Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: CO2

Synonyms: carbonic anhydride, carbonic acid gas, carbon dioxide

Chemical Formula: CO2

Molecular Weight: 44.01 Daltons

Monoisotopic Molecular Weight: 43.989829244199996 Daltons

SMILES: C(=O)=O

InChI: InChI=1S/CO2/c2-1-3

InChIKey: InChIKey=CURLTUGMZLYLDI-UHFFFAOYSA-N

Unification Links: CAS:124-38-9 , ChEBI:16526 , ChemSpider:274 , HMDB:HMDB01967 , IAF1260:33506 , KEGG:C00011 , MetaboLights:MTBLC16526 , PubChem:280 , UMBBD-Compounds:c0131

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -92.26 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

4-ethylphenol degradation (anaerobic) :
4-hydroxyacetophenone + CO2 + ATP + 2 H2O → 4-hydroxybenzoyl-acetate + AMP + 2 phosphate + 3 H+

acetone degradation II (to acetoacetate) :
acetone + CO2 + ATP + 2 H2O → acetoacetate + AMP + 2 phosphate + 3 H+

anaerobic energy metabolism (invertebrates, cytosol) :
oxaloacetate + ITP ← CO2 + phosphoenolpyruvate + IDP

biotin biosynthesis from 8-amino-7-oxononanoate I , biotin biosynthesis from 8-amino-7-oxononanoate II :
CO2 + 7,8-diaminopelargonate + ATP → dethiobiotin + ADP + phosphate + 3 H+

calystegine biosynthesis , hyoscyamine and scopolamine biosynthesis , superpathway of hyoscyamine and scopolamine biosynthesis :
N-methyl-Δ1-pyrrolinium cation + CO2 → hygrine

inosine-5'-phosphate biosynthesis II :
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ ← 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + CO2

isoleucine biosynthesis V :
2-methylbutanoate + CO2 → (S)-3-methyl-2-oxopentanoate

methanofuran biosynthesis :
pentane-1,3,4,5-tetracarboxylate + CO2 + 2 H+ → hexane-6-keto-1,3,4,6-tetracarboxylate + H2O

propylene degradation :
acetoacetate + coenzyme M + NADP+ ← 2-oxopropyl-CoM + CO2 + NADPH

reductive TCA cycle II :
ATP + 2-oxoglutarate + CO2 + H2O → oxalosuccinate + ADP + phosphate + 2 H+

salinosporamide A biosynthesis :
chloroethylmalonyl-CoA + NAD+ ← 4-chloro-crotonyl-CoA + CO2 + NADH

urea cycle :
ammonium + CO2 + 2 ATP + H2O → carbamoyl-phosphate + 2 ADP + phosphate + 3 H+

urea degradation I :
ATP + urea + CO2 + H2O → ADP + urea-1-carboxylate + phosphate + 2 H+

wybutosine biosynthesis :
7-[(3S)-4-methoxy-(3-amino-3-carboxypropyl)]-wyosine37 in tRNAPhe + CO2 + S-adenosyl-L-methionine → wybutosine37 in tRNAPhe + S-adenosyl-L-homocysteine + 2 H+

Not in pathways:
7-[4-methoxy-(2-hydroxy-3-amino-3-carboxypropyl)]-wyosine37 in tRNAPhe + CO2 + S-adenosyl-L-methionine → 2-hydroxy-wybutosine37 in tRNAPhe + S-adenosyl-L-homocysteine + 2 H+

Reactions known to produce the compound:

