diff --git a/code/modelCuration/GlycolysisCuration.m b/code/modelCuration/GlycolysisCuration.m new file mode 100644 index 00000000..2dbaab27 --- /dev/null +++ b/code/modelCuration/GlycolysisCuration.m @@ -0,0 +1,94 @@ +% This function is for adding new rxns annotated for glycolysis genes of GPRs identified by GPT. +rxnStruct = importTsvFile('../../data/modelCuration/addRxnGly_20230414.tsv'); +MetStruct = importTsvFile('../../data/modelCuration/addMetGly_20230414.tsv'); + +model = importYaml('Human-GEM.yml'); + +rxnsToAdd.rxns = rxnStruct.rxnID; +rxnsToAdd.eccodes = rxnStruct.ECNumber; +rxnsToAdd.equations = rxnStruct.Equation; +rxnsToAdd.rxnNames = rxnStruct.rxnID; +rxnsToAdd.lb = zeros(length(rxnStruct.rxnID),1); +rxnsToAdd.ub = repmat(1000,length(rxnStruct.rxnID),1); +idx = find(cell2mat(rxnStruct.Reversibility) == 1); +rxnsToAdd.lb(idx) = -1000; +rxnsToAdd.grRules = rxnStruct.grRules; +rxnsToAdd.subSystems = rxnStruct.Subsystems; +rxnsToAdd.rxnConfidenceScores = zeros(length(rxnStruct.rxnID),1); +[~,idx] = ismember(MetStruct.MetID,model.mets); +metsToAdd.mets = MetStruct.MetID(~idx,1); +metsToAdd.metNames = MetStruct.Name(~idx,1); +metsToAdd.compartments = MetStruct.Comp(~idx,1); +metsToAdd.metFormulas = MetStruct.Fromula(~idx,1); +metsToAdd.metCharges = MetStruct.Charge(~idx,1); +tmp = []; +for i = 1:length(metsToAdd.metCharges) + if ~isempty(metsToAdd.metCharges{i}) + tmp(i,1) = str2double(metsToAdd.metCharges{i}); + else + tmp(i,1) = NaN; + end +end +metsToAdd.metCharges = tmp; + +[newModel, modelChanges] = addMetabolicNetwork(model,rxnsToAdd,metsToAdd); + +% export the new mets, new reactions to the table +structure = importTsvFile('../../model/metabolites.tsv'); +[~,idx] = ismember(modelChanges.mets.mets,MetStruct.MetID); +MetStruct.emptyID(1:length(MetStruct.MetID),1) = {''}; +% metID metNames metFormulas metCharges compartments metKEGGID metPubChemID metChEBIID metMetaCycID metMetaNetXID +metNocomp = cellfun(@(s) s(1:8), MetStruct.MetID(idx,1), 'UniformOutput', false); +structure.mets = [structure.mets;MetStruct.MetID(idx,1)]; +structure.metBiGGID = [structure.metBiGGID;MetStruct.emptyID(idx,1)]; +structure.metKEGGID = [structure.metKEGGID;MetStruct.KEGG(idx,1)]; +structure.metsNoComp = [structure.metsNoComp;metNocomp]; +structure.metHMDBID = [structure.metHMDBID;MetStruct.emptyID(idx,1)]; +structure.metChEBIID = [structure.metChEBIID;MetStruct.CHEBI(idx,1)]; +structure.metPubChemID = [structure.metPubChemID;MetStruct.emptyID(idx,1)]; +structure.metLipidMapsID = [structure.metLipidMapsID;MetStruct.emptyID(idx,1)]; +structure.metEHMNID = [structure.metEHMNID;MetStruct.emptyID(idx,1)]; +structure.metHepatoNET1ID = [structure.metHepatoNET1ID;MetStruct.emptyID(idx,1)]; +structure.metRecon3DID = [structure.metRecon3DID;MetStruct.emptyID(idx,1)]; +structure.metMetaNetXID = [structure.metMetaNetXID;MetStruct.MetaNetx(idx,1)]; +structure.metHMR2ID = [structure.metHMR2ID;MetStruct.emptyID(idx,1)]; +structure.metRetired = [structure.metRetired;MetStruct.emptyID(idx,1)]; +% sort the order based on the model.mets +[~,idx] = ismember(model.mets,structure.mets); +structure.mets = structure.mets(idx); +structure.metsNoComp = structure.metsNoComp(idx); +structure.metBiGGID = structure.metBiGGID(idx,1); +structure.metKEGGID = structure.metKEGGID(idx,1); +structure.metHMDBID = structure.metHMDBID(idx,1); +structure.metChEBIID = structure.metChEBIID(idx,1); +structure.metPubChemID = structure.metPubChemID(idx,1); +structure.metLipidMapsID = structure.metLipidMapsID(idx,1); +structure.metEHMNID = structure.metEHMNID(idx,1); +structure.metHepatoNET1ID = structure.metHepatoNET1ID(idx,1); +structure.metRecon3DID = structure.metRecon3DID(idx,1); +structure.metMetaNetXID = structure.metMetaNetXID(idx,1); +structure.metHMR2ID = structure.metHMR2ID(idx,1); +structure.metRetired = structure.metRetired(idx,1); +exportTsvFile(structure, '../../model/metabolites.tsv') + +structure = importTsvFile('../../model/reactions.tsv'); +[~,idx] = ismember(modelChanges.rxns.rxns,rxnStruct.rxnID); +rxnStruct.emptyID(1:length(rxnStruct.rxnID),1) = {''}; +structure.rxns = [structure.rxns;rxnStruct.rxnID(idx,1) ]; +structure.rxnKEGGID = [structure.rxnKEGGID;rxnStruct.KEGG(idx,1) ]; +structure.rxnBiGGID= [structure.rxnBiGGID;rxnStruct.BiGG(idx,1) ]; +structure.rxnEHMNID = [structure.rxnEHMNID;rxnStruct.emptyID(idx,1) ]; +structure.rxnHepatoNET1ID = [structure.rxnHepatoNET1ID;rxnStruct.emptyID(idx,1) ]; +structure.rxnREACTOMEID = [structure.rxnREACTOMEID;rxnStruct.Reactome(idx,1) ]; +structure.rxnRecon3DID = [structure.rxnRecon3DID;rxnStruct.emptyID(idx,1) ]; +structure.rxnMetaNetXID = [structure.rxnMetaNetXID;rxnStruct.MetaNetx(idx,1) ]; +structure.rxnHMR2ID = [structure.rxnHMR2ID;rxnStruct.emptyID(idx,1) ]; +structure.rxnRatconID = [structure.rxnRatconID;rxnStruct.emptyID(idx,1) ]; +structure.rxnTCDBID = [structure.rxnTCDBID;rxnStruct.emptyID(idx,1) ]; +structure.spontaneous = [structure.spontaneous;zeros(length(rxnStruct.rxnID(idx,1)),1) ]; +structure.rxnRheaID = [structure.rxnRheaID;rxnStruct.RHEA(idx,1) ]; +structure.rxnRheaMasterID = [structure.rxnRheaMasterID;rxnStruct.emptyID(idx,1) ]; +structure.rxnRetired = [structure.rxnRetired;rxnStruct.emptyID(idx,1) ]; + +exportTsvFile(structure, '../../model/reactions.tsv') + diff --git a/data/modelCuration/addMetGly_20230414.tsv b/data/modelCuration/addMetGly_20230414.tsv new file mode 100644 index 00000000..2a4bfc4d --- /dev/null +++ b/data/modelCuration/addMetGly_20230414.tsv @@ -0,0 +1,127 @@ +MetID Name Fromula Charge Comp KEGG PubChem CHEBI MetaCyc MetaNetx +MAM02039n H+ H 1 n CHEBI:15378 MNXM1 +MAM20001n retinol C20H30O n CHEBI:50211 MNXM729111 +MAM20002n retinal C20H28O 0 n CHEBI:15035 MNXM1105989 +MAM02552n NAD+ C21H26N7O14P2 n CHEBI:57540 MNXM8 +MAM02553n NADH C21H27N7O14P2 -2 n CHEBI:57945 MNXM10 +MAM02039c H+ H 1 c CHEBI:15378 MNXM1 +MAM02552c NAD+ C21H26N7O14P2 c CHEBI:57540 MNXM8 +MAM01232n 9-cis-retinol C20H30O 0 n CHEBI:78272 MNXM1102095 +MAM01230n 9-cis-retinal C20H28O 0 n CHEBI:78273 MNXM1105991 +MAM20003n 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate C20H29O3 n CHEBI:76645 MNXM145653 +MAM20004n (5Z,8Z,11Z,14Z)-eicosatetraenedioate C20H28O4 n CHEBI:76647 MNXM23130 +MAM20005c 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate C20H29O3 c CHEBI:76645 MNXM145653 +MAM20006c (5Z,8Z,11Z,14Z)-eicosatetraenedioate C20H28O4 c CHEBI:76647 MNXM23130 +MAM00270n 10-HETE C20H31O3 n CHEBI:76624 MNXM732711 +MAM00270c 10-HETE C20H31O3 c CHEBI:76624 MNXM732711 +MAM20007n 1,4-benzoquinone C6H4O2 n CHEBI:16509 MNXM740100 +MAM20008n hydroquinone C6H6O2 n CHEBI:17594 MNXM376 +MAM20009c 1,4-benzoquinone C6H4O2 c CHEBI:16509 MNXM740100 +MAM20010c hydroquinone C6H6O2 c