.26) RQ 1 EV IPR013096; PF07883; sufficient; // AC GenProp1394 DE Trehalose degradation I (low osmolarity) TP PATHWAY AU Caspi R, Riley M TH 0 DC Trehalose degradation I (low osmolarity) DR MetaCyc; TREDEGLOW-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucokinase DN Glucokinase (EC 2.7.1.2) RQ 1 EV IPR000600; PF00480; sufficient; EV IPR004654; TIGR00744; sufficient; EV IPR003836; PF02685; sufficient; EV IPR003836; TIGR00749; sufficient; -- SN 2 ID Trehalose-6-phosphate hydrolase DN Trehalose-6-phosphate hydrolase (EC 3.2.1.93) RQ 1 EV IPR012769; TIGR02403; sufficient; // AC GenProp1395 DE Superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism TP PATHWAY AU Caspi R TH 0 DC Superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism DR MetaCyc; PWY-6358; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ins(1,4,5)P3 5-phosphatase DN Ins(1,4,5)P3 5-phosphatase (EC 3.1.3.56) RQ 1 EV IPR002013; PF02383; sufficient; EV IPR005135; PF03372; sufficient; EV IPR015047; PF08952; sufficient; EV IPR000198; PF00620; sufficient; EV IPR031995; PF16726; sufficient; EV IPR031896; PF16776; sufficient; -- SN 2 ID Inositol-1,3,4,5-tetrakisphosphate 3-phosphatase DN Inositol-1,3,4,5-tetrakisphosphate 3-phosphatase (EC 3.1.3.62) RQ 1 EV IPR000560; PF00328; sufficient; // AC GenProp1396 DE UTP and CTP dephosphorylation II TP PATHWAY AU Caspi R TH 1 DC UTP and CTP dephosphorylation II DR MetaCyc; PWY-7177; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID CTP synthetase DN CTP synthetase (EC 6.3.4.2) RQ 1 EV IPR004468; TIGR00337; sufficient; -- SN 2 ID UTP phosphohydrolase DN UTP phosphohydrolase (EC 3.6.1.5) RQ 1 EV IPR000407; PF01150; sufficient; EV IPR014078; TIGR02705; sufficient; -- SN 3 ID CTP diphosphatase DN CTP diphosphatase (EC 3.6.1.5) RQ 1 EV IPR014078; TIGR02705; sufficient; EV IPR000407; PF01150; sufficient; // AC GenProp1397 DE (Kdo)2-lipid A biosynthesis I TP PATHWAY AU Johnson A TH 0 DC (Kdo)2-lipid A biosynthesis I DR MetaCyc; KDO-LIPASYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lauroyl acyltransferase DN Lauroyl acyltransferase (EC 2.3.1.241) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011920; TIGR02207; sufficient; -- SN 2 ID Myristoyl-acyl carrier protein-dependent acyltransferase DN Myristoyl-acyl carrier protein-dependent acyltransferase (EC 2.3.1.243) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011921; TIGR02208; sufficient; // AC GenProp1398 DE Poly(glycerol phosphate) wall teichoic acid biosynthesis TP PATHWAY AU Caspi R, Wagg J TH 10 DC Poly(glycerol phosphate) wall teichoic acid biosynthesis DR MetaCyc; TEICHOICACID-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol-3-phosphate cytidylyltransferase DN Glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) RQ 1 EV IPR006409; TIGR01518; sufficient; -- SN 2 ID PG:teichoic acid D-alanyltransferase DN PG:teichoic acid D-alanyltransferase (EC 2.3.1.M32) RQ 1 EV IPR004299; PF03062; sufficient; EV IPR024024; TIGR04091; sufficient; -- SN 3 ID UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase DN UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.33) RQ 1 EV IPR000715; PF00953; sufficient; -- SN 4 ID D-alanine carrier protein:PG D-alanyltransferase DN D-alanine carrier protein:PG D-alanyltransferase (EC 2.3.1.M31) RQ 1 EV IPR006998; PF04914; sufficient; EV IPR023896; TIGR04092; sufficient; -- SN 5 ID D-alanine--[D-alanyl carrier protein] ligase DN D-alanine--[D-alanyl carrier protein] ligase RQ 1 EV IPR010072; TIGR01734; sufficient; -- SN 6 ID Poly(glycerol phosphate) teichoic acid transporter DN Poly(glycerol phosphate) teichoic acid transporter (EC 3.6.3.40) RQ 1 EV IPR003439; PF00005; sufficient; EV IPR013525; PF01061; sufficient; -- SN 7 ID N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase DN N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (EC 2.4.1.187) RQ 1 EV IPR004629; PF03808; sufficient; EV IPR004629; TIGR00696; sufficient; -- SN 8 ID Teichoic acid glycerol-phosphate primase DN Teichoic acid glycerol-phosphate primase (EC 2.7.8.44) RQ 1 EV IPR007554; PF04464; sufficient; -- SN 9 ID Teichoic acid glycerol-phosphate transferase DN Teichoic acid glycerol-phosphate transferase (EC 2.7.8.12) RQ 1 EV IPR007554; PF04464; sufficient; -- SN 10 ID Poly(glycerol-phosphate) alpha-glucosyltransferase DN Poly(glycerol-phosphate) alpha-glucosyltransferase (EC 2.4.1.52) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR015397; PF09318; sufficient; -- SN 11 ID Polyisoprenyl-major teichoic acid--peptidoglycan teichoic acid transferase DN Polyisoprenyl-major teichoic acid--peptidoglycan teichoic acid transferase (EC 2.7.8.M1) RQ 1 EV IPR004474; PF03816; sufficient; EV IPR004474; TIGR00350; sufficient; -- SN 12 ID UDP-N-acetylglucosamine 2-epimerase DN UDP-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) RQ 1 EV IPR029767; TIGR00236; sufficient; // AC GenProp1399 DE Superpathway of L-cysteine biosynthesis (mammalian) TP PATHWAY AU Caspi R TH 0 DC Superpathway of L-cysteine biosynthesis (mammalian) DR MetaCyc; PWY-6292; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID S-adenosylhomocysteine hydrolase DN S-adenosylhomocysteine hydrolase (EC 3.3.1.1) RQ 1 EV IPR000043; PF05221; sufficient; EV IPR000043; TIGR00936; sufficient; -- SN 2 ID Cystathionine beta-synthase DN Cystathionine beta-synthase (EC 4.2.1.22) RQ 1 EV IPR005857; TIGR01137; sufficient; // AC GenProp1400 DE Queuosine biosynthesis TP PATHWAY AU Caspi R, Keseler I TH 2 DC Queuosine biosynthesis DR MetaCyc; PWY-6700; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Epoxyqueuosine reductase DN Epoxyqueuosine reductase (EC 1.17.99.6) RQ 1 EV IPR004453; TIGR00276; sufficient; -- SN 2 ID tRNA-guanine transglycosylase DN tRNA-guanine transglycosylase (EC 2.4.2.29) RQ 1 EV IPR004803; TIGR00430; sufficient; -- SN 3 ID tRNA preQ134 S-adenosylmethionine ribosyltransferase-isomerase DN tRNA preQ134 S-adenosylmethionine ribosyltransferase-isomerase (EC 2.4.99.17) RQ 1 EV IPR003699; PF02547; sufficient; EV IPR003699; TIGR00113; sufficient; -- SN 4 ID 7-Cyano-7-deazaguanine reductase DN 7-Cyano-7-deazaguanine reductase (EC 1.7.1.13) RQ 1 EV IPR016428; TIGR03138; sufficient; EV IPR029500; PF14489; sufficient; // AC GenProp1401 DE Proline to cytochrome bo oxidase electron transfer TP PATHWAY AU Mackie A TH 0 DC Proline to cytochrome bo oxidase electron transfer DR MetaCyc; PWY0-1544; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; -- SN 2 ID Proline dehydrogenase DN Proline dehydrogenase (EC 1.5.5.2) RQ 1 EV IPR002872; PF01619; sufficient; EV IPR005933; TIGR01238; sufficient; EV IPR015590; PF00171; sufficient; EV IPR024082; PF14850; sufficient; // AC GenProp1402 DE Phenylethylamine degradation I TP PATHWAY AU Pellegrini-Toole A TH 0 DC Phenylethylamine degradation I DR MetaCyc; 2PHENDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Monoamine oxidase DN Monoamine oxidase (EC 1.4.3.21) RQ 1 EV IPR012854; PF07833; sufficient; EV IPR015798; PF01179; sufficient; EV IPR015800; PF02727; sufficient; EV IPR015802; PF02728; sufficient; -- SN 2 ID Phenylacetaldehyde dehydrogenase DN Phenylacetaldehyde dehydrogenase (EC 1.2.1.39) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1403 DE dTDP-N-acetylthomosamine biosynthesis TP PATHWAY AU Caspi R TH 2 DC dTDP-N-acetylthomosamine biosynthesis DR MetaCyc; PWY-7315; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID dTDP-glucose 4,6-dehydratase DN dTDP-glucose 4,6-dehydratase (EC 4.2.1.46) RQ 1 EV IPR005888; TIGR01181; sufficient; -- SN 2 ID Glucose-1-phosphate thymidylyltransferase DN Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) RQ 1 EV IPR005907; TIGR01207; sufficient; -- SN 3 ID dTDP-4-dehydro-6-deoxy-D-glucose transaminase DN dTDP-4-dehydro-6-deoxy-D-glucose transaminase (EC 2.6.1.59) RQ 1 EV IPR000653; PF01041; sufficient; EV IPR012749; TIGR02379; sufficient; -- SN 4 ID dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase DN dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase (EC 2.3.1.210) RQ 1 EV IPR012752; TIGR02382; sufficient; // AC GenProp1404 DE Superpathway of L-aspartate and L-asparagine biosynthesis TP PATHWAY AU N/A TH 2 DC Superpathway of L-aspartate and L-asparagine biosynthesis DR MetaCyc; ASPASN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Asparagine synthetase DN Asparagine synthetase (EC 6.3.1.1) RQ 1 EV IPR004618; PF03590; sufficient; EV IPR004618; TIGR00669; sufficient; EV IPR006426; TIGR01536; sufficient; -- SN 2 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 3 ID L-asparaginase DN L-asparaginase (EC 3.5.1.1) RQ 1 EV IPR006033; TIGR00519; sufficient; EV IPR004550; TIGR00520; sufficient; EV IPR000246; PF01112; sufficient; -- SN 4 ID Aspartate ammonia-lyase DN Aspartate ammonia-lyase (EC 4.3.1.1) RQ 1 EV IPR004708; TIGR00839; sufficient; // AC GenProp1405 DE Superpathway of branched chain amino acid biosynthesis TP PATHWAY AU LaRossa R TH 0 DC Superpathway of branched chain amino acid biosynthesis DR MetaCyc; BRANCHED-CHAIN-AA-SYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Isopropylmalate synthase DN 2-Isopropylmalate synthase (EC 2.3.3.13) RQ 1 EV IPR005671; TIGR00973; sufficient; -- SN 2 ID 2,3-Dihydroxy-isovalerate dehydratase DN 2,3-Dihydroxy-isovalerate dehydratase (EC 4.2.1.9) RQ 1 EV IPR000581; PF00920; sufficient; EV IPR004404; TIGR00110; sufficient; // AC GenProp1406 DE Superpathway of purine nucleotides de novo biosynthesis I TP PATHWAY AU Caspi R, Pellegrini-Toole A, Fulcher C TH 7 DC Superpathway of purine nucleotides de novo biosynthesis I DR MetaCyc; PWY-841; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID AMP kinase DN AMP kinase (EC 2.7.4.3) RQ 1 EV IPR006259; TIGR01351; sufficient; EV IPR006267; TIGR01360; sufficient; -- SN 2 ID Adenylosuccinate synthase DN Adenylosuccinate synthase (EC 6.3.4.4) RQ 1 EV IPR001114; PF00709; sufficient; EV IPR001114; TIGR00184; sufficient; -- SN 3 ID ADP reductase DN ADP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 4 ID Phosphoribosylaminoimidazole carboxylase DN Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) RQ 1 EV IPR000031; PF00731; sufficient; EV IPR000031; TIGR01162; sufficient; EV IPR003135; PF02222; sufficient; EV IPR005875; TIGR01161; sufficient; EV IPR028923; PF01259; sufficient; -- SN 5 ID Phosphoribosylformylglycinamide cyclo-ligase DN Phosphoribosylformylglycinamide cyclo-ligase (EC 6.3.3.1) RQ 1 EV IPR000115; TIGR00877; sufficient; EV IPR004733; TIGR00878; sufficient; EV IPR004607; TIGR00639; sufficient; -- SN 6 ID GDP reductase DN GDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 7 ID Guanylate kinase DN Guanylate kinase (EC 2.7.4.8) RQ 1 EV IPR017665; TIGR03263; sufficient; -- SN 8 ID Inosine-5'-monophosphate dehydrogenase DN Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) RQ 1 EV IPR005990; TIGR01302; sufficient; -- SN 9 ID IMP cyclohydrolase DN IMP cyclohydrolase (EC 3.5.4.10) RQ 1 EV IPR002695; PF01808; sufficient; EV IPR002695; TIGR00355; sufficient; // AC GenProp1407 DE Glycolysis II (from fructose 6-phosphate) TP PATHWAY AU Caspi R TH 9 DC Glycolysis II (from fructose 6-phosphate) DR MetaCyc; PWY-5484; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Enolase DN Enolase (EC 4.2.1.11) RQ 1 EV IPR000941; TIGR01060; sufficient; -- SN 2 ID 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) RQ 1 EV IPR005995; TIGR01307; sufficient; -- SN 3 ID 6-Phosphofructokinase DN 6-Phosphofructokinase (EC 2.7.1.11) RQ 1 EV IPR012828; TIGR02482; sufficient; EV IPR017583; TIGR03168; sufficient; -- SN 4 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase (EC 4.1.2.13) RQ 1 EV IPR002915; PF01791; sufficient; EV IPR000771; PF01116; sufficient; EV IPR000771; TIGR00167; sufficient; EV IPR006411; TIGR01520; sufficient; -- SN 5 ID Fructose 1,6-bisphosphatase DN Fructose 1,6-bisphosphatase (EC 3.1.3.11) RQ 1 EV IPR004464; PF03320; sufficient; EV IPR004464; TIGR00330; sufficient; EV IPR000150; TIGR00099; sufficient; EV IPR006379; TIGR01484; sufficient; EV IPR001952; PF00245; sufficient; -- SN 6 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 7 ID Pyruvate kinase DN Pyruvate kinase (EC 2.7.1.40) RQ 1 EV IPR001697; TIGR01064; sufficient; -- SN 8 ID Phosphoenolpyruvate synthetase DN Phosphoenolpyruvate synthetase (EC 2.7.9.2) RQ 1 EV IPR006319; TIGR01418; sufficient; -- SN 9 ID Phosphoglycerate kinase DN Phosphoglycerate kinase (EC 2.7.2.3) RQ 1 EV IPR001576; PF00162; sufficient; -- SN 10 ID 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.11) RQ 1 EV IPR005952; TIGR01258; sufficient; EV IPR013078; PF00300; sufficient; -- SN 11 ID Triose-phosphate isomerase DN Triose-phosphate isomerase (EC 5.3.1.1) RQ 1 EV IPR000652; PF00121; sufficient; EV IPR000652; TIGR00419; sufficient; // AC GenProp1408 DE 2-Oxoisovalerate decarboxylation to isobutanoyl-CoA TP PATHWAY AU Caspi R TH 1 DC 2-Oxoisovalerate decarboxylation to isobutanoyl-CoA DR MetaCyc; PWY-5046; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Keto-isovalerate dehydrogenase component DN 2-Keto-isovalerate dehydrogenase component (EC 1.2.4.4) RQ 1 EV IPR001017; PF00676; sufficient; EV IPR005475; PF02779; sufficient; EV IPR033248; PF02780; sufficient; -- SN 2 ID Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase DN Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) RQ 1 EV IPR000089; PF00364; sufficient; EV IPR001078; PF00198; sufficient; EV IPR004167; PF02817; sufficient; -- SN 3 ID Dihydrolipoyl dehydrogenase DN Dihydrolipoyl dehydrogenase (EC 1.8.1.4) RQ 1 EV IPR006258; TIGR01350; sufficient; // AC GenProp1409 DE Bis(guanylyl molybdenum cofactor) biosynthesis TP PATHWAY AU Caspi R TH 0 DC Bis(guanylyl molybdenum cofactor) biosynthesis DR MetaCyc; PWY-7639; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Bis(molybdenum cofactor) guanylyltransferase DN Bis(molybdenum cofactor) guanylyltransferase (EC 2.7.7.77) RQ 1 EV IPR013482; TIGR02665; sufficient; -- SN 2 ID Bis(molybdenum cofactor) synthase DN Bis(molybdenum cofactor) synthase RQ 1 EV IPR013482; TIGR02665; sufficient; // AC GenProp1410 DE Pyrimidine deoxyribonucleosides degradation TP PATHWAY AU Caspi R TH 1 DC Pyrimidine deoxyribonucleosides degradation DR MetaCyc; PWY-7181; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Deoxycytidine deaminase DN Deoxycytidine deaminase (EC 3.5.4.5) RQ 1 EV IPR006263; TIGR01355; sufficient; EV IPR006262; TIGR01354; sufficient; -- SN 2 ID Thymidine phosphorylase DN Thymidine phosphorylase (EC 2.4.2.4) RQ 1 EV IPR009664; PF06865; sufficient; EV IPR018090; TIGR02644; sufficient; EV IPR013465; TIGR02643; sufficient; -- SN 3 ID 2'-Deoxyuridine phosphorylase DN 2'-Deoxyuridine phosphorylase (EC 2.4.2.2) RQ 1 EV IPR010059; TIGR01719; sufficient; EV IPR018090; TIGR02644; sufficient; EV IPR013465; TIGR02643; sufficient; // AC GenProp1411 DE All-trans-farnesol biosynthesis TP PATHWAY AU Weerasinghe D TH 2 DC All-trans-farnesol biosynthesis DR MetaCyc; PWY-6859; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID Dimethylallyltransferase DN Dimethylallyltransferase (EC 2.5.1.1) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 3 ID Isopentenyl pyrophosphate isomerase DN Isopentenyl pyrophosphate isomerase (EC 5.3.3.2) RQ 1 EV IPR011876; TIGR02150; sufficient; -- SN 4 ID (2E,6E)-farnesyl diphosphate phosphatase DN (2E,6E)-farnesyl diphosphate phosphatase (EC 3.1.7.6) RQ 1 EV IPR001952; PF00245; sufficient; // AC GenProp1412 DE Glycogen degradation I TP PATHWAY AU Riley M TH 6 DC Glycogen degradation I DR MetaCyc; GLYCOCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Maltotriose 4-alpha-glucanotransferase DN Maltotriose 4-alpha-glucanotransferase (EC 2.4.1.25) RQ 1 EV IPR003385; PF02446; sufficient; EV IPR003385; TIGR00217; sufficient; -- SN 2 ID Glucokinase DN Glucokinase (EC 2.7.1.2) RQ 1 EV IPR003836; PF02685; sufficient; EV IPR003836; TIGR00749; sufficient; -- SN 3 ID Glycogen phosphorylase DN Glycogen phosphorylase (EC 2.4.1.1) RQ 1 EV IPR000811; PF00343; sufficient; EV IPR011833; TIGR02093; sufficient; -- SN 4 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005852; TIGR01132; sufficient; -- SN 5 ID Glycogen phosphorylase DN Glycogen phosphorylase (EC 2.4.1.1) RQ 1 EV IPR000811; PF00343; sufficient; EV IPR011833; TIGR02093; sufficient; -- SN 6 ID Limit dextrin alpha-1,6-glucohydrolase DN Limit dextrin alpha-1,6-glucohydrolase (EC 3.2.1.196) RQ 1 EV IPR011837; TIGR02100; sufficient; -- SN 7 ID Maltodextrin phosphorylase DN Maltodextrin phosphorylase (EC 2.4.1.1) RQ 1 EV IPR000811; PF00343; sufficient; EV IPR011833; TIGR02093; sufficient; -- SN 8 ID Maltodextrin glucosidase DN Maltodextrin glucosidase (EC 3.2.1.20) RQ 1 EV IPR004185; PF02903; sufficient; EV IPR006047; PF00128; sufficient; // AC GenProp1413 DE Mitochondrial L-carnitine shuttle TP PATHWAY AU Caspi R, Fulcher C TH 1 DC Mitochondrial L-carnitine shuttle DR MetaCyc; PWY-6111; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Carnitine palmitoyltransferase DN Carnitine palmitoyltransferase (EC 2.3.1.21) RQ 1 EV IPR000542; PF00755; sufficient; -- SN 2 ID Carnitine O-palmitoyltransferase DN Carnitine O-palmitoyltransferase (EC 2.3.1.21) RQ 1 EV IPR000542; PF00755; sufficient; -- SN 3 ID Transport of L-carnitine and O-acyl-L-carnitine DN Transport of L-carnitine and O-acyl-L-carnitine RQ 1 EV IPR018108; PF00153; sufficient; // AC GenProp1414 DE Glycine betaine degradation II (mammalian) TP PATHWAY AU Weerasinghe D, Caspi R TH 2 DC Glycine betaine degradation II (mammalian) DR MetaCyc; PWY-3661-1; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Betaine--homocysteine S-methyltransferase DN Betaine--homocysteine S-methyltransferase (EC 2.1.1.5) RQ 1 EV IPR003726; PF02574; sufficient; -- SN 2 ID Dimethylglycine dehydrogenase DN Dimethylglycine dehydrogenase (EC 1.5.8.4) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR006222; PF01571; sufficient; EV IPR013977; PF08669; sufficient; EV IPR032503; PF16350; sufficient; -- SN 3 ID 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase DN 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase (EC 2.1.2.1) RQ 1 EV IPR001085; PF00464; sufficient; -- SN 4 ID Sarcosine dehydrogenase DN Sarcosine dehydrogenase (EC 1.5.8) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR006222; PF01571; sufficient; EV IPR013977; PF08669; sufficient; EV IPR032503; PF16350; sufficient; // AC GenProp1415 DE Superpathway of fatty acid biosynthesis initiation (E. coli) TP PATHWAY AU Caspi R, Riley M TH 2 DC Superpathway of fatty acid biosynthesis initiation (E. coli) DR MetaCyc; FASYN-INITIAL-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetoacetyl-[acp] synthase DN Acetoacetyl-[acp] synthase (EC 2.3.1.179) RQ 1 EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; -- SN 2 ID Acetyl-CoA:ACP transacylase DN Acetyl-CoA:ACP transacylase (EC 2.3.1.86) RQ 1 EV IPR004655; TIGR00747; sufficient; -- SN 3 ID Malonyl-ACP decarboxylase DN Malonyl-ACP decarboxylase (EC 2.3.1) RQ 1 EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; -- SN 4 ID Malonyl CoA-acyl carrier protein transacylase, mitochondrial DN Malonyl CoA-acyl carrier protein transacylase, mitochondrial (EC 2.3.1.86) RQ 1 EV IPR004410; TIGR00128; sufficient; // AC GenProp1416 DE Allantoin degradation to glyoxylate III TP PATHWAY AU Caspi R TH 0 DC Allantoin degradation to glyoxylate III DR MetaCyc; PWY-5705; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ureidoglycolate urea-lyase DN Ureidoglycolate urea-lyase (EC 4.3.2.3) RQ 1 EV IPR007247; PF04115; sufficient; -- SN 2 ID Ureidoglycine aminohydrolase DN Ureidoglycine aminohydrolase (EC 3.5.3.26) RQ 1 EV IPR017627; TIGR03214; sufficient; // AC GenProp1417 DE Estradiol biosynthesis II TP PATHWAY AU Caspi R TH 1 DC Estradiol biosynthesis II DR MetaCyc; PWY-7306; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Testosterone 19-hydroxylase DN Testosterone 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID 19-Hydroxytestosterone 19-dehydrogenase DN 19-Hydroxytestosterone 19-dehydrogenase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID 19-Oxotestosterone 2-betahydroxylation DN 19-Oxotestosterone 2-betahydroxylation RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1418 DE UMP biosynthesis III TP PATHWAY AU Caspi R TH 4 DC UMP biosynthesis III DR MetaCyc; PWY-7791; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate carbamoyltransferase DN Aspartate carbamoyltransferase (EC 2.1.3.2) RQ 1 EV IPR002082; TIGR00670; sufficient; -- SN 2 ID Carbamoyl phosphate synthase DN Carbamoyl phosphate synthase (EC 6.3.5.5) RQ 1 EV IPR006274; TIGR01368; sufficient; EV IPR006275; TIGR01369; sufficient; -- SN 3 ID Dihydroorotase DN Dihydroorotase (EC 3.5.2.3) RQ 1 EV IPR004722; TIGR00857; sufficient; -- SN 4 ID Orotate phosphoribosyltransferase DN Orotate phosphoribosyltransferase (EC 2.4.2.10) RQ 1 EV IPR000836; PF00156; sufficient; EV IPR004467; TIGR00336; sufficient; -- SN 5 ID Dihydroorotate dehydrogenase DN Dihydroorotate dehydrogenase (EC 1.3.1.14) RQ 1 EV IPR001433; PF00175; sufficient; EV IPR019480; PF10418; sufficient; EV IPR005720; PF01180; sufficient; EV IPR005720; TIGR01037; sufficient; -- SN 6 ID Orotidine 5'-phosphate decarboxylase DN Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) RQ 1 EV IPR014732; TIGR01740; sufficient; // AC GenProp1419 DE Superpathway of L-methionine biosynthesis (transsulfuration) TP PATHWAY AU Caspi R TH 2 DC Superpathway of L-methionine biosynthesis (transsulfuration) DR MetaCyc; PWY-5347; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID Aspartate kinase DN Aspartate kinase (EC 2.7.2.4) RQ 1 EV IPR005260; TIGR00656; sufficient; -- SN 3 ID Homoserine dehydrogenase DN Homoserine dehydrogenase (EC 1.1.1.3) RQ 1 EV IPR001048; PF00696; sufficient; EV IPR001341; TIGR00657; sufficient; EV IPR001342; PF00742; sufficient; EV IPR002912; PF01842; sufficient; EV IPR005106; PF03447; sufficient; EV IPR027795; PF13840; sufficient; -- SN 4 ID Homoserine O-succinyltransferase DN Homoserine O-succinyltransferase (EC 2.3.1.46) RQ 1 EV IPR005697; PF04204; sufficient; EV IPR005697; TIGR01001; sufficient; // AC GenProp1420 DE Gibberellin inactivation II (methylation) TP PATHWAY AU Dreher K TH 2 DC Gibberellin inactivation II (methylation) DR MetaCyc; PWY-6477; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GA9 carboxyl methyltransferase DN GA9 carboxyl methyltransferase (EC 2.1.1.275) RQ 1 EV IPR005299; PF03492; sufficient; -- SN 2 ID GA4 carboxyl methyltransferase DN GA4 carboxyl methyltransferase (EC 2.1.1.276) RQ 1 EV IPR005299; PF03492; sufficient; -- SN 3 ID GA20 carboxyl methyltransferase DN GA20 carboxyl methyltransferase (EC 2.1.1) RQ 1 EV IPR005299; PF03492; sufficient; -- SN 4 ID GA4 carboxyl methyltransferase DN GA4 carboxyl methyltransferase (EC 2.1.1) RQ 1 EV IPR005299; PF03492; sufficient; // AC GenProp1421 DE Heme b biosynthesis I (aerobic) TP PATHWAY AU Caspi R, Fulcher C, Ying H TH 2 DC Heme b biosynthesis I (aerobic) DR MetaCyc; HEME-BIOSYNTHESIS-II; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Deferrochelatase DN Deferrochelatase (EC 4.99.1.1) RQ 1 EV IPR001015; PF00762; sufficient; EV IPR001015; TIGR00109; sufficient; -- SN 2 ID Protoporphyrinogen oxidase DN Protoporphyrinogen oxidase (EC 1.3.3.4) RQ 1 EV IPR004572; TIGR00562; sufficient; EV IPR005265; PF03653; sufficient; -- SN 3 ID Coproporphyrinogen III oxidase DN Coproporphyrinogen III oxidase (EC 1.3.3.3) RQ 1 EV IPR001260; PF01218; sufficient; -- SN 4 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase (EC 4.1.1.37) RQ 1 EV IPR006361; TIGR01464; sufficient; // AC GenProp1423 DE Sphingolipid biosynthesis (yeast) TP PATHWAY AU Caspi R, Hong E TH 6 DC Sphingolipid biosynthesis (yeast) DR MetaCyc; SPHINGOLIPID-SYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Ketodihydrosphingosine reductase DN 3-Ketodihydrosphingosine reductase (EC 1.1.1.102) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID Dihydrospingosine C-4 hydroxylase DN Dihydrospingosine C-4 hydroxylase (EC 1.14.18.5) RQ 1 EV IPR006694; PF04116; sufficient; -- SN 3 ID 4-Hydroxysphinganine N-acyltransferase DN 4-Hydroxysphinganine N-acyltransferase (EC 2.3.1.24) RQ 1 EV IPR006634; PF03798; sufficient; EV IPR013599; PF08390; sufficient; -- SN 4 ID Ceramide very long chain fatty acid hydroxylase DN Ceramide very long chain fatty acid hydroxylase (EC 1.14.18.6) RQ 1 EV IPR001199; PF00173; sufficient; EV IPR006694; PF04116; sufficient; -- SN 5 ID Inositol phosphoceramide synthase DN Inositol phosphoceramide synthase (EC 2.7.1) RQ 1 EV IPR013862; PF08552; sufficient; EV IPR026841; PF14378; sufficient; -- SN 6 ID Inositol phosphorylceramide mannosyltransferase DN Inositol phosphorylceramide mannosyltransferase (EC 2.4.1) RQ 1 EV IPR031581; PF16965; sufficient; -- SN 7 ID Mannosyl-inositol-phosphoceramide inositolphosphotransferase DN Mannosyl-inositol-phosphoceramide inositolphosphotransferase (EC 2.7.1) RQ 1 EV IPR026841; PF14378; sufficient; -- SN 8 ID Serine palmitoyltransferase DN Serine palmitoyltransferase (EC 2.3.1.50) RQ 1 EV IPR004839; PF00155; sufficient; // AC GenProp1424 DE Two-component alkanesulfonate monooxygenase TP PATHWAY AU Pellegrini-Toole A, Keseler I TH 0 DC Two-component alkanesulfonate monooxygenase DR MetaCyc; ALKANEMONOX-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID FMN reductase (NADPH) DN FMN reductase (NADPH) (EC 1.5.1.38) RQ 1 EV IPR020048; TIGR03567; sufficient; -- SN 2 ID Alkanesulfonate monooxygenase DN Alkanesulfonate monooxygenase (EC 1.14.14.5) RQ 1 EV IPR019911; TIGR03565; sufficient; // AC GenProp1425 DE Pyruvate fermentation to ethanol I TP PATHWAY AU Caspi R TH 1 DC Pyruvate fermentation to ethanol I DR MetaCyc; PWY-5480; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR003361; TIGR03215; sufficient; -- SN 2 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; EV IPR015590; PF00171; sufficient; -- SN 3 ID Pyruvate formate lyase DN Pyruvate formate lyase (EC 2.3.1.54) RQ 1 EV IPR005949; TIGR01255; sufficient; // AC GenProp1426 DE Aerobic respiration II (cytochrome c) (yeast) TP PATHWAY AU Foerster H TH 1 DC Aerobic respiration II (cytochrome c) (yeast) DR MetaCyc; PWY-7279; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ubiquinol-cytochrome C oxidoreductase DN Ubiquinol-cytochrome C oxidoreductase (EC 1.10.2.2) RQ 1 EV IPR019182; PF09796; sufficient; -- SN 2 ID Cytochrome c oxidase DN Cytochrome c oxidase (EC 1.9.3.1) RQ 1 EV IPR000883; PF00115; sufficient; EV IPR002124; PF01215; sufficient; EV IPR001349; PF02046; sufficient; EV IPR003204; PF02284; sufficient; EV IPR003213; PF02297; sufficient; EV IPR004202; PF02935; sufficient; EV IPR004203; PF02936; sufficient; -- SN 3 ID NADH:ubiquinone oxidoreductase 1 (external) DN NADH:ubiquinone oxidoreductase 1 (external) (EC 1.6.5.9) RQ 1 EV IPR023753; PF07992; sufficient; // AC GenProp1427 DE UMP biosynthesis I TP PATHWAY AU Foerster H, Caspi R TH 4 DC UMP biosynthesis I DR MetaCyc; PWY-5686; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate carbamoyltransferase DN Aspartate carbamoyltransferase (EC 2.1.3.2) RQ 1 EV IPR002082; TIGR00670; sufficient; EV IPR002801; TIGR00240; sufficient; EV IPR006274; TIGR01368; sufficient; EV IPR006275; TIGR01369; sufficient; -- SN 2 ID Carbamoyl phosphate synthase DN Carbamoyl phosphate synthase (EC 6.3.5.5) RQ 1 EV IPR006275; TIGR01369; sufficient; EV IPR006274; TIGR01368; sufficient; EV IPR002082; TIGR00670; sufficient; -- SN 3 ID Dihydroorotase DN Dihydroorotase (EC 3.5.2.3) RQ 1 EV IPR004721; TIGR00856; sufficient; EV IPR002082; TIGR00670; sufficient; EV IPR006274; TIGR01368; sufficient; EV IPR006275; TIGR01369; sufficient; -- SN 4 ID Dihydroorotate dehydrogenase DN Dihydroorotate dehydrogenase (EC 1.3.5.2) RQ 1 EV IPR005719; TIGR01036; sufficient; -- SN 5 ID Orotate phosphoribosyltransferase DN Orotate phosphoribosyltransferase (EC 2.4.2.10) RQ 1 EV IPR014732; TIGR01740; sufficient; -- SN 6 ID Orotidine 5'-phosphate decarboxylase DN Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) RQ 1 EV IPR014732; TIGR01740; sufficient; // AC GenProp1428 DE L-arginine degradation I (arginase pathway) TP PATHWAY AU Caspi R, Ying H TH 1 DC L-arginine degradation I (arginase pathway) DR MetaCyc; ARGASEDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arginase DN Arginase (EC 3.5.3.1) RQ 1 EV IPR006035; PF00491; sufficient; EV IPR014033; TIGR01229; sufficient; -- SN 2 ID Ornithine--oxo-glutarate aminotransferase DN Ornithine--oxo-glutarate aminotransferase (EC 2.6.1.13) RQ 1 EV IPR005814; PF00202; sufficient; EV IPR010164; TIGR01885; sufficient; -- SN 3 ID 1-Pyrroline-5-carboxylate dehydrogenase DN 1-Pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) RQ 1 EV IPR005931; TIGR01236; sufficient; // AC GenProp1429 DE GDP-L-fucose biosynthesis I (from GDP-D-mannose) TP PATHWAY AU N/A TH 0 DC GDP-L-fucose biosynthesis I (from GDP-D-mannose) DR MetaCyc; PWY-66; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GDP-fucose synthase DN GDP-fucose synthase (EC 1.1.1.271) RQ 1 EV IPR001509; PF01370; sufficient; -- SN 2 ID GDP-mannose 4,6-dehydratase DN GDP-mannose 4,6-dehydratase (EC 4.2.1.47) RQ 1 EV IPR006368; TIGR01472; sufficient; // AC GenProp1430 DE Adenine and adenosine salvage II TP PATHWAY AU Caspi R TH 0 DC Adenine and adenosine salvage II DR MetaCyc; PWY-6605; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine nucleosidase DN Adenosine nucleosidase (EC 3.2.2.7) RQ 1 EV IPR001910; PF01156; sufficient; -- SN 2 ID Adenine phosphoribosyltransferase DN Adenine phosphoribosyltransferase (EC 2.4.2.7) RQ 1 EV IPR005764; TIGR01090; sufficient; // AC GenProp1431 DE L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) TP PATHWAY AU Caspi R, Ying H TH 1 DC L-arginine degradation IV (arginine decarboxylase/agmatine deiminase DC pathway) DR MetaCyc; ARGDEG-III-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Agmatine deiminase DN Agmatine deiminase (EC 3.5.3.12) RQ 1 EV IPR007466; PF04371; sufficient; EV IPR017754; TIGR03380; sufficient; -- SN 2 ID Arginine decarboxylase DN Arginine decarboxylase (EC 4.1.1.19) RQ 1 EV IPR002985; TIGR01273; sufficient; EV IPR022643; PF00278; sufficient; EV IPR022644; PF02784; sufficient; -- SN 3 ID N-carbamolyputrescine amidohydrolase DN N-carbamolyputrescine amidohydrolase (EC 3.5.1.53) RQ 1 EV IPR003010; PF00795; sufficient; EV IPR017755; TIGR03381; sufficient; // AC GenProp1432 DE Mevalonate pathway I TP PATHWAY AU Pellegrini-Toole A TH 5 DC Mevalonate pathway I DR MetaCyc; PWY-922; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Hydroxy-3-methylglutaryl-coenzyme A reductase DN 3-Hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) RQ 1 EV IPR002202; PF00368; sufficient; EV IPR004554; TIGR00533; sufficient; EV IPR004816; TIGR00920; sufficient; -- SN 2 ID Acetoacetyl-CoA thiolase DN Acetoacetyl-CoA thiolase (EC 2.3.1.9) RQ 1 EV IPR002155; TIGR01930; sufficient; -- SN 3 ID Mevalonate diphosphate decarboxylase DN Mevalonate diphosphate decarboxylase (EC 4.1.1.33) RQ 1 EV IPR029765; TIGR01240; sufficient; -- SN 4 ID Hydroxymethyl glutaryl-CoA synthase DN Hydroxymethyl glutaryl-CoA synthase (EC 2.3.3.10) RQ 1 EV IPR010122; TIGR01833; sufficient; -- SN 5 ID Isopentenyl pyrophosphate isomerase DN Isopentenyl pyrophosphate isomerase (EC 5.3.3.2) RQ 1 EV IPR011876; TIGR02150; sufficient; -- SN 6 ID Mevalonate kinase DN Mevalonate kinase (EC 2.7.1.36) RQ 1 EV IPR006205; TIGR00549; sufficient; -- SN 7 ID Phosphomevalonate kinase DN Phosphomevalonate kinase (EC 2.7.4.2) RQ 1 EV IPR016005; TIGR01219; sufficient; EV IPR005919; PF04275; sufficient; EV IPR005919; TIGR01223; sufficient; // AC GenProp1433 DE Aminopropylcadaverine biosynthesis TP PATHWAY AU Johnson A TH 0 DC Aminopropylcadaverine biosynthesis DR MetaCyc; PWY0-1303; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-lysine decarboxylase DN L-lysine decarboxylase (EC 4.1.1.18) RQ 1 EV IPR000310; PF01276; sufficient; EV IPR005308; PF03709; sufficient; EV IPR008286; PF03711; sufficient; -- SN 2 ID Aminopropylcadaverine synthase DN Aminopropylcadaverine synthase (EC 2.5.1) RQ 1 EV IPR001045; TIGR00417; sufficient; // AC GenProp1434 DE Putrescine degradation II TP PATHWAY AU Keseler I, Caspi R TH 2 DC Putrescine degradation II DR MetaCyc; PWY0-1221; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutamate-putrescine ligase DN Glutamate-putrescine ligase (EC 6.3.1.11) RQ 1 EV IPR008146; PF00120; sufficient; -- SN 2 ID Gamma-glutamylputrescine oxidase DN Gamma-glutamylputrescine oxidase (EC 1.4.3.M3) RQ 1 EV IPR006076; PF01266; sufficient; -- SN 3 ID Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DN Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.99) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 4 ID Gamma-glutamyl-gamma-aminobutyrate hydrolase DN Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) RQ 1 EV IPR011697; PF07722; sufficient; // AC GenProp1436 DE Superpathway of mycolate biosynthesis TP PATHWAY AU Sarker M TH 10 DC Superpathway of mycolate biosynthesis DR MetaCyc; PWY-6113; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Beta-ketoacyl-[acyl-carrier-protein] synthase DN Beta-ketoacyl-[acyl-carrier-protein] synthase (EC 2.3.1.180) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 2 ID 3-Oxo-cerotoyl-[acp] synthase DN 3-Oxo-cerotoyl-[acp] synthase (EC 2.3.1.41) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 3 ID 3-Oxocerotoyl-[acp] reductase DN 3-Oxocerotoyl-[acp] reductase (EC 1.1.1.100) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 4 ID 3-Hydroxycerotyl-[acp] dehydrase DN 3-Hydroxycerotyl-[acp] dehydrase (EC 4.2.1.59) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 5 ID Trans-hexacos-2-enoyl-[acp] reductase DN Trans-hexacos-2-enoyl-[acp] reductase (EC 1.3.1.9) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 6 ID Acetoacetyl-[acyl-carrier protein] reductase DN Acetoacetyl-[acyl-carrier protein] reductase (EC 2.3.1.86) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 7 ID 3-Oxo-stearoyl-[acyl-carrier protein] synthase DN 3-Oxo-stearoyl-[acyl-carrier protein] synthase (EC 2.3.1.41) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 8 ID Trans-octadec-2-enoyl-[acyl-carrier-protein] reductase DN Trans-octadec-2-enoyl-[acyl-carrier-protein] reductase (EC 1.3.1.9) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 9 ID Trans hexadecenoyl-[acp] reductase DN Trans hexadecenoyl-[acp] reductase (EC 1.3.1.9) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 10 ID 3-Oxo-arachidoyl-[acp] synthase DN 3-Oxo-arachidoyl-[acp] synthase (EC 2.3.1.41) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 11 ID Trans-tetracos-2-enoyl-[acyl-carrier protein] reductase DN Trans-tetracos-2-enoyl-[acyl-carrier protein] reductase (EC 1.3.1.9) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; -- SN 12 ID Cerotoyl-[acyl-carrier protein] reductase DN Cerotoyl-[acyl-carrier protein] reductase (EC 2.3.1) RQ 1 EV IPR002539; PF01575; sufficient; EV IPR013565; PF08354; sufficient; EV IPR014030; PF00109; sufficient; EV IPR014031; PF02801; sufficient; EV IPR014043; PF00698; sufficient; // AC GenProp1437 DE Ethanol degradation III TP PATHWAY AU N/A TH 1 DC Ethanol degradation III DR MetaCyc; PWY66-161; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetyl CoA synthetase DN Acetyl CoA synthetase (EC 6.2.1.1) RQ 1 EV IPR011904; TIGR02188; sufficient; -- SN 2 ID Ethanol monooxygenase DN Ethanol monooxygenase (EC 1.14.14) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.3) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1438 DE Pentose phosphate pathway TP PATHWAY AU Ingraham J TH 1 DC Pentose phosphate pathway DR MetaCyc; PENTOSE-P-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ribose-5-phosphate isomerase A DN Ribose-5-phosphate isomerase A (EC 5.3.1.6) RQ 1 EV IPR004788; PF06026; sufficient; EV IPR004788; TIGR00021; sufficient; EV IPR003500; PF02502; sufficient; EV IPR003500; TIGR00689; sufficient; EV IPR004785; TIGR01120; sufficient; -- SN 2 ID Ribulose-phosphate 3-epimerase DN Ribulose-phosphate 3-epimerase (EC 5.1.3.1) RQ 1 EV IPR000056; PF00834; sufficient; EV IPR000056; TIGR01163; sufficient; -- SN 3 ID 6-Phosphogluconate dehydrogenase, decarboxylating DN 6-Phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) RQ 1 EV IPR006113; TIGR00873; sufficient; // AC GenProp1439 DE 2-Oxobutanoate degradation I TP PATHWAY AU Caspi R TH 2 DC 2-Oxobutanoate degradation I DR MetaCyc; PWY-5130; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Methylmalonyl-CoA epimerase DN Methylmalonyl-CoA epimerase (EC 5.1.99.1) RQ 1 EV IPR017515; TIGR03081; sufficient; -- SN 2 ID Methylmalonyl-CoA mutase DN Methylmalonyl-CoA mutase (EC 5.4.99.2) RQ 1 EV IPR006098; TIGR00641; sufficient; EV IPR006099; PF01642; sufficient; EV IPR006158; PF02310; sufficient; EV IPR006159; TIGR00640; sufficient; -- SN 3 ID Propionyl-CoA carboxylase DN Propionyl-CoA carboxylase (EC 6.4.1.3) RQ 1 EV IPR000089; PF00364; sufficient; EV IPR005479; PF02786; sufficient; EV IPR005481; PF00289; sufficient; EV IPR005482; PF02785; sufficient; -- SN 4 ID 2-Oxobutanoate dehydrogenase DN 2-Oxobutanoate dehydrogenase (EC 1.2.1.M8) RQ 1 EV IPR006258; TIGR01350; sufficient; // AC GenProp1441 DE Acetoacetate degradation (to acetyl CoA) TP PATHWAY AU Riley M, Ingraham J TH 0 DC Acetoacetate degradation (to acetyl CoA) DR MetaCyc; ACETOACETATE-DEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetoacetyl-CoA transferase DN Acetoacetyl-CoA transferase (EC 2.8.3.9) RQ 1 EV IPR004165; PF01144; sufficient; -- SN 2 ID Acetoacetyl-CoA thiolase DN Acetoacetyl-CoA thiolase (EC 2.3.1.9) RQ 1 EV IPR002155; TIGR01930; sufficient; // AC GenProp1442 DE Protein O-[N-acetyl]-glucosylation TP PATHWAY AU Caspi R TH 0 DC Protein O-[N-acetyl]-glucosylation DR MetaCyc; PWY-7437; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-N-acetylglucosamine:glycoprotein beta-N-acetylglucosaminyltransferase DN UDP-N-acetylglucosamine:glycoprotein beta-N-acetylglucosaminyltransferase (EC 2.4.1.255) RQ 1 EV IPR029489; PF13844; sufficient; -- SN 2 ID [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase DN [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase (EC 3.2.1.169) RQ 1 EV IPR011496; PF07555; sufficient; // AC GenProp1443 DE UDP-N-acetyl-D-glucosamine biosynthesis I TP PATHWAY AU Keseler I TH 3 DC UDP-N-acetyl-D-glucosamine biosynthesis I DR MetaCyc; UDPNAGSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucosamine-1-phosphate acetyltransferase DN Glucosamine-1-phosphate acetyltransferase (EC 2.3.1.157) RQ 1 EV IPR005882; TIGR01173; sufficient; -- SN 2 ID Phosphoglucosamine mutase DN Phosphoglucosamine mutase (EC 5.4.2.10) RQ 1 EV IPR006352; TIGR01455; sufficient; -- SN 3 ID Glutamine:fructose-6-phosphate amidotransferase DN Glutamine:fructose-6-phosphate amidotransferase (EC 2.6.1.16) RQ 1 EV IPR005855; TIGR01135; sufficient; -- SN 4 ID UDP-N-acetylglucosamine pyrophosphorylase DN UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) RQ 1 EV IPR005882; TIGR01173; sufficient; -- SN 5 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; // AC GenProp1444 DE Complex N-linked glycan biosynthesis (plants) TP PATHWAY AU Caspi R TH 9 DC Complex N-linked glycan biosynthesis (plants) DR MetaCyc; PWY-7920; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase DN Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) RQ 1 EV IPR004139; PF03071; sufficient; -- SN 2 ID Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase DN Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) RQ 1 EV IPR007754; PF05060; sufficient; -- SN 3 ID Glycoprotein 2-beta-D-xylosyltransferase DN Glycoprotein 2-beta-D-xylosyltransferase (EC 2.4.2.38) RQ 1 EV IPR007657; PF04577; sufficient; -- SN 4 ID Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase DN Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase (EC 3.2.1.114) RQ 1 EV IPR000602; PF01074; sufficient; EV IPR011682; PF07748; sufficient; EV IPR015341; PF09261; sufficient; -- SN 5 ID Glycoprotein 2-beta-D-xylosyltransferase DN Glycoprotein 2-beta-D-xylosyltransferase (EC 2.4.2.38) RQ 1 EV IPR007657; PF04577; sufficient; -- SN 6 ID Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase DN Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase (EC 3.2.1.114) RQ 1 EV IPR000602; PF01074; sufficient; EV IPR011682; PF07748; sufficient; EV IPR015341; PF09261; sufficient; -- SN 7 ID Glycoprotein 2-beta-D-xylosyltransferase DN Glycoprotein 2-beta-D-xylosyltransferase (EC 2.4.2.38) RQ 1 EV IPR007657; PF04577; sufficient; -- SN 8 ID Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase DN Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) RQ 1 EV IPR007754; PF05060; sufficient; -- SN 9 ID Glycoprotein 3-alpha-L-fucosyltransferase DN Glycoprotein 3-alpha-L-fucosyltransferase (EC 2.4.1.214) RQ 1 EV IPR001503; PF00852; sufficient; -- SN 10 ID N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase DN N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase (EC 2.4.1.86) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 11 ID 3-Galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase DN 3-Galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase (EC 2.4.1.65) RQ 1 EV IPR001503; PF00852; sufficient; // AC GenProp1445 DE L-threonine degradation IV TP PATHWAY AU Caspi R TH 0 DC L-threonine degradation IV DR MetaCyc; PWY-5436; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR003361; TIGR03215; sufficient; -- SN 2 ID L-threonine aldolase DN L-threonine aldolase (EC 4.1.2.5) RQ 1 EV IPR001597; PF01212; sufficient; // AC GenProp1446 DE Adenosine deoxyribonucleotides de novo biosynthesis II TP PATHWAY AU Caspi R TH 2 DC Adenosine deoxyribonucleotides de novo biosynthesis II DR MetaCyc; PWY-7220; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ADP reductase DN ADP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 2 ID DADP kinase DN DADP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; -- SN 3 ID ATP reductase DN ATP reductase (EC 1.1.98.6) RQ 1 EV IPR012833; PF13597; sufficient; EV IPR012833; TIGR02487; sufficient; -- SN 4 ID ADP reductase DN ADP reductase (EC 1.17.4.1) RQ 1 EV IPR026459; TIGR04170; sufficient; EV IPR000358; PF00268; sufficient; EV IPR026494; TIGR04171; sufficient; // AC GenProp1447 DE Methanogenesis from methylthiopropanoate TP PATHWAY AU Caspi R TH 0 DC Methanogenesis from methylthiopropanoate DR MetaCyc; PWY-5260; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID [methyl-Co(III) methanethiol-specific corrinoid protein]:coenzyme M methyltransferase DN [methyl-Co(III) methanethiol-specific corrinoid protein]:coenzyme M methyltransferase (EC 2.1.1.251) RQ 1 EV IPR000257; PF01208; sufficient; -- SN 2 ID 3-(Methylthio)propionate:MtpC protein methyltransferase DN 3-(Methylthio)propionate:MtpC protein methyltransferase (EC 2.1.1.251) RQ 1 EV IPR000257; PF01208; sufficient; // AC GenProp1448 DE UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) TP PATHWAY AU Caspi R TH 6 DC UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate DC containing) DR MetaCyc; PWY-6387; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-alanine-D-alanine ligase DN D-alanine-D-alanine ligase (EC 6.3.2.4) RQ 1 EV IPR005905; TIGR01205; sufficient; -- SN 2 ID Glutamate racemase DN Glutamate racemase (EC 5.1.1.3) RQ 1 EV IPR004391; TIGR00067; sufficient; EV IPR015942; PF01177; sufficient; -- SN 3 ID UDP-N-acetylmuramate-L-alanine ligase DN UDP-N-acetylmuramate-L-alanine ligase (EC 6.3.2.8) RQ 1 EV IPR005758; TIGR01082; sufficient; -- SN 4 ID UDP-N-acetylmuramoylalanine--D-glutamate ligase DN UDP-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) RQ 1 EV IPR005762; TIGR01087; sufficient; -- SN 5 ID UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate ligase DN UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate ligase (EC 6.3.2.10) RQ 1 EV IPR005863; TIGR01143; sufficient; -- SN 6 ID UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase DN UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase (EC 6.3.2.13) RQ 1 EV IPR005761; TIGR01085; sufficient; -- SN 7 ID UDP-N-acetylglucosamine 1-carboxyvinyltransferase DN UDP-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) RQ 1 EV IPR005750; TIGR01072; sufficient; -- SN 8 ID UDP-N-acetylenolpyruvoylglucosamine reductase DN UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) RQ 1 EV IPR003170; TIGR00179; sufficient; // AC GenProp1449 DE D-fructuronate degradation TP PATHWAY AU Caspi R TH 2 DC D-fructuronate degradation DR MetaCyc; PWY-7242; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Dehydro-3-deoxygluconate kinase DN 2-Dehydro-3-deoxygluconate kinase (EC 2.7.1.45) RQ 1 EV IPR011611; PF00294; sufficient; -- SN 2 ID 2-Dehydro-3-deoxy-phosphogluconate aldolase DN 2-Dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) RQ 1 EV IPR000887; PF01081; sufficient; EV IPR000887; TIGR01182; sufficient; -- SN 3 ID D-mannonate dehydratase DN D-mannonate dehydratase (EC 4.2.1.8) RQ 1 EV IPR004628; PF03786; sufficient; EV IPR004628; TIGR00695; sufficient; -- SN 4 ID D-mannonate dehydrogenase DN D-mannonate dehydrogenase (EC 1.1.1.57) RQ 1 EV IPR013118; PF08125; sufficient; EV IPR013131; PF01232; sufficient; // AC GenProp1450 DE L-tryptophan biosynthesis TP PATHWAY AU Fulcher C TH 4 DC L-tryptophan biosynthesis DR MetaCyc; TRPSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Anthranilate synthase DN Anthranilate synthase (EC 4.1.3.27) RQ 1 EV IPR005257; TIGR00565; sufficient; EV IPR005940; TIGR01245; sufficient; EV IPR010116; TIGR01820; sufficient; -- SN 2 ID Indole-3-glycerol phosphate synthase DN Indole-3-glycerol phosphate synthase (EC 4.1.1.48) RQ 1 EV IPR013798; PF00218; sufficient; EV IPR001240; PF00697; sufficient; -- SN 3 ID Phosphoribosylanthranilate isomerase DN Phosphoribosylanthranilate isomerase (EC 5.3.1.24) RQ 1 EV IPR001240; PF00697; sufficient; EV IPR013798; PF00218; sufficient; -- SN 4 ID Anthranilate phosphoribosyltransferase DN Anthranilate phosphoribosyltransferase (EC 2.4.2.18) RQ 1 EV IPR005940; TIGR01245; sufficient; -- SN 5 ID Indole-3-glycerol phosphate lyase DN Indole-3-glycerol phosphate lyase (EC 4.1.2.8) RQ 1 EV IPR002028; PF00290; sufficient; EV IPR002028; TIGR00262; sufficient; -- SN 6 ID Tryptophan synthase DN Tryptophan synthase (EC 4.2.1.122) RQ 1 EV IPR006316; TIGR01415; sufficient; EV IPR006654; TIGR00263; sufficient; // AC GenProp1451 DE Beta-carotene biosynthesis TP PATHWAY AU Caspi R TH 0 DC Beta-carotene biosynthesis DR MetaCyc; PWY-5943; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lycopene beta-monocyclase DN Lycopene beta-monocyclase (EC 5.5.1.19) RQ 1 EV IPR010108; TIGR01790; sufficient; -- SN 2 ID Gamma-carotene beta-cyclase DN Gamma-carotene beta-cyclase (EC 5.5.1.19) RQ 1 EV IPR010108; TIGR01790; sufficient; // AC GenProp1452 DE Gamma-linolenate biosynthesis II (animals) TP PATHWAY AU Caspi R TH 0 DC Gamma-linolenate biosynthesis II (animals) DR MetaCyc; PWY-6000; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Linoleoyl-CoA 6-desaturase DN Linoleoyl-CoA 6-desaturase (EC 1.14.19.3) RQ 1 EV IPR001199; PF00173; sufficient; EV IPR005804; PF00487; sufficient; -- SN 2 ID Linoleate:CoA ligase (AMP-forming) DN Linoleate:CoA ligase (AMP-forming) (EC 6.2.1.3) RQ 1 EV IPR000873; PF00501; sufficient; EV IPR025110; PF13193; sufficient; // AC GenProp1453 DE Cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) TP PATHWAY AU Fulcher C TH 0 DC Cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) DR MetaCyc; PWY-7509; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylethanolamine synthase DN Phosphatidylethanolamine synthase RQ 1 EV IPR025202; PF13091; sufficient; -- SN 2 ID Cardiolipin synthase DN Cardiolipin synthase (EC 2.7.8.41) RQ 1 EV IPR025202; PF13091; sufficient; // AC GenProp1454 DE Adenosylcobalamin biosynthesis from adenosylcobinamide-GDP I TP PATHWAY AU Caspi R TH 1 DC Adenosylcobalamin biosynthesis from adenosylcobinamide-GDP I DR MetaCyc; PWY-5509; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cobalamin 5'-phosphate synthase DN Cobalamin 5'-phosphate synthase (EC 2.7.8.26) RQ 1 EV IPR003805; PF02654; sufficient; EV IPR003805; TIGR00317; sufficient; -- SN 2 ID Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase DN Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) RQ 1 EV IPR017846; TIGR03160; sufficient; -- SN 3 ID Adenosylcobalamin 5'-phosphate phosphatase DN Adenosylcobalamin 5'-phosphate phosphatase (EC 3.1.3.73) RQ 1 EV IPR013078; PF00300; sufficient; EV IPR017578; TIGR03162; sufficient; // AC GenProp1455 DE Protein O-mannosylation III (mammals, core M3) TP PATHWAY AU Caspi R TH 3 DC Protein O-mannosylation III (mammals, core M3) DR MetaCyc; PWY-7979; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dolichyl-phosphate-mannose-protein mannosyltransferase DN Dolichyl-phosphate-mannose-protein mannosyltransferase (EC 2.4.1.109) RQ 1 EV IPR003342; PF02366; sufficient; EV IPR016093; PF02815; sufficient; EV IPR032421; PF16192; sufficient; -- SN 2 ID Dolichyl-phosphate mannose synthase DN Dolichyl-phosphate mannose synthase (EC 2.4.1.83) RQ 1 EV IPR009914; PF07297; sufficient; EV IPR013174; PF08285; sufficient; -- SN 3 ID Protein O-mannose kinase DN Protein O-mannose kinase (EC 2.7.1.183) RQ 1 EV IPR001245; PF07714; sufficient; -- SN 4 ID Beta-1,3-N-acetylgalactosaminyltransferase DN Beta-1,3-N-acetylgalactosaminyltransferase (EC 2.4.1.313) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 5 ID Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase DN Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase (EC 2.4.1.312) RQ 1 EV IPR007657; PF04577; sufficient; // AC GenProp1457 DE Thiamine diphosphate biosynthesis I (E. coli) TP PATHWAY AU Caspi R TH 0 DC Thiamine diphosphate biosynthesis I (E. coli) DR MetaCyc; PWY-6894; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Thiamin phosphate synthase DN Thiamin phosphate synthase (EC 2.5.1.3) RQ 1 EV IPR003733; PF02581; sufficient; EV IPR003733; TIGR00693; sufficient; -- SN 2 ID Thiamine-monophosphate kinase DN Thiamine-monophosphate kinase (EC 2.7.4.16) RQ 1 EV IPR006283; TIGR01379; sufficient; // AC GenProp1458 DE Cinnamate and 3-hydroxycinnamate degradation to 2-hydroxypentadienoate TP PATHWAY AU Caspi R TH 3 DC Cinnamate and 3-hydroxycinnamate degradation to 2-hydroxypentadienoate DR MetaCyc; PWY-6690; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Hydroxy-trans-cinnamate hydroxylase DN 3-Hydroxy-trans-cinnamate hydroxylase (EC 1.14.13.127) RQ 1 EV IPR002938; PF01494; sufficient; -- SN 2 ID 2-Hydroxy-6-oxononatrienedioate hydrolase DN 2-Hydroxy-6-oxononatrienedioate hydrolase (EC 3.7.1.14) RQ 1 EV IPR000073; PF12697; sufficient; -- SN 3 ID Cis-3-(2-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol dehydrogenase DN Cis-3-(2-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol dehydrogenase (EC 1.3.1.87) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 4 ID Cinnamate dioxygenase DN Cinnamate dioxygenase (EC 1.14.12.19) RQ 1 EV IPR000391; PF00866; sufficient; -- SN 5 ID 2,3-Dihydroxycinnamate dioxygenase DN 2,3-Dihydroxycinnamate dioxygenase (EC 1.13.11.16) RQ 1 EV IPR004183; PF02900; sufficient; // AC GenProp1459 DE D-galactose detoxification TP PATHWAY AU Caspi R TH 1 DC D-galactose detoxification DR MetaCyc; PWY-3821; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Galactokinase DN Galactokinase (EC 2.7.1.6) RQ 1 EV IPR000705; TIGR00131; sufficient; -- SN 2 ID UDP-galactose 4-epimerase DN UDP-galactose 4-epimerase (EC 5.1.3.2) RQ 1 EV IPR005886; TIGR01179; sufficient; -- SN 3 ID UDP-galactose pyrophosphorylase DN UDP-galactose pyrophosphorylase (EC 2.7.7.10) RQ 1 EV IPR002618; PF01704; sufficient; // AC GenProp1460 DE D-myo-inositol (3,4,5,6)-tetrakisphosphate biosynthesis TP PATHWAY AU Caspi R TH 2 DC D-myo-inositol (3,4,5,6)-tetrakisphosphate biosynthesis DR MetaCyc; PWY-6365; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol 1,3,4-triphosphate 6 kinase DN Inositol 1,3,4-triphosphate 6 kinase (EC 2.7.1.159) RQ 1 EV IPR008656; PF05770; sufficient; -- SN 2 ID Myo-inositol polyphosphate kinase DN Myo-inositol polyphosphate kinase (EC 2.7.1.134) RQ 1 EV IPR008656; PF05770; sufficient; -- SN 3 ID Myo-inositol-1,3,4,6-tetrakisphosphate 5-kinase DN Myo-inositol-1,3,4,6-tetrakisphosphate 5-kinase (EC 2.7.1.140) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 4 ID Myo-inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase DN Myo-inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase (EC 3.1.3) RQ 1 EV IPR008656; PF05770; sufficient; // AC GenProp1461 DE tRNA-uridine 2-thiolation (cytoplasmic) TP PATHWAY AU Caspi R TH 5 DC tRNA-uridine 2-thiolation (cytoplasmic) DR MetaCyc; PWY-7888; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID tRNA (carboxymethyluridine34-5-O)-methyltransferase DN tRNA (carboxymethyluridine34-5-O)-methyltransferase (EC 2.1.1.229) RQ 1 EV IPR005651; PF03966; sufficient; -- SN 2 ID tRNA-5-(2-methoxy-2-oxoethyl)uridine 2-sulfurtransferase DN tRNA-5-(2-methoxy-2-oxoethyl)uridine 2-sulfurtransferase (EC 2.8.1) RQ 1 EV IPR019407; PF10288; sufficient; -- SN 3 ID URM1 adenylyltransferase DN URM1 adenylyltransferase (EC 2.7.7) RQ 1 EV IPR000594; PF00899; sufficient; EV IPR001763; PF00581; sufficient; -- SN 4 ID URM1 sulfurtransferase DN URM1 sulfurtransferase (EC 2.8.1) RQ 1 EV IPR000594; PF00899; sufficient; EV IPR001763; PF00581; sufficient; -- SN 5 ID TUM1:MOCS3 sulfurtransferase DN TUM1:MOCS3 sulfurtransferase (EC 2.8.1) RQ 1 EV IPR000594; PF00899; sufficient; EV IPR001763; PF00581; sufficient; -- SN 6 ID Cysteine desulfurase:TUM1 sulfurtransferase DN Cysteine desulfurase:TUM1 sulfurtransferase (EC 2.8.1) RQ 1 EV IPR001763; PF00581; sufficient; -- SN 7 ID Cysteine desulfurase DN Cysteine desulfurase RQ 1 EV IPR010240; TIGR02006; sufficient; // AC GenProp1462 DE Yersiniabactin biosynthesis TP PATHWAY AU Caspi R TH 0 DC Yersiniabactin biosynthesis DR MetaCyc; PWY-6407; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Yersiniabactin synthase DN Yersiniabactin synthase (EC 2.3.1) RQ 1 EV IPR010091; TIGR01761; sufficient; -- SN 2 ID Salicilate adenylyltransferase DN Salicilate adenylyltransferase RQ 1 EV IPR000873; PF00501; sufficient; EV IPR025110; PF13193; sufficient; // AC GenProp1463 DE D-allose degradation TP PATHWAY AU Keseler I, Pellegrini-Toole A TH 1 DC D-allose degradation DR MetaCyc; PWY0-44; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-allose kinase DN D-allose kinase (EC 2.7.1.55) RQ 1 EV IPR000600; PF00480; sufficient; -- SN 2 ID Allose-6-phosphate isomerase DN Allose-6-phosphate isomerase (EC 5.3.1) RQ 1 EV IPR003500; PF02502; sufficient; EV IPR003500; TIGR00689; sufficient; EV IPR004785; TIGR01120; sufficient; -- SN 3 ID D-allulose-6-phosphate 3-epimerase DN D-allulose-6-phosphate 3-epimerase (EC 5.1.3) RQ 1 EV IPR000056; PF00834; sufficient; // AC GenProp1464 DE Indole-3-acetate biosynthesis I TP PATHWAY AU Caspi R, Schaeffer M TH 0 DC Indole-3-acetate biosynthesis I DR MetaCyc; PWYDQC-4; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-tryptophan:pyruvate aminotransferase DN L-tryptophan:pyruvate aminotransferase (EC 2.6.1.99) RQ 1 EV IPR006948; PF04864; sufficient; -- SN 2 ID Indole-3-pyruvate monooxygenase DN Indole-3-pyruvate monooxygenase (EC 1.14.13.168) RQ 1 EV IPR020946; PF00743; sufficient; // AC GenProp1465 DE Pyrimidine ribonucleosides salvage II TP PATHWAY AU Zhang P TH 0 DC Pyrimidine ribonucleosides salvage II DR MetaCyc; PWY-6556; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytidine deaminase DN Cytidine deaminase (EC 3.5.4.5) RQ 1 EV IPR006263; TIGR01355; sufficient; EV IPR006262; TIGR01354; sufficient; -- SN 2 ID Uridine nucleosidase DN Uridine nucleosidase (EC 3.2.2.3) RQ 1 EV IPR001910; PF01156; sufficient; // AC GenProp1466 DE L-ornithine biosynthesis I TP PATHWAY AU Fulcher C, Caspi R, Irina Iourovitski I TH 3 DC L-ornithine biosynthesis I DR MetaCyc; GLUTORN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetylglutamate kinase DN Acetylglutamate kinase (EC 2.7.2.8) RQ 1 EV IPR004662; TIGR00761; sufficient; -- SN 2 ID N-acetylornithinase DN N-acetylornithinase (EC 3.5.1.16) RQ 1 EV IPR002933; PF01546; sufficient; EV IPR010169; TIGR01892; sufficient; -- SN 3 ID N-acetylornithine aminotransferase DN N-acetylornithine aminotransferase (EC 2.6.1.11) RQ 1 EV IPR004636; TIGR00707; sufficient; EV IPR005814; PF00202; sufficient; EV IPR017652; TIGR03246; sufficient; EV IPR004632; TIGR00700; sufficient; -- SN 4 ID N-acetylglutamylphosphate reductase DN N-acetylglutamylphosphate reductase (EC 1.2.1.38) RQ 1 EV IPR000706; TIGR01850; sufficient; -- SN 5 ID Acetylglutamate synthase DN Acetylglutamate synthase (EC 2.3.1.1) RQ 1 EV IPR010167; TIGR01890; sufficient; // AC GenProp1467 DE L-valine degradation II TP PATHWAY AU Caspi R TH 1 DC L-valine degradation II DR MetaCyc; PWY-5057; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-valine:2-oxoglutarate aminotransferase DN L-valine:2-oxoglutarate aminotransferase (EC 2.6.1.42) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005786; TIGR01123; sufficient; -- SN 2 ID 2-Oxoisovalerate carboxy-lyase DN 2-Oxoisovalerate carboxy-lyase (EC 4.1.1.72) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 3 ID Isobutanol dehydrogenase DN Isobutanol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR014183; TIGR02818; sufficient; // AC GenProp1468 DE UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronate biosynthesis TP PATHWAY AU Caspi R TH 3 DC UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronate biosynthesis DR MetaCyc; PWY-7090; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-N-acetylglucosamine 6-dehydrogenase DN UDP-N-acetylglucosamine 6-dehydrogenase (EC 1.1.1.136) RQ 1 EV IPR017476; TIGR03026; sufficient; -- SN 2 ID UDP-2,3-diacetamido-2,3-dideoxyglucuronic acid 2-epimerase DN UDP-2,3-diacetamido-2,3-dideoxyglucuronic acid 2-epimerase (EC 5.1.3.23) RQ 1 EV IPR029767; TIGR00236; sufficient; -- SN 3 ID UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase DN UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase (EC 1.1.1.335) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR004104; PF02894; sufficient; -- SN 4 ID UDP-2-acetamido-3-amino-2,3-dideoxy-glucuronate N-acetyltransferase DN UDP-2-acetamido-3-amino-2,3-dideoxy-glucuronate N-acetyltransferase (EC 2.3.1.201) RQ 1 EV IPR001451; PF00132; sufficient; -- SN 5 ID UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase DN UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase (EC 2.6.1.98) RQ 1 EV IPR000653; PF01041; sufficient; // AC GenProp1469 DE Guanosine nucleotides degradation III TP PATHWAY AU Caspi R TH 2 DC Guanosine nucleotides degradation III DR MetaCyc; PWY-6608; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Guanine deaminase DN Guanine deaminase (EC 3.5.4.3) RQ 1 EV IPR014311; TIGR02967; sufficient; -- SN 2 ID 5'-GMP-nucleotidase DN 5'-GMP-nucleotidase (EC 3.1.3.5) RQ 1 EV IPR008380; PF05761; sufficient; EV IPR008380; TIGR02244; sufficient; EV IPR006439; TIGR01509; sufficient; -- SN 3 ID Guanosine phosphorylase DN Guanosine phosphorylase (EC 2.4.2.15) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR004402; TIGR00107; sufficient; -- SN 4 ID Xanthine:NAD+ oxidoreductase DN Xanthine:NAD+ oxidoreductase (EC 1.17.1.4) RQ 1 EV IPR000674; PF01315; sufficient; EV IPR001041; PF00111; sufficient; EV IPR002346; PF00941; sufficient; EV IPR002888; PF01799; sufficient; EV IPR005107; PF03450; sufficient; EV IPR008274; PF02738; sufficient; EV IPR014307; TIGR02963; sufficient; EV IPR014309; TIGR02965; sufficient; // AC GenProp1470 DE Superpathway of heme b biosynthesis from uroporphyrinogen-III TP PATHWAY AU Riley M, Caspi R TH 2 DC Superpathway of heme b biosynthesis from uroporphyrinogen-III DR MetaCyc; PWY0-1415; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Deferrochelatase DN Deferrochelatase (EC 4.99.1.1) RQ 1 EV IPR006314; PF04261; sufficient; EV IPR006314; TIGR01413; sufficient; EV IPR001015; PF00762; sufficient; EV IPR001015; TIGR00109; sufficient; -- SN 2 ID Protoporphyrinogen oxidase DN Protoporphyrinogen oxidase (EC 1.3.3.4) RQ 1 EV IPR026816; PF12724; sufficient; -- SN 3 ID Coproporphyrinogen III oxidase DN Coproporphyrinogen III oxidase (EC 1.3.3.3) RQ 1 EV IPR001260; PF01218; sufficient; -- SN 4 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase (EC 4.1.1.37) RQ 1 EV IPR006361; TIGR01464; sufficient; // AC GenProp1471 DE Beta-caryophyllene biosynthesis TP PATHWAY AU Pujar A TH 1 DC Beta-caryophyllene biosynthesis DR MetaCyc; PWY-6275; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID (E)-beta-caryophyllene synthase DN (E)-beta-caryophyllene synthase (EC 4.2.3.57) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 2 ID Alpha-humulene synthase DN Alpha-humulene synthase (EC 4.2.3.104) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 3 ID Beta-elemene synthase DN Beta-elemene synthase (EC 4.2.3) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; // AC GenProp1472 DE L-ornithine biosynthesis II TP PATHWAY AU Weerasinghe D TH 2 DC L-ornithine biosynthesis II DR MetaCyc; ARGININE-SYN4-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutamate dehydrogenase DN Glutamate dehydrogenase (EC 1.4.1.3) RQ 1 EV IPR006096; PF00208; sufficient; EV IPR006097; PF02812; sufficient; -- SN 2 ID Gamma-glutamyl kinase DN Gamma-glutamyl kinase (EC 2.7.2.11) RQ 1 EV IPR005766; TIGR01092; sufficient; EV IPR005715; TIGR01027; sufficient; -- SN 3 ID Glutamate-5-semialdehyde dehydrogenase DN Glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) RQ 1 EV IPR005766; TIGR01092; sufficient; EV IPR005715; TIGR01027; sufficient; -- SN 4 ID Ornithine--oxo-glutarate aminotransferase DN Ornithine--oxo-glutarate aminotransferase (EC 2.6.1.13) RQ 1 EV IPR005814; PF00202; sufficient; EV IPR010164; TIGR01885; sufficient; // AC GenProp1473 DE Cis-alkene biosynthesis TP PATHWAY AU Caspi R TH 2 DC Cis-alkene biosynthesis DR MetaCyc; PWY-7869; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acyl-CoA:acyl-CoA alkyltransferase DN Acyl-CoA:acyl-CoA alkyltransferase (EC 2.3.3.20) RQ 1 EV IPR013747; PF08541; sufficient; EV IPR013751; PF08545; sufficient; -- SN 2 ID 2-Alkyl-3-oxo-fatty acid reductase DN 2-Alkyl-3-oxo-fatty acid reductase (EC 1.1.1.412) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 3 ID 3-Alkyl-4-acyloxetan-2-one synthetase DN 3-Alkyl-4-acyloxetan-2-one synthetase (EC 6.1.3.1) RQ 1 EV IPR000873; PF00501; sufficient; -- SN 4 ID 3-Alkyl-4-alkyloxetan-2-one decarboxylase DN 3-Alkyl-4-alkyloxetan-2-one decarboxylase RQ 1 EV IPR000073; PF00561; sufficient; // AC GenProp1474 DE Nitrate reduction VIIIb (dissimilatory) TP PATHWAY AU Mackie A TH 0 DC Nitrate reduction VIIIb (dissimilatory) DR MetaCyc; PWY0-1573; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID NADH:ubiquinone oxidoreductase 1 (external) DN NADH:ubiquinone oxidoreductase 1 (external) (EC 1.6.5.9) RQ 1 EV IPR023753; PF07992; sufficient; -- SN 2 ID Ubiquinol:nitrate oxidoreductase DN Ubiquinol:nitrate oxidoreductase (EC 1.7.5.1) RQ 1 EV IPR006468; TIGR01580; sufficient; EV IPR006547; TIGR01660; sufficient; EV IPR003816; TIGR00351; sufficient; // AC GenProp1475 DE Superpathway of L-lysine, L-threonine and L-methionine biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Superpathway of L-lysine, L-threonine and L-methionine biosynthesis I DR MetaCyc; P4-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Homoserine dehydrogenase DN Homoserine dehydrogenase (EC 1.1.1.3) RQ 1 EV IPR001048; PF00696; sufficient; EV IPR001341; TIGR00657; sufficient; EV IPR001342; PF00742; sufficient; EV IPR002912; PF01842; sufficient; EV IPR005106; PF03447; sufficient; EV IPR027795; PF13840; sufficient; -- SN 2 ID Homoserine O-succinyltransferase DN Homoserine O-succinyltransferase (EC 2.3.1.46) RQ 1 EV IPR005697; PF04204; sufficient; EV IPR005697; TIGR01001; sufficient; // AC GenProp1476 DE Autoinducer AI-2 degradation TP PATHWAY AU Caspi R, Keseler I TH 1 DC Autoinducer AI-2 degradation DR MetaCyc; PWY0-1569; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase DN (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase (EC 5.3.1.32) RQ 1 EV IPR007138; PF03992; sufficient; -- SN 2 ID 3-Hydroxy-2,4-pentadione 5-phosphate thiolase DN 3-Hydroxy-2,4-pentadione 5-phosphate thiolase (EC 2.3.1.245) RQ 1 EV IPR002915; PF01791; sufficient; -- SN 3 ID Autoinducer-2 kinase DN Autoinducer-2 kinase (EC 2.7.1.189) RQ 1 EV IPR018484; PF00370; sufficient; EV IPR018485; PF02782; sufficient; // AC GenProp1477 DE Coenzyme B/coenzyme M regeneration III (coenzyme F420-dependent) TP PATHWAY AU Caspi R TH 0 DC Coenzyme B/coenzyme M regeneration III (coenzyme F420-dependent) DR MetaCyc; PWY-7866; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ferredoxin:CoB-CoM heterosulfide reductase DN Ferredoxin:CoB-CoM heterosulfide reductase (EC 1.8.7.3) RQ 1 EV IPR017678; TIGR03288; sufficient; EV IPR017680; TIGR03290; sufficient; -- SN 2 ID Coenzyme F420:CoB-CoM heterosulfide,ferredoxin reductase DN Coenzyme F420:CoB-CoM heterosulfide,ferredoxin reductase (EC 1.8.98.4) RQ 1 EV IPR017678; TIGR03288; sufficient; EV IPR017680; TIGR03290; sufficient; // AC GenProp1478 DE Chorismate biosynthesis from 3-dehydroquinate TP PATHWAY AU Weerasinghe D, Caspi R TH 4 DC Chorismate biosynthesis from 3-dehydroquinate DR MetaCyc; PWY-6163; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Phosphoshikimate 1-carboxyvinyltransferase DN 3-Phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) RQ 1 EV IPR006264; TIGR01356; sufficient; EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR031322; PF01202; sufficient; -- SN 2 ID 3-Dehydroquinate dehydratase DN 3-Dehydroquinate dehydratase (EC 4.2.1.10) RQ 1 EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR006264; TIGR01356; sufficient; EV IPR031322; PF01202; sufficient; -- SN 3 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; PF01264; sufficient; EV IPR000453; TIGR00033; sufficient; -- SN 4 ID Shikimate dehydrogenase DN Shikimate dehydrogenase (EC 1.1.1.282) RQ 1 EV IPR013708; PF08501; sufficient; -- SN 5 ID Shikimate dehydrogenase DN Shikimate dehydrogenase (EC 1.1.1.25) RQ 1 EV IPR011342; TIGR00507; sufficient; EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR006264; TIGR01356; sufficient; EV IPR031322; PF01202; sufficient; -- SN 6 ID Shikimate kinase DN Shikimate kinase (EC 2.7.1.71) RQ 1 EV IPR010189; TIGR01920; sufficient; EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR006264; TIGR01356; sufficient; EV IPR031322; PF01202; sufficient; // AC GenProp1479 DE Polyisoprenoid biosynthesis (E. coli) TP PATHWAY AU Caspi R, Riley M TH 1 DC Polyisoprenoid biosynthesis (E. coli) DR MetaCyc; POLYISOPRENSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID All-trans-octaprenyl-diphosphate synthase DN All-trans-octaprenyl-diphosphate synthase (EC 2.5.1.90) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 3 ID Di-trans,poly-cis-decaprenyl diphosphate:isopentenyl-diphosphate undecaprenylcistransferase DN Di-trans,poly-cis-decaprenyl diphosphate:isopentenyl-diphosphate undecaprenylcistransferase (EC 2.5.1.31) RQ 1 EV IPR001441; PF01255; sufficient; EV IPR001441; TIGR00055; sufficient; // AC GenProp1480 DE Peptidoglycan biosynthesis I (meso-diaminopimelate containing) TP PATHWAY AU Caspi R, Riley M TH 1 DC Peptidoglycan biosynthesis I (meso-diaminopimelate containing) DR MetaCyc; PEPTIDOGLYCANSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminlytransferase DN UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminlytransferase (EC 2.4.1.227) RQ 1 EV IPR006009; TIGR01133; sufficient; -- SN 2 ID UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase DN UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase (EC 2.7.8.13) RQ 1 EV IPR000715; PF00953; sufficient; EV IPR003524; TIGR00445; sufficient; -- SN 3 ID UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate ligase DN UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate ligase (EC 6.3.2.10) RQ 1 EV IPR005863; TIGR01143; sufficient; // AC GenProp1481 DE Superpathway of L-citrulline metabolism TP PATHWAY AU Caspi R TH 1 DC Superpathway of L-citrulline metabolism DR MetaCyc; PWY-5004; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Argininosuccinase DN Argininosuccinase (EC 4.3.2.1) RQ 1 EV IPR009049; TIGR00838; sufficient; -- SN 2 ID Argininosuccinate synthase DN Argininosuccinate synthase (EC 6.3.4.5) RQ 1 EV IPR001518; PF00764; sufficient; EV IPR001518; TIGR00032; sufficient; -- SN 3 ID Nitric-oxide synthase DN Nitric-oxide synthase (EC 1.14.13.39) RQ 1 EV IPR001433; PF00175; sufficient; EV IPR001478; PF00595; sufficient; EV IPR003097; PF00667; sufficient; EV IPR004030; PF02898; sufficient; EV IPR008254; PF00258; sufficient; // AC GenProp1482 DE S-methyl-5'-thioadenosine degradation I TP PATHWAY AU Caspi R TH 0 DC S-methyl-5'-thioadenosine degradation I DR MetaCyc; PWY-6754; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID MTR kinase DN MTR kinase (EC 2.7.1.100) RQ 1 EV IPR009212; TIGR01767; sufficient; -- SN 2 ID MTA nucleosidase DN MTA nucleosidase (EC 3.2.2.16) RQ 1 EV IPR010049; TIGR01704; sufficient; // AC GenProp1483 DE Glycogen biosynthesis II (from UDP-D-Glucose) TP PATHWAY AU Caspi R TH 2 DC Glycogen biosynthesis II (from UDP-D-Glucose) DR MetaCyc; PWY-5067; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-alpha-D-glucose:glycogenin alpha-D-glucosyltransferase DN UDP-alpha-D-glucose:glycogenin alpha-D-glucosyltransferase (EC 2.4.1.186) RQ 1 EV IPR002495; PF01501; sufficient; -- SN 2 ID UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase DN UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase (EC 2.4.1.186) RQ 1 EV IPR002495; PF01501; sufficient; -- SN 3 ID UDP-glucose:glycogenin 4-alpha-D-glucosyltransferase DN UDP-glucose:glycogenin 4-alpha-D-glucosyltransferase (EC 2.4.1.11) RQ 1 EV IPR008631; PF05693; sufficient; -- SN 4 ID 1,4-Alpha-glucan branching enzyme DN 1,4-Alpha-glucan branching enzyme (EC 2.4.1.18) RQ 1 EV IPR004193; PF02922; sufficient; EV IPR006047; PF00128; sufficient; EV IPR006048; PF02806; sufficient; // AC GenProp1484 DE Superpathway of guanosine nucleotides de novo biosynthesis II TP PATHWAY AU Caspi R TH 3 DC Superpathway of guanosine nucleotides de novo biosynthesis II DR MetaCyc; PWY-6125; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GDP kinase DN GDP kinase (EC 2.7.4.6) RQ 1 EV IPR006259; TIGR01351; sufficient; EV IPR001564; PF00334; sufficient; -- SN 2 ID GDP reductase DN GDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 3 ID Guanylate kinase DN Guanylate kinase (EC 2.7.4.8) RQ 1 EV IPR017665; TIGR03263; sufficient; -- SN 4 ID GTP reductase DN GTP reductase (EC 1.1.98.6) RQ 1 EV IPR012833; PF13597; sufficient; EV IPR012833; TIGR02487; sufficient; -- SN 5 ID 2'-Deoxyguanosine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase DN 2'-Deoxyguanosine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase (EC 1.17.4.1) RQ 1 EV IPR026459; TIGR04170; sufficient; EV IPR000358; PF00268; sufficient; EV IPR026494; TIGR04171; sufficient; // AC GenProp1485 DE Pyruvate fermentation to acetoin III TP PATHWAY AU Krieger C TH 1 DC Pyruvate fermentation to acetoin III DR MetaCyc; PWY3O-440; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pyruvate decarboxylase DN Pyruvate decarboxylase (EC 4.1.1.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID Pyruvate decarboxylase DN Pyruvate decarboxylase RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 3 ID Acetoin synthase DN Acetoin synthase RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; // AC GenProp1486 DE Oleate beta-oxidation TP PATHWAY AU Keseler I TH 0 DC Oleate beta-oxidation DR MetaCyc; PWY0-1337; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acyl-CoA thioesterase DN Acyl-CoA thioesterase (EC 3.1.2) RQ 1 EV IPR006684; TIGR00051; sufficient; -- SN 2 ID Delta3-cis-Delta2-trans-enoyl-CoA isomerase DN Delta3-cis-Delta2-trans-enoyl-CoA isomerase (EC 5.3.3.8) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012799; TIGR02437; sufficient; // AC GenProp1487 DE L-lysine degradation XI (mammalian) TP PATHWAY AU Weerasinghe D TH 3 DC L-lysine degradation XI (mammalian) DR MetaCyc; LYSINE-DEG1-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alpha-aminoadipic semialdehyde dehydrogenase DN Alpha-aminoadipic semialdehyde dehydrogenase (EC 1.2.1.31) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID L-lysine-alpha-ketoglutarate reductase DN L-lysine-alpha-ketoglutarate reductase (EC 1.5.1.8) RQ 1 EV IPR005097; PF03435; sufficient; EV IPR007886; PF05222; sufficient; EV IPR032095; PF16653; sufficient; -- SN 3 ID Saccharopine dehydrogenase DN Saccharopine dehydrogenase (EC 1.5.1.9) RQ 1 EV IPR005097; PF03435; sufficient; EV IPR007886; PF05222; sufficient; EV IPR032095; PF16653; sufficient; -- SN 4 ID 2-Aminoadipate-2-oxoglutarate aminotransferase DN 2-Aminoadipate-2-oxoglutarate aminotransferase (EC 2.6.1.39) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 5 ID 2-Oxoadipate dehydrogenase DN 2-Oxoadipate dehydrogenase (EC 1.2.1.M9) RQ 1 EV IPR011603; TIGR00239; sufficient; // AC GenProp1488 DE Oleate beta-oxidation (thioesterase-dependent, yeast) TP PATHWAY AU Foerster H TH 0 DC Oleate beta-oxidation (thioesterase-dependent, yeast) DR MetaCyc; PWY-7292; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acyl-CoA thioesterase DN Acyl-CoA thioesterase (EC 3.1.2) RQ 1 EV IPR003703; TIGR00189; sufficient; -- SN 2 ID Delta3-cis-Delta2-trans-enoyl-CoA isomerase DN Delta3-cis-Delta2-trans-enoyl-CoA isomerase (EC 5.3.3.8) RQ 1 EV IPR001753; PF00378; sufficient; // AC GenProp1489 DE Ammonia assimilation cycle I TP PATHWAY AU Caspi R TH 0 DC Ammonia assimilation cycle I DR MetaCyc; PWY-6963; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutamate synthase DN Glutamate synthase (EC 1.4.1.14) RQ 1 EV IPR006005; TIGR01317; sufficient; -- SN 2 ID Glutamine synthetase DN Glutamine synthetase (EC 6.3.1.2) RQ 1 EV IPR008146; PF00120; sufficient; EV IPR008147; PF03951; sufficient; // AC GenProp1490 DE Indole-3-acetate inactivation VIII TP PATHWAY AU Dreher K TH 5 DC Indole-3-acetate inactivation VIII DR MetaCyc; PWY-6219; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Indole-3-acetyl-alanine synthetase DN Indole-3-acetyl-alanine synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; -- SN 2 ID Indole-3-acetyl-leucine synthetase DN Indole-3-acetyl-leucine synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; -- SN 3 ID Indole-3-acetyl-aspatate synthetase DN Indole-3-acetyl-aspatate synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; -- SN 4 ID Indole-3-acetyl-glutamate synthetase DN Indole-3-acetyl-glutamate synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; -- SN 5 ID Indole-3-acetyl-glutamine synthetase DN Indole-3-acetyl-glutamine synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; -- SN 6 ID Indole-3-acetyl-valine synthetase DN Indole-3-acetyl-valine synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; -- SN 7 ID Indole-3-acetyl-phenylalanine synthetase DN Indole-3-acetyl-phenylalanine synthetase (EC 6.3) RQ 1 EV IPR004993; PF03321; sufficient; // AC GenProp1491 DE Ac/N-end rule pathway TP PATHWAY AU Caspi R TH 19 DC Ac/N-end rule pathway DR MetaCyc; PWY-7800; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.254) RQ 1 EV IPR019183; PF09797; sufficient; -- SN 2 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.254) RQ 1 EV IPR019183; PF09797; sufficient; -- SN 3 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.254) RQ 1 EV IPR019183; PF09797; sufficient; -- SN 4 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.254) RQ 1 EV IPR019183; PF09797; sufficient; -- SN 5 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.258) RQ 1 EV IPR007244; PF04112; sufficient; -- SN 6 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.256) RQ 1 EV IPR007244; PF04112; sufficient; -- SN 7 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.256) RQ 1 EV IPR007244; PF04112; sufficient; -- SN 8 ID N-terminal methionine N-alpha-acetyltransferase DN N-terminal methionine N-alpha-acetyltransferase (EC 2.3.1.256) RQ 1 EV IPR007244; PF04112; sufficient; -- SN 9 ID N-terminal L-methionine N-alpha-acetyltransferase DN N-terminal L-methionine N-alpha-acetyltransferase (EC 2.3.1.256) RQ 1 EV IPR007244; PF04112; sufficient; -- SN 10 ID N-terminal valine N-alpha-acetyltransferase DN N-terminal valine N-alpha-acetyltransferase (EC 2.3.1.255) RQ 1 EV IPR021183; PF12569; sufficient; -- SN 11 ID N-terminal alanine N-alpha-acetyltransferase DN N-terminal alanine N-alpha-acetyltransferase (EC 2.3.1.255) RQ 1 EV IPR021183; PF12569; sufficient; -- SN 12 ID N-terminal cysteine N-alpha-acetyltransferase DN N-terminal cysteine N-alpha-acetyltransferase (EC 2.3.1.255) RQ 1 EV IPR021183; PF12569; sufficient; -- SN 13 ID N-terminal glycine N-alpha-acetyltransferase DN N-terminal glycine N-alpha-acetyltransferase (EC 2.3.1.255) RQ 1 EV IPR021183; PF12569; sufficient; -- SN 14 ID N-terminal serine N-alpha-acetyltransferase DN N-terminal serine N-alpha-acetyltransferase (EC 2.3.1.255) RQ 1 EV IPR021183; PF12569; sufficient; -- SN 15 ID N-terminal threonine N-alpha-acetyltransferase DN N-terminal threonine N-alpha-acetyltransferase (EC 2.3.1.255) RQ 1 EV IPR021183; PF12569; sufficient; -- SN 16 ID Methionine aminopeptidase DN Methionine aminopeptidase (EC 3.4.11.18) RQ 1 EV IPR002467; TIGR00500; sufficient; EV IPR002468; TIGR00501; sufficient; -- SN 17 ID Methionine aminopeptidase DN Methionine aminopeptidase (EC 3.4.11.18) RQ 1 EV IPR002467; TIGR00500; sufficient; EV IPR002468; TIGR00501; sufficient; -- SN 18 ID Methionine aminopeptidase DN Methionine aminopeptidase (EC 3.4.11.18) RQ 1 EV IPR002467; TIGR00500; sufficient; EV IPR002468; TIGR00501; sufficient; -- SN 19 ID Methionine aminopeptidase DN Methionine aminopeptidase (EC 3.4.11.18) RQ 1 EV IPR002467; TIGR00500; sufficient; EV IPR002468; TIGR00501; sufficient; -- SN 20 ID Methionine aminopeptidase DN Methionine aminopeptidase (EC 3.4.11.18) RQ 1 EV IPR002468; TIGR00501; sufficient; -- SN 21 ID Methionine aminopeptidase DN Methionine aminopeptidase (EC 3.4.11.18) RQ 1 EV IPR002468; TIGR00501; sufficient; // AC GenProp1492 DE Sucrose degradation III (sucrose invertase) TP PATHWAY AU Caspi R TH 2 DC Sucrose degradation III (sucrose invertase) DR MetaCyc; PWY-621; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Neutral/alkaline invertase DN Neutral/alkaline invertase (EC 3.2.1.48) RQ 1 EV IPR024746; PF12899; sufficient; -- SN 2 ID ATP:D-fructose 6-phosphotransferase DN ATP:D-fructose 6-phosphotransferase (EC 2.7.1.4) RQ 1 EV IPR022672; PF00349; sufficient; EV IPR022673; PF03727; sufficient; -- SN 3 ID Glucokinase DN Glucokinase (EC 2.7.1.2) RQ 1 EV IPR022672; PF00349; sufficient; EV IPR022673; PF03727; sufficient; -- SN 4 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; // AC GenProp1493 DE Succinate to cytochrome bo oxidase electron transfer TP PATHWAY AU Mackie A, Nolan L, Krummenacker M TH 0 DC Succinate to cytochrome bo oxidase electron transfer DR MetaCyc; PWY0-1329; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; -- SN 2 ID Succinate dehydrogenase DN Succinate dehydrogenase (EC 1.3.5.1) RQ 1 EV IPR004489; TIGR00384; sufficient; EV IPR011281; TIGR01816; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR000701; PF01127; sufficient; EV IPR014314; TIGR02970; sufficient; EV IPR014312; TIGR02968; sufficient; // AC GenProp1494 DE Pyrimidine deoxyribonucleotide phosphorylation TP PATHWAY AU Caspi R TH 2 DC Pyrimidine deoxyribonucleotide phosphorylation DR MetaCyc; PWY-7197; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID DCDP kinase DN DCDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 2 ID DTDP kinase DN DTDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 3 ID Thymidylate kinase DN Thymidylate kinase (EC 2.7.4.12) RQ 1 EV IPR018094; TIGR00041; sufficient; -- SN 4 ID DCMP kinase DN DCMP kinase (EC 2.7.4.25) RQ 1 EV IPR003136; TIGR00017; sufficient; EV IPR006266; TIGR01359; sufficient; // AC GenProp1495 DE N-end rule pathway I (prokaryotic) TP PATHWAY AU Caspi R TH 0 DC N-end rule pathway I (prokaryotic) DR MetaCyc; PWY-7801; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Leucyl-tRNA-protein transferase DN Leucyl-tRNA-protein transferase (EC 2.3.2.6) RQ 1 EV IPR004616; PF03588; sufficient; EV IPR004616; TIGR00667; sufficient; -- SN 2 ID Leucyl-tRNA-protein transferase DN Leucyl-tRNA-protein transferase (EC 2.3.2.6) RQ 1 EV IPR004616; PF03588; sufficient; EV IPR004616; TIGR00667; sufficient; // AC GenProp1496 DE Hydrogen production V TP PATHWAY AU Weerasinghe D TH 0 DC Hydrogen production V DR MetaCyc; PWY-6772; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Formate dehydrogenase DN Formate dehydrogenase (EC 1.1.7) RQ 1 EV IPR006478; TIGR01591; sufficient; -- SN 2 ID Hydrogenase DN Hydrogenase RQ 1 EV IPR001694; PF00146; sufficient; // AC GenProp1497 DE Ethanol degradation I TP PATHWAY AU N/A TH 0 DC Ethanol degradation I DR MetaCyc; ETOH-ACETYLCOA-ANA-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR003361; TIGR03215; sufficient; -- SN 2 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; EV IPR015590; PF00171; sufficient; // AC GenProp1498 DE Superpathway of menaquinol-8 biosynthesis I TP PATHWAY AU Keseler I, Riley M, Caspi R TH 2 DC Superpathway of menaquinol-8 biosynthesis I DR MetaCyc; PWY-5838; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID S-adenosylmethionine:2-demethylquinol-8 methyltransferase DN S-adenosylmethionine:2-demethylquinol-8 methyltransferase (EC 2.1.1.163) RQ 1 EV IPR004033; PF01209; sufficient; EV IPR004033; TIGR01934; sufficient; -- SN 2 ID 1,4-Dihydroxy-2-naphthoate octaprenyltransferase DN 1,4-Dihydroxy-2-naphthoate octaprenyltransferase (EC 2.5.1.74) RQ 1 EV IPR000537; PF01040; sufficient; -- SN 3 ID All-trans-octaprenyl-diphosphate synthase DN All-trans-octaprenyl-diphosphate synthase (EC 2.5.1.90) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 4 ID 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase DN 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase (EC 3.1.2.28) RQ 1 EV IPR003736; TIGR00369; sufficient; EV IPR006683; PF03061; sufficient; // AC GenProp1499 DE L-selenocysteine biosynthesis I (bacteria) TP PATHWAY AU Ingraham J TH 1 DC L-selenocysteine biosynthesis I (bacteria) DR MetaCyc; PWY0-901; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Selenophosphate synthetase DN Selenophosphate synthetase (EC 2.7.9.3) RQ 1 EV IPR004536; TIGR00476; sufficient; -- SN 2 ID Selenocysteine synthase DN Selenocysteine synthase (EC 2.9.1.1) RQ 1 EV IPR004534; TIGR00474; sufficient; EV IPR018319; PF03841; sufficient; -- SN 3 ID Seryl-tRNAsec synthetase DN Seryl-tRNAsec synthetase (EC 6.1.1.11) RQ 1 EV IPR002317; TIGR00414; sufficient; // AC GenProp1501 DE Allantoin degradation to ureidoglycolate I (urea producing) TP PATHWAY AU Caspi R TH 0 DC Allantoin degradation to ureidoglycolate I (urea producing) DR MetaCyc; PWY-5697; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Allantoicase DN Allantoicase (EC 3.5.3.4) RQ 1 EV IPR005164; TIGR02961; sufficient; -- SN 2 ID Allantoinase DN Allantoinase (EC 3.5.2.5) RQ 1 EV IPR017593; TIGR03178; sufficient; // AC GenProp1502 DE NAD/NADP-NADH/NADPH cytosolic interconversion (yeast) TP PATHWAY AU Foerster H TH 3 DC NAD/NADP-NADH/NADPH cytosolic interconversion (yeast) DR MetaCyc; PWY-7268; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucose-6-phosphate dehydrogenase DN Glucose-6-phosphate dehydrogenase (EC 1.1.1.49) RQ 1 EV IPR001282; TIGR00871; sufficient; -- SN 2 ID NADP+-dependent isocitrate dehydrogenase DN NADP+-dependent isocitrate dehydrogenase (EC 1.1.1.42) RQ 1 EV IPR004790; TIGR00127; sufficient; -- SN 3 ID NAD kinase DN NAD kinase (EC 2.7.1.23) RQ 1 EV IPR002504; PF01513; sufficient; -- SN 4 ID NADH kinase DN NADH kinase (EC 2.7.1.86) RQ 1 EV IPR002504; PF01513; sufficient; -- SN 5 ID Acetaldehyde:NADP+ oxidoreductase DN Acetaldehyde:NADP+ oxidoreductase (EC 1.2.1.4) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1503 DE L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde TP PATHWAY AU Caspi R TH 3 DC L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde DR MetaCyc; PWY-5651; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Hydroxyanthranilate 3,4-dioxygenase DN 3-Hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) RQ 1 EV IPR010329; PF06052; sufficient; EV IPR010329; TIGR03037; sufficient; -- SN 2 ID 3-Hydroxy-L-kynurenine hydrolase DN 3-Hydroxy-L-kynurenine hydrolase (EC 3.7.1.3) RQ 1 EV IPR010111; TIGR01814; sufficient; -- SN 3 ID Arylformamidase DN Arylformamidase (EC 3.5.1.9) RQ 1 EV IPR013094; PF07859; sufficient; EV IPR004839; PF00155; sufficient; -- SN 4 ID Kynurenine 3-monooxygenase DN Kynurenine 3-monooxygenase (EC 1.14.13.9) RQ 1 EV IPR002938; PF01494; sufficient; -- SN 5 ID Tryptophan 2,3-dioxygenase DN Tryptophan 2,3-dioxygenase (EC 1.13.11.52) RQ 1 EV IPR004981; PF03301; sufficient; EV IPR000898; PF01231; sufficient; // AC GenProp1504 DE Nitrate reduction X (dissimilatory, periplasmic) TP PATHWAY AU Caspi R, Mackie A TH 1 DC Nitrate reduction X (dissimilatory, periplasmic) DR MetaCyc; PWY0-1584; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Nitrate reductase (cytochrome) DN Nitrate reductase (cytochrome) (EC 1.9.6.1) RQ 1 EV IPR010051; TIGR01706; sufficient; EV IPR005591; PF03892; sufficient; -- SN 2 ID Ubiquinol-[NapC cytochrome] reductase DN Ubiquinol-[NapC cytochrome] reductase (EC 1.10.2.2) RQ 1 EV IPR004494; TIGR00397; sufficient; EV IPR011886; TIGR02163; sufficient; -- SN 3 ID Sn-glycerol 3-phosphate:ubiquinone oxidoreductase DN Sn-glycerol 3-phosphate:ubiquinone oxidoreductase (EC 1.1.5.3) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR031656; PF16901; sufficient; // AC GenProp1505 DE Bacillithiol biosynthesis TP PATHWAY AU Keseler I TH 1 DC Bacillithiol biosynthesis DR MetaCyc; PWY8J2-1; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-malate glycosyltransferase DN L-malate glycosyltransferase RQ 1 EV IPR023881; TIGR03999; sufficient; -- SN 2 ID Malyl-N-acetyl-D-glucosamine N-acetyl hydrolase DN Malyl-N-acetyl-D-glucosamine N-acetyl hydrolase RQ 1 EV IPR003737; PF02585; sufficient; EV IPR023842; TIGR04001; sufficient; EV IPR023841; TIGR04000; sufficient; -- SN 3 ID Bacillithiol synthase DN Bacillithiol synthase RQ 1 EV IPR011199; PF10079; sufficient; EV IPR011199; TIGR03998; sufficient; // AC GenProp1506 DE 4-Aminobutanoate degradation I TP PATHWAY AU Caspi R TH 0 DC 4-Aminobutanoate degradation I DR MetaCyc; PWY-6535; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Aminobutyrate aminotransferase DN 4-Aminobutyrate aminotransferase (EC 2.6.1.19) RQ 1 EV IPR004631; TIGR00699; sufficient; EV IPR005814; PF00202; sufficient; EV IPR004632; TIGR00700; sufficient; -- SN 2 ID Succinate-semialdehyde dehydrogenase (NAD+) DN Succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) RQ 1 EV IPR010102; TIGR01780; sufficient; // AC GenProp1507 DE L-homocysteine biosynthesis TP PATHWAY AU Caspi R TH 0 DC L-homocysteine biosynthesis DR MetaCyc; PWY-5344; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID O-acetylhomoserine sulfhydrylase DN O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) RQ 1 EV IPR000277; PF01053; sufficient; EV IPR006235; TIGR01326; sufficient; -- SN 2 ID Homoserine O-acetyltransferase DN Homoserine O-acetyltransferase (EC 2.3.1.31) RQ 1 EV IPR008220; TIGR01392; sufficient; // AC GenProp1508 DE Violaxanthin, antheraxanthin and zeaxanthin interconversion TP PATHWAY AU Caspi R TH 2 DC Violaxanthin, antheraxanthin and zeaxanthin interconversion DR MetaCyc; PWY-5945; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Zeaxanthin epoxidase DN Zeaxanthin epoxidase RQ 1 EV IPR000253; PF00498; sufficient; EV IPR002938; PF01494; sufficient; -- SN 2 ID Antheraxanthin epoxidase DN Antheraxanthin epoxidase RQ 1 EV IPR000253; PF00498; sufficient; EV IPR002938; PF01494; sufficient; -- SN 3 ID Violaxanthin deepoxidase DN Violaxanthin deepoxidase RQ 1 EV IPR010788; PF07137; sufficient; -- SN 4 ID Violaxanthin de-epoxidase DN Violaxanthin de-epoxidase RQ 1 EV IPR010788; PF07137; sufficient; // AC GenProp1509 DE 1D-myo-inositol hexakisphosphate biosynthesis II (mammalian) TP PATHWAY AU Caspi R TH 3 DC 1D-myo-inositol hexakisphosphate biosynthesis II (mammalian) DR MetaCyc; PWY-6362; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol-1,4,5-trisphosphate 3-kinase DN Inositol-1,4,5-trisphosphate 3-kinase (EC 2.7.1.127) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 2 ID Inositol 1,3,4-triphosphate 6 kinase DN Inositol 1,3,4-triphosphate 6 kinase (EC 2.7.1.159) RQ 1 EV IPR008656; PF05770; sufficient; -- SN 3 ID Myo-inositol-1,3,4,6-tetrakisphosphate 5-kinase DN Myo-inositol-1,3,4,6-tetrakisphosphate 5-kinase (EC 2.7.1.140) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 4 ID Ins(1,3,4,5,6)P5 2-kinase DN Ins(1,3,4,5,6)P5 2-kinase (EC 2.7.1.158) RQ 1 EV IPR009286; PF06090; sufficient; -- SN 5 ID Inositol-1,3,4,5-tetrakisphosphate 5-phosphatase DN Inositol-1,3,4,5-tetrakisphosphate 5-phosphatase (EC 3.1.3.56) RQ 1 EV IPR005135; PF03372; sufficient; EV IPR000198; PF00620; sufficient; EV IPR031995; PF16726; sufficient; EV IPR031896; PF16776; sufficient; EV IPR002013; PF02383; sufficient; EV IPR015047; PF08952; sufficient; EV IPR000980; PF00017; sufficient; EV IPR001660; PF00536; sufficient; // AC GenProp1510 DE Fatty acid beta-oxidation II (peroxisome) TP PATHWAY AU Foerster H, Fulcher C, Zhang P TH 3 DC Fatty acid beta-oxidation II (peroxisome) DR MetaCyc; PWY-5136; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2,3,4-Saturated fatty acyl-CoA synthetase DN 2,3,4-Saturated fatty acyl-CoA synthetase (EC 6.2.1.3) RQ 1 EV IPR000873; PF00501; sufficient; -- SN 2 ID Enoyl-CoA hydratase DN Enoyl-CoA hydratase (EC 4.2.1.17) RQ 1 EV IPR001753; PF00378; sufficient; -- SN 3 ID 3-Ketoacyl-CoA thiolase DN 3-Ketoacyl-CoA thiolase (EC 2.3.1.16) RQ 1 EV IPR002155; TIGR01930; sufficient; -- SN 4 ID 3-Hydroxyacyl-CoA dehydrogenase DN 3-Hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) RQ 1 EV IPR001753; PF00378; sufficient; -- SN 5 ID Acyl-CoA oxidase DN Acyl-CoA oxidase (EC 1.3.3.6) RQ 1 EV IPR002655; PF01756; sufficient; EV IPR006091; PF02770; sufficient; EV IPR029320; PF14749; sufficient; EV IPR009075; PF00441; sufficient; EV IPR013786; PF02771; sufficient; // AC GenProp1511 DE D-myo-inositol-5-phosphate metabolism TP PATHWAY AU Caspi R TH 2 DC D-myo-inositol-5-phosphate metabolism DR MetaCyc; PWY-6367; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylinositol-5-phosphate 4-kinase DN Phosphatidylinositol-5-phosphate 4-kinase (EC 2.7.1.149) RQ 1 EV IPR002498; PF01504; sufficient; -- SN 2 ID 1-Phosphatidylinositol-4,5-bisphosphate phosphodiesterase DN 1-Phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) RQ 1 EV IPR000008; PF00168; sufficient; EV IPR000909; PF00388; sufficient; EV IPR001711; PF00387; sufficient; EV IPR015359; PF09279; sufficient; EV IPR014815; PF08703; sufficient; EV IPR000980; PF00017; sufficient; EV IPR001452; PF00018; sufficient; EV IPR000159; PF00788; sufficient; EV IPR001895; PF00617; sufficient; EV IPR001849; PF00169; sufficient; -- SN 3 ID Phosphatidylinositol-3,5-bisphosphate 3-phosphatase DN Phosphatidylinositol-3,5-bisphosphate 3-phosphatase (EC 3.1.3.95) RQ 1 EV IPR000306; PF01363; sufficient; EV IPR010569; PF06602; sufficient; -- SN 4 ID Phosphatidylinositol 4,5-bisphosphate 4-phosphatase DN Phosphatidylinositol 4,5-bisphosphate 4-phosphatase (EC 3.1.3.78) RQ 1 EV IPR019178; PF09788; sufficient; // AC GenProp1512 DE Fatty acid biosynthesis initiation I TP PATHWAY AU Caspi R, Zhang P TH 1 DC Fatty acid biosynthesis initiation I DR MetaCyc; PWY-4381; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Beta-ketoacyl-[acyl-carrier-protein] synthase DN Beta-ketoacyl-[acyl-carrier-protein] synthase (EC 2.3.1.180) RQ 1 EV IPR004655; TIGR00747; sufficient; -- SN 2 ID Malonyl CoA-acyl carrier protein transacylase, mitochondrial DN Malonyl CoA-acyl carrier protein transacylase, mitochondrial (EC 2.3.1.86) RQ 1 EV IPR004410; TIGR00128; sufficient; -- SN 3 ID Biotin carboxylase DN Biotin carboxylase (EC 2.1.3.15) RQ 1 EV IPR001095; PF03255; sufficient; EV IPR001095; TIGR00513; sufficient; EV IPR000438; TIGR00515; sufficient; // AC GenProp1513 DE Superpathway of thiamine diphosphate biosynthesis III (eukaryotes) TP PATHWAY AU Caspi R, Dreher K, Foerster H TH 1 DC Superpathway of thiamine diphosphate biosynthesis III (eukaryotes) DR MetaCyc; THISYNARA-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphomethylpyrimidine kinase DN Phosphomethylpyrimidine kinase (EC 2.7.4.7) RQ 1 EV IPR027574; TIGR04306; sufficient; -- SN 2 ID 4-Methyl-5-(beta-hydroxyethyl)thiazole phosphate synthase DN 4-Methyl-5-(beta-hydroxyethyl)thiazole phosphate synthase RQ 1 EV IPR002922; TIGR00292; sufficient; -- SN 3 ID Thiamine monophosphate pyrophosphorylase DN Thiamine monophosphate pyrophosphorylase (EC 2.5.1.3) RQ 1 EV IPR000417; PF02110; sufficient; EV IPR000417; TIGR00694; sufficient; // AC GenProp1514 DE D-glucarate degradation I TP PATHWAY AU Keseler I, Riley M TH 2 DC D-glucarate degradation I DR MetaCyc; GLUCARDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerate 2-kinase DN Glycerate 2-kinase (EC 2.7.1.165) RQ 1 EV IPR004381; PF02595; sufficient; EV IPR004381; TIGR00045; sufficient; -- SN 2 ID D-glucarate dehydratase DN D-glucarate dehydratase (EC 4.2.1.40) RQ 1 EV IPR017653; TIGR03247; sufficient; -- SN 3 ID Alpha-dehydro-beta-deoxy-D-glucarate aldolase DN Alpha-dehydro-beta-deoxy-D-glucarate aldolase (EC 4.1.2.20) RQ 1 EV IPR017648; TIGR03239; sufficient; -- SN 4 ID Tartronate semialdehyde reductase DN Tartronate semialdehyde reductase (EC 1.1.1.60) RQ 1 EV IPR006398; TIGR01505; sufficient; // AC GenProp1515 DE Succinate to cytochrome bd oxidase electron transfer TP PATHWAY AU Mackie A, Nolan L TH 0 DC Succinate to cytochrome bd oxidase electron transfer DR MetaCyc; PWY0-1353; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytochrome bd-I ubiquinol oxidase DN Cytochrome bd-I ubiquinol oxidase (EC 1.10.3.14) RQ 1 EV IPR002585; PF01654; sufficient; EV IPR003317; PF02322; sufficient; EV IPR003317; TIGR00203; sufficient; EV IPR011724; TIGR02106; sufficient; EV IPR012994; PF08173; sufficient; -- SN 2 ID Succinate dehydrogenase DN Succinate dehydrogenase (EC 1.3.5.1) RQ 1 EV IPR004489; TIGR00384; sufficient; EV IPR011281; TIGR01816; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR000701; PF01127; sufficient; EV IPR014314; TIGR02970; sufficient; EV IPR014312; TIGR02968; sufficient; // AC GenProp1516 DE Phosphatidylcholine biosynthesis V TP PATHWAY AU Fulcher C TH 1 DC Phosphatidylcholine biosynthesis V DR MetaCyc; PWY-6825; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylethanolamine N-methyltransferase DN Phosphatidylethanolamine N-methyltransferase (EC 2.1.1.17) RQ 1 EV IPR007318; PF04191; sufficient; -- SN 2 ID Phosphatidyl-N-methylethanolamine N-methyltransferase DN Phosphatidyl-N-methylethanolamine N-methyltransferase (EC 2.1.1.71) RQ 1 EV IPR007318; PF04191; sufficient; -- SN 3 ID Phosphatidyl-N-dimethylethanolamine N-methyltransferase DN Phosphatidyl-N-dimethylethanolamine N-methyltransferase (EC 2.1.1.71) RQ 1 EV IPR007318; PF04191; sufficient; // AC GenProp1517 DE Ganglio-series glycosphingolipids biosynthesis TP PATHWAY AU Caspi R TH 20 DC Ganglio-series glycosphingolipids biosynthesis DR MetaCyc; PWY-7836; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ganglioside GM3 beta-1,4 N-acetylgalactosaminyltransferase DN Ganglioside GM3 beta-1,4 N-acetylgalactosaminyltransferase (EC 2.4.1.92) RQ 1 EV IPR001173; PF00535; sufficient; -- SN 2 ID Lactosylceramide alpha-2,6-sialyltransferase DN Lactosylceramide alpha-2,6-sialyltransferase (EC 2.4.99.1) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 3 ID Ganglioside GM1a alpha-2,3-N-acetylneuraminyltransferase DN Ganglioside GM1a alpha-2,3-N-acetylneuraminyltransferase (EC 2.4.99.2) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 4 ID Lactosylceramide alpha-2,3-sialyltransferase DN Lactosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.9) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 5 ID Ceramide glucosyltransferase DN Ceramide glucosyltransferase (EC 2.4.1.80) RQ 1 EV IPR025993; PF13506; sufficient; -- SN 6 ID Ganglioside GM2 beta-1,3-galactosyltransferase DN Ganglioside GM2 beta-1,3-galactosyltransferase (EC 2.4.1.62) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 7 ID Glucosylceramide beta-1,4-galactosyltransferase DN Glucosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.274) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 8 ID Ganglioside GA2 beta-1,3-galactosyltransferase DN Ganglioside GA2 beta-1,3-galactosyltransferase (EC 2.4.1.62) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 9 ID Lactosylceramide beta-1,4 N-acetylgalactosaminyltransferase DN Lactosylceramide beta-1,4 N-acetylgalactosaminyltransferase (EC 2.4.1.92) RQ 1 EV IPR001173; PF00535; sufficient; -- SN 10 ID Ganglioside GD3 beta-1,4 N-acetylgalactosaminyltransferase DN Ganglioside GD3 beta-1,4 N-acetylgalactosaminyltransferase (EC 2.4.1.92) RQ 1 EV IPR001173; PF00535; sufficient; -- SN 11 ID Ganglioside GM3 alpha-2,8-sialyltransferase DN Ganglioside GM3 alpha-2,8-sialyltransferase (EC 2.4.99.8) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 12 ID Ganglioside GD2 beta-1,3-galactosyltransferase DN Ganglioside GD2 beta-1,3-galactosyltransferase (EC 2.4.1.62) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 13 ID Ganglioside GD1b alpha-2,3-N-acetylneuraminyltransferase DN Ganglioside GD1b alpha-2,3-N-acetylneuraminyltransferase (EC 2.4.99.2) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 14 ID Ganglioside GD1a alpha-2,8-sialyltransferase DN Ganglioside GD1a alpha-2,8-sialyltransferase (EC 2.4.99.8) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 15 ID Ganglioside GT1b alpha-2,8-sialyltransferase DN Ganglioside GT1b alpha-2,8-sialyltransferase (EC 2.4.99.8) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 16 ID Ganglioside GD3 alpha-2,8-sialyltransferase DN Ganglioside GD3 alpha-2,8-sialyltransferase (EC 2.4.99.8) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 17 ID Ganglioside GM1b alpha-2,8-sialyltransferase DN Ganglioside GM1b alpha-2,8-sialyltransferase (EC 2.4.99.8) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 18 ID Ganglioside GA1 alpha-2,3-sialyltransferase DN Ganglioside GA1 alpha-2,3-sialyltransferase (EC 2.4.99.4) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 19 ID Ganglioside GT3 beta-1,4 N-acetylgalactosaminyltransferase DN Ganglioside GT3 beta-1,4 N-acetylgalactosaminyltransferase (EC 2.4.1.92) RQ 1 EV IPR001173; PF00535; sufficient; -- SN 20 ID Ganglioside GT2 beta-1,3-galactosyltransferase DN Ganglioside GT2 beta-1,3-galactosyltransferase (EC 2.4.1.62) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 21 ID Ganglioside GT1c alpha-2,3-N-acetylneuraminyltransferase DN Ganglioside GT1c alpha-2,3-N-acetylneuraminyltransferase (EC 2.4.99.2) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 22 ID Ganglioside GQ1c alpha-2,8-sialyltransferase DN Ganglioside GQ1c alpha-2,8-sialyltransferase (EC 2.4.99.8) RQ 1 EV IPR001675; PF00777; sufficient; // AC GenProp1518 DE Lacto-series glycosphingolipids biosynthesis TP PATHWAY AU Caspi R TH 5 DC Lacto-series glycosphingolipids biosynthesis DR MetaCyc; PWY-7839; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase DN Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase (EC 2.4.1.206) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 2 ID Lactotriaosylceramide beta-1,3-galactosyltransferase DN Lactotriaosylceramide beta-1,3-galactosyltransferase (EC 2.4.1.86) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 3 ID Ceramide glucosyltransferase DN Ceramide glucosyltransferase (EC 2.4.1.80) RQ 1 EV IPR025993; PF13506; sufficient; -- SN 4 ID Lactotetraosylceramide alpha-2-fucosyltransferase DN Lactotetraosylceramide alpha-2-fucosyltransferase (EC 2.4.1.69) RQ 1 EV IPR002516; PF01531; sufficient; -- SN 5 ID Glucosylceramide beta-1,4-galactosyltransferase DN Glucosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.274) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 6 ID Lactotetraosylceramide alpha-2,3-sialyltransferase DN Lactotetraosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.9) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 7 ID Ganglioside 3'-isoLM1 alpha-2,6-sialyltransferase DN Ganglioside 3'-isoLM1 alpha-2,6-sialyltransferase (EC 2.4.99.1) RQ 1 EV IPR001675; PF00777; sufficient; // AC GenProp1520 DE Pentose phosphate pathway (oxidative branch) I TP PATHWAY AU Keseler I, Riley M, Ingraham J TH 1 DC Pentose phosphate pathway (oxidative branch) I DR MetaCyc; OXIDATIVEPENT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 6-Phosphogluconolactonase DN 6-Phosphogluconolactonase (EC 3.1.1.31) RQ 1 EV IPR019405; PF10282; sufficient; -- SN 2 ID Glucose-6-phosphate dehydrogenase DN Glucose-6-phosphate dehydrogenase (EC 1.1.1.49) RQ 1 EV IPR001282; TIGR00871; sufficient; -- SN 3 ID 6-Phosphogluconate dehydrogenase, decarboxylating DN 6-Phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) RQ 1 EV IPR006113; TIGR00873; sufficient; // AC GenProp1521 DE tRNA methylation (yeast) TP PATHWAY AU Caspi R TH 0 DC tRNA methylation (yeast) DR MetaCyc; PWY-6829; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID tRNA (guanine26-N2)-methyltransferase DN tRNA (guanine26-N2)-methyltransferase (EC 2.1.1.216) RQ 1 EV IPR002905; PF02005; sufficient; EV IPR002905; TIGR00308; sufficient; -- SN 2 ID tRNA (N2-methylguanine26-N2)-methyltransferase DN tRNA (N2-methylguanine26-N2)-methyltransferase (EC 2.1.1.216) RQ 1 EV IPR002905; PF02005; sufficient; EV IPR002905; TIGR00308; sufficient; // AC GenProp1522 DE Chitin degradation I (archaea) TP PATHWAY AU Fulcher C TH 5 DC Chitin degradation I (archaea) DR MetaCyc; PWY-6855; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Chitinase DN Chitinase (EC 3.2.1.14) RQ 1 EV IPR001223; PF00704; sufficient; EV IPR001919; PF00553; sufficient; EV IPR003610; PF02839; sufficient; -- SN 2 ID Glucosamine 6-phosphate isomerase DN Glucosamine 6-phosphate isomerase (EC 3.5.99.6) RQ 1 EV IPR001347; PF01380; sufficient; -- SN 3 ID N-acetyl-D-glucosamine deacetylase DN N-acetyl-D-glucosamine deacetylase (EC 3.5.1.33) RQ 1 EV IPR003737; PF02585; sufficient; -- SN 4 ID Exo-chitinase (non-reducing end) DN Exo-chitinase (non-reducing end) (EC 3.2.1.200) RQ 1 EV IPR001223; PF00704; sufficient; EV IPR001919; PF00553; sufficient; EV IPR003610; PF02839; sufficient; -- SN 5 ID N,N'-diacetylchitobiose deacetylase DN N,N'-diacetylchitobiose deacetylase (EC 3.5.1) RQ 1 EV IPR003737; PF02585; sufficient; -- SN 6 ID 2-Acetamido-4-O-(2-amino-2-deoxy-beta-D-glucopyranosyl)-2-deoxy-D-glucose exo-beta-D-glucosaminidase DN 2-Acetamido-4-O-(2-amino-2-deoxy-beta-D-glucopyranosyl)-2-deoxy-D-glucose exo-beta-D-glucosaminidase (EC 3.2.1) RQ 1 EV IPR013529; PF02449; sufficient; -- SN 7 ID ADP-dependent N-acetyl-D-glucosamine kinase DN ADP-dependent N-acetyl-D-glucosamine kinase (EC 2.7.1.147) RQ 1 EV IPR007666; PF04587; sufficient; // AC GenProp1523 DE 4-Aminobutanoate degradation III TP PATHWAY AU Caspi R TH 0 DC 4-Aminobutanoate degradation III DR MetaCyc; PWY-6536; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Aminobutyrate aminotransferase DN 4-Aminobutyrate aminotransferase (EC 2.6.1.19) RQ 1 EV IPR004631; TIGR00699; sufficient; EV IPR005814; PF00202; sufficient; -- SN 2 ID Succinate semialdehyde dehydrogenase DN Succinate semialdehyde dehydrogenase (EC 1.2.1.16) RQ 1 EV IPR010102; TIGR01780; sufficient; // AC GenProp1524 DE Complex N-linked glycan biosynthesis (vertebrates) TP PATHWAY AU Caspi R TH 8 DC Complex N-linked glycan biosynthesis (vertebrates) DR MetaCyc; PWY-7426; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase DN Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) RQ 1 EV IPR004139; PF03071; sufficient; -- SN 2 ID Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase DN Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) RQ 1 EV IPR007754; PF05060; sufficient; -- SN 3 ID Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase DN Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (EC 2.4.1.144) RQ 1 EV IPR006813; PF04724; sufficient; -- SN 4 ID Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase DN Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (EC 2.4.1.145) RQ 1 EV IPR006759; PF04666; sufficient; -- SN 5 ID Alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase DN Alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase (EC 2.4.1.155) RQ 1 EV IPR027833; PF15027; sufficient; -- SN 6 ID Glycoprotein 6-alpha-L-fucosyltransferase DN Glycoprotein 6-alpha-L-fucosyltransferase (EC 2.4.1.68) RQ 1 EV IPR001452; PF14604; sufficient; -- SN 7 ID Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase DN Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase (EC 3.2.1.114) RQ 1 EV IPR000602; PF01074; sufficient; EV IPR011682; PF07748; sufficient; EV IPR015341; PF09261; sufficient; -- SN 8 ID Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase DN Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase (EC 2.4.1.38) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 9 ID Beta-D-galactosyl-1,3-N-acetyl-D-galatosaminyl-glycoprotein alpha-2,3-N-acetylneuraminyltransferase DN Beta-D-galactosyl-1,3-N-acetyl-D-galatosaminyl-glycoprotein alpha-2,3-N-acetylneuraminyltransferase (EC 2.4.99.6) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 10 ID Beta-galactoside alpha-2,6-sialyltransferase DN Beta-galactoside alpha-2,6-sialyltransferase (EC 2.4.99.1) RQ 1 EV IPR001675; PF00777; sufficient; // AC GenProp1525 DE Tetrapyrrole biosynthesis II (from glycine) TP PATHWAY AU Caspi R TH 2 DC Tetrapyrrole biosynthesis II (from glycine) DR MetaCyc; PWY-5189; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 5-Aminolevulinate synthase DN 5-Aminolevulinate synthase (EC 2.3.1.37) RQ 1 EV IPR004839; PF00155; sufficient; EV IPR010961; TIGR01821; sufficient; EV IPR015118; PF09029; sufficient; -- SN 2 ID Porphobilinogen deaminase DN Porphobilinogen deaminase (EC 2.5.1.61) RQ 1 EV IPR000860; TIGR00212; sufficient; -- SN 3 ID Porphobilinogen synthase DN Porphobilinogen synthase (EC 4.2.1.24) RQ 1 EV IPR001731; PF00490; sufficient; -- SN 4 ID Uroporphyrinogen III cosynthetase DN Uroporphyrinogen III cosynthetase (EC 4.2.1.75) RQ 1 EV IPR003754; PF02602; sufficient; // AC GenProp1526 DE Chondroitin sulfate biosynthesis TP PATHWAY AU Caspi R TH 0 DR MetaCyc; PWY-6569; CC See MetaCyc for additional information and references relating to this CC property. -- SN 1 ID Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase DN Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135) RQ 1 EV IPR005027; PF03360; sufficient; -- SN 2 ID Glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase DN Glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase (EC 2.4.1.174) RQ 1 EV IPR008428; PF05679; sufficient; // AC GenProp1527 DE Myo-inositol degradation II TP PATHWAY AU Caspi R TH 3 DC Myo-inositol degradation II DR MetaCyc; PWY-7241; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Myo-inositol 2-dehydrogenase DN Myo-inositol 2-dehydrogenase (EC 1.1.1.18) RQ 1 EV IPR030827; TIGR04380; sufficient; -- SN 2 ID 2-Inosose 4-dehydrogenase DN 2-Inosose 4-dehydrogenase (EC 1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; -- SN 3 ID 2,4-Didehydro-inositol hydratase DN 2,4-Didehydro-inositol hydratase RQ 1 EV IPR003785; PF02633; sufficient; -- SN 4 ID 5-Dehydro-L-gluconate epimerase DN 5-Dehydro-L-gluconate epimerase (EC 5.3.3) RQ 1 EV IPR013022; PF01261; sufficient; -- SN 5 ID D-tagaturonate epimerase DN D-tagaturonate epimerase (EC 5.1.2.7) RQ 1 EV IPR032586; PF16257; sufficient; // AC GenProp1528 DE Guanine and guanosine salvage TP PATHWAY AU Caspi R TH 0 DC Guanine and guanosine salvage DR MetaCyc; PWY-6620; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Guanine phosphoribosyltransferase DN Guanine phosphoribosyltransferase (EC 2.4.2.8) RQ 1 EV IPR005904; TIGR01203; sufficient; -- SN 2 ID Guanosine phosphorylase DN Guanosine phosphorylase (EC 2.4.2.15) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR004402; TIGR00107; sufficient; // AC GenProp1529 DE Superpathway of fucose and rhamnose degradation TP PATHWAY AU N/A TH 2 DC Superpathway of fucose and rhamnose degradation DR MetaCyc; FUC-RHAMCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Fuculose-1-phosphate aldolase DN Fuculose-1-phosphate aldolase (EC 4.1.2.17) RQ 1 EV IPR004782; TIGR01086; sufficient; -- SN 2 ID NAD+ L-lactaldehyde dehydrogenase DN NAD+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 3 ID L-1,2-propanediol oxidoreductase DN L-1,2-propanediol oxidoreductase (EC 1.1.1.77) RQ 1 EV IPR013460; TIGR02638; sufficient; -- SN 4 ID Rhamnulose-1-phosphate aldolase DN Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) RQ 1 EV IPR013447; TIGR02624; sufficient; // AC GenProp1530 DE Superpathway of cholesterol biosynthesis TP PATHWAY AU N/A TH 2 DC Superpathway of cholesterol biosynthesis DR MetaCyc; PWY66-5; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID Dimethylallyltransferase DN Dimethylallyltransferase (EC 2.5.1.1) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 3 ID Isopentenyl pyrophosphate isomerase DN Isopentenyl pyrophosphate isomerase (EC 5.3.3.2) RQ 1 EV IPR011876; TIGR02150; sufficient; -- SN 4 ID Squalene synthase DN Squalene synthase (EC 2.5.1.21) RQ 1 EV IPR002060; PF00494; sufficient; EV IPR006449; TIGR01559; sufficient; // AC GenProp1533 DE L-isoleucine degradation I TP PATHWAY AU Caspi R, Ying H TH 4 DC L-isoleucine degradation I DR MetaCyc; ILEUDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Hydroxy-2-methylbutyryl-CoA dehydrogenase DN 3-Hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID S-2-methylbutryl-CoA:FAD oxidoreductase DN S-2-methylbutryl-CoA:FAD oxidoreductase (EC 1.3.8.5) RQ 1 EV IPR006091; PF02770; sufficient; EV IPR009075; PF00441; sufficient; EV IPR013786; PF02771; sufficient; -- SN 3 ID (S)-3-methyl-2-oxopentanoate dehydrogenase (acylating) DN (S)-3-methyl-2-oxopentanoate dehydrogenase (acylating) (EC 1.2.1.25) RQ 1 EV IPR006258; TIGR01350; sufficient; -- SN 4 ID L-isoleucine:2-oxoglutarate aminotransferase DN L-isoleucine:2-oxoglutarate aminotransferase (EC 2.6.1.42) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005785; TIGR01122; sufficient; -- SN 5 ID 2-Methylacetoacetyl-CoA thiolase DN 2-Methylacetoacetyl-CoA thiolase (EC 2.3.1.9) RQ 1 EV IPR002155; TIGR01930; sufficient; -- SN 6 ID Tiglyl-CoA hydratase DN Tiglyl-CoA hydratase (EC 4.2.1.17) RQ 1 EV IPR001753; PF00378; sufficient; // AC GenProp1534 DE Kanosamine biosynthesis II TP PATHWAY AU Keseler I TH 1 DC Kanosamine biosynthesis II DR MetaCyc; PWY8J2-22; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucose-6-phosphate 3-dehydrogenase DN Glucose-6-phosphate 3-dehydrogenase (EC 1.1.1.361) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR004104; PF02894; sufficient; -- SN 2 ID 3-Oxo-glucose-6-phosphate:glutamate aminotransferase DN 3-Oxo-glucose-6-phosphate:glutamate aminotransferase (EC 2.6.1.104) RQ 1 EV IPR000653; PF01041; sufficient; -- SN 3 ID Kanosamine-6-phosphate phosphatase DN Kanosamine-6-phosphate phosphatase (EC 3.1.3.92) RQ 1 EV IPR006379; TIGR01484; sufficient; // AC GenProp1535 DE Formate to trimethylamine N-oxide electron transfer TP PATHWAY AU Mackie A, Nolan L TH 0 DC Formate to trimethylamine N-oxide electron transfer DR MetaCyc; PWY0-1355; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Formate dehydrogenase (menaquinone) DN Formate dehydrogenase (menaquinone) (EC 1.17.5.3) RQ 1 EV