(-)-microperfuranone biosynthesis : 2 2-oxo-3-phenylpropanoate + 2 ATP + H2O → (-)-microperfuranone + 2 AMP + CO2 + 2 diphosphate (1'S,5'S)-averufin biosynthesis : a hexanoyl-[acyl-carrier-protein] + 7 malonyl-CoA + 5 H+ → norsolorinate anthrone + a holo-[acyl-carrier protein] + 7 CO2 + 7 coenzyme A + 2 H2O (5R)-carbapenem carboxylate biosynthesis : (3S,5S)-carbapenam-3-carboxylate + 2-oxoglutarate + oxygen → (5R)-carbapen-2-em-3-carboxylate + succinate + CO2 + H2O (S)-1-pyrroline-5-carboxylate + malonyl-CoA + H+ + H2O → (2S,5S)-5-carboxymethyl proline + CO2 + coenzyme A (R)-acetoin biosynthesis I , (S)-acetoin biosynthesis : (S)-2-acetolactate + an oxidized electron acceptor + H+ → diacetyl + CO2 + a reduced electron acceptor (R)-acetoin biosynthesis II : (S)-2-acetolactate + H+ → (R)-acetoin + CO2 (S)-reticuline biosynthesis I : L-tyrosine + H+CO2 + tyramine 4-hydroxyphenylpyruvate + H+CO2 + (4-hydroxyphenyl)acetaldehyde L-dopa + H+ → dopamine + CO2 (S)-reticuline biosynthesis II : L-tyrosine + H+CO2 + tyramine 3,4-dihydroxyphenylpyruvate + H+ → 3,4-dihydroxyphenylacetaldehyde + CO2 (Z)-9-tricosene biosynthesis : (15Z)-tetracos-15-enal + NADPH + oxygen + H+ → (Z)-9-tricosene + CO2 + NADP+ + H2O 1,4-dihydroxy-2-naphthoate biosynthesis I , 1,4-dihydroxy-2-naphthoate biosynthesis II (plants) : isochorismate + 2-oxoglutarate + H+ → 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate + CO2 2,2'-dihydroxybiphenyl degradation : 2,3-dihydroxybenzoate + NADH + oxygen + 2 H+ → pyrogallol + CO2 + NAD+ + H2O 2,3-dihydroxybenzoate degradation : (3E)-2-oxohex-3-enedioate + H+ → 2-oxopent-4-enoate + CO2 3-carboxy-2-hydroxymuconate semialdehyde + H+ → (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + CO2 2,4-dichlorophenoxyacetate degradation : 2,4-dichlorophenoxyacetate + 2-oxoglutarate + oxygen → 2,4-dichlorophenol + glyoxylate + succinate + CO2 2-amino-3-carboxymuconate semialdehyde degradation to 2-oxopentenoate : (3E)-2-oxohex-3-enedioate + H+ → 2-oxopent-4-enoate + CO2 aminocarboxymuconate semialdehyde + H+ → 2-aminomuconate 6-semialdehyde + CO2 2-amino-3-carboxymuconate semialdehyde degradation to glutaryl-CoA : 2-oxoadipate + coenzyme A + NAD+CO2 + glutaryl-CoA + NADH aminocarboxymuconate semialdehyde + H+ → 2-aminomuconate 6-semialdehyde + CO2 2-amino-3-hydroxycyclopent-2-enone biosynthesis , tetrapyrrole biosynthesis II (from glycine) : glycine + succinyl-CoA + H+CO2 + 5-aminolevulinate + coenzyme A 2-aminoethylphosphonate biosynthesis , fosfomycin biosynthesis : 3-phosphonopyruvate + H+ → phosphonoacetaldehyde + CO2 2-aminoethylphosphonate degradation III : (2-aminoethyl)phosphonate + 2-oxoglutarate + oxygen → (2-amino-1-hydroxyethyl)phosphonate + succinate + CO2 2-aminophenol degradation , 3-chlorocatechol degradation III (meta pathway) , catechol degradation to 2-oxopent-4-enoate II , orthanilate degradation : (3E)-2-oxohex-3-enedioate + H+ → 2-oxopent-4-enoate + CO2 2-chlorobenzoate degradation : 2-chlorobenzoate + NADH + oxygen + H+ → catechol + chloride + CO2 + NAD+ 2-heptyl-3-hydroxy-4(1H)-quinolone biosynthesis : anthraniloyl-CoA + 3-oxodecanoate + H+ → 2-heptyl-4(1H)-quinolone + CO2 + coenzyme A + H2O 2-hydroxyphenazine biosynthesis : 2-hydroxyphenazine-1-carboxylate + H+ → 2-hydroxyphenazine + CO2 2-methylketone biosynthesis : 3-oxo-myristate + H+ → 2-tridecanone + CO2 3-oxo-dodecanoate + H+CO2 + 2-undecanone 3-oxo-palmitate + H+ → 2-pentadecanone + CO2 2-nitrobenzoate degradation I : (3E)-2-oxohex-3-enedioate + H+ → 2-oxopent-4-enoate + CO2 aminocarboxymuconate semialdehyde + H+ → 2-aminomuconate 6-semialdehyde + CO2 2-nitrobenzoate degradation II , anthranilate degradation I (aerobic) , indole-3-acetate degradation VIII (bacterial) : anthranilate + NAD(P)H + oxygen + 3 H+ → catechol + CO2 + ammonium + NAD(P)+ 2-oxobutanoate degradation I , threonine degradation : 2-oxobutanoate + coenzyme A + NAD+ → propanoyl-CoA + CO2 + NADH 2-oxoglutarate decarboxylation to succinyl-CoA : 2-oxoglutarate + a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine + H+ → a [2-oxoglutarate dehydrogenase E2 protein] N6-S-succinyldihydrolipoyl-L-lysine + CO2 3-chlorobenzoate degradation I (via chlorocatechol) : 3-chloro-3,5-cyclohexadiene-l,2-diol-1-carboxylate + NAD+ → 3-chlorocatechol + CO2 + NADH 5-chloro-3,5-cyclohexadiene-l,2-diol-1-carboxylate + NAD+ → 4-chlorocatechol + CO2 + NADH 3-dimethylallyl-4-hydroxybenzoate biosynthesis : prephenate + NAD+ → 4-hydroxyphenylpyruvate + CO2 + NADH 3-dimethylallyl-4-hydroxymandelate + oxygen → 3-dimethylallyl-4-hydroxybenzoate + CO2 + H2O 3-dimethylallyl-4-hydroxyphenylpyruvate + oxygen → 3-dimethylallyl-4-hydroxymandelate + CO2 3-methylbutanol biosynthesis : (2S)-2-isopropyl-3-oxosuccinate + H+ → 4-methyl-2-oxopentanoate + CO2 4-methyl-2-oxopentanoate + H+ → 3-methylbutanal + CO2 4-amino-3-hydroxybenzoate degradation : (3E)-2-oxohex-3-enedioate + H+ → 2-oxopent-4-enoate + CO2 (2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde + H+ → (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + CO2 4-chloro-2-methylphenoxyacetate degradation : 4-chloro-2-methylphenoxyacetate + 2-oxoglutarate + oxygen → 2-methyl-4-chlorophenol + glyoxylate + succinate + CO2 4-chloronitrobenzene degradation : 2-oxopent-5-chloro-3-enoate + H+ → 2-oxo-5-chloro-4-pentenoate + CO2 4-hydroxy-2(1H)-quinolone biosynthesis : anthraniloyl-CoA + malonyl-CoA + H+ → 4-hydroxy-2(1H)-quinolone + CO2 + 2 coenzyme A 4-hydroxycoumarin and dicoumarol biosynthesis : salicyloyl-CoA + malonyl-CoA + H+ → 4-hydroxycoumarin + CO2 + 2 coenzyme A 4-hydroxymandelate degradation : 2-(4-hydroxyphenyl)-2-oxoacetate + H+ → 4-hydroxybenzaldehyde + CO2 4-hydroxyphenylacetate degradation : 5-carboxy-2-oxohept-3-enedioate + H+ → 2-hydroxyhepta-2,4-dienedioate + CO2 4-nitrotoluene degradation II : 5-methyl-2-oxo-3-hexene-1,6-dioate + H+ → 2-oxo-4-hexenoate + CO2 5,5'-dehydrodivanillate degradation : 5-carboxyvanillate + H+ → vanillate + CO2 5-hydroxymethylfurfural degradation : 2,5-dicarboxyfuran + H+ → 2-furoate + CO2 6-gingerol analog biosynthesis : 4-coumaryl-CoA + 3-oxooctanoyl-CoA + H2O → 4-coumaroylhexanoylmethane + CO2 + 2 coenzyme A 6-methoxymellein biosynthesis : acetyl-CoA + 2 malonyl-CoA + H+ → triacetate lactone + 2 CO2 + 3 coenzyme A acetyl-CoA + 4 malonyl-CoA + NADPH + 5 H+ → 6-hydroxymellein + 4 CO2 + 5 coenzyme A + NADP+ + H2O 7-(3-amino-3-carboxypropyl)-wyosine biosynthesis , methylwyosine biosynthesis : N1-methylguanine37 in tRNAPhe + pyruvate + S-adenosyl-L-methionine → 4-demethylwyosine37 in tRNAPhe + L-methionine + 5'-deoxyadenosine + CO2 + H2O 8-amino-7-oxononanoate biosynthesis I : a glutaryl-[acp] methyl ester + a malonyl-[acp] + H+ → a 3-oxo-pimeloyl-[acp] methyl ester + CO2 + a holo-[acyl-carrier protein] a malonyl-[acp] methyl ester + a malonyl-[acp] + H+ → a 3-oxo-glutaryl-[acp] methyl ester + CO2 + a holo-[acyl-carrier protein] a pimeloyl-[acp] + L-alanine + H+ → 8-amino-7-oxononanoate + CO2 + a holo-[acyl-carrier protein] 8-amino-7-oxononanoate biosynthesis II : a pimeloyl-[acp] + L-alanine + H+ → 8-amino-7-oxononanoate + CO2 + a holo-[acyl-carrier protein] 8-amino-7-oxononanoate biosynthesis III : pimeloyl-CoA + L-alanine + H+CO2 + 8-amino-7-oxononanoate + coenzyme A acetaldehyde biosynthesis I , acetaldehyde biosynthesis II , long chain fatty acid ester synthesis for microdiesel production , pyruvate fermentation to acetate VIII , pyruvate fermentation to ethanol II : pyruvate + H+ → acetaldehyde + CO2 acetoin biosynthesis III : pyruvate + acetaldehyde + H+ → acetoin + CO2 pyruvate + H+ → acetaldehyde + CO2 acetone degradation I (to methylglyoxal) , acetone degradation III (to propane-1,2-diol) , isopropanol biosynthesis , ketogenesis , pyruvate fermentation to acetone : acetoacetate + H+ → acetone + CO2 achromobactin biosynthesis : O-citryl-L-serine + H+O-citryl-ethanolamine + CO2 aclacinomycin biosynthesis : propanoyl-CoA + 9 malonyl-CoA + a polyketide synthase containing an [acp] domain + 10 H+ → 3,5,7,9,11,13,15,17,19-nonaoxohenicosanoyl-[acp] + 9 CO2 + 10 coenzyme A acridone alkaloid biosynthesis : N-methylanthraniloyl-CoA + 3 malonyl-CoA → 3 CO2 + 1,3-dihydroxy-N-methylacridone + 4 coenzyme A acrylate degradation : malonate semialdehyde + coenzyme A + NAD(P)+ → acetyl-CoA + CO2 + NAD(P)H actinorhodin biosynthesis : 8 malonyl-CoA + a polyketide synthase containing an [acp] domain → a 3,5,7,9,11,13,15-hepta-oxo-hexadecanoyl-[PKS-acp] + 8 CO2 + 8 coenzyme A aflatoxins B1 and G1 biosynthesis : 8-O-methylsterigmatocystin + 2 NADPH + 2 H+ + 2 oxygen → aflatoxin B1 + CO2 + methanol + 2 NADP+ + H2O aflatoxins B2 and G2 biosynthesis : 8-O-methyldihydrosterigmatocystin + 2 NADPH + 2 H+ + 2 oxygen → aflatoxin B2 + CO2 + methanol + 2 NADP+ + H2O ajmaline and sarpagine biosynthesis : polyneuridine aldehyde + H2O → methanol + CO2 + 16-epivellosimine aliphatic glucosinolate biosynthesis, side chain elongation cycle : 3-(7'-methylthio)heptylmalate → 2-oxo-10-methylthiodecanoate + CO2 + H+ 3-(6'-methylthio)hexylmalate → 2-oxo-9-methylthiononanoate + CO2 + H+ 3-(5'-methylthio)pentylmalate → 2-oxo-8-methylthiooctanoate + CO2 + H+ 3-(4'-methylthio)butylmalate → 2-oxo-7-methylthioheptanoate + CO2 + H+ 3-(3'-methylthio)propylmalate → 2-oxo-6-methylthiohexanoate + CO2 + H+ allantoin degradation to glyoxylate II : S-ureidoglycolate + 2 H+ + H2O → 2 ammonium + CO2 + glyoxylate allantoin degradation to ureidoglycolate II (ammonia producing) : allantoate + 2 H+ + H2O → S-ureidoglycine + ammonium + CO2 aloesone biosynthesis I : acetyl-CoA + 6 malonyl-CoA + 6 H+ → aloesone + 7 CO2 + 7 coenzyme A + H2O aloesone biosynthesis II : heptaketide pyrone intermediate + H+ → aloesone + CO2 7 malonyl-CoA + 6 H+ → heptaketide pyrone + 7 CO2 + 7 coenzyme A + H2O 6 malonyl-CoA + 5 H+ → hexaketide pyrone + 6 CO2 + 6 coenzyme A + H2O α-cyclopiazonate biosynthesis : acetyl-CoA + malonyl-CoA + a holo-[acyl-carrier protein] + H+ → acetoacetyl-ACP + CO2 + 2 coenzyme A aminopropanol phosphate biosynthesis I : L-threonine 3-O-phosphate + H+ → (R)-1-amino-2-propanol O-2-phosphate + CO2 aminopropanol phosphate biosynthesis II , threonine degradation III (to methylglyoxal) : 2-amino-3-oxobutanoate + 2 H+ → aminoacetone + CO2 aminopropylcadaverine biosynthesis , bisucaberin biosynthesis , desferrioxamine B biosynthesis , desferrioxamine E biosynthesis , lupanine biosynthesis , lysine degradation I , lysine degradation X : L-lysine + H+CO2 + cadaverine anaerobic energy metabolism (invertebrates, mitochondrial) , C4 photosynthetic carbon assimilation cycle, NAD-ME type , L-carnitine degradation III : (S)-malate + NAD+ → pyruvate + CO2 + NADH anthocyanin biosynthesis (cyanidin 3-O-glucoside) : leucocyanidin + 2-oxoglutarate + oxygen → a dihydroquercetin + succinate + CO2 + H2O leucocyanidin + 2-oxoglutarate + oxygen → cyanidin + succinate + CO2 + H+ + 2 H2O anthocyanin biosynthesis (delphinidin 3-O-glucoside) : leucodelphinidin + 2-oxoglutarate + oxygen → delphinidin + CO2 + succinate + H+ + 2 H2O anthocyanin biosynthesis (pelargonidin 3-O-glucoside) : leucopelargonidin + 2-oxoglutarate + oxygen → pelargonidin + succinate + CO2 + H+ + 2 H2O apigeninidin 5-O-glucoside biosynthesis : apiforol + 2-oxoglutarate + oxygen → apigeninidin + succinate + CO2 + 2 H2O arachidonate biosynthesis : malonyl-CoA + γ-linolenoyl-CoA + H+ → (8Z,11Z,14Z)-3-oxo-icosatrienoyl-CoA + CO2 + coenzyme A archaetidylserine and archaetidylethanolamine biosynthesis : unsaturated archaetidylserine + H+ → unsaturated archaetidylethanolamine + CO2 saturated archaetidylserine + H+ → saturated archaetidylethanolamine + CO2 arginine degradation II (AST pathway) : N2-succinyl-L-arginine + 2 H+ + 2 H2O → 2 ammonium + N2-succinyl-L-ornithine + CO2 arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) , putrescine biosynthesis II : N-carbamoylputrescine + 2 H+ + H2O → putrescine + CO2 + ammonium

