pyruvate transport in via proton symport
pyruvate decarboxylase (acetoin-forming)
(S)-Lactate:ferricytochrome-c 2-oxidoreductase
YGL205W, YIL160C, YKR009C, YLR284C, YNL202W, YOR180C
YGL205W, YIL160C, YKR009C, YLR284C, YNL202W
3',5'-cyclic-nucleotide phosphodiesterase
acetohydroxy acid isomeroreductase, mitochondrial
ketol-acid reductoisomerase (2-Aceto-2-hydroxybutanoate), mitochondrial
D1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
pyrimidine-nucleoside phosphorylase (uracil)
Alcohol Acetyltransferase (2-methylbutanol)
Alcohol Acetyltransferase (isoamyl alcohol)
Alcohol Acetyltransferase (isobutyl alcohol)
Octadecenoate (n-C18:1) transport in via uniport
Octadecanoate (n-C18:0) transport in via uniport
Octadecynoate (n-C18:2) transport in via uniport
phosphoadenylyl-sulfate reductase (thioredoxin)
purine-nucleoside phosphorylase (Xanthosine)
purine-nucleoside phosphorylase (Adenosine)
purine-nucleoside phosphorylase (Deoxyadenosine)
purine-nucleoside phosphorylase (Deoxyguanosine)
purine-nucleoside phosphorylase (Guanosine)
purine-nucleoside phosphorylase (Deoxyinosine)
purine-nucleoside phosphorylase (Inosine)
orntithine transport in via proton symport
ribonucleoside-triphosphate reductase (ATP)
ribonucleoside-diphosphate reductase (UDP)
ribonucleoside-diphosphate reductase (CDP)
Alcohol Acetyltransferase (Phenylethanol alcohol)
2-Oxo-4-methyl-3-carboxypentanoate decarboxylation
O-Phospho-4-hydroxy-L-threonine:2-oxoglutarate aminotransferase
YAL044C, YBR221C, YDR019C, YER178W, YMR189W
ribonucleoside-diphosphate reductase (GDP)
fatty-acid--CoA ligase (dodecanoate), peroxisomal
ribonucleoside-diphosphate reductase (ADP)
ribose transport in via proton symporter
riboflavin transport in via proton symport
Itaconate--CoA ligase (ADP-forming), mitochondrial
inositol transport in via proton symport
1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Phenylacetaldehyde transport (extracellular)
fatty-acid--CoA ligase (octanoate), peroxisomal
fatty-acid--CoA ligase (n-C26:0), peroxisomal
fatty-acid--CoA ligase (n-C24:0), peroxisomal
2,3-diketo-5-methylthio-1-phosphopentane degradation reaction
nucleoside-diphosphate kinase (ATP:dADP)
nucleoside-diphosphate kinase (ATP:dCDP)
deoxyinosine transport in via proton symport
nucleoside-diphosphate kinase (ATP:dUDP)
nucleoside-diphosphate kinase (ATP:dTDP)
nucleoside-diphosphate kinase (ATP:dGDP)
2-methylcitrate dehydratase, mitochondrial
D-mannose transport in via proton symport
acyl-CoA oxidase (octadecanoyl-CoA), peroxisomal
acyl-CoA oxidase (hexacanoyl-CoA), peroxisomal
acyl-CpA oxidase (tetradecanoyl-CoA), peroxisomal
fatty-acyl-ACP synthase (n-C10:0ACP), mitochondrial
acyl-CoA oxidase (hexadecanoyl-CoA), peroxisomal
5-Methylthio-5-deoxy-D-ribulose 1-phosphate dehydratase
fatty acid oxidation (octanoyl-CoA), peroxisomal
acyl-CoA oxidase (dodecanoyl-CoA), peroxisomal
fatty acid oxidation (tetradecansoyl-CoA), peroxisomal
N,N-bisformyl-dityrosine transport (extracellular)
fatty-acyl-ACP synthase (n-C16:0ACP), mitochondrial
3-hydroxyacyl-CoA dehydrogenase (3-oxodecanoyl-CoA), peroxisomal
3-Hydroxyacyl-CoA dehydrogenase (3-oxotetradecanoyl-CoA), peroxisomal
3-hydroxyacyl-CoA dehydrogenase (3-oxohexadecanoyl-CoA), peroxisomal
3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA), peroxisomal
nicotinamide-nucleotide adenylyltransferase
3-hydroxyacyl-CoA dehydrogenase (3-oxohexacosyl-CoA), peroxisomal
fatty-acyl-ACP synthase (n-C14:0ACP), mitochondrial
ammonia transport (efflux, cytosol to extracellular)
fatty-acyl-ACP synthase (n-C12:0ACP), mitochondrial
Dihydroneopterin monophosphate dephosphorylase
Dihydroneopterin triphosphate pyrophosphatase
