From 0eb0faf894741d808283fdd68a341ee6861e4812 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 18 Jul 2026 10:02:44 +0200 Subject: [PATCH 1/2] Fix metabolicTasks_Full.txt so it parses with parseTaskList The full metabolic task list was missing the leading (empty) column that metabolicTasks_Essential.txt has, so RAVEN parseTaskList read the whole file as a single task. Add the leading column to align the format; parseTaskList now returns 257 tasks and compareMultipleModels runs against the full list. No task definitions are changed. --- data/metabolicTasks/metabolicTasks_Full.txt | 952 ++++++++++---------- 1 file changed, 476 insertions(+), 476 deletions(-) diff --git a/data/metabolicTasks/metabolicTasks_Full.txt b/data/metabolicTasks/metabolicTasks_Full.txt index 0a7947c6..a367b5aa 100644 --- a/data/metabolicTasks/metabolicTasks_Full.txt +++ b/data/metabolicTasks/metabolicTasks_Full.txt @@ -1,476 +1,476 @@ -ID DESCRIPTION SHOULD FAIL IN IN LB IN UB OUT OUT LB OUT UB EQU EQU LB EQU UB CHANGED RXN CHANGED LB CHANGED UB PRINT FLUX COMMENTS -1 Aerobic rephosphorylation of ATP from glucose O2[e];glucose[e] H2O[e];CO2[e];H+[c] ATP[c] + H2O[c] => ADP[c] + Pi[c] + H+[c] 1 -2 Aerobic rephosphorylation of ATP from a fatty acid O2[e];palmitate[e] H2O[e];CO2[e];H+[c] ATP[c] + H2O[c] => ADP[c] + Pi[c] + H+[c] 1 -3 Aerobic rephosphorylation of GTP O2[e];glucose[e] H2O[e];CO2[e];H+[c] GTP[c] + H2O[c] => GDP[c] + Pi[c] + H+[c] 1 -4 Aerobic rephosphorylation of CTP O2[e];glucose[e] H2O[e];CO2[e];H+[c] CTP[c] + H2O[c] => CDP[c] + Pi[c] + H+[c] 1 -5 Aerobic rephosphorylation of UTP O2[e];glucose[e] H2O[e];CO2[e];H+[c] UTP[c] + H2O[c] => UDP[c] + Pi[c] + H+[c] 1 -6 Anaerobic rephosphorylation of ATP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] ATP[c] + H2O[c] => ADP[c] + Pi[c] + H+[c] 1 -7 Anaerobic rephosphorylation of GTP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] GTP[c] + H2O[c] => GDP[c] + Pi[c] + H+[c] 1 -8 Anaerobic rephosphorylation of CTP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] CTP[c] + H2O[c] => CDP[c] + Pi[c] + H+[c] 1 -9 Anaerobic rephosphorylation of UTP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] UTP[c] + H2O[c] => UDP[c] + Pi[c] + H+[c] 1 -10 ATP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - ATP[c] 1 -11 CTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - CTP[c] 1 -12 GTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - GTP[c] 1 -13 UTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - UTP[c] 1 -14 dATP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - dATP[c] 1 -15 dCTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - dCTP[c] 1 -16 dGTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - dGTP[c] 1 -17 dTTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - dTTP[c] 1 -18 ATP salvage from Adenosine Pi[e];H+[c] H2O[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] - adenosine[e] 1 1 ATP[e] 1 -19 ATP salvage from Hypoxanthine Pi[e];O2[e];NH3[e];H2O[e];H+[c] H2O[e];Pi[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] - hypoxanthine[e] 1 1 ATP[e] 1 - PRPP[c] 1 1 -20 dTTP salvage from Thymine Pi[e];O2[e];NH3[e];H2O[e];H+[c] H2O[e];PPi[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] - thymine[e] 1 1 dTTP[c] 1 - 2-deoxy-D-ribose-1-phosphate[c] 1 1 -21 Aerobic reduction of NAD+ glucose[e];O2[e] H2O[e];CO2[e] NADH[c] => NAD+[c] 1 This is not a proof since there can be net synthesis of NADH. However, if you look at the solution it's fine -22 Aerobic reduction of NADP+ glucose[e];O2[e] H2O[e];CO2[e] NADPH[c] => NADP+[c] 1 This is not a proof since there can be net synthesis of NADPH. However, if you look at the solution it's fine -23 Gluconeogenesis from Lactate O2[e];H2O[e];L-lactate[e] H2O[e];CO2[e] - glucose[e] 1 -24 Gluconeogenesis from Glycerol O2[e];H2O[e];glycerol[e] H2O[e];CO2[e] - glucose[e] 1 -25 Gluconeogenesis from Alanine O2[e];H2O[e];alanine[e] H2O[e];CO2[e];urea[e] - glucose[e] 1 -26 Gluconeogenesis from Lactate and optionally fatty acid O2[e];H2O[e];palmitate[e];L-lactate[e] H2O[e];CO2[e] - glucose[e] 1 -27 Gluconeogenesis from Glycerol and optionally fatty acid O2[e];H2O[e];palmitate[e];glycerol[e] H2O[e];CO2[e] - glucose[e] 1 -28 Gluconeogenesis from Alanine and fatty acid O2[e];H2O[e];palmitate[e];alanine[e] H2O[e];CO2[e] - glucose[e] 1 -29 Storage of glucose in Glycogen glucose[e] 11 11 H2O[e];CO2[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] - glycogenin[c] 1 1 glycogenin G11[c] 1 NADH[c] <=> NAD+[c] - O2[e] NADPH[c] <=> NADP+[c] -30 Release of glucose from Glycogen glycogenin G11[c] 1 1 glucose[e] 11 11 glucose-1-phosphate[c] + H2O[c] => glucose[c] + Pi[c] - H2O[e] glycogenin[c] 1 1 -31 Fructose degradation fructose[e];O2[e] 1 H2O[e];CO2[e] -32 Galactose degradation galactose[e];O2[e] 1 H2O[e];CO2[e] -33 UDP-glucose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - UDP-glucose[c] 1 -34 UDP-galactose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - UDP-galactose[c] 1 -35 UDP-glucuronate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - UDP-glucuronate[c] 1 -36 GDP-L-fucose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - GDP-L-fucose[c] 1 -37 GDP-mannose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - GDP-mannose[c] 1 -38 UDP-N-acetyl D-galactosamine de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - UDP-N-acetyl-D-galactosamine[c] 1 -39 CMP-N-acetylneuraminate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - CMP-N-acetylneuraminate[c] 1 -40 N-Acetylglucosamine de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - N-acetylglucosamine[c] 1 -41 Glucuronate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - glucuronate[c] 1 -42 Alanine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - alanine[e] 1 -43 Arginine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - arginine[e] 1 -44 Asparagine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - asparagine[e] 1 -45 Aspartate de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - aspartate[c] 1 -46 Glutamate de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - glutamate[e] 1 -47 Glycine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - glycine[e] 1 -48 Glutamine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - glutamine[e] 1 -49 Proline de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - proline[e] 1 -50 Serine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - serine[e] 1 -51 Histidine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - histidine[c] 1 -52 Histidine uptake histidine[e] 1 1 histidine[c] 1 -53 Isoleucine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - isoleucine[c] 1 -54 Isoleucine uptake isoleucine[e] 1 1 isoleucine[c] 1 -55 Leucine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - leucine[c] 1 -56 Leucine uptake leucine[e] 1 1 leucine[c] 1 -57 Lysine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - lysine[c] 1 -58 Lysine uptake lysine[e] 1 1 lysine[c] 1 -59 Methionine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - methionine[c] 1 -60 Methionine uptake methionine[e] 1 1 methionine[c] 1 -61 Phenylalanine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - phenylalanine[c] 1 -62 Phenylalanine uptake phenylalanine[e] 1 1 phenylalanine[c] 1 -63 Threonine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - threonine[c] 1 -64 Threonine uptake threonine[e] 1 1 threonine[c] 1 -65 Tryptophan de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - tryptophan[c] 1 -66 Tryptophan uptake tryptophan[e] 1 1 tryptophan[c] 1 -67 Valine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - valine[c] 