Reactions known to both consume and produce the compound:

(R)-acetoin biosynthesis I , (R)-acetoin biosynthesis II , (S)-acetoin biosynthesis , pyruvate fermentation to isobutanol (engineered) , valine biosynthesis :
2 pyruvate + H+ ↔ (S)-2-acetolactate + CO2

1-butanol autotrophic biosynthesis , anaerobic energy metabolism (invertebrates, mitochondrial) , photosynthetic 3-hydroxybutyrate biosynthesis (engineered) , pyruvate fermentation to acetate II , pyruvate fermentation to acetate V , superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass :
pyruvate + coenzyme A + NAD+ ↔ acetyl-CoA + CO2 + NADH

2-oxobutanoate degradation II , isoleucine biosynthesis IV :
2-oxobutanoate + 2 an oxidized ferredoxin + coenzyme A ↔ propanoyl-CoA + 2 a reduced ferredoxin + CO2 + H+

2-oxoisovalerate decarboxylation to isobutanoyl-CoA :
3-methyl-2-oxobutanoate + an [apo BCAA dehydrogenase E2 protein] N6-lipoyl-L-lysine + H+ ↔ an [apo BCAA dehydrogenase E2 protein] N6-S-[2-methylpropanoyl]dihydrolipoyl-L-lysine + CO2

acetyl-CoA biosynthesis II (NADP-dependent pyruvate dehydrogenase) :
pyruvate + coenzyme A + NADP+ ↔ acetyl-CoA + CO2 + NADPH

adenosine nucleotides degradation IV , Calvin-Benson-Bassham cycle , Rubisco shunt :
2 3-phospho-D-glycerate + 2 H+ ↔ D-ribulose-1,5-bisphosphate + CO2 + H2O

allantoin degradation IV (anaerobic) , citrulline degradation :
ammonium + CO2 + ATP ↔ carbamoyl-phosphate + ADP + 2 H+

anaerobic energy metabolism (invertebrates, cytosol) , gluconeogenesis III :
oxaloacetate + GTP ← CO2 + phosphoenolpyruvate + GDP

arginine degradation III (arginine decarboxylase/agmatinase pathway) , arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) , arginine dependent acid resistance , putrescine biosynthesis I , putrescine biosynthesis II , putrescine biosynthesis IV , spermidine biosynthesis III :
L-arginine + H+CO2 + agmatine

C4 photosynthetic carbon assimilation cycle, NAD-ME type , C4 photosynthetic carbon assimilation cycle, NADP-ME type , C4 photosynthetic carbon assimilation cycle, PEPCK type , CO2 fixation into oxaloacetate (anapleurotic) , cyanate degradation :
hydrogen carbonate + H+CO2 + H2O

carbon tetrachloride degradation II :
formate + NADP+CO2 + NADPH

crotonate fermentation (to acetate and cyclohexane carboxylate) , glutamate degradation V (via hydroxyglutarate) , glutaryl-CoA degradation :
(E)-glutaconyl-CoA + H+CO2 + crotonyl-CoA