CHEBI:17594 MNXM376 +MAM02833n retinoate C20H27O2 -1 n CHEBI:35291 MNXM1107683 +MAM02833c retinoate C20H27O2 -1 c CHEBI:35291 MNXM1107683 +MAM20011m (S)-3-hydroxybutanoate C4H7O3 -1 m CHEBI:11047 MNXM1104966 +MAM20012m (R)-2-hydroxyglutarate C5H6O5 -2 m CHEBI:15801 MNXM733230 +MAM01306m AKG C5H4O5 m CHEBI:16810 MNXM20 +MAM00970c 4-aminobutyrate C4H9NO2 c CHEBI:59888 MNXM192 +MAM02674c palmitate C16H31O2 -1 c CHEBI:7896 MNXM108 +MAM20013c octanal C8H16O 0 c CHEBI:17935 MNXM2705 +MAM02642c octanoic acid C8H15O2 c CHEBI:25646 MNXM750 +MAM02039g H+ H 1 g CHEBI:15378 MNXM1 +MAM20014g 15-oxoprostaglandin E2 C20H29O5 g CHEBI:57400 MNXM1619 +MAM20015g 13,14-dihydro-15-oxo-prostaglandin E2 C20H31O5 g CHEBI:57402 MNXM733372 +MAM02555g NADPH C21H26N7O17P3 -4 g CHEBI:57783 MNXM738702 +MAM02554g NADP+ C21H25N7O17P3 g CHEBI:58349 MNXM5 +MAM20016n 15-oxoprostaglandin E2 C20H29O5 n CHEBI:57400 MNXM1619 +MAM20017n 13,14-dihydro-15-oxo-prostaglandin E2 C20H31O5 n CHEBI:57402 MNXM733372 +MAM02554n NADP+ C21H25N7O17P3 n CHEBI:58349 MNXM5 +MAM02751r Pi HO4P r CHEBI:43474 MNXM9 +MAM01968r glucose-6-phosphate C6H11O9P -2 r CHEBI:61548 MNXM1105858 +MAM20018r 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate C20H33O3 r CHEBI:132024 MNXM163133 +MAM02039r H+ H 1 r CHEBI:15378 MNXM1 +MAM20019r FMNH2 C17H21N4O9P -2 r CHEBI:57618 MNXM1107623 +MAM20020r FMN C17H18N4O9P -3 r CHEBI:58210 MNXM1105928 +MAM02457r mead acid C20H33O2 r CHEBI:78043 MNXM735122 +MAM20021i 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate C20H33O3 i CHEBI:132024 MNXM163133 +MAM02040i H2O H2O i CHEBI:15377 WATER +MAM02039i H+ H 1 i CHEBI:15378 MNXM1 +MAM02630i O2 O2 i CHEBI:15379 MNXM735438 +MAM20022i FMNH2 C17H21N4O9P -2 i CHEBI:57618 MNXM1107623 +MAM20023i FMN C17H18N4O9P -3 i CHEBI:58210 MNXM1105928 +MAM02457i mead acid C20H33O2 i CHEBI:78043 MNXM735122 +MAM01784r EPA C20H29O2 r CHEBI:58562 MNXM727959 +MAM20024r 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate C20H29O3 r CHEBI:76636 MNXM146872 +MAM01784i EPA C20H29O2 i CHEBI:58562 MNXM727959 +MAM20025i 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate C20H29O3 i CHEBI:76636 MNXM146872 +MAM20026r 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate C22H31O3 r CHEBI:132025 MNXM35542 +MAM01689r DHA C22H31O2 r CHEBI:77016 MNXM7161 +MAM20027i 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate C22H31O3 i CHEBI:132025 MNXM35542 +MAM01689i DHA C22H31O2 i CHEBI:77016 MNXM7161 +MAM02344r lauric acid C12H23O2 r CHEBI:18262 MNXM402 +MAM20028r 11-hydroxydodecanoate C12H23O3 r CHEBI:76628 MNXM22530 +MAM02344i lauric acid C12H23O2 i CHEBI:18262 MNXM402 +MAM20029i 11-hydroxydodecanoate C12H23O3 i CHEBI:76628 MNXM22530 +MAM20030r 13-hydroxytetradecanoate C14H27O3 r CHEBI:132031 MNXM163120 +MAM02494r myristic acid C14H27O2 r CHEBI:30807 MNXM314 +MAM20031i 13-hydroxytetradecanoate C14H27O3 i CHEBI:132031 MNXM163120 +MAM02494i myristic acid C14H27O2 i CHEBI:30807 MNXM314 +MAM01019r 4-nitrocatechol C6H4NO4 r CHEBI:57730 MNXM1982 +MAM02754r PNP C6H4NO3 r CHEBI:57917 MNXM526 +MAM02554r NADP+ C21H25N7O17P3 r CHEBI:58349 MNXM5 +MAM01019i 4-nitrocatechol C6H4NO4 i CHEBI:57730 MNXM1982 +MAM02555i NADPH C21H26N7O17P3 -4 i CHEBI:57783 MNXM738702 +MAM02754i PNP C6H4NO3 i CHEBI:57917 MNXM526 +MAM02554i NADP+ C21H25N7O17P3 i CHEBI:58349 MNXM5 +MAM20032n beta-D-galactose C6H12O6 0 n CHEBI:27667 MNXM112 +MAM01910n galactose C6H12O6 0 n C00984 439357 CHEBI:28061 MNXM1108175 +MAM20033c beta-D-galactose C6H12O6 0 c CHEBI:27667 MNXM112 +MAM01388n beta-D-glucose C6H12O6 0 n CHEBI:15903 MNXM1105026 +MAM20034n alpha-D-glucose C6H12O6 0 n CHEBI:17925 MNXM1105027 +MAM20035c alpha-D-glucose C6H12O6 0 c CHEBI:17925 MNXM1105027 +MAM02554c NADP+ C21H25N7O17P3 c CHEBI:58349 MNXM5 +MAM20036c benzaldehyde C7H6O c CHEBI:17169 MNXM371 +MAM20037c hexanal C6H12O c CHEBI:88528 MNXM8718 +MAM20038c (E)-4-hydroxynon-2-enoate C9H15O3 -1 c CHEBI:142920 MNXM746911 +MAM20039c (2E)-octenoate C8H13O2 -1 c CHEBI:143526 MNXM1108529 +MAM20040c (2E)-octenal C8H14O 0 c CHEBI:61748 MNXM1108145 +MAM01837c formylglutathione C11H16N3O7S c CHEBI:57688 MNXM741595 +MAM02152c hydroxymethylglutathione C11H18N3O7S c CHEBI:58758 MNXM726277 +MAM02116r hexadecenal C16H30O r CHEBI:17585 MNXM728262 +MAM02552r NAD+ C21H26N7O14P2 r CHEBI:57540 MNXM8 +MAM20041r (E)-hexadec-2-enoate C16H29O2 r CHEBI:72745 MNXM31465 +MAM02116c hexadecenal C16H30O c CHEBI:17585 MNXM728262 +MAM20042c (E)-hexadec-2-enoate C16H29O2 c CHEBI:72745 MNXM31465 +MAM02674r palmitate C16H31O2 -1 r CHEBI:7896 MNXM108 +MAM20043r 22-oxodocosanoate C22H41O3 r CHEBI:76298 MNXM6762 +MAM20044c 22-oxodocosanoate C22H41O3 c CHEBI:76298 MNXM6762 +MAM00564r 2(S)-pristanal C19H38O r CHEBI:49189 MNXM1947 +MAM02766r pristanic acid C19H37O2 r CHEBI:77268 MNXM3342 +MAM00564c 2(S)-pristanal C19H38O c CHEBI:49189 MNXM1947 +MAM02766c pristanic acid C19H37O2 c CHEBI:77268 MNXM3342 +MAM20045r octadecanal C18H36O r CHEBI:17034 MNXM2269 +MAM02938r stearate C18H35O2 r CHEBI:25629 MNXM236 +MAM20046c octadecanal C18H36O c CHEBI:17034 MNXM2269 +MAM02938c stearate C18H35O2 c CHEBI:25629 MNXM236 +MAM20047r dodecanal C12H24O 0 r CHEBI:27836 MNXM11432 +MAM02344c lauric acid C12H23O2 c CHEBI:18262 MNXM402 +MAM20048c dodecanal C12H24O 0 c CHEBI:27836 MNXM11432 +MAM01648r decanoic acid C10H19O2 -1 r CHEBI:27689 MNXM1043 +MAM20049r decanal C10H20O r CHEBI:31457 MNXM7260 +MAM01648c decanoic acid C10H19O2 -1 c CHEBI:27689 MNXM1043 +MAM20050c decanal C10H20O c CHEBI:31457 MNXM7260 +MAM20051r tetradecanal C14H28O r CHEBI:84067 MNXM13002 +MAM02494c myristic acid C14H27O2 c CHEBI:30807 MNXM314 +MAM20052c tetradecanal C14H28O c CHEBI:84067 MNXM13002 +MAM20053r octanal C8H16O 0 r CHEBI:17935 MNXM2705 +MAM02642r octanoic acid C8H15O2 r CHEBI:25646 MNXM750 +MAM02108r heptylic acid C7H13O2 r CHEBI:32362 MNXM7416 +MAM20054r heptanal C7H14O r CHEBI:34787 MNXM8711 +MAM02108c heptylic acid C7H13O2 c CHEBI:32362 MNXM7416 +MAM20055c heptanal C7H14O c CHEBI:34787 MNXM8711 +MAM20056r (2E,6E)-farnesoate C15H23O2 r CHEBI:83276 MNXM735429 +MAM00677r 2-trans,6-trans-farnesal C15H24O 0 r C03461 CHEBI:15894 MNXM1959 +MAM20057c (2E,6E)-farnesoate C15H23O2 c CHEBI:83276 MNXM735429 +MAM20058c all-trans-4-hydroxyretinol C20H30O2 0 c CHEBI:132259 MNXM730551 +MAM20059c all-trans-4-hydroxyretinal C20H28O2 0 c CHEBI:139346 MNXM166395 +MAM20060c all-trans-4-oxoretinal C20H26O2 c CHEBI:139347 MNXM745787 +MAM01032c 4-oxoretinol C20H28O2 c CHEBI:44597 MNXM735096 \ No newline at end of file diff --git a/data/modelCuration/addRxnGly_20230414.tsv b/data/modelCuration/addRxnGly_20230414.tsv new file mode 100644 index 00000000..78d51551 --- /dev/null +++ b/data/modelCuration/addRxnGly_20230414.tsv @@ -0,0 +1,69 @@ +rxnID Equation Reversibility grRules Comp