Dolichyl-phosphate-mannose--protein mannosyltransferase, endoplasmic reticular
Dolichyl-phosphate D-mannosyltransferase
fatty-acyl-ACP synthase (n-C14:1ACP), mitochondrial
fatty acyl-ACP synthase (n-C8:0ACP), mitochondrial, lumped reaction
fatty acid synthase (n-C24:0), lumped reaction
fatty-acyl-ACP synthase (n-C16:1ACP), mitochondrial
Hydroxybenzoate octaprenyltransferase, mitochondrial
nicotinate-nucleotide diphosphorylase (carboxylating)
nicotinate-nucleotide adenylyltransferase
xanthosine transport in via proton symport
fatty-acyl-ACP synthase (n-C18:1ACP), mitochondrial
fatty-acyl-ACP synthase (n-C18:0ACP), mitochondrial
fatty-acyl-ACP synthase (n-C18:2ACP), mitochondrial
cytochrome P450 lanosterol 14-alpha-demethylase (NAD)
cytochrome P450 lanosterol 14-alpha-demethylase (NADP)
formate dehydrogenase, cytosolic/mitochondrial
fatty acyl-CoA synthase (n-C8:0CoA), lumped reaction
fatty acid synthase (n-C8:0), lumped reaction
hexadecenoate (n-C16:1) transport in via uniport
D-Fructose 1-phosphate D-glyceraldehyde-3-phosphate-lyase
Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase
xylitol dehydrogenase (D-xyulose-forming)
acteylornithine transaminase, mitochondrial
acid phosphatase, extracellular (secreted)
acyl carrier protein synthase, mitochondrial
Hexadecanoate (n-C16:0) transport in via uniport
cytosine transport in via proton symport
UDP-glucose:ergosterol glucosyltransferase
thymidine transport in via proton symport
hydrogen peroxide reductase (thioredoxin)
Tetrahydrofolate:L-glutamate gamma-ligase (ADP-forming)
Ubiquinol:ferricytochrome-c oxidoreductase
Methionyl-tRNA formyltransferase, mitochondrial
tetrahydrofolate aminomethyltransferase, mitochondrial
carnitine O-acetyltransferase, reverse direction, peroxisomal
ethanolamine transport via diffusion (extracellular)
hexaprenyldihydroxybenzoate methyltransferase
2-Hexaprenyl-6-methoxyphenol monooxygenase, mitochondrial
2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase, mitochondrial
cytidine transport in via proton symport
2-Methylbutanal transport (extracellular)
Thiamine transport in via proton symport
2-methyl-1-butanol transport (extracellular)
L-aspartate transport via proton symport
L-threonine transport via proton symport
5-Formyltetrahydrofolate:10-Formyltetrahydrofolate isomerase
D-fructose transport in via proton symport
5-formethyltetrahydrofolate cyclo-ligase
(R)-Lactate:ferricytochrome-c 2-oxidoreductase
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase (nadph)
2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate deaminase
deoxyadenosine transport in via proton symport
7,8-Diaminononanoate transport via proton symport
Glycolipid 1,3-alpha-D-mannosyltransferase, Golgi apparatus
glycero-3-phosphocholine transport (extracellular to cytosol)
glycerol-3-phosphate dehydrogenase (NAD)
glycerol-3-phosphate dehydrogenase (FAD), mitochondrial
glycero-3-phospho-1-inositol transport (extracellular to cytosol)
deoxyuridine transport in via proton symport
deoxyhypusine synthase, cytosolic/mitochondrial
L-asparagine transport via proton symport
3-hydroxyacyl-CoA dehydratase (3-hydroxytetradecanoyl-CoA), peroxisomal
3,4-Dihydroxy-2-butanone-4-phosphate synthase
3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA), peroxisomal
3-hydroxyacyl-CoA dehydratase (3-hydroxydecanoyl-CoA), peroxisomal
deoxycytidine transport in via proton symport
3-hydroxyacyl-CoA dehydratase (3-hydroxyhexacosyl-CoA), peroxisomal
asparagine synthase (glutamine-hydrolysing)
Myristicoyl-CoA desaturase (n-C14:0CoA -> n-C14:1CoA)
3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase
sucrose hydrolyzing enxyme, extracellular