Entner-Doudoroff pathway II (non-phosphorylative) , glutamate degradation VII (to butanoate) , glycerol degradation to butanol , isopropanol biosynthesis , pyruvate fermentation to acetate I , pyruvate fermentation to acetate III , pyruvate fermentation to acetate VI , pyruvate fermentation to acetate VII , pyruvate fermentation to acetone , pyruvate fermentation to butanoate , pyruvate fermentation to butanol I , pyruvate fermentation to ethanol III , pyruvate fermentation to hexanol , reductive monocarboxylic acid cycle :
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

ethylene biosynthesis V (engineered) , glutamine biosynthesis III , methylaspartate cycle , mixed acid fermentation , NAD/NADP-NADH/NADPH cytosolic interconversion (yeast) , TCA cycle I (prokaryotic) , TCA cycle IV (2-oxoglutarate decarboxylase) , TCA cycle VI (obligate autotrophs) , TCA cycle VII (acetate-producers) :
D-threo-isocitrate + NADP+ ↔ 2-oxoglutarate + CO2 + NADPH

ethylmalonyl pathway :
(S)-ethylmalonyl-CoA + NADP+ ↔ crotonyl-CoA + CO2 + NADPH

folate transformations I , folate transformations II , N10-formyl-tetrahydrofolate biosynthesis , photorespiration :
glycine + a tetrahydrofolate + NAD+ ↔ a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH

formate oxidation to CO2 , oxalate degradation III , purine nucleobases degradation I (anaerobic) :
formate + NAD+CO2 + NADH

gallate degradation III (anaerobic) :
gallate + H+CO2 + pyrogallol

gluconeogenesis II (Methanobacterium thermoautotrophicum) :
hydrogen carbonate + H+CO2 + H2O
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

glycine biosynthesis II , glycine cleavage :
glycine + a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + H+ ↔ a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine + CO2

incomplete reductive TCA cycle :
2-oxoglutarate + 2 an oxidized ferredoxin + coenzyme A ↔ succinyl-CoA + CO2 + 2 a reduced ferredoxin + H+
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

isoleucine biosynthesis V , isoleucine degradation I :
(S)-3-methyl-2-oxopentanoate + coenzyme A + NAD+ ↔ 2-methylbutanoyl-CoA + CO2 + NADH

methanogenesis from acetate :
carbon monoxide + an oxidized ferredoxin + H2O ↔ CO2 + a reduced ferredoxin + H+

methanogenesis from CO2 , methyl-coenzyme M oxidation to CO2 :
formyl-methanofuran + an oxidized electron acceptor + H2O + H+ ↔ a methanofuran + CO2 + a reduced electron acceptor

p-cumate degradation to 2-oxopent-4-enoate :
2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate + H+ ↔ 2-hydroxy-6-oxo-7-methyl-octa-2,4-dienoate + CO2

phenol degradation II (anaerobic) :
phenol-phosphate + CO2 + H2O ↔ 4-hydroxybenzoate + phosphate + H+

phenylacetate degradation II (anaerobic) :
phenylglyoxylate + coenzyme A + an oxidized electron acceptor + H+ ↔ benzoyl-CoA + CO2 + a reduced electron acceptor

phenylalanine biosynthesis (cytosolic, plants) , phenylalanine biosynthesis I :
prephenate + H+ ↔ 2-oxo-3-phenylpropanoate + CO2 + H2O

phenylalanine degradation II (anaerobic) , phenylalanine degradation III :
2-oxo-3-phenylpropanoate + H+CO2 + phenylacetaldehyde

purine nucleobases degradation II (anaerobic) :
formate + NAD+CO2 + NADH
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

pyruvate decarboxylation to acetyl CoA :
pyruvate + a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine + H+ ↔ a [pyruvate dehydrogenase E2 protein] N6-S-acetyldihydrolipoyl-L-lysine + CO2

reductive acetyl coenzyme A pathway :
carbon monoxide + an oxidized ferredoxin + H2O ↔ CO2 + a reduced ferredoxin + H+
formate + NADP+CO2 + NADPH

reductive TCA cycle I :
D-threo-isocitrate + NADP+ ↔ 2-oxoglutarate + CO2 + NADPH
2-oxoglutarate + 2 an oxidized ferredoxin + coenzyme A ↔ succinyl-CoA + CO2 + 2 a reduced ferredoxin + H+
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

reductive TCA cycle II :
2-oxoglutarate + 2 an oxidized ferredoxin + coenzyme A ↔ succinyl-CoA + CO2 + 2 a reduced ferredoxin + H+
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) :
D-threo-isocitrate + NADP+ ↔ 2-oxoglutarate + CO2 + NADPH
2-oxoglutarate + 2 an oxidized ferredoxin + coenzyme A ↔ succinyl-CoA + CO2 + 2 a reduced ferredoxin + H+

TCA cycle VIII (helicobacter) :
D-threo-isocitrate + NADP+ ↔ 2-oxoglutarate + CO2 + NADPH
2-oxoglutarate + 2 an oxidized ferredoxin + coenzyme A ↔ succinyl-CoA + CO2 + 2 a reduced ferredoxin + H+

urea degradation II :
urea + 2 H+ + H2O ↔ 2 ammonium + CO2

Not in pathways:
ferulate + H+ ↔ 4-vinylguaiacol + CO2
acetyl-CoA + 2 an oxidized ferredoxin + tetrahydrosarcinapterin + H2O ↔ CO2 + 2 a reduced ferredoxin + 5-methyl-tetrahydrosarcinapterin + coenzyme A + 2 H+
3-methyl-2-oxobutanoate + an oxidized ferredoxin + coenzyme A ↔ isobutanoyl-CoA + CO2 + a reduced ferredoxin + H+
indole-3-carboxylate + H+ ↔ indole + CO2
pyruvate + an oxidized flavodoxin + coenzyme A + H+ ↔ acetyl-CoA + CO2 + a reduced flavodoxin

