%* Data Describing the starting set of metabolites atom(Compound name, Atom number, Atom type). bond(Compound name, Chemical bond type, Atom number1, Greater Atom number2). *% % Mycosporine-like amino acids PWY-7751 atom("sedoheptulose-7-phosphate",1..5,carb). atom("sedoheptulose-7-phosphate",6,oxyg). atom("sedoheptulose-7-phosphate",7,carb). atom("sedoheptulose-7-phosphate",8,carb). atom("sedoheptulose-7-phosphate",9..12,oxyg). atom("sedoheptulose-7-phosphate",25,oxyg). atom("sedoheptulose-7-phosphate",26..29,oxyg). atom("sedoheptulose-7-phosphate",30,phos). bond("sedoheptulose-7-phosphate",single,1,2). bond("sedoheptulose-7-phosphate",single,2,3). bond("sedoheptulose-7-phosphate",single,3,4). bond("sedoheptulose-7-phosphate",single,4,5). bond("sedoheptulose-7-phosphate",singleR,4,25). bond("sedoheptulose-7-phosphate",single,5,6). bond("sedoheptulose-7-phosphate",single,1,6). bond("sedoheptulose-7-phosphate",singleR,5,7). bond("sedoheptulose-7-phosphate",singleS,3,10). bond("sedoheptulose-7-phosphate",singleR,1,8). bond("sedoheptulose-7-phosphate",singleS,5,12). bond("sedoheptulose-7-phosphate",single,7,11). bond("sedoheptulose-7-phosphate",singleS,2,9). bond("sedoheptulose-7-phosphate",single,9,26). bond("sedoheptulose-7-phosphate",single,26,30). bond("sedoheptulose-7-phosphate",single,27,30). bond("sedoheptulose-7-phosphate",double,28,30). bond("sedoheptulose-7-phosphate",single,29,30). atom("R-demethyl-4-deoxygadusol",1..7,carb). atom("R-demethyl-4-deoxygadusol",8,oxyg). atom("R-demethyl-4-deoxygadusol",9..12,oxyg). bond("R-demethyl-4-deoxygadusol",double,1,2). bond("R-demethyl-4-deoxygadusol",single,2,3). bond("R-demethyl-4-deoxygadusol",single,3,4). bond("R-demethyl-4-deoxygadusol",single,4,5). bond("R-demethyl-4-deoxygadusol",single,5,6). bond("R-demethyl-4-deoxygadusol",single,1,6). bond("R-demethyl-4-deoxygadusol",single,5,7). bond("R-demethyl-4-deoxygadusol",double,3,10). bond("R-demethyl-4-deoxygadusol",single,1,8). bond("R-demethyl-4-deoxygadusol",singleR,5,12). bond("R-demethyl-4-deoxygadusol",single,7,11). bond("R-demethyl-4-deoxygadusol",single,2,9). atom("S-demethyl-4-deoxygadusol",1..7,carb). atom("S-demethyl-4-deoxygadusol",8,oxyg). atom("S-demethyl-4-deoxygadusol",9..12,oxyg). bond("S-demethyl-4-deoxygadusol",double,1,2). bond("S-demethyl-4-deoxygadusol",single,2,3). bond("S-demethyl-4-deoxygadusol",single,3,4). bond("S-demethyl-4-deoxygadusol",single,4,5). bond("S-demethyl-4-deoxygadusol",single,5,6). bond("S-demethyl-4-deoxygadusol",single,1,6). bond("S-demethyl-4-deoxygadusol",single,5,7). bond("S-demethyl-4-deoxygadusol",double,3,10). bond("S-demethyl-4-deoxygadusol",single,1,8). bond("S-demethyl-4-deoxygadusol",singleS,5,12). bond("S-demethyl-4-deoxygadusol",single,7,11). bond("S-demethyl-4-deoxygadusol",single,2,9). atom("R-4-deoxygadusol",1..7,carb). atom("R-4-deoxygadusol",8,oxyg). atom("R-4-deoxygadusol",9..12,oxyg). atom("R-4-deoxygadusol",13,carb). bond("R-4-deoxygadusol",double,1,2). bond("R-4-deoxygadusol",single,2,3). bond("R-4-deoxygadusol",single,3,4). bond("R-4-deoxygadusol",single,4,5). bond("R-4-deoxygadusol",single,5,6). bond("R-4-deoxygadusol",single,1,6). bond("R-4-deoxygadusol",single,5,7). bond("R-4-deoxygadusol",double,3,10). bond("R-4-deoxygadusol",single,1,8). bond("R-4-deoxygadusol",singleR,5,12). bond("R-4-deoxygadusol",single,7,11). bond("R-4-deoxygadusol",single,2,9). bond("R-4-deoxygadusol",single,9,13). atom("S-4-deoxygadusol",1..7,carb). atom("S-4-deoxygadusol",8,oxyg). atom("S-4-deoxygadusol",9..12,oxyg). atom("S-4-deoxygadusol