IPR006443; TIGR01553; sufficient; EV IPR006470; TIGR01582; sufficient; EV IPR006471; TIGR01583; sufficient; -- SN 2 ID Trimethylamine-N-oxide reductase (menaquinone) DN Trimethylamine-N-oxide reductase (menaquinone) (EC 1.7.2.3) RQ 1 EV IPR009154; TIGR02162; sufficient; EV IPR006658; TIGR00509; sufficient; EV IPR011887; TIGR02164; sufficient; // AC GenProp1536 DE Pyruvate decarboxylation to acetyl CoA TP PATHWAY AU Caspi R, Ingraham J TH 1 DC Pyruvate decarboxylation to acetyl CoA DR MetaCyc; PYRUVDEHYD-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dihydrolipoamide dehydrogenase DN Dihydrolipoamide dehydrogenase (EC 1.8.1.4) RQ 1 EV IPR006258; TIGR01350; sufficient; -- SN 2 ID Dihydrolipoyllysine-residue acetyltransferase DN Dihydrolipoyllysine-residue acetyltransferase (EC 2.3.1.12) RQ 1 EV IPR006256; TIGR01348; sufficient; EV IPR006257; TIGR01349; sufficient; -- SN 3 ID Pyruvate dehydrogenase DN Pyruvate dehydrogenase (EC 1.2.4.1) RQ 1 EV IPR004660; TIGR00759; sufficient; EV IPR017597; TIGR03182; sufficient; // AC GenProp1537 DE NADH to fumarate electron transfer TP PATHWAY AU Mackie A, Krummenacker M TH 0 DC NADH to fumarate electron transfer DR MetaCyc; PWY0-1336; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Fumarate reductase DN Fumarate reductase (EC 1.3.5.4) RQ 1 EV IPR004489; TIGR00384; sufficient; EV IPR005884; TIGR01176; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR003510; PF02300; sufficient; EV IPR003418; PF02313; sufficient; -- SN 2 ID NADH:menaquinone oxidoreductase (H+-transporting) DN NADH:menaquinone oxidoreductase (H+-transporting) (EC 1.6.5) RQ 1 EV IPR000440; PF00507; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR001694; PF00146; sufficient; EV IPR010226; TIGR01971; sufficient; EV IPR001457; PF00499; sufficient; EV IPR001133; PF00420; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR010227; TIGR01972; sufficient; EV IPR010096; TIGR01770; sufficient; // AC GenProp1538 DE Superpathway of aromatic amino acid biosynthesis TP PATHWAY AU N/A TH 1 DC Superpathway of aromatic amino acid biosynthesis DR MetaCyc; COMPLETE-ARO-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Anthranilate synthase DN Anthranilate synthase (EC 4.1.3.27) RQ 1 EV IPR005257; TIGR00565; sufficient; EV IPR005940; TIGR01245; sufficient; -- SN 2 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; PF01264; sufficient; EV IPR000453; TIGR00033; sufficient; -- SN 3 ID Chorismate mutase DN Chorismate mutase (EC 5.4.99.5) RQ 1 EV IPR003099; PF02153; sufficient; EV IPR011277; TIGR01799; sufficient; EV IPR001086; PF00800; sufficient; EV IPR010952; TIGR01797; sufficient; // AC GenProp1539 DE Neolacto-series glycosphingolipids biosynthesis TP PATHWAY AU Caspi R TH 10 DC Neolacto-series glycosphingolipids biosynthesis DR MetaCyc; PWY-7841; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Neolactotetraosylceramide beta-1,3-galactosyltransferase DN Neolactotetraosylceramide beta-1,3-galactosyltransferase (EC 2.4.1.149) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 2 ID Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase DN Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase (EC 2.4.1.206) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 3 ID Neolactotetraosylceramide alpha-2,3-sialyltransferase DN Neolactotetraosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.6) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 4 ID Ceramide glucosyltransferase DN Ceramide glucosyltransferase (EC 2.4.1.80) RQ 1 EV IPR025993; PF13506; sufficient; -- SN 5 ID Glucosylceramide beta-1,4-galactosyltransferase DN Glucosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.274) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 6 ID Lactotriaosylceramide beta-1,4-galactosyltransferase DN Lactotriaosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.275) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 7 ID Neolactopentaosylceramide beta-1,4-galactosyltransferase DN Neolactopentaosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.275) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 8 ID Neolactohexaosylceramide beta-1,3-galactosyltransferase DN Neolactohexaosylceramide beta-1,3-galactosyltransferase (EC 2.4.1.149) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 9 ID Neolactoheptaosylceramide beta-1,4-galactosyltransferase DN Neolactoheptaosylceramide beta-1,4-galactosyltransferase (EC 2.4.1.275) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 10 ID Neolactooctaosylceramide alpha-2,3-sialyltransferase DN Neolactooctaosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.6) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 11 ID Neolactohexaosylceramide alpha-2,3-sialyltransferase DN Neolactohexaosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.6) RQ 1 EV IPR001675; PF00777; sufficient; -- SN 12 ID Neolactosylceramide alpha-2,6-sialyltransferase DN Neolactosylceramide alpha-2,6-sialyltransferase (EC 2.4.99.1) RQ 1 EV IPR001675; PF00777; sufficient; // AC GenProp1540 DE Pyrimidine ribonucleosides salvage III TP PATHWAY AU Caspi R TH 0 DC Pyrimidine ribonucleosides salvage III DR MetaCyc; PWY-7195; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytosine deaminase DN Cytosine deaminase (EC 3.5.4.1) RQ 1 EV IPR013108; PF07969; sufficient; EV IPR002125; PF00383; sufficient; -- SN 2 ID Cytidine nucleosidase DN Cytidine nucleosidase (EC 3.2.2.3) RQ 1 EV IPR001910; PF01156; sufficient; // AC GenProp1541 DE Superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) TP PATHWAY TH 0 DC Superpathway of geranylgeranyldiphosphate biosynthesis I (via DC mevalonate) DR MetaCyc; PWY-5910; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Geranylgeranyl diphosphate synthase DN Geranylgeranyl diphosphate synthase (EC 2.5.1.29) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; // AC GenProp1542 DE Phosphatidylethanolamine biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Phosphatidylethanolamine biosynthesis I DR MetaCyc; PWY-5669; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylserine decarboxylase DN Phosphatidylserine decarboxylase (EC 4.1.1.65) RQ 1 EV IPR003817; PF02666; sufficient; EV IPR033177; TIGR00163; sufficient; -- SN 2 ID Phosphatidylserine synthase DN Phosphatidylserine synthase (EC 2.7.8.8) RQ 1 EV IPR025202; PF13091; sufficient; // AC GenProp1543 DE Pyruvate fermentation to acetate IV TP PATHWAY AU Caspi R TH 1 DC Pyruvate fermentation to acetate IV DR MetaCyc; PWY-5485; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetate kinase DN Acetate kinase (EC 2.7.2.1) RQ 1 EV IPR000890; PF00871; sufficient; EV IPR004372; TIGR00016; sufficient; EV IPR005862; TIGR01142; sufficient; -- SN 2 ID Phosphotransacetylase DN Phosphotransacetylase (EC 2.3.1.8) RQ 1 EV IPR002505; PF01515; sufficient; EV IPR004614; TIGR00651; sufficient; EV IPR010766; PF07085; sufficient; -- SN 3 ID Pyruvate formate lyase DN Pyruvate formate lyase (EC 2.3.1.54) RQ 1 EV IPR005949; TIGR01255; sufficient; // AC GenProp1544 DE Fatty acid beta-oxidation (peroxisome, yeast) TP PATHWAY AU Foerster H TH 3 DC Fatty acid beta-oxidation (peroxisome, yeast) DR MetaCyc; PWY-7288; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2,3,4-Saturated fatty acyl-CoA synthetase DN 2,3,4-Saturated fatty acyl-CoA synthetase (EC 6.2.1.3) RQ 1 EV IPR000873; PF00501; sufficient; -- SN 2 ID 3-Ketoacyl-CoA thiolase DN 3-Ketoacyl-CoA thiolase (EC 2.3.1.16) RQ 1 EV IPR002155; TIGR01930; sufficient; -- SN 3 ID Acyl-CoA oxidase DN Acyl-CoA oxidase (EC 1.3.3.6) RQ 1 EV IPR002655; PF01756; sufficient; EV IPR006091; PF02770; sufficient; EV IPR029320; PF14749; sufficient; -- SN 4 ID (R)-specific enoyl-CoA hydratase DN (R)-specific enoyl-CoA hydratase (EC 4.2.1.119) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 5 ID 3-Hydroxyacyl-CoA dehydrogenase DN 3-Hydroxyacyl-CoA dehydrogenase (EC 1.1.1.M19) RQ 1 EV IPR002347; PF00106; sufficient; // AC GenProp1545 DE i antigen and I antigen biosynthesis TP PATHWAY AU Caspi R TH 3 DC i antigen and I antigen biosynthesis DR MetaCyc; PWY-7837; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Type 2 precursor disaccharide beta-1,3-galactosyltransferase DN Type 2 precursor disaccharide beta-1,3-galactosyltransferase (EC 2.4.1.149) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 2 ID N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase DN N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (EC 2.4.1.150) RQ 1 EV IPR003406; PF02485; sufficient; -- SN 3 ID Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase DN Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase (EC 2.4.1.38) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 4 ID Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase DN Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase (EC 2.4.1.38) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 5 ID Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase DN Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase (EC 2.4.1.38) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; // AC GenProp1546 DE Sulfoquinovosyl diacylglycerol biosynthesis TP PATHWAY AU Caspi R TH 0 DC Sulfoquinovosyl diacylglycerol biosynthesis DR MetaCyc; PWYQT-4427; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-sulfoquinovose synthase DN UDP-sulfoquinovose synthase (EC 3.13.1.1) RQ 1 EV IPR001509; PF01370; sufficient; -- SN 2 ID Sulfoquinovosyldiacylglycerol synthase DN Sulfoquinovosyldiacylglycerol synthase (EC 2.4.1.M2) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR028098; PF13439; sufficient; // AC GenProp1547 DE Anthocyanidin modification (Arabidopsis) TP PATHWAY AU Foerster H TH 7 DC Anthocyanidin modification (Arabidopsis) DR MetaCyc; PWY-7450; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cyanidin 3-O-glucoside 2''-O-xylosyltransferase DN Cyanidin 3-O-glucoside 2''-O-xylosyltransferase (EC 2.4.2.51) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 2 ID Cyanidin 3-O-glucoside-p-coumaroyltransferase DN Cyanidin 3-O-glucoside-p-coumaroyltransferase (EC 2.3.1) RQ 1 EV IPR003480; PF02458; sufficient; -- SN 3 ID Cyanidin 3-O-p-coumaroylglucoside 2-O-xylosyltransferase DN Cyanidin 3-O-p-coumaroylglucoside 2-O-xylosyltransferase (EC 2.4.2) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 4 ID Cyanidin 3-O-sambubioside 6''-O-p-coumaroyltransferase DN Cyanidin 3-O-sambubioside 6''-O-p-coumaroyltransferase (EC 2.3.1) RQ 1 EV IPR003480; PF02458; sufficient; -- SN 5 ID Cyanidin 3-O-[2-O-(xylosyl)-6-O-(p-coumaroyl) glucoside] 5-O-glucosyltransferase DN Cyanidin 3-O-[2-O-(xylosyl)-6-O-(p-coumaroyl) glucoside] 5-O-glucosyltransferase (EC 2.4.1) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 6 ID Cyanidin 3-O-[2-O-(xylosyl)-6-O-(p-coumaroyl) glucoside] 5-O-glucoside malonyltransferase DN Cyanidin 3-O-[2-O-(xylosyl)-6-O-(p-coumaroyl) glucoside] 5-O-glucoside malonyltransferase (EC 2.3.1) RQ 1 EV IPR003480; PF02458; sufficient; -- SN 7 ID Cyanidin 3-O-[2-O-(2'-O-(sinapoyl) xylosyl) 6-O-(p-coumaroyl) glucoside] 5-O-[6-O-(malonyl) glucoside] sinapoyltransferase DN Cyanidin 3-O-[2-O-(2'-O-(sinapoyl) xylosyl) 6-O-(p-coumaroyl) glucoside] 5-O-[6-O-(malonyl) glucoside] sinapoyltransferase (EC 2.3.1) RQ 1 EV IPR001563; PF00450; sufficient; -- SN 8 ID Cyanidin 3-O-[2-O-(2'-O-(sinapoyl) xylosyl) 6-O-(p-O-(glucosyl)-p-coumaroyl) glucoside] 5-O-[6-O-(malonyl) glucoside] acylglucose glucosyltransferase DN Cyanidin 3-O-[2-O-(2'-O-(sinapoyl) xylosyl) 6-O-(p-O-(glucosyl)-p-coumaroyl) glucoside] 5-O-[6-O-(malonyl) glucoside] acylglucose glucosyltransferase (EC 2.4.1) RQ 1 EV IPR001360; PF00232; sufficient; -- SN 9 ID Cyanidin 3-O-glucosyltransferase DN Cyanidin 3-O-glucosyltransferase (EC 2.4.1.115) RQ 1 EV IPR002213; PF00201; sufficient; // AC GenProp1548 DE D-myo-inositol (1,4,5)-trisphosphate biosynthesis TP PATHWAY AU Caspi R TH 3 DC D-myo-inositol (1,4,5)-trisphosphate biosynthesis DR MetaCyc; PWY-6351; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylinositol 4-kinase DN Phosphatidylinositol 4-kinase (EC 2.7.1.67) RQ 1 EV IPR000403; PF00454; sufficient; EV IPR001263; PF00613; sufficient; -- SN 2 ID Phosphatidylinositol-5-phosphate 4-kinase DN Phosphatidylinositol-5-phosphate 4-kinase (EC 2.7.1.149) RQ 1 EV IPR002498; PF01504; sufficient; -- SN 3 ID Phosphatidylinositol-4-phosphate 5-kinase DN Phosphatidylinositol-4-phosphate 5-kinase (EC 2.7.1.68) RQ 1 EV IPR002498; PF01504; sufficient; -- SN 4 ID CDP-diacylglycerol:myo-inositol phosphatidyltransferase DN CDP-diacylglycerol:myo-inositol phosphatidyltransferase (EC 2.7.8.11) RQ 1 EV IPR000462; PF01066; sufficient; -- SN 5 ID 1-Phosphatidylinositol-4,5-bisphosphate phosphodiesterase DN 1-Phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) RQ 1 EV IPR000008; PF00168; sufficient; EV IPR000909; PF00388; sufficient; EV IPR001711; PF00387; sufficient; EV IPR015359; PF09279; sufficient; EV IPR014815; PF08703; sufficient; EV IPR000980; PF00017; sufficient; EV IPR001452; PF00018; sufficient; EV IPR000159; PF00788; sufficient; EV IPR001895; PF00617; sufficient; EV IPR001849; PF00169; sufficient; // AC GenProp1549 DE UDP-N-acetyl-alpha-D-mannosaminouronate biosynthesis TP PATHWAY AU Caspi R TH 0 DC UDP-N-acetyl-alpha-D-mannosaminouronate biosynthesis DR MetaCyc; PWY-7335; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-N-acetylglucosamine 2-epimerase DN UDP-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) RQ 1 EV IPR029767; TIGR00236; sufficient; -- SN 2 ID UDP-N-acetyl-D-mannosamine dehydrogenase DN UDP-N-acetyl-D-mannosamine dehydrogenase (EC 1.1.1.336) RQ 1 EV IPR017476; TIGR03026; sufficient; // AC GenProp1550 DE Superpathway of L-tryptophan biosynthesis TP PATHWAY AU Caspi R TH 0 DC Superpathway of L-tryptophan biosynthesis DR MetaCyc; PWY-6629; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Anthranilate synthase DN Anthranilate synthase (EC 4.1.3.27) RQ 1 EV IPR005257; TIGR00565; sufficient; EV IPR005940; TIGR01245; sufficient; -- SN 2 ID Chorismate synthase DN Chorismate synthase (EC 4.2.3.5) RQ 1 EV IPR000453; PF01264; sufficient; EV IPR000453; TIGR00033; sufficient; // AC GenProp1551 DE L-tryptophan degradation X (mammalian, via tryptamine) TP PATHWAY AU Fulcher C TH 2 DC L-tryptophan degradation X (mammalian, via tryptamine) DR MetaCyc; PWY-6307; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Tryptophan decarboxylase DN Tryptophan decarboxylase (EC 4.1.1.105) RQ 1 EV IPR002129; PF00282; sufficient; -- SN 2 ID Indole acetaldehyde dehydrogenase DN Indole acetaldehyde dehydrogenase (EC 1.2.1.3) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 3 ID Indole acetaldehyde reductase DN Indole acetaldehyde reductase (EC 1.1.1.2) RQ 1 EV IPR023210; PF00248; sufficient; -- SN 4 ID Tryptamine oxidase DN Tryptamine oxidase (EC 1.4.3.4) RQ 1 EV IPR002937; PF01593; sufficient; // AC GenProp1552 DE Allopregnanolone biosynthesis TP PATHWAY AU Montanucci L TH 0 DC Allopregnanolone biosynthesis DR MetaCyc; PWY-7455; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 5-Alpha-progesterone reductase DN 5-Alpha-progesterone reductase (EC 1.3.1.22) RQ 1 EV IPR001104; PF02544; sufficient; -- SN 2 ID 3-Alpha-hydroxysteroid dehydrogenase DN 3-Alpha-hydroxysteroid dehydrogenase (EC 1.1.1.213) RQ 1 EV IPR023210; PF00248; sufficient; // AC GenProp1553 DE L-homoserine biosynthesis TP PATHWAY AU Paley S, Shearer A TH 1 DC L-homoserine biosynthesis DR MetaCyc; HOMOSERSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate-semialdehyde dehydrogenase DN Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) RQ 1 EV IPR011534; TIGR01745; sufficient; EV IPR005676; TIGR00978; sufficient; -- SN 2 ID Aspartate kinase DN Aspartate kinase (EC 2.7.2.4) RQ 1 EV IPR005260; TIGR00656; sufficient; -- SN 3 ID Homoserine dehydrogenase DN Homoserine dehydrogenase (EC 1.1.1.3) RQ 1 EV IPR001048; PF00696; sufficient; EV IPR001341; TIGR00657; sufficient; EV IPR001342; PF00742; sufficient; EV IPR002912; PF01842; sufficient; EV IPR005106; PF03447; sufficient; EV IPR027795; PF13840; sufficient; // AC GenProp1554 DE Nitrate reduction V (assimilatory) TP PATHWAY AU Caspi R TH 2 DC Nitrate reduction V (assimilatory) DR MetaCyc; PWY-5675; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutamine synthetase DN Glutamine synthetase (EC 6.3.1.2) RQ 1 EV IPR008146; PF00120; sufficient; EV IPR008147; PF03951; sufficient; -- SN 2 ID Glutamate dehydrogenase 2 (NADP-dependent) DN Glutamate dehydrogenase 2 (NADP-dependent) (EC 1.4.1.4) RQ 1 EV IPR006096; PF00208; sufficient; EV IPR006097; PF02812; sufficient; -- SN 3 ID Nitrate reductase DN Nitrate reductase (EC 1.7.1.3) RQ 1 EV IPR000572; PF00174; sufficient; EV IPR001199; PF00173; sufficient; EV IPR001433; PF00175; sufficient; EV IPR005066; PF03404; sufficient; EV IPR008333; PF00970; sufficient; -- SN 4 ID Nitrite reductase DN Nitrite reductase (EC 1.7.1.4) RQ 1 EV IPR005117; PF03460; sufficient; EV IPR006067; PF01077; sufficient; EV IPR007419; PF04324; sufficient; EV IPR012744; TIGR02374; sufficient; EV IPR017941; PF00355; sufficient; EV IPR023753; PF07992; sufficient; // AC GenProp1555 DE tRNA-uridine 2-thiolation (bacteria) TP PATHWAY AU Caspi R TH 6 DC tRNA-uridine 2-thiolation (bacteria) DR MetaCyc; PWY-7892; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID IscS:TusA sulfurtransferase DN IscS:TusA sulfurtransferase (EC 2.8.1) RQ 1 EV IPR001455; PF01206; sufficient; -- SN 2 ID TusD:TusE sulfurtransferase DN TusD:TusE sulfurtransferase (EC 2.8.1) RQ 1 EV IPR007453; PF04358; sufficient; EV IPR007453; TIGR03342; sufficient; -- SN 3 ID TusA:TusD sulfurtransferase DN TusA:TusD sulfurtransferase (EC 2.8.1) RQ 1 EV IPR007215; PF04077; sufficient; EV IPR007215; TIGR03011; sufficient; EV IPR017462; TIGR03010; sufficient; EV IPR017463; TIGR03012; sufficient; -- SN 4 ID 5-Carboxymethylaminomethyluridine-tRNA synthase DN 5-Carboxymethylaminomethyluridine-tRNA synthase RQ 1 EV IPR002218; PF01134; sufficient; EV IPR004416; TIGR00136; sufficient; EV IPR004520; TIGR00450; sufficient; -- SN 5 ID tRNA-specific 2-thiouridylase DN tRNA-specific 2-thiouridylase (EC 2.8.1.13) RQ 1 EV IPR004506; TIGR00420; sufficient; -- SN 6 ID Cysteine desulfurase DN Cysteine desulfurase RQ 1 EV IPR010240; TIGR02006; sufficient; -- SN 7 ID 5-Methylaminomethyl-2-thiouridine-forming methyltransferase DN 5-Methylaminomethyl-2-thiouridine-forming methyltransferase (EC 2.1.1.61) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR008471; PF05430; sufficient; EV IPR017610; TIGR03197; sufficient; -- SN 8 ID 5-Aminomethyl-2-thiouridine synthase DN 5-Aminomethyl-2-thiouridine synthase RQ 1 EV IPR006076; PF01266; sufficient; EV IPR008471; PF05430; sufficient; EV IPR017610; TIGR03197; sufficient; // AC GenProp1556 DE Glycolate and glyoxylate degradation II TP PATHWAY AU Riley M, Ingraham J TH 0 DC Glycolate and glyoxylate degradation II DR MetaCyc; GLYOXDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycolate oxidase DN Glycolate oxidase (EC 1.1.99.14) RQ 1 EV IPR004490; TIGR00387; sufficient; -- SN 2 ID Malate synthase DN Malate synthase (EC 2.3.3.9) RQ 1 EV IPR001465; PF01274; sufficient; EV IPR006253; TIGR01345; sufficient; // AC GenProp1557 DE Entner-Doudoroff pathway I TP PATHWAY AU Riley M, Ingraham J TH 0 DC Entner-Doudoroff pathway I DR MetaCyc; ENTNER-DOUDOROFF-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Dehydro-3-deoxy-phosphogluconate aldolase DN 2-Dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) RQ 1 EV IPR000887; PF01081; sufficient; EV IPR000887; TIGR01182; sufficient; -- SN 2 ID Phosphogluconate dehydratase DN Phosphogluconate dehydratase (EC 4.2.1.12) RQ 1 EV IPR000581; PF00920; sufficient; EV IPR004786; TIGR01196; sufficient; // AC GenProp1558 DE Sterol:steryl ester interconversion (yeast) TP PATHWAY AU Foerster H TH 2 DC Sterol:steryl ester interconversion (yeast) DR MetaCyc; PWY-7424; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lanosterol O-acyltransferase DN Lanosterol O-acyltransferase (EC 2.3.1.26) RQ 1 EV IPR004299; PF03062; sufficient; -- SN 2 ID Lanosterol esterase DN Lanosterol esterase (EC 3.1.1.13) RQ 1 EV IPR000073; PF00561; sufficient; EV IPR006693; PF04083; sufficient; -- SN 3 ID Ergosterol O-acyltransferase DN Ergosterol O-acyltransferase (EC 2.3.1.26) RQ 1 EV IPR004299; PF03062; sufficient; -- SN 4 ID Ergosterol esterase DN Ergosterol esterase (EC 3.1.1.13) RQ 1 EV IPR000073; PF00561; sufficient; EV IPR006693; PF04083; sufficient; // AC GenProp1559 DE 2'-Deoxy-alpha-D-ribose 1-phosphate degradation TP PATHWAY AU Caspi R TH 1 DC 2'-Deoxy-alpha-D-ribose 1-phosphate degradation DR MetaCyc; PWY-7180; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR003361; TIGR03215; sufficient; -- SN 2 ID D-deoxyribose 1,5-phosphomutase DN D-deoxyribose 1,5-phosphomutase (EC 5.4.2.7) RQ 1 EV IPR010045; TIGR01696; sufficient; -- SN 3 ID Deoxyribose-phosphate aldolase DN Deoxyribose-phosphate aldolase (EC 4.1.2.4) RQ 1 EV IPR002915; PF01791; sufficient; EV IPR011343; TIGR00126; sufficient; // AC GenProp1560 DE 2-Carboxy-1,4-naphthoquinol biosynthesis TP PATHWAY AU Keseler I, Caspi R TH 5 DC 2-Carboxy-1,4-naphthoquinol biosynthesis DR MetaCyc; PWY-5837; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase DN 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (EC 2.2.1.9) RQ 1 EV IPR004433; TIGR00173; sufficient; -- SN 2 ID Isochorismate synthase DN Isochorismate synthase (EC 5.4.4.2) RQ 1 EV IPR004561; TIGR00543; sufficient; -- SN 3 ID Naphthoyl-CoA synthase DN Naphthoyl-CoA synthase (EC 4.1.3.36) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR010198; TIGR01929; sufficient; -- SN 4 ID O-succinylbenzoate-CoA ligase DN O-succinylbenzoate-CoA ligase (EC 6.2.1.26) RQ 1 EV IPR010192; TIGR01923; sufficient; -- SN 5 ID O-succinylbenzoate synthase DN O-succinylbenzoate synthase (EC 4.2.1.113) RQ 1 EV IPR010197; TIGR01928; sufficient; -- SN 6 ID (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase DN (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20) RQ 1 EV IPR022485; TIGR03695; sufficient; -- SN 7 ID 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase DN 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase (EC 3.1.2.28) RQ 1 EV IPR006683; PF03061; sufficient; EV IPR003736; TIGR00369; sufficient; // AC GenProp1561 DE Superpathway of coenzyme A biosynthesis III (mammals) TP PATHWAY AU Weerasinghe D, Keseler I, Arnaud M, Foerster H TH 0 DC Superpathway of coenzyme A biosynthesis III (mammals) DR MetaCyc; COA-PWY-1; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pantothenate kinase DN Pantothenate kinase (EC 2.7.1.33) RQ 1 EV IPR004567; PF03630; sufficient; EV IPR004567; TIGR00555; sufficient; -- SN 2 ID Phosphopantothenate-cysteine ligase DN Phosphopantothenate-cysteine ligase (EC 6.3.2.51) RQ 1 EV IPR007085; PF04127; sufficient; // AC GenProp1562 DE Fatty acid salvage TP PATHWAY AU Caspi R TH 4 DC Fatty acid salvage DR MetaCyc; PWY-7094; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID (S)-3-hydroxydecanoyl-CoA dehydrogenase DN (S)-3-hydroxydecanoyl-CoA dehydrogenase (EC 1.1.1.35) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012799; TIGR02437; sufficient; -- SN 2 ID Beta-ketodecanoyl-[acyl-carrier-protein] synthase DN Beta-ketodecanoyl-[acyl-carrier-protein] synthase (EC 2.3.1.207) RQ 1 EV IPR013747; PF08541; sufficient; EV IPR013751; PF08545; sufficient; -- SN 3 ID Decanoate--CoA ligase DN Decanoate--CoA ligase (EC 6.2.1.3) RQ 1 EV IPR000873; PF00501; sufficient; EV IPR025110; PF13193; sufficient; -- SN 4 ID Decanoyl-CoA dehydrogenase DN Decanoyl-CoA dehydrogenase (EC 1.3.8.7) RQ 1 EV IPR006091; PF02770; sufficient; EV IPR009075; PF00441; sufficient; EV IPR013786; PF02771; sufficient; EV IPR015396; PF09317; sufficient; -- SN 5 ID Trans-Delta2-decenoyl-CoA hydratase DN Trans-Delta2-decenoyl-CoA hydratase (EC 4.2.1.17) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012799; TIGR02437; sufficient; -- SN 6 ID Acetyl-CoA C-octanoyltransferase DN Acetyl-CoA C-octanoyltransferase (EC 2.3.1.16) RQ 1 EV IPR002155; TIGR01930; sufficient; EV IPR012805; TIGR02445; sufficient; // AC GenProp1563 DE Glycerol-3-phosphate to cytochrome bo oxidase electron transfer TP PATHWAY AU Mackie A TH 0 DC Glycerol-3-phosphate to cytochrome bo oxidase electron transfer DR MetaCyc; PWY0-1561; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Sn-glycerol 3-phosphate:ubiquinone oxidoreductase DN Sn-glycerol 3-phosphate:ubiquinone oxidoreductase (EC 1.1.5.3) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR031656; PF16901; sufficient; -- SN 2 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; // AC GenProp1564 DE Trehalose degradation II (trehalase) TP PATHWAY AU Fulcher C, Keseler I, Caspi R TH 0 DC Trehalose degradation II (trehalase) DR MetaCyc; PWY0-1182; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucokinase DN Glucokinase (EC 2.7.1.2) RQ 1 EV IPR003836; PF02685; sufficient; EV IPR003836; TIGR00749; sufficient; -- SN 2 ID Trehalase DN Trehalase (EC 3.2.1.28) RQ 1 EV IPR001661; PF01204; sufficient; // AC GenProp1565 DE N-acetylglucosamine degradation II TP PATHWAY AU Caspi R TH 0 DC N-acetylglucosamine degradation II DR MetaCyc; PWY-6517; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID N-acetyl-D-glucosamine kinase DN N-acetyl-D-glucosamine kinase (EC 2.7.1.59) RQ 1 EV IPR000600; PF00480; sufficient; -- SN 2 ID N-acetylglucosamine-6-phosphate deacetylase DN N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) RQ 1 EV IPR003764; TIGR00221; sufficient; // AC GenProp1566 DE D-galactonate degradation TP PATHWAY AU Fulcher C, Keseler I, Riley M TH 1 DC D-galactonate degradation DR MetaCyc; GALACTCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Dehydro-3-deoxygalactonokinase DN 2-Dehydro-3-deoxygalactonokinase (EC 2.7.1.58) RQ 1 EV IPR007729; PF05035; sufficient; -- SN 2 ID 2-Dehydro-3-deoxy-6-phosphogalactonate aldolase DN 2-Dehydro-3-deoxy-6-phosphogalactonate aldolase (EC 4.1.2.21) RQ 1 EV IPR000887; PF01081; sufficient; -- SN 3 ID D-galactonate dehydratase DN D-galactonate dehydratase (EC 4.2.1.6) RQ 1 EV IPR013341; PF02746; sufficient; EV IPR029065; PF13378; sufficient; // AC GenProp1567 DE Glycerol degradation I TP PATHWAY AU Caspi R TH 0 DC Glycerol degradation I DR MetaCyc; PWY-4261; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol kinase DN Glycerol kinase (EC 2.7.1.30) RQ 1 EV IPR005999; TIGR01311; sufficient; -- SN 2 ID Glycerol-3-phosphate dehydrogenase DN Glycerol-3-phosphate dehydrogenase (EC 1.1.5.3) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR031656; PF16901; sufficient; // AC GenProp1568 DE Purine deoxyribonucleosides degradation II TP PATHWAY AU Weerasinghe D, Paley S, Caspi R TH 1 DC Purine deoxyribonucleosides degradation II DR MetaCyc; PWY-7179-1; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine deaminase DN Adenosine deaminase (EC 3.5.4.4) RQ 1 EV IPR006330; TIGR01430; sufficient; -- SN 2 ID Deoxyguanosine phosphorylase DN Deoxyguanosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; -- SN 3 ID Deoxyinosine phosphorylase DN Deoxyinosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; // AC GenProp1569 DE Very long chain fatty acid biosynthesis I TP PATHWAY AU Caspi R, Zhang P TH 2 DC Very long chain fatty acid biosynthesis I DR MetaCyc; PWY-5080; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Very-long-chain 3-hydroxyacyl-CoA dehydratase DN Very-long-chain 3-hydroxyacyl-CoA dehydratase (EC 4.2.1.134) RQ 1 EV IPR007482; PF04387; sufficient; -- SN 2 ID Very-long-chain 3-ketoacyl-CoA synthase DN Very-long-chain 3-ketoacyl-CoA synthase (EC 2.3.1.199) RQ 1 EV IPR013601; PF08392; sufficient; EV IPR013747; PF08541; sufficient; -- SN 3 ID Very-long-chain 3-oxoacyl-CoA reductase DN Very-long-chain 3-oxoacyl-CoA reductase (EC 1.1.1.330) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 4 ID Very-long-chain enoyl-CoA reductase DN Very-long-chain enoyl-CoA reductase (EC 1.3.1.93) RQ 1 EV IPR001104; PF02544; sufficient; // AC GenProp1570 DE N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis TP PATHWAY AU Keseler I TH 0 DC N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis DR MetaCyc; PWY0-1587; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Threonylcarbamoyl-AMP synthase DN Threonylcarbamoyl-AMP synthase (EC 2.7.7.87) RQ 1 EV IPR006070; PF01300; sufficient; -- SN 2 ID N6-L-threonylcarbamoyladenine synthase DN N6-L-threonylcarbamoyladenine synthase (EC 2.3.1.234) RQ 1 EV IPR017861; TIGR00329; sufficient; EV IPR022450; TIGR03723; sufficient; EV IPR003442; PF02367; sufficient; EV IPR003442; TIGR00150; sufficient; EV IPR022496; TIGR03725; sufficient; // AC GenProp1571 DE Spermine biosynthesis TP PATHWAY AU Foerster H, Caspi R, Ying H TH 0 DC Spermine biosynthesis DR MetaCyc; ARGSPECAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID S-adenosylmethionine decarboxylase DN S-adenosylmethionine decarboxylase (EC 4.1.1.50) RQ 1 EV IPR003826; PF02675; sufficient; EV IPR017716; TIGR03330; sufficient; EV IPR001985; PF01536; sufficient; -- SN 2 ID Spermine synthase DN Spermine synthase (EC 2.5.1.22) RQ 1 EV IPR001045; TIGR00417; sufficient; // AC GenProp1572 DE L-carnitine degradation I TP PATHWAY AU Caspi R TH 2 DC L-carnitine degradation I DR MetaCyc; CARNMET-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Crotonobetainyl-CoA hydratase DN Crotonobetainyl-CoA hydratase (EC 4.2.1.149) RQ 1 EV IPR001753; PF00378; sufficient; -- SN 2 ID Crotonobetainyl-CoA reductase DN Crotonobetainyl-CoA reductase (EC 1.3.8.13) RQ 1 EV IPR006091; PF02770; sufficient; EV IPR009075; PF00441; sufficient; EV IPR013786; PF02771; sufficient; -- SN 3 ID Carnitine-CoA ligase DN Carnitine-CoA ligase (EC 6.2.1.48) RQ 1 EV IPR000873; PF00501; sufficient; EV IPR025110; PF13193; sufficient; -- SN 4 ID Gamma-butyrobetainyl-CoA:carnitine CoA transferase DN Gamma-butyrobetainyl-CoA:carnitine CoA transferase (EC 2.8.3.21) RQ 1 EV IPR003673; PF02515; sufficient; // AC GenProp1573 DE Sulfate activation for sulfonation TP PATHWAY AU Caspi R TH 0 DC Sulfate activation for sulfonation DR MetaCyc; PWY-5340; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenylyl-sulfate kinase DN Adenylyl-sulfate kinase (EC 2.7.1.25) RQ 1 EV IPR002891; TIGR00455; sufficient; -- SN 2 ID Sulfate adenylyltransferase DN Sulfate adenylyltransferase (EC 2.7.7.4) RQ 1 EV IPR002891; TIGR00455; sufficient; EV IPR011784; TIGR02039; sufficient; EV IPR011779; TIGR02034; sufficient; // AC GenProp1574 DE Inositol diphosphates biosynthesis TP PATHWAY AU Caspi R TH 7 DC Inositol diphosphates biosynthesis DR MetaCyc; PWY-6369; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol hexakisphosphate kinase DN Inositol hexakisphosphate kinase (EC 2.7.4.21) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 2 ID 5-Diphosphoinositol-pentakisphosphate 1-kinase DN 5-Diphosphoinositol-pentakisphosphate 1-kinase (EC 2.7.4.24) RQ 1 EV IPR000560; PF00328; sufficient; -- SN 3 ID Inositol hexakisphosphate 3-kinase DN Inositol hexakisphosphate 3-kinase (EC 2.7.4.21) RQ 1 EV IPR000560; PF00328; sufficient; -- SN 4 ID Inositol hexakisphosphate 1-kinase DN Inositol hexakisphosphate 1-kinase (EC 2.7.4.24) RQ 1 EV IPR000560; PF00328; sufficient; -- SN 5 ID 3-Diphosphoinositol pentakisphosphate 5-kinase DN 3-Diphosphoinositol pentakisphosphate 5-kinase (EC 2.7.4.24) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 6 ID 1-Diphosphoinositol pentakisphosphate 5-kinase DN 1-Diphosphoinositol pentakisphosphate 5-kinase (EC 2.7.4.21) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 7 ID 5-Diphosphoinositol-pentakisphosphate 3-kinase DN 5-Diphosphoinositol-pentakisphosphate 3-kinase (EC 2.7.4.24) RQ 1 EV IPR000560; PF00328; sufficient; -- SN 8 ID Inositol-1,3,4,5,6-pentakisphosphate kinase DN Inositol-1,3,4,5,6-pentakisphosphate kinase (EC 2.7.1) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 9 ID Ins(1,3,4,5,6)P5 2-kinase DN Ins(1,3,4,5,6)P5 2-kinase (EC 2.7.1.158) RQ 1 EV IPR009286; PF06090; sufficient; // AC GenProp1575 DE Phospholipid remodeling (phosphatidylethanolamine, yeast) TP PATHWAY AU Foerster H TH 2 DC Phospholipid remodeling (phosphatidylethanolamine, yeast) DR MetaCyc; PWY-7409; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerophosphorylethanolamine phosphodiesterase DN Glycerophosphorylethanolamine phosphodiesterase (EC 3.1.4.46) RQ 1 EV IPR004331; PF03105; sufficient; EV IPR020683; PF12796; sufficient; EV IPR030395; PF03009; sufficient; -- SN 2 ID Lyso-phosphatidylethanolaminelipase DN Lyso-phosphatidylethanolaminelipase (EC 3.1.1.5) RQ 1 EV IPR002642; PF01735; sufficient; -- SN 3 ID Oleoyl-CoA:lysophosphatidylethanolamine acyltransferase DN Oleoyl-CoA:lysophosphatidylethanolamine acyltransferase (EC 2.3.1.23) RQ 1 EV IPR021771; PF11815; sufficient; EV IPR004299; PF03062; sufficient; -- SN 4 ID Phospholipase A2 DN Phospholipase A2 (EC 3.1.1.4) RQ 1 EV IPR021771; PF11815; sufficient; // AC GenProp1576 DE Pyrimidine ribonucleosides degradation TP PATHWAY AU Ingraham J TH 0 DC Pyrimidine ribonucleosides degradation DR MetaCyc; PWY0-1295; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cytidine deaminase DN Cytidine deaminase (EC 3.5.4.5) RQ 1 EV IPR006263; TIGR01355; sufficient; EV IPR006262; TIGR01354; sufficient; -- SN 2 ID Uridine phosphorylase DN Uridine phosphorylase (EC 2.4.2.3) RQ 1 EV IPR009664; PF06865; sufficient; EV IPR010059; TIGR01719; sufficient; EV IPR010058; TIGR01718; sufficient; // AC GenProp1577 DE Biotin biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Biotin biosynthesis I DR MetaCyc; BIOTIN-BIOSYNTHESIS-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 7,8-Diaminopelargonic acid aminotransferase DN 7,8-Diaminopelargonic acid aminotransferase (EC 2.6.1.62) RQ 1 EV IPR005814; PF00202; sufficient; EV IPR005815; TIGR00508; sufficient; -- SN 2 ID 8-Amino-7-oxononanoate synthase DN 8-Amino-7-oxononanoate synthase (EC 2.3.1.47) RQ 1 EV IPR004723; TIGR00858; sufficient; // AC GenProp1578 DE Methylglyoxal degradation I TP PATHWAY AU Caspi R TH 1 DC Methylglyoxal degradation I DR MetaCyc; PWY-5386; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-lactate dehydrogenase DN D-lactate dehydrogenase (EC 1.1.5.12) RQ 1 EV IPR006094; PF01565; sufficient; EV IPR015409; PF09330; sufficient; -- SN 2 ID Glyoxalase I DN Glyoxalase I (EC 4.4.1.5) RQ 1 EV IPR004361; TIGR00068; sufficient; -- SN 3 ID Hydroxyacylglutathione hydrolase DN Hydroxyacylglutathione hydrolase (EC 3.1.2.6) RQ 1 EV IPR000801; PF00756; sufficient; EV IPR014186; TIGR02821; sufficient; EV IPR017782; TIGR03413; sufficient; // AC GenProp1579 DE 4-Aminobutanoate degradation II TP PATHWAY AU Caspi R, Hong E TH 0 DC 4-Aminobutanoate degradation II DR MetaCyc; PWY-6537; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Aminobutyrate aminotransferase DN 4-Aminobutyrate aminotransferase (EC 2.6.1.19) RQ 1 EV IPR004632; TIGR00700; sufficient; EV IPR005814; PF00202; sufficient; -- SN 2 ID Succinate-semialdehyde dehydrogenase (NADP+) DN Succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) RQ 1 EV IPR010102; TIGR01780; sufficient; // AC GenProp1580 DE Homolactic fermentation TP PATHWAY AU Caspi R, Ying H TH 3 DC Homolactic fermentation DR MetaCyc; ANAEROFRUCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 6-Phosphofructokinase DN 6-Phosphofructokinase (EC 2.7.1.11) RQ 1 EV IPR009161; TIGR02478; sufficient; -- SN 2 ID Glucokinase DN Glucokinase (EC 2.7.1.2) RQ 1 EV IPR022672; PF00349; sufficient; EV IPR022673; PF03727; sufficient; -- SN 3 ID L-lactate dehydrogenase DN L-lactate dehydrogenase (EC 1.1.1.27) RQ 1 EV IPR011304; TIGR01771; sufficient; -- SN 4 ID Pyruvate kinase DN Pyruvate kinase (EC 2.7.1.40) RQ 1 EV IPR001697; TIGR01064; sufficient; -- SN 5 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; // AC GenProp1581 DE L-homoserine and L-methionine biosynthesis TP PATHWAY AU Paley S, Riley M TH 0 DC L-homoserine and L-methionine biosynthesis DR MetaCyc; METSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Homoserine dehydrogenase DN Homoserine dehydrogenase (EC 1.1.1.3) RQ 1 EV IPR001048; PF00696; sufficient; EV IPR001341; TIGR00657; sufficient; EV IPR001342; PF00742; sufficient; EV IPR005106; PF03447; sufficient; -- SN 2 ID Homoserine O-succinyltransferase DN Homoserine O-succinyltransferase (EC 2.3.1.46) RQ 1 EV IPR005697; PF04204; sufficient; EV IPR005697; TIGR01001; sufficient; // AC GenProp1582 DE Hydrogen to trimethylamine N-oxide electron transfer TP PATHWAY AU Mackie A TH 0 DC Hydrogen to trimethylamine N-oxide electron transfer DR MetaCyc; PWY0-1578; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Menaquinone hydrogenase (acceptor) DN Menaquinone hydrogenase (acceptor) (EC 1.12.99.6) RQ 1 EV IPR005614; PF03916; sufficient; EV IPR001821; TIGR00391; sufficient; EV IPR000516; TIGR02125; sufficient; -- SN 2 ID Trimethylamine-N-oxide reductase (menaquinone) DN Trimethylamine-N-oxide reductase (menaquinone) (EC 1.7.2.3) RQ 1 EV IPR009154; TIGR02162; sufficient; EV IPR006658; TIGR00509; sufficient; EV IPR011887; TIGR02164; sufficient; // AC GenProp1583 DE Nitrate reduction VIII (dissimilatory) TP PATHWAY AU Mackie A, Nolan L TH 0 DC Nitrate reduction VIII (dissimilatory) DR MetaCyc; PWY0-1352; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Menaquinol:nitrate oxidoreductase DN Menaquinol:nitrate oxidoreductase (EC 1.7.5.1) RQ 1 EV IPR006468; TIGR01580; sufficient; EV IPR006547; TIGR01660; sufficient; EV IPR003816; TIGR00351; sufficient; -- SN 2 ID NADH:menaquinone oxidoreductase (H+-transporting) DN NADH:menaquinone oxidoreductase (H+-transporting) (EC 1.6.5) RQ 1 EV IPR000440; PF00507; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR001694; PF00146; sufficient; EV IPR010226; TIGR01971; sufficient; EV IPR001457; PF00499; sufficient; EV IPR001133; PF00420; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR010227; TIGR01972; sufficient; EV IPR010096; TIGR01770; sufficient; // AC GenProp1584 DE L-aspartate degradation II TP PATHWAY AU Fulcher C TH 0 DC L-aspartate degradation II DR MetaCyc; MALATE-ASPARTATE-SHUTTLE-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate aminotransferase DN Aspartate aminotransferase (EC 2.6.1.1) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID Malate dehydrogenase (NAD) DN Malate dehydrogenase (NAD) (EC 1.1.1.37) RQ 1 EV IPR010945; TIGR01759; sufficient; EV IPR011274; TIGR01758; sufficient; EV IPR010097; TIGR01772; sufficient; // AC GenProp1585 DE Superpathway of ubiquinol-8 biosynthesis (prokaryotic) TP PATHWAY AU Keseler I, Riley M TH 2 DC Superpathway of ubiquinol-8 biosynthesis (prokaryotic) DR MetaCyc; UBISYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Hydroxybenzoate octaprenyltransferase DN 4-Hydroxybenzoate octaprenyltransferase (EC 2.5.1.39) RQ 1 EV IPR000537; PF01040; sufficient; EV IPR006370; TIGR01474; sufficient; -- SN 2 ID Chorismate lyase DN Chorismate lyase (EC 4.1.3.40) RQ 1 EV IPR007440; PF04345; sufficient; -- SN 3 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 4 ID All-trans-octaprenyl-diphosphate synthase DN All-trans-octaprenyl-diphosphate synthase (EC 2.5.1.90) RQ 1 EV IPR000092; PF00348; sufficient; // AC GenProp1586 DE Adenosine deoxyribonucleotides de novo biosynthesis TP PATHWAY AU Caspi R TH 0 DC Adenosine deoxyribonucleotides de novo biosynthesis DR MetaCyc; PWY-7227; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ADP reductase DN ADP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 2 ID DADP kinase DN DADP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; // AC GenProp1587 DE Oleate biosynthesis II (animals and fungi) TP PATHWAY AU Caspi R TH 0 DC Oleate biosynthesis II (animals and fungi) DR MetaCyc; PWY-5996; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Stearoyl-CoA 9-desaturase DN Stearoyl-CoA 9-desaturase (EC 1.14.19.1) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 2 ID Oleoyl-CoA hydrolase DN Oleoyl-CoA hydrolase (EC 3.1.2.2) RQ 1 EV IPR006862; PF04775; sufficient; EV IPR014940; PF08840; sufficient; // AC GenProp1588 DE Lipoxin biosynthesis TP PATHWAY AU Weerasinghe D TH 4 DC Lipoxin biosynthesis DR MetaCyc; PWY66-392; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arachidonate 5-lipoxygenase DN Arachidonate 5-lipoxygenase (EC 1.13.11.34) RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 2 ID Lipoxin A4 synthase DN Lipoxin A4 synthase (EC 1.13.11) RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 3 ID 15S-HETE synthase DN 15S-HETE synthase RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 4 ID Lipoxin A4 synthase DN Lipoxin A4 synthase (EC 1.13.11) RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 5 ID Lipoxin B4 synthase DN Lipoxin B4 synthase (EC 1.13.11) RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 6 ID Lipoxin B4 synthase DN Lipoxin B4 synthase (EC 1.13.11) RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; // AC GenProp1589 DE D-arabinose degradation I TP PATHWAY AU Keseler I TH 2 DC D-arabinose degradation I DR MetaCyc; DARABCATK12-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-ribulose-phosphate aldolase DN D-ribulose-phosphate aldolase RQ 1 EV IPR004782; TIGR01086; sufficient; -- SN 2 ID D-arabinose isomerase DN D-arabinose isomerase (EC 5.3.1.3) RQ 1 EV IPR005763; TIGR01089; sufficient; -- SN 3 ID D-ribulokinase DN D-ribulokinase RQ 1 EV IPR013450; TIGR02628; sufficient; -- SN 4 ID Glycolaldehyde dehydrogenase DN Glycolaldehyde dehydrogenase (EC 1.2.1.21) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1590 DE 4-Amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis TP PATHWAY AU Caspi R TH 0 DC 4-Amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis DR MetaCyc; PWY-6890; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID HMP-P synthase DN HMP-P synthase (EC 4.1.99.17) RQ 1 EV IPR002817; PF01964; sufficient; EV IPR002817; TIGR00190; sufficient; -- SN 2 ID Phosphomethylpyrimidine kinase DN Phosphomethylpyrimidine kinase (EC 2.7.4.7) RQ 1 EV IPR004399; TIGR00097; sufficient; EV IPR013749; PF08543; sufficient; // AC GenProp1591 DE Heme degradation I TP PATHWAY AU Caspi R TH 4 DC Heme degradation I DR MetaCyc; PWY-5874; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Biliverdin reductase DN Biliverdin reductase (EC 1.3.1.24) RQ 1 EV IPR000683; PF01408; sufficient; EV IPR015249; PF09166; sufficient; -- SN 2 ID Heme oxygenase DN Heme oxygenase (EC 1.14.14.18) RQ 1 EV IPR016053; PF01126; sufficient; -- SN 3 ID Bilirubin glucuronosyltransferase (C8 isomer-forming) DN Bilirubin glucuronosyltransferase (C8 isomer-forming) (EC 2.4.1.17) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 4 ID Bilirubin glucuronosyltransferase (C12 isomer-forming) DN Bilirubin glucuronosyltransferase (C12 isomer-forming) (EC 2.4.1.17) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 5 ID Bilirubin glucuronoside glucuronosyltransferase DN Bilirubin glucuronoside glucuronosyltransferase (EC 2.4.1.17) RQ 1 EV IPR002213; PF00201; sufficient; -- SN 6 ID Bilirubin glucuronoside glucuronosyltransferase DN Bilirubin glucuronoside glucuronosyltransferase (EC 2.4.1.17) RQ 1 EV IPR002213; PF00201; sufficient; // AC GenProp1592 DE Superpathway of purine nucleotides de novo biosynthesis II TP PATHWAY AU Arnaud M TH 3 DC Superpathway of purine nucleotides de novo biosynthesis II DR MetaCyc; DENOVOPURINE2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenylosuccinate synthase DN Adenylosuccinate synthase (EC 6.3.4.4) RQ 1 EV IPR001114; PF00709; sufficient; EV IPR001114; TIGR00184; sufficient; -- SN 2 ID Phosphoribosylformylglycinamide cyclo-ligase DN Phosphoribosylformylglycinamide cyclo-ligase (EC 6.3.3.1) RQ 1 EV IPR004733; TIGR00878; sufficient; -- SN 3 ID Inosine-5'-monophosphate dehydrogenase DN Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) RQ 1 EV IPR005990; TIGR01302; sufficient; -- SN 4 ID IMP cyclohydrolase DN IMP cyclohydrolase (EC 3.5.4.10) RQ 1 EV IPR002695; PF01808; sufficient; EV IPR002695; TIGR00355; sufficient; -- SN 5 ID 5-(Carboxyamino)imidazole ribonucleotide synthase DN 5-(Carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) RQ 1 EV IPR003135; PF02222; sufficient; EV IPR005875; TIGR01161; sufficient; // AC GenProp1593 DE Staphyloferrin A biosynthesis TP PATHWAY AU Caspi R TH 1 DC Staphyloferrin A biosynthesis DR MetaCyc; PWY-7990; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ornithine racemase DN Ornithine racemase (EC 5.1.1.12) RQ 1 EV IPR001608; PF01168; sufficient; -- SN 2 ID Staphyloferrin A synthase DN Staphyloferrin A synthase (EC 6.3.2) RQ 1 EV IPR007310; PF04183; sufficient; EV IPR022770; PF06276; sufficient; -- SN 3 ID D-ornithine--citrate ligase DN D-ornithine--citrate ligase (EC 6.3.2) RQ 1 EV IPR007310; PF04183; sufficient; EV IPR022770; PF06276; sufficient; // AC GenProp1594 DE Superpathway of ergosterol biosynthesis I TP PATHWAY AU Caspi R, Hong E TH 5 DC Superpathway of ergosterol biosynthesis I DR MetaCyc; ERGOSTEROL-SYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID 2,3-Oxidosqualene-lanosterol cyclase DN 2,3-Oxidosqualene-lanosterol cyclase (EC 5.4.99.7) RQ 1 EV IPR018333; TIGR01787; sufficient; -- SN 3 ID Squalene synthase DN Squalene synthase (EC 2.5.1.21) RQ 1 EV IPR002060; PF00494; sufficient; EV IPR006449; TIGR01559; sufficient; -- SN 4 ID Lanosterol 14a-demethylase DN Lanosterol 14a-demethylase (EC 1.14.13.70) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 5 ID SAM:C-24 sterol methyltransferase DN SAM:C-24 sterol methyltransferase (EC 2.1.1.41) RQ 1 EV IPR013216; PF08241; sufficient; EV IPR013705; PF08498; sufficient; -- SN 6 ID Zymosterol 3-dehydrogenase DN Zymosterol 3-dehydrogenase (EC 1.1.1.270) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 7 ID Squalene monooxygenase DN Squalene monooxygenase (EC 1.14.14.17) RQ 1 EV IPR013698; PF08491; sufficient; // AC GenProp1595 DE Heparan sulfate biosynthesis TP PATHWAY AU Caspi R TH 0 DC Heparan sulfate biosynthesis DR MetaCyc; PWY-6564; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase DN Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135) RQ 1 EV IPR005027; PF03360; sufficient; -- SN 2 ID Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase DN Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase (EC 2.4.1.223) RQ 1 EV IPR004263; PF03016; sufficient; // AC GenProp1596 DE Superpathway of polyamine biosynthesis I TP PATHWAY AU N/A TH 4 DC Superpathway of polyamine biosynthesis I DR MetaCyc; POLYAMSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Agmatinase DN Agmatinase (EC 3.5.3.11) RQ 1 EV IPR005925; TIGR01230; sufficient; EV IPR006035; PF00491; sufficient; -- SN 2 ID L-lysine decarboxylase DN L-lysine decarboxylase (EC 4.1.1.18) RQ 1 EV IPR000310; PF01276; sufficient; EV IPR005308; PF03709; sufficient; EV IPR008286; PF03711; sufficient; -- SN 3 ID Ornithine decarboxylase DN Ornithine decarboxylase (EC 4.1.1.17) RQ 1 EV IPR027568; TIGR04301; sufficient; -- SN 4 ID Aminopropylcadaverine synthase DN Aminopropylcadaverine synthase (EC 2.5.1) RQ 1 EV IPR001045; TIGR00417; sufficient; -- SN 5 ID S-adenosylmethionine decarboxylase DN S-adenosylmethionine decarboxylase (EC 4.1.1.50) RQ 1 EV IPR003826; PF02675; sufficient; EV IPR009165; TIGR03331; sufficient; -- SN 6 ID Spermidine synthase DN Spermidine synthase (EC 2.5.1.16) RQ 1 EV IPR001045; TIGR00417; sufficient; // AC GenProp1597 DE Pinolenate and coniferonate biosynthesis TP PATHWAY AU Caspi R, Zhang P TH 0 DC Pinolenate and coniferonate biosynthesis DR MetaCyc; PWY-7152; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alpha-linolenate 5-desaturase DN Alpha-linolenate 5-desaturase (EC 1.14.19.12) RQ 1 EV IPR001199; PF00173; sufficient; EV IPR005804; PF00487; sufficient; -- SN 2 ID Linoleate 5-desaturase DN Linoleate 5-desaturase (EC 1.14.19.12) RQ 1 EV IPR001199; PF00173; sufficient; EV IPR005804; PF00487; sufficient; // AC GenProp1598 DE Superoxide radicals degradation TP PATHWAY AU Caspi R, Riley M, Foerster H TH 0 DC Superoxide radicals degradation DR MetaCyc; DETOX1-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Catalase DN Catalase (EC 1.11.1.21) RQ 1 EV IPR000763; TIGR00198; sufficient; EV IPR006679; TIGR01178; sufficient; -- SN 2 ID Superoxide dismutase DN Superoxide dismutase (EC 1.15.1.1) RQ 1 EV IPR019831; PF00081; sufficient; EV IPR019832; PF02777; sufficient; EV IPR001424; PF00080; sufficient; // AC GenProp1599 DE Glycolysis III (from glucose) TP PATHWAY AU Weerasinghe D, Pellegrini-Toole A TH 8 DC Glycolysis III (from glucose) DR MetaCyc; ANAGLYCOLYSIS-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Enolase DN Enolase (EC 4.2.1.11) RQ 1 EV IPR000941; TIGR01060; sufficient; -- SN 2 ID 6-Phosphofructokinase DN 6-Phosphofructokinase (EC 2.7.1.11) RQ 1 EV IPR012828; TIGR02482; sufficient; EV IPR009161; TIGR02478; sufficient; -- SN 3 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase (EC 4.1.2.13) RQ 1 EV IPR000741; PF00274; sufficient; -- SN 4 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 5 ID Glucokinase DN Glucokinase (EC 2.7.1.2) RQ 1 EV IPR000600; PF00480; sufficient; EV IPR004654; TIGR00744; sufficient; -- SN 6 ID Pyruvate kinase DN Pyruvate kinase (EC 2.7.1.40) RQ 1 EV IPR001697; TIGR01064; sufficient; -- SN 7 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; -- SN 8 ID Phosphoglycerate kinase DN Phosphoglycerate kinase (EC 2.7.2.3) RQ 1 EV IPR000652; PF00121; sufficient; EV IPR000652; TIGR00419; sufficient; EV IPR001576; PF00162; sufficient; -- SN 9 ID 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.11) RQ 1 EV IPR004456; PF10143; sufficient; EV IPR004456; TIGR00306; sufficient; EV IPR005952; TIGR01258; sufficient; EV IPR013078; PF00300; sufficient; -- SN 10 ID Triose-phosphate isomerase DN Triose-phosphate isomerase (EC 5.3.1.1) RQ 1 EV IPR000652; PF00121; sufficient; EV IPR000652; TIGR00419; sufficient; EV IPR001576; PF00162; sufficient; // AC GenProp1600 DE Abscisic acid degradation by glucosylation TP PATHWAY AU Foerster H, Tissier C TH 0 DC Abscisic acid degradation by glucosylation DR MetaCyc; PWY-5272; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Abscisic acid glucose ester beta-glucosidase DN Abscisic acid glucose ester beta-glucosidase (EC 3.2.1.175) RQ 1 EV IPR001360; PF00232; sufficient; -- SN 2 ID Abscisic acid glycosyltransferase DN Abscisic acid glycosyltransferase (EC 2.4.1.263) RQ 1 EV IPR002213; PF00201; sufficient; // AC GenProp1601 DE Superpathway of coenzyme A biosynthesis I (bacteria) TP PATHWAY AU Arnaud M TH 2 DC Superpathway of coenzyme A biosynthesis I (bacteria) DR MetaCyc; PANTOSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate 1-decarboxylase DN Aspartate 1-decarboxylase (EC 4.1.1.11) RQ 1 EV IPR003190; PF02261; sufficient; EV IPR003190; TIGR00223; sufficient; -- SN 2 ID Phosphopantothenoylcysteine synthetase DN Phosphopantothenoylcysteine synthetase (EC 6.3.2.5) RQ 1 EV IPR005252; TIGR00521; sufficient; -- SN 3 ID Pantoate beta-alanine ligase DN Pantoate beta-alanine ligase (EC 6.3.2.1) RQ 1 EV IPR003721; PF02569; sufficient; EV IPR003721; TIGR00018; sufficient; -- SN 4 ID Pantothenate kinase DN Pantothenate kinase (EC 2.7.1.33) RQ 1 EV IPR004566; TIGR00554; sufficient; // AC GenProp1602 DE PreQ0 biosynthesis TP PATHWAY AU Caspi R, Keseler I TH 2 DC PreQ0 biosynthesis DR MetaCyc; PWY-6703; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GTP cyclohydrolase DN GTP cyclohydrolase (EC 3.5.4.16) RQ 1 EV IPR001474; TIGR00063; sufficient; -- SN 2 ID 7-Cyano-7-deazaguanine synthase DN 7-Cyano-7-deazaguanine synthase (EC 6.3.4.20) RQ 1 EV IPR018317; PF06508; sufficient; EV IPR018317; TIGR00364; sufficient; -- SN 3 ID 6-Carboxy-5,6,7,8-tetrahydropterin synthase DN 6-Carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) RQ 1 EV IPR007115; PF01242; sufficient; EV IPR007115; TIGR00039; sufficient; EV IPR007115; TIGR03367; sufficient; -- SN 4 ID 7-Carboxy-7-deazaguanine synthase DN 7-Carboxy-7-deazaguanine synthase (EC 4.3.99.3) RQ 1 EV IPR017742; TIGR03365; sufficient; // AC GenProp1603 DE C20 prostanoid biosynthesis TP PATHWAY AU Weerasinghe D, Trupp M TH 3 DC C20 prostanoid biosynthesis DR MetaCyc; PWY66-374; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Prostaglandin-H2 D-isomerase DN Prostaglandin-H2 D-isomerase (EC 5.3.99.2) RQ 1 EV IPR000566; PF00061; sufficient; EV IPR004045; PF02798; sufficient; EV IPR004046; PF14497; sufficient; -- SN 2 ID Prostaglandin E synthase DN Prostaglandin E synthase (EC 5.3.99.3) RQ 1 EV IPR001129; PF01124; sufficient; -- SN 3 ID Prostaglandin G/H synthase DN Prostaglandin G/H synthase (EC 1.14.99.1) RQ 1 EV IPR019791; PF03098; sufficient; -- SN 4 ID Prostacyclin synthase DN Prostacyclin synthase (EC 5.3.99.4) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 5 ID Thromboxane-A synthase DN Thromboxane-A synthase (EC 5.3.99.5) RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1604 DE Pyridoxal 5'-phosphate salvage I TP PATHWAY AU N/A TH 3 DC Pyridoxal 5'-phosphate salvage I DR MetaCyc; PLPSAL-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pyridoxine-5'-phosphate oxidase DN Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) RQ 1 EV IPR000659; TIGR00558; sufficient; -- SN 2 ID Pyridoxal kinase DN Pyridoxal kinase (EC 2.7.1.35) RQ 1 EV IPR004625; TIGR00687; sufficient; -- SN 3 ID Pyridoxine 5'-phosphate oxidase II DN Pyridoxine 5'-phosphate oxidase II (EC 1.4.3.5) RQ 1 EV IPR000659; TIGR00558; sufficient; -- SN 4 ID Pyridoxal kinase DN Pyridoxal kinase (EC 2.7.1.35) RQ 1 EV IPR004625; TIGR00687; sufficient; -- SN 5 ID Pyridoxal kinase DN Pyridoxal kinase (EC 2.7.1.35) RQ 1 EV IPR004625; TIGR00687; sufficient; // AC GenProp1605 DE D-myo-inositol (1,4,5)-trisphosphate degradation TP PATHWAY AU Caspi R TH 1 DC D-myo-inositol (1,4,5)-trisphosphate degradation DR MetaCyc; PWY-6363; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ins(1,4,5)P3 5-phosphatase DN Ins(1,4,5)P3 5-phosphatase (EC 3.1.3.56) RQ 1 EV IPR005135; PF03372; sufficient; EV IPR002013; PF02383; sufficient; EV IPR015047; PF08952; sufficient; EV IPR000198; PF00620; sufficient; EV IPR031995; PF16726; sufficient; EV IPR031896; PF16776; sufficient; -- SN 2 ID Inositol 1,4-bisphosphate 1-phosphatase DN Inositol 1,4-bisphosphate 1-phosphatase (EC 3.1.3.57) RQ 1 EV IPR000760; PF00459; sufficient; -- SN 3 ID Inositol-4-phosphate monophosphatase DN Inositol-4-phosphate monophosphatase (EC 3.1.3.25) RQ 1 EV IPR000760; PF00459; sufficient; // AC GenProp1606 DE Octopamine biosynthesis TP PATHWAY AU Fulcher C TH 0 DC Octopamine biosynthesis DR MetaCyc; PWY-7297; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Tyramine beta-monooxygenase DN Tyramine beta-monooxygenase (EC 1.14.17) RQ 1 EV IPR000323; PF01082; sufficient; EV IPR005018; PF03351; sufficient; EV IPR024548; PF03712; sufficient; -- SN 2 ID L-tyrosine decarboxylase DN L-tyrosine decarboxylase (EC 4.1.1.25) RQ 1 EV IPR002129; PF00282; sufficient; // AC GenProp1607 DE Purine deoxyribonucleosides salvage TP PATHWAY AU Caspi R TH 4 DC Purine deoxyribonucleosides salvage DR MetaCyc; PWY-7224; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID DADP kinase DN DADP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; -- SN 2 ID 2'-Deoxyadenosine kinase DN 2'-Deoxyadenosine kinase (EC 2.7.1.76) RQ 1 EV IPR031314; PF01712; sufficient; -- SN 3 ID DAMP kinase DN DAMP kinase (EC 2.7.4.11) RQ 1 EV IPR006267; TIGR01360; sufficient; -- SN 4 ID 2'-Deoxyguanosine kinase (ATP) DN 2'-Deoxyguanosine kinase (ATP) (EC 2.7.1.113) RQ 1 EV IPR031314; PF01712; sufficient; -- SN 5 ID DGDP kinase DN DGDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 6 ID DGMP kinase DN DGMP kinase (EC 2.7.4.12) RQ 1 EV IPR017665; TIGR03263; sufficient; // AC GenProp1608 DE NADH to cytochrome bd oxidase electron transfer I TP PATHWAY AU Mackie A, Nolan L, Krummenacker M TH 0 DC NADH to cytochrome bd oxidase electron transfer I DR MetaCyc; PWY0-1334; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID NADH dehydrogenase DN NADH dehydrogenase (EC 1.6.5.3) RQ 1 EV