1 -68 Valine uptake valine[e] 1 1 valine[c] 1 -69 Cysteine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e];sulfate[e] H2O[e];CO2[e] - cysteine[e] 1 -70 Cysteine de novo synthesis (minimal substrates and AA, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e];sulfate[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e] H2O[e];CO2[e] - cysteine[e] 1 -71 Cystine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e];sulfite[e] H2O[e];CO2[e] - cystine[e] 1 -72 Tyrosine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - tyrosine[e] 1 -73 Tyrosine de novo synthesis (minimal substrates with AA, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e];sulfate[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e] H2O[e];CO2[e] - tyrosine[e] 1 -74 Homocysteine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - homocysteine[c] 1 -75 Homocysteine de novo synthesis (minimal substrates with AA, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e];sulfate[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e] H2O[e];CO2[e] - homocysteine[c] 1 -76 beta-Alanine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - beta-alanine[e] 1 -77 Alanine degradation alanine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -78 Arginine degradation arginine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -79 Asparagine degradation asparagine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -80 Aspartate degradation aspartate[e];O2[e] 1 H2O[e];CO2[e];urate[e] -81 Cysteine degradation cysteine[e];O2[e] 1 H2O[e];CO2[e];urate[e];H2S[e] -82 Glutamate degradation glutamate[e];O2[e] 1 H2O[e];CO2[e];urate[e] -83 Glycine degradation glycine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -84 Histidine degradation histidine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -85 Isoleucine degradation isoleucine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -86 Glutamine degradation glutamine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -87 Leucine degradation leucine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -88 Lysine degradation lysine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -89 Methionine degradation methionine[e];O2[e] 1 H2O[e];CO2[e];urate[e];H2S[e] -90 Phenylalanine degradation phenylalanine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -91 Proline degradation proline[e];O2[e] 1 H2O[e];CO2[e];urate[e] -92 Serine degradation serine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -93 Threonine degradation threonine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -94 Tryptophan degradation tryptophan[e];O2[e] 1 H2O[e];CO2[e];urate[e] -95 Tyrosine degradation tyrosine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -96 Valine degradation valine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -97 Homocysteine degradation homocysteine[c];O2[e] 1 H2O[e];CO2[e];urate[e];H2S[e] -98 Ornithine degradation ornithine[e] 1 urea[e] 1 - O2[e] H2O[e];CO2[e] -99 beta-Alanine degradation beta-alanine[e];O2[e] 1 H2O[e];CO2[e];urate[e] -100 Urea from alanine alanine[e] 2 H2O[e];CO2[e] - O2[e] urea[e] 1 -101 Urea from glutamine glutamine[e] 1 H2O[e];CO2[e] - O2[e] urea[e] 1 -102 Creatine de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] - creatine[e] 1 -103 Heme de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];Fe2+[e] H2O[e];CO2[e] - heme[e] 1 -104 PC de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e];isoleucine[c] H2O[e];CO2[e];urate[e] - PC-LD pool[c] 1 -105 PE de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];ethanolamine[c] H2O[e];CO2[e] - PE-LD pool[c] 1 -106 PS de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] - PS-LD pool[c] 1 -107 PI de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];inositol[e] H2O[e];CO2[e] - PI pool[c] 1 -108 Cardiolipin de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] - CL pool[c] 1 -109 SM de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] - SM pool[c] 1 -110 Ceramide de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] - ceramide pool[c] 1 -111 Lactosylceramide de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] - LacCer pool[c] 1 -112 CoA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];methionine[e];pantothenate[e] CoA[c] 1 - CO2[e];urate[e];H2O[e] -113 NAD de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];nicotinamide[e] NADH[c] 1 - H2O[e];CO2[e] -114 NADP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];nicotinamide[e] NADPH[c] 1 - H2O[e];CO2[e] -115 FAD de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];riboflavin[e] FAD[c] 1 - H2O[e];CO2[e] -116 Thioredoxin de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e];valine[e] H2O[e];CO2[e];urate[e];H2S[e] - thioredoxin[c] 1 -117 THF de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];folate[e] H2O[e];CO2[e] - THF[c] 1 -118 Pyridoxal-P de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];pyridoxine[e] H2O[e];CO2[e] - pyridoxal-phosphate[c] 1 -119 Acetoacetate de novo synthesis O2[e];glucose[e] H2O[e];CO2[e] - acetoacetate[m] 1 -120 (R)-3-Hydroxybutanoate de novo synthesis O2[e];glucose[e] H2O[e];CO2[e] - (R)-3-hydroxybutanoate[c] 1 -121 Farnesyl-PP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];phenylalanine[e];Pi[e] H2O[e];CO2[e] - farnesyl-PP[c] 1 -122 Lauric acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - lauric acid[c] 1 -123 Tridecylic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - tridecylic acid[c] 1 -124 Myristic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - myristic acid[c] 1 -125 9E-tetradecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - (9E)-tetradecenoic acid[c] 1 -126 7Z-tetradecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - (7Z)-tetradecenoic acid[c] 1 -127 Physeteric acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - physeteric acid[c] 1 -128 Pentadecylic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - pentadecylic acid[c] 1 -129 Palmitate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - palmitate[c] 1 -130 Palmitolate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - palmitolate[c] 1 -131 7-palmitoleic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - 7-palmitoleic acid[c] 1 -132 Margaric acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - margaric acid[c] 1 -133 10Z-heptadecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - (10Z)-heptadecenoic acid[c] 1 -134 9-heptadecylenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - 9-heptadecylenic acid[c] 1 -135 Stearate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - stearate[c] 1 -136 13Z-octadecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - (13Z)-octadecenoic acid[c] 1 -137 cis-vaccenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - cis-vaccenic acid[c] 1 -138 Oleate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - oleate[c] 1 -139 Elaidate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - elaidate[c] 1 -140 7Z-octadecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - (7Z)-octadecenoic acid[c] 1 -141 6Z,9Z-octadecadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - (6Z,9Z)-octadecadienoic acid[c] 1 -142 Nonadecylic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - nonadecylic acid[c] 1 -143 Eicosanoate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - eicosanoate[c] 1 -144 13Z-Eicosenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - (13Z)-eicosenoic acid[c] 1 -145 cis-Gondoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - cis-gondoic acid[c] 1 -146 9-Eicosenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - 9-eicosenoic acid[c] 1 -147 8,11-Eicosadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - 8,11-eicosadienoic acid[c] 1 -148 Mead acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - mead acid[c] 1 -149 Heneicosanoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - heneicosanoic acid[c] 1 -150 Behenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - behenic acid[c] 1 -151 cis-Erucic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - cis-erucic acid[c] 1 -152 cis-Cetoleic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - cis-cetoleic acid[c] 1 -153 Tricosanoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] - tricosanoic acid[c] 1 -154 Lignocerate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - lignocerate[c] 1 -155 Nervonic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - nervonic acid[c] 1 -156 Cerotic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - cerotic acid[c] 1 -157 Ximenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] - ximenic acid[c] 1 -158 Linolenate de novo synthesis (minimal substrates, physiological excretion) TRUE O2[e];glucose[e] CO2[e];H2O[e] - linolenate[c] 1 -159 Stearidonic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - stearidonic acid[c] 1 -160 omega-3-Arachidonic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - omega-3-arachidonic acid[c] 1 -161 EPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - EPA[c] 1 -162 DPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - DPA[c] 1 -163 9Z,12Z,15Z,18Z,21Z-TPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - (9Z,12Z,15Z,18Z,21Z)-TPA[c] 1 -164 6Z,9Z,12Z,15Z,18Z,21Z-THA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - (6Z,9Z,12Z,15Z,18Z,21Z)-THA[c] 1 -165 DHA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - DHA[c] 1 -166 11Z,14Z,17Z-eicosatrienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - (11Z,14Z,17Z)-eicosatrienoic acid[c] 1 -167 13,16,19-docosatrienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - 13,16,19-docosatrienoic acid[c] 1 -168 10,13,16,19-docosatetraenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - 10,13,16,19-docosatetraenoic acid[c] 1 -169 12,15,18,21-tetracosatetraenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] - 12,15,18,21-tetracosatetraenoic acid[c] 1 -170 Linoleate de novo synthesis (minimal substrates, physiological excretion) TRUE O2[e];glucose[e] CO2[e];H2O[e] - linoleate[c] 1 -171 gamma-Linolenate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - gamma-linolenate[c] 1 -172 Dihomo-gamma-linolenate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - dihomo-gamma-linolenate[c] 1 -173 Arachidonate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - arachidonate[c] 1 -174 Adrenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - adrenic acid[c] 1 -175 9Z,12Z,15Z,18Z-TTA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - (9Z,12Z,15Z,18Z)-TTA[c] 1 -176 6Z,9Z,12Z,15Z,18Z-TPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - (6Z,9Z,12Z,15Z,18Z)-TPA[c] 1 -177 4Z,7Z,10Z,13Z,16Z-DPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - (4Z,7Z,10Z,13Z,16Z)-DPA[c] 1 -178 11Z,14Z-eicosadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - (11Z,14Z)-eicosadienoic acid[c] 1 -179 13Z,16Z-docosadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - (13Z,16Z)-docosadienoic acid[c] 1 -180 10,13,16-docosatriynoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] - 10,13,16-docosatriynoic acid[c] 1 -181 Lauric acid (complete oxidation) lauric acid[e] 1 1 CO2[e];H2O[e] - O2[e] -182 Tridecylic acid (complete oxidation) tridecylic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -183 Myristic acid (complete oxidation) myristic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -184 9E-tetradecenoic acid (complete oxidation) (9E)-tetradecenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -185 7Z-tetradecenoic acid (complete oxidation) (7Z)-tetradecenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -186 Physeteric acid (complete oxidation) physeteric acid[e] 1 1 CO2[e];H2O[e] - O2[e] -187 Pentadecylic acid (complete oxidation) pentadecylic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -188 Palmitate (complete oxidation) palmitate[e] 1 1 CO2[e];H2O[e] - O2[e] -189 Palmitolate (complete oxidation) palmitolate[e] 1 1 CO2[e];H2O[e] - O2[e] -190 7-palmitoleic acid (complete oxidation) 7-palmitoleic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -191 Margaric acid (complete oxidation) margaric acid[e] 1 1 CO2[e];H2O[e] - O2[e] -192 10Z-heptadecenoic acid (complete oxidation) (10Z)-heptadecenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -193 9-heptadecylenic acid (complete oxidation) 9-heptadecylenic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -194 Stearate (complete oxidation) stearate[e] 1 1 CO2[e];H2O[e] - O2[e] -195 13Z-octadecenoic acid (complete oxidation) (13Z)-octadecenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -196 cis-Vaccenic acid (complete oxidation) cis-vaccenic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -197 Oleate (complete oxidation) oleate[e] 1 1 CO2[e];H2O[e] - O2[e] -198 Elaidate (complete oxidation) elaidate[e] 1 1 CO2[e];H2O[e] - O2[e] -199 7Z-octadecenoic acid (complete oxidation) (7Z)-octadecenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -200 6Z,9Z-octadecadienoic acid (complete oxidation) (6Z,9Z)-octadecadienoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -201 Nonadecylic acid (complete oxidation) nonadecylic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -202 Eicosanoate (complete oxidation) eicosanoate[e] 1 1 CO2[e];H2O[e] - O2[e] -203 13Z-Eicosenoic acid (complete oxidation) (13Z)-eicosenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -204 cis-Gondoic acid (complete oxidation) cis-gondoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -205 9-Eicosenoic acid (complete oxidation) 9-eicosenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -206 8,11-Eicosadienoic acid (complete oxidation) 8,11-eicosadienoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -207 Mead acid (complete oxidation) mead acid[e] 1 1 CO2[e];H2O[e] - O2[e] -208 heneicosanoic acid (complete oxidation) heneicosanoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -209 Behenic acid (complete oxidation) behenic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -210 cis-Erucic acid (complete oxidation) cis-erucic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -211 cis-Cetoleic acid (complete oxidation) cis-cetoleic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -212 Tricosanoic acid (complete oxidation) tricosanoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -213 Lignocerate (complete oxidation) lignocerate[e] 1 1 CO2[e];H2O[e] - O2[e] -214 Nervonic acid (complete oxidation) nervonic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -215 Cerotic acid (complete oxidation) cerotic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -216 Ximenic acid (complete oxidation) ximenic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -217 Linolenate (complete oxidation) linolenate[e] 1 1 CO2[e];H2O[e] - O2[e] -218 Stearidonic acid (complete oxidation) stearidonic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -219 omega-3-Arachidonic acid (complete oxidation) omega-3-arachidonic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -220 EPA (complete oxidation) EPA[e] 1 1 CO2[e];H2O[e] - O2[e] -221 DPA (complete oxidation) DPA[e] 1 1 CO2[e];H2O[e] - O2[e] -222 9Z,12Z,15Z,18Z,21Z-TPA (complete oxidation) (9Z,12Z,15Z,18Z,21Z)-TPA[e] 1 1 CO2[e];H2O[e] - O2[e] -223 6Z,9Z,12Z,15Z,18Z,21Z-THA (complete