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fix: modify rxn and met IDs
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- These ids accidentally conflict with recent changes made to HumanGEM
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haowang-bioinfo committed May 16, 2023
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14 changes: 7 additions & 7 deletions data/zebrafishSpecificMets.tsv
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mets metNames metFormulas metCharges compartments metKEGGID metPubChemID metChEBIID metMetaCycID metMetaNetXID metsNoComp
"MAM20003c" "L-Allothreonine" "C4H9NO3" 0 "c" "C05519" "7864" "CHEBI:58585" "L-ALLO-THREONINE" "MNXM2125" "MAM20003"
"MAM20004c" "Benzenamine sulfate" "C6H6NO3S" -1 "c" "C06011" "440879" "CHEBI:3024" "BENZENAMINE-SULFATE" "MNXM8327" "MAM20004"
"MAM20005x" "1,3,7-Trimethyluric acid" "C8H10N4O3" 0 "x" "C16361" "47205669" "CHEBI:691622" "CPD-12480" "MNXM2761" "MAM20005"
"MAM20006x" "3,6,8-Trimethylallantoin" "C7H12N4O3" 0 "x" "C16362" "47205670" "CHEBI:80471" "CPD-12485" "MNXM6778" "MAM20006"
"MAM20008c" "L-histidinol phosphate" "C6H11N3O4P" -1 "c" "C01100" "439398" "CHEBI:16996" "L-HISTIDINOL-P" "MNXM1482" "MAM20008"
"MAM20009c" "L-histidinol" "C6H12N3O" 1 "c" "C00860" "165271" "CHEBI:16255" "HISTIDINOL" "MNXM1281" "MAM20009"
"MAM20010c" "pseudouridine" "C9H12N2O6" 0 "c" "C02067" "15047" "CHEBI:17802" "CPD-497" "MNXM1094063;MNXM4794" "MAM20010"
"MAM15003c" "L-Allothreonine" "C4H9NO3" 0 "c" "C05519" "7864" "CHEBI:58585" "L-ALLO-THREONINE" "MNXM2125" "MAM15003"
"MAM15004c" "Benzenamine sulfate" "C6H6NO3S" -1 "c" "C06011" "440879" "CHEBI:3024" "BENZENAMINE-SULFATE" "MNXM8327" "MAM15004"
"MAM15005x" "1,3,7-Trimethyluric acid" "C8H10N4O3" 0 "x" "C16361" "47205669" "CHEBI:691622" "CPD-12480" "MNXM2761" "MAM15005"
"MAM15006x" "3,6,8-Trimethylallantoin" "C7H12N4O3" 0 "x" "C16362" "47205670" "CHEBI:80471" "CPD-12485" "MNXM6778" "MAM15006"
"MAM15008c" "L-histidinol phosphate" "C6H11N3O4P" -1 "c" "C01100" "439398" "CHEBI:16996" "L-HISTIDINOL-P" "MNXM1482" "MAM15008"
"MAM15009c" "L-histidinol" "C6H12N3O" 1 "c" "C00860" "165271" "CHEBI:16255" "HISTIDINOL" "MNXM1281" "MAM15009"
"MAM15010c" "pseudouridine" "C9H12N2O6" 0 "c" "C02067" "15047" "CHEBI:17802" "CPD-497" "MNXM1094063;MNXM4794" "MAM15010"
"MAM01104x" "5-hydroxyisourate" "C5H4N4O4" 0 "x" "C11821" "" "CHEBI:250388" "5-HYDROXYISOURATE" "MNXM1137" "MAM01104"
"MAM10018x" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate" "C5H5N4O5" -1 "x" "C12248" "" "CHEBI:58639" "CPD-5821" "MNXM1805" "MAM10018"
24 changes: 12 additions & 12 deletions data/zebrafishSpecificRxns.tsv
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rxns equations ub lb eccodes subSystems grRules rxnReferences rxnConfidenceScores rxnKEGGID rxnMetaCycID rxnREACTOMEID rxnMetaNetXID
"MAR20001" "NAD+[m] + threonine[m] => NADH[m] + H+[m] + L-2-amino-3-oxobutanoic acid[m]" 1000 0 "1.1.1.103" "Glycine, serine and threonine metabolism" "tdh" "" 2 "R01465" "THREODEHYD-RXN" "R-HSA-6798667" "MNXR103402"
"MAR20003" "L-Allothreonine[c] <=> glycine[c] + acetaldehyde[c]" 1000 -1000 "4.1.2.48;4.1.2.49" "Glycine, serine and threonine metabolism" "tha1" "" 2 "R06171" "LTAA-RXN" "" "MNXR104834"
"MAR20004" "H2O[x] + 5-hydroxyisourate[x] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] + H+[x]" 1000 0 "3.5.2.17" "Purine metabolism" "uraha or urahb" "" 3 "R06601" "3.5.2.17-RXN" "" "MNXR100652"