",13,carb). bond("S-4-deoxygadusol",double,1,2). bond("S-4-deoxygadusol",single,2,3). bond("S-4-deoxygadusol",single,3,4). bond("S-4-deoxygadusol",single,4,5). bond("S-4-deoxygadusol",single,5,6). bond("S-4-deoxygadusol",single,1,6). bond("S-4-deoxygadusol",single,5,7). bond("S-4-deoxygadusol",double,3,10). bond("S-4-deoxygadusol",single,1,8). bond("S-4-deoxygadusol",singleS,5,12). bond("S-4-deoxygadusol",single,7,11). bond("S-4-deoxygadusol",single,2,9). bond("S-4-deoxygadusol",single,9,13). atom("mycosporin-glycine",1..7,carb). atom("mycosporin-glycine",8,nitr). atom("mycosporin-glycine",9..12,oxyg). atom("mycosporin-glycine",13..15,carb). atom("mycosporin-glycine",16..17,oxyg). bond("mycosporin-glycine",double,1,2). bond("mycosporin-glycine",single,2,3). bond("mycosporin-glycine",single,3,4). bond("mycosporin-glycine",single,4,5). bond("mycosporin-glycine",single,5,6). bond("mycosporin-glycine",single,1,6). bond("mycosporin-glycine",single,5,7). bond("mycosporin-glycine",double,3,10). bond("mycosporin-glycine",single,1,8). bond("mycosporin-glycine",singleS,5,12). bond("mycosporin-glycine",single,7,11). bond("mycosporin-glycine",single,2,9). bond("mycosporin-glycine",single,9,13). bond("mycosporin-glycine",single,8,14). bond("mycosporin-glycine",single,14,15). bond("mycosporin-glycine",double,15,16). bond("mycosporin-glycine",single,15,17). atom("shinorine",1..7,carb). atom("shinorine",8,nitr). atom("shinorine",9,oxyg). atom("shinorine",10,nitr). atom("shinorine",11..12,oxyg). atom("shinorine",13..15,carb). atom("shinorine",16..17,oxyg). atom("shinorine",18..19,carb). atom("shinorine",20,oxyg). atom("shinorine",21,carb). atom("shinorine",22..23,oxyg). bond("shinorine",double,1,2). bond("shinorine",single,2,3). bond("shinorine",single,3,4). bond("shinorine",single,4,5). bond("shinorine",single,5,6). bond("shinorine",single,1,6). bond("shinorine",single,5,7). bond("shinorine",double,3,10). bond("shinorine",single,1,8). bond("shinorine",singleS,5,12). bond("shinorine",single,7,11). bond("shinorine",single,2,9). bond("shinorine",single,9,13). bond("shinorine",single,8,14). bond("shinorine",single,14,15). bond("shinorine",double,15,16). bond("shinorine",single,15,17). bond("shinorine",single,10,18). bond("shinorine",single,18,19). bond("shinorine",single,19,20). bond("shinorine",single,18,21). bond("shinorine",double,21,22). bond("shinorine",single,21,23). % Other Mycosporine amino-acids atom("palythinol",1..7,carb). atom("palythinol",8,nitr). atom("palythinol",9,oxyg). atom("palythinol",10,nitr). atom("palythinol",11..12,oxyg). atom("palythinol",13..15,carb). atom("palythinol",16..17,oxyg). atom("palythinol",18..19,carb). atom("palythinol",20,oxyg). atom("palythinol",21,carb). bond("palythinol",double,1,2). bond("palythinol",single,2,3). bond("palythinol",single,3,4). bond("palythinol",single,4,5). bond("palythinol",single,5,6). bond("palythinol",single,1,6). bond("palythinol",single,5,7). bond("palythinol",double,3,10). bond("palythinol",single,1,8). bond("palythinol",singleS,5,12). bond("palythinol",single,7,11). bond("palythinol",single,2,9). bond("palythinol",single,9,13). bond("palythinol",single,8,14). bond("palythinol",single,14,15). bond("palythinol",double,15,16). bond("palythinol",single,15,17). bond("palythinol",single,10,18). bond("palythinol",single,18,19). bond("palythinol",single,19,20). bond("palythinol",single,18,21). atom("asterina-330",1..7,carb). atom("asterina-330",8,nitr). atom("asterina-330",9,oxyg). atom("asterina-330",10,nitr). atom("asterina-330",11..12,oxyg). atom("asterina-330",13..15,carb). atom("asterina-330",16..17,oxyg). atom("asterina-330",18..19,carb). atom("asterina-330",20,oxyg). bond("asterina-330",double,1,2). bond("asterina-330",single,2,3). bond("asterina-330",single,3,4). bond("asterina-330",single,4,5). bond("asterina-330",single,5,6). bond("asterina-330",single,1,6). bond("asterina-330",single,5,7). bond("asterina-330",double,3,10). bond("asterina-330",single,1,8). bond("asterina-330",singleS,5,12). bond("asterina-330",single,7,11). bond("asterina-330",single,2,9). bond("asterina-330",single,9,13). bond("asterina-330",single,8,14). bond("asterina-330",single,14,15). bond("asterina-330",double,15,16). bond("asterina-330",single,15,17). bond("asterina-330",single,10,18). bond("asterina-330",single,18,19). bond("asterina-330",single,19,20). atom("palythine",1..7,carb). atom("palythine",8,nitr). atom("palythine",9,oxyg). atom("palythine",10,nitr). atom("palythine",11..12,oxyg). atom("palythine",13..15,carb). atom("palythine",16..17,oxyg). bond("palythine",double,1,2). bond("palythine",single,2,3). bond("palythine",single,3,4). bond("palythine",single,4,5). bond("palythine",single,5,6). bond("palythine",single,1,6). bond("palythine",single,5,7). bond("palythine",double,3,10). bond("palythine",single,1,8). bond("palythine",singleS,5,12). bond("palythine",single,7,11). bond("palythine",single,2,9). bond("palythine",single,9,13). bond("palythine",single,8,14). bond("palythine",single,14,15). bond("palythine",double,15,16). bond("palythine",single,15,17). atom("porphyra-334",1..7,carb). atom("porphyra-334",8,nitr). atom("porphyra-334",9,oxyg). atom("porphyra-334",10,nitr). atom("porphyra-334",11..12,oxyg). atom("porphyra-334",13..15,carb). atom("porphyra-334",16..17,oxyg). atom("porphyra-334",18..19,carb). atom("porphyra-334",20,oxyg). atom("porphyra-334",21,carb). atom("porphyra-334",22..23,oxyg). atom("porphyra-334",24,carb). bond("porphyra-334",double,1,2). bond("porphyra-334",single,2,3). bond("porphyra-334",single,3,4). bond("porphyra-334",single,4,5). bond("porphyra-334",single,5,6). bond("porphyra-334",single,1,6). bond("porphyra-334",single,5,7). bond("porphyra-334",double,3,10). bond("porphyra-334",single,1,8). bond("porphyra-334",singleS,5,12). bond("porphyra-334",single,7,11). bond("porphyra-334",single,2,9). bond("porphyra-334",single,9,13). bond("porphyra-334",single,8,14). bond("porphyra-334",single,14,15). bond("porphyra-334",double,15,16). bond("porphyra-334",single,15,17). bond("porphyra-334",single,10,18). bond("porphyra-334",single,18,19). bond("porphyra-334",single,19,20). bond("porphyra-334",single,18,21). bond("porphyra-334",double,21,22). bond("porphyra-334",single,21,23). bond("porphyra-334",single,19,24). atom("z-palythenic acid",1..7,carb). atom("z-palythenic acid",8,nitr). atom("z-palythenic acid",9,oxyg). atom("z-palythenic acid",10,nitr). atom("z-palythenic acid",11..12,oxyg). atom("z-palythenic acid",13..15,carb). atom("z-palythenic acid",16..17,oxyg). atom("z-palythenic acid",18..19,carb). atom("z-palythenic acid",21,carb). atom("z-palythenic acid",22..23,oxyg). atom("z-palythenic acid",24,carb). bond("z-palythenic acid",double,1,2). bond("z-palythenic acid",single,2,3). bond("z-palythenic acid",single,3,4). bond("z-palythenic acid",single,4,5). bond("z-palythenic acid",single,5,6). bond("z-palythenic acid",single,1,6). bond("z-palythenic acid",single,5,7). bond("z-palythenic acid",double,3,10). bond("z-palythenic acid",single,1,8). bond("z-palythenic acid",singleS,5,12). bond("z-palythenic