In Reactions of unknown directionality:

fatty acids biosynthesis (yeast) : acetyl-CoA + n malonyl-CoA + 2n NADPH + 4n H+ = a long-chain acyl-CoA + n CO2 + n coenzyme A + 2n NADP+ glycolate degradation II : 6 glycolate + H+ = acetate + 2 succinate + 2 CO2 + 4 H2O oxalate degradation V : oxalate + H+ = formate + CO2 plumbagin biosynthesis : acetyl-CoA + 5 malonyl-CoA + 2 NADPH + 6 H+ + oxygen = hexaketide pyrone + 5 CO2 + 6 coenzyme A + 2 NADP+ + 3 H2O rhodoquinone-10 biosynthesis : ammonium + ubiquinone-10 + H2O = CO2 + rhodoquinone-10 + 7 H+ rhodoquinone-9 biosynthesis : ammonium + ubiquinone-9 + H2O = CO2 + rhodoquinone-9 + 7 H+ salicylate degradation III : salicylate + H+ = phenol + CO2 Not in pathways: stipitatonate = stipitatate + CO2 L-tartrate + H+ = D-glycerate + CO2 2,3-dihydroxybenzoate + H+ = CO2 + catechol N-[(R)-pantothenoyl]-L-cysteine + H+ = pantetheine + CO2 orsellinate + H+ = orcinol + CO2 protocatechuate + H+ = CO2 + catechol dihydroxyfumarate + H+ = CO2 + tartronate semialdehyde L-carnitine + H+ = CO2 + 2-methylcholine L-aspartate + H+ = CO2 + L-alanine 2,2-dialkylglycine + pyruvate + H+ = dialkyl ketone + L-alanine + CO2 oxaloacetate + diphosphate = CO2 + phosphoenolpyruvate + phosphate 4-hydroxybenzoate + H+ = CO2 + phenol 4,5-dihydroxyphthalate + H+ = CO2 + protocatechuate hydroxypyruvate + H+ = CO2 + glycolaldehyde 3-hydroxy-L-glutamate + H+ = 4-amino-3-hydroxybutanoate + CO2 gentisate + H+ = CO2 + benzene-1,4-diol L-methionine + H+ = CO2 + 3-methylthiopropanamine uracil 5-carboxylate + H+ = CO2 + uracil N-Benzyloxycarbonylglycine + H+ + H2O = glycine + CO2 + benzyl alcohol N(α)-benzyloxycarbonyl-L-leucine + 3 H+ + H2O = L-leucine + CO2 + benzyl alcohol (R)-3,3-dimethylmalate + NAD+ = CO2 + 3-methyl-2-oxobutanoate + NADH carbon monoxide + 2 an oxidized cytochrome b561 + H2O = CO2 + 2 a reduced cytochrome b561 + 2 H+ 2 hydrogen peroxide + palmitate + H+ = CO2 + pentadecanal + 3 H2O 4-coumarate + H+ = 4-vinylphenol + CO2 trans-cinnamate + H+ = styrene + CO2 indole carboxyl thiazole + H+ = camalexin + CO2 acetylenedicarboxylate + H+ + H2O = CO2 + pyruvate glycine + 2 acceptors = hydrogen cyanide + CO2 + 2 reduced acceptors 1,2-dihydroxy-6-methylcyclohexa-3,5-dienecarboxylate + NAD+ = CO2 + 3-methylcatechol + NADH 2-aryl-2-methylmalonate = CO2 + 2-arylpropionate 2-amino-4-carboxypyrimidine + L-alanine = lathyrine + CO2 + H2O isovaleryl-CoA + 2 malonyl-CoA + H+ = 6-isobutyl-4-hydroxy-2-pyrone + 2 CO2 + 3 coenzyme A isovaleryl-CoA + 3 malonyl-CoA + 2 H+ = 6-(4-methyl-2-oxopentyl)-4-hydroxy-2-pyrone + 3 CO2 + 4 coenzyme A anthranilate + H+ = aniline + CO2 4-aminobenzoate + H+ = aniline + CO2 D-dopachrome + H+ = 5,6-dihydroxyindole + CO2 an acyl-CoA + n (R)-methylmalonyl-CoA + 2n NADPH + 2n H+ = a multi-methyl-branched acyl-CoA + n CO2 + n coenzyme A + 2n NADP+ lauroyl-CoA + malonyl-CoA + H+ = 3-oxo-myristoyl-CoA + CO2 + coenzyme A myristoyl-CoA + malonyl-CoA + H+ = 3-oxo-palmitoyl-CoA + CO2 + coenzyme A urate + 2 H2O + oxygen = (S)-(+)-allantoin + CO2 + hydrogen peroxide pyruvate + formaldehyde + H+ = acetol + CO2 hexanoyl-CoA + 3 malonyl-CoA + 2 H+ = tetraketide pyrone + 3 CO2 + 4 coenzyme A phenylglyoxylate + coenzyme A + NAD+ = benzoyl-CoA + CO2 + NADH hexanoyl-CoA + 2 malonyl-CoA + H2O = triketide pyrone + 2 CO2 + 3 coenzyme A + OH- acetyl-CoA + malonyl-CoA + H+ = acetoacetyl-CoA + CO2 + coenzyme A prephenate + NADP+ = 4-hydroxyphenylpyruvate + CO2 + NADPH hexanoyl-CoA + 3 malonyl-CoA + 3 H+ = olivetol + 4 CO2 + 4 coenzyme A 4α-carboxy,4β,14α-dimethyl-9β,19-cyclo-5α-cholest-24-en-3β-ol + NAD+ = 4α,14α-dimethyl-9β,19-cyclo-5α-cholest-24-en-3-one + CO2 + NADH 4α-carboxy-5α-cholesta-7,24-dien-3β-ol + NAD+ = 5α-cholesta-7,24-dien-3-one + CO2 + NADH stearoyl-CoA + malonyl-CoA + 2 NAD(P)H + 3 H+ = arachidoyl-CoA + CO2 + coenzyme A + 2 NAD(P)+ + H2O carbon monoxide + H2O = CO2 + H2 acetyl-CoA + n