"MAR20005" "5-hydroxyisourate[x] <=> 5-hydroxyisourate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR20006" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR20007" "2 H2O[x] + O2[x] + 1,3,7-Trimethyluric acid[x] <=> CO2[x] + H2O2[x] + 3,6,8-Trimethylallantoin[x]" 1000 -1000 "1.7.3.3" "Caffeine metabolism" "uox" "" 2 "R07981" "" "" "MNXR111564"
"MAR20010" "PAPS[c] + aniline[c] => PAP[c] + Benzenamine sulfate[c] + H+[c]" 1000 0 "2.8.2.3" "Amine sulfotransferase" "sult3st1 or sult3st2 or sult3st3 or sult3st4 or sult3st5" "" 2 "R01861" "" "" "MNXR107208"
"MAR20011" "ATP[c] + glucuronate[c] => ADP[c] + D-glucuronate 1-phosphate[c] + H+[c]" 1000 0 "2.7.1.43" "Ascorbate and aldarate metabolism" "gkup" "" 2 "R01476" "GLUCURONOKINASE-RXN" "" "MNXR107016"
"MAR20012" "H2O[c] + L-histidinol phosphate[c] => Pi[c] + L-histidinol[c]" 1000 0 "3.1.3.15" "Histidine metabolism" "LOC101886429" "" 2 "R03013" "HISTIDPHOS-RXN" "" "MNXR100642"
"MAR20013" "ATP[c] + pseudouridine[c] <=> ADP[c] + pseudouridine-5-phosphate[c] + H+[c]" 1000 -1000 "2.7.1.83" "Pyrimidine metabolism" "zgc:136858" "" 2 "R03315" "PSEUDOURIDINE-KINASE-RXN" "" "MNXR108088;MNXR162394"
"MAR20014" "NADH[c] + O2[c] + H+[c] + cholesterol[c] => 2 H2O[c] + NAD+[c] + provitamin D3[c]" 1000 0 "1.14.19.21" "Hormone biosynthesis" "nvd-Dr" "" 2 "R11007" "RXN-16379" "" "MNXR120043"
"MAR20015" "NADPH[c] + O2[c] + H+[c] + cholesterol[c] => 2 H2O[c] + NADP+[c] + provitamin D3[c]" 1000 0 "1.14.19.21" "Hormone biosynthesis" "nvd-Dr" "" 2 "R11008" "RXN-16379" "" "MNXR120043"
"MAR15001" "NAD+[m] + threonine[m] => NADH[m] + H+[m] + L-2-amino-3-oxobutanoic acid[m]" 1000 0 "1.1.1.103" "Glycine, serine and threonine metabolism" "tdh" "" 2 "R01465" "THREODEHYD-RXN" "R-HSA-6798667" "MNXR103402"
"MAR15003" "L-Allothreonine[c] <=> glycine[c] + acetaldehyde[c]" 1000 -1000 "4.1.2.48;4.1.2.49" "Glycine, serine and threonine metabolism" "tha1" "" 2 "R06171" "LTAA-RXN" "" "MNXR104834"
"MAR15004" "H2O[x] + 5-hydroxyisourate[x] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] + H+[x]" 1000 0 "3.5.2.17" "Purine metabolism" "uraha or urahb" "" 3 "R06601" "3.5.2.17-RXN" "" "MNXR100652"
"MAR15005" "5-hydroxyisourate[x] <=> 5-hydroxyisourate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR15006" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR15007" "2 H2O[x] + O2[x] + 1,3,7-Trimethyluric acid[x] <=> CO2[x] + H2O2[x] + 3,6,8-Trimethylallantoin[x]" 1000 -1000 "1.7.3.3" "Caffeine metabolism" "uox" "" 2 "R07981" "" "" "MNXR111564"
"MAR15010" "PAPS[c] + aniline[c] => PAP[c] + Benzenamine sulfate[c] + H+[c]" 1000 0 "2.8.2.3" "Amine sulfotransferase" "sult3st1 or sult3st2 or sult3st3 or sult3st4 or sult3st5" "" 2 "R01861" "" "" "MNXR107208"
"MAR15011" "ATP[c] + glucuronate[c] => ADP[c] + D-glucuronate 1-phosphate[c] + H+[c]" 1000 0 "2.7.1.43" "Ascorbate and aldarate metabolism" "gkup" "" 2 "R01476" "GLUCURONOKINASE-RXN" "" "MNXR107016"
"MAR15012" "H2O[c] + L-histidinol phosphate[c] => Pi[c] + L-histidinol[c]" 1000 0 "3.1.3.15" "Histidine metabolism" "LOC101886429" "" 2 "R03013" "HISTIDPHOS-RXN" "" "MNXR100642"
"MAR15013" "ATP[c] + pseudouridine[c] <=> ADP[c] + pseudouridine-5-phosphate[c] + H+[c]" 1000 -1000 "2.7.1.83" "Pyrimidine metabolism" "zgc:136858" "" 2 "R03315" "PSEUDOURIDINE-KINASE-RXN" "" "MNXR108088;MNXR162394"
"MAR15014" "NADH[c] + O2[c] + H+[c] + cholesterol[c] => 2 H2O[c] + NAD+[c] + provitamin D3[c]" 1000 0 "1.14.19.21" "Hormone biosynthesis" "nvd-Dr" "" 2 "R11007" "RXN-16379" "" "MNXR120043"
"MAR15015" "NADPH[c] + O2[c] + H+[c] + cholesterol[c] => 2 H2O[c] + NADP+[c] + provitamin D3[c]" 1000 0 "1.14.19.21" "Hormone biosynthesis" "nvd-Dr" "" 2 "R11008" "RXN-16379" "" "MNXR120043"

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