IPR000440; PF00507; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR001694; PF00146; sufficient; EV IPR010226; TIGR01971; sufficient; EV IPR001457; PF00499; sufficient; EV IPR001133; PF00420; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR010227; TIGR01972; sufficient; EV IPR010096; TIGR01770; sufficient; -- SN 2 ID Cytochrome bd-I ubiquinol oxidase DN Cytochrome bd-I ubiquinol oxidase (EC 1.10.3.14) RQ 1 EV IPR002585; PF01654; sufficient; EV IPR003317; PF02322; sufficient; EV IPR003317; TIGR00203; sufficient; EV IPR011724; TIGR02106; sufficient; EV IPR012994; PF08173; sufficient; // AC GenProp1609 DE Ergosterol biosynthesis I TP PATHWAY AU Caspi R TH 3 DC Ergosterol biosynthesis I DR MetaCyc; PWY-6075; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID C-24 sterol reductase DN C-24 sterol reductase (EC 1.3.1.71) RQ 1 EV IPR001171; PF01222; sufficient; -- SN 2 ID SAM:C-24 sterol methyltransferase DN SAM:C-24 sterol methyltransferase (EC 2.1.1.41) RQ 1 EV IPR013216; PF08241; sufficient; EV IPR013705; PF08498; sufficient; -- SN 3 ID C-8 sterol isomerase DN C-8 sterol isomerase RQ 1 EV IPR006716; PF04622; sufficient; -- SN 4 ID Episterol C-5 desaturase DN Episterol C-5 desaturase (EC 1.14.19.20) RQ 1 EV IPR006694; PF04116; sufficient; -- SN 5 ID C-22 sterol desaturase DN C-22 sterol desaturase (EC 1.14.19.41) RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1610 DE Spermine and spermidine degradation I TP PATHWAY AU Fulcher C TH 3 DC Spermine and spermidine degradation I DR MetaCyc; PWY-6117; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID N1-acetylspermidine oxidase DN N1-acetylspermidine oxidase (EC 1.5.3.17) RQ 1 EV IPR002937; PF01593; sufficient; -- SN 2 ID Spermine oxidase DN Spermine oxidase (EC 1.5.3.16) RQ 1 EV IPR002937; PF01593; sufficient; -- SN 3 ID Spermine N1-acetyltransferase DN Spermine N1-acetyltransferase (EC 2.3.1.57) RQ 1 EV IPR000182; PF00583; sufficient; -- SN 4 ID N1-acetylspermine oxidase DN N1-acetylspermine oxidase (EC 1.5.3.13) RQ 1 EV IPR002937; PF01593; sufficient; -- SN 5 ID Spermidine N1-acetyltransferase DN Spermidine N1-acetyltransferase (EC 2.3.1.57) RQ 1 EV IPR000182; PF00583; sufficient; // AC GenProp1611 DE Xanthine and xanthosine salvage TP PATHWAY AU Caspi R, Sarker M, Arnaud M TH 0 DC Xanthine and xanthosine salvage DR MetaCyc; SALVPURINE2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Xanthine phosphoribosyltransferase DN Xanthine phosphoribosyltransferase (EC 2.4.2.22) RQ 1 EV IPR000836; PF00156; sufficient; -- SN 2 ID Xanthosine phosphorylase DN Xanthosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR009664; PF06865; sufficient; EV IPR010943; TIGR01699; sufficient; EV IPR011268; TIGR01697; sufficient; // AC GenProp1612 DE Gluconeogenesis III TP PATHWAY AU Caspi R, Weerasinghe D, Riley M TH 10 DC Gluconeogenesis III DR MetaCyc; PWY66-399; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Enolase DN Enolase (EC 4.2.1.11) RQ 1 EV IPR000941; TIGR01060; sufficient; -- SN 2 ID Phosphoenolpyruvate carboxykinase DN Phosphoenolpyruvate carboxykinase (EC 4.1.1.32) RQ 1 EV IPR008209; PF00821; sufficient; -- SN 3 ID Fructose-bisphosphate aldolase DN Fructose-bisphosphate aldolase (EC 4.1.2.13) RQ 1 EV IPR000741; PF00274; sufficient; -- SN 4 ID Fructose 1,6-bisphosphatase DN Fructose 1,6-bisphosphatase (EC 3.1.3.11) RQ 1 EV IPR033391; PF00316; sufficient; -- SN 5 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 6 ID Malate dehydrogenase (NAD) DN Malate dehydrogenase (NAD) (EC 1.1.1.37) RQ 1 EV IPR010097; TIGR01772; sufficient; EV IPR010945; TIGR01759; sufficient; EV IPR011274; TIGR01758; sufficient; -- SN 7 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; -- SN 8 ID Phosphoglycerate kinase DN Phosphoglycerate kinase (EC 2.7.2.3) RQ 1 EV IPR001576; PF00162; sufficient; -- SN 9 ID Pyruvate carboxylase DN Pyruvate carboxylase (EC 6.4.1.1) RQ 1 EV IPR005930; TIGR01235; sufficient; -- SN 10 ID 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase DN 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.11) RQ 1 EV IPR005952; TIGR01258; sufficient; EV IPR013078; PF00300; sufficient; -- SN 11 ID Glucose-6-phosphatase DN Glucose-6-phosphatase (EC 3.1.3.9) RQ 1 EV IPR000326; PF01569; sufficient; -- SN 12 ID Triose-phosphate isomerase DN Triose-phosphate isomerase (EC 5.3.1.1) RQ 1 EV IPR000652; PF00121; sufficient; EV IPR000652; TIGR00419; sufficient; // AC GenProp1613 DE Formate assimilation into 5,10-methylenetetrahydrofolate TP PATHWAY AU Caspi R TH 1 DC Formate assimilation into 5,10-methylenetetrahydrofolate DR MetaCyc; PWY-1722; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Formate--tetrahydrofolate ligase DN Formate--tetrahydrofolate ligase (EC 6.3.4.3) RQ 1 EV IPR000559; PF01268; sufficient; -- SN 2 ID Methenyltetrahydrofolate cyclohydrolase DN Methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9) RQ 1 EV IPR000559; PF01268; sufficient; -- SN 3 ID Methylenetetrahydrofolate dehydrogenase DN Methylenetetrahydrofolate dehydrogenase (EC 1.5.1.5) RQ 1 EV IPR000559; PF01268; sufficient; // AC GenProp1614 DE UMP biosynthesis II TP PATHWAY AU Caspi R TH 4 DC UMP biosynthesis II DR MetaCyc; PWY-7790; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aspartate carbamoyltransferase DN Aspartate carbamoyltransferase (EC 2.1.3.2) RQ 1 EV IPR002082; TIGR00670; sufficient; EV IPR006274; TIGR01368; sufficient; EV IPR006275; TIGR01369; sufficient; -- SN 2 ID Carbamoyl phosphate synthase DN Carbamoyl phosphate synthase (EC 6.3.5.5) RQ 1 EV IPR002082; TIGR00670; sufficient; EV IPR006274; TIGR01368; sufficient; EV IPR006275; TIGR01369; sufficient; -- SN 3 ID Dihydroorotase DN Dihydroorotase (EC 3.5.2.3) RQ 1 EV IPR004721; TIGR00856; sufficient; -- SN 4 ID Orotate phosphoribosyltransferase DN Orotate phosphoribosyltransferase (EC 2.4.2.10) RQ 1 EV IPR000836; PF00156; sufficient; EV IPR004467; TIGR00336; sufficient; -- SN 5 ID Orotidine 5'-phosphate decarboxylase DN Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) RQ 1 EV IPR014732; TIGR01740; sufficient; -- SN 6 ID Dihydroorotate dehydrogenase DN Dihydroorotate dehydrogenase (EC 1.3.98.1) RQ 1 EV IPR005720; PF01180; sufficient; EV IPR005720; TIGR01037; sufficient; // AC GenProp1615 DE Ammonia assimilation cycle III TP PATHWAY AU Pellegrini-Toole A TH 0 DC Ammonia assimilation cycle III DR MetaCyc; AMMASSIM-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutamate synthase DN Glutamate synthase (EC 1.4.1.13) RQ 1 EV IPR006006; TIGR01318; sufficient; -- SN 2 ID Glutamine synthetase DN Glutamine synthetase (EC 6.3.1.2) RQ 1 EV IPR004809; TIGR00653; sufficient; // AC GenProp1616 DE Tetrahydrofolate biosynthesis TP PATHWAY AU Caspi R TH 1 DC Tetrahydrofolate biosynthesis DR MetaCyc; PWY-6614; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Dihydrofolate reductase DN Dihydrofolate reductase (EC 1.5.1.3) RQ 1 EV IPR000398; TIGR03284; sufficient; -- SN 2 ID Dihydrofolate synthetase DN Dihydrofolate synthetase (EC 6.3.2.12) RQ 1 EV IPR001645; TIGR01499; sufficient; -- SN 3 ID Dihydropteroate synthase DN Dihydropteroate synthase (EC 2.5.1.15) RQ 1 EV IPR000489; PF00809; sufficient; EV IPR006390; TIGR01496; sufficient; // AC GenProp1617 DE Pyrimidine deoxyribonucleotides de novo biosynthesis I TP PATHWAY AU Caspi R TH 7 DC Pyrimidine deoxyribonucleotides de novo biosynthesis I DR MetaCyc; PWY-7184; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID CDP reductase DN CDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; -- SN 2 ID DCDP kinase DN DCDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 3 ID DTDP kinase DN DTDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 4 ID Thymidylate kinase DN Thymidylate kinase (EC 2.7.4.12) RQ 1 EV IPR018094; TIGR00041; sufficient; -- SN 5 ID DUDP kinase DN DUDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; -- SN 6 ID DUTP pyrophosphohydrolase DN DUTP pyrophosphohydrolase (EC 3.6.1.23) RQ 1 EV IPR008181; TIGR00576; sufficient; -- SN 7 ID CTP triphosphatase DN CTP triphosphatase (EC 3.6.1.15) RQ 1 EV IPR004948; PF03266; sufficient; -- SN 8 ID Thymidylate synthase DN Thymidylate synthase (EC 2.1.1.45) RQ 1 EV IPR000398; TIGR03284; sufficient; -- SN 9 ID UDP reductase DN UDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; // AC GenProp1619 DE L-histidine degradation I TP PATHWAY AU Caspi R TH 2 DC L-histidine degradation I DR MetaCyc; HISDEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Formiminoglutamate formiminohydrolase DN Formiminoglutamate formiminohydrolase (EC 3.5.3.8) RQ 1 EV IPR005923; TIGR01227; sufficient; EV IPR006035; PF00491; sufficient; -- SN 2 ID Histidase DN Histidase (EC 4.3.1.3) RQ 1 EV IPR001106; PF00221; sufficient; EV IPR005921; TIGR01225; sufficient; -- SN 3 ID Imidazolonepropionase DN Imidazolonepropionase (EC 3.5.2.7) RQ 1 EV IPR005920; TIGR01224; sufficient; -- SN 4 ID Urocanase DN Urocanase (EC 4.2.1.49) RQ 1 EV IPR023637; PF01175; sufficient; EV IPR023637; TIGR01228; sufficient; // AC GenProp1620 DE Pyruvate fermentation to acetate VIII TP PATHWAY AU Caspi R TH 0 DC Pyruvate fermentation to acetate VIII DR MetaCyc; PWY-5768; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pyruvate decarboxylase DN Pyruvate decarboxylase (EC 4.1.1.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID Acetaldehyde:NADP+ oxidoreductase DN Acetaldehyde:NADP+ oxidoreductase (EC 1.2.1.4) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1621 DE Pyrimidine deoxyribonucleotides de novo biosynthesis II TP PATHWAY AU Caspi R TH 5 DC Pyrimidine deoxyribonucleotides de novo biosynthesis II DR MetaCyc; PWY-7187; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID DCTP deaminase DN DCTP deaminase (EC 3.5.4.13) RQ 1 EV IPR011962; TIGR02274; sufficient; -- SN 2 ID DTDP kinase DN DTDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 3 ID Thymidylate kinase DN Thymidylate kinase (EC 2.7.4.12) RQ 1 EV IPR018094; TIGR00041; sufficient; -- SN 4 ID DUTP pyrophosphohydrolase DN DUTP pyrophosphohydrolase (EC 3.6.1.23) RQ 1 EV IPR000086; PF00293; sufficient; -- SN 5 ID CTP reductase DN CTP reductase (EC 1.1.98.6) RQ 1 EV IPR012833; PF13597; sufficient; EV IPR012833; TIGR02487; sufficient; -- SN 6 ID UTP reductase DN UTP reductase (EC 1.1.98.6) RQ 1 EV IPR012833; PF13597; sufficient; EV IPR012833; TIGR02487; sufficient; -- SN 7 ID Thymidylate synthase DN Thymidylate synthase (EC 2.1.1.45) RQ 1 EV IPR000398; TIGR03284; sufficient; // AC GenProp1622 DE Mycocyclosin biosynthesis TP PATHWAY AU Caspi R TH 0 DC Mycocyclosin biosynthesis DR MetaCyc; PWY-7236; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Mycocyclosin synthase DN Mycocyclosin synthase (EC 1.14.21.9) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID Cyclo(L-tyrosyl-L-tyrosyl) synthase DN Cyclo(L-tyrosyl-L-tyrosyl) synthase (EC 2.3.2.21) RQ 1 EV IPR030903; PF16715; sufficient; EV IPR030903; TIGR04539; sufficient; // AC GenProp1623 DE Anhydromuropeptides recycling I TP PATHWAY AU Keseler I, Caspi R TH 10 DC Anhydromuropeptides recycling I DR MetaCyc; PWY0-1261; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glucosamine-1-phosphate acetyltransferase DN Glucosamine-1-phosphate acetyltransferase (EC 2.3.1.157) RQ 1 EV IPR005882; TIGR01173; sufficient; -- SN 2 ID Phosphoglucosamine mutase DN Phosphoglucosamine mutase (EC 5.4.2.10) RQ 1 EV IPR006352; TIGR01455; sufficient; -- SN 3 ID UDP-N-acetylglucosamine pyrophosphorylase DN UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) RQ 1 EV IPR005882; TIGR01173; sufficient; -- SN 4 ID N-acetylglucosamine-6-phosphate deacetylase DN N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) RQ 1 EV IPR003764; TIGR00221; sufficient; -- SN 5 ID UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase DN UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (EC 6.3.2.45) RQ 1 EV IPR005757; TIGR01081; sufficient; -- SN 6 ID Anhydro-N-acetylmuramic acid kinase DN Anhydro-N-acetylmuramic acid kinase (EC 2.7.1.170) RQ 1 EV IPR005338; PF03702; sufficient; -- SN 7 ID N-acetylmuramic acid 6-phosphate etherase DN N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) RQ 1 EV IPR005488; TIGR00274; sufficient; -- SN 8 ID N-acetylmuramoyl-L-alanine amidase DN N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) RQ 1 EV IPR002502; PF01510; sufficient; -- SN 9 ID GlcNAc-1,6-anhMurNAcaminidase DN GlcNAc-1,6-anhMurNAcaminidase (EC 3.2.1.52) RQ 1 EV IPR001764; PF00933; sufficient; -- SN 10 ID Muramoyltetrapeptide carboxypeptidase DN Muramoyltetrapeptide carboxypeptidase (EC 3.4.17.13) RQ 1 EV IPR003507; PF02016; sufficient; -- SN 11 ID UDP-N-acetylglucosamine 1-carboxyvinyltransferase DN UDP-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) RQ 1 EV IPR005750; TIGR01072; sufficient; -- SN 12 ID UDP-N-acetylenolpyruvoylglucosamine reductase DN UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) RQ 1 EV IPR003170; TIGR00179; sufficient; // AC GenProp1624 DE Fructoselysine and psicoselysine degradation TP PATHWAY AU Arnaud M TH 1 DC Fructoselysine and psicoselysine degradation DR MetaCyc; PWY0-521; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Fructoselysine 3-epimerase DN Fructoselysine 3-epimerase (EC 5.1.3.41) RQ 1 EV IPR013022; PF01261; sufficient; -- SN 2 ID Fructoselysine 6-kinase DN Fructoselysine 6-kinase (EC 2.7.1.218) RQ 1 EV IPR011611; PF00294; sufficient; -- SN 3 ID Fructoselysine 6-phosphate deglycase DN Fructoselysine 6-phosphate deglycase RQ 1 EV IPR001347; PF01380; sufficient; // AC GenProp1625 DE Lipoate biosynthesis and incorporation III (Bacillus) TP PATHWAY AU Caspi R TH 1 DC Lipoate biosynthesis and incorporation III (Bacillus) DR MetaCyc; PWY-6987; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GcvH:[lipoyl domain] amidotransferase DN GcvH:[lipoyl domain] amidotransferase (EC 2.3.1.204) RQ 1 EV IPR004143; PF03099; sufficient; -- SN 2 ID Octanoyl:GcvH transferase DN Octanoyl:GcvH transferase (EC 2.3.1.181) RQ 1 EV IPR004143; PF03099; sufficient; -- SN 3 ID Lipoyl synthase DN Lipoyl synthase (EC 2.8.1.8) RQ 1 EV IPR003698; TIGR00510; sufficient; // AC GenProp1626 DE L-alanine degradation I TP PATHWAY AU Riley M TH 0 DC L-alanine degradation I DR MetaCyc; ALADEG-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alanine racemase DN Alanine racemase (EC 5.1.1.1) RQ 1 EV IPR000821; TIGR00492; sufficient; -- SN 2 ID D-alanine dehydrogenase DN D-alanine dehydrogenase (EC 1.4.5) RQ 1 EV IPR006076; PF01266; sufficient; // AC GenProp1627 DE Cardiolipin biosynthesis I TP PATHWAY AU Caspi R TH 1 DC Cardiolipin biosynthesis I DR MetaCyc; PWY-5668; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cardiolipin synthase DN Cardiolipin synthase (EC 2.7.8) RQ 1 EV IPR022924; TIGR04265; sufficient; -- SN 2 ID Phosphatidylglycerolphosphate phosphatase DN Phosphatidylglycerolphosphate phosphatase (EC 3.1.3.27) RQ 1 EV IPR006435; TIGR01545; sufficient; -- SN 3 ID Phosphatidylglycerolphosphate synthase DN Phosphatidylglycerolphosphate synthase (EC 2.7.8.5) RQ 1 EV IPR000462; PF01066; sufficient; EV IPR004570; TIGR00560; sufficient; // AC GenProp1628 DE 5-Aminoimidazole ribonucleotide biosynthesis II TP PATHWAY AU Caspi R TH 3 DC 5-Aminoimidazole ribonucleotide biosynthesis II DR MetaCyc; PWY-6122; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoribosylformylglycinamide cyclo-ligase DN Phosphoribosylformylglycinamide cyclo-ligase (EC 6.3.3.1) RQ 1 EV IPR004733; TIGR00878; sufficient; -- SN 2 ID Phosphoribosylformylglycinamidine synthetase DN Phosphoribosylformylglycinamidine synthetase (EC 6.3.5.3) RQ 1 EV IPR010073; TIGR01735; sufficient; -- SN 3 ID Phosphoribosylglycinamide formyltransferase DN Phosphoribosylglycinamide formyltransferase (EC 2.1.2) RQ 1 EV IPR005862; TIGR01142; sufficient; -- SN 4 ID Phosphoribosylamine-glycine ligase DN Phosphoribosylamine-glycine ligase (EC 6.3.4.13) RQ 1 EV IPR000115; TIGR00877; sufficient; -- SN 5 ID Phosphoribosylpyrophosphate amidotransferase DN Phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) RQ 1 EV IPR005854; TIGR01134; sufficient; // AC GenProp1629 DE Propanoyl CoA degradation I TP PATHWAY AU Riley M TH 1 DC Propanoyl CoA degradation I DR MetaCyc; PROPIONMET-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Methylmalonyl-CoA epimerase DN Methylmalonyl-CoA epimerase (EC 5.1.99.1) RQ 1 EV IPR017515; TIGR03081; sufficient; -- SN 2 ID Methylmalonyl-CoA mutase DN Methylmalonyl-CoA mutase (EC 5.4.99.2) RQ 1 EV IPR006098; TIGR00641; sufficient; EV IPR006099; PF01642; sufficient; EV IPR006158; PF02310; sufficient; EV IPR006159; TIGR00640; sufficient; -- SN 3 ID Propionyl-CoA carboxylase DN Propionyl-CoA carboxylase (EC 6.4.1.3) RQ 1 EV IPR000089; PF00364; sufficient; EV IPR005479; PF02786; sufficient; EV IPR005481; PF00289; sufficient; EV IPR005482; PF02785; sufficient; // AC GenProp1630 DE Aminomethylphosphonate degradation TP PATHWAY AU Caspi R TH 6 DC Aminomethylphosphonate degradation DR MetaCyc; PWY-7805; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenine phosphoribosyltransferase DN Adenine phosphoribosyltransferase (EC 2.4.2.7) RQ 1 EV IPR005764; TIGR01090; sufficient; -- SN 2 ID Inorganic pyrophosphatase DN Inorganic pyrophosphatase (EC 3.6.1.1) RQ 1 EV IPR001952; PF00245; sufficient; EV IPR008162; PF00719; sufficient; -- SN 3 ID Alpha-D-ribose-1-(2-N-acetamidomethylphosphonate)-5-triphosphate synthase DN Alpha-D-ribose-1-(2-N-acetamidomethylphosphonate)-5-triphosphate synthase (EC 2.7.8.37) RQ 1 EV IPR009609; PF06754; sufficient; EV IPR009609; TIGR03293; sufficient; EV IPR008772; PF05845; sufficient; EV IPR008772; TIGR03292; sufficient; EV IPR008773; PF05861; sufficient; EV IPR012701; TIGR02324; sufficient; -- SN 4 ID Alpha-D-ribose-1-(2-N-acetamidomethylphosphonate)-5-triphosphate diphosphatase DN Alpha-D-ribose-1-(2-N-acetamidomethylphosphonate)-5-triphosphate diphosphatase (EC 3.6.1.63) RQ 1 EV IPR012696; TIGR02318; sufficient; -- SN 5 ID Carbon-phosphorous lyase DN Carbon-phosphorous lyase (EC 4.7.1.1) RQ 1 EV IPR010306; PF06007; sufficient; -- SN 6 ID Ribose 1,5-bisphosphate phosphokinase DN Ribose 1,5-bisphosphate phosphokinase (EC 2.7.4.23) RQ 1 EV IPR012699; TIGR02322; sufficient; -- SN 7 ID Phosphoribosyl 1,2-cyclic phosphodiesterase DN Phosphoribosyl 1,2-cyclic phosphodiesterase (EC 3.1.4.55) RQ 1 EV IPR017693; TIGR03307; sufficient; -- SN 8 ID Aminomethylphosphonate N-acetyltransferase DN Aminomethylphosphonate N-acetyltransferase (EC 2.3.1.M28) RQ 1 EV IPR000182; PF00583; sufficient; // AC GenProp1631 DE Superpathway of pyrimidine deoxyribonucleosides degradation TP PATHWAY AU Ingraham J TH 1 DC Superpathway of pyrimidine deoxyribonucleosides degradation DR MetaCyc; PWY0-1298; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-deoxyribose 1,5-phosphomutase DN D-deoxyribose 1,5-phosphomutase (EC 5.4.2.7) RQ 1 EV IPR010045; TIGR01696; sufficient; -- SN 2 ID Thymidine phosphorylase DN Thymidine phosphorylase (EC 2.4.2.4) RQ 1 EV IPR009664; PF06865; sufficient; EV IPR013465; TIGR02643; sufficient; EV IPR018090; TIGR02644; sufficient; -- SN 3 ID 2'-Deoxyuridine phosphorylase DN 2'-Deoxyuridine phosphorylase (EC 2.4.2.2) RQ 1 EV IPR013465; TIGR02643; sufficient; EV IPR018090; TIGR02644; sufficient; // AC GenProp1632 DE Erythro-tetrahydrobiopterin biosynthesis I TP PATHWAY AU Caspi R TH 1 DC Erythro-tetrahydrobiopterin biosynthesis I DR MetaCyc; PWY-5663; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 6-Pyruvoyltetrahydropterin synthase DN 6-Pyruvoyltetrahydropterin synthase (EC 4.2.3.12) RQ 1 EV IPR007115; PF01242; sufficient; EV IPR007115; TIGR00039; sufficient; -- SN 2 ID GTP cyclohydrolase DN GTP cyclohydrolase (EC 3.5.4.16) RQ 1 EV IPR001474; TIGR00063; sufficient; -- SN 3 ID Sepiapterin reductase [(6R)-tetrahydrobiopterin-forming] DN Sepiapterin reductase [(6R)-tetrahydrobiopterin-forming] (EC 1.1.1.153) RQ 1 EV IPR002347; PF00106; sufficient; EV IPR006393; TIGR01500; sufficient; // AC GenProp1633 DE Pyridoxal 5'-phosphate biosynthesis I TP PATHWAY AU Sarker M, Riley M TH 5 DC Pyridoxal 5'-phosphate biosynthesis I DR MetaCyc; PYRIDOXSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 1-Deoxy-D-xylulose 5-phosphate synthase DN 1-Deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7) RQ 1 EV IPR005477; PF13292; sufficient; EV IPR005477; TIGR00204; sufficient; -- SN 2 ID D-erythrose-4-phosphate dehydrogenase DN D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) RQ 1 EV IPR006422; TIGR01532; sufficient; -- SN 3 ID Erythronate-4-phosphate dehydrogenase DN Erythronate-4-phosphate dehydrogenase (EC 1.1.1.290) RQ 1 EV IPR006139; PF00389; sufficient; EV IPR006140; PF02826; sufficient; EV IPR024531; PF11890; sufficient; -- SN 4 ID Pyridoxine 5'-phosphate synthase DN Pyridoxine 5'-phosphate synthase (EC 2.6.99.2) RQ 1 EV IPR004569; PF03740; sufficient; EV IPR004569; TIGR00559; sufficient; -- SN 5 ID Pyridoxine 5'-phosphate oxidase II DN Pyridoxine 5'-phosphate oxidase II (EC 1.4.3.5) RQ 1 EV IPR000659; TIGR00558; sufficient; -- SN 6 ID Phosphohydroxythreonine aminotransferase DN Phosphohydroxythreonine aminotransferase (EC 2.6.1.52) RQ 1 EV IPR022278; TIGR01364; sufficient; -- SN 7 ID 4-Hydroxythreonine-4-phosphate dehydrogenase DN 4-Hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262) RQ 1 EV IPR005255; PF04166; sufficient; EV IPR005255; TIGR00557; sufficient; // AC GenProp1634 DE CMP phosphorylation TP PATHWAY AU Caspi R TH 0 DC CMP phosphorylation DR MetaCyc; PWY-7205; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID CDP kinase DN CDP kinase (EC 2.7.4.6) RQ 1 EV IPR001564; PF00334; sufficient; EV IPR006259; TIGR01351; sufficient; -- SN 2 ID CMP kinase DN CMP kinase (EC 2.7.4.25) RQ 1 EV IPR003136; TIGR00017; sufficient; EV IPR006266; TIGR01359; sufficient; // AC GenProp1635 DE Superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis TP PATHWAY AU Caspi R TH 3 DC Superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis DR MetaCyc; PWY-7211; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID CTP synthetase DN CTP synthetase (EC 6.3.4.2) RQ 1 EV IPR004468; TIGR00337; sufficient; -- SN 2 ID Orotidine 5'-phosphate decarboxylase DN Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) RQ 1 EV IPR014732; TIGR01740; sufficient; -- SN 3 ID UMP kinase DN UMP kinase (EC 2.7.4.14) RQ 1 EV IPR006266; TIGR01359; sufficient; EV IPR015963; TIGR02075; sufficient; -- SN 4 ID CTP triphosphatase DN CTP triphosphatase (EC 3.6.1.15) RQ 1 EV IPR004948; PF03266; sufficient; -- SN 5 ID UDP reductase DN UDP reductase (EC 1.17.4.1) RQ 1 EV IPR000358; PF00268; sufficient; // AC GenProp1636 DE D-galacturonate degradation I TP PATHWAY AU Keseler I, Riley M TH 3 DC D-galacturonate degradation I DR MetaCyc; GALACTUROCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Tagaturonate reductase DN Tagaturonate reductase (EC 1.1.1.58) RQ 1 EV IPR013118; PF08125; sufficient; EV IPR013131; PF01232; sufficient; -- SN 2 ID D-altronate dehydratase DN D-altronate dehydratase (EC 4.2.1.7) RQ 1 EV IPR007392; PF04295; sufficient; EV IPR013974; PF08666; sufficient; -- SN 3 ID 2-Dehydro-3-deoxygluconate kinase DN 2-Dehydro-3-deoxygluconate kinase (EC 2.7.1.45) RQ 1 EV IPR011611; PF00294; sufficient; -- SN 4 ID D-galacturonate isomerase DN D-galacturonate isomerase (EC 5.3.1.12) RQ 1 EV IPR003766; PF02614; sufficient; -- SN 5 ID 2-Dehydro-3-deoxy-phosphogluconate aldolase DN 2-Dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) RQ 1 EV IPR000887; PF01081; sufficient; EV IPR000887; TIGR01182; sufficient; // AC GenProp1637 DE Aerobic respiration I (cytochrome c) TP PATHWAY AU Foerster H TH 1 DC Aerobic respiration I (cytochrome c) DR MetaCyc; PWY-3781; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ubiquinol-cytochrome C oxidoreductase DN Ubiquinol-cytochrome C oxidoreductase (EC 1.10.2.2) RQ 1 EV IPR007863; PF05193; sufficient; EV IPR011765; PF00675; sufficient; -- SN 2 ID Cytochrome c oxidase DN Cytochrome c oxidase (EC 1.9.3.1) RQ 1 EV IPR002124; PF01215; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014241; TIGR02891; sufficient; -- SN 3 ID NADH dehydrogenase DN NADH dehydrogenase (EC 1.6.5.3) RQ 1 EV IPR010226; TIGR01971; sufficient; EV IPR008698; PF05676; sufficient; EV IPR009346; PF06212; sufficient; EV IPR019329; PF10183; sufficient; EV IPR019342; PF10200; sufficient; EV IPR007763; PF05071; sufficient; EV IPR017384; PF15879; sufficient; EV IPR010029; TIGR01676; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR006806; PF04716; sufficient; EV IPR006885; PF04800; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR001694; PF00146; sufficient; // AC GenProp1638 DE (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene biosynthesis TP PATHWAY AU Dreher K TH 0 DC (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene biosynthesis DR MetaCyc; PWY-6668; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID (E,E)-geranyllinalool synthase DN (E,E)-geranyllinalool synthase (EC 4.2.3.144) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 2 ID TMTT synthase DN TMTT synthase (EC 1.14.14.58) RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1639 DE Sucrose degradation II (sucrose synthase) TP PATHWAY AU Caspi R TH 3 DC Sucrose degradation II (sucrose synthase) DR MetaCyc; PWY-3801; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ATP:D-fructose 6-phosphotransferase DN ATP:D-fructose 6-phosphotransferase (EC 2.7.1.4) RQ 1 EV IPR022672; PF00349; sufficient; EV IPR022673; PF03727; sufficient; -- SN 2 ID UDP-glucose pyrophosphorylase DN UDP-glucose pyrophosphorylase (EC 2.7.7.9) RQ 1 EV IPR002618; PF01704; sufficient; -- SN 3 ID Glucose-6-phosphate isomerase DN Glucose-6-phosphate isomerase (EC 5.3.1.9) RQ 1 EV IPR001672; PF00342; sufficient; -- SN 4 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005843; PF00408; sufficient; EV IPR005844; PF02878; sufficient; EV IPR005845; PF02879; sufficient; EV IPR005846; PF02880; sufficient; -- SN 5 ID Sucrose synthase DN Sucrose synthase (EC 2.4.1.13) RQ 1 EV IPR012820; TIGR02470; sufficient; // AC GenProp1640 DE L-serine biosynthesis TP PATHWAY AU Riley M TH 1 DC L-serine biosynthesis DR MetaCyc; SERSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Phosphoglycerate dehydrogenase DN 3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) RQ 1 EV IPR006236; TIGR01327; sufficient; -- SN 2 ID Phosphoserine aminotransferase DN Phosphoserine aminotransferase (EC 2.6.1.52) RQ 1 EV IPR022278; TIGR01364; sufficient; -- SN 3 ID L-3-phosphoserine phosphatase DN L-3-phosphoserine phosphatase (EC 3.1.3.3) RQ 1 EV IPR006383; TIGR01488; sufficient; // AC GenProp1641 DE NADH to cytochrome bo oxidase electron transfer II TP PATHWAY AU Mackie A TH 0 DC NADH to cytochrome bo oxidase electron transfer II DR MetaCyc; PWY0-1567; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; -- SN 2 ID NADH:ubiquinone oxidoreductase 1 (external) DN NADH:ubiquinone oxidoreductase 1 (external) (EC 1.6.5.9) RQ 1 EV IPR023753; PF07992; sufficient; // AC GenProp1643 DE Chorismate biosynthesis I TP PATHWAY AU Caspi R, Ingraham J TH 0 DC Chorismate biosynthesis I DR MetaCyc; ARO-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Dehydroquinate dehydratase DN 3-Dehydroquinate dehydratase (EC 4.2.1.10) RQ 1 EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR011342; TIGR00507; sufficient; EV IPR006264; TIGR01356; sufficient; EV IPR031322; PF01202; sufficient; -- SN 2 ID 3-Dehydroquinate synthase DN 3-Dehydroquinate synthase (EC 4.2.3.4) RQ 1 EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR006264; TIGR01356; sufficient; EV IPR031322; PF01202; sufficient; // AC GenProp1644 DE Mineralocorticoid biosynthesis TP PATHWAY AU Caspi R, Weerasinghe D, Trupp M TH 2 DC Mineralocorticoid biosynthesis DR MetaCyc; PWY66-382; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Progesterone 21-hydroxylase DN Progesterone 21-hydroxylase (EC 1.14.13) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID 11-Deoxycorticosterone hydroxylase DN 11-Deoxycorticosterone hydroxylase (EC 1.14.15.4) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID Cytochrome P450 11B2, mitochondrial DN Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 4 ID 18-Hydroxycorticosterone 18-methyl oxidase DN 18-Hydroxycorticosterone 18-methyl oxidase (EC 1.14.15.5) RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1645 DE Zeaxanthin biosynthesis TP PATHWAY AU Caspi R TH 0 DC Zeaxanthin biosynthesis DR MetaCyc; PWY-5944; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Beta-carotene hydroxylase DN Beta-carotene hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 2 ID Beta-cryptoxanthin 3'-hydroxylase DN Beta-cryptoxanthin 3'-hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; // AC GenProp1646 DE L-threonine degradation II TP PATHWAY AU Caspi R, Wagg J TH 0 DC L-threonine degradation II DR MetaCyc; THREONINE-DEG2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Amino-3-ketobutyrate coenzyme A ligase DN 2-Amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) RQ 1 EV IPR011282; TIGR01822; sufficient; -- SN 2 ID L-threonine dehydrogenase DN L-threonine dehydrogenase (EC 1.1.1.103) RQ 1 EV IPR004627; TIGR00692; sufficient; // AC GenProp1647 DE Superpathway of lipopolysaccharide biosynthesis TP PATHWAY AU Sarker M, Johnson A TH 5 DC Superpathway of lipopolysaccharide biosynthesis DR MetaCyc; LPSSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Deoxy-manno-octulosonate cytidylyltransferase DN 3-Deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) RQ 1 EV IPR003329; PF02348; sufficient; EV IPR004528; TIGR00466; sufficient; -- SN 2 ID Lipid IVA (2-6) 3-deoxy-D-manno-octulosonic acid transferase DN Lipid IVA (2-6) 3-deoxy-D-manno-octulosonic acid transferase (EC 2.4.99.12) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR007507; PF04413; sufficient; -- SN 3 ID KDO transferase DN KDO transferase (EC 2.4.99.13) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR007507; PF04413; sufficient; -- SN 4 ID Lauroyl acyltransferase DN Lauroyl acyltransferase (EC 2.3.1.241) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011920; TIGR02207; sufficient; -- SN 5 ID Myristoyl-acyl carrier protein-dependent acyltransferase DN Myristoyl-acyl carrier protein-dependent acyltransferase (EC 2.3.1.243) RQ 1 EV IPR004960; PF03279; sufficient; EV IPR011921; TIGR02208; sufficient; -- SN 6 ID ADP-heptose:Kdo2-lipid A heptosyltransferase DN ADP-heptose:Kdo2-lipid A heptosyltransferase (EC 2.4) RQ 1 EV IPR002201; PF01075; sufficient; EV IPR011908; TIGR02193; sufficient; -- SN 7 ID Tetraacyldisaccharide 4'-kinase DN Tetraacyldisaccharide 4'-kinase (EC 2.7.1.130) RQ 1 EV IPR003758; PF02606; sufficient; EV IPR003758; TIGR00682; sufficient; // AC GenProp1648 DE Colanic acid building blocks biosynthesis TP PATHWAY AU Keseler I, Pellegrini-Toole A, Caspi R TH 3 DC Colanic acid building blocks biosynthesis DR MetaCyc; COLANSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Mannose-1-phosphate guanylyltransferase DN Mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) RQ 1 EV IPR006375; TIGR01479; sufficient; -- SN 2 ID GDP-mannose 4,6-dehydratase DN GDP-mannose 4,6-dehydratase (EC 4.2.1.47) RQ 1 EV IPR006368; TIGR01472; sufficient; -- SN 3 ID UDP-glucose pyrophosphorylase DN UDP-glucose pyrophosphorylase (EC 2.7.7.9) RQ 1 EV IPR005771; TIGR01099; sufficient; -- SN 4 ID UDP-galactose 4-epimerase DN UDP-galactose 4-epimerase (EC 5.1.3.2) RQ 1 EV IPR005886; TIGR01179; sufficient; -- SN 5 ID UDP-glucose dehydrogenase DN UDP-glucose dehydrogenase (EC 1.1.1.22) RQ 1 EV IPR017476; TIGR03026; sufficient; // AC GenProp1649 DE Dehydro-D-arabinono-1,4-lactone biosynthesis TP PATHWAY AU Foerster H, Vincent B, Krieger C TH 1 DC Dehydro-D-arabinono-1,4-lactone biosynthesis DR MetaCyc; PWY3O-6; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-arabinose dehydrogenase DN D-arabinose dehydrogenase (EC 1.1.1.117) RQ 1 EV IPR023210; PF00248; sufficient; -- SN 2 ID D-arabinono-1,4-lactone oxidase DN D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) RQ 1 EV IPR030654; TIGR01678; sufficient; -- SN 3 ID D-arabinose dehydrogenase DN D-arabinose dehydrogenase (EC 1.1.1.116) RQ 1 EV IPR023210; PF00248; sufficient; // AC GenProp1650 DE Guanosine ribonucleotides de novo biosynthesis TP PATHWAY AU Caspi R TH 2 DC Guanosine ribonucleotides de novo biosynthesis DR MetaCyc; PWY-7221; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GDP kinase DN GDP kinase (EC 2.7.4.6) RQ 1 EV IPR006259; TIGR01351; sufficient; EV IPR001564; PF00334; sufficient; -- SN 2 ID Xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming) DN Xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming) (EC 6.3.5.2) RQ 1 EV IPR001674; PF00958; sufficient; EV IPR001674; TIGR00884; sufficient; EV IPR004739; TIGR00888; sufficient; EV IPR017926; PF00117; sufficient; EV IPR022310; PF02540; sufficient; -- SN 3 ID Guanylate kinase DN Guanylate kinase (EC 2.7.4.8) RQ 1 EV IPR017665; TIGR03263; sufficient; -- SN 4 ID Inosine-5'-monophosphate dehydrogenase DN Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) RQ 1 EV IPR005990; TIGR01302; sufficient; // AC GenProp1651 DE Lipid A-core biosynthesis TP PATHWAY AU Sarker M, Johnson A TH 8 DC Lipid A-core biosynthesis DR MetaCyc; LIPA-CORESYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ADP-heptose-LPS heptosyltransferase DN ADP-heptose-LPS heptosyltransferase (EC 2.4.1) RQ 1 EV IPR002201; PF01075; sufficient; EV IPR011910; TIGR02195; sufficient; -- SN 2 ID ADP-heptose:Kdo2-lipid A heptosyltransferase DN ADP-heptose:Kdo2-lipid A heptosyltransferase (EC 2.4) RQ 1 EV IPR002201; PF01075; sufficient; EV IPR011908; TIGR02193; sufficient; -- SN 3 ID Lipopolysaccharide glucosyltransferase DN Lipopolysaccharide glucosyltransferase (EC 2.4.1) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR028098; PF13439; sufficient; -- SN 4 ID Lipopolysaccharide core heptose (I) kinase DN Lipopolysaccharide core heptose (I) kinase (EC 2.7.1) RQ 1 EV IPR010440; PF06293; sufficient; -- SN 5 ID Lipopolysaccharide core heptosyltransferase DN Lipopolysaccharide core heptosyltransferase (EC 2.4) RQ 1 EV IPR002201; PF01075; sufficient; EV IPR011916; TIGR02201; sufficient; -- SN 6 ID Lipopolysaccharide core heptose (II) kinase DN Lipopolysaccharide core heptose (II) kinase (EC 2.7.1) RQ 1 EV IPR009330; PF06176; sufficient; -- SN 7 ID Lipopolysaccharide 1,6-galactosyltransferase DN Lipopolysaccharide 1,6-galactosyltransferase (EC 2.4.1.44) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR028098; PF13439; sufficient; -- SN 8 ID UDP-D-glucose:(glucosyl)LPS alpha-1,3-glucosyltransferase DN UDP-D-glucose:(glucosyl)LPS alpha-1,3-glucosyltransferase (EC 2.4.1.73) RQ 1 EV IPR002495; PF01501; sufficient; -- SN 9 ID Lipopolysaccharide glucosyltransferase DN Lipopolysaccharide glucosyltransferase (EC 2.4.1.58) RQ 1 EV IPR002495; PF01501; sufficient; -- SN 10 ID Lipid A-core heptosyl transferase DN Lipid A-core heptosyl transferase (EC 2.4) RQ 1 EV IPR002201; PF01075; sufficient; // AC GenProp1652 DE Urate conversion to allantoin I TP PATHWAY AU Caspi R TH 1 DC Urate conversion to allantoin I DR MetaCyc; PWY-5691; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Hydroxyisourate hydrolase DN Hydroxyisourate hydrolase (EC 3.5.2.17) RQ 1 EV IPR001360; PF00232; sufficient; EV IPR014306; TIGR02962; sufficient; -- SN 2 ID OHCU decarboxylase DN OHCU decarboxylase (EC 4.1.1.97) RQ 1 EV IPR014306; TIGR02962; sufficient; -- SN 3 ID Urate hydroxylase DN Urate hydroxylase (EC 1.7.3.3) RQ 1 EV IPR002042; PF01014; sufficient; EV IPR002042; TIGR03383; sufficient; // AC GenProp1653 DE Leukotriene biosynthesis TP PATHWAY AU Trupp M TH 4 DC Leukotriene biosynthesis DR MetaCyc; PWY66-375; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Arachidonate 5-lipoxygenase DN Arachidonate 5-lipoxygenase RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 2 ID Leukotriene A-4 hydrolase DN Leukotriene A-4 hydrolase (EC 3.3.2.6) RQ 1 EV IPR012777; TIGR02411; sufficient; -- SN 3 ID Leukotriene C4 synthase DN Leukotriene C4 synthase (EC 4.4.1.20) RQ 1 EV IPR001129; PF01124; sufficient; -- SN 4 ID (6E,8Z,11Z,14Z)-(5S)-5-hydroperoxyicosa-6,8,11,14-tetraenoate dehydratase DN (6E,8Z,11Z,14Z)-(5S)-5-hydroperoxyicosa-6,8,11,14-tetraenoate dehydratase RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013819; PF00305; sufficient; -- SN 5 ID Leukotriene-C4 gamma-glutamyl transferase DN Leukotriene-C4 gamma-glutamyl transferase (EC 2.3.2.2) RQ 1 EV IPR000101; PF01019; sufficient; -- SN 6 ID LTD4 dipeptidase DN LTD4 dipeptidase (EC 3.4.13.19) RQ 1 EV IPR008257; PF01244; sufficient; // AC GenProp1654 DE Homocysteine and cysteine interconversion TP PATHWAY AU Pellegrini-Toole A TH 2 DC Homocysteine and cysteine interconversion DR MetaCyc; PWY-801; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-cystathionine beta-lyase DN L-cystathionine beta-lyase (EC 4.4.1.13) RQ 1 EV IPR000277; PF01053; sufficient; EV IPR006238; TIGR01329; sufficient; -- SN 2 ID Cystathionine beta-synthase DN Cystathionine beta-synthase (EC 4.2.1.22) RQ 1 EV IPR005857; TIGR01137; sufficient; -- SN 3 ID O-succinylhomoserine(thiol)-lyase DN O-succinylhomoserine(thiol)-lyase (EC 2.5.1.48) RQ 1 EV IPR000277; PF01053; sufficient; -- SN 4 ID Cystathionine gamma-lyase DN Cystathionine gamma-lyase (EC 4.4.1.1) RQ 1 EV IPR000277; PF01053; sufficient; // AC GenProp1655 DE L-methionine degradation III TP PATHWAY AU Caspi R TH 1 DC L-methionine degradation III DR MetaCyc; PWY-5082; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Oxo-4-methylthiobutanoate carboxy-lyase DN 2-Oxo-4-methylthiobutanoate carboxy-lyase RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 2 ID Methionol reductase DN Methionol reductase (EC 1.1.1.1) RQ 1 EV IPR014183; TIGR02818; sufficient; -- SN 3 ID Methionine--phenylpyruvate transaminase DN Methionine--phenylpyruvate transaminase (EC 2.6.1.28) RQ 1 EV IPR004839; PF00155; sufficient; // AC GenProp1656 DE Xylose degradation I TP PATHWAY AU Riley M, Ingraham J TH 0 DC Xylose degradation I DR MetaCyc; XYLCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Xylose isomerase DN Xylose isomerase (EC 5.3.1.5) RQ 1 EV IPR013452; TIGR02630; sufficient; -- SN 2 ID D-xylulokinase DN D-xylulokinase (EC 2.7.1.17) RQ 1 EV IPR006000; TIGR01312; sufficient; // AC GenProp1657 DE Ethylene biosynthesis I (plants) TP PATHWAY AU Irina Iourovitski I, Pujar A TH 1 DC Ethylene biosynthesis I (plants) DR MetaCyc; ETHYL-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 1-Aminocyclopropane-1-carboxylate synthase DN 1-Aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID 1-Aminocyclopropane-1-carboxylate oxidase DN 1-Aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) RQ 1 EV IPR005123; PF03171; sufficient; EV IPR026992; PF14226; sufficient; -- SN 3 ID Methionine adenosyltransferase DN Methionine adenosyltransferase (EC 2.5.1.6) RQ 1 EV IPR002133; TIGR01034; sufficient; // AC GenProp1658 DE NAD salvage pathway III TP PATHWAY AU Caspi R, Ying H TH 3 DC NAD salvage pathway III DR MetaCyc; NAD-BIOSYNTHESIS-II; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Nicotinamide mononucleotide adenylyltransferase DN Nicotinamide mononucleotide adenylyltransferase (EC 2.7.7.1) RQ 1 EV IPR004821; PF01467; sufficient; EV IPR004821; TIGR00125; sufficient; EV IPR006417; TIGR01526; sufficient; EV IPR001387; PF01381; sufficient; -- SN 2 ID NAD pyrophosphatase DN NAD pyrophosphatase (EC 3.6.1.22) RQ 1 EV IPR006420; TIGR01530; sufficient; -- SN 3 ID Ribosylnicotinamide kinase DN Ribosylnicotinamide kinase (EC 2.7.1.22) RQ 1 EV IPR004821; PF01467; sufficient; EV IPR004821; TIGR00125; sufficient; EV IPR006417; TIGR01526; sufficient; EV IPR001387; PF01381; sufficient; -- SN 4 ID NADP phosphatase DN NADP phosphatase (EC 3.1.3.2) RQ 1 EV IPR005519; PF03767; sufficient; EV IPR006423; TIGR01533; sufficient; -- SN 5 ID NMN 5'-nucleotidase DN NMN 5'-nucleotidase (EC 3.1.3.5) RQ 1 EV IPR006420; TIGR01530; sufficient; EV IPR005519; PF03767; sufficient; EV IPR006423; TIGR01533; sufficient; // AC GenProp1660 DE L-asparagine biosynthesis III (tRNA-dependent) TP PATHWAY AU Caspi R TH 0 DC L-asparagine biosynthesis III (tRNA-dependent) DR MetaCyc; PWY490-4; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Anspartyl-tRNA(Asn) amidotransferase DN Anspartyl-tRNA(Asn) amidotransferase (EC 6.3.5.6) RQ 1 EV IPR004412; TIGR00132; sufficient; EV IPR004413; TIGR00133; sufficient; EV IPR003837; PF02686; sufficient; EV IPR003837; TIGR00135; sufficient; -- SN 2 ID Aspartate--tRNA ligase DN Aspartate--tRNA ligase (EC 6.1.1.23) RQ 1 EV IPR004523; TIGR00458; sufficient; // AC GenProp1661 DE D-galactose degradation V (Leloir pathway) TP PATHWAY AU Caspi R, Montanucci L TH 3 DC D-galactose degradation V (Leloir pathway) DR MetaCyc; PWY66-422; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Mutarotase DN Mutarotase (EC 5.1.3.3) RQ 1 EV IPR008183; PF01263; sufficient; -- SN 2 ID Galactokinase DN Galactokinase (EC 2.7.1.6) RQ 1 EV IPR000705; TIGR00131; sufficient; -- SN 3 ID Galactose-1-phosphate uridylyltransferase DN Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) RQ 1 EV IPR001937; TIGR00209; sufficient; -- SN 4 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005843; PF00408; sufficient; EV IPR005844; PF02878; sufficient; EV IPR005845; PF02879; sufficient; EV IPR005846; PF02880; sufficient; -- SN 5 ID UDP-galactose 4-epimerase DN UDP-galactose 4-epimerase (EC 5.1.3.2) RQ 1 EV IPR005886; TIGR01179; sufficient; // AC GenProp1662 DE L-lactaldehyde degradation (aerobic) TP PATHWAY AU Keseler I TH 0 DC L-lactaldehyde degradation (aerobic) DR MetaCyc; PWY0-1317; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lactate oxidation DN Lactate oxidation RQ 1 EV IPR000262; PF01070; sufficient; -- SN 2 ID NAD+ L-lactaldehyde dehydrogenase DN NAD+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) RQ 1 EV IPR013454; TIGR02632; sufficient; // AC GenProp1663 DE Heme b biosynthesis IV (Gram-positive bacteria) TP PATHWAY AU Caspi R TH 2 DC Heme b biosynthesis IV (Gram-positive bacteria) DR MetaCyc; PWY-7766; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Coproporphyrinogen III oxidase (coproporphyrin-forming) DN Coproporphyrinogen III oxidase (coproporphyrin-forming) (EC 1.3.3.15) RQ 1 EV IPR004572; TIGR00562; sufficient; -- SN 2 ID Coproporphyrin ferrochelatase DN Coproporphyrin ferrochelatase (EC 4.99.1.9) RQ 1 EV IPR001015; PF00762; sufficient; EV IPR001015; TIGR00109; sufficient; -- SN 3 ID Coproheme III oxidative decarboxylase DN Coproheme III oxidative decarboxylase (EC 1.3.99) RQ 1 EV IPR010644; PF06778; sufficient; -- SN 4 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase (EC 4.1.1.37) RQ 1 EV IPR006361; TIGR01464; sufficient; // AC GenProp1664 DE Gamma-glutamyl cycle TP PATHWAY AU Caspi R TH 4 DC Gamma-glutamyl cycle DR MetaCyc; PWY-4041; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 5-Oxoprolinase DN 5-Oxoprolinase (EC 3.5.2.9) RQ 1 EV IPR002821; PF01968; sufficient; EV IPR003692; PF02538; sufficient; EV IPR008040; PF05378; sufficient; -- SN 2 ID Gamma-glutamyl cyclotransferase DN Gamma-glutamyl cyclotransferase (EC 4.3.2.9) RQ 1 EV IPR009288; PF06094; sufficient; -- SN 3 ID Glutathione synthetase DN Glutathione synthetase (EC 6.3.2.3) RQ 1 EV IPR005615; PF03917; sufficient; EV IPR005615; TIGR01986; sufficient; -- SN 4 ID Glutamate-cysteine ligase DN Glutamate-cysteine ligase (EC 6.3.2.2) RQ 1 EV IPR004308; PF03074; sufficient; -- SN 5 ID Gamma-glutamyl transpeptidase DN Gamma-glutamyl transpeptidase (EC 2.3.2.2) RQ 1 EV IPR000101; PF01019; sufficient; -- SN 6 ID Cysteinylglycine dipeptidase DN Cysteinylglycine dipeptidase (EC 3.4.13.18) RQ 1 EV IPR014782; PF01433; sufficient; EV IPR024571; PF11838; sufficient; EV IPR000819; PF00883; sufficient; EV IPR008283; PF02789; sufficient; // AC GenProp1665 DE Sphingolipid biosynthesis (mammals) TP PATHWAY AU Caspi R TH 0 DC Sphingolipid biosynthesis (mammals) DR MetaCyc; PWY-7277; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Sphingomyelin synthase DN Sphingomyelin synthase (EC 2.7.8.27) RQ 1 EV IPR025749; PF14360; sufficient; -- SN 2 ID Dihydroceramide 4-desaturase DN Dihydroceramide 4-desaturase (EC 1.14.19.17) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR013866; PF08557; sufficient; // AC GenProp1666 DE Glucocorticoid biosynthesis TP PATHWAY AU Caspi R, Trupp M TH 1 DC Glucocorticoid biosynthesis DR MetaCyc; PWY66-381; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Progesterone 17-hydroxylase DN Progesterone 17-hydroxylase (EC 1.14.14.19) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID 17-Hydroxyprogesterone 21-hydroxylase DN 17-Hydroxyprogesterone 21-hydroxylase (EC 1.14.13) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID 11-Deoxycortisol oxidase DN 11-Deoxycortisol oxidase (EC 1.14.15.4) RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1667 DE L-alanine biosynthesis I TP PATHWAY AU Riley M, Shearer A TH 1 DC L-alanine biosynthesis I DR MetaCyc; ALANINE-VALINESYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Alanine racemase DN Alanine racemase (EC 5.1.1.1) RQ 1 EV IPR000821; TIGR00492; sufficient; -- SN 2 ID L-valine:2-oxoglutarate aminotransferase DN L-valine:2-oxoglutarate aminotransferase (EC 2.6.1.42) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005785; TIGR01122; sufficient; -- SN 3 ID Valine-pyruvate aminotransferase DN Valine-pyruvate aminotransferase (EC 2.6.1.66) RQ 1 EV IPR004839; PF00155; sufficient; // AC GenProp1668 DE Gadusol biosynthesis TP PATHWAY AU Caspi R TH 1 DC Gadusol biosynthesis DR MetaCyc; PWY-7752; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Epi-5-epi-valiolone dehydrogenase DN 2-Epi-5-epi-valiolone dehydrogenase (EC 1.1.1.M23) RQ 1 EV IPR002935; PF01596; sufficient; -- SN 2 ID Desmethyl gadusol O-methyltransferase DN Desmethyl gadusol O-methyltransferase (EC 2.1.1.M22) RQ 1 EV IPR002935; PF01596; sufficient; -- SN 3 ID 2-Epi-5-epi-valiolone synthase DN 2-Epi-5-epi-valiolone synthase (EC 4.2.3.152) RQ 1 EV IPR030960; PF01761; sufficient; // AC GenProp1669 DE CO2 fixation into oxaloacetate (anaplerotic) TP PATHWAY AU Tissier C, Caspi R TH 0 DC CO2 fixation into oxaloacetate (anaplerotic) DR MetaCyc; PWYQT-4429; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoenolpyruvate carboxylase DN Phosphoenolpyruvate carboxylase (EC 4.1.1.31) RQ 1 EV IPR021135; PF00311; sufficient; -- SN 2 ID Beta-carbonic anhydrase DN Beta-carbonic anhydrase (EC 4.2.1.1) RQ 1 EV IPR001765; PF00484; sufficient; // AC GenProp1670 DE Di-trans,poly-cis-undecaprenyl phosphate biosynthesis TP PATHWAY AU Caspi R TH 0 DC Di-trans,poly-cis-undecaprenyl phosphate biosynthesis DR MetaCyc; PWY-5785; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Di-trans,poly-cis-decaprenyl diphosphate:isopentenyl-diphosphate undecaprenylcistransferase DN Di-trans,poly-cis-decaprenyl diphosphate:isopentenyl-diphosphate undecaprenylcistransferase (EC 2.5.1.31) RQ 1 EV IPR001441; PF01255; sufficient; EV IPR001441; TIGR00055; sufficient; -- SN 2 ID Undecaprenyl pyrophosphate phosphatase DN Undecaprenyl pyrophosphate phosphatase (EC 3.6.1.27) RQ 1 EV IPR003824; PF02673; sufficient; EV IPR003824; TIGR00753; sufficient; // AC GenProp1671 DE Ceramide de novo biosynthesis TP PATHWAY AU Weerasinghe D, Evsikov A TH 2 DC Ceramide de novo biosynthesis DR MetaCyc; PWY3DJ-12; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Ketodihydrosphingosine reductase DN 3-Ketodihydrosphingosine reductase (EC 1.1.1.102) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID Dihydroceramide 4-desaturase DN Dihydroceramide 4-desaturase (EC 1.14.19.17) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR013866; PF08557; sufficient; -- SN 3 ID Sphinganine N-acyltransferase DN Sphinganine N-acyltransferase (EC 2.3.1) RQ 1 EV IPR006634; PF03798; sufficient; -- SN 4 ID Serine palmitoyltransferase DN Serine palmitoyltransferase (EC 2.3.1.50) RQ 1 EV IPR024512; PF11779; sufficient; // AC GenProp1672 DE Hydrogen to fumarate electron transfer TP PATHWAY AU Mackie A TH 0 DC Hydrogen to fumarate electron transfer DR MetaCyc; PWY0-1576; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Fumarate reductase DN Fumarate reductase (EC 1.3.5.4) RQ 1 EV IPR004489; TIGR00384; sufficient; EV IPR005884; TIGR01176; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR003510; PF02300; sufficient; EV IPR003418; PF02313; sufficient; -- SN 2 ID Menaquinone hydrogenase (acceptor) DN Menaquinone hydrogenase (acceptor) (EC 1.12.99.6) RQ 1 EV IPR005614; PF03916; sufficient; EV IPR001821; TIGR00391; sufficient; // AC GenProp1673 DE L-leucine degradation I TP PATHWAY AU Fulcher C, Caspi R, Wagg J TH 4 DC L-leucine degradation I DR MetaCyc; LEU-DEG2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Methyl-2-oxopentanoate dehydrogenase (acylating) DN 4-Methyl-2-oxopentanoate dehydrogenase (acylating) (EC 1.2.1.25) RQ 1 EV IPR006258; TIGR01350; sufficient; -- SN 2 ID Leucine transaminase DN Leucine transaminase (EC 2.6.1.42) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005785; TIGR01122; sufficient; -- SN 3 ID Hydroxymethylglutaryl-CoA lyase DN Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) RQ 1 EV IPR000891; PF00682; sufficient; -- SN 4 ID 3-Methylcrotonyl-CoA carboxylase DN 3-Methylcrotonyl-CoA carboxylase (EC 6.4.1.4) RQ 1 EV IPR000089; PF00364; sufficient; EV IPR005479; PF02786; sufficient; EV IPR005481; PF00289; sufficient; EV IPR005482; PF02785; sufficient; -- SN 5 ID 3-Methylglutaconyl-CoA hydratase DN 3-Methylglutaconyl-CoA hydratase (EC 4.2.1.18) RQ 1 EV IPR001753; PF00378; sufficient; -- SN 6 ID Isovaleryl-CoA:FAD oxidoreductase DN Isovaleryl-CoA:FAD oxidoreductase (EC 1.3.8.4) RQ 1 EV IPR006091; PF02770; sufficient; EV IPR009075; PF00441; sufficient; EV IPR013786; PF02771; sufficient; // AC GenProp1674 DE Thiamine formation from pyrithiamine and oxythiamine (yeast) TP PATHWAY AU Foerster H TH 4 DC Thiamine formation from pyrithiamine and oxythiamine (yeast) DR MetaCyc; PWY-7357; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 4-Amino-2-methyl-5-hydroxymethylpyrimidine kinase DN 4-Amino-2-methyl-5-hydroxymethylpyrimidine kinase (EC 2.7.1.49) RQ 1 EV IPR027574; TIGR04306; sufficient; -- SN 2 ID Phosphomethylpyrimidine kinase DN Phosphomethylpyrimidine kinase (EC 2.7.4.7) RQ 1 EV IPR027574; TIGR04306; sufficient; -- SN 3 ID Thiaminase II DN Thiaminase II (EC 3.5.99) RQ 1 EV IPR027574; TIGR04306; sufficient; -- SN 4 ID Thiaminase II DN Thiaminase II (EC 3.5.99) RQ 1 EV IPR027574; TIGR04306; sufficient; -- SN 5 ID Thiamine monophosphate pyrophosphorylase DN Thiamine monophosphate pyrophosphorylase (EC 2.5.1.3) RQ 1 EV IPR000417; PF02110; sufficient; EV IPR000417; TIGR00694; sufficient; -- SN 6 ID Hydroxyethylthiazole kinase DN Hydroxyethylthiazole kinase (EC 2.7.1.50) RQ 1 EV IPR000417; PF02110; sufficient; EV IPR000417; TIGR00694; sufficient; // AC GenProp1675 DE Superpathway of D-glucarate and D-galactarate degradation TP PATHWAY AU Caspi R, Riley M TH 0 DC Superpathway of D-glucarate and D-galactarate degradation DR MetaCyc; GLUCARGALACTSUPER-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerate 2-kinase DN Glycerate 2-kinase (EC 2.7.1.165) RQ 1 EV IPR004381; PF02595; sufficient; EV IPR004381; TIGR00045; sufficient; -- SN 2 ID Tartronate semialdehyde reductase DN Tartronate semialdehyde reductase (EC 1.1.1.60) RQ 1 EV IPR006398; TIGR01505; sufficient; // AC GenProp1676 DE Nitrate reduction IX (dissimilatory) TP PATHWAY AU Mackie A TH 0 DC Nitrate reduction IX (dissimilatory) DR MetaCyc; PWY0-1581; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol-3-phosphate dehydrogenase, anaerobic DN Glycerol-3-phosphate dehydrogenase, anaerobic (EC 1.1.5.3) RQ 1 EV IPR017752; TIGR03377; sufficient; EV IPR009158; TIGR03378; sufficient; EV IPR017753; TIGR03379; sufficient; -- SN 2 ID Menaquinol:nitrate oxidoreductase DN Menaquinol:nitrate oxidoreductase (EC 1.7.5.1) RQ 1 EV IPR006468; TIGR01580; sufficient; EV IPR006547; TIGR01660; sufficient; EV IPR003816; TIGR00351; sufficient; // AC GenProp1677 DE NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) TP PATHWAY AU Foerster H TH 3 DC NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) DR MetaCyc; PWY-7269; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aldehyde dehydrogenase DN Aldehyde dehydrogenase (EC 1.2.1.4) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID Aldehyde dehydrogenase DN Aldehyde dehydrogenase (EC 1.2.1.3) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 3 ID NAD kinase DN NAD kinase (EC 2.7.1.23) RQ 1 EV IPR002504; PF01513; sufficient; -- SN 4 ID NADH kinase DN NADH kinase (EC 2.7.1.86) RQ 1 EV IPR002504; PF01513; sufficient; -- SN 5 ID NADH:ubiquinone oxidoreductase 1 (external) DN NADH:ubiquinone oxidoreductase 1 (external) (EC 1.6.5.9) RQ 1 EV IPR023753; PF07992; sufficient; // AC GenProp1678 DE Beta-alanine biosynthesis IV TP PATHWAY AU Caspi R TH 0 DC Beta-alanine biosynthesis IV DR MetaCyc; PWY-5760; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Aminopropanal:NAD(P)+ oxidoreductase DN 3-Aminopropanal:NAD(P)+ oxidoreductase (EC 1.2.1.