oxidation) (6Z,9Z,12Z,15Z,18Z,21Z)-THA[e] 1 1 CO2[e];H2O[e] - O2[e] -224 DHA (complete oxidation) DHA[e] 1 1 CO2[e];H2O[e] - O2[e] -225 11Z,14Z,17Z-eicosatrienoic acid (complete oxidation) (11Z,14Z,17Z)-eicosatrienoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -226 13,16,19-docosatrienoic acid (complete oxidation) 13,16,19-docosatrienoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -227 10,13,16,19-docosatetraenoic acid (complete oxidation) 10,13,16,19-docosatetraenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -228 12,15,18,21-tetracosatetraenoic acid (complete oxidation) 12,15,18,21-tetracosatetraenoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -229 Linoleate (complete oxidation) linoleate[e] 1 1 CO2[e];H2O[e] - O2[e] -230 gamma-Linolenate (complete oxidation) gamma-linolenate[e] 1 1 CO2[e];H2O[e] - O2[e] -231 Dihomo-gamma-linolenate (complete oxidation) dihomo-gamma-linolenate[e] 1 1 CO2[e];H2O[e] - O2[e] -232 Arachidonate (complete oxidation) arachidonate[e] 1 1 CO2[e];H2O[e] - O2[e] -233 Adrenic acid (complete oxidation) adrenic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -234 9Z,12Z,15Z,18Z-TTA (complete oxidation) (9Z,12Z,15Z,18Z)-TTA[e] 1 1 CO2[e];H2O[e] - O2[e] -235 6Z,9Z,12Z,15Z,18Z-TPA (complete oxidation) (6Z,9Z,12Z,15Z,18Z)-TPA[e] 1 1 CO2[e];H2O[e] - O2[e] -236 4Z,7Z,10Z,13Z,16Z-DPA (complete oxidation) (4Z,7Z,10Z,13Z,16Z)-DPA[e] 1 1 CO2[e];H2O[e] - O2[e] -237 11Z,14Z-eicosadienoic acid (complete oxidation) (11Z,14Z)-eicosadienoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -238 13Z,16Z-docosadienoic acid (complete oxidation) (13Z,16Z)-docosadienoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -239 10,13,16-docosatriynoic acid (complete oxidation) 10,13,16-docosatriynoic acid[e] 1 1 CO2[e];H2O[e] - O2[e] -240 Triacylglycerol de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];linoleate[e];linolenate[e] H2O[e];CO2[e] - TAG-LD pool[c] 1 -241 Glycocholate de novo synthesis and excretion (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];phenylalanine[e] H2O[e];CO2[e];urea[e] - glycocholate[e] 1 -242 Glycochenodeoxycholate de novo synthesis and excretion O2[e];glucose[e];Pi[e];phenylalanine[e] H2O[e];CO2[e];urea[e] - glycochenodeoxycholate[e] 1 -243 Taurocholate de novo synthesis and excretion (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];phenylalanine[e];cysteine[e] H2O[e];CO2[e];urea[e] - taurocholate[e] 1 -244 Taurochenodeoxycholate de novo synthesis and excretion (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];phenylalanine[e];cysteine[e] H2O[e];CO2[e];urea[e] - taurochenodeoxycholate[e] 1 -245 PAPS de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];NH3[e];sulfate[e];histidine[e];valine[e] H2O[e];CO2[e];urate[e] - PAPS[c] 1 -246 PAP degradation PAPS[c] CO2[e];H2O[e];urate[e];Pi[e];H2S[e] - O2[e] -247 SAM de novo synthesis (minimal substrates, physiological excretion) O2[e];NH3[e];glucose[e];methionine[e] H2O[e];CO2[e];urate[e] - SAM[c] 1 -248 GSH de novo synthesis (minimal substrates, physiological excretion) O2[e];NH3[e];glucose[e];methionine[e] H2O[e];CO2[e];urate[e] - GSH[c] 1 -249 Bilirubin conjugation (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];bilirubin[e] H2O[e];CO2[e] - bilirubin-bisglucuronoside[e] 1 -250 NH3 import and degradation NH3[e];O2[e];glucose[e] CO2[e];H2O[e] - urea[e] 1 -251 Ethanol import and degradation (minimal substrates, minimalexcretion) ethanol[e] 1 1 CO2[e];H2O[e] - O2[e] -252 Oxidative phosphorylation succinate[m] 1 1 fumarate[m] 1 1 ATP[m] + H2O[m] => ADP[m] + Pi[m] + H+[m] 1 - NADH[m];H+[m] 1 1 NAD+[m] 1 1 - O2[e] H2O[e] -253 Oxidative decarboxylation pyruvate[m];NAD+[m];CoA[m] 1 1 acetyl-CoA[m];NADH[m];CO2[e] 1 1 -254 Krebs cycle NADH acetyl-CoA[m];GDP[m];ubiquinone[m] 1 1 CoA[m];ubiquinol[m];GTP[m] 1 1 - NAD+[m] 3 3 NADH[m] 3 3 - Pi[m];H2O[e] CO2[e];H+[c];H+[m] -255 Ubiquinol-to-proton ubiquinol[m] 1 1 ubiquinone[m] 1 1 - O2[e];H+[m] H2O[e] - H+[c] 6 -256 Ubiquinol-to-ATP ubiquinol[m] 1 1 ubiquinone[m] 1 1 ATP[m] + H2O[m] => ADP[m] + Pi[m] + H+[m] 1 - O2[e];H+[m] H2O[e];H+[m];H+[c] -257 Biosynthesis of Vitamin C (ascorbate) TRUE O2[e];glucose[e] ascorbate[c] 1 - H2O[e];CO2[e] + ID DESCRIPTION SHOULD FAIL IN IN LB IN UB OUT OUT LB OUT UB EQU EQU LB EQU UB CHANGED RXN CHANGED LB CHANGED UB PRINT FLUX COMMENTS + 1 Aerobic rephosphorylation of ATP from glucose O2[e];glucose[e] H2O[e];CO2[e];H+[c] ATP[c] + H2O[c] => ADP[c] + Pi[c] + H+[c] 1 + 2 Aerobic rephosphorylation of ATP from a fatty acid O2[e];palmitate[e] H2O[e];CO2[e];H+[c] ATP[c] + H2O[c] => ADP[c] + Pi[c] + H+[c] 1 + 3 Aerobic rephosphorylation of GTP O2[e];glucose[e] H2O[e];CO2[e];H+[c] GTP[c] + H2O[c] => GDP[c] + Pi[c] + H+[c] 1 + 4 Aerobic rephosphorylation of CTP O2[e];glucose[e] H2O[e];CO2[e];H+[c] CTP[c] + H2O[c] => CDP[c] + Pi[c] + H+[c] 1 + 5 Aerobic rephosphorylation of UTP O2[e];glucose[e] H2O[e];CO2[e];H+[c] UTP[c] + H2O[c] => UDP[c] + Pi[c] + H+[c] 1 + 6 Anaerobic rephosphorylation of ATP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] ATP[c] + H2O[c] => ADP[c] + Pi[c] + H+[c] 1 + 7 Anaerobic rephosphorylation of GTP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] GTP[c] + H2O[c] => GDP[c] + Pi[c] + H+[c] 1 + 8 Anaerobic rephosphorylation of CTP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] CTP[c] + H2O[c] => CDP[c] + Pi[c] + H+[c] 1 + 9 Anaerobic rephosphorylation of UTP glucose[e] H2O[e];L-lactate[e];CO2[e];H+[c] UTP[c] + H2O[c] => UDP[c] + Pi[c] + H+[c] 1 + 10 ATP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + ATP[c] 1 + 11 CTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + CTP[c] 1 + 12 GTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + GTP[c] 1 + 13 UTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + UTP[c] 1 + 14 dATP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + dATP[c] 1 + 15 dCTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + dCTP[c] 1 + 16 dGTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + dGTP[c] 1 + 17 dTTP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + dTTP[c] 1 + 18 ATP salvage from Adenosine Pi[e];H+[c] H2O[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] + adenosine[e] 1 1 ATP[e] 1 + 19 ATP salvage from Hypoxanthine Pi[e];O2[e];NH3[e];H2O[e];H+[c] H2O[e];Pi[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] + hypoxanthine[e] 1 1 ATP[e] 1 + PRPP[c] 1 1 + 20 dTTP salvage from Thymine Pi[e];O2[e];NH3[e];H2O[e];H+[c] H2O[e];PPi[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] + thymine[e] 1 1 dTTP[c] 1 + 2-deoxy-D-ribose-1-phosphate[c] 1 1 + 21 Aerobic reduction of NAD+ glucose[e];O2[e] H2O[e];CO2[e] NADH[c] => NAD+[c] 1 This is not a proof since there can be net synthesis of NADH. However, if you look at the solution it's fine + 22 Aerobic reduction of NADP+ glucose[e];O2[e] H2O[e];CO2[e] NADPH[c] => NADP+[c] 1 This is not a proof since there can be net synthesis of NADPH. However, if you look at the solution it's fine + 23 Gluconeogenesis from Lactate O2[e];H2O[e];L-lactate[e] H2O[e];CO2[e] + glucose[e] 1 + 24 Gluconeogenesis from Glycerol O2[e];H2O[e];glycerol[e] H2O[e];CO2[e] + glucose[e] 1 + 25 Gluconeogenesis from Alanine O2[e];H2O[e];alanine[e] H2O[e];CO2[e];urea[e] + glucose[e] 1 + 26 Gluconeogenesis from Lactate and optionally fatty acid O2[e];H2O[e];palmitate[e];L-lactate[e] H2O[e];CO2[e] + glucose[e] 1 + 27 Gluconeogenesis from Glycerol and optionally fatty acid O2[e];H2O[e];palmitate[e];glycerol[e] H2O[e];CO2[e] + glucose[e] 1 + 28 Gluconeogenesis from Alanine and fatty acid O2[e];H2O[e];palmitate[e];alanine[e] H2O[e];CO2[e] + glucose[e] 