succinate dehydrogenase (ubiquinone-6), mitochondrial
L-erythro-4-Hydroxyglutamate:2-oxoglutarate aminotransferase
3-hydroxyacyl-CoA dehydratase (3-hydroxyhexadecanoyl-CoA), peroxisomal
3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA), peroxisomal
4-Aminobenzoate mitochondrial transport via diffusion
L-Tryptophan:oxygen 2,3-oxidoreductase (decyclizing)
tryptophan synthase (indoleglycerol phosphate)
3-Hexaprenyl-4,5-dihydroxybenzoate hydroxylase, mitochondrial
S-adenosyl-L-methionine transport in via proton symport
L-tryptophan transport via proton symport
N-acetylputrescine: oxygen oxireductase (deaminating)
YBR221C, YER178W, YFL018C, YGR193C, YNL071W
L-4-hydroxyglutamate semialdehyde dehydrogenase, mitochondrial
L-2-amino-3-oxobutanoate decarboxylation (spontaneous)
UDPglucose--hexose-1-phosphate uridylyltransferase
cholestenol delta-isomerase, lumped reaction
thiazole phosphate synthesis (xylulose 5-phosphate), yeast-specific
thiazole phosphate synthesis (ribose 5-phosphate), yeast-specifc
4-Hydroxyphenylpyruvate:oxygen oxidoreductase
2-methylpropanal transport (extracellular)
coproporphyrinogen oxidase (O2 required)
carnitine O-aceyltransferase, mitochondrial
3-methylbutanal transport (extracellular)
3-Hexaprenyl-4-hydroxy-5-methoxybenzoate decarboxylase, mitochondrial
S-adenosyl-L-methionine:3-hexaprenyl-4,5-dihydroxylate O-methyltransferase, mitochondrial
fatty-acid--CoA ligase (decanoate), peroxisomal
alpha,alpha-trehalose-phosphate synthase (UDP-forming)
trehalose transport in via proton symporter
2-aceto-2-hydroxybutanoate synthase, mitochondrial
N-acteylglutamate synthase, mitochondrial
acyl-CoA oxidase (decanoyl-CoA), peroxisomal
acetyl-CoA acyltransferase (tetracosanoyl-CoA), peroxisomal
N-acetylglucosamine-6-phosphate synthase
This is the model described in the article: Towards a genome-scale kinetic model of cellular metabolism Smallbone K, Simeonidis E, Swainston N, Mendes P. BMC Syst Biol. 2010 Jan 28;4(1):6. PMID: 20109182 , doi: 10.1186/1752-0509-4-6 Abstract: CKGROUND: Advances in bioinformatic techniques and analyses have led to the availability of genome-scale metabolic reconstructions. The size and complexity of such networks often means that their potential behaviour can only be analysed with constraint-based methods. Whilst requiring minimal experimental data, such methods are unable to give insight into cellular substrate concentrations. Instead, the long-term goal of systems biology is to use kinetic modelling to characterize fully the mechanics of each enzymatic reaction, and to combine such knowledge to predict system behaviour. RESULTS: We describe a method for building a parameterized genome-scale kinetic model of a metabolic network. Simplified linlog kinetics are used and the parameters are extracted from a kinetic model repository. We demonstrate our methodology by applying it to yeast metabolism. The resultant model has 956 metabolic reactions involving 820 metabolites, and, whilst approximative, has considerably broader remit than any existing models of its type. Control analysis is used to identify key steps within the system. CONCLUSIONS: Our modelling framework may be considered a stepping-stone toward the long-term goal of a fully-parameterized model of yeast metabolism. The model (see additional file 1) is available in SBML format from the BioModels database (BioModels ID: MODEL1001200000) and at http://www.mcisb.org/resources/genomescale/ . This SBML representation of the yeast metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org). This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
4-aminobutyrate transport in via proton symport
urea transport via proton symport (2 H+)