RHEA MetaNetx KEGG BiGG EC number MetaCyc Subsystems Reactome +MAR20001 NAD+[n] + retinol[n] => H+[n] + NADH[n] + retinal[n] FALSE ENSG00000198099 n RHEA:21284 MNXR189842 R02124 HMR_6633;RDH1;R_HMR_6633;R_RDH1;R_TRETINOLOR1;TRETINOLOR1 1.1.1.105 RETINOL-DEHYDROGENASE-RXN Retinol metabolism +MAR20002 NAD+[c] + retinol[c] => H+[c] + NADH[c] + retinal[c] FALSE ENSG00000198099 or ENSG00000196616 c RHEA:21284 MNXR189842 R02124 HMR_6633;RDH1;R_HMR_6633;R_RDH1;R_TRETINOLOR1;TRETINOLOR1 1.1.1.105 RETINOL-DEHYDROGENASE-RXN Retinol metabolism +MAR20003 9-cis-retinol[n] + NAD+[n] => 9-cis-retinal[n] + H+[n] + NADH[n] FALSE ENSG00000198099 n RHEA:42052 MNXR103441 R08382 RDH2;R_RDH2 1.1.1.315 RXN-12562 Retinol metabolism +MAR20004 9-cis-retinol[c] + NAD+[c] => 9-cis-retinal[c] + H+[c] + NADH[c] FALSE ENSG00000198099 c RHEA:42052 MNXR103441 R08382 RDH2;R_RDH2 1.1.1.315 RXN-12562 Retinol metabolism +MAR20005 "20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate[n] + H2O[n] + NAD+[n] => (5Z,8Z,11Z,14Z)-eicosatetraenedioate[n] + 2 H+[n] + NADH[n]" FALSE ENSG00000198099 n RHEA:39803 MNXR167709 Retinol metabolism +MAR20006 "20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate[c] + H2O[c] + NAD+[c] => (5Z,8Z,11Z,14Z)-eicosatetraenedioate[c] + 2 H+[c] + NADH[c]" FALSE ENSG00000198099 or ENSG00000197894 c RHEA:39803 MNXR167709 Retinol metabolism +MAR20007 "10-HETE[n] + NAD+[n] => 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate[n] + H+[n] + NADH[n]" FALSE ENSG00000198099 n RHEA:39799 MNXR167708 Retinol metabolism +MAR20008 "10-HETE[c] + NAD+[c] => 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate[c] + H+[c] + NADH[c]" FALSE ENSG00000198099 or ENSG00000197894 c RHEA:39799 MNXR167708 Retinol metabolism +MAR20009 "1,4-benzoquinone[n] + H+[n] + NADH[n] => NAD+[n] + hydroquinone[n]" FALSE ENSG00000198099 n RHEA:60660 MNXR133773 1.1.1.328;1.11.1.1;1.6.5.2 1.6.5.2;1.6.5.9 Isolated +MAR20010 "1,4-benzoquinone[c] + H+[c] + NADH[c] => NAD+[c] + hydroquinone[c]" FALSE ENSG00000198099 c RHEA:60660 MNXR133773 1.1.1.328;1.11.1.1;1.6.5.2 Isolated +MAR20011 H2O[n] + NAD+[n] + retinal[n] => 2 H+[n] + NADH[n] + retinoate[n] FALSE ENSG00000184254 n RHEA:42080 MNXR146215 R02123 HMR_6647;RADH;R_HMR_6647;R_RADH 1.2.1.36 RETINAL-DEHYDROGENASE-RXN Retinol metabolism +MAR20012 H2O[c] + NAD+[c] + retinal[c] => 2 H+[c] + NADH[c] + retinoate[c] FALSE ENSG00000184254 c RHEA:42080 MNXR146215 R02123 HMR_6647;RADH;R_HMR_6647;R_RADH 1.2.1.36 RETINAL-DEHYDROGENASE-RXN Retinol metabolism +MAR20013 (S)-3-hydroxybutanoate[m] + AKG[m] => (R)-2-hydroxyglutarate[m] + acetoacetate[m] FALSE ENSG00000147576 m RHEA:23048 MNXR108031 R03225 1.1.99.24 HYDROXYACID-OXOACID-TRANSHYDROGENASE-RXN Isolated +MAR20014 4-trimethylammoniobutanal[c] + H2O[c] + NAD+[c] => 2 H+[c] + NADH[c] + gamma-butyrobetaine[c] FALSE ENSG00000143149 c RHEA:17985 MNXR104876 R03283 R_TMABADH;TMABADH 1.2.1.47 1.2.1.47-RXN Lysine degradation +MAR20015 4-aminobutanal[c] + H2O[c] + NAD+[c] => 4-aminobutyrate[c] + 2 H+[c] + NADH[c] FALSE ENSG00000143149 c RHEA:19105 MNXR95191 R02549 ABUTD;ABUTDm;R_ABUTD;R_ABUTDm 1.2.1.19 AMINOBUTDEHYDROG-RXN Arginine and proline metabolism +MAR20016 2 H+[c] + NADH[c] + palmitate[c] => H2O[c] + NAD+[c] + hexadecanal[c] FALSE ENSG00000132746 or ENSG00000132746 or ENSG00000006534 or ENSG00000072210 c RHEA:33739 MNXR95739 R01704 ALDD16;R_ALDD16 1.2.1.48 RXN-16655 Fatty acid metabolism +MAR20017 H2O[c] + NAD+[c] + octanal[c] => 2 H+[c] + NADH[c] + octanoic acid[c] FALSE ENSG00000132746 or ENSG00000132746 or ENSG00000006534 or ENSG00000072210 c RHEA:44100 MNXR95760 ALDD8;R_ALDD8 1.2.1.3;1.2.1.48;1.2.1.5 R222-RXN octane oxidation +MAR20018 "13,14-dihydro-15-oxo-prostaglandin E2[g] + NADP+[g] => 15-oxoprostaglandin E2[g] + H+[g] + NADPH[g]" FALSE ENSG00000180011 or ENSG00000180011 g RHEA:11912 MNXR108965 R04557 1.3.1.48 15-OXOPROSTAGLANDIN-13-REDUCTASE-RXN " Arachidonic acid metabolism" R-HSA-2161692.2 +MAR20019 "13,14-dihydro-15-oxo-prostaglandin E2[n] + NADP+[n] => 15-oxoprostaglandin E2[n] + H+[n] + NADPH[n]" FALSE ENSG00000180011 or ENSG00000180011 n RHEA:11912 MNXR108965 R04557 1.3.1.48 15-OXOPROSTAGLANDIN-13-REDUCTASE-RXN " Arachidonic acid metabolism" R-HSA-2161692.2 +MAR20020 glucose-6-phosphate[r] + H2O[r] => glucose[r] + Pi[r] FALSE ENSG00000131482 or ENSG00000141349 r RHEA:16689 MNXR195425 R00303 G6PP;G6PPer;R_G6PP;R_G6PPer 3.1.3.9; 3.1.3.58 RXN66-526 Starch and sucrose metabolism +MAR20021 "mead acid[r] + FMNH2[r] + O2[r] => 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate[r] + FMN[r] + H+[r] + H2O[r]" FALSE ENSG00000130649 r RHEA:50076 MNXR169432 Fatty acid metabolism +MAR20022 "mead acid[i] + FMNH2[i] + O2[i] => 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate[i] + FMN[i] + H+[i] + H2O[i]" FALSE ENSG00000130649 i RHEA:50076 MNXR169432 Fatty acid metabolism +MAR20023 "EPA[r] + FMNH2[r] + O2[r] => 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate[r] + FMN[r] + H+[r] + H2O[r]" FALSE ENSG00000130649 r RHEA:39787 MNXR167706 Fatty acid metabolism +MAR20024 "EPA[i] + FMNH2[i] + O2[i] => 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate[i] + FMN[i] + H+[i] + H2O[i]" FALSE ENSG00000130649 i RHEA:39787 MNXR167706 Fatty acid metabolism +MAR20025 "DHA[r] + FMNH2[r] + O2[r] => 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate[r] + FMN[r] + H+[r] + H2O[r]" FALSE ENSG00000130649 r RHEA:50088 MNXR169433 Fatty acid metabolism +MAR20026 "DHA[i] + FMNH2[i] + O2[i] => 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate[i] + FMN[i] + H+[i] + H2O[i]" FALSE ENSG00000130649 i RHEA:50088 MNXR169433 Fatty acid metabolism +MAR20027 FMNH2[r] + O2[r] + lauric acid[r] => 11-hydroxydodecanoate[r] + FMN[r] + H+[r] + H2O[r] FALSE ENSG00000130649 r RHEA:39751 MNXR167698 Fatty acid metabolism +MAR20028 FMNH2[i] + O2[i] + lauric acid[i] => 11-hydroxydodecanoate[i] + FMN[i] + H+[i] + H2O[i] FALSE ENSG00000130649 i RHEA:39751 MNXR167698 Fatty acid metabolism +MAR20029 FMNH2[r] + O2[r] + myristic acid[r] => 13-hydroxytetradecanoate[r] + FMN[r] + H+[r] + H2O[r] FALSE ENSG00000130649 r RHEA:50096 MNXR169435 Fatty acid metabolism +MAR20030 FMNH2[i] + O2[i] + myristic acid[i] => 13-hydroxytetradecanoate[i] + FMN[i] + H+[i] + H2O[i] FALSE ENSG00000130649 i RHEA:50096 MNXR169435 Fatty acid metabolism +MAR20031 PNP[r] + H+[r] + NADPH[r] + O2[r] => 4-nitrocatechol[r] + H2O[r] + NADP+[r] FALSE ENSG00000130649 r RHEA:26205 MNXR102281 P4502E1;R_P4502E1 1.14.13.n7 Fatty acid metabolism +MAR20032 PNP[i] + H+[i] + NADPH[i] + O2[i] => 4-nitrocatechol[i] + H2O[i] + NADP+[i] FALSE ENSG00000130649 i RHEA:26205 MNXR102281 P4502E1;R_P4502E1 1.14.13.n7 Fatty acid metabolism +MAR20033 galactose[n] => beta-D-galactose[n] FALSE ENSG00000143891 n