-) RQ 1 EV IPR015590; PF00171; sufficient; -- SN 2 ID Spermine oxidase DN Spermine oxidase (EC 1.5.3.16) RQ 1 EV IPR002937; PF01593; sufficient; // AC GenProp1679 DE L-phenylalanine degradation I (aerobic) TP PATHWAY AU Fulcher C TH 1 DC L-phenylalanine degradation I (aerobic) DR MetaCyc; PHENYLALANINE-DEG1-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Pterin-4alpha-carbinolamine dehydratase DN Pterin-4alpha-carbinolamine dehydratase (EC 4.2.1.96) RQ 1 EV IPR001533; PF01329; sufficient; -- SN 2 ID Dihydropteridine reductase DN Dihydropteridine reductase (EC 1.5.1) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 3 ID Phenylalanine hydroxylase DN Phenylalanine hydroxylase (EC 1.14.16.1) RQ 1 EV IPR005961; TIGR01268; sufficient; // AC GenProp1680 DE Fucose degradation TP PATHWAY AU Keseler I, Riley M, Ingraham J TH 2 DC Fucose degradation DR MetaCyc; FUCCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-fucose isomerase DN L-fucose isomerase (EC 5.3.1.25) RQ 1 EV IPR005763; TIGR01089; sufficient; -- SN 2 ID Fuculose-1-phosphate aldolase DN Fuculose-1-phosphate aldolase (EC 4.1.2.17) RQ 1 EV IPR004782; TIGR01086; sufficient; -- SN 3 ID L-fuculokinase DN L-fuculokinase (EC 2.7.1.51) RQ 1 EV IPR013450; TIGR02628; sufficient; -- SN 4 ID L-fucose mutarotase DN L-fucose mutarotase (EC 5.1.3.29) RQ 1 EV IPR007721; PF05025; sufficient; // AC GenProp1681 DE L-cysteine degradation III TP PATHWAY AU Caspi R TH 0 DC L-cysteine degradation III DR MetaCyc; PWY-5329; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cysteine aminotransferase DN Cysteine aminotransferase (EC 2.6.1.3) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID 3-Mercaptopyruvate sulfurtransferase DN 3-Mercaptopyruvate sulfurtransferase (EC 2.8.1.2) RQ 1 EV IPR001763; PF00581; sufficient; // AC GenProp1682 DE Factor 420 polyglutamylation TP PATHWAY AU Caspi R TH 0 DC Factor 420 polyglutamylation DR MetaCyc; PWY-5199; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID F420-0-glutamyl ligase DN F420-0-glutamyl ligase (EC 6.3.2.31) RQ 1 EV IPR008225; TIGR01916; sufficient; -- SN 2 ID F420-1:gamma-glutamyl ligase DN F420-1:gamma-glutamyl ligase (EC 6.3.2.34) RQ 1 EV IPR008225; TIGR01916; sufficient; // AC GenProp1683 DE Epoxysqualene biosynthesis TP PATHWAY AU Caspi R TH 0 DC Epoxysqualene biosynthesis DR MetaCyc; PWY-5670; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Squalene synthase DN Squalene synthase (EC 2.5.1.21) RQ 1 EV IPR002060; PF00494; sufficient; EV IPR006449; TIGR01559; sufficient; -- SN 2 ID Squalene monooxygenase DN Squalene monooxygenase (EC 1.14.14.17) RQ 1 EV IPR013698; PF08491; sufficient; // AC GenProp1684 DE Kdo transfer to lipid IVA I TP PATHWAY AU Riley M TH 0 DC Kdo transfer to lipid IVA I DR MetaCyc; KDOSYN-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lipid IVA (2-6) 3-deoxy-D-manno-octulosonic acid transferase DN Lipid IVA (2-6) 3-deoxy-D-manno-octulosonic acid transferase (EC 2.4.99.12) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR007507; PF04413; sufficient; -- SN 2 ID KDO transferase DN KDO transferase (EC 2.4.99.13) RQ 1 EV IPR001296; PF00534; sufficient; EV IPR007507; PF04413; sufficient; // AC GenProp1685 DE Hydrogen sulfide biosynthesis II (mammalian) TP PATHWAY AU Caspi R, Weerasinghe D TH 4 DC Hydrogen sulfide biosynthesis II (mammalian) DR MetaCyc; PWY66-426; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Homocysteine desulfhydrase DN Homocysteine desulfhydrase (EC 4.4.1.2) RQ 1 EV IPR000277; PF01053; sufficient; -- SN 2 ID L-cysteine desulfhydrase DN L-cysteine desulfhydrase (EC 4.4.1.28) RQ 1 EV IPR000277; PF01053; sufficient; -- SN 3 ID L-homolanthionine synthase DN L-homolanthionine synthase RQ 1 EV IPR000277; PF01053; sufficient; -- SN 4 ID L-serine beta-synthase DN L-serine beta-synthase (EC 4.2.1.22) RQ 1 EV IPR005857; TIGR01137; sufficient; -- SN 5 ID Lanthionine beta-synthase DN Lanthionine beta-synthase (EC 4.2.1.22) RQ 1 EV IPR005857; TIGR01137; sufficient; EV IPR000277; PF01053; sufficient; -- SN 6 ID L-cystathionine synthase DN L-cystathionine synthase (EC 4.2.1.22) RQ 1 EV IPR005857; TIGR01137; sufficient; EV IPR000277; PF01053; sufficient; // AC GenProp1686 DE Heme b biosynthesis II (anaerobic) TP PATHWAY AU Keseler I, Caspi R, Riley M TH 2 DC Heme b biosynthesis II (anaerobic) DR MetaCyc; HEMESYN2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Coproporphyrinogen dehydrogenase DN Coproporphyrinogen dehydrogenase (EC 1.3.98.3) RQ 1 EV IPR004558; TIGR00538; sufficient; -- SN 2 ID Deferrochelatase DN Deferrochelatase (EC 4.99.1.1) RQ 1 EV IPR001015; PF00762; sufficient; EV IPR001015; TIGR00109; sufficient; -- SN 3 ID Protoporphyrinogen dehydrogenase DN Protoporphyrinogen dehydrogenase (EC 1.3.5.3) RQ 1 EV IPR026816; PF12724; sufficient; -- SN 4 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase (EC 4.1.1.37) RQ 1 EV IPR006361; TIGR01464; sufficient; // AC GenProp1687 DE 2-Methylcitrate cycle I TP PATHWAY AU Pellegrini-Toole A, Caspi R TH 3 DC 2-Methylcitrate cycle I DR MetaCyc; PWY0-42; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Methylcitrate dehydratase DN 2-Methylcitrate dehydratase (EC 4.2.1.79) RQ 1 EV IPR005656; PF03972; sufficient; EV IPR012705; TIGR02330; sufficient; -- SN 2 ID 2-Methylcitrate synthase DN 2-Methylcitrate synthase (EC 2.3.3.5) RQ 1 EV IPR002020; PF00285; sufficient; EV IPR011278; TIGR01800; sufficient; -- SN 3 ID (2R,3S)-2-methylisocitrate hydro-lyase DN (2R,3S)-2-methylisocitrate hydro-lyase (EC 4.2.1.99) RQ 1 EV IPR004406; TIGR00117; sufficient; EV IPR006249; TIGR01341; sufficient; -- SN 4 ID 2-Methylcitrate lyase DN 2-Methylcitrate lyase (EC 4.1.3.30) RQ 1 EV IPR012695; TIGR02317; sufficient; -- SN 5 ID Propionyl-CoA synthetase DN Propionyl-CoA synthetase (EC 6.2.1.17) RQ 1 EV IPR012694; TIGR02316; sufficient; EV IPR011904; TIGR02188; sufficient; // AC GenProp1688 DE Heme degradation VII TP PATHWAY AU Caspi R TH 0 DC Heme degradation VII DR MetaCyc; PWY-7848; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Heme oxygenase (mycobilin a-producing) DN Heme oxygenase (mycobilin a-producing) (EC 1.14.99.57) RQ 1 EV IPR007138; PF03992; sufficient; -- SN 2 ID Heme oxygenase (mycobilin b-producing) DN Heme oxygenase (mycobilin b-producing) (EC 1.14.99.57) RQ 1 EV IPR007138; PF03992; sufficient; // AC GenProp1689 DE Superpathway of 5-aminoimidazole ribonucleotide biosynthesis TP PATHWAY AU Caspi R TH 3 DC Superpathway of 5-aminoimidazole ribonucleotide biosynthesis DR MetaCyc; PWY-6277; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphoribosylformylglycinamide cyclo-ligase DN Phosphoribosylformylglycinamide cyclo-ligase (EC 6.3.3.1) RQ 1 EV IPR004733; TIGR00878; sufficient; -- SN 2 ID Phosphoribosylformylglycinamidine synthetase DN Phosphoribosylformylglycinamidine synthetase (EC 6.3.5.3) RQ 1 EV IPR010073; TIGR01735; sufficient; -- SN 3 ID Phosphoribosylglycinamide formyltransferase DN Phosphoribosylglycinamide formyltransferase (EC 2.1.2) RQ 1 EV IPR005862; TIGR01142; sufficient; -- SN 4 ID Phosphoribosylamine-glycine ligase DN Phosphoribosylamine-glycine ligase (EC 6.3.4.13) RQ 1 EV IPR000115; TIGR00877; sufficient; -- SN 5 ID Phosphoribosylpyrophosphate amidotransferase DN Phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) RQ 1 EV IPR005854; TIGR01134; sufficient; // AC GenProp1690 DE Glycolipid desaturation TP PATHWAY AU Zhang P TH 25 DC Glycolipid desaturation DR MetaCyc; PWY-782; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 1-18:1-2-16:0-Monogalactosyldiacylglycerol desaturase DN 1-18:1-2-16:0-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.42) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 2 ID 1-18:1-2-16:0-Monogalactosyldiacylglycerol desaturase DN 1-18:1-2-16:0-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 3 ID 1-18:2-2-16:0-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:0-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 4 ID 1-18:1-2-16:1-Monogalactosyldiacylglyceroldesaturase DN 1-18:1-2-16:1-Monogalactosyldiacylglyceroldesaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 5 ID 1-18:2-2-16:1-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:1-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 6 ID 1-18:1-2-16:2-Monogalactosyldiacylglycerol desaturase DN 1-18:1-2-16:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 7 ID 1-18:2-2-16:2-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 8 ID 1-18:1-2-16:3-Monogalactosyldiacylglycerol desaturase DN 1-18:1-2-16:3-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 9 ID 1-18:2-2-16:3-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:3-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 10 ID 1-18:1-2-16:2-Monogalactosyldiacylglycerol synthase DN 1-18:1-2-16:2-Monogalactosyldiacylglycerol synthase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 11 ID 1-18:1-2-16:2-Monogalactosyldiacylglycerol desaturase DN 1-18:1-2-16:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 12 ID 1-18:2-2-16:0-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:0-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.42) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 13 ID 1-18:2-2-16:1-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:1-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 14 ID 1-18:2-2-16:2-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-16:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 15 ID 1-18:3-2-16:0-Monogalactosyldiacylglycerol desaturase DN 1-18:3-2-16:0-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.42) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 16 ID 1-18:3-2-16:1-Monogalactosyldiacylglycerol desaturase DN 1-18:3-2-16:1-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 17 ID 1-18:3-2-16:2-Monogalactosyldiacylglycerol desaturase DN 1-18:3-2-16:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 18 ID 1-18:2-2-18:2-Digalactosyldiacylglycerol desaturase DN 1-18:2-2-18:2-Digalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 19 ID 1-18:3-2-18:2-Digalactosyldiacylglycerol desaturase DN 1-18:3-2-18:2-Digalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 20 ID 1-18:2-2-18:2-Digalactosyldiacylglycerol desaturas DN 1-18:2-2-18:2-Digalactosyldiacylglycerol desaturas (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 21 ID 1-18:2-2-18:3-Digalactosyldiacylglycerol desaturase DN 1-18:2-2-18:3-Digalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 22 ID 1-18:1-2-16:0-Digalactosyldiacylglycerol desaturase DN 1-18:1-2-16:0-Digalactosyldiacylglycerol desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 23 ID 1-18:2-2-16:0-Digalactosyldiacylglycerol desaturase DN 1-18:2-2-16:0-Digalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 24 ID 1-18:2-2-18:2-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-18:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 25 ID 1-18:2-2-18:2-Monogalactosyldiacylglycerol desaturase DN 1-18:2-2-18:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 26 ID 1-18:2-2-18:3-Monogalactosyldiacylglyceroldesaturase DN 1-18:2-2-18:3-Monogalactosyldiacylglyceroldesaturase (EC 1.14.19.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 27 ID 1-18:3-2-18:2-Monogalactosyldiacylglycerol desaturase DN 1-18:3-2-18:2-Monogalactosyldiacylglycerol desaturase (EC 1.14.99.35) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; // AC GenProp1691 DE Superpathway of glycolysis and the Entner-Doudoroff pathway TP PATHWAY AU Caspi R TH 3 DC Superpathway of glycolysis and the Entner-Doudoroff pathway DR MetaCyc; GLYCOLYSIS-E-D; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 6-Phosphogluconolactonase DN 6-Phosphogluconolactonase (EC 3.1.1.31) RQ 1 EV IPR019405; PF10282; sufficient; -- SN 2 ID Glyceraldehyde-3-phosphate dehydrogenase DN Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 3 ID Glucose-6-phosphate dehydrogenase DN Glucose-6-phosphate dehydrogenase (EC 1.1.1.49) RQ 1 EV IPR001282; TIGR00871; sufficient; -- SN 4 ID 2-Dehydro-3-deoxy-phosphogluconate aldolase DN 2-Dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) RQ 1 EV IPR000887; PF01081; sufficient; EV IPR000887; TIGR01182; sufficient; -- SN 5 ID Phosphogluconate dehydratase DN Phosphogluconate dehydratase (EC 4.2.1.12) RQ 1 EV IPR000581; PF00920; sufficient; EV IPR004786; TIGR01196; sufficient; // AC GenProp1692 DE D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis TP PATHWAY AU Caspi R TH 2 DC D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis DR MetaCyc; PWY-6366; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inositol 1,3,4-triphosphate 6 kinase DN Inositol 1,3,4-triphosphate 6 kinase (EC 2.7.1.159) RQ 1 EV IPR008656; PF05770; sufficient; -- SN 2 ID Myo-inositol-1,3,4,6-tetrakisphosphate 5-kinase DN Myo-inositol-1,3,4,6-tetrakisphosphate 5-kinase (EC 2.7.1.140) RQ 1 EV IPR005522; PF03770; sufficient; -- SN 3 ID Inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase DN Inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase (EC 3.1.3) RQ 1 EV IPR000560; PF00328; sufficient; -- SN 4 ID Myo-inositol-1,4,5,6-tetrakrisphosphate 3-kinase DN Myo-inositol-1,4,5,6-tetrakrisphosphate 3-kinase (EC 2.7.1.151) RQ 1 EV IPR005522; PF03770; sufficient; // AC GenProp1693 DE TCA cycle III (animals) TP PATHWAY AU Weerasinghe D, Caspi R TH 9 DC TCA cycle III (animals) DR MetaCyc; PWY66-398; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Oxoglutarate decarboxylase DN 2-Oxoglutarate decarboxylase (EC 1.2.4.2) RQ 1 EV IPR011603; TIGR00239; sufficient; -- SN 2 ID Aconitase DN Aconitase RQ 1 EV IPR006248; TIGR01340; sufficient; -- SN 3 ID Cis-aconitate hydratase DN Cis-aconitate hydratase RQ 1 EV IPR006248; TIGR01340; sufficient; -- SN 4 ID Citrate synthase DN Citrate synthase (EC 2.3.3.1) RQ 1 EV IPR002020; PF00285; sufficient; EV IPR010109; TIGR01793; sufficient; -- SN 5 ID Fumarase B DN Fumarase B (EC 4.2.1.2) RQ 1 EV IPR005677; TIGR00979; sufficient; -- SN 6 ID Isocitrate dehydrogenase DN Isocitrate dehydrogenase (EC 1.1.1.41) RQ 1 EV IPR004434; TIGR00175; sufficient; -- SN 7 ID Malate dehydrogenase (NAD) DN Malate dehydrogenase (NAD) (EC 1.1.1.37) RQ 1 EV IPR010097; TIGR01772; sufficient; EV IPR010945; TIGR01759; sufficient; EV IPR011274; TIGR01758; sufficient; -- SN 8 ID Dihydrolipoyltranssuccinylase DN Dihydrolipoyltranssuccinylase (EC 2.3.1.61) RQ 1 EV IPR006255; TIGR01347; sufficient; -- SN 9 ID Succinyl-CoA synthetase DN Succinyl-CoA synthetase (EC 6.2.1.5) RQ 1 EV IPR005809; TIGR01016; sufficient; EV IPR005810; TIGR01019; sufficient; -- SN 10 ID Succinyl-CoA synthetase DN Succinyl-CoA synthetase (EC 6.2.1.4) RQ 1 EV IPR005810; TIGR01019; sufficient; EV IPR005809; TIGR01016; sufficient; -- SN 11 ID Succinate dehydrogenase DN Succinate dehydrogenase (EC 1.3.5.1) RQ 1 EV IPR011281; TIGR01816; sufficient; EV IPR014006; TIGR01812; sufficient; EV IPR004489; TIGR00384; sufficient; EV IPR000701; PF01127; sufficient; EV IPR014314; TIGR02970; sufficient; // AC GenProp1694 DE Superpathway of demethylmenaquinol-8 biosynthesis I TP PATHWAY AU Caspi R TH 1 DC Superpathway of demethylmenaquinol-8 biosynthesis I DR MetaCyc; PWY-5861; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 1,4-Dihydroxy-2-naphthoate octaprenyltransferase DN 1,4-Dihydroxy-2-naphthoate octaprenyltransferase (EC 2.5.1.74) RQ 1 EV IPR000537; PF01040; sufficient; -- SN 2 ID All-trans-octaprenyl-diphosphate synthase DN All-trans-octaprenyl-diphosphate synthase (EC 2.5.1.90) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 3 ID 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase DN 1,4-Dihydroxy-2-naphthoyl-CoA thioesterase (EC 3.1.2.28) RQ 1 EV IPR003736; TIGR00369; sufficient; EV IPR006683; PF03061; sufficient; // AC GenProp1695 DE Serotonin and melatonin biosynthesis TP PATHWAY AU Weerasinghe D, Evsikov A TH 2 DC Serotonin and melatonin biosynthesis DR MetaCyc; PWY-6030; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetylserotonin O-methyltransferase DN Acetylserotonin O-methyltransferase (EC 2.1.1.4) RQ 1 EV IPR001077; PF00891; sufficient; EV IPR031725; PF16864; sufficient; -- SN 2 ID 5-Hydroxy-L-tryptophan decarboxylase DN 5-Hydroxy-L-tryptophan decarboxylase (EC 4.1.1.28) RQ 1 EV IPR002129; PF00282; sufficient; -- SN 3 ID Serotonin N-acetyltransferase DN Serotonin N-acetyltransferase (EC 2.3.1.87) RQ 1 EV IPR000182; PF00583; sufficient; -- SN 4 ID Tryptophan 5-hydroxylase DN Tryptophan 5-hydroxylase (EC 1.14.16.4) RQ 1 EV IPR005963; TIGR01270; sufficient; // AC GenProp1696 DE Curcumin degradation TP PATHWAY AU Fulcher C TH 0 DC Curcumin degradation DR MetaCyc; PWY0-1527; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID NADPH-dependent curcumin reductase DN NADPH-dependent curcumin reductase RQ 1 EV IPR013149; PF00107; sufficient; -- SN 2 ID NADPH-dependent dihydrocurcumin reductase DN NADPH-dependent dihydrocurcumin reductase RQ 1 EV IPR013149; PF00107; sufficient; // AC GenProp1697 DE Thiazole biosynthesis III (eukaryotes) TP PATHWAY AU Foerster H, Caspi R TH 0 DC Thiazole biosynthesis III (eukaryotes) DR MetaCyc; PWY-6909; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Thiazole synthase (eucaryotic) DN Thiazole synthase (eucaryotic) RQ 1 EV IPR002922; TIGR00292; sufficient; -- SN 2 ID 4-Methyl-5-(beta-hydroxyethyl)thiazole phosphate synthase DN 4-Methyl-5-(beta-hydroxyethyl)thiazole phosphate synthase RQ 1 EV IPR002922; TIGR00292; sufficient; // AC GenProp1698 DE L-phenylalanine degradation III TP PATHWAY AU Caspi R TH 2 DC L-phenylalanine degradation III DR MetaCyc; PWY-5079; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID L-phenylalanine:pyruvate aminotransferase DN L-phenylalanine:pyruvate aminotransferase (EC 2.6.1.58) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 2 ID L-phenylalanine:2-oxoglutarate aminotransferase DN L-phenylalanine:2-oxoglutarate aminotransferase (EC 2.6.1.57) RQ 1 EV IPR004839; PF00155; sufficient; -- SN 3 ID Phenylpyruvate decarboxylase DN Phenylpyruvate decarboxylase (EC 4.1.1.43) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; -- SN 4 ID 2-Phenylethanol dehydrogenase DN 2-Phenylethanol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR014183; TIGR02818; sufficient; // AC GenProp1699 DE Glycosaminoglycan-protein linkage region biosynthesis TP PATHWAY AU Caspi R TH 2 DC Glycosaminoglycan-protein linkage region biosynthesis DR MetaCyc; PWY-6557; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-galactose:beta-xylose beta-1,4-galactosyltransferase DN UDP-galactose:beta-xylose beta-1,4-galactosyltransferase (EC 2.4.1.133) RQ 1 EV IPR027791; PF02709; sufficient; EV IPR027995; PF13733; sufficient; -- SN 2 ID Galactosylxylosylprotein 3-beta-galactosyltransferase DN Galactosylxylosylprotein 3-beta-galactosyltransferase (EC 2.4.1.134) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 3 ID Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase DN Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135) RQ 1 EV IPR005027; PF03360; sufficient; -- SN 4 ID Protein xylosyltransferase DN Protein xylosyltransferase (EC 2.4.2.26) RQ 1 EV IPR003406; PF02485; sufficient; EV IPR024448; PF12529; sufficient; // AC GenProp1701 DE Tetrapyrrole biosynthesis I (from glutamate) TP PATHWAY AU Caspi R TH 4 DC Tetrapyrrole biosynthesis I (from glutamate) DR MetaCyc; PWY-5188; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutamyl-tRNAGlu synthetase DN Glutamyl-tRNAGlu synthetase (EC 6.1.1.17) RQ 1 EV IPR004527; TIGR00464; sufficient; -- SN 2 ID Glutamyl-tRNA reductase DN Glutamyl-tRNA reductase (EC 1.2.1.70) RQ 1 EV IPR000343; TIGR01035; sufficient; -- SN 3 ID Glutamate-1-semialdehyde 2,1-aminomutase DN Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) RQ 1 EV IPR004639; TIGR00713; sufficient; EV IPR005814; PF00202; sufficient; -- SN 4 ID Porphobilinogen deaminase DN Porphobilinogen deaminase (EC 2.5.1.61) RQ 1 EV IPR000860; TIGR00212; sufficient; -- SN 5 ID Porphobilinogen synthase DN Porphobilinogen synthase (EC 4.2.1.24) RQ 1 EV IPR001731; PF00490; sufficient; -- SN 6 ID Uroporphyrinogen III cosynthetase DN Uroporphyrinogen III cosynthetase (EC 4.2.1.75) RQ 1 EV IPR003754; PF02602; sufficient; // AC GenProp1702 DE Thiamine diphosphate biosynthesis IV (eukaryotes) TP PATHWAY AU Caspi R TH 1 DC Thiamine diphosphate biosynthesis IV (eukaryotes) DR MetaCyc; PWY-6908; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acid phosphatase DN Acid phosphatase (EC 3.1.3.100) RQ 1 EV IPR006384; TIGR01489; sufficient; EV IPR016965; PF06888; sufficient; -- SN 2 ID Thiamine monophosphate pyrophosphorylase DN Thiamine monophosphate pyrophosphorylase (EC 2.5.1.3) RQ 1 EV IPR000417; PF02110; sufficient; EV IPR000417; TIGR00694; sufficient; -- SN 3 ID Thiamine pyrophosphokinase DN Thiamine pyrophosphokinase (EC 2.7.6.2) RQ 1 EV IPR006282; TIGR01378; sufficient; // AC GenProp1703 DE Retinol biosynthesis TP PATHWAY AU Caspi R TH 5 DC Retinol biosynthesis DR MetaCyc; PWY-6857; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Lecithin:all-trans retinol acyltransferase DN Lecithin:all-trans retinol acyltransferase (EC 2.3.1.135) RQ 1 EV IPR007053; PF04970; sufficient; -- SN 2 ID All-trans-retinol dehydrogenase DN All-trans-retinol dehydrogenase (EC 1.1.1.300) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 3 ID Cellular retinol-binding protein DN Cellular retinol-binding protein RQ 1 EV IPR000566; PF00061; sufficient; -- SN 4 ID Plasma retinol-binding protein DN Plasma retinol-binding protein RQ 1 EV IPR000566; PF00061; sufficient; -- SN 5 ID All-trans retinyl-ester hydrolase DN All-trans retinyl-ester hydrolase (EC 3.1.1.1) RQ 1 EV IPR002018; PF00135; sufficient; -- SN 6 ID TriacylGlycerol Lipase DN TriacylGlycerol Lipase (EC 3.1.1.3) RQ 1 EV IPR001024; PF01477; sufficient; EV IPR013818; PF00151; sufficient; -- SN 7 ID Beta,beta-carotene 15,15'-dioxygenase DN Beta,beta-carotene 15,15'-dioxygenase (EC 1.13.11.63) RQ 1 EV IPR004294; PF03055; sufficient; // AC GenProp1704 DE Trans, trans-farnesyl diphosphate biosynthesis TP PATHWAY AU Tissier C TH 1 DC Trans, trans-farnesyl diphosphate biosynthesis DR MetaCyc; PWY-5123; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Omega,E,E-farnesyl diphosphate synthase DN Omega,E,E-farnesyl diphosphate synthase (EC 2.5.1.10) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 2 ID Dimethylallyltransferase DN Dimethylallyltransferase (EC 2.5.1.1) RQ 1 EV IPR000092; PF00348; sufficient; -- SN 3 ID Isopentenyl pyrophosphate isomerase DN Isopentenyl pyrophosphate isomerase (EC 5.3.3.2) RQ 1 EV IPR011876; TIGR02150; sufficient; // AC GenProp1705 DE Sedoheptulose bisphosphate bypass TP PATHWAY AU Keseler I TH 0 DC Sedoheptulose bisphosphate bypass DR MetaCyc; PWY0-1517; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Sedoheptulose-7-phosphate kinase DN Sedoheptulose-7-phosphate kinase (EC 2.7.1) RQ 1 EV IPR012828; TIGR02482; sufficient; -- SN 2 ID Sedoheptulose-1,7-bisphosphate aldolase DN Sedoheptulose-1,7-bisphosphate aldolase (EC 4.1.2) RQ 1 EV IPR000771; PF01116; sufficient; EV IPR000771; TIGR00167; sufficient; EV IPR006411; TIGR01520; sufficient; // AC GenProp1706 DE Protein N-glycosylation processing phase (yeast) TP PATHWAY AU Caspi R TH 2 DC Protein N-glycosylation processing phase (yeast) DR MetaCyc; PWY-7918; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glc3Man9GlcNAc2 alpha-1,2-glucosidase DN Glc3Man9GlcNAc2 alpha-1,2-glucosidase (EC 3.2.1.106) RQ 1 EV IPR031335; PF03200; sufficient; EV IPR031631; PF16923; sufficient; -- SN 2 ID Glc2Man9GlcNAc2 alpha-1,3-glucosidase DN Glc2Man9GlcNAc2 alpha-1,3-glucosidase RQ 1 EV IPR000322; PF01055; sufficient; -- SN 3 ID Glc1Man9GlcNAc2 alpha-1,3-glucosidase DN Glc1Man9GlcNAc2 alpha-1,3-glucosidase RQ 1 EV IPR000322; PF01055; sufficient; -- SN 4 ID Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase DN Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase RQ 1 EV IPR001382; PF01532; sufficient; // AC GenProp1707 DE tRNA splicing II TP PATHWAY AU Caspi R TH 0 DC tRNA splicing II DR MetaCyc; PWY-7803; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID tRNA-splicing endonuclease DN tRNA-splicing endonuclease (EC 4.6.1.16) RQ 1 EV IPR006676; TIGR00324; sufficient; -- SN 2 ID tRNA-splicing ligase DN tRNA-splicing ligase (EC 6.5.1.8) RQ 1 EV IPR019265; PF10036; sufficient; EV IPR001233; PF01139; sufficient; EV IPR024887; PF15323; sufficient; EV IPR018797; PF10239; sufficient; // AC GenProp1708 DE L-phenylalanine biosynthesis I TP PATHWAY AU Fulcher C, Ingraham J, Caspi R, Riley M TH 1 DC L-phenylalanine biosynthesis I DR MetaCyc; PHESYN; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Chorismate mutase DN Chorismate mutase (EC 5.4.99.5) RQ 1 EV IPR003099; PF02153; sufficient; EV IPR011277; TIGR01799; sufficient; EV IPR001086; PF00800; sufficient; EV IPR010952; TIGR01797; sufficient; -- SN 2 ID L-phenylalanine:2-oxoglutarate aminotransferase DN L-phenylalanine:2-oxoglutarate aminotransferase (EC 2.6.1.57) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR005785; TIGR01122; sufficient; -- SN 3 ID Prephenate dehydratase DN Prephenate dehydratase (EC 4.2.1.51) RQ 1 EV IPR001086; PF00800; sufficient; EV IPR010952; TIGR01797; sufficient; // AC GenProp1709 DE Trichome monoterpenes biosynthesis TP PATHWAY AU Pujar A TH 5 DC Trichome monoterpenes biosynthesis DR MetaCyc; PWY-6447; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Neryl diphosphate synthase DN Neryl diphosphate synthase (EC 2.5.1.28) RQ 1 EV IPR001441; PF01255; sufficient; EV IPR001441; TIGR00055; sufficient; -- SN 2 ID Alpha-terpinene synthase (neryl-diphosphate-cyclizing) DN Alpha-terpinene synthase (neryl-diphosphate-cyclizing) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 3 ID (+)-2-Carene synthase (neryl-diphosphate-cyclizing) DN (+)-2-Carene synthase (neryl-diphosphate-cyclizing) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 4 ID (-)-Alpha-pinene synthase (neryl-diphosphate-cyclizing) DN (-)-Alpha-pinene synthase (neryl-diphosphate-cyclizing) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 5 ID Phellandrene synthase DN Phellandrene synthase RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 6 ID (4S)-limonene synthase (neryl-diphosphate-cyclizing) DN (4S)-limonene synthase (neryl-diphosphate-cyclizing) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 7 ID Beta-phellandrene synthase (neryl-diphosphate-cyclizing) DN Beta-phellandrene synthase (neryl-diphosphate-cyclizing) (EC 4.2.3.51) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; // AC GenProp1710 DE Superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass TP PATHWAY AU Caspi R TH 1 DC Superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate DC bypass DR MetaCyc; GLYCOLYSIS-TCA-GLYOX-BYPASS; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Citrate synthase DN Citrate synthase (EC 2.3.3.1) RQ 1 EV IPR002020; PF00285; sufficient; EV IPR010953; TIGR01798; sufficient; EV IPR011278; TIGR01800; sufficient; -- SN 2 ID Pyruvate kinase DN Pyruvate kinase (EC 2.7.1.40) RQ 1 EV IPR001697; TIGR01064; sufficient; -- SN 3 ID Pyruvate dehydrogenase DN Pyruvate dehydrogenase (EC 1.2.1.M10) RQ 1 EV IPR004660; TIGR00759; sufficient; EV IPR006256; TIGR01348; sufficient; EV IPR006258; TIGR01350; sufficient; // AC GenProp1711 DE Molybdenum cofactor biosynthesis TP PATHWAY AU Caspi R TH 6 DC Molybdenum cofactor biosynthesis DR MetaCyc; PWY-6823; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Molybdopterin-synthase adenylyltransferase DN Molybdopterin-synthase adenylyltransferase (EC 2.7.7.80) RQ 1 EV IPR012730; TIGR02355; sufficient; -- SN 2 ID Molybdopterin synthase sulfurtransferase DN Molybdopterin synthase sulfurtransferase (EC 2.8.1.11) RQ 1 EV IPR000594; PF00899; sufficient; EV IPR001763; PF00581; sufficient; -- SN 3 ID Cyclic pyranopterin monophosphate synthase DN Cyclic pyranopterin monophosphate synthase (EC 4.6.1.17) RQ 1 EV IPR023045; TIGR00581; sufficient; -- SN 4 ID GTP 3',8'-cyclase DN GTP 3',8'-cyclase (EC 4.1.99.22) RQ 1 EV IPR013483; TIGR02666; sufficient; -- SN 5 ID Molybdopterin synthase DN Molybdopterin synthase (EC 2.8.1.12) RQ 1 EV IPR003448; PF02391; sufficient; EV IPR003749; PF02597; sufficient; EV IPR010034; TIGR01682; sufficient; -- SN 6 ID Molybdopterin adenylyltransferase DN Molybdopterin adenylyltransferase (EC 2.7.7.75) RQ 1 EV IPR001453; PF00994; sufficient; EV IPR001453; TIGR00177; sufficient; EV IPR005110; PF03453; sufficient; EV IPR005111; PF03454; sufficient; -- SN 7 ID Molybdopterin molybdotransferase DN Molybdopterin molybdotransferase (EC 2.10.1.1) RQ 1 EV IPR001453; PF00994; sufficient; EV IPR001453; TIGR00177; sufficient; EV IPR005110; PF03453; sufficient; EV IPR005111; PF03454; sufficient; -- SN 8 ID Cysteine desulfurase DN Cysteine desulfurase RQ 1 EV IPR010240; TIGR02006; sufficient; // AC GenProp1712 DE Mucin core 1 and core 2 O-glycosylation TP PATHWAY AU Caspi R TH 3 DC Mucin core 1 and core 2 O-glycosylation DR MetaCyc; PWY-7433; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Core 2 beta-1,6-N-acetylglucosaminyltransferase DN Core 2 beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.102) RQ 1 EV IPR003406; PF02485; sufficient; -- SN 2 ID [glycoprotein]-N-acetylgalactosamine beta-1,3-galactosyltransferase DN [glycoprotein]-N-acetylgalactosamine beta-1,3-galactosyltransferase (EC 2.4.1.122) RQ 1 EV IPR003378; PF02434; sufficient; -- SN 3 ID Beta-1,3-galactosyl-O-glycosyl-[glycoprotein] beta-1,3-N-acetylglucosaminyltransferase DN Beta-1,3-galactosyl-O-glycosyl-[glycoprotein] beta-1,3-N-acetylglucosaminyltransferase (EC 2.4.1.146) RQ 1 EV IPR002659; PF01762; sufficient; -- SN 4 ID Polypeptide N-acetylgalactosaminyltransferase DN Polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41) RQ 1 EV IPR000772; PF00652; sufficient; EV IPR001173; PF00535; sufficient; -- SN 5 ID CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase DN CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.4) RQ 1 EV IPR001675; PF00777; sufficient; // AC GenProp1713 DE UDP-beta-L-rhamnose biosynthesis TP PATHWAY AU Caspi R, Tissier C TH 1 DC UDP-beta-L-rhamnose biosynthesis DR MetaCyc; PWY-3261; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-4-keto-rhamnose-4-keto-reductase DN UDP-4-keto-rhamnose-4-keto-reductase (EC 1.1.1) RQ 1 EV IPR005888; TIGR01181; sufficient; -- SN 2 ID UDP-4-dehydro-6-deoxy-alpha-D-glucose 3,5-epimerase DN UDP-4-dehydro-6-deoxy-alpha-D-glucose 3,5-epimerase (EC 5.1.3) RQ 1 EV IPR005888; TIGR01181; sufficient; -- SN 3 ID UDP-glucose 4,6-dehydratase DN UDP-glucose 4,6-dehydratase (EC 4.2.1.76) RQ 1 EV IPR005888; TIGR01181; sufficient; // AC GenProp1715 DE Ethanol degradation II TP PATHWAY AU Wagg J TH 1 DC Ethanol degradation II DR MetaCyc; PWY66-21; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetyl CoA synthetase DN Acetyl CoA synthetase (EC 6.2.1.1) RQ 1 EV IPR011904; TIGR02188; sufficient; -- SN 2 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; -- SN 3 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.3) RQ 1 EV IPR015590; PF00171; sufficient; // AC GenProp1716 DE Superpathay of heme b biosynthesis from glutamate TP PATHWAY AU Caspi R TH 0 DC Superpathay of heme b biosynthesis from glutamate DR MetaCyc; PWY-5918; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase (EC 4.1.1.37) RQ 1 EV IPR006361; TIGR01464; sufficient; -- SN 2 ID Uroporphyrinogen III cosynthetase DN Uroporphyrinogen III cosynthetase (EC 4.2.1.75) RQ 1 EV IPR003754; PF02602; sufficient; // AC GenProp1717 DE Fatty acid beta-oxidation I TP PATHWAY AU Foerster H, Caspi R, Riley M TH 5 DC Fatty acid beta-oxidation I DR MetaCyc; FAO-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acyl-CoA dehydrogenase DN Acyl-CoA dehydrogenase (EC 1.3.8) RQ 1 EV IPR006091; PF02770; sufficient; EV IPR009075; PF00441; sufficient; EV IPR013786; PF02771; sufficient; EV IPR015396; PF09317; sufficient; -- SN 2 ID 2,3,4-Saturated fatty acyl-CoA synthetase DN 2,3,4-Saturated fatty acyl-CoA synthetase (EC 6.2.1.3) RQ 1 EV IPR000873; PF00501; sufficient; EV IPR025110; PF13193; sufficient; -- SN 3 ID Dodecenoyl-CoA D-isomerase DN Dodecenoyl-CoA D-isomerase (EC 5.3.3.8) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012799; TIGR02437; sufficient; EV IPR012802; TIGR02440; sufficient; -- SN 4 ID Enoyl-CoA hydratase DN Enoyl-CoA hydratase (EC 4.2.1.17) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012799; TIGR02437; sufficient; EV IPR012802; TIGR02440; sufficient; -- SN 5 ID 3-Ketoacyl-CoA thiolase DN 3-Ketoacyl-CoA thiolase (EC 2.3.1.16) RQ 1 EV IPR002155; TIGR01930; sufficient; EV IPR012806; TIGR02446; sufficient; EV IPR012805; TIGR02445; sufficient; -- SN 6 ID 3-Hydroxyacyl-CoA dehydrogenase DN 3-Hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012802; TIGR02440; sufficient; EV IPR002347; PF00106; sufficient; EV IPR012799; TIGR02437; sufficient; -- SN 7 ID 3-Hydroxyacyl-CoA epimerase DN 3-Hydroxyacyl-CoA epimerase (EC 5.1.2.3) RQ 1 EV IPR001753; PF00378; sufficient; EV IPR012802; TIGR02440; sufficient; EV IPR012799; TIGR02437; sufficient; // AC GenProp1718 DE Phospholipid remodeling (phosphatidylcholine, yeast) TP PATHWAY AU Foerster H TH 1 DC Phospholipid remodeling (phosphatidylcholine, yeast) DR MetaCyc; PWY-7416; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phospholipase A2 DN Phospholipase A2 (EC 3.1.1.4) RQ 1 EV IPR021771; PF11815; sufficient; -- SN 2 ID Acyl-CoA:lyso-phosphatidylcholine acyltransferase DN Acyl-CoA:lyso-phosphatidylcholine acyltransferase (EC 2.3.1.23) RQ 1 EV IPR004299; PF03062; sufficient; -- SN 3 ID Phospholipid:diacylglycerol acyltransferase DN Phospholipid:diacylglycerol acyltransferase (EC 2.3.1.158) RQ 1 EV IPR002123; PF01553; sufficient; // AC GenProp1719 DE L-methionine salvage from L-homocysteine TP PATHWAY AU Weerasinghe D TH 1 DC L-methionine salvage from L-homocysteine DR MetaCyc; ADENOSYLHOMOCYSCAT-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Betaine--homocysteine S-methyltransferase DN Betaine--homocysteine S-methyltransferase (EC 2.1.1.5) RQ 1 EV IPR003726; PF02574; sufficient; -- SN 2 ID Methionine synthase DN Methionine synthase (EC 2.1.1.13) RQ 1 EV IPR011822; TIGR02082; sufficient; -- SN 3 ID Homocysteine S-methyltransferase DN Homocysteine S-methyltransferase (EC 2.1.1.10) RQ 1 EV IPR003726; PF02574; sufficient; // AC GenProp1720 DE Superpathway of b heme biosynthesis from glycine TP PATHWAY AU Weerasinghe D, Caspi R TH 0 DC Superpathway of b heme biosynthesis from glycine DR MetaCyc; PWY-5920; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Uroporphyrinogen decarboxylase DN Uroporphyrinogen decarboxylase (EC 4.1.1.37) RQ 1 EV IPR006361; TIGR01464; sufficient; -- SN 2 ID Uroporphyrinogen III cosynthetase DN Uroporphyrinogen III cosynthetase (EC 4.2.1.75) RQ 1 EV IPR003754; PF02602; sufficient; // AC GenProp1721 DE Glutathione-peroxide redox reactions TP PATHWAY AU Caspi R TH 1 DC Glutathione-peroxide redox reactions DR MetaCyc; PWY-4081; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glutathione peroxidase DN Glutathione peroxidase (EC 1.11.1.12) RQ 1 EV IPR000889; PF00255; sufficient; -- SN 2 ID Glutathione peroxidase DN Glutathione peroxidase (EC 1.11.1.9) RQ 1 EV IPR000889; PF00255; sufficient; -- SN 3 ID Glutathione reductase DN Glutathione reductase (EC 1.8.1.7) RQ 1 EV IPR006322; TIGR01421; sufficient; // AC GenProp1722 DE Chitin degradation to ethanol TP PATHWAY AU Weerasinghe D TH 4 DC Chitin degradation to ethanol DR MetaCyc; PWY-7118; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Malic enzyme (NAD) DN Malic enzyme (NAD) (EC 1.1.1.39) RQ 1 EV IPR012301; PF00390; sufficient; EV IPR012302; PF03949; sufficient; -- SN 2 ID Acetyl CoA synthetase DN Acetyl CoA synthetase (EC 6.2.1.1) RQ 1 EV IPR011904; TIGR02188; sufficient; -- SN 3 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; -- SN 4 ID Chitin deacetylase DN Chitin deacetylase (EC 3.5.1.41) RQ 1 EV IPR002509; PF01522; sufficient; -- SN 5 ID Malate synthase DN Malate synthase (EC 2.3.3.9) RQ 1 EV IPR001465; PF01274; sufficient; EV IPR006252; TIGR01344; sufficient; -- SN 6 ID Pyruvate decarboxylase DN Pyruvate decarboxylase (EC 4.1.1.1) RQ 1 EV IPR011766; PF02775; sufficient; EV IPR012000; PF00205; sufficient; EV IPR012001; PF02776; sufficient; // AC GenProp1723 DE Conversion of succinate to propanoate TP PATHWAY AU Keseler I, Pellegrini-Toole A TH 1 DC Conversion of succinate to propanoate DR MetaCyc; PWY0-43; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Methylmalonyl-CoA mutase DN Methylmalonyl-CoA mutase (EC 5.4.99.2) RQ 1 EV IPR006098; TIGR00641; sufficient; EV IPR006099; PF01642; sufficient; EV IPR006158; PF02310; sufficient; EV IPR006159; TIGR00640; sufficient; -- SN 2 ID Propionyl-CoA:succinate CoA transferase DN Propionyl-CoA:succinate CoA transferase (EC 2.8.3) RQ 1 EV IPR003702; PF02550; sufficient; EV IPR017821; TIGR03458; sufficient; -- SN 3 ID Methylmalonyl-CoA decarboxylase DN Methylmalonyl-CoA decarboxylase (EC 4.1.1.M5) RQ 1 EV IPR001753; PF00378; sufficient; // AC GenProp1724 DE Chlorophyll a biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Chlorophyll a biosynthesis I DR MetaCyc; PWY-5086; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3,8-Divinyl-chlorophyllide 8-vinyl reductase DN 3,8-Divinyl-chlorophyllide 8-vinyl reductase (EC 1.3.1.75) RQ 1 EV IPR016040; PF13460; sufficient; -- SN 2 ID Chlorophyll synthetase DN Chlorophyll synthetase (EC 2.5.1.62) RQ 1 EV IPR000537; PF01040; sufficient; EV IPR006372; TIGR01476; sufficient; EV IPR011799; TIGR02056; sufficient; // AC GenProp1725 DE Thiamine diphosphate biosynthesis II (Bacillus) TP PATHWAY AU Caspi R TH 0 DC Thiamine diphosphate biosynthesis II (Bacillus) DR MetaCyc; PWY-6893; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Thiamine phosphate synthase DN Thiamine phosphate synthase (EC 2.5.1.3) RQ 1 EV IPR003733; PF02581; sufficient; EV IPR003733; TIGR00693; sufficient; -- SN 2 ID Thiamine-monophosphate kinase DN Thiamine-monophosphate kinase (EC 2.7.4.16) RQ 1 EV IPR006283; TIGR01379; sufficient; // AC GenProp1726 DE Starch degradation II TP PATHWAY AU Dreher K TH 7 DC Starch degradation II DR MetaCyc; PWY-6724; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Starch, water dikinase DN Starch, water dikinase (EC 2.7.9.4) RQ 1 EV IPR002192; PF01326; sufficient; -- SN 2 ID 6-Phosphoglucan starch, water dikinase DN 6-Phosphoglucan starch, water dikinase (EC 2.7.9.5) RQ 1 EV IPR002044; PF00686; sufficient; EV IPR002192; PF01326; sufficient; -- SN 3 ID 6-Phosophogluco-starch phosphatase DN 6-Phosophogluco-starch phosphatase (EC 3.1.3) RQ 1 EV IPR000340; PF00782; sufficient; EV IPR032640; PF16561; sufficient; -- SN 4 ID 6-Phosophogluco-3-phosphogluco-starch phosphatase DN 6-Phosophogluco-3-phosphogluco-starch phosphatase (EC 3.1.3) RQ 1 EV IPR000340; PF00782; sufficient; EV IPR032640; PF16561; sufficient; -- SN 5 ID 1,4-A-D-glucan maltohydrolase DN 1,4-A-D-glucan maltohydrolase (EC 3.2.1.2) RQ 1 EV IPR001554; PF01373; sufficient; -- SN 6 ID 1,4-Alpha-D-glucan maltohydrolase DN 1,4-Alpha-D-glucan maltohydrolase (EC 3.2.1.2) RQ 1 EV IPR001554; PF01373; sufficient; -- SN 7 ID Isoamylase DN Isoamylase (EC 3.2.1.68) RQ 1 EV IPR004193; PF02922; sufficient; EV IPR006047; PF00128; sufficient; -- SN 8 ID Beta-amylase DN Beta-amylase (EC 3.2.1.2) RQ 1 EV IPR001554; PF01373; sufficient; -- SN 9 ID Maltotriose alpha-1,4-glucanotransferase DN Maltotriose alpha-1,4-glucanotransferase (EC 2.4.1.25) RQ 1 EV IPR003385; PF02446; sufficient; EV IPR003385; TIGR00217; sufficient; // AC GenProp1727 DE 4-Aminobenzoate biosynthesis TP PATHWAY AU Caspi R, Pujar A TH 0 DC 4-Aminobenzoate biosynthesis DR MetaCyc; PWY-6543; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Aminodeoxychorismate lyase DN Aminodeoxychorismate lyase (EC 4.1.3.38) RQ 1 EV IPR001544; PF01063; sufficient; EV IPR017824; TIGR03461; sufficient; -- SN 2 ID Aminodeoxychorismate synthase DN Aminodeoxychorismate synthase (EC 2.6.1.85) RQ 1 EV IPR005802; TIGR00553; sufficient; // AC GenProp1728 DE Thyroid hormone biosynthesis TP PATHWAY AU Fulcher C TH 4 DC Thyroid hormone biosynthesis DR MetaCyc; PWY-6241; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID [thyroglobulin]-3-iodotyrosine synthase DN [thyroglobulin]-3-iodotyrosine synthase (EC 1.11.1.8) RQ 1 EV IPR019791; PF03098; sufficient; -- SN 2 ID [thyroglobulin]-3,5-diiodotyrosine synthase DN [thyroglobulin]-3,5-diiodotyrosine synthase (EC 1.11.1.8) RQ 1 EV IPR019791; PF03098; sufficient; -- SN 3 ID [thyroglobulin]-triiodothyronine synthase DN [thyroglobulin]-triiodothyronine synthase (EC 1.11.1.8) RQ 1 EV IPR019791; PF03098; sufficient; -- SN 4 ID [thyroglobulin]-L-thyroxine synthase DN [thyroglobulin]-L-thyroxine synthase (EC 1.11.1.8) RQ 1 EV IPR019791; PF03098; sufficient; -- SN 5 ID [thyroglobulin]-3,5,3'-triiodo-L-thyronine hydrolase DN [thyroglobulin]-3,5,3'-triiodo-L-thyronine hydrolase RQ 1 EV IPR000668; PF00112; sufficient; EV IPR012599; PF08127; sufficient; EV IPR013201; PF08246; sufficient; EV IPR012848; PF07966; sufficient; EV IPR033121; PF00026; sufficient; -- SN 6 ID [thyroglobulin]-L-thyroxine hydrolase DN [thyroglobulin]-L-thyroxine hydrolase RQ 1 EV IPR000668; PF00112; sufficient; EV IPR012599; PF08127; sufficient; EV IPR013201; PF08246; sufficient; // AC GenProp1729 DE Glycerol-3-phosphate to hydrogen peroxide electron transport TP PATHWAY AU Mackie A TH 0 DC Glycerol-3-phosphate to hydrogen peroxide electron transport DR MetaCyc; PWY0-1591; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol-3-phosphate dehydrogenase, anaerobic DN Glycerol-3-phosphate dehydrogenase, anaerobic (EC 1.1.5.3) RQ 1 EV IPR017752; TIGR03377; sufficient; EV IPR009158; TIGR03378; sufficient; EV IPR017753; TIGR03379; sufficient; -- SN 2 ID Cytochrome c peroxidase DN Cytochrome c peroxidase (EC 1.11.1) RQ 1 EV IPR004852; PF03150; sufficient; EV IPR009056; PF00034; sufficient; EV IPR025992; PF14376; sufficient; // AC GenProp1730 DE Inosine-5'-phosphate biosynthesis I TP PATHWAY AU Caspi R TH 4 DC Inosine-5'-phosphate biosynthesis I DR MetaCyc; PWY-6123; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenylosuccinate lyase DN Adenylosuccinate lyase (EC 4.3.2.2) RQ 1 EV IPR004769; TIGR00928; sufficient; -- SN 2 ID AICAR transformylase DN AICAR transformylase (EC 2.1.2.3) RQ 1 EV IPR002695; PF01808; sufficient; EV IPR002695; TIGR00355; sufficient; -- SN 3 ID IMP cyclohydrolase DN IMP cyclohydrolase (EC 3.5.4.10) RQ 1 EV IPR002695; PF01808; sufficient; EV IPR002695; TIGR00355; sufficient; -- SN 4 ID 5-(Carboxyamino)imidazole ribonucleotide synthase DN 5-(Carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) RQ 1 EV IPR003135; PF02222; sufficient; EV IPR005875; TIGR01161; sufficient; -- SN 5 ID N5-carboxyaminoimidazole ribonucleotide mutase DN N5-carboxyaminoimidazole ribonucleotide mutase (EC 5.4.99.18) RQ 1 EV IPR000031; PF00731; sufficient; EV IPR000031; TIGR01162; sufficient; -- SN 6 ID Phosphoribosylaminoimidazole-succinocarboxamide synthase DN Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) RQ 1 EV IPR001636; TIGR00081; sufficient; // AC GenProp1731 DE 3-Dehydroquinate biosynthesis I TP PATHWAY AU Caspi R TH 0 DC 3-Dehydroquinate biosynthesis I DR MetaCyc; PWY-6164; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3-Dehydroquinate synthase DN 3-Dehydroquinate synthase (EC 4.2.3.4) RQ 1 EV IPR001381; PF01487; sufficient; EV IPR001381; TIGR01093; sufficient; EV IPR006264; TIGR01356; sufficient; EV IPR031322; PF01202; sufficient; -- SN 2 ID DAHP synthase DN DAHP synthase (EC 2.5.1.54) RQ 1 EV IPR006219; TIGR00034; sufficient; // AC GenProp1732 DE Pentose phosphate pathway (oxidative branch) II TP PATHWAY AU Caspi R TH 0 DC Pentose phosphate pathway (oxidative branch) II DR MetaCyc; PWY-7796; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Hexulose-6-phosphate synthase DN Hexulose-6-phosphate synthase (EC 4.1.2.43) RQ 1 EV IPR017552; TIGR03127; sufficient; -- SN 2 ID 6-Phospho-3-hexuloisomerase DN 6-Phospho-3-hexuloisomerase (EC 5.3.1.27) RQ 1 EV IPR017552; TIGR03127; sufficient; // AC GenProp1733 DE Putrescine biosynthesis II TP PATHWAY AU Caspi R TH 1 DC Putrescine biosynthesis II DR MetaCyc; PWY-43; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Agmatine deiminase DN Agmatine deiminase (EC 3.5.3.12) RQ 1 EV IPR007466; PF04371; sufficient; EV IPR017754; TIGR03380; sufficient; -- SN 2 ID Arginine decarboxylase DN Arginine decarboxylase (EC 4.1.1.19) RQ 1 EV IPR002985; TIGR01273; sufficient; -- SN 3 ID N-carbamolyputrescine amidohydrolase DN N-carbamolyputrescine amidohydrolase (EC 3.5.1.53) RQ 1 EV IPR017755; TIGR03381; sufficient; // AC GenProp1734 DE Flavin biosynthesis I (bacteria and plants) TP PATHWAY AU Riley M, Keseler I TH 7 DC Flavin biosynthesis I (bacteria and plants) DR MetaCyc; RIBOSYN2-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 3,4-Dihydroxy-2-butanone-4-phosphate synthase DN 3,4-Dihydroxy-2-butanone-4-phosphate synthase (EC 4.1.99.12) RQ 1 EV IPR000422; PF00926; sufficient; EV IPR000422; TIGR00506; sufficient; EV IPR000926; TIGR00505; sufficient; -- SN 2 ID FAD synthetase DN FAD synthetase (EC 2.7.7.2) RQ 1 EV IPR002606; TIGR00083; sufficient; EV IPR006439; TIGR01509; sufficient; EV IPR006439; TIGR01549; sufficient; -- SN 3 ID GTP cyclohydrolase DN GTP cyclohydrolase (EC 3.5.4.25) RQ 1 EV IPR000422; PF00926; sufficient; EV IPR000422; TIGR00506; sufficient; EV IPR000926; TIGR00505; sufficient; -- SN 4 ID 6,7-Dimethyl-8-ribityllumazine synthase DN 6,7-Dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) RQ 1 EV IPR002180; PF00885; sufficient; EV IPR002180; TIGR00114; sufficient; -- SN 5 ID Riboflaving synthase DN Riboflaving synthase (EC 2.5.1.9) RQ 1 EV IPR001783; TIGR00187; sufficient; -- SN 6 ID Riboflavin kinase DN Riboflavin kinase (EC 2.7.1.26) RQ 1 EV IPR002606; TIGR00083; sufficient; EV IPR006439; TIGR01509; sufficient; EV IPR006439; TIGR01549; sufficient; -- SN 7 ID Diaminohydroxyphosphoribosylaminopyrimidine deaminase DN Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC 3.5.4.26) RQ 1 EV IPR004794; TIGR00326; sufficient; -- SN 8 ID 5-Amino-6-(5-phosphoribosylamino)uracil reductase DN 5-Amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) RQ 1 EV IPR004794; TIGR00326; sufficient; -- SN 9 ID 5-Amino-6-(5-phospho-D-ribitylamino)uracil phosphatase DN 5-Amino-6-(5-phospho-D-ribitylamino)uracil phosphatase (EC 3.1.3.104) RQ 1 EV IPR006439; TIGR01549; sufficient; EV IPR000150; TIGR00099; sufficient; EV IPR006379; TIGR01484; sufficient; // AC GenProp1735 DE Archaeosine biosynthesis I TP PATHWAY AU Caspi R TH 0 DC Archaeosine biosynthesis I DR MetaCyc; PWY-6711; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 7-Cyano-7-deazaguanine tRNA-ribosyltransferase DN 7-Cyano-7-deazaguanine tRNA-ribosyltransferase (EC 2.4.2.48) RQ 1 EV IPR004804; TIGR00432; sufficient; -- SN 2 ID Archaeosine synthase DN Archaeosine synthase (EC 2.6.1.97) RQ 1 EV IPR002478; PF01472; sufficient; EV IPR004521; TIGR00451; sufficient; // AC GenProp1736 DE NADH repair TP PATHWAY AU Caspi R TH 2 DC NADH repair DR MetaCyc; PWY-6938; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID ATP-dependent NADH-hydrate dehydratase DN ATP-dependent NADH-hydrate dehydratase (EC 4.2.1.93) RQ 1 EV IPR000631; PF01256; sufficient; EV IPR000631; TIGR00196; sufficient; -- SN 2 ID NADHX epimerase DN NADHX epimerase (EC 5.1.99.6) RQ 1 EV IPR004443; PF03853; sufficient; EV IPR004443; TIGR00197; sufficient; -- SN 3 ID NADH hydratase DN NADH hydratase RQ 1 EV IPR006424; TIGR01534; sufficient; -- SN 4 ID NADH hydratase DN NADH hydratase RQ 1 EV IPR006424; TIGR01534; sufficient; // AC GenProp1737 DE CMP-N-acetylneuraminate biosynthesis I (eukaryotes) TP PATHWAY AU Fulcher C TH 3 DC CMP-N-acetylneuraminate biosynthesis I (eukaryotes) DR MetaCyc; PWY-6138; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID N-acetylmannosamine kinase DN N-acetylmannosamine kinase (EC 2.7.1.60) RQ 1 EV IPR000600; PF00480; sufficient; EV IPR020004; TIGR03568; sufficient; -- SN 2 ID UDP-N-acetylglucosamine 2-epimerase DN UDP-N-acetylglucosamine 2-epimerase (EC 3.2.1.183) RQ 1 EV IPR000600; PF00480; sufficient; EV IPR020004; TIGR03568; sufficient; -- SN 3 ID N-acetylneuraminate 9-phosphate synthase DN N-acetylneuraminate 9-phosphate synthase (EC 2.5.1.57) RQ 1 EV IPR013132; PF03102; sufficient; EV IPR013974; PF08666; sufficient; -- SN 4 ID N-acetylneuraminate-9-phosphate phosphatase DN N-acetylneuraminate-9-phosphate phosphatase (EC 3.1.3.29) RQ 1 EV IPR006439; TIGR01549; sufficient; EV IPR011950; TIGR02253; sufficient; -- SN 5 ID Cytidine 5'-monophosphate N-acetylneuraminate synthetase DN Cytidine 5'-monophosphate N-acetylneuraminate synthetase (EC 2.7.7.43) RQ 1 EV IPR003329; PF02348; sufficient; // AC GenProp1739 DE Ent-kaurene biosynthesis I TP PATHWAY AU N/A TH 0 DC Ent-kaurene biosynthesis I DR MetaCyc; PWY-5032; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ent-kaurene synthase DN Ent-kaurene synthase (EC 4.2.3.19) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; -- SN 2 ID Ent-copalyl diphosphate synthase DN Ent-copalyl diphosphate synthase (EC 5.5.1.13) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; // AC GenProp1740 DE Pregnenolone biosynthesis TP PATHWAY AU Trupp M TH 1 DC Pregnenolone biosynthesis DR MetaCyc; PWY66-377; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Cholesterol 22-beta-hydroxylase DN Cholesterol 22-beta-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID 22-Beta-hydroxycholesterol 20-alpha-hydroxylation DN 22-Beta-hydroxycholesterol 20-alpha-hydroxylation RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID 20-Alpha-22-beta-dihydroxycholesterol side-chain lyase DN 20-Alpha-22-beta-dihydroxycholesterol side-chain lyase RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1741 DE Adenine and adenosine salvage V TP PATHWAY AU Caspi R TH 1 DC Adenine and adenosine salvage V DR MetaCyc; PWY-6611; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenosine deaminase DN Adenosine deaminase (EC 3.5.4.4) RQ 1 EV IPR006330; TIGR01430; sufficient; -- SN 2 ID Adenosine phosphorylase DN Adenosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; EV IPR009664; PF06865; sufficient; -- SN 3 ID Inosine kinase DN Inosine kinase (EC 2.7.1.73) RQ 1 EV IPR011611; PF00294; sufficient; // AC GenProp1742 DE Androgen biosynthesis TP PATHWAY AU Trupp M TH 4 DC Androgen biosynthesis DR MetaCyc; PWY66-378; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Androstenedione reductase DN Androstenedione reductase (EC 1.1.1.64) RQ 1 EV IPR002347; PF00106; sufficient; -- SN 2 ID Pregnenolone 17-alpha-hydroxylase DN Pregnenolone 17-alpha-hydroxylase (EC 1.14.14.19) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID 17-Alpha-hydroxypregnenolone 17,20-lyase DN 17-Alpha-hydroxypregnenolone 17,20-lyase (EC 1.14.14.32) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 4 ID DHA dehydrogenase DN DHA dehydrogenase (EC 1.1.1.145) RQ 1 EV IPR002225; PF01073; sufficient; -- SN 5 ID Testosterone reductase DN Testosterone reductase (EC 1.3.1.22) RQ 1 EV IPR001104; PF02544; sufficient; -- SN 6 ID Androstenedione isomerase DN Androstenedione isomerase (EC 5.3.3.1) RQ 1 EV IPR002225; PF01073; sufficient; // AC GenProp1743 DE UDP-alpha-D-glucose biosynthesis I TP PATHWAY AU Caspi R TH 0 DC UDP-alpha-D-glucose biosynthesis I DR MetaCyc; PWY-7343; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID UDP-glucose pyrophosphorylase DN UDP-glucose pyrophosphorylase (EC 2.7.7.9) RQ 1 EV IPR002618; PF01704; sufficient; EV IPR005771; TIGR01099; sufficient; -- SN 2 ID Phosphoglucomutase DN Phosphoglucomutase (EC 5.4.2.2) RQ 1 EV IPR005852; TIGR01132; sufficient; // AC GenProp1744 DE Ubiquinol-8 biosynthesis (prokaryotic) TP PATHWAY AU Caspi R TH 6 DC Ubiquinol-8 biosynthesis (prokaryotic) DR MetaCyc; PWY-6708; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Octaprenyl-6-methoxyphenol hydroxylase DN 2-Octaprenyl-6-methoxyphenol hydroxylase (EC 1.14.13.M56) RQ 1 EV IPR010971; TIGR01988; sufficient; EV IPR011295; TIGR01984; sufficient; -- SN 2 ID 2-Octaprenyl-6-hydroxyphenyl methylase DN 2-Octaprenyl-6-hydroxyphenyl methylase (EC 2.1.1.222) RQ 1 EV IPR010233; TIGR01983; sufficient; -- SN 3 ID 2-Octaprenyl-6-methoxy-1,4-benzoquinone methylase DN 2-Octaprenyl-6-methoxy-1,4-benzoquinone methylase (EC 2.1.1.201) RQ 1 EV IPR004033; PF01209; sufficient; EV IPR004033; TIGR01934; sufficient; -- SN 4 ID 2-Octaprenylphenol hydroxylase DN 2-Octaprenylphenol hydroxylase RQ 1 EV IPR010971; TIGR01988; sufficient; -- SN 5 ID 3-Octaprenyl-4-hydroxybenzoate decarboxylase DN 3-Octaprenyl-4-hydroxybenzoate decarboxylase (EC 4.1.1.98) RQ 1 EV IPR002830; PF01977; sufficient; EV IPR002830; TIGR00148; sufficient; -- SN 6 ID 4-Hydroxybenzoate octaprenyltransferase DN 4-Hydroxybenzoate octaprenyltransferase (EC 2.5.1.39) RQ 1 EV IPR000537; PF01040; sufficient; EV IPR006370; TIGR01474; sufficient; -- SN 7 ID 3-Demethylubiquinone-8 3-O-methyltransferase DN 3-Demethylubiquinone-8 3-O-methyltransferase (EC 2.1.1.64) RQ 1 EV IPR010233; TIGR01983; sufficient; -- SN 8 ID 5-Demethoxyubiquinol-8 5-hydroxylase DN 5-Demethoxyubiquinol-8 5-hydroxylase RQ 1 EV IPR010971; TIGR01988; sufficient; // AC GenProp1745 DE GA12 biosynthesis TP PATHWAY AU N/A TH 4 DC GA12 biosynthesis DR MetaCyc; PWY-5034; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ent-kaurene 19-hydroxylase DN Ent-kaurene 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID Ent-kaurenoate monooxygenase DN Ent-kaurenoate monooxygenase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 3 ID Ent-kaurenol 19-dehydrogenase DN Ent-kaurenol 19-dehydrogenase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 4 ID Ent-kaurenal 19-hydroxylase DN Ent-kaurenal 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 5 ID Ent-7-alpha-hydroxykaur-16-en-19-oate monooxygenase DN Ent-7-alpha-hydroxykaur-16-en-19-oate monooxygenase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 6 ID GA12-aldehyde monooxygenase DN GA12-aldehyde monooxygenase RQ 1 EV IPR001128; PF00067; sufficient; // AC GenProp1746 DE Alkylnitronates degradation TP PATHWAY AU Fulcher C TH 0 DC Alkylnitronates degradation DR MetaCyc; PWY-723; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ethylnitronate monooxygenase DN Ethylnitronate monooxygenase (EC 1.13.12.16) RQ 1 EV IPR004136; PF03060; sufficient; -- SN 2 ID Nitrite reductase DN Nitrite reductase (EC 1.7.1.4) RQ 1 EV IPR005117; PF03460; sufficient; EV IPR006067; PF01077; sufficient; EV IPR007419; PF04324; sufficient; EV IPR012744; TIGR02374; sufficient; EV IPR017941; PF00355; sufficient; EV IPR023753; PF07992; sufficient; // AC GenProp1747 DE Photorespiration TP PATHWAY AU N/A TH 7 DC Photorespiration DR MetaCyc; PWY-181; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycine decarboxylase DN Glycine decarboxylase RQ 1 EV IPR002930; PF01597; sufficient; EV IPR017453; TIGR00527; sufficient; -- SN 2 ID D-glycerate 3-kinase DN D-glycerate 3-kinase (EC 2.7.1.31) RQ 1 EV IPR006083; PF00485; sufficient; -- SN 3 ID Hydroxypyruvate reductase DN Hydroxypyruvate reductase (EC 1.1.1.29) RQ 1 EV IPR006139; PF00389; sufficient; EV IPR006140; PF02826; sufficient; -- SN 4 ID Glycine transaminase DN Glycine transaminase (EC 2.6.1.4) RQ 1 EV IPR000192; PF00266; sufficient; EV IPR004839; PF00155; sufficient; -- SN 5 ID 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase DN 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase (EC 2.1.2.1) RQ 1 EV IPR001085; PF00464; sufficient; -- SN 6 ID Phosphoglycolate phosphatase DN Phosphoglycolate phosphatase (EC 3.1.3.18) RQ 1 EV IPR006349; TIGR01452; sufficient; EV IPR006357; PF13344; sufficient; EV IPR006357; TIGR01460; sufficient; -- SN 7 ID D-ribulose-1,5-bisphosphate cleaving dioxygenase DN D-ribulose-1,5-bisphosphate cleaving dioxygenase (EC 1.13.11) RQ 1 EV IPR000894; PF00101; sufficient; EV IPR024680; PF12338; sufficient; EV IPR000685; PF00016; sufficient; EV IPR017443; PF02788; sufficient; -- SN 8 ID Glycolate oxidase DN Glycolate oxidase (EC 1.1.3.15) RQ 1 EV IPR000262; PF01070; sufficient; -- SN 9 ID L-serine:glyoxylate aminotransferase DN L-serine:glyoxylate aminotransferase (EC 2.6.1.45) RQ 1 EV IPR000192; PF00266; sufficient; // AC GenProp1748 DE Phosphopantothenate biosynthesis I TP PATHWAY AU Foerster H, Keseler I, Arnaud M TH 2 DC Phosphopantothenate biosynthesis I DR MetaCyc; PANTO-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID 2-Dehydropantoate 2-reductase DN 2-Dehydropantoate 2-reductase (EC 1.1.1.169) RQ 1 EV IPR003710; TIGR00745; sufficient; EV IPR013023; TIGR00465; sufficient; -- SN 2 ID Ketopantoate hydroxymethyltransferase DN Ketopantoate hydroxymethyltransferase (EC 2.1.2.11) RQ 1 EV IPR003700; PF02548; sufficient; EV IPR003700; TIGR00222; sufficient; -- SN 3 ID Pantoate beta-alanine ligase DN Pantoate beta-alanine ligase (EC 6.3.2.1) RQ 1 EV IPR003721; PF02569; sufficient; EV IPR003721; TIGR00018; sufficient; -- SN 4 ID Pantothenate kinase DN Pantothenate kinase (EC 2.7.1.33) RQ 1 EV IPR004567; PF03630; sufficient; EV IPR004567; TIGR00555; sufficient; EV IPR004566; TIGR00554; sufficient; // AC GenProp1749 DE Superpathway of acetate utilization and formation TP PATHWAY AU Pellegrini-Toole A, Ingraham J TH 1 DC Superpathway of acetate utilization and formation DR MetaCyc; ACETATEUTIL-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetyl CoA synthetase DN Acetyl CoA synthetase (EC 6.2.1.1) RQ 1 EV IPR011904; TIGR02188; sufficient; -- SN 2 ID Acetate kinase DN Acetate kinase (EC 2.7.2.1) RQ 1 EV IPR000890; PF00871; sufficient; EV IPR004372; TIGR00016; sufficient; EV IPR005862; TIGR01142; sufficient; -- SN 3 ID Phosphotransacetylase DN Phosphotransacetylase (EC 2.3.1.8) RQ 1 EV IPR002505; PF01515; sufficient; EV IPR004614; TIGR00651; sufficient; EV IPR010766; PF07085; sufficient; // AC GenProp1750 DE Glycerol-3-phosphate shuttle TP PATHWAY AU Caspi R TH 0 DC Glycerol-3-phosphate shuttle DR MetaCyc; PWY-6118; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol-3-phosphate dehydrogenase DN Glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) RQ 1 EV IPR017751; TIGR03376; sufficient; -- SN 2 ID Glycerol-3-phosphate dehydrogenase DN Glycerol-3-phosphate dehydrogenase (EC 1.1.5.3) RQ 1 EV IPR006076; PF01266; sufficient; EV IPR031656; PF16901; sufficient; EV IPR002048; PF13499; sufficient; // AC GenProp1751 DE NADH to cytochrome bo oxidase electron transfer I TP PATHWAY AU Mackie A, Nolan L, Krummenacker M TH 0 DC NADH to cytochrome bo oxidase electron transfer I DR MetaCyc; PWY0-1335; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID NADH dehydrogenase DN NADH dehydrogenase (EC 1.6.5.3) RQ 1 EV IPR000440; PF00507; sufficient; EV IPR006138; TIGR01957; sufficient; EV