Aminobutyraldehyde dehydrogenase, mitochondrial
L-arabinitol transport via passive diffusion
acetyl-CoA C-acyltransferase (decanoyl-CoA), peroxisomal
acetyl-CoA C-acetyltransferase (dodecanoyl), peroxisomal
acetyl-CoA C-acetyltransferase (octanoyl-CoA), peroxisomal
acetyl-CoA acyltransferase (tetradecanoyl-CoA), peroxisomal
acetyl-CoA acyltransferase (hexadecanoyl-CoA), peroxisomal
uroporphyrinogen decarboxylase (uroporphyrinogen III)
2-keto-4-methylthiobutyrate transamination
5-Aminolevulinate transport in via proton symport
8-Amino-7-oxononanoate transport via proton symport
Aminoacetone:oxygen oxidoreductase(deaminating)(flavin-containing)
L-aminoadipate-semialdehyde dehydrogenase (NADPH)
L-aminoadipate-semialdehyde dehydrogenase (NADH)
Ferrocytochrome-c:hydrogen-peroxide oxidoreductase
alkaline ceramidase (ceramide-2), endoplasmic reticulum
alkaline ceramidase (ceramide-1), endoplasmic reticulum
Palmitoyl-CoA desaturase (n-C16:0CoA -> n-C16:1CoA)
C-4 sterol methyl oxidase (4,4-dimethylzymosterol)
carbamoyl-phosphate synthase (glutamine-hydrolysing)
C-4 sterol methyl oxidase (4-methylzymosterol)
stearoyl-CoA desaturase (n-C18:0CoA -> n-C18:1CoA)
Oleoyl-CoA desaturase (n-C18:1CoA -> n-C18:2CoA)
dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate), mitochondrial
dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate), mitochondrial
deoxyguanosine transport in via proton symport
C-s24 sterol reductase, endoplamic reticular
C-3 sterol dehydrogenase (4-methylzymosterol)
C-3 sterol keto reductase (4-methylzymosterol)
Squalene epoxidase, endoplasmic reticular (NADP)
adenosine transport in via proton symport
glycine-cleavage complex (lipoamide), mitochondrial
glycine-cleavage complex (lipoylprotein), mitochondrial
glycine-cleavage system (lipoamide), mitochondrial
isobutyl alcohol transport (extracellular)
Isobutyl acetate transport (extracellular)
Indoleacetaldehyde transport (extracellular)
3-phosphoshikimate 1-carboxyvinyltransferase
succinate-semialdehyde dehydrogenase (NADP)
Squalene epoxidase, endoplasmic reticular (NAD)
N-acetyl-g-glutamyl-phosphate reductase, mitochondrial
hypoxanthine phosphoribosyltransferase (Hypoxanthine)
4-amino-5-hydroxymethyl-2-methylpyrimidine synthetase
Isoamyl acetate transport (extracellular)
1-alpha-D-Galactosyl-myo-inositol galactohydrolase
galactose-1-phosphate uridylyltransferase
hypoxanthine transport via proton symport
UTP-glucose-1-phosphate uridylyltransferase
L-hydroxyproline dehydrogenase (NADP), mitochondrial
D-galactose transport in via proton symport
glyceraldehyde-3-phosphate dehydrogenase
phosphoribosylglycinamide formyltransferase
YGL205W, YIL160C, YKR009C, YNL202W, YOR180C
pantetheine-phosphate adenylyltransferase
isoamyl alcohol transport (extracellular)
putrescine transport in via proton antiport
putrescine excretion (cytosol to extracellular)
YBR026C, YER061C, YHR067W, YKL055C, YKL192C, YOR221C
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase, mitochondrial
L-hydroxyproline dehydrogenase (NAD), mitochondrial
oxoglutarate dehydrogenase (dihydrolipoamide S-succinyltransferase)
phosphoribosylaminoimidazole carboxylase
phosphoribosylaminoimidazolecarboxamide formyltransferase
L-glutamine transport via proton symport
YBR127C, YDL185W, YEL027W, YEL051W, YGR020C, YHR026W, YHR039C-A, YKL080W, YLR447C, YOR270C, YOR332W, YPL234C, YPR036W
protoporphyrinogen oxidase, mitochondrial
trans-pentaprenyltranstransferase, mitochondrial
glutamine-fructose-6-phosphate transaminase
L-histidine transport via proton symport
aldehyde dehydrogenase (2-methylbutanol, NAD)
Homogentisate:oxygen 1,2-oxidoreductase (decyclizing)
phosphoribosylformylglycinamidine synthase
