3-Hexaprenyl-4-hydroxy-5-methoxybenzoate decarboxylase, mitochondrial
Ubiquinol:ferricytochrome-c oxidoreductase
hexaprenyldihydroxybenzoate methyltransferase
sphingolipid long chain base kinase (phytosphingosine)
N-acetyl-g-glutamyl-phosphate reductase, mitochondrial
L-aminoadipate-semialdehyde dehydrogenase (NADH)
aldehyde dehydrogenase (tryptophol, NAD)
glycero-3-phosphocholine transport (extracellular to cytosol)
3-Hexaprenyl-4,5-dihydroxybenzoate hydroxylase, mitochondrial
aldehyde dehydrogenase (indole-3-acetaldehyde, NAD), mitochondrial
Squalene epoxidase, endoplasmic reticular (NAD)
5-Formyltetrahydrofolate:10-Formyltetrahydrofolate isomerase
fatty-acid--CoA ligase (decanoate), peroxisomal
L-glutamine transport via proton symport
spermidine excretion (cytosol to extracellular)
putrescine transport in via proton antiport
2-methylpropanal transport (extracellular)
7,8-Diaminononanoate transport via proton symport
2-keto-4-methylthiobutyrate transamination
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase (nadph)
Dolichyl-phosphate-mannose--protein mannosyltransferase, endoplasmic reticular
L-tryptophan transport via proton symport
tryptophan synthase (indoleglycerol phosphate)
alkaline ceramidase (ceramide-1), endoplasmic reticulum
inositol transport in via proton symport
trehalose transport in via proton symporter
ribonucleoside-diphosphate reductase (CDP)
sphingoid base-phosphate phosphatase (sphinganine 1-phosphatase), endoplasmic reticulum
ribose transport in via proton symporter
aldehyde dehydrogenase (isoamyl alcohol, NAD)
L-histidine transport via proton symport
riboflavin transport in via proton symport
Methionyl-tRNA formyltransferase, mitochondrial
3-methylbutanal transport (extracellular)
acyl-CoA oxidase (hexadecanoyl-CoA), peroxisomal
aldehyde dehydrogenase (2-methylbutanol, NAD)
L-isoleucine transport via proton symport
nucleoside-diphosphate kinase (ATP:dADP)
YBR127C, YDL185W, YEL027W, YEL051W, YGR020C, YHR026W, YHR039C-A, YKL080W, YLR447C, YMR054W, YOR332W, YPL234C, YPR036W
L-erythro-4-Hydroxyglutamate:2-oxoglutarate aminotransferase
glycine-cleavage complex (lipoylprotein), mitochondrial
purine-nucleoside phosphorylase (Xanthosine)
3-hydroxyacyl-CoA dehydratase (3-hydroxydecanoyl-CoA), peroxisomal
3-hydroxyacyl-CoA dehydrogenase (3-oxohexacosyl-CoA), peroxisomal
2-methylcitrate dehydratase, mitochondrial
Pantothenate transport via proton symport
2-Hexaprenyl-6-methoxyphenol monooxygenase, mitochondrial
acetyl-CoA C-acetyltransferase (octanoyl-CoA), peroxisomal
Alcohol Acetyltransferase (isoamyl alcohol)
deoxyguanosine transport in via proton symport
2-hydroxybutyrate cotransport with proton
Hexadecanoate (n-C16:0) transport in via uniport
(S)-Lactate:ferricytochrome-c 2-oxidoreductase
glycerol-3-phosphate dehydrogenase (NAD)
Isoamyl acetate transport (extracellular)
N-acteylglutamate synthase, mitochondrial
1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
adenosine transport in via proton symport
aldehyde dehydrogenase (indole-3-acetaldehyde, NADP)
3,4-Dihydroxy-2-butanone-4-phosphate synthase
fatty-acyl-ACP synthase (n-C10:0ACP), mitochondrial
L-methionine transport via proton symport
C-4 sterol methyl oxidase (4-methylzymosterol)
pyruvate decarboxylase (acetoin-forming)
3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase
deoxyinosine transport in via proton symport
putrescine excretion (cytosol to extracellular)
fatty acid synthase (n-C24:0), lumped reaction
oxoglutarate dehydrogenase (dihydrolipoamide S-succinyltransferase)
fatty-acyl-ACP synthase (n-C18:0ACP), mitochondrial
galactose-1-phosphate uridylyltransferase
phosphoadenylyl-sulfate reductase (thioredoxin)
2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate deaminase
YDR204W, YGL119W, YGR255C, YLR201C, YML110C, YOL096C, YOR125C
carnitine O-acetyltransferase, reverse direction, peroxisomal
Ferrocytochrome-c:hydrogen-peroxide oxidoreductase
carnitine O-aceyltransferase, mitochondrial
5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
Dolichyl-phosphate D-mannosyltransferase
asparagine synthase (glutamine-hydrolysing)
L-sorbitol dehydrogenase (L-sorbose-producing)
methylenetetrahydrofolate dehydrogenase (NAD)
sphingoid base-phosphate phosphatase (phytosphingosine 1-phosphate), endoplasmic reticulum
Alcohol Acetyltransferase (Phenylethanol alcohol)
S-adenosyl-L-methionine:3-hexaprenyl-4,5-dihydroxylate O-methyltransferase, mitochondrial
ribonucleoside-diphosphate reductase (ADP)
acteylornithine transaminase, mitochondrial
5-diphosphoinositol-1,2,3,4,6-pentakisphosphate diphosphohydrolase
L-arabinitol transport via passive diffusion
acyl-CoA oxidase (octadecanoyl-CoA), peroxisomal
xanthosine transport in via proton symport
acetohydroxy acid isomeroreductase, mitochondrial
purine-nucleoside phosphorylase (Deoxyadenosine)
3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA), peroxisomal
coproporphyrinogen oxidase (O2 required)
Palmitoyl-CoA desaturase (n-C16:0CoA -> n-C16:1CoA)
2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase, mitochondrial
acetyl-CoA C-acyltransferase (decanoyl-CoA), peroxisomal
Alcohol Acetyltransferase (2-methylbutanol)
dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate), mitochondrial
aldehyde dehydrogenase (3-aminopropanal, NAD)
sulfite transport (efflux, cytosol to extracellular)
alcohol dehydrogenase, forward rxn (ethanol -> acetaldehyde)
pyrimidine-nucleoside phosphorylase (uracil)
2-aceto-2-hydroxybutanoate synthase, mitochondrial
N-acetylputrescine: oxygen oxireductase (deaminating)
C-s24 sterol reductase, endoplamic reticular
phosphopantothenoylcysteine decarboxylase
cytochrome P450 lanosterol 14-alpha-demethylase (NADP)
NADH dehydrogenase, cytosolic/mitochondrial
tetrahydrofolate aminomethyltransferase, mitochondrial
fatty acyl-CoA synthase (n-C8:0CoA), lumped reaction
YBR221C, YER178W, YFL018C, YGR193C, YNL071W
thymidine transport in via proton symport
sucrose hydrolyzing enxyme, extracellular
deoxyuridine transport in via proton symport
UTP-glucose-1-phosphate uridylyltransferase
L-glutamate transport via proton symport
succinate dehydrogenase (ubiquinone-6), mitochondrial
inositol-1,3,4,5,6-pentakisphosphate 2-kinase, nuclear
fatty-acid--CoA ligase (n-C24:0), peroxisomal
8-Amino-7-oxononanoate transport via proton symport
ribonucleoside-diphosphate reductase (GDP)
alkaline ceramidase (ceramide-2), endoplasmic reticulum
3-hydroxyacyl-CoA dehydrogenase (3-oxodecanoyl-CoA), peroxisomal
YGL205W, YIL160C, YKR009C, YLR284C, YNL202W
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase, mitochondrial
ribonucleoside-diphosphate reductase (UDP)