IPR010218; TIGR01961; sufficient; EV IPR022885; TIGR01962; sufficient; EV IPR002023; TIGR01958; sufficient; EV IPR011537; TIGR01959; sufficient; EV IPR010228; TIGR01973; sufficient; EV IPR001694; PF00146; sufficient; EV IPR010226; TIGR01971; sufficient; EV IPR001457; PF00499; sufficient; EV IPR001133; PF00420; sufficient; EV IPR003945; TIGR01974; sufficient; EV IPR010227; TIGR01972; sufficient; EV IPR010096; TIGR01770; sufficient; -- SN 2 ID Ubiquinol oxidase (H+-transporting) DN Ubiquinol oxidase (H+-transporting) (EC 1.10.3.10) RQ 1 EV IPR006333; TIGR01433; sufficient; EV IPR000883; PF00115; sufficient; EV IPR014207; TIGR02843; sufficient; EV IPR014206; TIGR02842; sufficient; EV IPR005171; PF03626; sufficient; EV IPR014210; TIGR02847; sufficient; // AC GenProp1752 DE Superpathway of purine deoxyribonucleosides degradation TP PATHWAY AU Ingraham J TH 2 DC Superpathway of purine deoxyribonucleosides degradation DR MetaCyc; PWY0-1297; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID D-deoxyribose 1,5-phosphomutase DN D-deoxyribose 1,5-phosphomutase (EC 5.4.2.7) RQ 1 EV IPR010045; TIGR01696; sufficient; -- SN 2 ID Deoxyadenosine phosphorylase DN Deoxyadenosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; -- SN 3 ID Deoxyguanosine phosphorylase DN Deoxyguanosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; -- SN 4 ID Deoxyinosine phosphorylase DN Deoxyinosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR004402; TIGR00107; sufficient; // AC GenProp1753 DE Inosine 5'-phosphate degradation TP PATHWAY AU Caspi R TH 2 DC Inosine 5'-phosphate degradation DR MetaCyc; PWY-5695; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Inosine-5'-monophosphate dehydrogenase DN Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) RQ 1 EV IPR005990; TIGR01302; sufficient; -- SN 2 ID Xanthine:NAD+ oxidoreductase DN Xanthine:NAD+ oxidoreductase (EC 1.17.1.4) RQ 1 EV IPR000674; PF01315; sufficient; EV IPR001041; PF00111; sufficient; EV IPR002346; PF00941; sufficient; EV IPR002888; PF01799; sufficient; EV IPR005107; PF03450; sufficient; EV IPR008274; PF02738; sufficient; EV IPR014307; TIGR02963; sufficient; EV IPR014309; TIGR02965; sufficient; -- SN 3 ID Xanthosine phosphorylase DN Xanthosine phosphorylase (EC 2.4.2.1) RQ 1 EV IPR011268; TIGR01697; sufficient; EV IPR011270; TIGR01700; sufficient; EV IPR009664; PF06865; sufficient; EV IPR010943; TIGR01699; sufficient; -- SN 4 ID XMP phosphohydrolase DN XMP phosphohydrolase (EC 3.1.3.5) RQ 1 EV IPR008380; PF05761; sufficient; EV IPR008380; TIGR02244; sufficient; // AC GenProp1754 DE Protein ubiquitination TP PATHWAY AU Caspi R TH 7 DC Protein ubiquitination DR MetaCyc; PWY-7511; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ubiquitin-conjugating enzyme E2 DN Ubiquitin-conjugating enzyme E2 (EC 2.3.2.23) RQ 1 EV IPR000608; PF00179; sufficient; -- SN 2 ID HECT-type E3 ubiquitin transferase DN HECT-type E3 ubiquitin transferase (EC 2.3.2.26) RQ 1 EV IPR000008; PF00168; sufficient; EV IPR000569; PF00632; sufficient; EV IPR001202; PF00397; sufficient; -- SN 3 ID HECT-type E3 ubiquitin transferase DN HECT-type E3 ubiquitin transferase (EC 2.3.2.26) RQ 1 EV IPR000008; PF00168; sufficient; EV IPR000569; PF00632; sufficient; EV IPR001202; PF00397; sufficient; -- SN 4 ID RING-type E3 ubiquitin transferase DN RING-type E3 ubiquitin transferase (EC 2.3.2.27) RQ 1 EV IPR003126; PF02207; sufficient; EV IPR003769; PF02617; sufficient; EV IPR001373; PF00888; sufficient; EV IPR019559; PF10557; sufficient; EV IPR024766; PF12678; sufficient; EV IPR016072; PF01466; sufficient; EV IPR016073; PF03931; sufficient; EV IPR001810; PF12937; sufficient; EV IPR011016; PF12906; sufficient; -- SN 5 ID N-terminal E2 ubiquitin-conjugating enzyme DN N-terminal E2 ubiquitin-conjugating enzyme RQ 1 EV IPR000608; PF00179; sufficient; -- SN 6 ID N-terminal E2 ubiquitin-conjugating enzyme DN N-terminal E2 ubiquitin-conjugating enzyme RQ 1 EV IPR000608; PF00179; sufficient; -- SN 7 ID Ubiquitin-conjugating enzyme E2 (E3-independent) DN Ubiquitin-conjugating enzyme E2 (E3-independent) (EC 2.3.2.24) RQ 1 EV IPR000608; PF00179; sufficient; -- SN 8 ID Ubiquitin-conjugating enzyme E2 (E3-independent) DN Ubiquitin-conjugating enzyme E2 (E3-independent) (EC 2.3.2.24) RQ 1 EV IPR000608; PF00179; sufficient; -- SN 9 ID Ubiquitin-activating enzyme DN Ubiquitin-activating enzyme (EC 6.2.1.45) RQ 1 EV IPR018075; TIGR01408; sufficient; // AC GenProp1755 DE PpGpp biosynthesis TP PATHWAY AU Fulcher C, Riley M TH 4 DC PpGpp biosynthesis DR MetaCyc; PPGPPMET-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID GDP kinase DN GDP kinase (EC 2.7.4.6) RQ 1 EV IPR006259; TIGR01351; sufficient; EV IPR001564; PF00334; sufficient; -- SN 2 ID GDP diphosphokinase DN GDP diphosphokinase (EC 2.7.6.5) RQ 1 EV IPR004811; TIGR00691; sufficient; -- SN 3 ID GTP pyrophosphokinase DN GTP pyrophosphokinase (EC 2.7.6.5) RQ 1 EV IPR004811; TIGR00691; sufficient; -- SN 4 ID Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase DN Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase (EC 3.1.7.2) RQ 1 EV IPR004811; TIGR00691; sufficient; -- SN 5 ID Guanosine-5'-triphosphate,3'-diphosphate phosphatase DN Guanosine-5'-triphosphate,3'-diphosphate phosphatase (EC 3.6.1.40) RQ 1 EV IPR003695; PF02541; sufficient; -- SN 6 ID Guanosine 3'-diphosphate 5'-triphosphate 3'-diphosphatase DN Guanosine 3'-diphosphate 5'-triphosphate 3'-diphosphatase (EC 3.1.7.2) RQ 1 EV IPR004811; TIGR00691; sufficient; // AC GenProp1756 DE Poly(3-O-beta-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall teichoic acid biosynthesis TP PATHWAY AU Caspi R TH 9 DC Poly(3-O-beta-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall DC teichoic acid biosynthesis DR MetaCyc; PWY-7819; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Glycerol-3-phosphate cytidylyltransferase DN Glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) RQ 1 EV IPR006409; TIGR01518; sufficient; -- SN 2 ID UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase DN UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.33) RQ 1 EV IPR000715; PF00953; sufficient; -- SN 3 ID Poly(glucosyl N-acetylgalactosamine 1-phosphate) N-acetylgalactosamine 1-phosphate primase DN Poly(glucosyl N-acetylgalactosamine 1-phosphate) N-acetylgalactosamine 1-phosphate primase (EC 2.4.1) RQ 1 EV IPR007554; PF04464; sufficient; -- SN 4 ID Poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase DN Poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase (EC 2.4.1) RQ 1 EV IPR001173; PF00535; sufficient; -- SN 5 ID Poly(glucosyl N-acetylgalactosamine 1-phosphate) N-acetylgalactosamine 1-phosphate transferase DN Poly(glucosyl N-acetylgalactosamine 1-phosphate) N-acetylgalactosamine 1-phosphate transferase (EC 2.4.1) RQ 1 EV IPR007554; PF04464; sufficient; -- SN 6 ID Poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase DN Poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase (EC 2.4.1) RQ 1 EV IPR001173; PF00535; sufficient; -- SN 7 ID Polyisoprenyl-minor teichoic acid--peptidoglycan teichoic acid transferase DN Polyisoprenyl-minor teichoic acid--peptidoglycan teichoic acid transferase (EC 2.7.8.M1) RQ 1 EV IPR004474; PF03816; sufficient; EV IPR004474; TIGR00350; sufficient; -- SN 8 ID N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase DN N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (EC 2.4.1.187) RQ 1 EV IPR004629; PF03808; sufficient; EV IPR004629; TIGR00696; sufficient; -- SN 9 ID Teichoic acid glycerol-phosphate primase DN Teichoic acid glycerol-phosphate primase (EC 2.7.8.44) RQ 1 EV IPR007554; PF04464; sufficient; -- SN 10 ID Poly(3-O-beta-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) teichoic acid transporter DN Poly(3-O-beta-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) teichoic acid transporter RQ 1 EV IPR003439; PF00005; sufficient; EV IPR013525; PF01061; sufficient; -- SN 11 ID UDP-N-acetylglucosamine 2-epimerase DN UDP-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) RQ 1 EV IPR029767; TIGR00236; sufficient; // AC GenProp1757 DE Inosine-5'-phosphate biosynthesis II TP PATHWAY AU Caspi R TH 3 DC Inosine-5'-phosphate biosynthesis II DR MetaCyc; PWY-6124; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Adenylosuccinate lyase DN Adenylosuccinate lyase (EC 4.3.2.2) RQ 1 EV IPR004769; TIGR00928; sufficient; -- SN 2 ID AICAR transformylase DN AICAR transformylase (EC 2.1.2.3) RQ 1 EV IPR002695; PF01808; sufficient; EV IPR002695; TIGR00355; sufficient; -- SN 3 ID Phosphoribosylaminoimidazole carboxylase DN Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) RQ 1 EV IPR000031; PF00731; sufficient; EV IPR000031; TIGR01162; sufficient; EV IPR003135; PF02222; sufficient; EV IPR005875; TIGR01161; sufficient; EV IPR028923; PF01259; sufficient; -- SN 4 ID IMP cyclohydrolase DN IMP cyclohydrolase (EC 3.5.4.10) RQ 1 EV IPR002695; PF01808; sufficient; EV IPR002695; TIGR00355; sufficient; -- SN 5 ID Phosphoribosylaminoimidazole-succinocarboxamide synthase DN Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) RQ 1 EV IPR001636; TIGR00081; sufficient; // AC GenProp1758 DE 3-Phosphoinositide biosynthesis TP PATHWAY AU Caspi R TH 6 DC 3-Phosphoinositide biosynthesis DR MetaCyc; PWY-6352; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Phosphatidylinositol 3-kinase DN Phosphatidylinositol 3-kinase (EC 2.7.1.137) RQ 1 EV IPR000403; PF00454; sufficient; EV IPR001263; PF00613; sufficient; EV IPR002420; PF00792; sufficient; EV IPR000719; PF00069; sufficient; -- SN 2 ID Phosphatidylinositol 4-kinase DN Phosphatidylinositol 4-kinase (EC 2.7.1.67) RQ 1 EV IPR000403; PF00454; sufficient; EV IPR001263; PF00613; sufficient; -- SN 3 ID Phoshatidylinositol-3-phosphate 5-kinase DN Phoshatidylinositol-3-phosphate 5-kinase (EC 2.7.1.150) RQ 1 EV IPR002423; PF00118; sufficient; -- SN 4 ID Phosphatidylinositol-4,5-bisphosphate 3-kinase DN Phosphatidylinositol-4,5-bisphosphate 3-kinase (EC 2.7.1.153) RQ 1 EV IPR019522; PF10486; sufficient; -- SN 5 ID Phosphatidylinositol-4,5-bisphosphate 3-kinase DN Phosphatidylinositol-4,5-bisphosphate 3-kinase (EC 2.7.1.154) RQ 1 EV IPR000008; PF00168; sufficient; EV IPR000341; PF00794; sufficient; EV IPR000403; PF00454; sufficient; EV IPR001263; PF00613; sufficient; EV IPR001683; PF00787; sufficient; EV IPR002420; PF00792; sufficient; -- SN 6 ID Phosphatidylinositol-4-phosphate 5-kinase DN Phosphatidylinositol-4-phosphate 5-kinase (EC 2.7.1.68) RQ 1 EV IPR002498; PF01504; sufficient; -- SN 7 ID CDP-diacylglycerol:myo-inositol phosphatidyltransferase DN CDP-diacylglycerol:myo-inositol phosphatidyltransferase (EC 2.7.8.11) RQ 1 EV IPR000462; PF01066; sufficient; -- SN 8 ID Phosphatidylinositol 3,5-bisphosphate 5-phosphatase DN Phosphatidylinositol 3,5-bisphosphate 5-phosphatase (EC 3.1.3) RQ 1 EV IPR002013; PF02383; sufficient; // AC GenProp1759 DE Spermidine hydroxycinnamic acid conjugates biosynthesis TP PATHWAY AU Zhang P TH 5 DC Spermidine hydroxycinnamic acid conjugates biosynthesis DR MetaCyc; PWY-6442; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Spermidine:4-coumaroyl-CoA N-acyltransferase DN Spermidine:4-coumaroyl-CoA N-acyltransferase (EC 2.3.1.M34) RQ 1 EV IPR003480; PF02458; sufficient; -- SN 2 ID Spermidine:caffeoyl-CoA N-acyltransferase DN Spermidine:caffeoyl-CoA N-acyltransferase (EC 2.3.1.M34) RQ 1 EV IPR003480; PF02458; sufficient; -- SN 3 ID Spermidine:feruloyl-CoA N-acyltransferase DN Spermidine:feruloyl-CoA N-acyltransferase (EC 2.3.1.M34) RQ 1 EV IPR003480; PF02458; sufficient; -- SN 4 ID Tricoumaroyl spermidine hydroxylase DN Tricoumaroyl spermidine hydroxylase (EC 1.14.99) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 5 ID Tricaffeoyl spermidine O-methyltransferase DN Tricaffeoyl spermidine O-methyltransferase (EC 2.1.1) RQ 1 EV IPR002935; PF01596; sufficient; -- SN 6 ID Triferuloyl spermidine hydroxylase DN Triferuloyl spermidine hydroxylase (EC 1.14.99) RQ 1 EV IPR001128; PF00067; sufficient; -- SN 7 ID Trihydroxyferuloyl spermidine O-methyltransferase DN Trihydroxyferuloyl spermidine O-methyltransferase (EC 2.1.1) RQ 1 EV IPR002935; PF01596; sufficient; // AC GenProp1760 DE Superpathway of gibberellin GA12 biosynthesis TP PATHWAY AU N/A TH 0 DC Superpathway of gibberellin GA12 biosynthesis DR MetaCyc; PWY-5053; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Ent-kaurene 19-hydroxylase DN Ent-kaurene 19-hydroxylase RQ 1 EV IPR001128; PF00067; sufficient; -- SN 2 ID Ent-kaurene synthase DN Ent-kaurene synthase (EC 4.2.3.19) RQ 1 EV IPR001906; PF01397; sufficient; EV IPR005630; PF03936; sufficient; // AC GenProp1761 DE Linoleate biosynthesis I (plants) TP PATHWAY AU Caspi R TH 2 DC Linoleate biosynthesis I (plants) DR MetaCyc; PWY-5995; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Oleoyl-lipid 12-desaturase DN Oleoyl-lipid 12-desaturase (EC 1.14.19.23) RQ 1 EV IPR005804; PF00487; sufficient; -- SN 2 ID Lysophospholipid linoleoyltransferase DN Lysophospholipid linoleoyltransferase (EC 2.3.1.23) RQ 1 EV IPR004299; PF03062; sufficient; -- SN 3 ID Fatty acid desaturase DN Fatty acid desaturase (EC 1.14.19.22) RQ 1 EV IPR005804; PF00487; sufficient; EV IPR021863; PF11960; sufficient; -- SN 4 ID Lysophospholipid oleoyltransferase DN Lysophospholipid oleoyltransferase (EC 2.3.1.23) RQ 1 EV IPR004299; PF03062; sufficient; // AC GenProp1762 DE Ethanolamine utilization TP PATHWAY AU Caspi R, Keseler I TH 3 DC Ethanolamine utilization DR MetaCyc; PWY0-1477; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Acetaldehyde dehydrogenase DN Acetaldehyde dehydrogenase (EC 1.2.1.10) RQ 1 EV IPR003361; TIGR03215; sufficient; -- SN 2 ID Acetate kinase DN Acetate kinase (EC 2.7.2.1) RQ 1 EV IPR000890; PF00871; sufficient; EV IPR004372; TIGR00016; sufficient; EV IPR010424; PF06249; sufficient; EV IPR012381; PF10662; sufficient; EV IPR012381; TIGR02528; sufficient; EV IPR005862; TIGR01142; sufficient; -- SN 3 ID Alcohol dehydrogenase DN Alcohol dehydrogenase (EC 1.1.1.1) RQ 1 EV IPR013149; PF00107; sufficient; EV IPR013154; PF08240; sufficient; EV IPR001670; PF00465; sufficient; EV IPR015590; PF00171; sufficient; -- SN 4 ID Ethanolamine ammonia-lyase DN Ethanolamine ammonia-lyase (EC 4.3.1.7) RQ 1 EV IPR010628; PF06751; sufficient; EV IPR009246; PF05985; sufficient; -- SN 5 ID Phosphotransacetylase DN Phosphotransacetylase (EC 2.3.1.8) RQ 1 EV IPR008300; PF06130; sufficient; // AC GenProp1763 DE Superpathway of carotenoid biosynthesis in plants TP PATHWAY AU Lukas Mueller L, Tissier C TH 8 DC Superpathway of carotenoid biosynthesis in plants DR MetaCyc; CAROTENOID-PWY; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID Zeaxanthin epoxidase DN Zeaxanthin epoxidase RQ 1 EV IPR000253; PF00498; sufficient; EV IPR002938; PF01494; sufficient; -- SN 2 ID Antheraxanthin epoxidase DN Antheraxanthin epoxidase RQ 1 EV IPR000253; PF00498; sufficient; EV IPR002938; PF01494; sufficient; -- SN 3 ID Beta-carotene hydroxylase DN Beta-carotene hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 4 ID Beta-cryptoxanthin 3'-hydroxylase DN Beta-cryptoxanthin 3'-hydroxylase RQ 1 EV IPR006694; PF04116; sufficient; -- SN 5 ID Prolycopene isomerase DN Prolycopene isomerase (EC 5.2.1.13) RQ 1 EV IPR014101; TIGR02730; sufficient; -- SN 6 ID Lycopene epsilon cyclase DN Lycopene epsilon cyclase (EC 5.5.1.18) RQ 1 EV IPR010108; TIGR01790; sufficient; -- SN 7 ID Delta-carotene beta-cyclase DN Delta-carotene beta-cyclase (EC 5.5.1.19) RQ 1 EV IPR010108; TIGR01790; sufficient; -- SN 8 ID Lycopene beta-monocyclase DN Lycopene beta-monocyclase (EC 5.5.1.19) RQ 1 EV IPR010108; TIGR01790; sufficient; -- SN 9 ID Gamma-carotene beta-cyclase DN Gamma-carotene beta-cyclase (EC 5.5.1.19) RQ 1 EV IPR010108; TIGR01790; sufficient; -- SN 10 ID Neoxanthin synthase DN Neoxanthin synthase (EC 5.3.99.9) RQ 1 EV IPR010108; TIGR01790; sufficient; // AC GenProp1764 DE Flavin biosynthesis IV (mammalian) TP PATHWAY AU Trupp M TH 0 DC Flavin biosynthesis IV (mammalian) DR MetaCyc; PWY66-366; CC This property has been automatically generated from MetaCyc and has not CC been manually verified to check the validity of the InterPro signatures CC used for the evidence. See MetaCyc for additional information and CC references relating to this property. -- SN 1 ID FAD synthetase DN FAD synthetase (EC 2.7.7.2) RQ 1 EV IPR001453; PF00994; sufficient; EV IPR002500; PF01507; sufficient; -- SN 2 ID Riboflavin kinase DN Riboflavin kinase (EC 2.7.1.26) RQ 1 EV IPR015865; PF01687; sufficient; // AC GenProp1765 DE Vitamin Biosynthesis TP CATEGORY AU Richardson L TH 0 CC The process of synthesising vitamins from simpler starting CC materials. -- SN 1 ID Biotin biosynthesis from 8-amino-7-oxononanoate I RQ 0 EV GenProp1377; -- SN 2 ID Biotin biosynthesis I RQ 0 EV GenProp1577; -- SN 3 ID 2-Methyladeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP RQ 0 EV GenProp1366; -- SN 4 ID Adeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP RQ 0 EV GenProp1378; -- SN 5 ID Adenosylcobalamin biosynthesis from adenosylcobinamide-GDP I RQ 0 EV GenProp1454; -- SN 6 ID Aminopropanol phosphate biosynthesis I RQ 0 EV GenProp1312; -- SN 7 ID Flavin biosynthesis I (bacteria and plants) RQ 0 EV GenProp1734; -- SN 8 ID Flavin biosynthesis IV (mammalian) RQ 0 EV GenProp1764; -- SN 9 ID Tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate RQ 0 EV GenProp1216; -- SN 10 ID N10-formyl-tetrahydrofolate biosynthesis RQ 0 EV GenProp1356; -- SN 11 ID Tetrahydrofolate biosynthesis RQ 0 EV GenProp1616; -- SN 12 ID 4-Aminobenzoate biosynthesis RQ 0 EV GenProp1727; -- SN 13 ID Phosphopantothenate biosynthesis I RQ 0 EV GenProp1748; -- SN 14 ID 4-Amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis RQ 0 EV GenProp1590; -- SN 15 ID Thiamine diphosphate biosynthesis I (E. coli) RQ 0 EV GenProp1457; -- SN 16 ID Thiamine diphosphate biosynthesis IV (eukaryotes) RQ 0 EV GenProp1702; -- SN 17 ID Thiamine diphosphate biosynthesis II (Bacillus) RQ 0 EV GenProp1725; -- SN 18 ID Hydroxymethylpyrimidine salvage RQ 0 EV GenProp1218; -- SN 19 ID Thiamine salvage I RQ 0 EV GenProp1219; -- SN 20 ID Thiamine salvage II RQ 0 EV GenProp1289; -- SN 21 ID Thiazole biosynthesis III (eukaryotes) RQ 0 EV GenProp1697; -- SN 22 ID Thiamine formation from pyrithiamine and oxythiamine (yeast) RQ 0 EV GenProp1674; -- SN 23 ID Retinoate biosynthesis II RQ 0 EV GenProp1236; -- SN 24 ID Retinoate biosynthesis I RQ 0 EV GenProp1321; -- SN 25 ID Retinol biosynthesis RQ 0 EV GenProp1703; -- SN 26 ID Pyridoxal 5'-phosphate salvage I RQ 0 EV GenProp1604; -- SN 27 ID Pyridoxal 5'-phosphate biosynthesis I RQ 0 EV GenProp1633; -- SN 28 ID Dehydro-D-arabinono-1,4-lactone biosynthesis RQ 0 EV GenProp1649; -- SN 29 ID Superpathway of thiamine diphosphate biosynthesis II RQ 0 EV GenProp1266; -- SN 30 ID Superpathway of tetrahydrofolate biosynthesis RQ 0 EV GenProp1332; -- SN 31 ID Superpathway of adenosylcobalamin salvage from cobinamide I RQ 0 EV GenProp1349; -- SN 32 ID Superpathway of thiamine diphosphate biosynthesis III (eukaryotes) RQ 0 EV GenProp1513; // AC GenProp1766 DE Hormone biosynthesis TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the formation of CC hormones. -- SN 1 ID Indole-3-acetate biosynthesis I RQ 0 EV GenProp1464; -- SN 2 ID Cytokinins 7-N-glucoside biosynthesis RQ 0 EV GenProp1261; -- SN 3 ID Ethylene biosynthesis I (plants) RQ 0 EV GenProp1657; -- SN 4 ID Ent-kaurene biosynthesis I RQ 0 EV GenProp1739; -- SN 5 ID GA12 biosynthesis RQ 0 EV GenProp1745; -- SN 6 ID Estradiol biosynthesis I (via estrone) RQ 0 EV GenProp1338; -- SN 7 ID Progesterone biosynthesis RQ 0 EV GenProp1385; -- SN 8 ID Estradiol biosynthesis II RQ 0 EV GenProp1417; -- SN 9 ID Lipoxin biosynthesis RQ 0 EV GenProp1588; -- SN 10 ID C20 prostanoid biosynthesis RQ 0 EV GenProp1603; -- SN 11 ID Mineralocorticoid biosynthesis RQ 0 EV GenProp1644; -- SN 12 ID Leukotriene biosynthesis RQ 0 EV GenProp1653; -- SN 13 ID Glucocorticoid biosynthesis RQ 0 EV GenProp1666; -- SN 14 ID Serotonin and melatonin biosynthesis RQ 0 EV GenProp1695; -- SN 15 ID Thyroid hormone biosynthesis RQ 0 EV GenProp1728; -- SN 16 ID Pregnenolone biosynthesis RQ 0 EV GenProp1740; -- SN 17 ID Androgen biosynthesis RQ 0 EV GenProp1742; -- SN 18 ID Superpathway of steroid hormone biosynthesis RQ 0 EV GenProp1217; -- SN 19 ID Superpathway of gibberellin GA12 biosynthesis RQ 0 EV GenProp1760; // AC GenProp1767 DE Secondary metabolites biosynthesis TP CATEGORY AU Richardson L TH 0 CC The process of creating secondary metabolites from simpler starting CC materials. -- SN 1 ID Pyocyanin biosynthesis RQ 0 EV GenProp1331; -- SN 2 ID Spermidine hydroxycinnamic acid conjugates biosynthesis RQ 0 EV GenProp1759; -- SN 3 ID Anthocyanidin modification (Arabidopsis) RQ 0 EV GenProp1547; -- SN 4 ID Pterostilbene biosynthesis RQ 0 EV GenProp1388; -- SN 5 ID Kanosamine biosynthesis II RQ 0 EV GenProp1534; -- SN 6 ID 1D-myo-inositol hexakisphosphate biosynthesis I (from Ins(1,4,5)P3) RQ 0 EV GenProp1249; -- SN 7 ID 1D-myo-inositol hexakisphosphate biosynthesis II (mammalian) RQ 0 EV GenProp1509; -- SN 8 ID D-myo-inositol (1,3,4)-trisphosphate biosynthesis RQ 0 EV GenProp1229; -- SN 9 ID Myo-inositol biosynthesis RQ 0 EV GenProp1244; -- SN 10 ID D-myo-inositol (3,4,5,6)-tetrakisphosphate biosynthesis RQ 0 EV GenProp1460; -- SN 11 ID D-myo-inositol (1,4,5)-trisphosphate biosynthesis RQ 0 EV GenProp1548; -- SN 12 ID Inositol diphosphates biosynthesis RQ 0 EV GenProp1574; -- SN 13 ID D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis RQ 0 EV GenProp1692; -- SN 14 ID Beta-carotene biosynthesis RQ 0 EV GenProp1451; -- SN 15 ID Zeaxanthin biosynthesis RQ 0 EV GenProp1645; -- SN 16 ID Phytyl diphosphate biosynthesis RQ 0 EV GenProp1382; -- SN 17 ID Methylerythritol phosphate pathway I RQ 0 EV GenProp1295; -- SN 18 ID Mevalonate pathway I RQ 0 EV GenProp1432; -- SN 19 ID Trichome monoterpenes biosynthesis RQ 0 EV GenProp1709; -- SN 20 ID Beta-caryophyllene biosynthesis RQ 0 EV GenProp1471; -- SN 21 ID (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene biosynthesis RQ 0 EV GenProp1638; -- SN 22 ID PreQ0 biosynthesis RQ 0 EV GenProp1602; -- SN 23 ID Mycocyclosin biosynthesis RQ 0 EV GenProp1622; -- SN 24 ID Gadusol biosynthesis RQ 0 EV GenProp1668; -- SN 25 ID Superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism RQ 0 EV GenProp1395; -- SN 26 ID Superpathway of carotenoid biosynthesis in plants RQ 0 EV GenProp1763; // AC GenProp1768 DE Alcohols degradation TP CATEGORY AU Richardson L TH 0 CC Any metabolic process involving the breakdown of alcohols CC into smaller products. -- SN 1 ID Ethanol degradation IV RQ 0 EV GenProp1379; -- SN 2 ID Ethanol degradation III RQ 0 EV GenProp1437; -- SN 3 ID Ethanol degradation I RQ 0 EV GenProp1497; -- SN 4 ID Ethanol degradation II RQ 0 EV GenProp1715; -- SN 5 ID Glycerol degradation V RQ 0 EV GenProp1324; -- SN 6 ID Glycerol degradation I RQ 0 EV GenProp1567; -- SN 7 ID Ethylene glycol degradation RQ 0 EV GenProp1370; -- SN 8 ID Superpathway of glycol metabolism and degradation RQ 0 EV GenProp1297; // AC GenProp1769 DE Amines and polyamines catabolism TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the breakdown of amines CC and polyamines. -- SN 1 ID GABA shunt RQ 0 EV GenProp1288; -- SN 2 ID 4-Aminobutanoate degradation I RQ 0 EV GenProp1506; -- SN 3 ID 4-Aminobutanoate degradation III RQ 0 EV GenProp1523; -- SN 4 ID 4-Aminobutanoate degradation II RQ 0 EV GenProp1579; -- SN 5 ID Allantoin degradation to glyoxylate I RQ 0 EV GenProp1257; -- SN 6 ID Allantoin degradation to ureidoglycolate II (ammonia producing) RQ 0 EV GenProp1326; -- SN 7 ID Allantoin degradation to glyoxylate II RQ 0 EV GenProp1393; -- SN 8 ID Allantoin degradation to glyoxylate III RQ 0 EV GenProp1416; -- SN 9 ID Allantoin degradation to ureidoglycolate I (urea producing) RQ 0 EV GenProp1501; -- SN 10 ID L-carnitine degradation I RQ 0 EV GenProp1572; -- SN 11 ID Choline degradation I RQ 0 EV GenProp1390; -- SN 12 ID Glycine betaine degradation II (mammalian) RQ 0 EV GenProp1414; -- SN 13 ID N-acetylglucosamine degradation I RQ 0 EV GenProp1303; -- SN 14 ID N-acetylglucosamine degradation II RQ 0 EV GenProp1565; -- SN 15 ID Phenylethylamine degradation I RQ 0 EV GenProp1402; -- SN 16 ID Putrescine degradation V RQ 0 EV GenProp1276; -- SN 17 ID Putrescine degradation I RQ 0 EV GenProp1362; -- SN 18 ID Putrescine degradation II RQ 0 EV GenProp1434; -- SN 19 ID Spermine and spermidine degradation III RQ 0 EV GenProp1272; -- SN 20 ID Spermine and spermidine degradation I RQ 0 EV GenProp1610; -- SN 21 ID Ethanolamine utilization RQ 0 EV GenProp1762; // AC GenProp1770 DE Carbohydrates degradation TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the breakdown CC of carbohydrates. -- SN 1 ID Chitin degradation I (archaea) RQ 0 EV GenProp1522; -- SN 2 ID Glycogen degradation II RQ 0 EV GenProp1259; -- SN 3 ID Glycogen degradation I RQ 0 EV GenProp1412; -- SN 4 ID Starch degradation II RQ 0 EV GenProp1726; -- SN 5 ID D-arabinose degradation I RQ 0 EV GenProp1589; -- SN 6 ID Entner-Doudoroff pathway I RQ 0 EV GenProp1557; -- SN 7 ID D-galactose degradation I (Leloir pathway) RQ 0 EV GenProp1310; -- SN 8 ID D-galactose degradation V (Leloir pathway) RQ 0 EV GenProp1661; -- SN 9 ID L-arabinose degradation I RQ 0 EV GenProp1368; -- SN 10 ID Sucrose degradation III (sucrose invertase) RQ 0 EV GenProp1492; -- SN 11 ID Sucrose degradation II (sucrose synthase) RQ 0 EV GenProp1639; -- SN 12 ID Trehalose degradation I (low osmolarity) RQ 0 EV GenProp1394; -- SN 13 ID Trehalose degradation II (trehalase) RQ 0 EV GenProp1564; -- SN 14 ID Xylose degradation I RQ 0 EV GenProp1656; -- SN 15 ID Chitobiose degradation RQ 0 EV GenProp1293; -- SN 16 ID 2-O-alpha-mannosyl-D-glycerate degradation RQ 0 EV GenProp1299; -- SN 17 ID D-allose degradation RQ 0 EV GenProp1463; -- SN 18 ID 2'-Deoxy-alpha-D-ribose 1-phosphate degradation RQ 0 EV GenProp1559; -- SN 19 ID Fucose degradation RQ 0 EV GenProp1680; -- SN 20 ID Superpathway of fucose and rhamnose degradation RQ 0 EV GenProp1529; -- SN 21 ID Superpathway of D-glucarate and D-galactarate degradation RQ 0 EV GenProp1675; // AC GenProp1771 DE Carboxylates degradation TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the breakdown of CC carboxylates. -- SN 1 ID 2-Oxobutanoate degradation I RQ 0 EV GenProp1439; -- SN 2 ID Pyruvate fermentation to acetate IV RQ 0 EV GenProp1543; -- SN 3 ID Pyruvate fermentation to acetate VIII RQ 0 EV GenProp1620; -- SN 4 ID Acetate formation from acetyl-CoA I RQ 0 EV GenProp1345; -- SN 5 ID Glycolate and glyoxylate degradation I RQ 0 EV GenProp1374; -- SN 6 ID Glycolate and glyoxylate degradation II RQ 0 EV GenProp1556; -- SN 7 ID 2-Methylcitrate cycle I RQ 0 EV GenProp1687; -- SN 8 ID Propanoyl CoA degradation I RQ 0 EV GenProp1629; -- SN 9 ID Conversion of succinate to propanoate RQ 0 EV GenProp1723; -- SN 10 ID D-galactarate degradation I RQ 0 EV GenProp1225; -- SN 11 ID D-galacturonate degradation I RQ 0 EV GenProp1636; -- SN 12 ID D-glucarate degradation I RQ 0 EV GenProp1514; -- SN 13 ID L-idonate degradation RQ 0 EV GenProp1228; -- SN 14 ID D-fructuronate degradation RQ 0 EV GenProp1449; -- SN 15 ID D-galactonate degradation RQ 0 EV GenProp1566; -- SN 16 ID 2-Hydroxypenta-2,4-dienoate degradation RQ 0 EV GenProp1231; -- SN 17 ID Pyruvate decarboxylation to acetyl CoA RQ 0 EV GenProp1536; -- SN 18 ID Superpathway of beta-D-glucuronosides degradation RQ 0 EV GenProp1387; -- SN 19 ID Superpathway of acetate utilization and formation RQ 0 EV GenProp1749; // AC GenProp1772 DE Fatty acid degradation TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the breakdown of CC fatty acids. -- SN 1 ID Fatty acid beta-oxidation VI (peroxisome) RQ 0 EV GenProp1308; -- SN 2 ID Oleate beta-oxidation RQ 0 EV GenProp1486; -- SN 3 ID Oleate beta-oxidation (thioesterase-dependent, yeast) RQ 0 EV GenProp1488; -- SN 4 ID Fatty acid beta-oxidation II (peroxisome) RQ 0 EV GenProp1510; -- SN 5 ID Fatty acid beta-oxidation (peroxisome, yeast) RQ 0 EV GenProp1544; -- SN 6 ID Fatty acid beta-oxidation I RQ 0 EV GenProp1717; // AC GenProp1773 DE Lipid degradation TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the breakdown of lipids. -- SN 1 ID Sphingosine and sphingosine-1-phosphate metabolism RQ 0 EV GenProp1277; -- SN 2 ID Ceramide degradation RQ 0 EV GenProp1335; -- SN 3 ID Phosphatidylcholine resynthesis via glycerophosphocholine RQ 0 EV GenProp1352; -- SN 4 ID Sphingolipid recycling and degradation (yeast) RQ 0 EV GenProp1363; -- SN 5 ID Mitochondrial L-carnitine shuttle RQ 0 EV GenProp1413; -- SN 6 ID Acetoacetate degradation (to acetyl CoA) RQ 0 EV GenProp1441; // AC GenProp1774 DE Inorganic nutrients metabolism TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the utilisation and CC metabolism of inorganic nutrients, including sulphur compounds and CC nitrogen compounds. -- SN 1 ID Ammonia assimilation cycle I RQ 0 EV GenProp1489; -- SN 2 ID Ammonia assimilation cycle III RQ 0 EV GenProp1615; -- SN 3 ID Nitrate reduction III (dissimilatory) RQ 0 EV GenProp1329; -- SN 4 ID Nitrate reduction VIIIb (dissimilatory) RQ 0 EV GenProp1474; -- SN 5 ID Nitrate reduction X (dissimilatory, periplasmic) RQ 0 EV GenProp1504; -- SN 6 ID Nitrate reduction V (assimilatory) RQ 0 EV GenProp1554; -- SN 7 ID Nitrate reduction VIII (dissimilatory) RQ 0 EV GenProp1583; -- SN 8 ID Nitrate reduction IX (dissimilatory) RQ 0 EV GenProp1676; -- SN 9 ID Urea cycle RQ 0 EV GenProp1300; -- SN 10 ID Methylphosphonate degradation I RQ 0 EV GenProp1381; -- SN 11 ID Aminomethylphosphonate degradation RQ 0 EV GenProp1630; -- SN 12 ID Hydrogen sulfide biosynthesis I RQ 0 EV GenProp1281; -- SN 13 ID Hydrogen sulfide biosynthesis II (mammalian) RQ 0 EV GenProp1685; -- SN 14 ID Sulfate reduction I (assimilatory) RQ 0 EV GenProp1283; -- SN 15 ID Sulfate reduction II (assimilatory) RQ 0 EV GenProp1392; -- SN 16 ID Two-component alkanesulfonate monooxygenase RQ 0 EV GenProp1424; -- SN 17 ID Methanogenesis from methylthiopropanoate RQ 0 EV GenProp1447; -- SN 18 ID Superpathway of sulfate assimilation and cysteine biosynthesis RQ 0 EV GenProp1301; // AC GenProp1775 DE Secondary metabolites degradation TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the degradation and CC catabolism of secondary metabolites. -- SN 1 ID Anhydromuropeptides recycling I RQ 0 EV GenProp1623; -- SN 2 ID D-myo-inositol (1,4,5)-trisphosphate degradation RQ 0 EV GenProp1605; -- SN 3 ID Myo-, chiro- and scyllo-inositol degradation RQ 0 EV GenProp1271; -- SN 4 ID Myo-inositol degradation I RQ 0 EV GenProp1286; -- SN 5 ID Myo-inositol degradation II RQ 0 EV GenProp1527; -- SN 6 ID Fructoselysine and psicoselysine degradation RQ 0 EV GenProp1624; -- SN 7 ID Autoinducer AI-2 degradation RQ 0 EV GenProp1476; -- SN 8 ID Curcumin degradation RQ 0 EV GenProp1696; // AC GenProp1776 DE Nucleosides and nucleotides degradation TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways resulting in the degradation of CC nucleosides and nucleotides. -- SN 1 ID Adenosine nucleotides degradation II RQ 0 EV GenProp1255; -- SN 2 ID Guanosine nucleotides degradation III RQ 0 EV GenProp1469; -- SN 3 ID Purine ribonucleosides degradation RQ 0 EV GenProp1278; -- SN 4 ID Purine deoxyribonucleosides degradation I RQ 0 EV GenProp1323; -- SN 5 ID Purine deoxyribonucleosides degradation II RQ 0 EV GenProp1568; -- SN 6 ID Inosine 5'-phosphate degradation RQ 0 EV GenProp1753; -- SN 7 ID Pyrimidine deoxyribonucleosides degradation RQ 0 EV GenProp1410; -- SN 8 ID Thymine degradation RQ 0 EV GenProp1273; -- SN 9 ID UTP and CTP dephosphorylation II RQ 0 EV GenProp1396; -- SN 10 ID Pyrimidine ribonucleosides degradation RQ 0 EV GenProp1576; -- SN 11 ID S-methyl-5'-thioadenosine degradation I RQ 0 EV GenProp1482; -- SN 12 ID Superpathway of pyrimidine ribonucleosides degradation RQ 0 EV GenProp1380; -- SN 13 ID Superpathway of pyrimidine deoxyribonucleosides degradation RQ 0 EV GenProp1631; -- SN 14 ID Superpathway of purine deoxyribonucleosides degradation RQ 0 EV GenProp1752; // AC GenProp1777 DE Nucleic acids processing TP CATEGORY AU Richardson L TH 0 CC The chemical reactions and pathways involved in the processing CC of nucleic acids. -- SN 1 ID tRNA splicing II RQ 0 EV GenProp1707; -- SN 2 ID Wybutosine biosynthesis RQ 0 EV GenProp1241; -- SN 3 ID tRNA-uridine 2-thiolation (mammalian mitochondria) RQ 0 EV GenProp1313; -- SN 4 ID 5-(Carboxymethoxy)uridine biosynthesis RQ 0 EV GenProp1340; -- SN 5 ID mRNA capping I RQ 0 EV GenProp1354; -- SN 6 ID tRNA processing RQ 0 EV GenProp1360; -- SN 7 ID Queuosine biosynthesis RQ 0 EV GenProp1400; -- SN 8 ID tRNA-uridine 2-thiolation (cytoplasmic) RQ 0 EV GenProp1461; -- SN 9 ID tRNA methylation (yeast) RQ 0 EV GenProp1521; -- SN 10 ID tRNA-uridine 2-thiolation (bacteria) RQ 0 EV GenProp1555; -- SN 11 ID N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis RQ 0 EV GenProp1570; -- SN 12 ID Archaeosine biosynthesis I RQ 0 EV GenProp1735; // AC GenProp1778 DE Hormone systems TP CATEGORY AU Richardson L TH 0 CC Properties related to hormone biosynthesis, activation, signalling CC and secretion. -- SN 1 ID Renin-Angiotensin system RQ 0 EV GenProp2085; -- SN 2 ID Pro-insulin activation RQ 0 EV GenProp2086; -- SN 3 ID Proglucagon activation RQ 0 EV GenProp2087; -- SN 4 ID Insulin signaling pathway - glycogenesis RQ 0 EV GenProp2088; -- SN 5 ID Glucagon signaling pathway for glycogenolysis RQ 0 EV GenProp2089; -- SN 6 ID Insulin signaling pathway - glucose uptake RQ 0 EV GenProp2090; -- SN 7 ID Insulin secretion via PKA RQ 0 EV GenProp2095; -- SN 8 ID Insulin secretion via PKC RQ 0 EV GenProp2096; -- SN 9 ID Insulin secretion via IP3 RQ 0 EV GenProp2098; -- SN 10 ID Insulin secretion via glucose RQ 0 EV GenProp2099; // AC GenProp2002 DE Fibrinogen TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 7649481 RT Resolution of spontaneous bleeding events but failure of pregnancy in RT fibrinogen-deficient mice. RA Suh TT, Holmback K, Jensen NJ, Daugherty CC, Small K, Simon DI, RA Potter S, Degen JL; RL Genes Dev. 1995;9:2020-2033. DC Complement and coagulation cascades DR KEGG; map04610; CC Fibrinogen is the precursor of fibrin. During hemostasis, thrombin CC activates fibrin which then cross-links to form an insoluble matrix. CC Three subunits, alpha, beta and gamma, form fibrinogen [1]. Thrombin CC releases fibrinopeptides A and B from the N-termini of the alpha and CC beta chains respectively. Factor XIII is an transglutaminase which CC catalyses formation of isopeptide bonds between subunits via the CC newly exposed N-termini. -- SN 1 ID Fibrinogen alpha chain RQ 1 EV IPR037579; PTHR19143:SF232; sufficient; TG GO:0005577; -- SN 2 ID Fibrinogen beta chain RQ 1 EV IPR037580; PTHR19143:SF332; sufficient; TG GO:0005577; -- SN 3 ID Fibrinogen gamma chain RQ 0 EV IPR037581; PTHR19143:SF338; sufficient; TG GO:0005577; // AC GenProp2007 DE Complement activation, common pathway 1 TP PATHWAY AU Rawlings ND TH 2 RN [1] RM 26489954 RT Complement activation, regulation, and molecular basis for complement- RT related diseases. RA Bajic G; Degn SE; Thiel S; Andersen GR; RL EMBO J. 2015;34:2735-2757. DC Complement and coagulation cascades DR KEGG; map04610; CC Complement is a ring-shaped complex that forms pores in bacterial CC cell membranes, making the cells leak and thus kill invading bacteria CC and other pathogens. There are three pathways by which complement is CC activated, known as the classical, alternative and lectin pathways. CC Activation involves proteolytic cascades which are different for each CC of the activation pathways. The classical and lectin pathways converge CC at the activation of the C2/C4 complex, whereas the alternative pathway CC converges at C5 activation [1]. The pathways are found only in CC chordates. -- SN 1 ID Complement C2 DN Complement C2 (EC:3.4.21.43) RQ 1 EV IPR037568; PTHR19325:SF387; sufficient; -- SN 2 ID Complement C4 DN Complement C4 RQ 1 EV IPR037569; PTHR11412:SF134; sufficient; -- SN 4 ID Complement C3 DN Complement C3 RQ 1 EV IPR035711; PTHR11412:SF81; sufficient; // AC GenProp2010 DE Fibrinolysis TP METAPATH AU Rawlings ND TH 1 RN [1] RM 26324800 RT Coagulation and anticoagulation in idiopathic pulmonary fibrosis. RA Crooks MG; Hart SP; RL Eur Respir Rev. 2015;24:392-399. DC Complement and coagulation cascades DR KEGG; map04610; CC Fibrinolysis is the disolving of the blood clot and naturally CC follows coagulation. Plasmin cleaves alpha, beta and gamma chains CC of fibrin, thereby releasing the N-terminal peptides where the CC isopeptide bonds, which cross-link fibrin fibres, are formed [1]. -- SN 1 ID Plasminogen activator DN Plasminogen activator RQ 1 EV IPR034813; PTHR44459:SF2; sufficient; EV IPR034814; PTHR24264:SF38; sufficient; EV IPR034811; PTHR44617; sufficient; -- SN 2 ID Plasmin DN Plasmin (EC:3.4.21.7) RQ 1 EV IPR023317; PIRSF001150; sufficient; -- SN 3 ID Fibrinogen RQ 1 EV GenProp2002; TG GO:0005577; // AC GenProp2011 DE Eukaryote 20S proteasome TP COMPLEX AU Rawlings ND TH 13 RN [1] RM 9087403 RT Structure of 20S proteasome from yeast at 2.4 A resolution. RA Groll M; Ditzel L; Löwe J; Stock D; Bochtler M; Bartunik HD; Huber R; RL Nature 1997;386:463-471. RN [2] RM 12015144 RT The structure of the mammalian 20S proteasome at 2.75 A resolution. RA Unno M; Mizushima T; Morimoto Y; Tomisugi Y; Tanaka K; Yasuoka N; RA Tsukihara T; RL Structure 2002;10:609-618. RN [3] RM 28460188 RT Proteasomal and Autophagic Degradation Systems. RA Dikic I; RL Annu Rev Biochem. 2017;86:193-224. DC Proteasome DR KEGG; map03050; CC The 20S proteasome is an intracellular complex of fourteen homologous CC proteins known as alpha and beta subunits. The subunits are arranged CC in rings of seven and then stacked. Each ring contains only alpha or CC beta subunits, and these are arranged alpha-beta-beta-alpha in the CC stack. Three of the beta components are N-terminal nucleophile CC hydrolases that are threonine-type endopeptidases, with the N-terminal CC threonine being the nucleophile in the reaction. The active sites are CC directed towards the central cavity, so that a protein threaded through CC the central cavity is processed into short peptides. The three CC catalytically active beta subunits have different specificities, CC known as trypsin-like, chymotrypsin-like and caspase-like [1,2]. CC Substrates include intracellular proteins tagged for degradation by CC polyubiquitination and viral proteins. Peptide products may be CC trafficked to the major histocompatability complex for presentation CC as antigens on T-cells. Modified versions of the proteasome occur in CC immune cells, the thymus and the testis; in these some of the beta or CC alpha subunits are replaced. Most protein substrates must be CC denatured before being cleaved by the proteasome, and an additional CC complex, known as the 19S cap, can be added to either or both ends of CC the proteasome. The 19S cap includes ATPases and a deubiquitinating CC enzyme. This larger complex of the 20S proteasome and 19S cap is CC known as the 26S proteasome [3]. CC The 20S proteasome is found in all eukaryotes. In archaea and some CC bacteria, a much simpler assembly exists in which each ring is a CC homoheptamer of a single alpha or beta subunit. -- SN 1 ID Proteasome subunit alpha type-1 DN Proteasome subunit alpha type-1 RQ 1 EV IPR035144; cd03749; sufficient; TG GO:0000502; EV IPR035144; PTHR11599:SF12; sufficient; TG GO:0000502; -- SN 2 ID Proteasome subunit alpha type-2 DN Proteasome subunit alpha type-2 RQ 1 EV IPR034644; PTHR11599:SF16; sufficient; TG GO:0000502; -- SN 3 ID Proteasome subunit alpha type-3 DN Proteasome subunit alpha type-3 RQ 1 EV IPR037555; PTHR11599:SF10; sufficient; TG GO:0000502; EV IPR035150; PTHR11599:SF103; sufficient; TG GO:0000502; -- SN 4 ID Proteasome subunit alpha type-4 DN Proteasome subunit alpha type-4 RQ 1 EV IPR034647; PTHR11599:SF13; sufficient; TG GO:0000502; -- SN 5 ID Proteasome subunit alpha type-5 DN Proteasome subunit alpha type-5 RQ 1 EV IPR033812; cd03753; sufficient; TG GO:0000502; -- SN 6 ID Proteasome subunit alpha type-6 DN Proteasome subunit alpha type-6 RQ 1 EV IPR034642; PTHR11599:SF11; sufficient; TG GO:0000502; EV IPR034642; cd03754; sufficient; TG GO:0000502; -- SN 7 ID Proteasome subunit alpha type-7 DN Proteasome subunit alpha type-7 RQ 1 EV IPR035190; PTHR11599:SF40; sufficient; TG GO:0000502; -- SN 8 ID Proteasome subunit beta type-1 DN Proteasome subunit beta type-1 RQ 1 EV IPR035202; PTHR11599:SF59; sufficient; TG GO:0000502; EV IPR035202; PTHR11599:SF55; sufficient; TG GO:0000502; -- SN 9 ID Proteasome subunit beta type-2 DN Proteasome subunit beta type-2 RQ 1 EV IPR035206; PTHR11599:SF6; sufficient; TG GO:0000502; EV IPR035206; cd03758; sufficient; TG GO:0000502; -- SN 10 ID Proteasome subunit beta type-3 DN Proteasome subunit beta type-3 RQ 1 EV IPR033811; PTHR11599:SF62; sufficient; TG GO:0000502; EV IPR033811; cd03759; sufficient; TG GO:0000502; -- SN 11 ID Proteasome subunit beta type-4 DN Proteasome subunit beta type-4 RQ 1 EV IPR016295; PTHR11599:SF5; sufficient; TG GO:0000502; EV IPR016295; cd03760; sufficient; TG GO:0000502; -- SN 12 ID Proteasome subunit beta type-5 DN Proteasome subunit beta type-5 (EC 3.4.25.1) RQ 0 EV IPR037558; PTHR11599:SF51; sufficient; TG GO:0000502; TG GO:0043161; -- SN 13 ID Proteasome subunit beta type-6 DN Proteasome subunit beta type-6 (EC 3.4.25.1) RQ 1 EV IPR035140; PTHR11599:SF46; sufficient; TG GO:0000502; TG GO:0043161; -- SN 14 ID Proteasome subunit beta type-7 DN Proteasome subunit beta type-7 (EC 3.4.25.1) RQ 1 EV IPR035216; PTHR11599:SF42; sufficient; TG GO:0000502; TG GO:0043161; EV IPR035216; PTHR11599:SF44; sufficient; TG GO:0000502; TG GO:0043161; // AC GenProp2012 DE 19S proteasome cap TP COMPLEX AU Rawlings ND TH 3 RN [1] RM 1317798 RT Demonstration that a human 26S proteolytic complex consists of a RT proteasome and multiple associated protein components and hydrolyzes RT ATP and ubiquitin-ligated proteins by closely linked mechanisms. RA Kanayama HO; Tamura T; Ugai S; Kagawa S; Tanahashi N; Yoshimura T; RA Tanaka K; Ichihara A; RL Eur J Biochem. 1992;206:567-578. RN [2] RM 27428775 RT An atomic structure of the human 26S proteasome. RA Huang X; Luan B; Wu J; Shi Y; RL Nat Struct Mol Biol. 2016;23:778-785. RN [3] RM 15826667 RT Structure of S5a bound to monoubiquitin provides a model for RT polyubiquitin recognition. RA Wang Q; Young P; Walters KJ; RL J. Mol. Biol. 2005;348:727-739. RN [4] RM 19490896 RT Assembly pathway of the mammalian proteasome base subcomplex is RT mediated by multiple specific chaperones. RA Kaneko T; Hamazaki J; Iemura S; Sasaki K; Furuyama K; Natsume T; RA Tanaka K; Murata S; RL Cell 2009;137:914-925. RN [5] RM 19412159 RT Chaperone-mediated pathway of proteasome regulatory particle assembly. RA Roelofs J; Park S; Haas W; Tian G; McAllister FE; Huo Y; Lee BH; RA Zhang F; Shi Y; Gygi SP; Finley D; RL Nature 2009;459:861-865. DC Proteasome DR KEGG; map03050; CC The 20S proteasome is converted to the 26S proteasome by addition of CC the 19S cap. This is a complex of eighteen proteins, six AAA-ATPases CC and fourteen that are not ATPases. Non-ATPase regulatory subunit 14 CC is a metallo-dependent deubiquitinating enzyme from peptidase family CC M67. Non-ATPase regulatory subunit 4 binds ubiquitin. Ubiquitin CC receptor ADRM1 also binds ubiquitin and activates non-ATPase regulatory CC subunit 14, but is absent from the solved tertiary structures [1,2]. CC Non-ATPase regulatory subunits 5, 9, 10 and 11 are required for CC proteasome assembly. The 19S complex consists of a base, containing the CC six AAA-ATPases and three non-ATPase regulatory subunits, and a lid CC containing all the remaining non-ATPase regulatory subunits [4,5]. CC The functions of the 19S cap are to remove ubiquitin from targeted CC proteins, and to denature proteins prior to entry into the central CC cavity of the proteasome [3]. -- SN 1 ID 26S protease regulatory subunit 4/PSMC1 DN 26S protease regulatory subunit 4 RQ 1 EV IPR035244; PTHR23073:SF24; sufficient; TG GO:0016887; -- SN 2 ID 26S protease regulatory subunit 7/PSMC2 DN 26S protease regulatory subunit 7 RQ 1 EV IPR035245; PTHR23073:SF13; sufficient; TG GO:0016887; -- SN 3 ID 26S protease regulatory subunit 6a/PSMC3 DN 26S protease regulatory subunit 6a RQ 1 EV IPR035254; PTHR23073:SF7; sufficient; TG GO:0016887; -- SN 4 ID 26S protease regulatory subunit 6b/PSMC4 DN 26S protease regulatory subunit 6b RQ 1 EV IPR035256; PTHR23073:SF8; sufficient; TG GO:0016887; -- SN 5 ID 26S protease regulatory subunit 8/PSMC5 DN 26S protease regulatory subunit 8 RQ 1 EV IPR035261; PTHR23073:SF12; sufficient; TG GO:0016887; -- SN 6 ID 26S protease regulatory subunit 10b/PSMC6 DN 26S protease regulatory subunit 10b RQ 1 EV IPR035263; PTHR23073:SF59; sufficient; TG GO:0016887; -- SN 7 ID 26S proteasome non-ATPase regulatory subunit 1/PSMD1 DN 26S proteasome non-ATPase regulatory subunit 1 RQ 1 EV IPR035266; PTHR10943:SF2; sufficient; TG GO:0030234 -- SN 8 ID 26S proteasome non-ATPase regulatory subunit 2/PSMD2 DN 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit RQ 1 EV IPR016643; PTHR10943:SF1; sufficient; TG GO:0030234 -- SN 9 ID 26S proteasome non-ATPase regulatory subunit 3/PSMD3 DN 26S proteasome non-ATPase regulatory subunit 3 RQ 1 EV IPR035267; PTHR10758:SF2; sufficient; TG GO:0030234 -- SN 10 ID 26S proteasome non-ATPase regulatory subunit 4/PSMD4 DN Proteasome subunit Rpn10 RQ 1 EV IPR027040; PTHR10223:SF6; sufficient; TG GO:0031593 -- SN 11 ID 26S proteasome non-ATPase regulatory subunit 5/PSMD5 DN 26S proteasome non-ATPase regulatory subunit 5 RQ 0 EV IPR019538; PF10508; sufficient; EV IPR019538; PTHR13554; sufficient; TG GO:0070682 -- SN 12 ID 26S proteasome non-ATPase regulatory subunit 6/PSMD6 DN 26S proteasome non-ATPase regulatory subunit 6 RQ 1 EV IPR035268; PTHR14145:SF1; sufficient; -- SN 13 ID 26S proteasome non-ATPase regulatory subunit 7/PSMD7 DN 26S Proteasome non-ATPase regulatory subunit 7/8 RQ 1 EV IPR033858; PTHR10540:SF7; sufficient; EV IPR033858; cd08062; sufficient; -- SN 14 ID 26S proteasome non-ATPase regulatory subunit 8/PSMD8 DN 26S proteasome non-ATPase regulatory subunit Rpn12 RQ 1 EV IPR006746; PTHR12387; sufficient; -- SN 15 ID 26S proteasome non-ATPase regulatory subunit 9/PSMD9 DN 26S proteasome non-ATPase regulatory subunit 9 RQ 0 EV IPR035269; PTHR12651; sufficient; TG GO:0070682 -- SN 16 ID 26S proteasome non-ATPase regulatory subunit 10/PSMD10 DN 26S proteasome non-ATPase regulatory subunit 10-like RQ 0 EV IPR039334; PTHR44187; sufficient; TG GO:0070682 -- SN 17 ID 26S proteasome non-ATPase regulatory subunit 11/PSMD11 DN 26S proteasome non-ATPase regulatory subunit 11 RQ 1 EV IPR035295; PTHR10678:SF6; sufficient; TG GO:0070682 -- SN 18 ID 26S proteasome non-ATPase regulatory subunit 12/PSMD12 DN 26S proteasome non-ATPase regulatory subunit 12 RQ 1 EV IPR035297; PTHR10855:SF1; sufficient; -- SN 19 ID 26S proteasome non-ATPase regulatory subunit 13/PSMD13 DN 26S proteasome non-ATPase regulatory subunit 13 RQ 1 EV IPR035298; PTHR10539; sufficient; -- SN 20 ID 26S proteasome non-ATPase regulatory subunit 14/PSMD14 DN 26S proteasome non-ATPase regulatory subunit 14 RQ 1 EV IPR035299; PTHR10410:SF13; sufficient; TG GO:0061578 -- SN 21 ID 26S proteasome complex subunit SEM1/SEM1 DN DSS1/SEM1 RQ 1 EV IPR007834; PTHR16771; sufficient; EV IPR007834; PF05160; sufficient; EV IPR007834; SM01385; sufficient; -- SN 22 ID Proteasomal ubiquitin receptor ADRM1/ADRM1 DN 26S proteasome complex ubiquitin receptor, subunit Rpn13 RQ 0 EV IPR006773; PTHR12225; sufficient; // AC GenProp2013 DE 26S proteasome TP METAPATH AU Rawlings ND TH 1 RN [1] RM 1317798 RT Demonstration that a human 26S proteolytic complex consists of a RT proteasome and multiple associated protein components and hydrolyzes RT ATP and ubiquitin-ligated proteins by closely linked mechanisms. RA Kanayama HO; Tamura T; Ugai S; Kagawa S; Tanahashi N; Yoshimura T; RA Tanaka K; Ichihara A; RL Eur J Biochem. 1992;206:567-578. RN [2] RM 27428775 RT An atomic structure of the human 26S proteasome. RA Huang X; Luan B; Wu J; Shi Y; RL Nat Struct Mol Biol. 2016;23:778-785. DC Proteasome DR KEGG; map03050; CC The 26S proteasome is a complex of the 20S proteasome and the 19S CC proteasome cap. The cap denatures proteins tagged with ubiquitin CC for degradation, releases ubiquitin and controls access to the CC central cavity of the 20S proteasome where degradation takes place CC [1]. -- SN 1 ID Eukaryote 20S proteasome RQ 1 EV GenProp2011; -- SN 2 ID 19S proteasome cap RQ 1 EV GenProp2012; // AC GenProp2014 DE Immunoproteasome TP COMPLEX AU Rawlings ND TH 12 RN [1] RM 12015144 RT The structure of the mammalian 20S proteasome at 2.75 A resolution. RA Unno M; Mizushima T; Morimoto Y; Tomisugi Y; Tanaka K; Yasuoka N; RA Tsukihara T; RL Structure 2002;10:609-618. RN [2] RM 11265247 RT Antigen processing by the proteasome. RA Kloetzel PM; RL Nat Rev Mol Cell Biol. 2001;2:179-188. RN [3] RM 28460188 RT Proteasomal and Autophagic Degradation Systems. RA Dikic I; RL Annu Rev Biochem. 2017;86:193-224. DC Proteasome DR KEGG; map03050; CC The immunoproteasome is a specialist form of the eukaryote 20S CC proteasome [1] in which the three catalytic beta subunits are replaced CC by three different catalytic beta subunits known as beta1i (beta CC type-9), beta2i (beta type-10) and beta5i (beta type-8) [2]. Interferon CC gamma induces production of these subunits as well as the down-regulation CC of production of the usual beta1, beta2 and beta5 subunits. The CC interferon-induced subunits have modified specificities and the CC immunoproteasome generates peptides that act as ligands for the CC major histocompatibility complex [3]. -- SN 1 ID proteasome subunit alpha type-1 DN Proteasome subunit alpha 1 RQ 1 EV IPR035144; PTHR11599:SF12; sufficient; TG GO:0000502; -- SN 2 ID Proteasome subunit alpha type-2 DN Proteasome subunit alpha2 RQ 1 EV IPR034644; PTHR11599:SF16; sufficient; TG GO:0000502; -- SN 3 ID Proteasome subunit alpha type-3 DN Proteasome subunit alpha 3 RQ 1 EV IPR037555; PTHR11599:SF10; sufficient; TG GO:0000502; -- SN 4 ID Proteasome subunit alpha type-4 DN Proteasome subunit alpha4 RQ 1 EV IPR034647; PTHR11599:SF13; sufficient; TG GO:0000502; -- SN 5 ID Proteasome subunit alpha type-5 DN Proteasome subunit alpha5 RQ 1 EV IPR033812; cd03753; sufficient; TG GO:0000502; -- SN 6 ID Proteasome subunit alpha type-6 DN Proteasome subunit alpha6 RQ 1 EV IPR034642; PTHR11599:SF11; sufficient; TG GO:0000502; EV IPR034642; cd03754; sufficient; TG GO:0000502; -- SN 7 ID Proteasome subunit alpha type-7 DN Proteasome subunit alpha 7 RQ 1 EV IPR035190; PTHR11599:SF40; sufficient; TG GO:0000502; EV IPR037560; PTHR11599:SF15; sufficient; TG GO:0000502; -- SN 8 ID Proteasome subunit beta type-1 DN Proteasome subunit beta 1 RQ 1 EV IPR035202; PTHR11599:SF59; sufficient; TG GO:0000502; -- SN 9 ID Proteasome subunit beta type-2 DN Proteasome subunit beta 2 RQ 1 EV IPR035206; PTHR11599:SF6; sufficient; TG GO:0000502; -- SN 10 ID Proteasome subunit beta type-3 DN Proteasome beta 3 subunit RQ 1 EV IPR033811; PTHR11599:SF62; sufficient; TG GO:0000502; EV IPR033811; cd03759; sufficient; TG GO:0000502; -- SN 11 ID Proteasome subunit beta type-4 DN Proteasome endopeptidase complex, beta subunit RQ 1 EV IPR016295; PTHR11599:SF5; sufficient; TG GO:0000502; EV IPR016295; PIRSF001213; sufficient; TG GO:0000502; EV IPR016295; cd03760; sufficient; TG GO:0000502; -- SN 12 ID Proteasome subunit beta type-8 DN Proteasome subunit beta type-8 (EC 3.4.25.1) RQ 1 EV IPR035705; PTHR11599:SF53; sufficient; TG GO:0000502; TG GO:0043161; -- SN 13 ID Proteasome subunit beta type-9 DN Proteasome subunit beta type-9 (EC 3.4.25.1) RQ 1 EV IPR034383; PTHR11599:SF50; sufficient; TG GO:0000502; TG GO:0043161; -- SN 14 ID Proteasome subunit beta type-10 DN Proteasome subunit beta type 10 (EC 3.4.25.1) RQ 1 EV IPR034384; PTHR11599:SF41; sufficient; TG GO:0000502; TG GO:0043161; // AC GenProp2015 DE Thymoproteasome TP COMPLEX AU Rawlings ND TH 12 RN [1] RM 11265247 RT Antigen processing by the proteasome. RA Kloetzel PM; RL Nat Rev Mol Cell Biol. 2001;2:179-188. RN [2] RM 17540904 RT Regulation of CD8+ T cell development by thymus-specific proteasomes. RA Murata S; Sasaki K; Kishimoto T; Niwa S; Hayashi H; Takahama Y; Tanaka K; RL Science 2007;316:1349-1353. RN [3] RM 12015144 RT The structure of the mammalian 20S proteasome at 2.75 A resolution. RA Unno M; Mizushima T; Morimoto Y; Tomisugi Y; Tanaka K; Yasuoka N; RA Tsukihara T; RL Structure 2002;10:609-618. RN [4] RM 28460188 RT Proteasomal and Autophagic Degradation Systems. RA Dikic I; RL Annu Rev Biochem. 2017;86:193-224. DC Proteasome DR KEGG; map03050; CC The thymooproteasome is a specialist form of the immunoproteasome [1] in CC which the beta5i component (also known as beta type-8) is replaced by CC beta5t (also known as beta type-11)[2]. -- SN 1 ID proteasome subunit alpha type-1 DN Proteasome subunit alpha 1 RQ 1 EV IPR035144; PTHR11599:SF12; sufficient; TG GO:0000502; EV IPR035144; cd03749; sufficient; TG GO:0000502; -- SN 2 ID Proteasome subunit alpha type-2 DN Proteasome subunit alpha2 RQ 1 EV IPR034644; PTHR11599:SF16; sufficient; TG GO:0000502; -- SN 3 ID Proteasome subunit alpha type-3 DN Proteasome subunit alpha 3 RQ 1 EV IPR037555; PTHR11599:SF10; sufficient; TG GO:0000502; -- SN 4 ID Proteasome subunit alpha type-4 DN Proteasome subunit alpha4 RQ 1 EV IPR034647; PTHR11599:SF13; sufficient; TG GO:0000502; -- SN 5 ID Proteasome subunit alpha type-5 DN Proteasome subunit alpha5 RQ 1 EV IPR033812; cd03753; sufficient; TG GO:0000502; -- SN 6 ID Proteasome subunit alpha type-6 DN Proteasome subunit alpha6 RQ 1 EV IPR034642; PTHR11599:SF11; sufficient; TG GO:0000502; EV IPR034642; cd03754; sufficient; TG GO:0000502; -- SN 7 ID Proteasome subunit alpha type-7 DN Proteasome subunit alpha 7 RQ 1 EV IPR035190; PTHR11599:SF40; sufficient; TG GO:0000502; EV IPR037560; PTHR11599:SF15; sufficient; TG GO:0000502; -- SN 8 ID Proteasome subunit beta type-1 DN Proteasome subunit beta 1 RQ 1 EV IPR035202; PTHR11599:SF59; sufficient; TG GO:0000502; -- SN 9 ID Proteasome subunit beta type-2 DN Proteasome subunit beta 2 RQ 1 EV IPR035206; PTHR11599:SF6; sufficient; TG GO:0000502; EV IPR035206; cd03758; sufficient; TG GO:0000502; -- SN 10 ID Proteasome subunit beta type-3 DN Proteasome beta 3 subunit RQ 1 EV IPR033811; PTHR11599:SF62; sufficient; TG GO:0000502; EV IPR033811; cd03759; sufficient; TG GO:0000502; -- SN 11 ID Proteasome subunit beta type-4 DN Proteasome endopeptidase complex, beta subunit RQ 1 EV IPR016295; PTHR11599:SF5; sufficient; TG GO:0000502; EV IPR016295; PIRSF001213; sufficient; TG GO:0000502; EV IPR016295; cd03760; sufficient; TG GO:0000502; -- SN 12 ID Proteasome subunit beta type-11 DN Proteasome subunit beta type 11 (EC 3.4.25.1) RQ 1 EV IPR034385; PTHR11599:SF48; sufficient; TG GO:0000502; TG GO:0043161; -- SN 13 ID Proteasome subunit beta type-9 DN Proteasome subunit beta type-9 (EC 3.4.25.1) RQ 1 EV IPR034383; PTHR11599:SF50; sufficient; TG GO:0000502; TG GO:0043161; -- SN 14 ID Proteasome subunit beta type-10 DN Proteasome subunit beta type 10 (EC 3.4.25.1) RQ 1 EV IPR034384; PTHR11599:SF41; sufficient; TG GO:0000502; TG GO:0043161; // AC GenProp2016 DE Mammalian spermatoproteasome TP COMPLEX AU Rawlings ND TH 13 RN [1] RM 12015144 RT The structure of the mammalian 20S proteasome at 2.75 A resolution. RA Unno M; Mizushima T; Morimoto Y; Tomisugi Y; Tanaka K; Yasuoka N; RA Tsukihara T; RL Structure 2002;10:609-618. RN [2] RM 28460188 RT Proteasomal and Autophagy Degradation Systems. RA Dikic I; RL Annu Rev Biochem. 