malonyl-CoA + 2n NADPH + 2n H+ = a long-chain fatty acid + n CO2 + (n+1) coenzyme A + 2n NADP+ 2-oxoglutarate + glyoxylate + H+ = 2-hydroxy-3-oxoadipate + CO2 2-oxoglutarate + coenzyme A + NADP+ = succinyl-CoA + CO2 + NADPH (2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH 4-phospho-hydroxy-L-threonine + NAD+ = 3-amino-1-hydroxyacetone 1-phosphate + CO2 + NADH (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD+ = protocatechuate + CO2 + NADH (S)-ethylmalonyl-CoA + H+ = butanoyl-CoA + CO2 a palmitoyl-[acp] + malonyl-CoA = 1-heptadecene + 2 CO2 + a holo-[acyl-carrier protein] + coenzyme A a heptodecanoyl-[acp] + malonyl-CoA + 3 H+ = 1-octadecene + 2 CO2 + a holo-[acyl-carrier protein] + coenzyme A a stearoyl-[acp] + malonyl-CoA + 3 H+ = 1-nonadecene + 2 CO2 + a holo-[acyl-carrier protein] + coenzyme A indole-3-pyruvate + an oxidized ferredoxin + coenzyme A = S-2-(indol-3 yl)acetyl-CoA + CO2 + a reduced ferredoxin 2-oxo-2-[4,5,7,10-tetrahydroxy-3-(3-oxobutanoyl)anthracen-2-yl]acetyl-[PKS-acp] + acetoacetate = 1-[4,5,7,10-tetrahydroxy-3-(3-oxobutanoyl)anthracen-2-yl]pentane-1,2,4-trione + a polyketide synthase containing an [acp] domain + CO2 a [protein] N6,N6-dimethyl-L-lysine + 2-oxoglutarate + oxygen = a [protein] N6-methyl-L-lysine + succinate + formaldehyde + CO2 formate + an electron-transfer-related quinone + H+ = CO2 + an electron-transfer-related quinol glutaryl-CoA + an oxidized electron-transfer flavoprotein = crotonyl-CoA + CO2 + a reduced electron-transfer flavoprotein a ferricytochrome b1 + formate = a ferrocytochrome b1 + CO2 + H+ L-valine + H+ = CO2 + 2-methylpropanamine D-threo-isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH malonate semialdehyde + coenzyme A + NADP+ = acetyl-CoA + CO2 + NADPH pyruvate + thiamin diphosphate + H+ = 2-(α-hydroxyethyl)thiamine diphosphate + CO2 an all-trans-polyisoprenyl diphosphate + 1,4-dihydroxy-2-naphthoate + H+ = CO2 + a demethylmenaquinol + diphosphate 5-carboxy-2-oxohept-3-enedioate + H+ = 2-oxohept-3-enedioate + CO2 (S)-methylmalonyl-CoA + H+ = CO2 + propanoyl-CoA a 2-oxo carboxylate + H+ = an aldehyde + CO2 carboxyphosphonoenolpyruvate = CO2 + phosphinopyruvate a long-chain acyl-CoA + n malonyl-CoA = a very long chain fatty acyl-CoA + n CO2 + n coenzyme A 3β-hydroxy-4β-methyl-5α-cholest-7-ene-4α-carboxylate + NAD(P)+ = 4α-methyl-5α-cholest-7-en-3-one + CO2 + NAD(P)H a 3β-hydroxy-4α-carboxysteroid + NAD(P)+ = a 3-oxosteroid + CO2 + NAD(P)H L-cysteate + H+ = taurine + CO2 N, N-dihydroxytrihomomethionine + H+ = 6-methylthiohexanaldoxime + CO2 + H2O hexanoyl-CoA + 3 malonyl-CoA + 3 H+ = 3,5,7-trioxododecanoyl-CoA + 3 CO2 + 3 coenzyme A L-threonine + NAD+ = aminoacetone + CO2 + NADH cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate + NAD(P)+ = CO2 + 4-methylcatechol + NAD(P)H malonate + H+ = acetate + CO2 2 4-coumaryl-CoA + malonyl-CoA + H2O + H+ = bisdemethoxycurcumin + 2 CO2 + 3 coenzyme A an acyl-[acyl-carrier protein] + a malonyl-[acp] + H+ = a 3-oxoacyl-[acp] + CO2 + a holo-[acyl-carrier protein] arachidoyl-CoA + a malonyl-[acp] + H+ = a 3-oxo-behenoyl-[acp] + CO2 + coenzyme A an eicosapentaenoyl-[acp] + a malonyl-[acp] + H+ = a 3-oxo-docosapentaenoyl [acp] + a holo-[acyl-carrier protein] + CO2 2-benzyl-3-hydroxybutanedioate + NAD+ = 2-oxo-4-phenylbutanoate + CO2 + NADH vitamin K 2,3-epoxide + a [protein] 4-carboxy-L-glutamate + H2O = a [protein]-α-L-glutamate + CO2 + phylloquinone + oxygen + H+ uroporphyrinogen-I + 4 H+ = coproporphyrinogen I + 4 CO2 L-arogenate + NAD(P)+ = L-tyrosine + CO2 + NAD(P)H carbonic acid = CO2 + H2O carbon disulfide + 2 H2O = CO2 + 2 hydrogen sulfide a 2-oxo carboxylate + 2 an oxidized ferredoxin + coenzyme A = an acyl-CoA + CO2 + 2 a reduced ferredoxin + H+ UDP-α-D-galacturonate + H+ = UDP-β-L-arabinopyranose + CO2 15-demethoxy-ε-rhodomycinone + a reduced electron acceptor + oxygen + H+ = β-rhodomycinone + CO2 + an oxidized electron acceptor + H2O 15-demethoxy-aclacinomycin A + a reduced electron acceptor + H+ + oxygen = 10-decarboxymethyl, 10-hydroxyaclacinomycin A + CO2 + an oxidized electron acceptor + H2O 15-demethoxyaclacinomycin T + a reduced electron acceptor + H+ + oxygen = 10-decarboxymethylaclacinomycin T + CO2 + an oxidized electron acceptor + H2O 2-(hydroxymethyl)-3-(acetamidomethylene)succinate + H+ + 2 H2O = 2-hydroxymethyl-4-oxobutanoate + acetate + CO2 + ammonium cyanate + hydrogen carbonate + 3 H+ = ammonium + 2 CO2 (Z)-2-methylureidoacrylate peracid + H+ + H2O = (Z)-2-methyl-peroxyaminoacrylate + ammonium + CO2 N-carbamoyl-L-aspartate + 2 H+ + H2O = ammonium + CO2 + L-aspartate urethan + H+ + H2O = ammonium + CO2 + ethanol an N-carbamoyl D-amino acid + H+ + H2O = a D-amino acid + ammonium + CO2 (Z)-3-ureidoacrylate peracid + H+ + H2O = (Z)-3-peroxyaminoacrylate + ammonium + CO2 methylenediurea + 2 H+ + 2 H2O = N-(hydroxymethyl)urea + 2 ammonium + CO2 N,N-dihydroxypentahomomethionine + H+ = 8-methylthiooctanaldoxime + CO2 + H2O N,N-dihydroxyhexahomomethioniate + H+ = 9-methylthiononanaldoxime + CO2 + H2O N, N-dihydroxy-tetrahomomethionine + H+ = 7-methylthioheptanaldoxime + CO2 + H2O N,N-dihydroxyhomomethionine + H+ = 4-methylthiobutanaldoxime + CO2 + H2O N,N-dihydroxy-L-dihomomethionine + H+ = 5-methylthiopentanaldoxime + CO2 + H2O a 4-hydroxy-3-polyprenylbenzoate + H+ = a 2-polyprenylphenol + CO2 2 3-amino-4-hydroxybenzoate + N-acetyl-L-cysteine + 2 oxygen + H+ = grixazone B + CO2 + 4 H2O a C-terminal [cypemycin]-L-Cys-L-Leu-L-Val-L-Cys + an oxidized electron acceptor + H+ = a C-terminal C3.19,S21-[cyclocypemycin]-L-Ala-L-Leu-L-valinamide + CO2 + hydrogen sulfide + a reduced electron acceptor O-carbamoyl-L-serine = 2-aminoprop-2-enoate + CO2 + ammonium O-carbamoyl-L-serine + H2O + H+ = pyruvate + CO2 + 2 ammonium formate + an oxidized coenzyme F420 + H+ = CO2 + a reduced coenzyme F420 (S)-3-methyl-2-oxopentanoate + an [apo BCAA dehydrogenase E2 protein] N6-lipoyl-L-lysine + H+ = an [apo BCAA dehydrogenase E2 protein] N6-S-[2-methylbutanoyl]dihydrolipoyl-L-lysine + CO2 an acetyl-[acp] + 9 malonyl-CoA + 8 H+ = tetracenomycin F2 + a holo-[acyl-carrier protein] + 9 CO2 + 9 coenzyme A + 2 H2O acetyl-CoA + 5 malonyl-CoA + 3 NADPH + 7 H+ = 5-methyl-1-naphthoate + 5 CO2 + 6 coenzyme A + 3 NADP+ + 4 H2O acetyl-CoA + 5 malonyl-CoA + 2 NADPH + 6 H+ = 2-hydroxy-5-methyl-1-naphthoate + 5 CO2 + 6 coenzyme A + 2 NADP+ + 3 H2O pyruvate + (E)-non-3-en-2-one + H+ = (S)-3-pentanylhexane-2,5-dione + CO2 pyruvate + (E)-dec-3-en-2-one + H+ = (S)-3-hexanylhexane-2,5-dione + CO2 pyruvate + (E)-4-phenylbut-3-en-2-one + H+ = (R)-phenylhexane-2,5-dione + CO2 pyruvate + 2-hydroxychalcone + H+ = 3-(2-hydroxyphenyl)-1-phenylpentane-1,4-dione + CO2 pyruvate + an α,β-unsaturated aldehyde + H+ = a (3R,4E)-3-hydroxy-2-keto-alk-4-ene + CO2 pyruvate + an α,β-unsaturated carbonyl compound + H+ = CO2 + an n-acetyl-(n-2)-oxo-compound pyruvate + an (E)-2-oxo-alk-3-ene + H+ = CO2 + an (4S)-4-acetyl-2-oxo compound pyruvate + trans-chalcone + H+ = (R)-1,3-diphenyl-pentane-1,4-dione + CO2 an N-carbamoyl-L-amino acid + H2O + 2 H+ = an L-amino acid + ammonium + CO2 xanthine + 2-oxoglutarate + oxygen = urate + succinate + CO2 an N10-formyl-tetrahydrofolate + NADP+ + H2O = a tetrahydrofolate + CO2 + NADPH + H+ 2 an oxidized cytochrome c-553 + formate = 2 a reduced cytochrome c-553 + CO2 + H+ N-ethylammeline + CO2 + 7 H+ = N-isopropylammelide + ammonium + H2O D-glycerate + CO2 + NAD(P)+ = 2-hydroxy-3-oxosuccinate + NAD(P)H + 2 H+

In Transport reactions:
CO2[periplasmic space]CO2[cytosol]

In Redox half-reactions:
acetate[in] + CO2[in] + 2 H+[in] + 2 e- → pyruvate[in] + H2O[in] ,
CO2[out] + H+[out] + 2 e- → formate[out]


References

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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