RHEA:28675 MNXR153745 R10619 GALM2;GALM2pp;R_GALM2;R_GALM2pp 5.1.3.3 ALDOSE1EPIM-RXN Galactose metabolism +MAR20034 galactose[c] => beta-D-galactose[c] FALSE ENSG00000143891 c RHEA:28675 MNXR153745 R10619 GALM2;GALM2pp;R_GALM2;R_GALM2pp 5.1.3.3 ALDOSE1EPIM-RXN Galactose metabolism +MAR20035 alpha-D-glucose[n] => beta-D-glucose[n] FALSE ENSG00000143891 n RHEA:10264 MNXR107082 R01602 A1E;GalMr;R_A1E;R_GalMr 5.1.3.3 ALDOSE-1-EPIMERASE-RXN Glycolysis / Gluconeogenesis +MAR20036 alpha-D-glucose[c] => beta-D-glucose[c] FALSE ENSG00000143891 c RHEA:10264 MNXR107082 R01602 A1E;GalMr;R_A1E;R_GalMr 5.1.3.3 ALDOSE-1-EPIMERASE-RXN Glycolysis / Gluconeogenesis +MAR20037 H2O[c] + NADP+[c] + octanal[c] => 2 H+[c] + NADPH[c] + octanoic acid[c] FALSE ENSG00000006534 c RHEA:59904 MNXR133380 1.2.1.3;1.2.1.5 Glycolysis / Gluconeogenesis +MAR20038 H2O[c] + NADP+[c] + benzaldehyde[c] => 2 H+[c] + NADPH[c] + benzoate[c] FALSE ENSG00000006534 c RHEA:21660 MNXR106982 R01420 1.2.1.7 BENZALDEHYDE-DEHYDROGENASE-NADP%2b-RXN Toluene degradation +MAR20039 H2O[c] + NAD+[c] + benzaldehyde[c] => 2 H+[c] + NADH[c] + benzoate[c] FALSE ENSG00000006534 c RHEA:11840 MNXR96365 R01419 BZDH;R_BZDH 1.2.1.28 BENZALDEHYDE-DEHYDROGENASE-NAD%2b-RXN Toluene degradation +MAR20040 H2O[c] + NADP+[c] + hexanal[c] => 2 H+[c] + Hexanoate (N-C6:0)[c] + NADPH[c] FALSE ENSG00000006534 c RHEA:59908 MNXR133381 1.2.1.3;1.2.1.5 Glycolysis / Gluconeogenesis +MAR20041 4-hydroxy-2-nonenal[c] + H2O[c] + NADP+[c] => (E)-4-hydroxynon-2-enoate[c] + 2 H+[c] + NADPH[c] FALSE ENSG00000006534 c RHEA:59912 MNXR171402 Glycolysis / Gluconeogenesis +MAR20042 (2E)-octenal[c] + H2O[c] + NADP+[c] => (2E)-octenoate[c] + 2 H+[c] + NADPH[c] FALSE ENSG00000006534 c RHEA:59916 MNXR133378 1.2.1.5 Glycolysis / Gluconeogenesis +MAR20043 (2E)-octenal[c] + H2O[c] + NAD+[c] => (2E)-octenoate[c] + 2 H+[c] + NADH[c] FALSE ENSG00000006534 c RHEA:59920 MNXR171404 Glycolysis / Gluconeogenesis +MAR20044 NADP+[c] + hydroxymethylglutathione[c] => H+[c] + NADPH[c] + formylglutathione[c] FALSE ENSG00000197894 c RHEA:19981 MNXR110840 R07140 1.1.1.284 RXN-2962 Isolated +MAR20045 NAD+[c] + hydroxymethylglutathione[c] => H+[c] + NADH[c] + formylglutathione[c] FALSE ENSG00000197894 c RHEA:19985 MNXR146812 R06983 FALDH2;R_FALDH2;R_r1378;r1378 1.1.1.284 RXN-2962 Isolated +MAR20046 hexadecenal[r] + H2O[r] + NAD+[r] => (E)-hexadec-2-enoate[r] + 2 H+[r] + NADH[r] FALSE ENSG00000072210 r RHEA:36135 MNXR120270 1.2.1.3 Fatty acid metabolism +MAR20047 hexadecenal[c] + H2O[c] + NAD+[c] => (E)-hexadec-2-enoate[c] + 2 H+[c] + NADH[c] FALSE ENSG00000072210 c RHEA:36135 MNXR120270 1.2.1.3 Fatty acid metabolism +MAR20048 2 H+[r] + NADH[r] + palmitate[r] => H2O[r] + NAD+[r] + hexadecanal[r] FALSE ENSG00000072210 r RHEA:33739 MNXR95739 R01704 ALDD16;R_ALDD16 1.2.1.48 RXN-16655 Fatty acid metabolism +MAR20049 22-oxodocosanoate[r] + H2O[r] + NAD+[r] => Docosanedioicacid[r] + 2 H+[r] + NADH[r] FALSE ENSG00000072210 r RHEA:39015 MNXR167567 Fatty acid metabolism +MAR20050 22-oxodocosanoate[c] + H2O[c] + NAD+[c] => Docosanedioicacid[c] + 2 H+[c] + NADH[c] FALSE ENSG00000072210 c RHEA:39015 MNXR167567 Fatty acid metabolism +MAR20051 2(S)-pristanal[r] + H2O[r] + NAD+[r] => pristanic acid[r] + 2 H+[r] + NADH[r] FALSE ENSG00000072210 r RHEA:44016 MNXR95747 ALDD21;RE3076X;R_ALDD21;R_RE3076X Fatty acid metabolism +MAR20052 2(S)-pristanal[c] + H2O[c] + NAD+[c] => pristanic acid[c] + 2 H+[c] + NADH[c] FALSE ENSG00000072210 c RHEA:44016 MNXR95747 ALDD21;RE3076X;R_ALDD21;R_RE3076X Fatty acid metabolism +MAR20053 H2O[r] + NAD+[r] + octadecanal[r] => 2 H+[r] + NADH[r] + stearate[r] FALSE ENSG00000072210 r RHEA:44020 MNXR95741 ALDD18;R_ALDD18 1.2.1.48 Fatty acid metabolism +MAR20054 H2O[c] + NAD+[c] + octadecanal[c] => 2 H+[c] + NADH[c] + stearate[c] FALSE ENSG00000072210 c RHEA:44020 MNXR95741 ALDD18;R_ALDD18 1.2.1.48 Fatty acid metabolism +MAR20055 2 H+[r] + NADH[r] + lauric acid[r] => H2O[r] + NAD+[r] + dodecanal[r] FALSE ENSG00000072210 r RHEA:44168 MNXR95735 ALDD12;R_ALDD12 1.2.1.3;1.2.1.48;1.2.1.5 RXN-16654 Fatty acid metabolism +MAR20056 2 H+[c] + NADH[c] + lauric acid[c] => H2O[c] + NAD+[c] + dodecanal[c] FALSE ENSG00000072210 c RHEA:44168 MNXR95735 ALDD12;R_ALDD12 1.2.1.3;1.2.1.48;1.2.1.5 RXN-16654 Fatty acid metabolism +MAR20057 H2O[r] + NAD+[r] + decanal[r] => 2 H+[r] + NADH[r] + decanoic acid[r] FALSE ENSG00000072210 r RHEA:44104 MNXR95733 ALDD10;R_ALDD10 1.2.1.3;1.2.1.48;1.2.1.5 RXN-16653 Fatty acid metabolism +MAR20058 H2O[c] + NAD+[c] + decanal[c] => 2 H+[c] + NADH[c] + decanoic acid[c] FALSE ENSG00000072210 c RHEA:44104 MNXR95733 ALDD10;R_ALDD10 1.2.1.3;1.2.1.48;1.2.1.5 RXN-16653 Fatty acid metabolism +MAR20059 H2O[r] + NAD+[r] + tetradecanal[r] => 2 H+[r] + NADH[r] + myristic acid[r] FALSE ENSG00000072210 r RHEA:44172 MNXR95737 ALDD14;R_ALDD14 1.2.1.48;1.2.1.5 Fatty acid metabolism +MAR20060 H2O[c] + NAD+[c] + tetradecanal[c] => 2 H+[c] + NADH[c] + myristic acid[c] FALSE ENSG00000072210 c RHEA:44172 MNXR95737 ALDD14;R_ALDD14 1.2.1.48;1.2.1.5 Fatty acid metabolism +MAR20061 H2O[r] + NAD+[r] + octanal[r] => 2 H+[r] + NADH[r] + octanoic acid[r] FALSE ENSG00000072210 r RHEA:44100 MNXR95760 ALDD8;R_ALDD8 1.2.1.3;1.2.1.48;1.2.1.5 R222-RXN octane oxidation +MAR20062 H2O[r] + NAD+[r] + heptanal[r] => 2 H+[r] + NADH[r] + heptylic acid[r] FALSE ENSG00000072210 r RHEA:44108 MNXR95759 ALDD7;R_ALDD7 1.2.1.3;1.2.1.5 Fatty acid metabolism +MAR20063 H2O[c] + NAD+[c] + heptanal[c] => 2 H+[c] + NADH[c] + heptylic acid[c] FALSE ENSG00000072210 c RHEA:44108 MNXR95759 ALDD7;R_ALDD7 1.2.1.3;1.2.1.5 Fatty acid metabolism +MAR20064 "2-trans,6-trans-farnesal[r] + H2O[r] + NAD+[r] => (2E,6E)-farnesoate[r] + 2 H+[r] + NADH[r]" FALSE ENSG00000072210 r RHEA:24216 MNXR111724 R08146 1.2.1.94 RXN-11619 Insect hormone biosynthesis +MAR20065 "2-trans,6-trans-farnesal[c] + H2O[c] + NAD+[c] => (2E,6E)-farnesoate[c] + 2 H+[c] + NADH[c]" FALSE ENSG00000072210 c RHEA:24216 MNXR111724 R08146 1.2.1.94 RXN-11619 Insect hormone biosynthesis +MAR20066 2 H2O2[x] => 2 H2O[x] + O2[x] FALSE ENSG00000121691 x RHEA:20309 MNXR96455 R00009 CAT;CATm;CATp;CATpp;CATr;R_CAT;R_CATm;R_CATp;R_CATpp;R_CATr 1.11.1.6; 1.11.1.21 CATAL-RXN Glyoxylate and dicarboxylate metabolism +MAR20067 NAD+[c] + all-trans-4-hydroxyretinol[c] => H+[c] + NADH[c] + all-trans-4-hydroxyretinal[c] FALSE ENSG00000196616 c RHEA:55936 MNXR133799 1.1.1.1 Fatty acid metabolism +MAR20068 NAD+[c] + 4-oxoretinol[c] => H+[c] + NADH[c] + all-trans-4-oxoretinal[c] FALSE ENSG00000196616 c RHEA:60632 MNXR171534 Fatty acid degradation \ No newline at end of file diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6ca25a50..4533e9bd 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -4,7 +4,7 @@ short_name: "Human-GEM" full_name: "Generic genome-scale metabolic model of Homo sapiens" version: "" - date: "2023-04-14" + date: "2023-04-17" authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas" email: "jonrob@chalmers.se" organization: "Chalmers University of Technology" @@ -66908,6 +66908,702 @@ - charge: -4 - inchis: "" - metFrom: "" + - !!omap + - id: "MAM20001n" + - name: "retinol" + - compartment: "n" + - formula: "C20H30O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20002n" + - name: "retinal" + - compartment: "n" + - formula: "C20H28O" + - charge: 0 + - inchis: "InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3" + - metFrom: "" + - !!omap + - id: "MAM02553n" + - name: "NADH" + - compartment: "n" + - formula: "C21H27N7O14P2" + - charge: -2 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01232n" + - name: "9-cis-retinol" + - compartment: "n" + - formula: "C20H30O" + - charge: 0 + - inchis: "InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+" + - metFrom: "" + - !!omap + - id: "MAM01230n" + - name: "9-cis-retinal" + - compartment: "n" + - formula: "C20H28O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20003n" + - name: "20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate" + - compartment: "n" + - formula: "C20H29O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20004n" + - name: "(5Z,8Z,11Z,14Z)-eicosatetraenedioate" + - compartment: "n" + - formula: "C20H28O4" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20005c" + - name: "20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate" + - compartment: "c" + - formula: "C20H29O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20006c" + - name: "(5Z,8Z,11Z,14Z)-eicosatetraenedioate" + - compartment: "c" + - formula: "C20H28O4" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM00270n" + - name: "10-HETE" + - compartment: "n" + - formula: "C20H31O3" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20007n" + - name: "1,4-benzoquinone" + - compartment: "n" + - formula: "C6H4O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20008n" + - name: "hydroquinone" + - compartment: "n" + - formula: "C6H6O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20009c" + - name: "1,4-benzoquinone" + - compartment: "c" + - formula: "C6H4O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20010c" + - name: "hydroquinone" + - compartment: "c" + - formula: "C6H6O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20011m" + - name: "(S)-3-hydroxybutanoate" + - compartment: "m" + - formula: "C4H7O3" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20012m" + - name: "(R)-2-hydroxyglutarate" + - compartment: "m" + - formula: "C5H6O5" + - charge: -2 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20013c" + - name: "octanal" + - compartment: "c" + - formula: "C8H16O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20014g" + - name: "15-oxoprostaglandin E2" + - compartment: "g" + - formula: "C20H29O5" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20015g" + - name: "13,14-dihydro-15-oxo-prostaglandin E2" + - compartment: "g" + - formula: "C20H31O5" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02555g" + - name: "NADPH" + - compartment: "g" + - formula: "C21H26N7O17P3" + - charge: -4 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02554g" + - name: "NADP+" + - compartment: "g" + - formula: "C21H25N7O17P3" + - charge: -3 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20016n" + - name: "15-oxoprostaglandin E2" + - compartment: "n" + - formula: "C20H29O5" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20017n" + - name: "13,14-dihydro-15-oxo-prostaglandin E2" + - compartment: "n" + - formula: "C20H31O5" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20018r" + - name: "19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate" + - compartment: "r" + - formula: "C20H33O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20019r" + - name: "FMNH2" + - compartment: "r" + - formula: "C17H21N4O9P" + - charge: -2 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20020r" + - name: "FMN" + - compartment: "r" + - formula: "C17H18N4O9P" + - charge: -2 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20021i" + - name: "19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate" + - compartment: "i" + - formula: "C20H33O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02040i" + - name: "H2O" + - compartment: "i" + - formula: "H2O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02630i" + - name: "O2" + - compartment: "i" + - formula: "O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20022i" + - name: "FMNH2" + - compartment: "i" + - formula: "C17H21N4O9P" + - charge: -2 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20023i" + - name: "FMN" + - compartment: "i" + - formula: "C17H18N4O9P" + - charge: -2 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02457i" + - name: "mead acid" + - compartment: "i" + - formula: "C20H33O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20024r" + - name: "19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate" + - compartment: "r" + - formula: "C20H29O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01784i" + - name: "EPA" + - compartment: "i" + - formula: "C20H29O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20025i" + - name: "19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate" + - compartment: "i" + - formula: "C20H29O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20026r" + - name: "21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate" + - compartment: "r" + - formula: "C22H31O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20027i" + - name: "21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate" + - compartment: "i" + - formula: "C22H31O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01689i" + - name: "DHA" + - compartment: "i" + - formula: "C22H31O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20028r" + - name: "11-hydroxydodecanoate" + - compartment: "r" + - formula: "C12H23O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02344i" + - name: "lauric acid" + - compartment: "i" + - formula: "C12H23O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20029i" + - name: "11-hydroxydodecanoate" + - compartment: "i" + - formula: "C12H23O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20030r" + - name: "13-hydroxytetradecanoate" + - compartment: "r" + - formula: "C14H27O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20031i" + - name: "13-hydroxytetradecanoate" + - compartment: "i" + - formula: "C14H27O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02494i" + - name: "myristic acid" + - compartment: "i" + - formula: "C14H27O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01019r" + - name: "4-nitrocatechol" + - compartment: "r" + - formula: "C6H4NO4" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02754r" + - name: "PNP" + - compartment: "r" + - formula: "C6H4NO3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01019i" + - name: "4-nitrocatechol" + - compartment: "i" + - formula: "C6H4NO4" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02555i" + - name: "NADPH" + - compartment: "i" + - formula: "C21H26N7O17P3" + - charge: -4 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02754i" + - name: "PNP" + - compartment: "i" + - formula: "C6H4NO3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02554i" + - name: "NADP+" + - compartment: "i" + - formula: "C21H25N7O17P3" + - charge: -3 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20032n" + - name: "beta-D-galactose" + - compartment: "n" + - formula: "C6H12O6" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01910n" + - name: "galactose" + - compartment: "n" + - formula: "C6H12O6" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20033c" + - name: "beta-D-galactose" + - compartment: "c" + - formula: "C6H12O6" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM01388n" + - name: "beta-D-glucose" + - compartment: "n" + - formula: "C6H12O6" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20034n" + - name: "alpha-D-glucose" + - compartment: "n" + - formula: "C6H12O6" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20035c" + - name: "alpha-D-glucose" + - compartment: "c" + - formula: "C6H12O6" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20036c" + - name: "benzaldehyde" + - compartment: "c" + - formula: "C7H6O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20037c" + - name: "hexanal" + - compartment: "c" + - formula: "C6H12O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20038c" + - name: "(E)-4-hydroxynon-2-enoate" + - compartment: "c" + - formula: "C9H15O3" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20039c" + - name: "(2E)-octenoate" + - compartment: "c" + - formula: "C8H13O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20040c" + - name: "(2E)-octenal" + - compartment: "c" + - formula: "C8H14O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02116r" + - name: "hexadecenal" + - compartment: "r" + - formula: "C16H30O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20041r" + - name: "(E)-hexadec-2-enoate" + - compartment: "r" + - formula: "C16H29O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20042c" + - name: "(E)-hexadec-2-enoate" + - compartment: "c" + - formula: "C16H29O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20043r" + - name: "22-oxodocosanoate" + - compartment: "r" + - formula: "C22H41O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20044c" + - name: "22-oxodocosanoate" + - compartment: "c" + - formula: "C22H41O3" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM00564r" + - name: "2(S)-pristanal" + - compartment: "r" + - formula: "C19H38O" + - charge: 0 + - inchis: "InChI=1/C19H38O/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)15-20/h15-19H,6-14H2,1-5H3" + - metFrom: "" + - !!omap + - id: "MAM02766r" + - name: "pristanic acid" + - compartment: "r" + - formula: "C19H37O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20045r" + - name: "octadecanal" + - compartment: "r" + - formula: "C18H36O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20046c" + - name: "octadecanal" + - compartment: "c" + - formula: "C18H36O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20047r" + - name: "dodecanal" + - compartment: "r" + - formula: "C12H24O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20048c" + - name: "dodecanal" + - compartment: "c" + - formula: "C12H24O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20049r" + - name: "decanal" + - compartment: "r" + - formula: "C10H20O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20050c" + - name: "decanal" + - compartment: "c" + - formula: "C10H20O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20051r" + - name: "tetradecanal" + - compartment: "r" + - formula: "C14H28O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20052c" + - name: "tetradecanal" + - compartment: "c" + - formula: "C14H28O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20053r" + - name: "octanal" + - compartment: "r" + - formula: "C8H16O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02642r" + - name: "octanoic acid" + - compartment: "r" + - formula: "C8H15O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM02108r" + - name: "heptylic acid" + - compartment: "r" + - formula: "C7H13O2" + - charge: -1 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20054r" + - name: "heptanal" + - compartment: "r" + - formula: "C7H14O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20055c" + - name: "heptanal" + - compartment: "c" + - formula: "C7H14O" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM20056r" + - name: "(2E,6E)-farnesoate" + - compartment: "r" + - formula: "C15H23O2" + - charge: 0 + - inchis: "" + - metFrom: "" + - !!omap + - id: "MAM00677r" + - name: "2-trans,6-trans-farnesal" + - compartment: "r" + - formula: "C15H24O" + - charge: 0 + - inchis: "" + - metFrom: 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rxnFrom: "" + - eccodes: "1.2.1.94" + - references: "" + - subsystem: + - "Insect hormone biosynthesis" + - confidence_score: 0 + - !!omap + - id: "MAR20066" + - name: "MAR20066" + - metabolites: !!omap + - MAM02040x: 2 + - MAM02041x: -2 + - MAM02630x: 1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000121691" + - rxnNotes: "" + - rxnFrom: "" + - eccodes: "1.11.1.6; 1.11.1.21" + - references: "" + - subsystem: + - "Glyoxylate and dicarboxylate metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20067" + - name: "MAR20067" + - metabolites: !!omap + - MAM02039c: 1 + - MAM02552c: -1 + - MAM02553c: 1 + - MAM20058c: -1 + - MAM20059c: 1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000196616" + - rxnNotes: "" + - rxnFrom: "" + - eccodes: "1.1.1.1" + - references: "" + - subsystem: + - "Fatty acid metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20068" + - name: "MAR20068" + - metabolites: !!omap + - MAM01032c: -1 + - MAM02039c: 1 + - MAM02552c: -1 + - MAM02553c: 1 + - MAM20060c: 1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000196616" + - rxnNotes: "" + - rxnFrom: "" + - eccodes: "" + - references: "" + - subsystem: + - "Fatty acid degradation" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 833153a2..243418f5 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -8361,3 +8361,90 