1 + 29 Storage of glucose in Glycogen glucose[e] 11 11 H2O[e];CO2[e] ATP[c] + H2O[c] <=> ADP[c] + Pi[c] + H+[c] + glycogenin[c] 1 1 glycogenin G11[c] 1 NADH[c] <=> NAD+[c] + O2[e] NADPH[c] <=> NADP+[c] + 30 Release of glucose from Glycogen glycogenin G11[c] 1 1 glucose[e] 11 11 glucose-1-phosphate[c] + H2O[c] => glucose[c] + Pi[c] + H2O[e] glycogenin[c] 1 1 + 31 Fructose degradation fructose[e];O2[e] 1 H2O[e];CO2[e] + 32 Galactose degradation galactose[e];O2[e] 1 H2O[e];CO2[e] + 33 UDP-glucose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + UDP-glucose[c] 1 + 34 UDP-galactose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + UDP-galactose[c] 1 + 35 UDP-glucuronate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + UDP-glucuronate[c] 1 + 36 GDP-L-fucose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + GDP-L-fucose[c] 1 + 37 GDP-mannose de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + GDP-mannose[c] 1 + 38 UDP-N-acetyl D-galactosamine de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + UDP-N-acetyl-D-galactosamine[c] 1 + 39 CMP-N-acetylneuraminate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + CMP-N-acetylneuraminate[c] 1 + 40 N-Acetylglucosamine de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + N-acetylglucosamine[c] 1 + 41 Glucuronate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + glucuronate[c] 1 + 42 Alanine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + alanine[e] 1 + 43 Arginine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + arginine[e] 1 + 44 Asparagine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + asparagine[e] 1 + 45 Aspartate de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + aspartate[c] 1 + 46 Glutamate de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + glutamate[e] 1 + 47 Glycine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + glycine[e] 1 + 48 Glutamine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + glutamine[e] 1 + 49 Proline de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + proline[e] 1 + 50 Serine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + serine[e] 1 + 51 Histidine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + histidine[c] 1 + 52 Histidine uptake histidine[e] 1 1 histidine[c] 1 + 53 Isoleucine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + isoleucine[c] 1 + 54 Isoleucine uptake isoleucine[e] 1 1 isoleucine[c] 1 + 55 Leucine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + leucine[c] 1 + 56 Leucine uptake leucine[e] 1 1 leucine[c] 1 + 57 Lysine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + lysine[c] 1 + 58 Lysine uptake lysine[e] 1 1 lysine[c] 1 + 59 Methionine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + methionine[c] 1 + 60 Methionine uptake methionine[e] 1 1 methionine[c] 1 + 61 Phenylalanine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + phenylalanine[c] 1 + 62 Phenylalanine uptake phenylalanine[e] 1 1 phenylalanine[c] 1 + 63 Threonine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + threonine[c] 1 + 64 Threonine uptake threonine[e] 1 1 threonine[c] 1 + 65 Tryptophan de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + tryptophan[c] 1 + 66 Tryptophan uptake tryptophan[e] 1 1 tryptophan[c] 1 + 67 Valine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + valine[c] 1 + 68 Valine uptake valine[e] 1 1 valine[c] 1 + 69 Cysteine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e];sulfate[e] H2O[e];CO2[e] + cysteine[e] 1 + 70 Cysteine de novo synthesis (minimal substrates and AA, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e];sulfate[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e] H2O[e];CO2[e] + cysteine[e] 1 + 71 Cystine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e];sulfite[e] H2O[e];CO2[e] + cystine[e] 1 + 72 Tyrosine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + tyrosine[e] 1 + 73 Tyrosine de novo synthesis (minimal substrates with AA, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e];sulfate[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e] H2O[e];CO2[e] + tyrosine[e] 1 + 74 Homocysteine de novo synthesis (minimal substrates, minimal excretion) TRUE O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + homocysteine[c] 1 + 75 Homocysteine de novo synthesis (minimal substrates with AA, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e];sulfate[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e] H2O[e];CO2[e] + homocysteine[c] 1 + 76 beta-Alanine de novo synthesis (minimal substrates, minimal excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + beta-alanine[e] 1 + 77 Alanine degradation alanine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 78 Arginine degradation arginine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 79 Asparagine degradation asparagine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 80 Aspartate degradation aspartate[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 81 Cysteine degradation cysteine[e];O2[e] 1 H2O[e];CO2[e];urate[e];H2S[e] + 82 Glutamate degradation glutamate[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 83 Glycine degradation glycine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 84 Histidine degradation histidine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 85 Isoleucine degradation isoleucine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 86 Glutamine degradation glutamine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 87 Leucine degradation leucine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 88 Lysine degradation lysine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 89 Methionine degradation methionine[e];O2[e] 1 H2O[e];CO2[e];urate[e];H2S[e] + 90 Phenylalanine degradation phenylalanine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 91 Proline degradation proline[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 92 Serine degradation serine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 93 Threonine degradation threonine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 94 Tryptophan degradation tryptophan[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 95 Tyrosine degradation tyrosine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 96 Valine degradation valine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 97 Homocysteine degradation homocysteine[c];O2[e] 1 H2O[e];CO2[e];urate[e];H2S[e] + 98 Ornithine degradation ornithine[e] 1 urea[e] 1 + O2[e] H2O[e];CO2[e] + 99 beta-Alanine degradation beta-alanine[e];O2[e] 1 H2O[e];CO2[e];urate[e] + 100 Urea from alanine alanine[e] 2 H2O[e];CO2[e] + O2[e] urea[e] 1 + 101 Urea from glutamine glutamine[e] 1 H2O[e];CO2[e] + O2[e] urea[e] 1 + 102 Creatine de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e] H2O[e];CO2[e] + creatine[e] 1 + 103 Heme de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];Fe2+[e] H2O[e];CO2[e] + heme[e] 1 + 104 PC de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e];isoleucine[c] H2O[e];CO2[e];urate[e] + PC-LD pool[c] 1 + 105 PE de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];ethanolamine[c] H2O[e];CO2[e] + PE-LD pool[c] 1 + 106 PS de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] + PS-LD pool[c] 1 + 107 PI de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];inositol[e] H2O[e];CO2[e] + PI pool[c] 1 + 108 Cardiolipin de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] + CL pool[c] 1 + 109 SM de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] + SM pool[c] 1 + 110 Ceramide de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] + ceramide pool[c] 1 + 