acid",single,7,11). bond("z-palythenic acid",single,2,9). bond("z-palythenic acid",single,9,13). bond("z-palythenic acid",single,8,14). bond("z-palythenic acid",single,14,15). bond("z-palythenic acid",double,15,16). bond("z-palythenic acid",single,15,17). bond("z-palythenic acid",single,10,18). bond("z-palythenic acid",double,18,19). bond("z-palythenic acid",single,18,21). bond("z-palythenic acid",double,21,22). bond("z-palythenic acid",single,21,23). bond("z-palythenic acid",single,19,24). atom("palythene",1..7,carb). atom("palythene",8,nitr). atom("palythene",9,oxyg). atom("palythene",10,nitr). atom("palythene",11..12,oxyg). atom("palythene",13..15,carb). atom("palythene",16..17,oxyg). atom("palythene",18..19,carb). atom("palythene",24,carb). bond("palythene",double,1,2). bond("palythene",single,2,3). bond("palythene",single,3,4). bond("palythene",single,4,5). bond("palythene",single,5,6). bond("palythene",single,1,6). bond("palythene",single,5,7). bond("palythene",double,3,10). bond("palythene",single,1,8). bond("palythene",singleS,5,12). bond("palythene",single,7,11). bond("palythene",single,2,9). bond("palythene",single,9,13). bond("palythene",single,8,14). bond("palythene",single,14,15). bond("palythene",double,15,16). bond("palythene",single,15,17). bond("palythene",single,10,18). bond("palythene",double,18,19). bond("palythene",single,19,24). %* Shared domain *% % Definition of a cyclohexene atomDomain(cyclohexene,1,carb). atomDomain(cyclohexene,2,carb). atomDomain(cyclohexene,3,carb). atomDomain(cyclohexene,4,carb). atomDomain(cyclohexene,5,carb). atomDomain(cyclohexene,6,carb). bondDomain(cyclohexene,double,1,2). bondDomain(cyclohexene,single,2,3). bondDomain(cyclohexene,single,3,4). bondDomain(cyclohexene,single,4,5). bondDomain(cyclohexene,single,5,6). bondDomain(cyclohexene,single,1,6). %* Known reactions %%%%%%%%%%%%%%%%%%% reaction(Reaction type (name), Compound 1 [, Active site atom number], [Compound 2 , Active site atom number], Resulting compound) *% % Known sterol reactions (inferred from other organisms) % Mycosporine amino-acids known reactions. % Reactions from PWY-7751. reaction(rxn_17372, "sedoheptulose-7-phosphate", "R-demethyl-4-deoxygadusol"). reaction(rxn_17895, "R-demethyl-4-deoxygadusol", "S-demethyl-4-deoxygadusol"). reaction(rxn_17366, "R-demethyl-4-deoxygadusol", "R-4-deoxygadusol"). reaction(rxn_17370, "R-4-deoxygadusol", "S-4-deoxygadusol"). reaction(rxn_17896, "S-demethyl-4-deoxygadusol", "S-4-deoxygadusol"). reaction(aminoacid_C_1_transfer, "S-4-deoxygadusol", "mycosporin-glycine"). reaction(aminoacid_C_3_transfer_serine,"mycosporin-glycine","shinorine"). % Extended reaction from serine to threonine (as proposed in Brawley et al., 2017) reaction(aminoacid_C_3_transfer_threonine,"mycosporin-glycine","porphyra-334"). % Other reactions from bibliography (Carreto and Carignan, 2011) reaction(hydrogenation,"shinorine","palythinol"). reaction(demethylation,"palythinol", "asterina-330"). reaction(dehydration,"porphyra-334", "z-palythenic acid"). reaction(decarboxylation_1,"z-palythenic acid","palythene"). reaction(decarboxylation_2,"shinorine","asterina-330"). reaction(hydrolysis,"palythene","palythine"). % MZ expected in mycosporine amino-acids pathway. mzfiltering(2702720). mzfiltering(3023117). % defining absent molecules absentmolecules("z-palythenic acid"). absentmolecules("palythinol"). % Source molecule for inference. source("sedoheptulose-7-phosphate"). % Initiation of incremental grounding. goal(pathway("sedoheptulose-7-phosphate","palythine")).