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM10041c" "MAM10041" "" "" "" "" "119046" "" "" "" "" "" "" "m10041c" "MAM10041e" "MAM10041" "" "" "" "" "119046" "" "" "" "" "" "" "m10041s" "MAM10042c" "MAM10042" "" "C17689" "" "" "" "" "" "" "" "" "" "m10042c" +"MAM20001n" "MAM20001" "" "" "" "CHEBI:50211" "" "" "" "" "" "MNXM729111" "" "" +"MAM20002n" "MAM20002" "" "" "" "CHEBI:15035" "" "" "" "" "" "MNXM1105989" "" "" +"MAM02553n" "MAM02553" "" "" "" "CHEBI:57945" "" "" "" "" "" "MNXM10" "" "" +"MAM01232n" "MAM01232" "" "" "" "CHEBI:78272" "" "" "" "" "" "MNXM1102095" "" "" +"MAM01230n" "MAM01230" "" "" "" "CHEBI:78273" "" "" "" "" "" "MNXM1105991" "" "" +"MAM20003n" "MAM20003" "" "" "" "CHEBI:76645" "" "" "" "" "" "MNXM145653" "" "" +"MAM20004n" "MAM20004" "" "" "" "CHEBI:76647" "" "" "" "" "" "MNXM23130" "" "" +"MAM20005c" "MAM20005" "" "" "" "CHEBI:76645" "" "" "" "" "" "MNXM145653" "" "" +"MAM20006c" "MAM20006" "" "" "" "CHEBI:76647" "" "" "" "" "" "MNXM23130" "" "" +"MAM00270n" "MAM00270" "" "" "" "CHEBI:76624" "" "" "" "" "" "MNXM732711" "" "" +"MAM20007n" "MAM20007" "" "" "" "CHEBI:16509" "" "" "" "" "" "MNXM740100" "" "" +"MAM20008n" "MAM20008" "" "" "" "CHEBI:17594" "" "" "" "" "" "MNXM376" "" "" +"MAM20009c" "MAM20009" "" "" "" "CHEBI:16509" "" "" "" "" "" "MNXM740100" "" "" +"MAM20010c" "MAM20010" "" "" "" "CHEBI:17594" "" "" "" "" "" "MNXM376" "" "" +"MAM20011m" "MAM20011" "" "" "" "CHEBI:11047" "" "" "" "" "" "MNXM1104966" "" "" +"MAM20012m" "MAM20012" "" "" "" "CHEBI:15801" "" "" "" "" "" "MNXM733230" "" "" +"MAM20013c" "MAM20013" "" "" "" "CHEBI:17935" "" "" "" "" "" "MNXM2705" "" "" +"MAM20014g" "MAM20014" "" "" "" "CHEBI:57400" "" "" "" "" "" "MNXM1619" "" "" +"MAM20015g" "MAM20015" "" "" "" "CHEBI:57402" "" "" "" "" "" "MNXM733372" "" "" +"MAM02555g" "MAM02555" "" "" "" "CHEBI:57783" "" "" "" "" "" "MNXM738702" "" "" +"MAM02554g" "MAM02554" "" "" "" "CHEBI:58349" "" "" "" "" "" "MNXM5" "" "" +"MAM20016n" "MAM20016" "" "" "" "CHEBI:57400" "" "" "" "" "" "MNXM1619" "" "" +"MAM20017n" "MAM20017" "" "" "" "CHEBI:57402" "" "" "" "" "" "MNXM733372" "" "" +"MAM20018r" "MAM20018" "" "" "" "CHEBI:132024" "" "" "" "" "" "MNXM163133" "" "" +"MAM20019r" "MAM20019" "" "" "" "CHEBI:57618" "" "" "" "" "" "MNXM1107623" "" "" +"MAM20020r" "MAM20020" "" "" "" "CHEBI:58210" "" "" "" "" "" "MNXM1105928" "" "" +"MAM20021i" "MAM20021" "" "" "" "CHEBI:132024" "" "" "" "" "" "MNXM163133" "" "" +"MAM02040i" "MAM02040" "" "" "" "CHEBI:15377" "" "" "" "" "" "WATER" "" "" +"MAM02630i" "MAM02630" "" "" "" "CHEBI:15379" "" "" "" "" "" "MNXM735438" "" "" +"MAM20022i" "MAM20022" "" "" "" "CHEBI:57618" "" "" "" "" "" "MNXM1107623" "" "" +"MAM20023i" "MAM20023" "" "" "" "CHEBI:58210" "" "" "" "" "" "MNXM1105928" "" "" +"MAM02457i" "MAM02457" "" "" "" "CHEBI:78043" "" "" "" "" "" "MNXM735122" "" "" +"MAM20024r" "MAM20024" "" "" "" "CHEBI:76636" "" "" "" "" "" "MNXM146872" "" "" +"MAM01784i" "MAM01784" "" "" "" "CHEBI:58562" "" "" "" "" "" "MNXM727959" "" "" +"MAM20025i" "MAM20025" "" "" "" "CHEBI:76636" "" "" "" "" "" "MNXM146872" "" "" +"MAM20026r" "MAM20026" "" "" "" "CHEBI:132025" "" "" "" "" "" "MNXM35542" "" "" +"MAM20027i" "MAM20027" "" "" "" "CHEBI:132025" "" "" "" "" "" "MNXM35542" "" "" +"MAM01689i" "MAM01689" "" "" "" "CHEBI:77016" "" "" "" "" "" "MNXM7161" "" "" +"MAM20028r" "MAM20028" "" "" "" "CHEBI:76628" "" "" "" "" "" "MNXM22530" "" "" +"MAM02344i" "MAM02344" "" "" "" "CHEBI:18262" "" "" "" "" "" "MNXM402" "" "" +"MAM20029i" "MAM20029" "" "" "" "CHEBI:76628" "" "" "" "" "" "MNXM22530" "" "" +"MAM20030r" "MAM20030" "" "" "" "CHEBI:132031" "" "" "" "" "" "MNXM163120" "" "" +"MAM20031i" "MAM20031" "" "" "" "CHEBI:132031" "" "" "" "" "" "MNXM163120" "" "" +"MAM02494i" "MAM02494" "" "" "" "CHEBI:30807" "" "" "" "" "" "MNXM314" "" "" +"MAM01019r" "MAM01019" "" "" "" "CHEBI:57730" "" "" "" "" "" "MNXM1982" "" "" +"MAM02754r" "MAM02754" "" "" "" "CHEBI:57917" "" "" "" "" "" "MNXM526" "" "" +"MAM01019i" "MAM01019" "" "" "" "CHEBI:57730" "" "" "" "" "" "MNXM1982" "" "" +"MAM02555i" "MAM02555" "" "" "" "CHEBI:57783" "" "" "" "" "" "MNXM738702" "" "" +"MAM02754i" "MAM02754" "" "" "" "CHEBI:57917" "" "" "" "" "" "MNXM526" "" "" +"MAM02554i" "MAM02554" "" "" "" "CHEBI:58349" "" "" "" "" "" "MNXM5" "" "" +"MAM20032n" "MAM20032" "" "" "" "CHEBI:27667" "" "" "" "" "" "MNXM112" "" "" +"MAM01910n" "MAM01910" "" "C00984" "" "CHEBI:28061" "" "" "" "" "" "MNXM1108175" "" "" +"MAM20033c" "MAM20033" "" "" "" "CHEBI:27667" "" "" "" "" "" "MNXM112" "" "" +"MAM01388n" "MAM01388" "" "" "" "CHEBI:15903" "" "" "" "" "" "MNXM1105026" "" "" +"MAM20034n" "MAM20034" "" "" "" "CHEBI:17925" "" "" "" "" "" "MNXM1105027" "" "" +"MAM20035c" "MAM20035" "" "" "" "CHEBI:17925" "" "" "" "" "" "MNXM1105027" "" "" +"MAM20036c" "MAM20036" "" "" "" "CHEBI:17169" "" "" "" "" "" "MNXM371" "" "" +"MAM20037c" "MAM20037" "" "" "" "CHEBI:88528" "" "" "" "" "" "MNXM8718" "" "" +"MAM20038c" "MAM20038" "" "" "" "CHEBI:142920" "" "" "" "" "" "MNXM746911" "" "" +"MAM20039c" "MAM20039" "" "" "" "CHEBI:143526" "" "" "" "" "" "MNXM1108529" "" "" +"MAM20040c" "MAM20040" "" "" "" "CHEBI:61748" "" "" "" "" "" "MNXM1108145" "" "" +"MAM02116r" "MAM02116" "" "" "" "CHEBI:17585" "" "" "" "" "" "MNXM728262" "" "" +"MAM20041r" "MAM20041" "" "" "" "CHEBI:72745" "" "" "" "" "" "MNXM31465" "" "" +"MAM20042c" "MAM20042" "" "" "" "CHEBI:72745" "" "" "" "" "" "MNXM31465" "" "" +"MAM20043r" "MAM20043" "" "" "" "CHEBI:76298" "" "" "" "" "" "MNXM6762" "" "" +"MAM20044c" "MAM20044" "" "" "" "CHEBI:76298" "" "" "" "" "" "MNXM6762" "" "" +"MAM00564r" "MAM00564" "" "" "" "CHEBI:49189" "" "" "" "" "" "MNXM1947" "" "" +"MAM02766r" "MAM02766" "" "" "" "CHEBI:77268" "" "" "" "" "" "MNXM3342" "" "" +"MAM20045r" "MAM20045" "" "" "" "CHEBI:17034" "" "" "" "" "" "MNXM2269" "" "" +"MAM20046c" "MAM20046" "" "" "" "CHEBI:17034" "" "" "" "" "" "MNXM2269" "" "" +"MAM20047r" "MAM20047" "" "" "" "CHEBI:27836" "" "" "" "" "" "MNXM11432" "" "" +"MAM20048c" "MAM20048" "" "" "" "CHEBI:27836" "" "" "" "" "" "MNXM11432" "" "" +"MAM20049r" "MAM20049" "" "" "" "CHEBI:31457" "" "" "" "" "" "MNXM7260" "" "" +"MAM20050c" "MAM20050" "" "" "" "CHEBI:31457" "" "" "" "" "" "MNXM7260" "" "" +"MAM20051r" "MAM20051" "" "" "" "CHEBI:84067" "" "" "" "" "" "MNXM13002" "" "" +"MAM20052c" "MAM20052" "" "" "" "CHEBI:84067" "" "" "" "" "" "MNXM13002" "" "" +"MAM20053r" "MAM20053" "" "" "" "CHEBI:17935" "" "" "" "" "" "MNXM2705" "" "" +"MAM02642r" "MAM02642" "" "" "" "CHEBI:25646" "" "" "" "" "" "MNXM750" "" "" +"MAM02108r" "MAM02108" "" "" "" "CHEBI:32362" "" "" "" "" "" "MNXM7416" "" "" +"MAM20054r" "MAM20054" "" "" "" "CHEBI:34787" "" "" "" "" "" "MNXM8711" "" "" +"MAM20055c" "MAM20055" "" "" "" "CHEBI:34787" "" "" "" "" "" "MNXM8711" "" "" +"MAM20056r" "MAM20056" "" "" "" "CHEBI:83276" "" "" "" "" "" "MNXM735429" "" "" +"MAM00677r" "MAM00677" "" "C03461" "" "CHEBI:15894" "" "" "" "" "" "MNXM1959" "" "" +"MAM20057c" "MAM20057" "" "" "" "CHEBI:83276" "" "" "" "" "" "MNXM735429" "" "" +"MAM20058c" "MAM20058" "" "" "" "CHEBI:132259" "" "" "" "" "" "MNXM730551" "" "" +"MAM20059c" "MAM20059" "" "" "" "CHEBI:139346" "" "" "" "" "" "MNXM166395" "" "" +"MAM20060c" "MAM20060" "" "" "" "CHEBI:139347" "" "" "" "" "" "MNXM745787" "" "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 