111 Lactosylceramide de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];Pi[e];linoleate[e];linolenate[e];choline[e] H2O[e];CO2[e] + LacCer pool[c] 1 + 112 CoA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];methionine[e];pantothenate[e] CoA[c] 1 + CO2[e];urate[e];H2O[e] + 113 NAD de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];nicotinamide[e] NADH[c] 1 + H2O[e];CO2[e] + 114 NADP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];nicotinamide[e] NADPH[c] 1 + H2O[e];CO2[e] + 115 FAD de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];NH3[e];Pi[e];riboflavin[e] FAD[c] 1 + H2O[e];CO2[e] + 116 Thioredoxin de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];histidine[e];isoleucine[e];leucine[e];lysine[e];methionine[e];phenylalanine[e];threonine[e];tryptophan[e];valine[e] H2O[e];CO2[e];urate[e];H2S[e] + thioredoxin[c] 1 + 117 THF de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];folate[e] H2O[e];CO2[e] + THF[c] 1 + 118 Pyridoxal-P de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];pyridoxine[e] H2O[e];CO2[e] + pyridoxal-phosphate[c] 1 + 119 Acetoacetate de novo synthesis O2[e];glucose[e] H2O[e];CO2[e] + acetoacetate[m] 1 + 120 (R)-3-Hydroxybutanoate de novo synthesis O2[e];glucose[e] H2O[e];CO2[e] + (R)-3-hydroxybutanoate[c] 1 + 121 Farnesyl-PP de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];phenylalanine[e];Pi[e] H2O[e];CO2[e] + farnesyl-PP[c] 1 + 122 Lauric acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + lauric acid[c] 1 + 123 Tridecylic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + tridecylic acid[c] 1 + 124 Myristic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + myristic acid[c] 1 + 125 9E-tetradecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + (9E)-tetradecenoic acid[c] 1 + 126 7Z-tetradecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + (7Z)-tetradecenoic acid[c] 1 + 127 Physeteric acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + physeteric acid[c] 1 + 128 Pentadecylic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + pentadecylic acid[c] 1 + 129 Palmitate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + palmitate[c] 1 + 130 Palmitolate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + palmitolate[c] 1 + 131 7-palmitoleic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + 7-palmitoleic acid[c] 1 + 132 Margaric acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + margaric acid[c] 1 + 133 10Z-heptadecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + (10Z)-heptadecenoic acid[c] 1 + 134 9-heptadecylenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + 9-heptadecylenic acid[c] 1 + 135 Stearate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + stearate[c] 1 + 136 13Z-octadecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + (13Z)-octadecenoic acid[c] 1 + 137 cis-vaccenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + cis-vaccenic acid[c] 1 + 138 Oleate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + oleate[c] 1 + 139 Elaidate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + elaidate[c] 1 + 140 7Z-octadecenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + (7Z)-octadecenoic acid[c] 1 + 141 6Z,9Z-octadecadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + (6Z,9Z)-octadecadienoic acid[c] 1 + 142 Nonadecylic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + nonadecylic acid[c] 1 + 143 Eicosanoate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + eicosanoate[c] 1 + 144 13Z-Eicosenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + (13Z)-eicosenoic acid[c] 1 + 145 cis-Gondoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + cis-gondoic acid[c] 1 + 146 9-Eicosenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + 9-eicosenoic acid[c] 1 + 147 8,11-Eicosadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + 8,11-eicosadienoic acid[c] 1 + 148 Mead acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + mead acid[c] 1 + 149 Heneicosanoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + heneicosanoic acid[c] 1 + 150 Behenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + behenic acid[c] 1 + 151 cis-Erucic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + cis-erucic acid[c] 1 + 152 cis-Cetoleic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + cis-cetoleic acid[c] 1 + 153 Tricosanoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] + tricosanoic acid[c] 1 + 154 Lignocerate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + lignocerate[c] 1 + 155 Nervonic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + nervonic acid[c] 1 + 156 Cerotic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + cerotic acid[c] 1 + 157 Ximenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e] CO2[e];H2O[e] + ximenic acid[c] 1 + 158 Linolenate de novo synthesis (minimal substrates, physiological excretion) TRUE O2[e];glucose[e] CO2[e];H2O[e] + linolenate[c] 1 + 159 Stearidonic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + stearidonic acid[c] 1 + 160 omega-3-Arachidonic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + omega-3-arachidonic acid[c] 1 + 161 EPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + EPA[c] 1 + 162 DPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + DPA[c] 1 + 163 9Z,12Z,15Z,18Z,21Z-TPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + (9Z,12Z,15Z,18Z,21Z)-TPA[c] 1 + 164 6Z,9Z,12Z,15Z,18Z,21Z-THA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + (6Z,9Z,12Z,15Z,18Z,21Z)-THA[c] 1 + 165 DHA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + DHA[c] 1 + 166 11Z,14Z,17Z-eicosatrienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + (11Z,14Z,17Z)-eicosatrienoic acid[c] 1 + 167 13,16,19-docosatrienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + 13,16,19-docosatrienoic acid[c] 1 + 168 10,13,16,19-docosatetraenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + 10,13,16,19-docosatetraenoic acid[c] 1 + 169 12,15,18,21-tetracosatetraenoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linolenate[e] CO2[e];H2O[e] + 12,15,18,21-tetracosatetraenoic acid[c] 1 + 170 Linoleate de novo synthesis (minimal substrates, physiological excretion) TRUE O2[e];glucose[e] CO2[e];H2O[e] + linoleate[c] 1 + 171 gamma-Linolenate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + gamma-linolenate[c] 1 + 172 Dihomo-gamma-linolenate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + dihomo-gamma-linolenate[c] 1 + 173 Arachidonate de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + arachidonate[c] 1 + 174 Adrenic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + adrenic acid[c] 1 + 175 9Z,12Z,15Z,18Z-TTA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + (9Z,12Z,15Z,18Z)-TTA[c] 1 + 176 6Z,9Z,12Z,15Z,18Z-TPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + (6Z,9Z,12Z,15Z,18Z)-TPA[c] 1 + 177 4Z,7Z,10Z,13Z,16Z-DPA de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + (4Z,7Z,10Z,13Z,16Z)-DPA[c] 1 + 178 11Z,14Z-eicosadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + (11Z,14Z)-eicosadienoic acid[c] 1 + 179 13Z,16Z-docosadienoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + (13Z,16Z)-docosadienoic acid[c] 1 + 180 10,13,16-docosatriynoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];linoleate[e] CO2[e];H2O[e] + 10,13,16-docosatriynoic acid[c] 1 + 181 Lauric acid (complete oxidation) lauric acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 182 Tridecylic acid (complete oxidation) tridecylic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 183 Myristic acid (complete oxidation) myristic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 