"TF"	"Target"	"_comments"
"crp"	"cyaA"	"Disabled because of negative feedback in acetate - cyaA -> cAMP -> cAMP-crp"
"bglJ"	"leuO"	"Remove feedback loop between bglJ <-> leuO"
"leuO"	"bglJ"	"Remove feedback loop between bglJ <-> leuO"
"fnr"	"arcA"	"Remove to get expression of arcA"
"leuO"	"leuA"	"Remove for more steady expression of LeuA - need better control of LeuO expression"
"lrp"	"rplR"	"Remove to increase ribosome counts in with amino acid conditions when simulating with ppGpp"
"argR"	"rpsO"	"Remove to increase ribosome counts in with amino acid conditions when simulating with ppGpp"
"crp"	"rpsO"	"Remove to increase ribosome counts in with amino acid conditions when simulating with ppGpp"
"fis"	"rpsO"	"Remove to increase ribosome counts in with amino acid conditions when simulating with ppGpp"
"fis"	"gltX"	"Remove to get higher charging in with amino acid conditions when simulating with ppGpp"
"argP"	"gdhA"	"Remove to get stable growth with mechanistic translation supply due to complexity of ArgP signaling and Lys pathway control"
"crp"	"rplI"	"Remove to get expression in ppGpp"
"crp"	"rpsF"	"Remove to get expression in ppGpp"
"crp"	"rpsR"	"Remove to get expression in ppGpp"
"lrp"	"ilvA"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (regulation reduced Ile synthesis rate to near 0)"
"lrp"	"glnA"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (regulation reduced Gln synthesis rate to near 0)"
"lrp"	"serA"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (regulation reduced Ser synthesis rate to near 0)"
"lrp"	"aspC"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (regulation reduced Asp synthesis rate to near 0)"
"lrp"	"can"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (shut down Arg synthesis)"
"lrp"	"ilvD"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (shut down Val synthesis)"
"lrp"	"pyrI"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (shut down UTP synthesis)"
"lrp"	"ilvE"	"Remove to get stable growth with ppGpp regulation and amino acid supply especially with Leu added (catalyzes the forward and reverse reaction for the last step of multiple amino acids but only account for the reverse direction with the current amino acid synthesis implementation)"
"argR"	"hisL"	"Remove to get sufficient expression of histidine biosynthesis enzymes in the His operon when operon structures are used"
"lexA"	"rpsU"	"Remove to get sufficient expression of the ribosomal subunit rpsU when ppGpp regulation and operon structures are used"
"fis"	"rrfH"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"fis"	"rrlG"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"fis"	"rrsG"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"fis"	"rrsH"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"hns"	"rrfH"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"hns"	"rrlG"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"hns"	"rrsG"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"hns"	"rrsH"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"lrp"	"rrfH"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"lrp"	"rrlG"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"lrp"	"rrsG"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"
"lrp"	"rrsH"	"Remove to eliminate operon-specific regulation of rRNAs by certain TFs"