45db7ee1..fc63cc03 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -13012,3 +13012,71 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR13085" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR13086" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR13087" "R02243" "" "" "" "" "" "MNXR107402" "" "" "" 0 "RHEA:15254" "RHEA:15253" "" +"MAR20001" "R02124" "HMR_6633;RDH1;R_HMR_6633;R_RDH1;R_TRETINOLOR1;TRETINOLOR1" "" "" "" "" "MNXR189842" "" "" "" 0 "RHEA:21284" "" "" +"MAR20002" "R02124" "HMR_6633;RDH1;R_HMR_6633;R_RDH1;R_TRETINOLOR1;TRETINOLOR1" "" "" "" "" "MNXR189842" "" "" "" 0 "RHEA:21284" "" "" +"MAR20003" "R08382" "RDH2;R_RDH2" "" "" "" "" "MNXR103441" "" "" "" 0 "RHEA:42052" "" "" +"MAR20004" "R08382" "RDH2;R_RDH2" "" "" "" "" "MNXR103441" "" "" "" 0 "RHEA:42052" "" "" +"MAR20005" "" "" "" "" "" "" "MNXR167709" "" "" "" 0 "RHEA:39803" "" "" +"MAR20006" "" "" "" "" "" "" "MNXR167709" "" "" "" 0 "RHEA:39803" "" "" +"MAR20007" "" "" "" "" "" "" "MNXR167708" "" "" "" 0 "RHEA:39799" "" "" +"MAR20008" "" "" "" "" "" "" "MNXR167708" "" "" "" 0 "RHEA:39799" "" "" +"MAR20009" "" "" "" "" "" "" "MNXR133773" "" "" "" 0 "RHEA:60660" "" "" +"MAR20010" "" "" "" "" "" "" "MNXR133773" "" "" "" 0 "RHEA:60660" "" "" +"MAR20011" "R02123" "HMR_6647;RADH;R_HMR_6647;R_RADH" "" "" "" "" "MNXR146215" "" "" "" 0 "RHEA:42080" "" "" +"MAR20012" "R02123" "HMR_6647;RADH;R_HMR_6647;R_RADH" "" "" "" "" "MNXR146215" "" "" "" 0 "RHEA:42080" "" "" +"MAR20013" "R03225" "" "" "" "" "" "MNXR108031" "" "" "" 0 "RHEA:23048" "" "" +"MAR20014" "R03283" "R_TMABADH;TMABADH" "" "" "" "" "MNXR104876" "" "" "" 0 "RHEA:17985" "" "" +"MAR20015" "R02549" "ABUTD;ABUTDm;R_ABUTD;R_ABUTDm" "" "" "" "" "MNXR95191" "" "" "" 0 "RHEA:19105" "" "" +"MAR20016" "R01704" "ALDD16;R_ALDD16" "" "" "" "" "MNXR95739" "" "" "" 0 "RHEA:33739" "" "" +"MAR20017" "" "ALDD8;R_ALDD8" "" "" "" "" "MNXR95760" "" "" "" 0 "RHEA:44100" "" "" +"MAR20018" "R04557" "" "" "" "R-HSA-2161692.2" "" "MNXR108965" "" "" "" 0 "RHEA:11912" "" "" +"MAR20019" "R04557" "" "" "" "R-HSA-2161692.2" "" "MNXR108965" "" "" "" 0 "RHEA:11912" "" "" +"MAR20020" "R00303" "G6PP;G6PPer;R_G6PP;R_G6PPer" "" "" "" "" "MNXR195425" "" "" "" 0 "RHEA:16689" "" "" +"MAR20021" "" "" "" "" "" "" "MNXR169432" "" "" "" 0 "RHEA:50076" "" "" +"MAR20022" "" "" "" "" "" "" "MNXR169432" "" "" "" 0 "RHEA:50076" "" "" +"MAR20023" "" "" "" "" "" "" "MNXR167706" "" "" "" 0 "RHEA:39787" "" "" +"MAR20024" "" "" "" "" "" "" "MNXR167706" "" "" "" 0 "RHEA:39787" "" "" +"MAR20025" "" "" "" "" "" "" "MNXR169433" "" "" "" 0 "RHEA:50088" "" "" +"MAR20026" "" "" "" "" "" "" "MNXR169433" "" "" "" 0 "RHEA:50088" "" "" +"MAR20027" "" "" "" "" "" "" "MNXR167698" "" "" "" 0 "RHEA:39751" "" "" +"MAR20028" "" "" "" "" "" "" "MNXR167698" "" "" "" 0 "RHEA:39751" "" "" +"MAR20029" "" "" "" "" "" "" "MNXR169435" "" "" "" 0 "RHEA:50096" "" "" +"MAR20030" "" "" "" "" "" "" "MNXR169435" "" "" "" 0 "RHEA:50096" "" "" +"MAR20031" "" "P4502E1;R_P4502E1" "" "" "" "" "MNXR102281" "" "" "" 0 "RHEA:26205" "" "" +"MAR20032" "" "P4502E1;R_P4502E1" "" "" "" "" "MNXR102281" "" "" "" 0 "RHEA:26205" "" "" +"MAR20033" "R10619" "GALM2;GALM2pp;R_GALM2;R_GALM2pp" "" "" "" "" "MNXR153745" "" "" "" 0 "RHEA:28675" "" "" +"MAR20034" "R10619" "GALM2;GALM2pp;R_GALM2;R_GALM2pp" "" "" "" "" "MNXR153745" "" "" "" 0 "RHEA:28675" "" "" +"MAR20035" "R01602" "A1E;GalMr;R_A1E;R_GalMr" "" "" "" "" "MNXR107082" "" "" "" 0 "RHEA:10264" "" "" +"MAR20036" "R01602" "A1E;GalMr;R_A1E;R_GalMr" "" "" "" "" "MNXR107082" "" "" "" 0 "RHEA:10264" "" "" +"MAR20037" "" "" "" "" "" "" "MNXR133380" "" "" "" 0 "RHEA:59904" "" "" +"MAR20038" "R01420" "" "" "" "" "" "MNXR106982" "" "" "" 0 "RHEA:21660" "" "" +"MAR20039" "R01419" "BZDH;R_BZDH" "" "" "" "" "MNXR96365" "" "" "" 0 "RHEA:11840" "" "" +"MAR20040" "" "" "" "" "" "" "MNXR133381" "" "" "" 0 "RHEA:59908" "" "" +"MAR20041" "" "" "" "" "" "" "MNXR171402" "" "" "" 0 "RHEA:59912" "" "" +"MAR20042" "" "" "" "" "" "" "MNXR133378" "" "" "" 0 "RHEA:59916" "" "" +"MAR20043" "" "" "" "" "" "" "MNXR171404" "" "" "" 0 "RHEA:59920" "" "" +"MAR20044" "R07140" "" "" "" "" "" "MNXR110840" "" "" "" 0 "RHEA:19981" "" "" +"MAR20045" "R06983" "FALDH2;R_FALDH2;R_r1378;r1378" "" "" "" "" "MNXR146812" "" "" "" 0 "RHEA:19985" "" "" +"MAR20046" "" "" "" "" "" "" "MNXR120270" "" "" "" 0 "RHEA:36135" "" "" +"MAR20047" "" "" "" "" "" "" "MNXR120270" "" "" "" 0 "RHEA:36135" "" "" +"MAR20048" "R01704" "ALDD16;R_ALDD16" "" "" "" "" "MNXR95739" "" "" "" 0 "RHEA:33739" "" "" +"MAR20049" "" "" "" "" "" "" "MNXR167567" "" "" "" 0 "RHEA:39015" "" "" +"MAR20050" "" "" "" "" "" "" "MNXR167567" "" "" "" 0 "RHEA:39015" "" "" +"MAR20051" "" "ALDD21;RE3076X;R_ALDD21;R_RE3076X" "" "" "" "" "MNXR95747" "" "" "" 0 "RHEA:44016" "" "" +"MAR20052" "" "ALDD21;RE3076X;R_ALDD21;R_RE3076X" "" "" "" "" "MNXR95747" "" "" "" 0 "RHEA:44016" "" "" +"MAR20053" "" "ALDD18;R_ALDD18" "" "" "" "" "MNXR95741" "" "" "" 0 "RHEA:44020" "" "" +"MAR20054" "" "ALDD18;R_ALDD18" "" "" "" "" "MNXR95741" "" "" "" 0 "RHEA:44020" "" "" +"MAR20055" "" "ALDD12;R_ALDD12" "" "" "" "" "MNXR95735" "" "" "" 0 "RHEA:44168" "" "" +"MAR20056" "" "ALDD12;R_ALDD12" "" "" "" "" "MNXR95735" "" "" "" 0 "RHEA:44168" "" "" +"MAR20057" "" "ALDD10;R_ALDD10" "" "" "" "" "MNXR95733" "" "" "" 0 "RHEA:44104" "" "" +"MAR20058" "" "ALDD10;R_ALDD10" "" "" "" "" "MNXR95733" "" "" "" 0 "RHEA:44104" "" "" +"MAR20059" "" "ALDD14;R_ALDD14" "" "" "" "" "MNXR95737" "" "" "" 0 "RHEA:44172" "" "" +"MAR20060" "" "ALDD14;R_ALDD14" "" "" "" "" "MNXR95737" "" "" "" 0 "RHEA:44172" "" "" +"MAR20061" "" "ALDD8;R_ALDD8" "" "" "" "" "MNXR95760" "" "" "" 0 "RHEA:44100" "" "" +"MAR20062" "" "ALDD7;R_ALDD7" "" "" "" "" "MNXR95759" "" "" "" 0 "RHEA:44108" "" "" +"MAR20063" "" "ALDD7;R_ALDD7" "" "" "" "" "MNXR95759" "" "" "" 0 "RHEA:44108" "" "" +"MAR20064" "R08146" "" "" "" "" "" "MNXR111724" "" "" "" 0 "RHEA:24216" "" "" +"MAR20065" "R08146" "" "" "" "" "" "MNXR111724" "" "" "" 0 "RHEA:24216" "" "" +"MAR20066" "R00009" "CAT;CATm;CATp;CATpp;CATr;R_CAT;R_CATm;R_CATp;R_CATpp;R_CATr" "" "" "" "" "MNXR96455" "" "" "" 0 "RHEA:20309" "" "" +"MAR20067" "" "" "" "" "" "" "MNXR133799" "" "" "" 0 "RHEA:55936" "" "" +"MAR20068" "" "" "" "" "" "" "MNXR171534" "" "" "" 0 "RHEA:60632" "" ""