184 9E-tetradecenoic acid (complete oxidation) (9E)-tetradecenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 185 7Z-tetradecenoic acid (complete oxidation) (7Z)-tetradecenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 186 Physeteric acid (complete oxidation) physeteric acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 187 Pentadecylic acid (complete oxidation) pentadecylic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 188 Palmitate (complete oxidation) palmitate[e] 1 1 CO2[e];H2O[e] + O2[e] + 189 Palmitolate (complete oxidation) palmitolate[e] 1 1 CO2[e];H2O[e] + O2[e] + 190 7-palmitoleic acid (complete oxidation) 7-palmitoleic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 191 Margaric acid (complete oxidation) margaric acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 192 10Z-heptadecenoic acid (complete oxidation) (10Z)-heptadecenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 193 9-heptadecylenic acid (complete oxidation) 9-heptadecylenic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 194 Stearate (complete oxidation) stearate[e] 1 1 CO2[e];H2O[e] + O2[e] + 195 13Z-octadecenoic acid (complete oxidation) (13Z)-octadecenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 196 cis-Vaccenic acid (complete oxidation) cis-vaccenic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 197 Oleate (complete oxidation) oleate[e] 1 1 CO2[e];H2O[e] + O2[e] + 198 Elaidate (complete oxidation) elaidate[e] 1 1 CO2[e];H2O[e] + O2[e] + 199 7Z-octadecenoic acid (complete oxidation) (7Z)-octadecenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 200 6Z,9Z-octadecadienoic acid (complete oxidation) (6Z,9Z)-octadecadienoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 201 Nonadecylic acid (complete oxidation) nonadecylic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 202 Eicosanoate (complete oxidation) eicosanoate[e] 1 1 CO2[e];H2O[e] + O2[e] + 203 13Z-Eicosenoic acid (complete oxidation) (13Z)-eicosenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 204 cis-Gondoic acid (complete oxidation) cis-gondoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 205 9-Eicosenoic acid (complete oxidation) 9-eicosenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 206 8,11-Eicosadienoic acid (complete oxidation) 8,11-eicosadienoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 207 Mead acid (complete oxidation) mead acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 208 heneicosanoic acid (complete oxidation) heneicosanoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 209 Behenic acid (complete oxidation) behenic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 210 cis-Erucic acid (complete oxidation) cis-erucic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 211 cis-Cetoleic acid (complete oxidation) cis-cetoleic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 212 Tricosanoic acid (complete oxidation) tricosanoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 213 Lignocerate (complete oxidation) lignocerate[e] 1 1 CO2[e];H2O[e] + O2[e] + 214 Nervonic acid (complete oxidation) nervonic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 215 Cerotic acid (complete oxidation) cerotic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 216 Ximenic acid (complete oxidation) ximenic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 217 Linolenate (complete oxidation) linolenate[e] 1 1 CO2[e];H2O[e] + O2[e] + 218 Stearidonic acid (complete oxidation) stearidonic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 219 omega-3-Arachidonic acid (complete oxidation) omega-3-arachidonic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 220 EPA (complete oxidation) EPA[e] 1 1 CO2[e];H2O[e] + O2[e] + 221 DPA (complete oxidation) DPA[e] 1 1 CO2[e];H2O[e] + O2[e] + 222 9Z,12Z,15Z,18Z,21Z-TPA (complete oxidation) (9Z,12Z,15Z,18Z,21Z)-TPA[e] 1 1 CO2[e];H2O[e] + O2[e] + 223 6Z,9Z,12Z,15Z,18Z,21Z-THA (complete oxidation) (6Z,9Z,12Z,15Z,18Z,21Z)-THA[e] 1 1 CO2[e];H2O[e] + O2[e] + 224 DHA (complete oxidation) DHA[e] 1 1 CO2[e];H2O[e] + O2[e] + 225 11Z,14Z,17Z-eicosatrienoic acid (complete oxidation) (11Z,14Z,17Z)-eicosatrienoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 226 13,16,19-docosatrienoic acid (complete oxidation) 13,16,19-docosatrienoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 227 10,13,16,19-docosatetraenoic acid (complete oxidation) 10,13,16,19-docosatetraenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 228 12,15,18,21-tetracosatetraenoic acid (complete oxidation) 12,15,18,21-tetracosatetraenoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 229 Linoleate (complete oxidation) linoleate[e] 1 1 CO2[e];H2O[e] + O2[e] + 230 gamma-Linolenate (complete oxidation) gamma-linolenate[e] 1 1 CO2[e];H2O[e] + O2[e] + 231 Dihomo-gamma-linolenate (complete oxidation) dihomo-gamma-linolenate[e] 1 1 CO2[e];H2O[e] + O2[e] + 232 Arachidonate (complete oxidation) arachidonate[e] 1 1 CO2[e];H2O[e] + O2[e] + 233 Adrenic acid (complete oxidation) adrenic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 234 9Z,12Z,15Z,18Z-TTA (complete oxidation) (9Z,12Z,15Z,18Z)-TTA[e] 1 1 CO2[e];H2O[e] + O2[e] + 235 6Z,9Z,12Z,15Z,18Z-TPA (complete oxidation) (6Z,9Z,12Z,15Z,18Z)-TPA[e] 1 1 CO2[e];H2O[e] + O2[e] + 236 4Z,7Z,10Z,13Z,16Z-DPA (complete oxidation) (4Z,7Z,10Z,13Z,16Z)-DPA[e] 1 1 CO2[e];H2O[e] + O2[e] + 237 11Z,14Z-eicosadienoic acid (complete oxidation) (11Z,14Z)-eicosadienoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 238 13Z,16Z-docosadienoic acid (complete oxidation) (13Z,16Z)-docosadienoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 239 10,13,16-docosatriynoic acid (complete oxidation) 10,13,16-docosatriynoic acid[e] 1 1 CO2[e];H2O[e] + O2[e] + 240 Triacylglycerol de novo synthesis (physiological substrates, physiological excretion) O2[e];glucose[e];linoleate[e];linolenate[e] H2O[e];CO2[e] + TAG-LD pool[c] 1 + 241 Glycocholate de novo synthesis and excretion (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];phenylalanine[e] H2O[e];CO2[e];urea[e] + glycocholate[e] 1 + 242 Glycochenodeoxycholate de novo synthesis and excretion O2[e];glucose[e];Pi[e];phenylalanine[e] H2O[e];CO2[e];urea[e] + glycochenodeoxycholate[e] 1 + 243 Taurocholate de novo synthesis and excretion (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];phenylalanine[e];cysteine[e] H2O[e];CO2[e];urea[e] + taurocholate[e] 1 + 244 Taurochenodeoxycholate de novo synthesis and excretion (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];phenylalanine[e];cysteine[e] H2O[e];CO2[e];urea[e] + taurochenodeoxycholate[e] 1 + 245 PAPS de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];NH3[e];sulfate[e];histidine[e];valine[e] H2O[e];CO2[e];urate[e] + PAPS[c] 1 + 246 PAP degradation PAPS[c] CO2[e];H2O[e];urate[e];Pi[e];H2S[e] + O2[e] + 247 SAM de novo synthesis (minimal substrates, physiological excretion) O2[e];NH3[e];glucose[e];methionine[e] H2O[e];CO2[e];urate[e] + SAM[c] 1 + 248 GSH de novo synthesis (minimal substrates, physiological excretion) O2[e];NH3[e];glucose[e];methionine[e] H2O[e];CO2[e];urate[e] + GSH[c] 1 + 249 Bilirubin conjugation (minimal substrates, physiological excretion) O2[e];glucose[e];Pi[e];bilirubin[e] H2O[e];CO2[e] + bilirubin-bisglucuronoside[e] 1 + 250 NH3 import and degradation NH3[e];O2[e];glucose[e] CO2[e];H2O[e] + urea[e] 1 + 251 Ethanol import and degradation (minimal substrates, minimalexcretion) ethanol[e] 1 1 CO2[e];H2O[e] + O2[e] + 252 Oxidative phosphorylation succinate[m] 1 1 fumarate[m] 1 1 ATP[m] + H2O[m] => ADP[m] + Pi[m] + H+[m] 