D-sorbitol dehydrogenase (D-fructose producing)
Itaconate--CoA ligase (ADP-forming), mitochondrial
N,N-bisformyl-dityrosine transport (extracellular)
YBR127C, YDL185W, YEL027W, YEL051W, YGR020C, YHR026W, YHR039C-A, YKL080W, YLR447C, YOR270C, YOR332W, YPL234C, YPR036W
O-Phospho-4-hydroxy-L-threonine:2-oxoglutarate aminotransferase
acid phosphatase, extracellular (secreted)
aldehyde dehydrogenase (isoamyl alcohol, NADP)
5-diphosphoinositol-1,2,3,4,6-pentakisphosphate synthase
hexadecenoate (n-C16:1) transport in via uniport
nicotinamide-nucleotide adenylyltransferase
Aminobutyraldehyde dehydrogenase, mitochondrial
acyl-CoA oxidase (hexacanoyl-CoA), peroxisomal
Isobutyl acetate transport (extracellular)
ketol-acid reductoisomerase (2-Aceto-2-hydroxybutanoate), mitochondrial
purine-nucleoside phosphorylase (Guanosine)
nicotinate-nucleotide adenylyltransferase
isoamyl alcohol transport (extracellular)
cytidine transport in via proton symport
fatty-acyl-ACP synthase (n-C12:0ACP), mitochondrial
3-hydroxyacyl-CoA dehydratase (3-hydroxytetradecanoyl-CoA), peroxisomal
glycylpeptide N-tetradecanoyltransferase
Alcohol Acetyltransferase (isobutyl alcohol)
acetyl-CoA C-acetyltransferase (dodecanoyl), peroxisomal
aldehyde dehydrogenase (acetylaldehyde, NAD), mitochondrial
dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate), mitochondrial
saccharopine dehydrogenase (NADP, L-glutamate forming)
alcohol dehydrogenase, reverse rxn (acetaldehyde -> ethanol)
glycerol-3-phosphate dehydrogenase (FAD), mitochondrial
fatty-acyl-ACP synthase (n-C14:1ACP), mitochondrial
ribonucleoside-triphosphate reductase (GTP)
D1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Phenylacetaldehyde transport (extracellular)
5-Methylthio-5-deoxy-D-ribulose 1-phosphate dehydratase
C-3 sterol dehydrogenase (4-methylzymosterol)
cytochrome P450 lanosterol 14-alpha-demethylase (NAD)
Tetrahydrofolate:L-glutamate gamma-ligase (ADP-forming)
pyruvate transport in via proton symport
Myristicoyl-CoA desaturase (n-C14:0CoA -> n-C14:1CoA)
fatty acid synthase (n-C8:0), lumped reaction
2,3-diketo-5-methylthio-1-phosphopentane degradation reaction
fatty acyl-ACP synthase (n-C8:0ACP), mitochondrial, lumped reaction
glycine-cleavage complex (lipoamide), mitochondrial
phosphoribosylaminoimidazolesuccinocarboxamide synthase
3',5'-cyclic-nucleotide phosphodiesterase
acyl-CoA oxidase (decanoyl-CoA), peroxisomal
D-galactose transport in via proton symport
uroporphyrinogen decarboxylase (uroporphyrinogen III)
3-Hydroxyacyl-CoA dehydrogenase (3-oxotetradecanoyl-CoA), peroxisomal
Octadecanoate (n-C18:0) transport in via uniport
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-Hydroxyphenylpyruvate:oxygen oxidoreductase
inositol-1,3,4,5-triphosphate 6-kinase, nucleus
glutamine-fructose-6-phosphate transaminase
cholestenol delta-isomerase, lumped reaction
YGL205W, YIL160C, YKR009C, YLR284C, YNL202W, YOR180C
D-fructose transport in via proton symport
stearoyl-CoA desaturase (n-C18:0CoA -> n-C18:1CoA)
aldehyde dehydrogenase (2-methylbutanol, NADP)
L-threonine transport via proton symport
5,10-methylenetetrahydrofolatereductase (NADPH)
purine-nucleoside phosphorylase (Deoxyguanosine)
acetyl-CoA acyltransferase (tetracosanoyl-CoA), peroxisomal
2-Oxo-4-methyl-3-carboxypentanoate decarboxylation
methylenetetrahydrofolate dehydrogenase (NADP)