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
phosphoribosylaminoimidazolesuccinocarboxamide synthase
YDR204W, YGL119W, YGR255C, YLR201C, YML110C, YOL096C, YOR125C
YBR127C, YDL185W, YEL027W, YEL051W, YGR020C, YHR026W, YHR039C-A, YKL080W, YLR447C, YMR054W, YOR332W, YPL234C, YPR036W
aldehyde dehydrogenase (isoamyl alcohol, NADP)
aldehyde dehydrogenase (isobutyl alcohol, NADP)
aldehyde dehydrogenase (isoamyl alcohol, NAD)
aldehyde dehydrogenase (2-phenylethanol, NADP)
aldehyde dehydrogenase (2-phenylethanol, NAD)
ribonucleoside-triphosphate reductase (GTP)
ribonucleoside-triphosphate reductase (UTP)
ribonucleoside-triphosphate reductase (CTP)
L-glutamate transport via proton symport
methylenetetrahydrofolate dehydrogenase (NADP)
5-diphosphoinositol-1,2,3,4,6-pentakisphosphate synthase
5-diphosphoinositol-1,2,3,4,6-pentakisphosphate diphosphohydrolase
inositol-1,4,5-triphosphate 6-kinase, nucleus
inositol-1,4,5-trisphosphate 3-kinase, nucleus
3-methyl-2-oxobutanoate hydroxymethyltransferase
diphosphoinositol-1,3,4,6-tetrakisphosphate synthase
diphosphoinositol-1,3,4,6-tetrakisphosphate diphosphohydrolase
D-sorbitol dehydrogenase (D-fructose producing)
sphingoid base-phosphate phosphatase (phytosphingosine 1-phosphate), endoplasmic reticulum
sphingoid base-phosphate phosphatase (sphinganine 1-phosphatase), endoplasmic reticulum
S-adenosyl-methionine delta-24-sterol-c-methyltransferase
saccharopine dehydrogenase (NAD, L-lysine forming)
aldehyde dehydrogenase (isobutyl alcohol, NAD)
aldehyde dehydrogenase (2-methylbutanol, NADP)
saccharopine dehydrogenase (NADP, L-glutamate forming)
glutamine phosphoribosyldiphosphate amidotransferase
aldehyde dehydrogenase (phenylacetaldehyde, NAD)
aldehyde dehydrogenase (indole-3-acetaldehyde, NAD), mitochondrial
aldehyde dehydrogenase (indole-3-acetaldehyde, NADP)
L-sorbitol dehydrogenase (L-sorbose-producing)
2-hydroxybutyrate cotransport with proton
glycylpeptide N-tetradecanoyltransferase
L-methionine transport via proton symport
L-sorbitol transport via passive diffusion
D-sorbitol transport via passive diffusion
phosphopantothenoylcysteine decarboxylase
5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
inositol-1,3,4,5,6-pentakisphosphate 2-kinase, nuclear
aldehyde dehydrogenase (tryptophol, NAD)
inositol-1,3,4,5-triphosphate 6-kinase, nucleus
inositol-1,4,5,6- tetrakisphosphate 3-kinase, nucleus
alcohol dehydrogenase, forward rxn (ethanol -> acetaldehyde)
Pantothenate transport via proton symport
alcohol dehydrogenase, reverse rxn (acetaldehyde -> ethanol)
adenosylmethionine-8-amino-7-oxononanoate transaminase
guanosine transport in via proton symport
sphingolipid long chain base kinase (phytosphingosine)
sphingolipid long chain base kinase (sphinganine)
O-succinylhomoserine lyase (elimination)
aldehyde dehydrogenase (acetaldehyde, NADP)
aldehyde dehydrogenase (acetylaldehyde, NAD), mitochondrial
aldehyde dehydrogenase (3-aminopropanal, NAD)
sulfite transport (efflux, cytosol to extracellular)
L-isoleucine transport via proton symport
L-1-Pyrroline-3-hydroxy-5-carboxylate spontaneous conversion to L-4-Hydroxyglutamate semialdehyde, mitochondrial
L-1-pyrroline-3-hydroxy-5-carboxylate dehydrogenase
Phenethyl acetate transport (extracellular)
N4-Acetylaminobutanal:NAD+ oxidoreductase
L-phenylalanine transport via proton symport
Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)
NADH dehydrogenase, cytosolic/mitochondrial
spermidine transport in via proton antiport
methylenetetrahydrofolate dehydrogenase (NAD)
5,10-methylenetetrahydrofolatereductase (NADPH)
spermidine excretion (cytosol to extracellular)
5-methylthioribose-1-phosphate isomerase