2017;:-. RN [3] RM 24286712 RT The unique functions of tissue-specific proteasomes. RA Kniepert A; Groettrup M; RL Trends Biochem Sci. 2014;39:17-24. RN [4] RM 24668818 RT Characterization of the testis-specific proteasome subunit alpha4s in RT mammals. RA Uechi H, Hamazaki J, Murata S; RL J Biol Chem. 2014;289:12365-12374. RN [5] RM 23706739 RT Acetylation-mediated proteasomal degradation of core histones during RT DNA repair and spermatogenesis. RA Qian MX; Pang Y; Liu CH; Haratake K; Du BY; Ji DY; Wang GF; Zhu QQ; RA Song W; Yu Y; Zhang XX; Huang HT; Miao S; Chen LB; Zhang ZH; Liang YN; RA Liu S; Cha H; Yang D; Zhai Y; Komatsu T; Tsuruta F; Li H; Cao C; Li W; RA Li GH; Cheng Y; Chiba T; Wang L; Goldberg AL; Shen Y; Qiu XB; RL Cell 2013;39:1012-1024. DC Proteasome DR KEGG; map03050; CC The spermatoproteasome is a specialist version of the 20S proteasome CC [1,2] found in the mammalian testis where the alpha4 subunit is replaced CC by the alpha4S subunit [3,4]. The spermatoprotasome degrades histones [5]. CC Ubiquitinated proteins are not degraded. -- SN 1 ID proteasome subunit alpha type-1 DN Proteasome subunit alpha 1 RQ 1 EV IPR035144; PTHR11599:SF12; sufficient; TG GO:0000502; EV IPR035144; cd03749; sufficient; TG GO:0000502; -- SN 2 ID Proteasome subunit alpha type-2 DN Proteasome subunit alpha2 RQ 1 EV IPR034644; PTHR11599:SF16; sufficient; TG GO:0000502; -- SN 3 ID Proteasome subunit alpha type-3 DN Proteasome subunit alpha 3 RQ 1 EV IPR037555; PTHR11599:SF10; sufficient; TG GO:0000502; -- SN 4 ID Proteasome subunit alpha type-7-like/alpha 4s/PSMA8 DN Proteasome subunit alpha type-7-like RQ 1 EV IPR037560; PTHR11599:SF47; sufficient; TG GO:0000502; -- SN 5 ID Proteasome subunit alpha type-5 DN Proteasome subunit alpha5 RQ 1 EV IPR033812; cd03753; sufficient; TG GO:0000502; -- SN 6 ID Proteasome subunit alpha type-6 DN Proteasome subunit alpha6 RQ 1 EV IPR034642; PTHR11599:SF11; sufficient; TG GO:0000502; EV IPR034642; cd03754; sufficient; TG GO:0000502; -- SN 7 ID Proteasome subunit alpha type-7 DN Proteasome subunit alpha type-7 RQ 1 EV IPR035190; PTHR11599:SF40; sufficient; TG GO:0000502; -- SN 8 ID Proteasome subunit beta type-1 DN Proteasome subunit beta 1 RQ 1 EV IPR035202; PTHR11599:SF59; sufficient; TG GO:0000502; -- SN 9 ID Proteasome subunit beta type-2 DN Proteasome subunit beta 2 RQ 1 EV IPR035206; PTHR11599:SF6; sufficient; TG GO:0000502; EV IPR035206; cd03758; sufficient; TG GO:0000502; -- SN 10 ID Proteasome subunit beta type-3 DN Proteasome beta 3 subunit RQ 1 EV IPR033811; PTHR11599:SF62; sufficient; TG GO:0000502; EV IPR033811; cd03759; sufficient; TG GO:0000502; -- SN 11 ID Proteasome subunit beta type-4 DN Proteasome endopeptidase complex, beta subunit RQ 1 EV IPR016295; PTHR11599:SF5; sufficient; TG GO:0000502; EV IPR016295; PIRSF001213; sufficient; TG GO:0000502; EV IPR016295; cd03760; sufficient; TG GO:0000502; -- SN 12 ID Proteasome subunit beta type-5 DN Proteasome subunit beta type-5 (EC 3.4.25.1) RQ 1 EV IPR037558; PTHR11599:SF51; sufficient; TG GO:0000502; TG GO:0043161; -- SN 13 ID Proteasome subunit beta type-6 DN Proteasome subunit beta 6 (EC 3.4.25.1) RQ 1 EV IPR035140; PTHR11599:SF46; sufficient; TG GO:0000502; TG GO:0043161; EV IPR037559; PTHR11599:SF4; sufficient; TG GO:0000502; TG GO:0043161; -- SN 14 ID Proteasome subunit beta type-7 DN Proteasome subunit beta 7 (EC 3.4.25.1) RQ 1 EV IPR035216; PTHR11599:SF42; sufficient; TG GO:0000502; TG GO:0043161; EV IPR035216; PTHR11599:SF44; sufficient; TG GO:0000502; TG GO:0043161; -- SN 15 ID Proteasome activator complex subunit 4 DN Proteasome activator complex subunit 4 RQ 1 EV IPR035309; PTHR32170; sufficient; TG GO:0070628; TG GO:0070577; // AC GenProp2017 DE Gamma secretase TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 28320827 RT Structural and Chemical Biology of Presenilin Complexes. RA Johnson DS, Li YM, Pettersson M, St George-Hyslop PH; RL Cold Spring Harb Perspect Med. 2017; [Epub ahead of print] DC Alzheimer's disease DR KEGG; ko05010; CC Gamma secretase is a complex found in cell membranes and initially CC identified as the peptidase responsible for the gamma, varepsilon and CC zeta cleavages of the transmembrane domains of Type I membrane proteins CC including amyloid precursor protein (APP) and Notch. Release of the CC amyloid beta (A-beta) peptide from APP is an important step in the CC development of Alzheimer's disease and forms the plaques that are CC characteristic of the pathology. Release of the A-beta peptide requires CC two proteolytic cleavages, cleavage by beta-secretase in the extracellular CC domain, and then cleavage at the gamma and epsilon sites by gamma CC secretase. The proteolytic component of gamma secretase is presenilin CC which is an aspartic endopeptidase [1]. -- SN 1 ID Presenilin DN Presenilin RQ 1 EV IPR002031; PTHR10202; sufficient; TG GO:0042500; TG GO:0042987; -- SN 2 ID Gamma-secretase subunit APH-1A DN Gamma-secretase subunit Aph-1 RQ 1 EV IPR009294; PTHR12889; sufficient; EV IPR009294; PF06105; sufficient; TG GO:0043085; -- SN 3 ID Nicastrin DN Nicastrin RQ 1 EV IPR008710; PTHR21092; sufficient; EV IPR008710; PF05450; sufficient; TG GO:0043085; -- SN 4 ID Gamma-secretase subunit PEN-2 DN Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit RQ 1 EV IPR019379; PTHR16318; sufficient; EV IPR019379; PF10251; sufficient; TG GO:0043085; // AC GenProp2018 DE Initiator caspases of the apoptosis extrinsic pathway TP GUILD AU Rawlings ND TH 0 RN [1] RM 14499155 RT Apoptosis: the complex scenario for a silent cell death. RA Bohm I, Schild H; RL Mol Imaging Biol. 2003;5:2-14. RN [2] RM 9006941 RT FLICE induced apoptosis in a cell-free system. Cleavage of caspase RT zymogens. RA Muzio M; Salvesen GS; Dixit VM; RL J Biol Chem. 1997;272:2952-2956. DC Apoptosis DR KEGG; map04210; CC Apoptosis or programmed cell death is the mechanism by which cells CC in eukaryotes are killed. Cysteine endopeptidases known as caspases CC are activated and these deactivate cellular proteins, often by CC cleaving within interdomain regions, thereby separating binding CC domains of signal reception and transduction domains [1]. Caspases CC have a specificity for aspartyl bonds, which occur frequently in CC surface loops and interdomain regions of proteins. Caspases involved CC in apoptosis are of two kinds: initiators and executors. Initiator CC caspases activate the executor caspases which cleave other proteins CC in the cell [2]. There are at least four routes by which the CC initiator caspase precursors are activated. This Genome Property CC includes the extrinsic pathway initiator caspases. -- SN 1 ID Caspase-8 DN Caspase-8 (EC:3.4.22.61) RQ 1 EV IPR033170; PTHR10454:SF162; sufficient; TG GO:0097199; -- SN 2 ID Caspase-10 DN Caspase-10 (EC:3.4.22.63) RQ 1 EV IPR035701; PTHR10454:SF26; sufficient; TG GO:0097199; // AC GenProp2019 DE Executor caspases of apoptosis TP GUILD AU Rawlings ND TH 0 RN [1] RM 14499155 RT Apoptosis: the complex scenario for a silent cell death. RA Bohm I, Schild H; RL Mol Imaging Biol. 2003;5:2-14. RN [2] RM 21456965 RT Caspase substrates and cellular remodeling. RA Crawford ED; Wells JA; RL Annu Rev Biochem. 2001;80:1055-1087. RN [3] RM 9852092 RT Granzyme B mimics apical caspases. Description of a unified pathway RT for trans-activation of executioner caspase-3 and -7. RA Yang X; Stennicke HR; Wang B; Green DR; Jänicke RU; Srinivasan A; RA Seth P; Salvesen GS; Froelich CJ; RL J Biol Chem. 1998;273:34278-34283. RN [4] RM 8900201 RT The Ced-3/interleukin 1beta converting enzyme-like homolog Mch6 and RT the lamin-cleaving enzyme Mch2alpha are substrates for the apoptotic RT mediator CPP32. RA Srinivasula SM; Fernandes-Alnemri T; Zangrilli J; Robertson N; RA Armstrong RC; Wang L; Trapani JA; Tomaselli KJ; Litwack G; Alnemri RA ES; RL J Biol Chem. 1998;271:27099-27106. DC Apoptosis DR KEGG; map04210; CC Apoptosis or programmed cell death is the mechanism by which cells CC in eukaryotes are killed. Cysteine endopeptidases known as caspases CC are activated and these deactivate cellular proteins, often by CC cleaving within interdomain regions, thereby separating binding CC domains or signal reception and transduction domains [1]. Caspases have CC a specificity for aspartyl bonds, which occur frequently in surface CC loops and interdomain regions of proteins [2]. Caspases involved in CC apoptosis are of two kinds: initiators and executors. Initiator CC caspases activate the executor caspases which cleave other proteins CC in the cell [3,4]. This Genome Property includes the executor CC caspases. -- SN 1 ID Caspase-3/7 DN Caspase-3/7 (EC:3.4.22.-) RQ 1 EV IPR015471; PTHR10454:SF31; sufficient; TG GO:0097200; -- SN 3 ID Caspase-6 DN Caspase-6 (EC:3.4.22.59) RQ 1 EV IPR037554; PTHR10454:SF164; sufficient; TG GO:0097200; // AC GenProp2021 DE Apoptosome TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 14499155 RT Apoptosis: the complex scenario for a silent cell death. RA Bohm I, Schild H; RL Mol Imaging Biol. 2003;5:2-14. RN [2] RM 21456965 RT Caspase substrates and cellular remodeling. RA Crawford ED; Wells JA; RL Annu Rev Biochem. 2001;80:1055-1087. RN [3] RM 26543158 RT Atomic structure of the apoptosome: mechanism of cytochrome c- and RT dATP-mediated activation of Apaf-1. RA Zhou M; Li Y; Hu Q; Bai XC; Huang W; Yan C; Scheres SH; Shi Y; RL Genes Dev. 2015;29:2349-2361. DC Apoptosis DR KEGG; map04210; CC Apoptosis or programmed cell death is the mechanism by which cells CC in eukaryotes are killed. Cysteine endopeptidases known as caspases CC are activated and these deactivate cellular proteins, often by CC cleaving within interdomain regions, thereby separating binding CC domains of signal reception and transduction domains [1]. Caspases have CC a specificity for aspartyl bonds, which occur frequently in surface CC loops and interdomain regions of proteins [2]. Caspases involved in CC apoptosis are of two kinds: initiators and executors. Initiator CC caspases activate the executor caspases which cleave other proteins CC in the cell. There are at least four routes by which the initiator CC caspase precursors are activated. This Genome Property includes CC the apoptosome, which includes the precursor of initiator caspase 9 CC from the intrinsic (or mitochondrial) pathway [3]. When it binds CC cytochrome c and dATP, Apaf1 oligomerizes into a heptameric ring. -- SN 1 ID Cytochrome c DN Cytochrome c RQ 1 EV IPR002327; PTHR11961; sufficient; TG GO:0008635; -- SN 2 ID Apoptotic protease-activating factor 1 DN Apoptotic protease-activating factor 1 RQ 1 EV IPR017251; PIRSF037646; sufficient; TG GO:0006919; -- SN 3 ID Caspase-9 DN Caspase-9 (EC:3.4.22.62) RQ 1 EV IPR033171; PTHR10454:SF157; sufficient; TG GO:0006919; // AC GenProp2026 DE KICSTOR complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 28199306 RT KICSTOR recruits GATOR1 to the lysosome and is necessary for RT nutrients to regulate mTORC1. RA Wolfson RL; Chantranupong L; Wyant GA; Gu X; Orozco JM; Shen K; RA Condon KJ; Petri S; Kedir J; Scaria SM; Abu-Remaileh M; Frankel WN; RA Sabatini DM; RL Nature. 2017;543:438-442. DC mTOR signaling pathway DR KEGG; map04150; CC The KICSTOR complex functions in the TORC1 signaling pathway and is CC an amino acid-sensor. In the absence of amino acids, KICSTOR CC recruits the GATOR1 complex to lysosomal membranes and permits CC interaction with GATOR2 and the RAG GTPases. This negatively CC regulates mTORC1 signaling. In the absence of KICSTOR, mTORC1 is CC localized to the lysosome and activated. The mTORC1 complex is a CC regulator of cell growth [1]. -- SN 1 ID KICSTOR complex protein kaptin DN KICSTOR complex protein kaptin/1 RQ 1 EV IPR029982; PTHR15435; sufficient; TG GO:1904262; TG GO:0034198; -- SN 2 ID KICSTOR complex protein ITFG2 DN KICSTOR complex protein ITFG2/2 RQ 1 EV IPR031793; PF15907; sufficient; TG GO:1904262; TG GO:0034198; -- SN 3 ID KICSTOR complex protein C12orf66 DN KICSTOR complex protein C12orf66/3 RQ 1 EV IPR018544; PF09404; sufficient; TG GO:1904262; TG GO:0034198; -- SN 4 ID KICSTOR complex protein SZT2 DN KICSTOR complex protein SZT2/4 RQ 1 EV IPR033228; PTHR14918; sufficient; TG GO:1904262; TG GO:0034198; // AC GenProp2028 DE GATOR1 complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 23723238 RT A Tumor suppressor complex with GAP activity for the Rag GTPases RT that signal amino acid sufficiency to mTORC1. RA Bar-Peled L; Chantranupong L; Cherniack AD; Chen WW; Ottina KA; RA Grabiner BC; Spear ED; Carter SL; Meyerson M; Sabatini DM; RL Science. 2013;340:1100-1106. DC mTOR signaling pathway DR KEGG; map04150; CC The GATOR1 complex inhibits the amino acid-sensing branch of the CC TORC1 pathway by leading to the release of mTORC1 from the CC lysosomal surface [1]. -- SN 1 ID GATOR complex protein DEPDC5 DN GATOR complex protein DEPDC5 /1 RQ 1 EV IPR027244; PF12257; sufficient; TG GO:0005096; -- SN 2 ID GATOR complex protein NPRL2 DN GATOR complex protein NPRL2 /2 RQ 1 EV IPR009348; PF06218; sufficient; TG GO:0005096; -- SN 3 ID GATOR complex protein NPRL3 DN GATOR complex protein NPRL3/3 RQ 1 EV IPR005365; PF03666; sufficient; TG GO:0005096; // AC GenProp2029 DE GATOR2 complex TP COMPLEX AU Rawlings ND TH 2 RN [1] RM 23723238 RT A Tumor suppressor complex with GAP activity for the Rag GTPases RT that signal amino acid sufficiency to mTORC1. RA Bar-Peled L; Chantranupong L; Cherniack AD; Chen WW; Ottina KA; RA Grabiner BC; Spear ED; Carter SL; Meyerson M; Sabatini DM; RL Science. 2013;340:1100-1106. DC mTOR signaling pathway DR KEGG; map04150; CC The GATOR2 subcomplex inhibits the GATOR1 subcomplex, thereby CC activating the TORC1 pathway [1]. -- SN 1 ID GATOR complex protein WDR24 DN GATOR complex protein WDR24 RQ 1 EV IPR037590; PTHR22850:SF131; sufficient; TG GO:0032008; -- SN 2 ID GATOR complex protein WDR59 DN GATOR complex protein WDR59 RQ 1 EV IPR037591; PTHR22850:SF116; sufficient; TG GO:0032008; -- SN 3 ID GATOR complex protein MIOS DN GATOR complex protein MIOS RQ 1 EV IPR037593; PTHR16453:SF9; sufficient; TG GO:0032008; -- SN 4 ID Protein SEC13 homolog DN Protein SEC13 homolog RQ 1 EV IPR037596; PTHR11024:SF2; sufficient; TG GO:0032008; -- SN 5 ID Nucleoporin SEH1 DN Nucleoporin SEH1 RQ 1 EV IPR037597; PTHR11024:SF3; sufficient; TG GO:0032008; // AC GenProp2030 DE mTORC1 complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 12150925 RT mTOR interacts with raptor to form a nutrient-sensitive complex RT that signals to the cell growth machinery. RA Kim DH; Sarbassov DD; Ali SM; King JE; Latek RR; RA Erdjument-Bromage H; Tempst P; Sabatini DM; RL Cell. 2002;110:163-175. RN [2] RM 18497260 RT The Rag GTPases bind raptor and mediate amino acid signaling to RT mTORC1. RA Sancak Y; Peterson TR; Shaul YD; Lindquist RA; Thoreen CC; RA Bar-Peled L; Sabatini DM; RL Science. 2008;320:1496-1501. RN [3] RM 12718876 RT GbetaL, a positive regulator of the rapamycin-sensitive pathway RT required for the nutrient-sensitive interaction between raptor RT and mTOR. RA Kim DH; Sarbassov DD; Ali SM; Latek RR; Guntur KV; RA Erdjument-Bromage H; Tempst P; Sabatini DM; RL Mol Cell. 2003;11:895-904. RN [4] RM 17386266 RT PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein RT kinase. RA Sancak Y; Thoreen CC; Peterson TR; Lindquist RA; Kang SA; RA Spooner E; Carr SA; Sabatini DM; RL Mol Cell. 2007;25:903-915. RN [5] RM 19446321 RT DEPTOR is an mTOR inhibitor frequently overexpressed in RT multiple myeloma cells and required for their survival. RA Peterson TR; Laplante M; Thoreen CC; Sancak Y; Kang SA; RA Kuehl WM; Gray NS; Sabatini DM; RL Cell. 2009;137:873-886. DC mTOR signaling pathway DR KEGG; map04150; CC mTORC1 (mammalian target of rapamycin complex 1 or mechanistic CC target of rapamycin complex 1) is a nutrient sensor which CC controls protein synthesis by activating protein translation [1]. CC Protein synthesis requires a supply of amino acids, an energy CC source, oxygen abundance and the required growth factors. When CC these conditons are met, Rag GTPase heterodimers are activated, CC interact with Raptor, and mTORC1 is localized to the lysosomal CC membrane surface where it can interact with the G protein Rheb CC and ATP [2, 3]. The pathway is controlled by two complexes that CC interact with the Rag GTPase, GATOR1 (inhibitor) and GATOR2 CC (activator) [4]. -- SN 1 ID Serine/threonine-protein kinase mTOR DN Serine/threonine-protein kinase mTOR (EC:2.7.11.1) RQ 1 EV IPR026683; PTHR11139:SF9; sufficient; TG GO:0004674; -- SN 2 ID Regulatory-associated protein of mTOR DN Regulatory-associated protein of mTOR RQ 1 EV IPR004083; PTHR12848; sufficient; -- SN 3 ID Target of rapamycin complex subunit LST8 DN Target of rapamycin complex subunit LST8 RQ 1 EV IPR037588; PTHR19842; sufficient; TG GO:0032008; -- SN 4 ID Proline-rich AKT1 substrate 1 DN Proline-rich AKT1 substrate 1 RQ 1 EV IPR026682; PF15798; sufficient; TG GO:0032007; -- SN 5 ID DEP domain-containing mTOR-interacting protein DN DEP domain-containing mTOR-interacting protein RQ 1 EV IPR037589; PTHR22829:SF18; sufficient; TG GO:0032007; // AC GenProp2031 DE Ragulator complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 20381137 RT Ragulator-Rag complex targets mTORC1 to the lysosomal surface RT and is necessary for its activation by amino acids. RA Sancak Y; Bar-Peled L; Zoncu R; Markhard AL; Nada S; RA Sabatini DM; RL Cell. 2010;141:290-303. RN [2] RM 22980980 RT Ragulator is a GEF for the rag GTPases that signal amino acid RT levels to mTORC1. RA Bar-Peled L; Schweitzer LD; Zoncu R; Sabatini DM; RL Cell. 2012;150:1196-1208. DC mTOR signaling pathway DR KEGG; map04150; CC The Ragulator complex is required for the activation of the CC mTORC1 sensor complex, which promotes protein synthesis when CC there is sufficient energy and amino acids [1]. Ragulator CC functions as a guanine nucleotide exchange factor and activates CC the small GTPases Rag [2]. -- SN 1 ID Ragulator complex protein LAMTOR1 DN Ragulator complex protein LAMTOR1 RQ 1 EV IPR026310; PTHR13401; sufficient; TG GO:0051020; -- SN 2 ID Ragulator complex protein LAMTOR2 DN Ragulator complex protein LAMTOR2 RQ 1 EV IPR037587; PTHR13323; sufficient; TG GO:0032008; -- SN 3 ID Ragulator complex protein LAMTOR3 DN Ragulator complex protein LAMTOR3 RQ 1 EV IPR015019; PTHR13378; sufficient; TG GO:0032008; -- SN 4 ID Ragulator complex protein LAMTOR4 DN Ragulator complex protein LAMTOR4 RQ 1 EV IPR034601; PTHR33967; sufficient; TG GO:0032008; -- SN 5 ID Ragulator complex protein LAMTOR5 DN Ragulator complex protein LAMTOR5 RQ 1 EV IPR024135; PTHR13342; sufficient; TG GO:0032008; // AC GenProp2032 DE Rag complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 23723238 RT A Tumor suppressor complex with GAP activity for the Rag GTPases RT that signal amino acid sufficiency to mTORC1. RA Bar-Peled L; Chantranupong L; Cherniack AD; Chen WW; Ottina KA; RA Grabiner BC; Spear ED; Carter SL; Meyerson M; Sabatini DM; RL Science. 2013;340:1100-1106. RN [2] RM 20381137 RT Ragulator-Rag complex targets mTORC1 to the lysosomal surface RT and is necessary for its activation by amino acids. RA Sancak Y; Bar-Peled L; Zoncu R; Markhard AL; Nada S; RA Sabatini DM; RL Cell. 2010;141:290-303. DC mTOR signaling pathway DR KEGG; map04150; CC The RAG complex is a component of the the TORC1 sensor pathway CC which promotes protein synthesis in the presence of adequate CC energy and amino acids. The heterodimeric Rag complex CC alternates between an active ATP-bound form and an inactive GDP- CC bound form [1]. When active, the Rag complex relocalizes the CC mTORC1 complex to the lysosome membrane surface, where it is CC activated by the GTPase Rheb [2]. Activity of the RAG complex is CC controlled by the GATOR1 and GATOR2 complexes. -- SN 1 ID Ras-related GTP-binding protein A/B DN RagA-like RQ 1 EV IPR039397; cd11384; sufficient; TG GO:0003924; -- SN 2 ID Ras-related GTP-binding protein C/D DN RagC-like RQ 1 EV IPR039400; cd11385; sufficient; TG GO:0003924; // AC GenProp2033 DE mTORC1 activation TP METAPATH AU Rawlings ND TH 1 RN [1] RM 12271141 RT Tuberous sclerosis complex-1 and -2 gene products function RT together to inhibit mammalian target of rapamycin (mTOR)-mediated RT downstream signaling. RA Tee AR; Fingar DC; Manning BD; Kwiatkowski DJ; Cantley LC; RA Blenis J; RL Proc Natl Acad Sci U S A. 2002;99:13571-13576. RN [2] RM 15340059 RT Biochemical and functional characterizations of small GTPase Rheb RT and TSC2 GAP activity. RA Li Y; Inoki K; Guan KL; RL Mol Cell Biol. 2004;24:7965-7975. RN [3] RM 12869586 RT Rheb GTPase is a direct target of TSC2 GAP activity and regulates RT mTOR signaling. RA Inoki K; Li Y; Xu T; Guan KL; RL Genes Dev. 2003;17:1829-1834. DC mTOR signaling pathway DR KEGG; map04150; CC The mTORC1 complex is a sensor detecting energy levels and amino CC acid abundance. Once activated, the mTORC1 complex leads to CC protein synthesis. Activation of mTORC1 occurs on the surface CC of the lysosome membrane [1,2,3]. -- SN 1 ID Hamartin DN Hamartin (TSC1) RQ 1 EV IPR007483; PTHR15154; sufficient; TG GO:0051087; -- SN 2 ID Tuberin DN Tuberin (TSC2) RQ 1 EV IPR003913; PR01431; sufficient; TG GO:0005096; -- SN 3 ID GTP-binding protein Rheb DN GTP-binding protein Rheb RQ 1 EV IPR037586; PTHR24070:SF264; sufficient; TG GO:0005525; -- SN 4 ID mTORC1 complex DN mTORC1 complex RQ 1 EV GenProp2030; -- SN 5 ID Rag complex DN Rag complex RQ 1 EV GenProp2032; -- SN 6 ID GATOR1 complex DN GATOR1 complex RQ 1 EV GenProp2028; -- SN 7 ID GATOR2 complex DN GATOR2 complex RQ 1 EV GenProp2029; -- SN 8 ID Ragulator complex DN Ragulator complex RQ 1 EV GenProp2031; // AC GenProp2034 DE eIF4F complex TP COMPLEX AU Rawlings ND TH 2 RN [1] RM 9372926 RT Human eukaryotic translation initiation factor 4G (eIF4G) possesses RT two separate and independent binding sites for eIF4A. RA Imataka H; Sonenberg N; RL Mol Cell Biol. 1997;17:6940-6947. RN [2] RM 19204291 RT Crystal structure of the eIF4A-PDCD4 complex. RA Chang JH; Cho YH; Sohn SY; Choi JM; Kim A; Kim YC; Jang SK; Cho Y; RL Proc Natl Acad Sci U S A. 2009;106:3148-3153. RN [3] RM 16271312 RT Structural basis for mRNA Cap-Binding regulation of eukaryotic RT initiation factor 4E by 4E-binding protein, studied by spectroscopic, RT X-ray crystal structural, and molecular dynamics simulation methods. RA Tomoo K; Matsushita Y; Fujisaki H; Abiko F; Shen X; Taniguchi T; RA Miyagawa H; Kitamura K; Miura K; Ishida T; RL Proc Natl Acad Sci U S A. 2009;106:3148-3153. RN [4] RM 9418880 RT A novel functional human eukaryotic translation initiation factor 4G. RA Gradi A; Imataka H; Svitkin YV; Rom E; Raught B; Morino S; Sonenberg N; RL Mol Cell Biol. 1998;18:334-342. DC RNA transport DR KEGG; map03013; CC Eukaryote initiation factor 4F (eI4F) is a complex involved in CC protein translation [1,4]. It recognizes the mRNA cap, recruits mRNA to CC the ribosome and unwinds 5'-terminal secondary structure in an ATP- CC dependent manner [3]. The composition of the complex varies with the CC external and internal conditions. -- SN 1 ID Eukaryotic initiation factor 4A DN Eukaryotic initiation factor 4A (EC:3.6.4.13) RQ 1 EV IPR037583; PTHR24031:SF226; sufficient; TG GO:0004004; -- SN 2 ID Eukaryotic translation initiation factor 4 gamma 1 DN Eukaryotic translation initiation factor 4 gamma 1 RQ 1 EV IPR037584; PTHR23253:SF10; sufficient; TG GO:0008190; -- SN 3 ID Eukaryotic translation initiation factor 4 gamma 3 DN Eukaryotic translation initiation factor 4 gamma 3 RQ 1 EV IPR037585; PTHR23253:SF23; sufficient; TG GO:0000339; -- SN 4 ID Eukaryotic translation initiation factor 4E DN Eukaryotic translation initiation factor 4E RQ 1 EV IPR001040; PTHR11960; sufficient; TG GO:0000339; // AC GenProp2035 DE mTORC1 pathway TP METAPATH AU Rawlings ND TH 1 RN [1] RM 7935836 RT Insulin-dependent stimulation of protein synthesis by RT phosphorylation of a regulator of 5'-cap function. RA Pause A; Belsham GJ; Gingras AC; Donzé O; Lin TA; Lawrence JC Jr; RA Sonenberg N; RL Nature. 1994;371:762-767. RN [2] RM 14673156 RT mTOR controls cell cycle progression through its cell growth RT effectors S6K1 and 4E-BP1/eukaryotic translation initiation RT factor 4E. RA Fingar DC; Richardson CJ; Tee AR; Cheatham L; Tsou C; Blenis J; RL Mol Cell Biol. 2004;24:200-216. DC mTOR signaling pathway DR KEGG; map04150; CC The mTORC1 (mammalian target of rapamycin) complex is a sensor CC detecting energy levels and amino acid abundance. Once activated, CC the mTORC1 complex leads to protein synthesis [1]. Activation of CC mTORC1 occurs on the surface of the lysosome membrane. The mTORC1 CC complex leads to activation of eukaryote initiation factor 4F via CC S6K1, and removes inhibition by EIF4EBP1. EIF4EBP1 prevents CC assembly of the eIF4F complex [2]. -- SN 1 ID mTORC1 complex DN mTORC1 complex RQ 1 EV GenProp2030; -- SN 2 ID Eukaryotic translation initiation factor 4E-binding protein 1 DN Eukaryotic translation initiation factor 4E-binding protein 1 RQ 1 EV IPR037582; PTHR12669:SF14; sufficient; TG GO:0008190; -- SN 3 ID Ribosomal protein S6 kinase beta-1 DN Ribosomal protein S6 kinase beta-1 (EC:2.7.11.1) RQ 1 EV IPR016238; PIRSF000605; sufficient; TG GO:0004674; -- SN 4 ID eI4F complex DN eI4F complex RQ 1 EV GenProp2034; // AC GenProp2036 DE Nuclear pore complex, vertebrate TP COMPLEX AU Rawlings ND TH 3 RN [1] RM 15229283 RT Nucleoporins as components of the nuclear pore complex core RT structure and Tpr as the architectural element of the nuclear RT basket. RA Krull S; Thyberg J; Björkroth B; Rackwitz HR; Cordes VC; RL Mol Biol Cell. 2004;15:4261-4277. RN [2] RM 11684705 RT Novel vertebrate nucleoporins Nup133 and Nup160 play a role in RT mRNA export. RA Vasu S; Shah S; Orjalo A; Park M; Fischer WH; Forbes DJ; RL J. Cell Biol. 2001;155:339-354. RN [3] RM 18287282 RT Structural constraints on autoprocessing of the human nucleoporin RT Nup98. RA Sun Y; Guo HC; RL Protein Sci. 2008;17:494-505. RN [4] RM 12552102 RT Depletion of a single nucleoporin, Nup107, prevents the assembly RT of a subset of nucleoporins into the nuclear pore complex. RA Boehmer T; Enninga J; Dales S; Blobel G; Zhong H; RL Proc. Natl. Acad. Sci. U.S.A. 2003;100:981-985. RN [5] RM 11564755 RT An evolutionarily conserved NPC subcomplex, which redistributes RT in part to kinetochores in mammalian cells. RA Belgareh N; Rabut G; Baï SW; van Overbeek M; Beaudouin J; RA Daigle N; Zatsepina OV; Pasteau F; Labas V; Fromont-Racine M; RA Ellenberg J; Doye V; RL J Cell Biol. 2001;154:1147-1160. RN [6] RM 12802065 RT Direct interaction with nup153 mediates binding of Tpr to the RT periphery of the nuclear pore complex. RA Hase ME; Cordes VC; RL Mol Biol Cell. 2003;14:1923-1940. RN [7] RM 9864356 RT Functional analysis of Tpr: identification of nuclear pore complex RT association and nuclear localization domains and a role in mRNA RT export. RA Bangs P; Burke B; Powers C; Craig R; Purohit A; Doxsey S; RL J Cell Biol. 1998;143:1801-1812. DC RNA transport DR KEGG; map03013; CC The vertebrate nuclear pore complex (NPC) has eight-fold radial CC symmetry. The core complex consists of globular subunits that CC are sandwiched between two coaxial ring-like structures. The CC ring facing the nuclear interior is capped by a fibrous structure CC called the nuclear basket [1]. NUP160, NUP133, NUP107 and NUP96 CC form the Nup160 subcomplex [4,5], which plays a role in RNA export CC and tethering NUP98 and NUP153 to the nucleus [2]. Nup98 must CC process itself autoproteolytically [3]. Tpr forms the nuclear CC basket. The Tpr N terminus interacts with NUP153 in the NPC [6] CC while the acidic C terminus is transported into the nuclear CC interior, where is interacts with soluble transport factors and CC can mediate export of macromolecules from the nucleus [7]. -- SN 1 ID Nuclear pore complex protein Nup98-Nup96 DN Nuclear pore complex protein Nup98-Nup96 RQ 1 EV IPR037637; PTHR23198:SF6; sufficient; TG GO:0017056 -- SN 2 ID Nuclear pore complex protein Nup107 DN Nuclear pore protein 84/107 RQ 1 EV IPR007252; PF04121; sufficient; EV IPR007252; PTHR13003; sufficient; TG GO:0017056; -- SN 3 ID Nuclear pore complex protein Nup133 DN Nuclear pore complex protein Nup133-like RQ 1 EV IPR037624; PTHR13405; sufficient; TG GO:0017056; -- SN 4 ID Nuclear pore complex protein Nup160 DN Nucleoporin Nup120/160 RQ 1 EV IPR021717; PF11715; sufficient; TG GO:0031080; -- SN 5 ID Nuclear pore complex protein Nup153 DN Nuclear pore complex protein Nup153 RQ 1 EV IPR037625; PTHR23193:SF31; sufficient; TG GO:0017056; -- SN 6 ID Nucleoprotein TPR DN Nucleoprotein TPR/MLP1 RQ 1 EV IPR012929; PF07926; sufficient; TG GO:0044615; // AC GenProp2037 DE Nuclear pore subcomplex Nup107-160 TP COMPLEX AU Rawlings ND TH 4 RN [1] RM 15146057 RT The entire Nup107-160 complex, including three new members, is RT targeted as one entity to kinetochores in mitosis. RA Loïodice I; Alves A; Rabut G; Van Overbeek M; Ellenberg J; RA Sibarita JB; Doye V; RL Mol Biol Cell. 2004;15:3333-44. RN [2] RM 17363900 RT The human Nup107-160 nuclear pore subcomplex contributes to RT proper kinetochore functions. RA Zuccolo M; Alves A; Galy V; Bolhy S; Formstecher E; Racine V; RA Sibarita JB; Fukagawa T; Shiekhattar R; Yen T; Doye V; RL EMBO J. 2007;26:1853-1864. RN [3] RM 17360435 RT Cell-cycle-dependent phosphorylation of the nuclear pore RT Nup107-160 subcomplex. RA Glavy JS; Krutchinsky AN; Cristea IM; Berke IC; Boehmer T; RA Blobel G; Chait BT; RL Proc Natl Acad Sci U S A. 2007;104:3811-3816. DC RNA transport DR KEGG; map03013; CC The Nup107-160 subcomplex of the nuclear pore complex (NPC) CC consists of NUP160, NUP133, NUP107, NUP98, NUP85, NUP43, NUP37, CC SEH1 and SEC13. This subcomplex is required for the assembly of CC a functional NPC [1]. This subcomplex is also required for CC normal kinetochore microtubule attachment, mitotic progression CC and chromosome segregation [2]. Phosphorylation of the CC subcomplex regulates its association with the NPC and other CC proteins [3]. -- SN 1 ID Nucleoporin Nup37 DN Nucleoporin Nup37 RQ 1 EV IPR037626; PTHR22806; sufficient; TG GO:0031080 -- SN 2 ID Nucleoporin Nup43 DN Nucleoporin Nup43 RQ 1 EV IPR037628; PTHR22652; sufficient; TG GO:0031080 -- SN 3 ID Nuclear pore complex protein Nup85 DN Nucleoporin Nup85-like RQ 1 EV IPR011502; PF07575; sufficient; EV IPR011502; PTHR13373; sufficient; TG GO:0017056 -- SN 4 ID Nuclear pore complex protein Nup98-Nup96 DN Nuclear pore complex protein NUP98-NUP96 RQ 1 EV IPR037637; PTHR23198:SF6; sufficient; TG GO:0017056 -- SN 5 ID Nuclear pore complex protein Nup107 DN Nuclear pore protein 84/107 RQ 1 EV IPR007252; PF04121; sufficient; EV IPR007252; PTHR13003; sufficient; TG GO:0017056; -- SN 6 ID Nuclear pore complex protein Nup133 DN Nuclear pore complex protein Nup133-like RQ 1 EV IPR037624; PTHR13405; sufficient; TG GO:0017056; -- SN 7 ID Nuclear pore complex protein Nup160 DN Nucleoporin Nup120/160 RQ 1 EV IPR021717; PF11715; sufficient; TG GO:0031080; -- SN 8 ID Nucleoporin SEH1 DN Nucleoporin Seh1 RQ 1 EV IPR037597; PTHR11024:SF3; sufficient; TG GO:0006999; -- SN 9 ID Protein SEC13 homolog DN Protein Sec13 RQ 1 EV IPR037596; PTHR11024:SF2; sufficient; TG GO:0031080; // AC GenProp2038 DE Microsomal signal peptidase complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 1846444 RT Yeast signal peptidase contains a glycoprotein and the Sec11 RT gene product. RA YaDeau JT; Klein C; Blobel G; RL Proc Natl Acad Sci U S A. 1991;88:517-521. RN [2] RM 9148931 RT The yeast SPC22/23 homolog Spc3p is essential for signal RT peptidase activity. RA Meyer HA; Hartmann E; RL J Biol Chem. 1997;272:13159-13164. RN [3] RM 14559916 RT Genetic complementation in yeast reveals functional RT similarities between the catalytic subunits of mammalian RT signal peptidase complex. RA Liang H; VanValkenburgh C; Chen X; Mullins C; Van Kaer L; RA Green N; Fang H; RL J Biol Chem. 2003;278:50932-50939. DC Protein export DR KEGG; map03060; CC Microsomal signal peptidase removes signal peptides from CC newly transcribed proteins that are destined for entry into CC the secretory pathway. Microsomal signal peptidase is a CC complex consisting of SEC11A, SEC11C, SPCS1, SPCS2 and SPCS3. CC In the yeast Saccharomyces cerevisiae, there is only one CC SEC11 component [1,2]. SEC11A and SEC11C are both serine CC endopeptidases with overlapping specificities [3]. -- SN 1 ID Signal peptidase complex catalytic subunit SEC11A DN Signal peptidase complex catalytic subunit SEC11A RQ 1 EV IPR037712; PTHR10806:SF8; sufficient; TG GO:0031080 -- SN 2 ID Signal peptidase complex catalytic subunit SEC11C DN Signal peptidase complex catalytic subunit SEC11C RQ 0 EV IPR037710; PTHR10806:SF12; sufficient; TG GO:0006465 -- SN 3 ID Signal peptidase complex subunit 1 DN Signal peptidase complex subunit 1 RQ 1 EV IPR037713; PTHR13202:SF0; sufficient; TG GO:0005787 -- SN 4 ID Signal peptidase complex subunit 2 DN Signal peptidase complex subunit 2 RQ 1 EV IPR009582; PF06703; sufficient; EV IPR009582; PTHR13085; sufficient; TG GO:0005787 -- SN 5 ID Signal peptidase complex subunit 3 DN Signal peptidase complex subunit 3 RQ 1 EV IPR007653; PF04573; sufficient; EV IPR007653; PIRSF016089; sufficient; EV IPR007653; PTHR12804; sufficient; TG GO:0005787; // AC GenProp2039 DE Mitochondrial protein processing TP SYSTEM AU Rawlings ND TH 1 RN [1] RM 11470436 RT Crystal structures of mitochondrial processing peptidase RT reveal the mode for specific cleavage of import signal RT sequences. RA Taylor AB; Smith BS; Kitada S; Kojima K; Miyaura H; RA Otwinowski Z; Ito A; Deisenhofer J; RL Structure 2001;9:615-625. RN [2] RM 8035833 RT MIP1, a new yeast gene homologous to the rat mitochondrial RT intermediate peptidase gene, is required for oxidative RT metabolism in Saccharomyces cerevisiae. RA Isaya G; Miklos D; Rollins RA; RL Mol Cell Biol. 1994;14:5603-5616. CC Mitocondrial processing peptidase (MPP) removes the first, CC N-terminal targeting sequence from nuclear-encoded proteins CC that are destined for import into the mitochondrion. MPP CC is a heterodimer of two homologous subunits, MMPalpha and CC MPPbeta. Only the beta subunit has peptidase activity [1]. CC The initial targeting signal may be followed by a second CC signal that targets a protein to the mitochondrial matrix CC or inner membrane. This second signal is removed by CC mitochondrial intermediate peptidase [2]. -- SN 1 ID Mitochondrial-processing peptidase subunit alpha DN Mitochondrial-processing peptidase subunit alpha RQ 1 EV IPR037715; PTHR11851:SF183; sufficient; TG GO:0006627 -- SN 2 ID Mitochondrial-processing peptidase subunit beta DN Mitochondrial-processing peptidase subunit beta RQ 1 EV IPR037718; PTHR11851:SF103; sufficient; TG GO:0017087 -- SN 3 ID Mitochondrial intermediate peptidase DN Mitochondrial intermediate peptidase RQ 0 EV IPR033851; PTHR11804:SF5; sufficient; EV IPR033851; cd06457; sufficient; TG GO:0006627 // AC GenProp2040 DE Mitochondrial inner membrane peptidase complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 8132591 RT Purified inner membrane protease I of yeast mitochondria RT is a heterodimer. RA Schneider A; Oppliger W; Jenö P; RL J Biol Chem. 1994 Mar 25;269(12):8635-8638. RN [2] RM 8879245 RT SOM 1, a small new gene required for mitochondrial inner RT membrane peptidase function in Saccharomyces cerevisiae. RA Esser K; Pratje E; Michaelis G; RL Mol Gen Genet. 1996;252:437-445. DC Protein export DR KEGG; map03060; CC The mitochondrial inner membrane peptidase (MIP) complex CC removes the N-terminal signal peptide from proteins that CC are synthesized in the mitochondrial matrix but destined for CC the inter-membrane space. There are two subunits that have CC proteolytic activity, IMP1 and IMP2 [1]. SOM1 is required CC for correct processing of cytochrome oxidase subunit 2 and CC cytochrome b2 [2]. -- SN 1 ID Mitochondrial inner membrane protease subunit 1 DN Mitochondrial inner membrane protease subunit 1 RQ 1 EV IPR026730; PTHR12383:SF16; sufficient; TG GO:0042720 -- SN 2 ID Mitochondrial inner membrane protease subunit 2 DN Mitochondrial inner membrane protease subunit 2 RQ 1 EV IPR037730; PTHR12383:SF3; sufficient; TG GO:0042720 -- SN 3 ID Protein SOM1, mitochondrial DN Mitochondrial export protein Som1 RQ 1 EV IPR024645; PF11093; sufficient; TG GO:0042720 // AC GenProp2043 DE Nuclear pore complex 107-120, Schizosaccharomyces TP COMPLEX AU Rawlings ND TH 3 RN [1] RM 15226438 RT The fission yeast Nup107-120 complex functionally interacts with RT the small GTPase Ran/Spi1 and is required for mRNA export, nuclear RT pore distribution, and proper cell division. RA Baï SW; Rouquette J; Umeda M; Faigle W; Loew D; Sazer S; Doye V; RL Mol Cell Biol. 2004;24:6379-6392. RN [2] RM 15116432 RT Identification of genes encoding putative nucleoporins and RT transport factors in the fission yeast Schizosaccharomyces pombe: RT a deletion analysis. RA Chen XQ; Du X; Liu J; Balasubramanian MK; Balasundaram D; RL Yeast 2004;21:495-509. DC RNA transport DR KEGG; map03013; CC The NPC107-120 nuclear pore complex (NPC) from Schizosaccharomyes CC is required for mRNA export, nuclear pore distribution, and cell CC division [1]. Components of the NPC have been identified by CC mutation studies [2]. -- SN 1 ID Nucleoporin nup85 DN Nucleoporin Nup85-like RQ 1 EV IPR011502; PF07575; sufficient; EV IPR011502; PTHR13373; sufficient; TG GO:0017056; -- SN 2 ID Nucleoporin nup107 DN Nuclear pore protein 84/107 RQ 1 EV IPR007252; PF04121; sufficient; EV IPR007252; PTHR13003; sufficient; TG GO:0017056; -- SN 3 ID Nucleoporin nup120 DN Nucleoporin Nup120/160 RQ 1 EV IPR021717; PF11715; sufficient; TG GO:0031080; -- SN 4 ID Nucleoporin nup131 DN Nuclear pore complex protein Nup133-like RQ 1 EV IPR037624; PTHR13405; sufficient; TG GO:0017056; -- SN 5 ID Nucleoporin nup132 DN Nuclear pore complex protein Nup133-like RQ 1 EV IPR037624; PTHR13405; sufficient; TG GO:0017056; -- SN 6 ID Nucleoporin seh1 DN Nucleoporin Seh1 RQ 1 EV IPR037597; PTHR11024:SF3; sufficient; TG GO:0031080; // AC GenProp2047 DE COP9 Signalosome, eukaryote TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 26456823 RT CSNAP Is a Stoichiometric Subunit of the COP9 Signalosome. RA Rozen S; Füzesi-Levi MG; Ben-Nissan G; Mizrachi L; Gabashvili A; RA Levin Y; Ben-Dor S; Eisenstein M; Sharon M; RL Cell Rep. 2015;13:585-598. RN [2] RM 12183637 RT Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage RT of Nedd8 from Cul1. RA Cope GA; Suh GS; Aravind L; Schwarz SE; Zipursky SL; Koonin EV; RA Deshaies RJ; RL Science 2002;298:608-611. CC The COP9 signalosome (CSN) consists of COPS1/GPS1, COPS2, COPS3, CC COPS4, COPS5, COPS6, COPS7 (COPS7A or COPS7B), COPS8 and COPS9 CC isoform 1 [1]. CSN subunit 5 is a metallo-isopeptidase that CC releases the ubiquitin-like protein Nedd8 from the Cul1 subunit CC of SCF ubiquitin ligases [2]. -- SN 1 ID COP9 signalosome complex subunit 1/GPS1 DN COP9 signalosome complex subunit 1 RQ 1 EV IPR033008; PTHR14145:SF2; sufficient; TG GO:0008180; TG GO:0000338; -- SN 2 ID COP9 signalosome complex subunit 2 DN COP9 signalosome complex subunit 2 RQ 1 EV IPR037750; PTHR10678:SF3; sufficient; TG GO:0008180; -- SN 3 ID COP9 signalosome complex subunit 3 DN COP9 signalosome complex subunit 3 RQ 1 EV IPR037753; PTHR10758:SF1; sufficient; TG GO:0008180; -- SN 4 ID COP9 signalosome complex subunit 4 DN COP9 signalosome complex subunit 4 RQ 1 EV IPR037754; PTHR10855:SF2; sufficient; TG GO:0008180; -- SN 5 ID COP9 signalosome complex subunit 5 DN COP9 signalosome complex subunit 5 RQ 1 EV IPR037740; PTHR10410:SF6; sufficient; TG GO:0008180; -- SN 6 ID COP9 signalosome complex subunit 6 DN COP9 signalosome complex subunit 6 RQ 1 EV IPR033859; PTHR10540:SF8; sufficient; EV IPR033859; cd08063; sufficient; TG GO:0008180; -- SN 7 ID COP9 signalosome complex subunit 7 DN COP9 signalosome complex subunit 7a/b RQ 1 EV IPR037757; PTHR15350:SF7; sufficient; EV IPR027530; PTHR15350:SF8; sufficient; TG GO:0008180; -- SN 8 ID COP9 signalosome complex subunit 8 DN COP9 signalosome complex subunit 8 RQ 1 EV IPR033205; PTHR13339; sufficient; TG GO:0008180; -- SN 9 ID COP9 signalosome complex subunit 9 DN COP9 signalosome complex subunit 9, metazoa RQ 1 EV IPR029391; PF15004; sufficient; EV IPR029391; PTHR28562; sufficient; TG GO:0008180; // AC GenProp2048 DE General transcription factor IIH TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 8157004 RT Correction of xeroderma pigmentosum repair defect by basal RT transcription factor BTF2 (TFIIH). RA van Vuuren AJ; Vermeulen W; Ma L; Weeda G; Appeldoorn E; Jaspers RA NG; van der Eb AJ; Bootsma D; Hoeijmakers JH; Humbert S; RL EMBO J. 1994;13:1645-1653. RN [2] RM 10024882 RT Reconstitution of the transcription factor TFIIH: assignment of RT functions for the three enzymatic subunits, XPB, XPD, and cdk7. RA Tirode F; Busso D; Coin F; Egly JM; RL Mol Cell. 1999;3:87-95. RN [3] RM 9852112 RT Immunoaffinity purification and functional characterization of RT human transcription factor IIH and RNA polymerase II from clonal RT cell lines that conditionally express epitope-tagged subunits of RT the multiprotein complexes. RA Kershnar E; Wu SY; Chiang CM; RL J Biol Chem. 1998;273:34444-34453. DC Basal transcription factors DR KEGG; map03022; CC The core-TFIIH basal transcription factor is involved in CC nucleotide excision repair (NER) of DNA [1]. It consists of six CC subunits where the sixth component is a helicase, either XPB [2] CC or XPD [3]. The complex associates with the CAK complex to form CC the TFIIH basal transcription factor [2]. -- SN 1 ID General transcription factor IIH subunit 1 DN TFIIH subunit Tfb1/GTF2H1 RQ 1 EV IPR027079; PTHR12856; sufficient; TG GO:0006289; TG GO:0000439; -- SN 2 ID General transcription factor IIH subunit 2 DN TFIIH subunit Ssl1/p44 RQ 1 EV IPR012170; PIRSF015919; sufficient; EV IPR012170; PTHR12695; sufficient; EV IPR012170; TIGR00622; sufficient; TG GO:0006289; TG GO:0000439; -- SN 3 ID General transcription factor IIH subunit 3 DN TFIIH subunit Tfb4/GTF2H3 RQ 1 EV IPR004600; PF03850; sufficient; EV IPR004600; PTHR12831; sufficient; EV IPR004600; TIGR00627; sufficient; TG GO:0006289; TG GO:0000439; -- SN 4 ID General transcription factor IIH subunit 4 DN Transcription factor TFIIH subunit p52/Tfb2 RQ 1 EV IPR004598; PF03849; sufficient; EV IPR004598; PTHR13152; sufficient; EV IPR004598; TIGR00625; sufficient; TG GO:0006289; TG GO:0000439; -- SN 5 ID General transcription factor IIH subunit 5 DN TFIIH subunit TTDA/Tfb5 RQ 1 EV IPR009400; PF06331; sufficient; EV IPR009400; PTHR28580; sufficient; EV IPR009400; SM01395; sufficient; TG GO:0006289; TG GO:0000439; -- SN 6 ID TFIIH basal transcription factor complex helicase XPB subunit DN Helicase XPB/Ssl2 (EC:3.6.4.12) RQ 1 EV IPR001161; TIGR00603; sufficient; TG GO:0006289; TG GO:0004003; -- SN 7 ID TFIIH basal transcription factor complex helicase XPD subunit DN RAD3/XPD family (EC:3.6.4.12) RQ 0 EV IPR001945; PR00852; sufficient; EV IPR001945; PTHR11472:SF1; sufficient; TG GO:0006289; TG GO:0004003; // AC GenProp2049 DE CDK-activating kinase (CAK) complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 10024882 RT Reconstitution of the transcription factor TFIIH: assignment of RT functions for the three enzymatic subunits, XPB, XPD, and cdk7. RA Tirode F; Busso D; Coin F; Egly JM; RL Mol Cell. 1999;3:87-95. RN [2] RM 8230216 RT The kin28 protein kinase is associated with a cyclin in RT Saccharomyces cerevisiae. RA Valay JG; Simon M; Faye G; RL J Mol Biol. 1993;234:307-310. DC Cell cycle DR KEGG; map04110; CC The CAK complex consists of cyclin-dependent kinase 7 (CDK7), CC cyclin-H (CCNH) and MAT1. The complex associates with the CC core-TFIIH complex to form the TFIIH basal transcription factor CC [1]. In the yeast Saccharomyces cerevisiae, CDK7 is known as CC KIN28 and cyclin H is known as CCL1. Together they form a CC heterodimer known as TFIIK [2]. -- SN 1 ID Cyclin-dependent kinase 7 DN Cyclin-dependent kinase 7 (EC 2.7.11.22/EC 2.7.11.23) RQ 1 EV IPR037770; PTHR24056:SF0; sufficient; TG GO:0004693; TG GO:0006289; -- SN 2 ID Cyclin-H DN CyclinH/Ccl1 RQ 1 EV IPR027081; TIGR00569; sufficient; TG GO:0016538; TG GO:0070985; -- SN 3 ID CDK-activating kinase assembly factor MAT1 DN Cdk-activating kinase assembly factor MAT1/Tfb3 RQ 1 EV IPR004575; PIRSF003338; sufficient; EV IPR004575; PTHR12683:SF13; sufficient; EV IPR004575; TIGR00570; sufficient; TG GO:0006289; TG GO:0005675; // AC GenProp2050 DE TFIIH basal transcription factor TP METAPATH AU Rawlings ND TH 1 RN [1] RM 10024882 RT Reconstitution of the transcription factor TFIIH: assignment of RT functions for the three enzymatic subunits, XPB, XPD, and cdk7. RA Tirode F; Busso D; Coin F; Egly JM; RL Mol Cell. 1999;3:87-95. RN [2] RM 15494306 RT Selective regulation of vitamin D receptor-responsive genes by RT TFIIH. RA Drané P; Compe E; Catez P; Chymkowitch P; Egly JM; RL Mol Cell. 2004;16:187-197. DC Basal transcription factors DR KEGG; map03022; CC The core-TFIIH basal transcription factor associates with the CAK CC complex to form the TFIIH basal transcription factor [1]. TFIIH CC is required for transcription initiation and nucleotide excision CC repair [2]. -- SN 1 ID General transcription factor IIH RQ 1 EV GenProp2048; -- SN 2 ID CDK-activating kinase (CAK) complex RQ 1 EV GenProp2049; // AC GenProp2052 DE SAGA-like (SLIK) complex TP METAPATH AU Rawlings ND TH 3 RN [1] RM 15647753 RT Chd1 chromodomain links histone H3 methylation with SAGA- and RT SLIK-dependent acetylation. RA Pray-Grant MG; Daniel JA; Schieltz D; Yates JR 3rd; Grant PA; RL Nature 2005;433:434-438. CC The yeast SLIK (SAGA-like) complex is a multi-subunit histone CC acetyltransferase complex that preferentially acetylates CC histones H3 and H2B and deubiquitinates histone H2B. It is an CC embellishment of the SAGA complex. It consists of at least CC TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, CC UBP8, GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9 [1]. -- SN 1 ID SALSA complex RQ 1 EV GenProp2053; TG GO:0000124; -- SN 2 ID Chromo domain-containing protein 1 DN Chromo domain-containing protein 1 (EC 3.6.4.-)/CHD1 RQ 1 EV IPR037780; PTHR10799:SF838; sufficient; TG GO:0000124; -- SN 3 ID High-affinity glucose transporter RGT2 DN High-affinity glucose transporter RGT2 RQ 1 EV IPR037792; PTHR23500:SF343; sufficient; TG GO:0000124; -- SN 4 ID Ubiquitin carboxyl-terminal hydrolase 8 DN Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)/UBP8 RQ 1 EV IPR037798; PTHR43961:SF2; sufficient; TG GO:0000124; -- SN 5 ID SAGA-associated factor 29 DN SAGA-associated factor 29/SGF29 RQ 1 EV IPR037802; PTHR21539; sufficient; TG GO:0000124; -- SN 6 ID Transcription initiation factor TFIID subunit 10 DN Transcription initiation factor TFIID subunit 10/TAF10 RQ 1 EV IPR003923; PIRSF017246; sufficient; EV IPR003923; PR01443; sufficient; EV IPR003923; PTHR21242; sufficient; EV IPR003923; cd07982; sufficient; TG GO:0000124; -- SN 7 ID Transcription initiation factor TFIID subunit 9 DN Transcription initiation factor TFIID subunit 9/TAF9 RQ 1 EV IPR003162; PF02291; sufficient; EV IPR003162; cd07979; sufficient; TG GO:0000124; // AC GenProp2053 DE SALSA complex TP COMPLEX AU Rawlings ND TH 5 RN [1] RM 12186975 RT SALSA, a variant of yeast SAGA, contains truncated Spt7, which RT correlates with activated transcription. RA Sterner DE; Belotserkovskaya R; Berger SL; RL Proc Natl Acad Sci U S A 2002;99:11622-11627. CC The yeast SALSA complex is an altered form of the SAGA complex CC and consists of at least TRA1, SPT7 (C-terminal truncated CC form), TAF5, ADA3, SPT20, TAF12, TAF6, HFI1, GCN5, ADA2 and CC SPT3 [1]. -- SN 1 ID Transcription-associated protein 1 DN Transcription-associated protein 1/TRA1 RQ 1 EV IPR033317; PTHR11139:SF1; sufficient; TG GO:0000124; -- SN 2 ID Transcriptional activator SPT7 DN Transcriptional activator SPT7 RQ 1 EV IPR037782; PTHR22880:SF223; sufficient; TG GO:0000124; -- SN 3 ID Transcription initiation factor TFIID subunit 5 DN Transcription initiation factor TFIID subunit 5/TAF5 RQ 1 EV IPR037783; PTHR19879:SF1; sufficient; TG GO:0000124; -- SN 4 ID Chromatin-remodeling complexes subunit NGG1 (ADA3) DN Chromatin-remodeling complexes subunit NGG1 (ADA3) RQ 1 EV IPR019340; PTHR13556; sufficient; EV IPR019340; PF10198; sufficient; TG GO:0000124; -- SN 5 ID Transcription factor SPT20 DN Transcription factor SPT20 RQ 1 EV IPR021950; PF12090; sufficient; TG GO:0000124; -- SN 6 ID Transcription initiation factor TFIID subunit 12 DN Transcription initiation factor TFIID subunit 12/TAF12 RQ 1 EV IPR037794; PTHR12264:SF21; sufficient; TG GO:0000124; -- SN 7 ID Transcription initiation factor TFIID subunit 6 DN Transcription initiation factor TFIID subunit 6/TAF6 RQ 1 EV IPR037796; PTHR10221; sufficient; TG GO:0000124; -- SN 8 ID Transcriptional coactivator HFI1/ADA1 DN Transcriptional coactivator HFI1/ADA1 RQ 1 EV IPR024738; PF12767; sufficient; EV IPR024738; PTHR21277; sufficient; TG GO:0000124; -- SN 9 ID Histone acetyltransferase GCN5 DN Histone acetyltransferase GCN5 (EC 2.3.1.48) RQ 1 EV IPR037800; PTHR22880:SF124; sufficient; TG GO:0000124; -- SN 10 ID Transcriptional adapter 2 (ADA2) DN Transcriptional adapter 2 (ADA2) RQ 1 EV IPR016827; PIRSF025024; sufficient; TG GO:0000124; -- SN 11 ID Protein SPT3 DN Protein SPT3/TAF13 RQ 1 EV IPR003195; PF02269; sufficient; EV IPR003195; PTHR11380; sufficient; EV IPR003195; cd07978; sufficient; TG GO:0000124; // AC GenProp2054 DE TFIID complex TP COMPLEX AU Rawlings ND TH 6 RN [1] RM 12138208 RT Molecular characterization of Saccharomyces cerevisiae TFIID. RA Sanders SL; Garbett KA; Weil PA; RL Mol Cell Biol. 2002;22:6000-6013. RN [2] RM 10788514 RT Identification of two novel TAF subunits of the yeast RT Saccharomyces cerevisiae TFIID complex. RA Sanders SL; Weil PA; RL J Biol Chem. 2000;275:13895-13900. DC Basal transcription factors DR KEGG; map03022; CC The TFIID complex is a general purpose translation initiator CC factor. It is composed of the TATA binding protein (TBP) and CC 14 TBP-associated factors. One copy of each TAF1, TAF2, TAF3, CC TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, CC TAF9, TAF10, TAF12, and three copies of TAF14 [1,2]. -- SN 1 ID TATA-box-binding protein DN TATA-box-binding protein/TBP RQ 1 EV IPR033710; cd04516; sufficient; TG GO:0005669; TG GO:0006352; -- SN 2 ID Transcription initiation factor TFIID subunit 1 DN Transcription initiation factor TFIID subunit 1/TAF1 RQ 1 EV IPR011177; PTHR19879:SF1; sufficient; TG GO:0005669; -- SN 3 ID Transcription initiation factor TFIID subunit 2 DN Transcription initiation factor TFIID subunit 2/TAF2 RQ 1 EV IPR037813; PTHR15137; sufficient; TG GO:0005669; -- SN 4 ID Transcription initiation factor TFIID subunit 3 DN Transcription initiation factor TFIID subunit 3/TAF3 RQ 1 EV IPR037815; PTHR12321:SF95; sufficient; TG GO:0005669; -- SN 5 ID Transcription initiation factor TFIID subunit 4 DN Transcription initiation factor TFIID subunit 4/TAF4 RQ 1 EV IPR007900; PF05236; sufficient; EV IPR007900; cd08045; sufficient; TG GO:0005669; -- SN 6 ID Transcription initiation factor TFIID subunit 5 DN Transcription initiation factor TFIID subunit 5/TAF5 RQ 1 EV IPR037783; PTHR19879:SF1; sufficient; TG GO:0005669; -- SN 7 ID Transcription initiation factor TFIID subunit 6 DN Transcription initiation factor TFIID subunit 6/TAF6 RQ 1 EV IPR037796; PTHR10221; sufficient; TG GO:0005669; -- SN 8 ID Transcription initiation factor TFIID subunit 7 DN Transcription initiation factor TFIID subunit 7/TAF7 RQ 1 EV IPR037817; PTHR12228; sufficient; TG GO:0005669; -- SN 9 ID Transcription initiation factor TFIID subunit 8 DN Transcription initiation factor TFIID subunit 8/TAF8 RQ 1 EV IPR037818; PTHR12321:SF102; sufficient; TG GO:0005669; -- SN 10 ID Transcription initiation factor TFIID subunit 9 DN Transcription initiation factor TFIID subunit 9/TAF9 RQ 1 EV IPR003162; PF02291; sufficient; EV IPR003162; cd07979; sufficient; TG GO:0005669; -- SN 11 ID Transcription initiation factor TFIID subunit 10 DN Transcription initiation factor TFIID subunit 10/TAF10 RQ 1 EV IPR003923; PIRSF017246; sufficient; EV IPR003923; PR01443; sufficient; EV IPR003923; PTHR21242; sufficient; EV IPR003923; cd07982; sufficient; TG GO:0005669; -- SN 12 ID Transcription initiation factor TFIID subunit 11 DN Transcription initiation factor TFIID subunit 11/TAF11 RQ 1 EV IPR006809; PTHR13218; sufficient; EV IPR006809; PF04719; sufficient; EV IPR006809; cd08048; sufficient; TG GO:0005669; -- SN 13 ID Transcription initiation factor TFIID subunit 12 DN Transcription initiation factor TFIID subunit 12/TAF12 RQ 1 EV IPR003228; PD012998; sufficient; EV IPR003228; PF03847; sufficient; EV IPR003228; cd07981; sufficient; TG GO:0005669; -- SN 14 ID Transcription initiation factor TFIID subunit 13 DN Transcription initiation factor TFIID subunit 13/TAF13 RQ 1 EV IPR003195; PF02269; sufficient; EV IPR003195; PTHR11380; sufficient; EV IPR003195; cd07978; sufficient; TG GO:0005669; -- SN 15 ID Transcription initiation factor TFIID subunit 14 DN Transcription initiation factor TFIID subunit 14/TAF14 RQ 1 EV IPR016665; PIRSF016551; sufficient; EV IPR016665; PTHR23195:SF2; sufficient; TG GO:0005669; // AC GenProp2055 DE ADA complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 9224714 RT Yeast Gcn5 functions in two multisubunit complexes to RT acetylate nucleosomal histones: characterization of an Ada RT complex and the SAGA (Spt/Ada) complex. RA Grant PA; Duggan L; Côté J; Roberts SM; Brownell JE; Candau RA R; Ohba R; Owen-Hughes T; Allis CD; Winston F; Berger SL; RA Workman JL; RL Genes Dev. 1997;11:1640-1650. CC The ADA complex is a transcription regulatory histone CC acetylation (HAT) complex. ADA preferentially acetylates CC nucleosomal histones H3 (at 'Lys-14' and 'Lys-18') and H2B. CC The complex consists of at least ADA2, ADA3, AHC1, and GCN5. CC AHC1 is required for the overall structural integrity of the CC ADA complex [1]. -- SN 1 ID Transcriptional adapter 2 (ADA2) DN Transcriptional adapter 2 (ADA2) RQ 1 EV IPR016827; PIRSF025024; sufficient; TG GO:0000124; -- SN 2 ID Chromatin-remodeling complexes subunit NGG1 (ADA3) DN Histone acetyltransferases subunit 3 (ADA3) RQ 1 EV IPR019340; PTHR13556; sufficient; EV IPR019340; PF10198; sufficient; TG GO:0000124; -- SN 3 ID Protein AHC1 DN Protein AHC1 RQ 1 EV IPR037807; PTHR13585:SF19; sufficient; -- SN 4 ID Histone acetyltransferase GCN5 DN Histone acetyltransferase GCN5 (EC 2.3.1.48) RQ 1 EV IPR037800; PTHR22880:SF124; sufficient; TG GO:0000124; // AC GenProp2057 DE TFTC-HAT complex TP COMPLEX AU Rawlings ND TH 9 RN [1] RM 10373431 RT Identification of TATA-binding protein-free TAFII- RT containing complex subunits suggests a role in nucleosome RT acetylation and signal transduction. RA Brand M; Yamamoto K; Staub A; Tora L; RL J Biol Chem. 1999;274:18285-18289. RN [2] RM 10788514 RT Identification of two novel TAF subunits of the yeast RT Saccharomyces cerevisiae TFIID complex. RA Sanders SL; Weil PA; RL J Biol Chem. 2000;275:13895-13900. CC The TATA-binding protein (TBP)-free TAFII-containing CC complex (TFTC) acetylates histones that are free or CC nucleosomal. The TFTC-HAT complex is composed of at least CC TAF5L, TAF6L, TAF3, TADA3L, SUPT3H/SPT3, TAF2/TAFII150, CC TAF4/TAFII135, TAF5/TAFII100, KAT2A/GCN5L2, TAF10 and CC TRRAP [1]. -- SN 1 ID TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L (TAF5L) DN TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L (TAF5L) RQ 1 EV IPR037826; PTHR19879:SF6; sufficient; TG GO:0033276; -- SN 2 ID TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L) DN Transcription initiation factor TFIID subunit 6 (TAF6L) RQ 1 EV IPR037796; PTHR10221; sufficient; TG GO:0033276; -- SN 3 ID Transcription initiation factor TFIID subunit 3 (TAF3) DN Transcription initiation factor TFIID subunit 3 (TAF3) RQ 1 EV IPR037815; PTHR12321:SF34; sufficient; TG GO:0033276; -- SN 4 ID Transcriptional adapter 3 (TADA3L) DN Histone acetyltransferases subunit 3 (TADA3L) RQ 1 EV IPR019340; PF10198; sufficient; EV IPR019340; PTHR13556; sufficient; TG GO:0033276; -- SN 5 ID Transcription initiation protein SPT3 homolog (SUPT3H/SPT3) DN Transcription initiation protein SPT3 homolog (SUPT3H/SPT3) RQ 1 EV IPR003195; PF02269; sufficient; EV IPR003195; PTHR11380; sufficient; EV IPR003195; cd07978; sufficient; TG GO:0033276; -- SN 6 ID Transcription initiation factor TFIID subunit 2 (TAF2/TAFII150) DN Transcription initiation factor TFIID subunit 2 (TAF2/TAFII150) RQ 1 EV IPR037813; PTHR15137; sufficient; TG GO:0033276; -- SN 7 ID Transcription initiation factor TFIID subunit 4 (TAF4/TAFII135) DN Transcription initiation factor TFIID subunit 4 (TAF4/TAFII135) RQ 1 EV IPR007900; PF05236; sufficient; EV IPR007900; d08045; sufficient; TG GO:0033276; -- SN 8 ID Transcription initiation factor TFIID subunit 5 (TAF5/TAFII100) DN Transcription initiation factor TFIID subunit 5 (TAF5/TAFII100) RQ 1 EV IPR037783; PTHR19879:SF4; sufficient; TG GO:0033276; -- SN 9 ID Histone acetyltransferase KAT2A DN Histone acetyltransferase KAT2A RQ 1 EV IPR037800; PTHR22880:SF124; sufficient; TG GO:0033276; TG GO:0016573; -- SN 10 ID Transcription initiation factor TFIID subunit 10 (TAF10) DN Transcription initiation factor TFIID subunit 10 (TAF10) RQ 1 EV IPR003923; PF03540; sufficient; EV IPR003923; PIRSF017246; sufficient; EV IPR003923; PR01443; sufficient; EV IPR003923; PTHR21242; sufficient; EV IPR003923; cd07982; sufficient; TG GO:0033276; -- SN 11 ID Transformation/transcription domain-associated protein (TRRAP) DN Transformation/transcription domain-associated protein (TRRAP) RQ 1 EV IPR033317; PTHR11139:SF1; sufficient; TG GO:0033276; // AC GenProp2059 DE Set1B histone H3-Lys4 methyltransferase complex TP COMPLEX AU Rawlings ND TH 6 RN [1] RM 17355966 RT Identification and characterization of the human Set1B histone RT H3-Lys4 methyltransferase complex. RA Lee JH; Tate CM; You JS; Skalnik DG; RL J Biol Chem. 2007;282:13419-13428. CC The SET1 complex is a methyltransferase that that produces CC trimethylated histone H3 at Lys(4). It is composed of at least CC the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, CC ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30 [1]. -- SN 1 ID Histone-lysine N-methyltransferase SET1 DN Histone-lysine N-methyltransferase SET1 (EC 2.1.1.43) RQ 1 EV IPR037841; PTHR22884:SF295; sufficient; EV IPR037842; PTHR22884:SF475; sufficient; EV IPR037861; PTHR22884:SF464; sufficient; TG GO:0048188; TG GO:0018024; -- SN 2 ID WD repeat-containing protein 5 DN WD repeat-containing protein 5 (WDR5) RQ 1 EV IPR037834; PTHR22847:SF560; sufficient; TG GO:0048188; -- SN 3 ID WD repeat-containing protein 82 (WDR82) DN WD repeat-containing protein 82 (WDR82) RQ 1 EV IPR037846; PTHR19861:SF2; sufficient; TG GO:0048188; -- SN 4 ID Retinoblastoma-binding protein 5 (RBBP5) DN Retinoblastoma-binding protein 5 (RBBP5) RQ 1 EV IPR037850; PTHR44040; sufficient; TG GO:0048188; -- SN 5 ID Set1/Ash2 histone methyltransferase complex subunit ASH2 DN Set1/Ash2 histone methyltransferase complex subunit ASH2 RQ 1 EV IPR037353; PTHR10598; sufficient; TG GO:0048188; -- SN 6 ID CXXC-type zinc finger protein 1 (CXXC1) DN CXXC-type zinc finger protein 1 (CXXC1) RQ 1 EV IPR037852; PTHR12321:SF58; sufficient; EV IPR037852; PTHR12321:SF99; sufficient; TG GO:0048188; -- SN 7 ID Host cell factor 1 (HCFC1) DN Host cell factor 1 (HCFC1) RQ 1 EV IPR037854; PTHR23244:SF339; sufficient; TG GO:0048188; -- SN 8 ID Protein dpy-30 homolog (DPY30) DN Protein dpy-30 homolog (DPY30) RQ 1 EV IPR037856; PTHR23356:SF0; sufficient; TG GO:0048188; // AC GenProp2060 DE COMPASS methyltransferase complex TP COMPLEX AU Rawlings ND TH 2 RN [1] RM 9398665 RT SET1, a yeast member of the trithorax family, functions in RT transcriptional silencing and diverse cellular processes. RA Nislow C; Ray E; Pillus L; RL Mol Biol Cell. 1997;8:2421-2436. RN [2] RM 11742990 RT The Saccharomyces cerevisiae Set1 complex includes an Ash2 RT homologue and methylates histone 3 lysine 4. RA Miller T; Krogan NJ; Dover J; Erdjument-Bromage H; Tempst P; RA Johnston M; Greenblatt JF; Shilatifard A; RL EMBO J. 2001;20:7137-7148. RN [3] RM 11687631 RT COMPASS: a complex of proteins associated with a trithorax- RT related SET domain protein. RA Roguev A; Schaft D; Shevchenko A; Pijnappel WW; Wilm M; RA Aasland R; Stewart AF; RL Proc Natl Acad Sci U S A 2001;98:12902-12907. CC The COMPASS (Complex Proteins Associated with Set1 or Set1C) CC complex mono-, di- and trimethylates histone H3 to form CC H3K4me1/2/3. This is important for telomere length CC maintenance and regulation of transcription elongation [1]. CC The complex consists of SET1, BRE2, SPP1, SDC1, SHG1, SWD1, CC SWD2, and SWD3 [2,3]. -- SN 1 ID Histone-lysine N-methyltransferase SET1 DN Histone-lysine N-methyltransferase SET1 (EC 2.1.1.43) RQ 1 EV IPR017111; PIRSF037104; sufficient; EV IPR017111; PS51572; sufficient; TG GO:0042800; TG GO:0048188; -- SN 2 ID WD40-repeat-containing protein SWD3-like DN WD40-repeat-containing protein SWD3-like RQ 1 EV IPR037866; PTHR22847:SF603; sufficient; TG GO:0048188; -- SN 3 ID COMPASS component SWD2 DN COMPASS component SWD2 RQ 1 EV IPR037867; PTHR19861:SF0; sufficient; TG GO:0048188; -- SN 4 ID COMPASS component SWD1 DN COMPASS component SWD1 RQ 1 EV IPR037850; PTHR44040; sufficient; TG GO:0048188; -- SN 5 ID COMPASS component BRE2 DN COMPASS component BRE2 RQ 1 EV IPR037353; PTHR10598; sufficient; TG GO:0048188; -- SN 6 ID COMPASS component SPP1 DN COMPASS component SPP1 RQ 1 EV IPR037869; PTHR12321:SF97; sufficient; TG GO:0048188; -- SN 7 ID COMPASS component SHG1 DN COMPASS component SHG1 RQ 1 EV IPR007870; PD086658; sufficient; TG GO:0048188; -- SN 8 ID COMPASS component SDC1 DN COMPASS component SDC1 RQ 1 EV IPR037870; PTHR23356:SF8; sufficient; TG GO:0048188; // AC GenProp2063 DE NSL complex TP COMPLEX AU Rawlings ND TH 5 RN [1] RM 20018852 RT Subunit composition and substrate specificity of a MOF- RT containing histone acetyltransferase distinct from the RT male-specific lethal (MSL) complex. RA Cai Y; Jin J; Swanson SK; Cole MD; Choi SH; Florens L; RA Washburn MP; Conaway JW; Conaway RC; RL J. Biol. Chem. 2010;285:4268-4272. CC The NSL complex is involved in acetylation of nucleosomal CC histone H4 on several lysine residues and therefore may be CC involved in the regulation of transcription. The complex CC is composed of at least MOF/KAT8, KANSL1, KANSL2, KANSL3, CC MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1 [1]. -- SN 1 ID Histone acetyltransferase KAT8 DN Histone acetyltransferase KAT8 (EC 2.3.1.48) (MOF/KAT8) RQ 1 EV IPR037906; PTHR10615:SF82; sufficient; TG GO:0004402; TG GO:0000123; -- SN 2 ID KAT8 regulatory NSL complex subunit 1 DN KAT8 regulatory NSL complex subunit 1 (KANSL1) RQ 1 EV IPR026180; PTHR22443; sufficient; TG GO:0000123; -- SN 3 ID KAT8 regulatory NSL complex subunit 2 DN KAT8 regulatory NSL complex subunit 2 (KANSL2) RQ 1 EV IPR026316; PTHR13453; sufficient; TG GO:0000123; -- SN 4 ID KAT8 regulatory NSL complex subunit 3 DN KAT8 regulatory NSL complex subunit 3 (KANSL3) RQ 1 EV IPR026555; PTHR13136; sufficient; TG GO:0000123; -- SN 5 ID Microspherule protein 1 DN Microspherule protein 1 (MCRS1) RQ 1 EV IPR037912; PTHR13233; sufficient; TG GO:0000123; -- SN 6 ID PHD finger protein 20 DN PHD finger protein 20 (PHF20) RQ 1 EV IPR037915; PTHR15856:SF27; sufficient; TG GO:0000123; -- SN 7 ID WD repeat-containing protein 5 DN WD repeat-containing protein 5 (WDR5) RQ 1 EV IPR037834; PTHR22847:SF560; sufficient; TG GO:0000123; -- SN 8 ID UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit DN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (EC 2.4.1.255) (OGT1/OGT) RQ 1 EV IPR037919; PTHR44366; sufficient; TG GO:0000123; TG GO:0097363; -- SN 9 ID Host cell factor 1 DN Host cell factor 1 (HCFC1) RQ 1 EV IPR037854; PTHR23244:SF339; sufficient; TG GO:0000123; // AC GenProp2064 DE MSL complex TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 22547026 RT Structural insight into the regulation of MOF in the RT male-specific lethal complex and the non-specific lethal RT complex. RA Huang J; Wan B; Wu L; Yang Y; Dou Y; Lei M; RL Cell Res. 2012;22:1078-1081. CC The MSL histone acetyltransferase complex acetylates CC histone H4 Lys16 (H4K16) along the male X-chromosome. CC The complex consists of at least MOF/KAT8, MSL1/hampin, CC MSL2 and MSL3 [1]. -- SN 1 ID Histone acetyltransferase KAT8 DN Histone acetyltransferase KAT8 (EC 2.3.1.48) (MOF/KAT8) RQ 1 EV IPR037906; PTHR10615:SF82; sufficient; TG GO:0004402; TG GO:0000123; TG GO:0072487; -- SN 2 ID Male-specific lethal 1 homolog (MSL1/hampin) DN Male-specific lethal 1 homolog (MSL1/hampin) RQ 1 EV IPR026711; PTHR21656; sufficient; TG GO:0072487; -- SN 3 ID E3 ubiquitin-protein ligase MSL2 (EC 6.3.2.-) DN E3 ubiquitin-protein ligase MSL2 (EC 6.3.2.-) RQ 1 EV IPR037922; PTHR16048; sufficient; TG GO:0072487; -- SN 4 ID Male-specific lethal 3 homolog (MSL3) DN Male-specific lethal 3 homolog (MSL3) RQ 1 EV IPR037921; PTHR10880:SF26; sufficient; TG GO:0072487; // AC GenProp2066 DE RuvB-like helicase TP COMPLEX AU Rawlings ND TH 1 RN [1] RM 10428817 RT TIP49b, a new RuvB-like DNA helicase, is included in a RT complex together with another RuvB-like DNA helicase, RT TIP49a. RA Kanemaki M; Kurokawa Y; Matsu-ura T; Makino Y; Masani A; RA Okazaki K; Morishita T; Tamura TA; RL J Biol Chem. 1999;274:22437-22444. CC The RuvB-like helicase is a heteroligomer consisting of CC a hexameric ring of subunit RUVBL1 and a hexameric ring CC of subunit RUVBL2, one stacked upon the other. Each CC is assumed to be a homohexamer, but this is not CC confirmed experimentally [1]. This complex itself is a CC component in many other complexes. -- SN 1 ID RuvB-like 1 (RUVBL1/TIP49a) DN RuvB-like 1 (EC 3.6.4.12) RQ 1 EV IPR037938; PTHR11093:SF6; sufficient; TG GO:0071339; TG GO:0043141; -- SN 2 ID RuvB-like 2 (RUVBL2/TIP49b) DN RuvB-like 2 (EC 3.6.4.12) RQ 1 EV IPR037942; PTHR11093:SF2; sufficient; TG GO:0071339; TG GO:0043141; // AC GenProp2067 DE MLL-HCF complex TP COMPLEX AU Rawlings ND TH 5 RN [1] RM 15199122 RT Leukemia proto-oncoprotein MLL forms a SET1-like histone RT methyltransferase complex with menin to regulate Hox RT gene expression. RA Yokoyama A; Wang Z; Wysocka J; Sanyal M; Aufiero DJ; RA Kitabayashi I; Herr W; Cleary ML; RL Mol Cell Biol. 2004;24:5639-5649. CC The MLL-HCF complex is a SET1-like histone CC methyltransferase complex that regulates Hox gene CC expression. The complex is at least composed of KMT2A/MLL1, CC MEN1, ASH2L, RBBP5, DPY30, WDR5, HCFC1 and HCFC2 [1]. -- SN 1 ID Histone-lysine N-methyltransferase 2A (EC 2.1.1.43) DN Histone-lysine N-methyltransferase 2A (EC 2.1.1.43) RQ 1 EV IPR037927; PTHR22884:SF387; sufficient; TG GO:0071339; TG GO:0042800; -- SN 2 ID WD repeat-containing protein 5 DN WD repeat-containing protein 5 (WDR5) RQ 1 EV IPR037834; PTHR22847:SF560; sufficient; TG GO:0071339; -- SN 3 ID Retinoblastoma-binding protein 5 (RBBP5) DN Retinoblastoma-binding protein 5 (RBBP5) RQ 1 EV IPR037850; PTHR44040; sufficient; TG GO:0071339; -- SN 4 ID Set1/Ash2 histone methyltransferase complex subunit ASH2 DN Set1/Ash2 histone methyltransferase complex subunit ASH2 RQ 1 EV IPR037353; PTHR10598; sufficient; TG GO:0071339; -- SN 5 ID Protein dpy-30 homolog (DPY30) DN Protein dpy-30 homolog (DPY30) RQ 1 EV IPR037856; PTHR23356:SF0; sufficient; TG GO:0071339; -- SN 6 ID Menin (MEN1) DN Menin RQ 1 EV IPR007747; PF05053; sufficient; EV IPR007747; PTHR12693; sufficient; EV IPR007747; cd14456; sufficient; TG GO:0071339; -- SN 7 ID Host cell factor 1 (HCFC1) DN Host cell factor 1 RQ 1 EV IPR037854; PTHR23244:SF339; sufficient; TG GO:0071339; -- SN 8 ID Host cell factor 2 (HCFC2) DN Host cell factor 2 RQ 1 EV IPR037932; PTHR23244:SF325; sufficient; TG GO:0071339; // AC GenProp2069 DE THAP1/THAP3-HCFC1-OGT complex TP COMPLEX AU Rawlings ND TH 2 RN [1] RM 20200153 RT The THAP-zinc finger protein THAP1 associates with RT coactivator HCF-1 and O-GlcNAc transferase: a link RT between DYT6 and DYT3 dystonias. RA Mazars R; Gonzalez-de-Peredo A; Cayrol C; Lavigne AC; RA Vogel JL; Ortega N; Lacroix C; Gautier V; Huet G; Ray A; RA Monsarrat B; Kristie TM, Girard JP; RL J Biol Chem. 2010;285:13364-13371. CC THAP1/THAP3-HCFC1-OGT complex is required for the CC regulation of the transcriptional activity of RRM1. CC The complex contains either THAP1 or THAP3, HCFC1 and CC OGT. -- SN 1 ID THAP domain-containing protein (THAP1/THAP3) DN THAP domain-containing protein (THAP1/THAP3) RQ 1 EV IPR026516; PTHR23080:SF85; sufficient; EV IPR026520; PTHR23080:SF64; sufficient; -- SN 2 ID Host cell factor 1 (HCFC1) DN Host cell factor 1 RQ 1 EV IPR037854; PTHR23244:SF339; sufficient; -- SN 3 ID UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT) DN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (EC 2.4.1.255) RQ 1 EV IPR037919; PTHR44366; sufficient; TG GO:0097363; // AC GenProp2080 DE BAF53 complex TP COMPLEX AU Rawlings ND TH 3 RN [1] RM 11839798 RT BAF53 forms distinct nuclear complexes and functions as a RT critical c-Myc-interacting nuclear cofactor for oncogenic RT transformation. RA Park J; Wood MA; Cole MD; RL Mol Cell Biol. 2002;22:1307-1316. CC The BAF53 complex is at least composed of ACTL6A/BAF53A, CC RUVBL1/TIP49, SMARCA2/BRM, and TRRAP/PAF400 [1]. -- SN 1 ID Actin-like protein 6A (ACTL6A/BAF53A) DN Actin-like protein 6A RQ 1 EV IPR029912; PTHR11937:SF191; sufficient; -- SN 2 ID RuvB-like helicase 1 (RUVBL1/TIP49) DN RuvB-like helicase 1 (EC 3.6.4.12) RQ 1 EV IPR037938; PTHR11093:SF6; sufficient; TG GO:0043141; -- SN 3 ID Probable global transcription activator SNF2L2 (SMARCA2/BRM) DN Probable global transcription activator SNF2L2 (EC 3.6.4.-) RQ 1 EV IPR030088; PTHR10799:SF541; sufficient; TG GO:0016887; -- SN 4 ID Transformation/transcription domain-associated protein (TRRAP/PAF400) DN Transformation/transcription domain-associated protein RQ 1 EV IPR033317; PTHR11139:SF1; sufficient; // AC GenProp2081 DE npBAF complex TP COMPLEX AU Rawlings ND TH 9 RN [1] RM 17640523 RT An essential switch in subunit composition of a chromatin RT remodeling complex during neural development. RA Lessard J; Wu JI; Ranish JA; Wan M; Winslow MM; Staahl BT; RA Wu H; Aebersold R; Graef IA; Crabtree GR; RL Neuron 2007;55:201-215. CC The switch that forces mammalian neural stem cells to CC differentiate is the change in the composition of the CC neural, ATP-dependent SWI/SNF-like chromatin remodeling CC complexes. As progenitors exit mitosis and differentiate CC into neurons, components in the npBAF complex are CC replaced to form the nBAF complex [1]. CC The npBAF complex is composed of at least ARID1A/BAF250A CC or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, CC SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, CC SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, CC ACTL6A/BAF53A and actin. -- SN 1 ID AT-rich interactive domain-containing protein 1A/1B (ARID1A/BAF250A or ARID1B/BAF250B) DN AT-rich interactive domain-containing protein 1A/1B RQ 1 EV IPR030094; PTHR12656:SF12; sufficient; EV IPR038040; PTHR12656:SF11; sufficient; TG GO:0071564; -- SN 2 ID SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 (SMARCD1/BAF60A) DN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 RQ 1 EV IPR038041; PTHR13844:SF1; sufficient; TG GO:0071564; -- SN 3 ID Probable global transcription activator SNF2L2 (SMARCA2/BRM/BAF190B) DN Probable global transcription activator SNF2L2 (EC 3.6.4.-) RQ 1 EV IPR030088; PTHR10799:SF541; sufficient; TG GO:0071564; -- SN 4 ID Transcription activator BRG1 (SMARCA4/BRG1/BAF190A) DN Transcription activator BRG1 (EC 3.6.4.-) RQ 1 EV IPR030100; PTHR10799:SF76; sufficient; TG GO:0071564; -- SN 5 ID SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1/BAF47) DN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 RQ 1 EV IPR006939; PF04855; sufficient; EV IPR006939; PTHR10019; sufficient; TG GO:0071564; -- SN 6 ID SWI/SNF complex subunit SMARCC1 (SMARCC1/BAF155) DN SWI/SNF complex subunit SMARCC1 RQ 1 EV IPR030087; PTHR12802:SF9; sufficient; TG GO:0071564; -- SN 7 ID SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1/BAF57) DN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 RQ 1 EV IPR030089; PTHR13711:SF206; sufficient; TG GO:0071564; -- SN 8 ID SWI/SNF complex subunit SMARCC2 (SMARCC2/BAF170) DN SWI/SNF complex subunit SMARCC2 RQ 1 EV IPR038044; PTHR12802:SF38; sufficient; TG GO:0071564; -- SN 9 ID PHD finger protein 10 (PHF10/BAF45A) DN PHD finger protein 10 RQ 1 EV IPR038045; PTHR10615:SF133; sufficient; TG GO:0071564; -- SN 10 ID Actin-like protein 6A (ACTL6A/BAF53A) DN Actin-like protein 6A RQ 1 EV IPR029912; PTHR11937:SF191; sufficient; TG GO:0071564; -- SN 11 ID Actin DN Actin RQ 1 EV IPR004000; PF00022; sufficient; EV IPR004000; PR00190; sufficient; EV IPR004000; PTHR11937; sufficient; EV IPR004000; SM00268; sufficient; TG GO:0071564; // AC GenProp2084 DE SWI/SNF complex TP COMPLEX AU Rawlings ND TH 5 RN [1] RM 22952240 RT SWI/SNF chromatin-remodeling factors: multiscale analyses and RT diverse functions. RA Euskirchen G; Auerbach RK; Snyder M; RL J Biol Chem. 2012;287:30897-30905. CC The complex contains a catalytic subunit (either CC SMARCA4/BRG1/BAF190A or SMARCA2/BRM/BAF190B) and at least CC SMARCE1, ACTL6A/BAF53, SMARCC1/BAF155, SMARCC2/BAF170, and CC SMARCB1/SNF5/BAF47. DC Hepatocellular carcinoma DR KEGG; map05225; -- SN 1 ID Transcription activator BRG1/SNF2L2 (SMARCA4/BRG1/BAF190A or SMARCA2/BRM/BAF190B) DN Transcription activator BRG1 (EC 3.6.4.-) RQ 1 EV IPR030100; PTHR10799:SF76; sufficient; EV IPR030088; PTHR10799:SF541; sufficient; TG GO:0016514; -- SN 2 ID SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1/BAF57) DN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 RQ 1 EV IPR030089; PTHR13711:SF206; sufficient; TG GO:0016514; -- SN 3 ID Actin-like protein 6A (ACTL6A/BAF53) DN Actin-like protein 6A RQ 1 EV IPR029912; PTHR11937:SF191; sufficient; TG GO:0016514; -- SN 4 ID SWI/SNF complex subunit SMARCC1 (SMARCC1/BAF155) DN SWI/SNF complex subunit SMARCC1 RQ 1 EV IPR030087; PTHR12802:SF9; sufficient; TG GO:0016514; -- SN 5 ID SWI/SNF complex subunit SMARCC2 (SMARCC2/BAF170) DN SWI/SNF complex subunit SMARCC2 RQ 1 EV IPR038044; PTHR12802:SF38; sufficient; TG GO:0016514; -- SN 6 ID SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1/BAF47) DN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 RQ 1 EV IPR006939; PF04855; sufficient; EV IPR006939; PTHR10019; sufficient; TG GO:0016514; // AC GenProp2085 DE Renin-Angiotensin system TP SYSTEM AU Rawlings ND TH 1 RN [1] RM 10619573 RT The renin-angiotensin-aldosterone system: a specific target RT for hypertension management. RA Weir MR; Dzau VJ; RL Am J Hypertens 1999;12:205S-213S. RN [2] RM 11707427 RT Evidence that the angiotensin IV (AT(4)) receptor is the RT enzyme insulin-regulated aminopeptidase. RA Albiston AL; McDowall SG; Matsacos D; Sim P; Clune E; RA Mustafa T; Lee J;Mendelsohn FA; Simpson RJ; Connolly LM; RA Chai SY; RL J Biol Chem. 2001;276:48623-48626. RN [3] RM 1653799 RT Evidence that prolyl endopeptidase participates in the RT processing of brain angiotensin. RA Welches WR; Santos RA; Chappell MC; Brosnihan KB; Greene LJ; RA Ferrario CM; RL J Hypertens 1991;9:631-638. RN [4] RM 26102692 RT The role of neprilysin in angiotensin 1-7 formation in the RT kidney. RA Domenig O; Manzel A; Grobe N; Kaltenecker C; Kovarik J; RA Stegbauer J; Gurley SB; Antlanger M; Elased K; Saemann M; RA Linker R; Poglitsch M; RL J Hypertens 2015;33 Suppl 1:e114-e115. RN [5] RM 15809376 RT G-protein-coupled receptor Mas is a physiological antagonist RT of the angiotensin II type 1 receptor. RA Kostenis E; Milligan G; Christopoulos A; Sanchez-Ferrer CF; RA Heringer-Walther S; Sexton PM; Gembardt F; Kellett E; RA Martini L; Vanderheyden P; Schultheiss HP; Walther T; RL Circulation 2005;111:1806-1813. RN [6] RM 24760442 RT New components of the renin-angiotensin system: alamandine RT and the MAS-related G protein-coupled receptor D. RA Etelvino GM; Peluso AA; Santos RA; RL Curr Hypertens Rep 2014;16:433. CC Blood pressure and hydro-electrolyte balance is regulated by CC the peptide hormone angiotensin, which is secreted as a CC precursor, angiotensinogen, by the kidney. The aspastic CC endopeptidase releases the active decapeptide angiotensin I CC which is in turn cleaved by the metalloendopeptidase ACE CC (angiotensin-converting enzyme) to generate angiotensin II. CC The binding of angiotensin II to its cell-surface receptor CC AT1R brings about vasoconstriction, absorption of sodium in CC the kidney and aldosterone secretion, all of which increase CC blood pressure and hypertension. Glutamyl aminopeptidase CC converts angiotensin II to angiotensin III, which leads to CC aldosterone release from the adrenal glands. Aldosterone CC is essential for sodium conservation in the kidney, salivary CC glands, sweat glands and colon [1]. Membrane alanyl CC aminopeptidase (aminopeptidase N) generates angiotensin IV. CC Cystinyl aminopeptidase is the angiotensin IV receptor [2]. CC Neprilysin and prolyl oligopeptidase generate angiotensin CC 1-7 [3,4]. MAS1 is the angiotensin 1-7 receptor and an CC antagnoist of AT1R [5]. Alamandine is derived from CC angiotensin 1-7 by decarboxylation or by cleavage of CC angiotensin A by ACE2. Alamandine binds to the Mas-related CC G protein coupled receptor D and induces vasorelaxation [6]. DC Renin-angiotensin system DR KEGG; map04614; -- SN 1 ID Angiotensinogen DN Angiotensinogen RQ 1 EV IPR000227; PR00654; sufficient; EV IPR000227; PTHR11461:SF13; sufficient; TG GO:0002016; -- SN 2 ID Renin DN Renin (EC 3.4.23.15) RQ 1 EV IPR034135; cd05487; sufficient; TG GO:0002016; TG GO:0004190; -- SN 3 ID Angiotensin-converting enzyme DN Angiotensin-converting enzyme (EC 3.4.15.1) RQ 1 EV IPR001548; PF01401; sufficient; EV IPR001548; PR00791; sufficient; EV IPR001548; PTHR10514; sufficient; EV IPR001548; cd06461; sufficient; TG GO:0002016; TG GO:0008241; -- SN 4 ID Angiotensin II receptor DN Angiotensin II receptor RQ 1 EV IPR000248; PR00241; sufficient; TG GO:0001595; -- SN 5 ID Glutamyl aminopeptidase DN Glutamyl aminopeptidase (EC 3.4.11.7) RQ 1 EV IPR033508; PTHR11533:SF242; sufficient; TG GO:0002016; TG GO:0070006; -- SN 6 ID Aminopeptidase N DN Aminopeptidase N (EC 3.4.11.2) RQ 1 EV IPR034016; cd09601; sufficient; TG GO:0002016; TG GO:0070006; -- SN 7 ID Cystinyl aminopeptidase DN Cystinyl aminopeptidase (EC 3.4.11.3) RQ 1 EV IPR034017; PTHR11533:SF42; sufficient; TG GO:0001595; -- SN 8 ID Neprilysin DN Neprilysin (EC 3.4.24.11) RQ 1 EV IPR029727; PTHR11733:SF114; sufficient; TG GO:0004222; -- SN 9 ID Prolyl oligopeptidase DN Prolyl oligopeptidase (EC 3.4.21.26) RQ 1 EV IPR002470; PR00862; sufficient; TG GO:0002016; TG GO:0004252; -- SN 10 ID Acidic amino acid decarboxylase GADL1 DN Acidic amino acid decarboxylase GADL1 (EC 4.1.1.11) RQ 1 EV IPR039025; PTHR11999:SF95; sufficient; TG GO:0004068; -- SN 11 ID Proto-oncogene Mas DN Proto-oncogene Mas (MAS1) RQ 1 EV IPR000820; PR00533; sufficient; TG GO:0001595; -- SN 12 ID Mas-related G-protein coupled receptor member D DN Mas-related G-protein coupled receptor member D RQ 1 EV IPR026232; PR02110; sufficient; EV IPR026232; cd15108; sufficient; TG GO:0001595; // AC GenProp2086 DE Pro-insulin activation TP METAPATH AU Rawlings ND TH 3 RN [1] RM 14426955 RT Amino-acid sequence of human insulin. RA Nicol DS; Smith LF; RL Nature 1960;187:483-485. RN [2] RM 7845206 RT Pro-protein convertases of subtilisin/kexin family. RA Seidah NG; Chrétien M; RL Methods Enzymol 1994;244:175-188. RN [3] RM 10966857 RT Translational regulation of proinsulin biosynthesis and RT proinsulin conversion in the pancreatic beta-cell. RA Goodge KA; Hutton JC; RL Semin Cell Dev Biol 2000;11:235-242. CC Insulin is synthesized as a precursor. It is processed to CC generate insulin A and B chains, which are disulfide-linked, CC and the C-peptide [1]. Processing occurs at dibasic CC residues [2] and the C-terminal dibasics are removed CC sequentially by a carboxypeptidase [3]. -- SN 1 ID Pro-insulin DN Insulin RQ 1 EV IPR004825; PR00277; sufficient; TG GO:0005179; -- SN 2 ID Microsomal signal peptidase complex RQ 1 EV GenProp2038; TG GO:0005787; TG GO:0006465; -- SN 3 ID Neuroendocrine convertase 1 DN Prohormone convertase enzyme (EC 3.4.21.93) RQ 1 EV IPR022005; PF12177; sufficient; TG GO:0004252; TG GO:0016486; -- SN 4 ID Carboxypeptidase E DN Carboxypeptidase E (EC 3.4.17.10) RQ 1 EV IPR034232; cd03865; sufficient; TG GO:0004181; TG GO:0007218; // AC GenProp2087 DE Proglucagon activation TP METAPATH AU Rawlings ND TH 4 RN [1] RM 2901414 RT Glucagon gene expression in vertebrate brain. RA Drucker DJ; Asa S; RL J Biol Chem 1988;263:13475-13478. RN [2] RM 12651102 RT Expression, purification, and PC1-mediated processing of RT human proglucagon, glicentin, and major proglucagon RT fragment. RA Bonic A; Mackin RB; RL Protein Expr Purif 2003;28:15-24. RN [3] RM 9287128 RT Role of the prohormone convertase PC2 in the processing RT of proglucagon to glucagon. RA Rouillé Y; Bianchi M; Irminger JC; Halban PA; RL FEBS Lett 1997;413:119-123. RN [4] RM 11375130 RT Attenuated processing of proglucagon and glucagon-like RT peptide-1 in carboxypeptidase E-deficient mice. RA Friis-Hansen L; Lacourse KA; Samuelson LC; Holst JJ; RL J Endocrinol 2001;169:595-602. CC Glucagon is synthesized as a precursor [1]. It is CC processed to generate glicentin, oxyntomodulin, CC glucagon and glucagon-like peptides 1 and 2. Processing CC occurs at dibasic residues [2,3] and the C-terminal CC dibasics are removed sequentially by a carboxypeptidase CC [4]. -- SN 1 ID Proglucagon DN Glucagon RQ 1 EV IPR015550; PTHR11418; sufficient; TG GO:0005179; -- SN 2 ID Microsomal signal peptidase complex RQ 1 EV GenProp2038; TG GO:0005787; TG GO:0006465; -- SN 3 ID Neuroendocrine convertase 1 DN Prohormone convertase enzyme (EC 3.4.21.93) RQ 1 EV IPR022005; PF12177; sufficient; TG GO:0004252; TG GO:0016486; -- SN 4 ID Neuroendocrine convertase 2 DN Kexin/furin catalytic domain (EC 3.4.21.94) RQ 1 EV IPR034182; cd04059; sufficient; TG GO:0004252; TG GO:0016486; -- SN 5 ID Carboxypeptidase E DN Carboxypeptidase E, carboxypeptidase domain (EC 3.4.17.10) RQ 1 EV IPR034232; cd03865; sufficient; TG GO:0004181; TG GO:0007218; // AC GenProp2088 DE Insulin signaling pathway - glycogenesis TP PATHWAY AU Rawlings ND TH 7 RN [1] RM 8276809 RT Direct activation of the phosphatidylinositol 3'- RT kinase by the insulin receptor. RA Van Horn DJ; Myers MG Jr; Backer JM; RL J Biol Chem 1994;269:29-32. RN [2] RM 15733744 RT Positive and negative regulation of insulin signaling RT through IRS-1 phosphorylation. RA Gual P; Le Marchand-Brustel Y; Tanti JF; RL Biochimie 2005;87:99-109. RN [3] RM 16314505 RT Tyrosine phosphorylation of phosphoinositide- RT dependent kinase 1 by the insulin receptor is RT necessary for insulin metabolic signaling. RA Fiory F; Alberobello AT; Miele C; Oriente F; RA Esposito I; Corbo V; Ruvo M; Tizzano B; RA Rasmussen TE; Gammeltoft S; Formisano P; RA Beguinot F; RL Mol Cell Biol 2005;25:10803-10814. RN [4] RM 9512493 RT Activation of protein kinase B beta and gamma RT isoforms by insulin in vivo and by 3- RT phosphoinositide-dependent protein kinase-1 in RT vitro: comparison with protein kinase B alpha. RA Walker KS; Deak M; Paterson A; Hudson K; Cohen P; RA Alessi DR; RL Biochem J 1998;331:299-308. RN [5] RM 9736715 RT Phosphoinositide-3-OH kinase-dependent regulation RT of glycogen synthase kinase 3 and protein kinase RT B/AKT by the integrin-linked kinase. RA Delcommenne M; Tan C; Gray V; Rue L; Woodgett J; RA Dedhar S; RL Proc Natl Acad Sci U S A 1998;95:11211-11216. RN [6] RM 8226927 RT Inactivation of rabbit muscle glycogen synthase by RT glycogen synthase kinase-3. Dominant role of the RT phosphorylation of Ser-640 (site-3a). RA Wang Y; Roach PJ; RL J Biol Chem 1993;268:23876-23880. DC Insulin signaling pathway DR KEGG; map04910; CC The binding of insulin to its receptor INSR leads to the CC phosphorylation and activation of the receptor, which is CC also a tyrosine kinase [1]. INSR then phosphorylates CC various proteins known as insulin receptor substrates. CC These then associate with the regulatory subunit of CC phosphoinositide 3-kinase (PI3K) [2]. PI3K activates CC 3-phosphoinositide-dependent protein kinase 1 [3], which in CC turn activates serine kinase Akt [4]. Akt deactivates CC glycogen synthase kinase 3 [5] which leads to the activation CC of glycogen synthase and thus glycogen synthesis [6]. -- SN 1 ID Insulin DN Insulin RQ 1 EV IPR004825; PR00277; sufficient; TG GO:0005179; -- SN 2 ID Insulin receptor (INSR) DN Tyrosine-protein kinase, insulin-like receptor RQ 1 EV IPR016246; PIRSF000620; sufficient; TG GO:0005009; TG GO:0004713; -- SN 3 ID Insulin receptor substrate DN Insulin receptor substrate RQ 1 EV IPR039011; PTHR10614; sufficient; TG GO:0005158; -- SN 4 ID Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) DN Phosphatidylinositol kinase (EC 2.7.1.153) RQ 1 EV IPR015433; PTHR10048; sufficient; TG GO:0004674; -- SN 5 ID Phosphatidylinositol 3-kinase regulatory subunit (PIK3R1) DN PI3K p85/p55 subunit RQ 1 EV IPR001720; PTHR10155; sufficient; TG GO:0001784; -- SN 6 ID 3-phosphoinositide-dependent protein kinase 1 (PDPK1) DN PDPK1 family (EC 2.7.11.1) RQ 1 EV IPR039046; PTHR24356:SF163; sufficient; TG GO:0004674; -- SN 7 ID RAC-gamma serine/threonine-protein kinase (AKT1) DN Serine/threonine-protein kinase RAC (EC 2.7.11.1) RQ 1 EV IPR039027; PTHR24356:SF176; sufficient; EV IPR039029; PTHR24356:SF190; sufficient; TG GO:0004674; -- SN 8 ID Glycogen synthase kinase-3 beta (GSK3B) DN Glycogen synthase kinase-3 beta (EC 2.7.11.26) RQ 1 EV IPR033573; PTHR24057:SF8; sufficient; TG GO:0004674; -- SN 9 ID Glycogen [starch] synthase, muscle (GYS1) DN Glycogen synthase (EC 2.4.1.11) RQ 1 EV IPR008631; PF05693; sufficient; EV IPR008631; PTHR10176; sufficient; EV IPR008631; cd03793; sufficient; TG GO:0004373; // AC GenProp2089 DE Glucagon signaling pathway for glycogenolysis TP PATHWAY AU Rawlings ND TH 8 RN [1] RM 17110384 RT Conditional stimulation of type V and VI adenylyl RT cyclases by G protein betagamma subunits. RA Gao X; Sadana R; Dessauer CW; Patel TB; RL J Biol Chem 2007;282:294-302. RN [2] RM 26206488 RT Adenylyl cyclase 5 regulation by Gbetagamma involves RT isoform-specific use of multiple interaction sites. RA Brand CS; Sadana R; Malik S; Smrcka AV; Dessauer CW; RL Mol Pharmacol 2015;88:758-767. RN [3] RM 22796337 RT Emerging role of AMP-activated protein kinase in RT endocrine control of metabolism in the liver. RA Hasenour CM; Berglund ED; Wasserman DH; RL Mol Cell Endocrinol 2013;366:152-162. RN [4] RM 10487978 RT Phosphorylase kinase: the complexity of its RT regulation is reflected in the complexity of its RT structure. RA Brushia RJ; Walsh DA; RL Front Biosci 1999;4:D618-D641. RN [5] RM 29483195 RT The dynamic life of the glycogen granule. RA Prats C; Graham TE; Shearer J; RL J Biol Chem 2018 (in press). RN [6] RM 1701966 RT Liver glucose transporter: a basolateral protein in RT hepatocytes and intestine and kidney cells. RA Thorens B; Cheng ZQ; Brown D; Lodish HF; RL Am J Physiol 1990;259:C279-C285. DC Glucagon signaling pathway DR KEGG; map04922; CC Glucagon is counter-regulatory to insulin and increases the CC levels of glucose in the blood by promoting its release from CC stores of glycogen, increasing biosynthesis of glucose and CC glycogen, and reducing glycolysis. The activation of CC adenylate cyclase is crucial to all these roles [1,2]. CC Production of cAMP activates protein kinase A [3], which CC phosphorylates many cellular proteins including phosphorylase CC kinase [4]. Glycogenolysis [5] is brought about by CC phosphorylation of glycogen phosphorylase. Glucose-1- CC phosphate is released from glycogen, converted to glucose by CC glucose-6-phosphatase and transported across the plasma CC membrane by facilitated glucose transporters [6]. -- SN 1 ID Glucagon DN Glucagon RQ 1 EV IPR015550; PTHR11418; sufficient; TG GO:0005179; -- SN 2 ID Glucagon receptor DN GPCR, family 2, glucagon receptor RQ 1 EV IPR003291; PR01354; sufficient; TG GO:0004967; TG GO:0004930; -- SN 3 ID Guanine nucleotide-binding protein G(s) subunit alpha DN Guanine nucleotide binding protein (G-protein), alpha subunit RQ 1 EV IPR001019; PF00503; sufficient; EV IPR001019; PR00318; sufficient; EV IPR001019; PTHR10218; sufficient; EV IPR001019; SM00275; sufficient; EV IPR001019; cd00066; sufficient; TG GO:0005525; -- SN 4 ID Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta DN Guanine nucleotide-binding protein, beta subunit RQ 1 EV IPR016346; PTHR19850; sufficient; TG GO:0003924; -- SN 5 ID Guanine nucleotide-binding protein G(T) subunit gamma-T1 DN G-protein, gamma subunit RQ 1 EV IPR001770; PR00321; sufficient; EV IPR001770; PTHR13809; sufficient; TG GO:0003924; -- SN 6 ID Adenylate cyclase type 2 DN Adenylate cyclase (EC 4.6.1.1) RQ 1 EV IPR030672; PIRSF039050; sufficient; TG GO:0004016; -- SN 7 ID cAMP-dependent protein kinase catalytic subunit alpha DN cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) RQ 1 EV IPR039035; PTHR24353:SF82; sufficient; TG GO:0004674; -- SN 8 ID Phosphorylase b kinase alpha/beta subunits DN Phosphorylase kinase alpha/beta subunit RQ 1 EV IPR008734; PTHR10749; sufficient; TG GO:0005964; -- SN 9 ID Phosphorylase b kinase gamma subunit DN Phosphorylase kinase, gamma catalytic subunit (EC 2.7.11.19) RQ 1 EV IPR002291; PR01049; sufficient; TG GO:0004689; TG GO:0005964; -- SN 10 ID Calmodulin DN Calmodulin RQ 1 EV IPR039030; PTHR23050:SF311; sufficient; TG GO:0005964; -- SN 11 ID Glycogen phosphorylase DN Glycogen/starch/alpha-glucan phosphorylase (EC 2.4.1.1) RQ 1 EV IPR011833; TIGR02093; sufficient; EV IPR011833; cd04300; sufficient; TG GO:0008184; -- SN 12 ID Glucose-6-phosphatase DN Glucose-6-phosphatase (G6PC) (EC 3.1.3.9) RQ 1 EV IPR016275; PIRSF000905; sufficient; TG GO:0004346; -- SN 13 ID Solute carrier family 2, facilitated glucose transporter DN Glucose transporter, type 1/2 (GLUT1/2) RQ 1 EV IPR002439; PR01190; sufficient; EV IPR002440; PR01191; sufficient; TG GO:0005355; // AC GenProp2090 DE Insulin signaling pathway - glucose uptake TP PATHWAY AU Rawlings ND TH 7 RN [1] RM 8276809 RT Direct activation of the phosphatidylinositol 3'- RT kinase by the insulin receptor. RA Van Horn DJ; Myers MG Jr; Backer JM; RL J Biol Chem 1994;269:29-32. RN [2] RM 15733744 RT Positive and negative regulation of insulin signaling RT through IRS-1 phosphorylation. RA Gual P; Le Marchand-Brustel Y; Tanti JF; RL Biochimie 2005;87:99-109. RN [3] RM 16314505 RT Tyrosine phosphorylation of phosphoinositide- RT dependent kinase 1 by the insulin receptor is RT necessary for insulin metabolic signaling. RA Fiory F; Alberobello AT; Miele C; Oriente F; RA Esposito I; Corbo V; Ruvo M; Tizzano B; RA Rasmussen TE; Gammeltoft S; Formisano P; RA Beguinot F; RL Mol Cell Biol 2005;25:10803-10814. RN [4] RM 9512493 RT Activation of protein kinase B beta and gamma RT isoforms by insulin in vivo and by 3- RT phosphoinositide-dependent protein kinase-1 in RT vitro: comparison with protein kinase B alpha. RA Walker KS; Deak M; Paterson A; Hudson K; Cohen P; RA Alessi DR; RL Biochem J 1998;331:299-308. RN [5] RM 15971998 RT AS160, the Akt substrate regulating GLUT4 RT translocation, has a functional Rab GTPase- RT activating protein domain. RA Mîinea CP; Sano H; Kane S; Sano E; Fukuda M; RA Peränen J; Lane WS; Lienhard GE; RL Biochem J 2005;391:87-93. RN [6] RM 12637568 RT Insulin-stimulated phosphorylation of a Rab GTPase- RT activating protein regulates GLUT4 translocation. RA Sano H; Kane S; Sano E; Mîinea CP; Asara JM; Lane WS; RA Garner CW; Lienhard GE; RL J Biol Chem. 2003;278:14599-14602. DC Insulin signaling pathway DR KEGG; map04910; CC The binding of insulin to its receptor INSR leads to the CC phosphorylation and activation of the receptor, which is CC also a tyrosine kinase [1]. INSR then phosphorylates CC various proteins known as insulin receptor substrates. CC These then associate with the regulatory subunit of CC phosphoinositide 3-kinase (PI3K) [2]. PI3K activates CC 3-phosphoinositide-dependent protein kinase 1 [3], which in CC turn activates serine kinase Akt [4]. Akt phosphorylates CC the Rab protein TBC1D4, inhibiting its GTPase activating CC domain and allowing it to change from its GDP- to its GTP- CC bound state. Other proteins in the cascade remain in their CC activated state, stimulating the glucose transporter GLUT4 CC to be expressed on the plasma membrane, leading to glucose CC uptake. -- SN 1 ID Insulin DN Insulin RQ 1 EV IPR004825; PR00277; sufficient; TG GO:0005179; -- SN 2 ID Insulin receptor DN Tyrosine-protein kinase, insulin-like receptor RQ 1 EV IPR016246; PIRSF000620; sufficient; TG GO:0005009; TG GO:0004713; -- SN 3 ID Insulin receptor substrate DN Insulin receptor substrate RQ 1 EV IPR039011; PTHR10614; sufficient; TG GO:0005158; -- SN 4 ID Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha DN Phosphatidylinositol kinase (EC 2.7.1.153) RQ 1 EV IPR015433; PTHR10048; sufficient; TG GO:0004674; -- SN 5 ID Phosphatidylinositol 3-kinase regulatory subunit DN PI3K p85/p55 subunit RQ 1 EV IPR001720; PTHR10155; sufficient; TG GO:0001784; -- SN 6 ID 3-phosphoinositide-dependent protein kinase 1 DN PDPK1 family (EC 2.7.11.1) RQ 1 EV IPR039046; PTHR24356:SF163; sufficient; TG GO:0004674; -- SN 7 ID RAC-gamma serine/threonine-protein kinase DN Serine/threonine-protein kinase RAC (EC 2.7.11.1) RQ 1 EV IPR039027; PTHR24356:SF176; sufficient; EV IPR039029; PTHR24356:SF190; sufficient; TG GO:0004674; -- SN 8 ID TBC1 domain family member 4 DN TBC1 domain family member 4 RQ 1 EV IPR033564; PTHR22957:SF195; sufficient; TG GO:0032869; -- SN 9 ID Solute carrier family 2, facilitated glucose transporter member 4 DN Glucose transporter, type 4 (GLUT4) RQ 1 EV IPR002441; PR01193; sufficient; TG GO:0017137; TG GO:0005355; // AC GenProp2092 DE GLP-1 signalled increase in cAMP TP SYSTEM AU Rawlings ND TH 1 RN [1] RM 17306374 RT Mechanisms of action of glucagon-like peptide 1 in RT the pancreas. RA Doyle ME; Egan JM; RL Pharmacol Ther 2007;113:546-593. RN [2] RM 8405712 RT Cloning and functional expression of the human islet RT GLP-1 receptor. Demonstration that exendin-4 is an RT agonist and exendin-(9-39) an antagonist of the RT receptor. RA Thorens B; Porret A; Bühler L; Deng SP; Morel P; RA Widmann C; RL Diabetes 1993;42:1678-1682. RN [3] RM 19817800 RT Roles of cAMP signalling in insulin granule exocytosis. RA Seino S; Takahashi H; Fujimoto W; Shibasaki T; RL Diabetes Obes Metab 2009;11 Suppl 4:180-188. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter, and metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels, causing an influx of calcium into CC the cell. Alternatively, there are surface receptors CC for peptide hormones such as glucogon-like peptide 1. CC Binding triggers adenylyl cyclase activation, an CC increase in cAMP, activation of cAMP-dependent second CC messengers such as protein kinase A, and secretion of CC insulin from vesicles [1-3]. This property describes CC the steps of the pathway leading to an increase in CC cAMP. -- SN 1 ID Glucagon-like peptide-1 DN Glucagon (GLP-1) RQ 1 EV IPR015550; PR00277; sufficient; TG GO:0005179; -- SN 2 ID Glucagon-like peptide 1 receptor DN GPCR, family 2, glucagon-like peptide-1 receptor (GLP-1R) RQ 1 EV IPR003292; PR01355; sufficient; EV IPR003292; PTHR12011:SF245; sufficient; EV IPR003292; cd15268; sufficient; TG GO:0044508; -- SN 3 ID Guanine nucleotide-binding protein G subunit alpha DN Guanine nucleotide binding protein (G-protein), alpha subunit (GNA) RQ 1 EV IPR001019; PF00503; sufficient; EV IPR001019; PR00318; sufficient; EV IPR001019; PTHR10218; sufficient; EV IPR001019; SM00275; sufficient; EV IPR001019; cd00066; sufficient; TG GO:0019001; -- SN 4 ID Guanine nucleotide-binding protein G subunit beta DN Guanine nucleotide-binding protein G subunit beta (GNB) RQ 1 EV IPR016346; PTHR19850; sufficient; TG GO:0003924; -- SN 5 ID Guanine nucleotide-binding protein G subunit gamma DN Guanine nucleotide-binding protein G subunit gamma (GNG) RQ 1 EV IPR001770; PTHR13809; sufficient; EV IPR001770; PR00321; sufficient; TG GO:0003924; -- SN 6 ID Adenylate cyclase DN Adenylate cyclase (AC) RQ 1 EV IPR030672; PIRSF039050; sufficient; TG GO:0004016; // AC GenProp2093 DE GIP signalled increase in cAMP TP SYSTEM AU Rawlings ND TH 1 RN [1] RM 15533777 RT Clinical endocrinology and metabolism. Glucose- RT dependent insulinotropic polypeptide/gastric RT inhibitory polypeptide. RA Meier JJ; Nauck MA; RL Best Pract Res Clin Endocrinol Metab 2004;18:587-606. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter, and metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels, causing an influx of calcium into CC the cell. Alternatively, there are surface receptors CC for peptide hormones such as GIP [1]. CC Binding triggers adenylyl cyclase activation, an CC increase in cAMP, activation of cAMP-dependent second CC messengers such as protein kinase A, and secretion of CC insulin from vesicles [1]. This property describes CC the steps of the pathway leading to an increase in CC cAMP. -- SN 1 ID Gastric inhibitory polypeptide DN Gastric inhibitory polypeptide (GIP) RQ 1 EV IPR039078; PTHR15211; sufficient; TG GO:0005179; -- SN 2 ID Glucose-dependent insulinotropic receptor DN Glucose-dependent insulinotropic receptor (GIPR) RQ 1 EV IPR028336; PTHR22750:SF7; sufficient; EV IPR028336; SF7cd15104; sufficient; TG GO:0004930; -- SN 3 ID Guanine nucleotide-binding protein G subunit alpha DN Guanine nucleotide binding protein (G-protein), alpha subunit (GNA) RQ 1 EV IPR001019; PF00503; sufficient; EV IPR001019; PR00318; sufficient; EV IPR001019; PTHR10218; sufficient; EV IPR001019; SM00275; sufficient; EV IPR001019; cd00066; sufficient; TG GO:0019001; -- SN 4 ID Guanine nucleotide-binding protein G subunit beta DN Guanine nucleotide-binding protein G subunit beta (GNB) RQ 1 EV IPR016346; PTHR19850; sufficient; TG GO:0003924; -- SN 5 ID Guanine nucleotide-binding protein G subunit gamma DN Guanine nucleotide-binding protein G subunit gamma (GNG) RQ 1 EV IPR001770; PTHR13809; sufficient; EV IPR001770; PR00321; sufficient; TG GO:0003924; -- SN 6 ID Adenylate cyclase DN Adenylate cyclase (AC) RQ 1 EV IPR030672; PIRSF039050; sufficient; TG GO:0004016; // AC GenProp2094 DE PACAP signalled increase in cAMP TP SYSTEM AU Rawlings ND TH 1 RN [1] RM 7902709 RT Molecular cloning and functional expression of a cDNA RT encoding a human pituitary adenylate cyclase activating RT polypeptide receptor. RA Ogi K; Miyamoto Y; Masuda Y; Habata Y; Hosoya M; Ohtaki RA T; Masuo Y; Onda H; Fujino M; RL Best Pract Res Clin Endocrinol Metab 2004;18:587-606. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter, and metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels, causing an influx of calcium into CC the cell. Alternatively, there are surface receptors CC for peptide hormones such as PACAP [1]. CC Binding triggers adenylyl cyclase activation, an CC increase in cAMP, activation of cAMP-dependent second CC messengers such as protein kinase A, and secretion of CC insulin from vesicles [1]. -- SN 1 ID Pituitary adenylate cyclase-activating polypeptide DN Pituitary adenylate cyclase-activating polypeptide (PACAP) RQ 1 EV IPR039080; PTHR11213:SF1; sufficient; TG GO:0005184; -- SN 2 ID Pituitary adenylate cyclase-activating polypeptide type I receptor DN GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor (PACAPR) RQ 1 EV IPR002285; PR01156; sufficient; EV IPR002285; PTHR12011:SF228; sufficient; TG GO:0007166; -- SN 3 ID Guanine nucleotide-binding protein G subunit alpha DN Guanine nucleotide binding protein (G-protein), alpha subunit (GNA) RQ 1 EV IPR001019; PF00503; sufficient; EV IPR001019; PR00318; sufficient; EV IPR001019; PTHR10218; sufficient; EV IPR001019; SM00275; sufficient; EV IPR001019; cd00066; sufficient; TG GO:0019001; -- SN 4 ID Guanine nucleotide-binding protein G subunit beta DN Guanine nucleotide-binding protein G subunit beta (GNB) RQ 1 EV IPR016346; PTHR19850; sufficient; TG GO:0003924; -- SN 5 ID Guanine nucleotide-binding protein G subunit gamma DN Guanine nucleotide-binding protein G subunit gamma (GNG) RQ 1 EV IPR001770; PTHR13809; sufficient; EV IPR001770; PR00321; sufficient; TG GO:0003924; -- SN 6 ID Adenylate cyclase DN Adenylate cyclase (AC) RQ 1 EV IPR030672; PIRSF039050; sufficient; TG GO:0004016; // AC GenProp2095 DE Insulin secretion via PKA TP METAPATH AU Rawlings ND TH 1 RN [1] RM 9914469 RT Molecular mechanisms and regulation of insulin RT exocytosis as a paradigm of endocrine secretion. RA Lang J; RL Eur J Biochem 1999;259:3-17. RN [2] RM 26206488 RT Adenylyl cyclase 5 regulation by Gbetagamma involves RT isoform-specific use of multiple interaction sites. RA Brand CS; Sadana R; Malik S; Smrcka AV; Dessauer CW; RL Mol Pharmacol 2015;88:758-767. RN [3] RM 9715374 RT Protein kinases, protein phosphorylation, and the RT regulation of insulin secretion from pancreatic beta- RT cells. RA Jones PMl Persaud SJ; RL Endocr Rev 1998;19:429-461. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter. Metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels, causing an influx of calcium into CC the cell [1]. Alternatively, there are surface CC receptors for peptide hormones such as glucagon-like CC peptide 1. Binding triggers an increase in cAMP, CC activation of G proteins, leading to insulin secretion CC via binding of storage vesicles to the membrane [2]. CC Depolarization of the plasma membrane leads to an CC influx of calcium, activation of calcium/calmodulin- CC dependent protein kinase and translocation of insulin- CC containing vesicles to the cell surface [3]. -- SN 1 ID Peptide hormone initiated increase in cAMP DN Peptide hormone initiated increase in cAMP RQ 1 EV GenProp2092; EV GenProp2093; EV GenProp2094; -- SN 5 ID cAMP-dependent protein kinase catalytic subunits DN cAMP-dependent protein kinase catalytic subunits (PRKACA, PRKACB, PRKACG) (EC 2.7.11.11) RQ 1 EV IPR039035; PTHR24353:SF82; sufficient; EV IPR039083; PTHR24353:SF116; sufficient; EV IPR039084; PTHR24353:SF113; sufficient; TG GO:0004674; TG GO:0004691; -- SN 6 ID cAMP-dependent protein kinase regulatory subunits DN cAMP-dependent protein kinase regulatory subunits (PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B) RQ 1 EV IPR012198; PIRSF000548; sufficient; TG GO:0000166; -- SN 7 ID Voltage-dependent L-type calcium channel subunits alpha DN Voltage-dependent L-type calcium channel subunits alpha (CACNA1C, CACNA1D, CACNA1F, CACNA1S) RQ 1 EV IPR005446; PR01630; sufficient; TG GO:0005245; -- SN 8 ID Calcium/calmodulin-dependent protein kinase type II DN Calcium/calmodulin-dependent protein kinase type II (CAMK2A, CAMK2B, CAMK2D, CAMK2G) RQ 1 EV IPR039071; PTHR43940; sufficient; TG GO:0004683; -- SN 9 ID Insulin release from secretory granules RQ 1 EV GenProp2097; // AC GenProp2096 DE Insulin secretion via PKC TP METAPATH AU Rawlings ND TH 3 RN [1] RM 9914469 RT Molecular mechanisms and regulation of insulin RT exocytosis as a paradigm of endocrine secretion. RA Lang J; RL Eur J Biochem 1999;259:3-17. RN [2] RM 3014651 RT Studies and perspectives of protein kinase C. RA Nishizuka Y; RL Science 1986;233:305-312. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter, and metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels, causing an influx of calcium into CC the cell [1]. Alternatively, there are surface CC receptors for acetylcholine, CCK and FA. Binding CC leads to activation of PLC, which generates the second CC messenger diacylglycerol, and PKC [2], followed by CC release of insulin from insulin secretory granules. -- SN 1 ID Cholecystokinin/acetylcholine/free fatty acid receptor DN Cholecystokinin/acetylcholine/free fatty acid receptor (CCKAR/CHRM3/FFAR1) RQ 1 EV IPR000596; PR00524; sufficient; EV IPR001183; PR00540; sufficient; EV IPR001183; cd15299; sufficient; EV IPR013313; PR01905; sufficient; EV IPR013313; cd15169; sufficient; TG GO:0007186; -- SN 2 ID Guanine nucleotide-binding protein subunit alpha-11/G(q) subunit alpha DN Guanine nucleotide-binding protein subunit alpha-11 (GNA11)/Guanine nucleotide-binding protein G(q) subunit alpha (GNAQ) RQ 1 EV IPR000654; PR00442; sufficient; TG GO:0001664; -- SN 4 ID 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta DN 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta (PLCB1, PLCB2, PLCB3, PLCB4) (EC 3.1.4.11) RQ 1 EV IPR016280; PIRSF000956; sufficient; TG GO:0004435; -- SN 5 ID Protein kinase C DN Protein kinase C (PRKCA, PRKCB, PRKCG) (EC 2.7.11.13) RQ 1 EV IPR014375; PIRSF000550; sufficient; TG GO:0004697; -- SN 6 ID Insulin release from secretory granules RQ 1 EV GenProp2097; // AC GenProp2097 DE Insulin release from secretory granules TP PATHWAY AU Rawlings ND TH 1 RN [1] RM 9914469 RT Molecular mechanisms and regulation of insulin RT exocytosis as a paradigm of endocrine secretion. RA Lang J; RL Eur J Biochem 1999;259:3-17. RN [2] RM 9715374 RT Protein kinases, protein phosphorylation, and the RT regulation of insulin secretion from pancreatic beta- RT cells. RA Jones PMl Persaud SJ; RL Endocr Rev 1998;19:429-461. RN [3] RM 9759724 RT Crystal structure of a SNARE complex involved in RT synaptic exocytosis at 2.4 A resolution. RA Sutton RB; Fasshauer D; Jahn R; Brunger AT; RL Nature 1998;395:347-353. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. There CC are numerous stilumi that promote release of the CC hormone from secretory granules [1,2]. Fusion of the CC granule and plasma membranes is brought about by the CC association of VAMP2 with the syntaxin/SNAP25 complex CC [3]. -- SN 1 ID Vesicle-associated membrane protein 2 DN Vesicle-associated membrane protein 2 (VAMP2) RQ 1 EV IPR028717; PTHR21136:SF91; sufficient; TG GO:0006887; TG GO:0019905; -- SN 2 ID Syntaxin-1A DN Syntaxin 1A RQ 1 EV IPR028669; PTHR19957:SF84; sufficient; TG GO:0031629; TG GO:0045921; -- SN 3 ID Synaptosomal-associated protein 25 DN Synaptosomal-associated protein 25 (SNAP25) RQ 1 EV IPR039077; PTHR19305:SF5; sufficient; TG GO:0017075; -- SN 4 ID Insulin DN Insulin RQ 1 EV IPR004825; PR00277; sufficient; TG GO:0005179; // AC GenProp2098 DE Insulin secretion via IP3 TP METAPATH AU Rawlings ND TH 5 RN [1] RM 9914469 RT Molecular mechanisms and regulation of insulin RT exocytosis as a paradigm of endocrine secretion. RA Lang J; RL Eur J Biochem 1999;259:3-17. RN [2] RM 2541501 RT Studies of inositol phospholipid-specific phospholipase RT C. RA Rhee SG; Suh PG; Ryu SH; Lee SY; RL Science 1989;244:546-550. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter, and metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels, causing an influx of calcium into CC the cell [1]. Alternatively, there are surface CC receptors for acetylcholine, CCK and FA. Binding CC leads to activation of PLC, which generates the second CC messenger inositol 1,4,5-trisphosphate (IP3) [2]. The CC binding of IP3 to a receptor of the endoplasmic CC reticulum surface, leads to calcium release into the CC cyoplasm and activation of CAMK. This leads to release CC of insulin from insulin secretory granules. -- SN 1 ID Cholecystokinin/acetylcholine/free fatty acid receptor DN Cholecystokinin/acetylcholine/free fatty acid receptor (CCKAR/CHRM3/FFAR1) RQ 1 EV IPR000596; PR00524; sufficient; EV IPR001183; PR00540; sufficient; EV IPR001183; cd15299; sufficient; EV IPR013313; PR01905; sufficient; EV IPR013313; cd15169; sufficient; TG GO:0007186; -- SN 2 ID Guanine nucleotide-binding protein subunit alpha-11/G(q) subunit alpha DN Guanine nucleotide-binding protein subunit alpha-11 (GNA11)/Guanine nucleotide-binding protein G(q) subunit alpha (GNAQ) RQ 1 EV IPR000654; PR00442; sufficient; TG GO:0001664; -- SN 4 ID 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta DN 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta (PLCB1, PLCB2, PLCB3, PLCB4) (EC 3.1.4.11) RQ 1 EV IPR016280; PIRSF000956; sufficient; TG GO:0004435; -- SN 5 ID Inositol 1,4,5-trisphosphate receptor type 3 DN Inositol 1,4,5-trisphosphate receptor type 3 (ITPR3) RQ 1 EV IPR000493; PR00779; sufficient; TG GO:0000822; TG GO:0005220; -- SN 6 ID Calcium/calmodulin-dependent protein kinase type II DN Calcium/calmodulin-dependent protein kinase type II (CAMK2A, CAMK2B, CAMK2D, CAMK2G) EV IPR039071; PTHR43940; sufficient; TG GO:0004683; -- SN 7 ID Insulin release from secretory granules RQ 1 EV GenProp2097; // AC GenProp2099 DE Insulin secretion via glucose TP METAPATH AU Rawlings ND TH 5 RN [1] RM 9914469 RT Molecular mechanisms and regulation of insulin RT exocytosis as a paradigm of endocrine secretion. RA Lang J; RL Eur J Biochem 1999;259:3-17. RN [2] RM 9683320 RT Correlating structure and function in ATP-sensitive RT K+ channels. RA Ashcroft FM; Gribble FM; RL Trends Neurosci 1998;21:288-294. RN [3] RM 17855752 RT A mutation in the ATP-binding site of the Kir6.2 RT subunit of the KATP channel alters coupling with the RT SUR2A subunit. RA Tammaro P; Ashcroft F; RL J Physiol 2007;584:743-753. DC Insulin secretion DR KEGG; map04911; CC Insulin is secreted by the pancreatic beta cells. Its CC secretion can be stimulated by the import of glucose CC via a surface transporter, and metabolism of glucose CC increases intracellular ATP, inhibiting ATP-sensitive CC potassium channels [2,3], causing an influx of calcium CC into the cell [1]. -- SN 1 ID Solute carrier family 2, facilitated glucose transporter DN Glucose transporter, type 1/2 (GLUT1/SLC2A1, GLUT2/SLC2A2) EV IPR002439; PR01190; sufficient; EV IPR002440; PR01191; sufficient; TG GO:0005355; -- SN 2 ID Glucokinase DN Glucokinase, chordate (GCK) (EC 2.7.1.2) EV IPR039073; PTHR19443:SF3; sufficient; TG GO:0004340; -- SN 3 ID TCA cycle RQ 1 EV GenProp0033; -- SN 4 ID Transient receptor potential cation channel subfamily M member 4 DN Transient receptor potential cation channel subfamily M member 4 (TRPM4) EV IPR029581; PTHR13800:SF6; sufficient; TG GO:0005272; -- SN 5 ID Sodium/potassium-transporting ATPase subunit alpha-1 DN P-type ATPase subfamily IIC, subunit alpha (ATP1A1, ATP1A2, ATP1A3, ATP1A4) EV IPR005775; TIGR01106; sufficient; EV IPR005775; cd02608; sufficient; TG GO:0005391; -- SN 6 ID Sodium/potassium-transporting ATPase subunit beta-1 DN Sodium/potassium-transporting ATPase subunit beta (ATP1B1, ATP1B2, ATP1B3) EV IPR000402; PF00287; sufficient; EV IPR000402; PS00390; sufficient; EV IPR000402; PS00391; sufficient; EV IPR000402; PTHR11523; sufficient; EV IPR000402; TIGR01107; sufficient; TG GO:0005391; -- SN 7 ID ATP-binding cassette sub-family C member 8 DN ATP-binding cassette subfamily C member 8 (ABCC8) EV IPR000844; PR01093; sufficient; EV IPR000844; PTHR24223:SF187; sufficient; TG GO:0005267; -- SN 8 ID ATP-sensitive inward rectifier potassium channel 11 DN Potassium channel, inwardly rectifying, Kir6.2 (KCNJ11) EV IPR003279; PR01332; sufficient; EV IPR003279; PTHR11767:SF44; sufficient; TG GO:0005249; -- SN 9 ID Voltage-dependent L-type calcium channel subunits alpha DN Voltage-dependent calcium channel, L-type, alpha-1 subunit (CACNA1C, CACNA1D, CACNA1F, CACNA1S) RQ 1 EV IPR005446; PR01630; sufficient; TG GO:0005245; -- SN 10 ID Calcium/calmodulin-dependent protein kinase type II DN Calcium/calmodulin-dependent protein kinase type II (CAMK2A, CAMK2B, CAMK2D, CAMK2G) RQ 1 EV IPR039071; PTHR43940; sufficient; TG GO:0004683; -- SN 11 ID Insulin release from secretory granules RQ 1 EV GenProp2097; //