4-Aminobenzoate mitochondrial transport via diffusion
S-adenosyl-L-methionine transport in via proton symport
acyl carrier protein synthase, mitochondrial
aldehyde dehydrogenase (2-phenylethanol, NAD)
diphosphoinositol-1,3,4,6-tetrakisphosphate diphosphohydrolase
4-aminobutyrate transport in via proton symport
isobutyl alcohol transport (extracellular)
YBR026C, YER061C, YHR067W, YKL055C, YKL192C, YOR221C
hypoxanthine transport via proton symport
orntithine transport in via proton symport
Dihydroneopterin monophosphate dephosphorylase
ribonucleoside-triphosphate reductase (UTP)
UDPglucose--hexose-1-phosphate uridylyltransferase
acetyl-CoA acyltransferase (tetradecanoyl-CoA), peroxisomal
fatty-acid--CoA ligase (dodecanoate), peroxisomal
aldehyde dehydrogenase (acetaldehyde, NADP)
alpha,alpha-trehalose-phosphate synthase (UDP-forming)
L-4-hydroxyglutamate semialdehyde dehydrogenase, mitochondrial
4-amino-5-hydroxymethyl-2-methylpyrimidine synthetase
saccharopine dehydrogenase (NAD, L-lysine forming)
adenosylmethionine-8-amino-7-oxononanoate transaminase
protoporphyrinogen oxidase, mitochondrial
glycero-3-phospho-1-inositol transport (extracellular to cytosol)
L-1-Pyrroline-3-hydroxy-5-carboxylate spontaneous conversion to L-4-Hydroxyglutamate semialdehyde, mitochondrial
ribonucleoside-triphosphate reductase (CTP)
inositol-1,4,5-triphosphate 6-kinase, nucleus
fatty-acid--CoA ligase (n-C26:0), peroxisomal
succinate-semialdehyde dehydrogenase (NADP)
L-2-amino-3-oxobutanoate decarboxylation (spontaneous)
hydrogen peroxide reductase (thioredoxin)
YAL044C, YBR221C, YDR019C, YER178W, YMR189W
nucleoside-diphosphate kinase (ATP:dGDP)
L-1-pyrroline-3-hydroxy-5-carboxylate dehydrogenase
glycine-cleavage system (lipoamide), mitochondrial
L-hydroxyproline dehydrogenase (NADP), mitochondrial
D-sorbitol transport via passive diffusion
fatty-acyl-ACP synthase (n-C18:1ACP), mitochondrial
deoxyhypusine synthase, cytosolic/mitochondrial
3-hydroxyacyl-CoA dehydrogenase (3-oxohexadecanoyl-CoA), peroxisomal
nucleoside-diphosphate kinase (ATP:dTDP)
Octadecenoate (n-C18:1) transport in via uniport
O-succinylhomoserine lyase (elimination)
inositol-1,4,5,6- tetrakisphosphate 3-kinase, nucleus
Aminoacetone:oxygen oxidoreductase(deaminating)(flavin-containing)
thiazole phosphate synthesis (xylulose 5-phosphate), yeast-specific
5-formethyltetrahydrofolate cyclo-ligase
Oleoyl-CoA desaturase (n-C18:1CoA -> n-C18:2CoA)
aldehyde dehydrogenase (isobutyl alcohol, NAD)
fatty acid oxidation (tetradecansoyl-CoA), peroxisomal
5-methylthioribose-1-phosphate isomerase
xylitol dehydrogenase (D-xyulose-forming)
purine-nucleoside phosphorylase (Inosine)
L-aspartate transport via proton symport
(R)-Lactate:ferricytochrome-c 2-oxidoreductase
diphosphoinositol-1,3,4,6-tetrakisphosphate synthase
3-methyl-2-oxobutanoate hydroxymethyltransferase
pantetheine-phosphate adenylyltransferase
phosphoribosylaminoimidazolecarboxamide formyltransferase
ethanolamine transport via diffusion (extracellular)
deoxyadenosine transport in via proton symport
nicotinate-nucleotide diphosphorylase (carboxylating)
UDP-glucose:ergosterol glucosyltransferase
1-alpha-D-Galactosyl-myo-inositol galactohydrolase
Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)
Dihydroneopterin triphosphate pyrophosphatase