1 + NADH[m];H+[m] 1 1 NAD+[m] 1 1 + O2[e] H2O[e] + 253 Oxidative decarboxylation pyruvate[m];NAD+[m];CoA[m] 1 1 acetyl-CoA[m];NADH[m];CO2[e] 1 1 + 254 Krebs cycle NADH acetyl-CoA[m];GDP[m];ubiquinone[m] 1 1 CoA[m];ubiquinol[m];GTP[m] 1 1 + NAD+[m] 3 3 NADH[m] 3 3 + Pi[m];H2O[e] CO2[e];H+[c];H+[m] + 255 Ubiquinol-to-proton ubiquinol[m] 1 1 ubiquinone[m] 1 1 + O2[e];H+[m] H2O[e] + H+[c] 6 + 256 Ubiquinol-to-ATP ubiquinol[m] 1 1 ubiquinone[m] 1 1 ATP[m] + H2O[m] => ADP[m] + Pi[m] + H+[m] 1 + O2[e];H+[m] H2O[e];H+[m];H+[c] + 257 Biosynthesis of Vitamin C (ascorbate) TRUE O2[e];glucose[e] ascorbate[c] 1 + H2O[e];CO2[e] From 050f648a03a87331d3b878c8064e333b4f557354 Mon Sep 17 00:00:00 2001 From: edkerk <7326655+edkerk@users.noreply.github.com> Date: Sat, 18 Jul 2026 08:19:32 +0000 Subject: [PATCH 2/2] chore: update model QC results [skip ci] --- data/testResults/README.md | 10 ++-- data/testResults/model_qc_summary.md | 72 ++++++++++++++-------------- 2 files changed, 41 insertions(+), 41 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 6ed6d67d..5930c830 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -21,11 +21,11 @@ own files. The pull request in each row is the one whose run last wrote those fi | Result file(s) | Produced by | Last updated by | | --- | --- | --- | -| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) | -| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) | -| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) | -| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) | -| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) | +| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1070** (model QC checks) | +| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1070** (model QC checks) | +| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1070** (model QC checks) | +| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1070** (MACAW and balance) | +| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1070** (MEMOTE) | | `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) | ## 2. What each check means diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index fdac8f39..22a681f6 100644 --- a/data/testResults/model_qc_summary.md +++ b/data/testResults/model_qc_summary.md @@ -1,59 +1,59 @@ ## Model quality report -:warning: **6 pre-existing finding(s), no regressions vs `main`.** Non-blocking. +:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking. -_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md)._ +_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md)._ ### Model checks _Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report._ -| Check | Result | Δ vs `main` | | +| Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#duplicate-omap-keys) | 0 | new | :white_check_mark: | -| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: | -| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-with-no-metabolites) | 0 | new | :white_check_mark: | -| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | new | :white_check_mark: | -| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: | -| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-formula) | 0 | new | :white_check_mark: | -| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-charge) | 0 | new | :white_check_mark: | -| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | new | :white_check_mark: | -| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | new | :white_check_mark: | -| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-metabolites) | 0 | new | :white_check_mark: | -| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-genes) | 0 | new | :white_check_mark: | -| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#malformed-cross-references) | 0 | new | :white_check_mark: | -| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_annotation_issues.csv) | new | :warning: | +| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: | +| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: | +| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: | +| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: | +| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: | +| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: | +| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: | +| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: | +| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: | +| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: | +| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: | +| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: | +| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/qc_annotation_issues.csv) | 0 | :warning: | ### MACAW and mass/charge balance -| Check | Result | Δ vs `main` | | +| Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -703 | :warning: | -| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -2 | :warning: | -| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: | -| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: | -| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_structure_consistency.csv) | new | :warning: | +| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/macaw_results.csv) | 0 | :warning: | +| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/macaw_results.csv) | 0 | :warning: | +| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/balance_results.csv) | 0 | :warning: | +| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/balance_results.csv) | 0 | :warning: | +| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/qc_structure_consistency.csv) | 0 | :warning: | ### Model file and metabolic tasks | Check | Result | | | --- | ---: | :---: | -| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: | -| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: | -| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: | -| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: | -| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: | +| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: | +| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: | +| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: | +| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: | +| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: | -### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#memote) +### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#memote) -**Total score: 63.2%** (core subset)   +**Total score: 63.2%** (core subset)   0 | Section | Score | Δ vs base | | --- | ---: | ---: | -| consistency | 42.4% | | -| annotation_met | 73.0% | | -| annotation_rxn | 72.7% | | -| annotation_gene | 46.7% | | -| annotation_sbo | 81.7% | | +| consistency | 42.4% | 0 | +| annotation_met | 73.0% | 0 | +| annotation_rxn | 72.7% | 0 | +| annotation_gene | 46.7% | 0 | +| annotation_sbo | 81.7% | 0 |
Per-test scores @@ -89,11 +89,11 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
-**Full suite: 64.2%**   · _from the last_ `/run memote`. +**Full suite: 64.2%**   0 · _from the last_ `/run memote`. _The score above is the fast core subset. Comment_ `/run memote` _to run the full suite on this pull request; the score updates here when it finishes._ -### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#gene-essentiality-hart-2015) +### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/metabolicTasks-Full-parse/data/testResults/README.md#gene-essentiality-hart-2015) _Not run automatically (it takes hours). Comment_ `/run gene-essentiality` _to run it on this pull request; the result posts as its own comment._