Squalene epoxidase, endoplasmic reticular (NADP)
2-Methylbutanal transport (extracellular)
acetyl-CoA acyltransferase (hexadecanoyl-CoA), peroxisomal
urea transport via proton symport (2 H+)
trans-pentaprenyltranstransferase, mitochondrial
Phenethyl acetate transport (extracellular)
cytosine transport in via proton symport
inositol-1,4,5-trisphosphate 3-kinase, nucleus
glutamine phosphoribosyldiphosphate amidotransferase
fatty-acid--CoA ligase (octanoate), peroxisomal
acyl-CoA oxidase (dodecanoyl-CoA), peroxisomal
phosphoribosylglycinamide formyltransferase
3-phosphoshikimate 1-carboxyvinyltransferase
D-Fructose 1-phosphate D-glyceraldehyde-3-phosphate-lyase
nucleoside-diphosphate kinase (ATP:dUDP)
5-Aminolevulinate transport in via proton symport
3-hydroxyacyl-CoA dehydratase (3-hydroxyhexadecanoyl-CoA), peroxisomal
L-sorbitol transport via passive diffusion
phosphoribosylformylglycinamidine synthase
glyceraldehyde-3-phosphate dehydrogenase
3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA), peroxisomal
Octadecynoate (n-C18:2) transport in via uniport
sphingolipid long chain base kinase (sphinganine)
L-aminoadipate-semialdehyde dehydrogenase (NADPH)
L-asparagine transport via proton symport
Glycolipid 1,3-alpha-D-mannosyltransferase, Golgi apparatus
hypoxanthine phosphoribosyltransferase (Hypoxanthine)
YGL205W, YIL160C, YKR009C, YNL202W, YOR180C
thiazole phosphate synthesis (ribose 5-phosphate), yeast-specifc
aldehyde dehydrogenase (phenylacetaldehyde, NAD)
L-hydroxyproline dehydrogenase (NAD), mitochondrial
fatty acid oxidation (octanoyl-CoA), peroxisomal
N4-Acetylaminobutanal:NAD+ oxidoreductase
ribonucleoside-triphosphate reductase (ATP)
purine-nucleoside phosphorylase (Deoxyinosine)
aldehyde dehydrogenase (2-phenylethanol, NADP)
spermidine transport in via proton antiport
Indoleacetaldehyde transport (extracellular)
phosphoribosylaminoimidazole carboxylase
fatty-acyl-ACP synthase (n-C16:1ACP), mitochondrial
guanosine transport in via proton symport
2-methyl-1-butanol transport (extracellular)
fatty-acyl-ACP synthase (n-C16:0ACP), mitochondrial
C-3 sterol keto reductase (4-methylzymosterol)
fatty-acyl-ACP synthase (n-C14:0ACP), mitochondrial
N-acetylglucosamine-6-phosphate synthase
Homogentisate:oxygen 1,2-oxidoreductase (decyclizing)
L-Tryptophan:oxygen 2,3-oxidoreductase (decyclizing)
C-4 sterol methyl oxidase (4,4-dimethylzymosterol)
deoxycytidine transport in via proton symport
fatty-acyl-ACP synthase (n-C18:2ACP), mitochondrial
carbamoyl-phosphate synthase (glutamine-hydrolysing)
S-adenosyl-methionine delta-24-sterol-c-methyltransferase
Thiamine transport in via proton symport
aldehyde dehydrogenase (isobutyl alcohol, NADP)
acyl-CpA oxidase (tetradecanoyl-CoA), peroxisomal
formate dehydrogenase, cytosolic/mitochondrial
L-phenylalanine transport via proton symport
Hydroxybenzoate octaprenyltransferase, mitochondrial
Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase
purine-nucleoside phosphorylase (Adenosine)
nucleoside-diphosphate kinase (ATP:dCDP)
3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA), peroxisomal
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
3-hydroxyacyl-CoA dehydratase (3-hydroxyhexacosyl-CoA), peroxisomal
ammonia transport (efflux, cytosol to extracellular)
D-mannose transport in via proton symport