MODEL1008240001
type: SBMLModel
volume units: 290956
species: 471843
species: 471871
length unit: 821056
reaction: 471940
species: 471920
reaction: 471958
reaction: 472038
reaction: 471954
notes: This is an SBML version of the reaction network used in the article: Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks Tunahan Çakir, Betül Kirdar, Kutlu Ö. Ülgen. Biotechnol Bioeng 2004 86:251-60; PubmedID: 15083505 ; DOI: 10.1002/bit.20020 Abstract: Central carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast. Resultant elementary modes were used for gene deletion phenotype analysis and for the analysis of robustness of the central metabolism and network functionality. Control-effective fluxes, determined by calculating the efficiency of each mode, were used for the prediction of transcript ratios of metabolic genes in different growth media (glucose-ethanol and galactose-ethanol). A high correlation was obtained between the theoretical and experimental expression levels of 38 genes when ethanol and glucose media were considered. Such analysis was shown to be a bridge between transcriptomics and fluxomics. Control-effective flux distribution was found to be promising in in silico predictions by incorporating functionality and regulation into the metabolic network structure. Some typographical errors in the paper have been corrected: Reaction (49) has substrate NADcyt (rather than NADmit) Reaction (53) is missing products 90 NADPcyt CO2 and O2 are also set as external metabolites 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. For more information see the terms of use . 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, curate…
reaction: 472036
reaction: 471952
species: 471918
species: 471877
reaction: 471966
reaction: 472016
reaction: 471964
name: Çakir2004 - Central Carbon Metabolism of S.cerevisiae
species: 471845
reaction: 472020
compartment: metaid cell
species: 471849
reaction: 471938
curated: false
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reaction: 471978
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species: 471867
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substance units: 867736
reaction: 472034
reaction: 471950
is described by: http://identifiers.org/pubmed/15083505
reaction: 472032
reaction: 472030
reaction: 471962
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metaid cell
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471940
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YMR303C PROTEIN_ASSOCIATION:ADH2
fast: false
reversible: false
name: alcohol dehydrogenase

MODEL1008240001#
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value: Infinity

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value: 0.0

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value: -0.2889

472114
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value: 11.32

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472182
type: LocalParameter
value: 1.2

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type: LocalParameter
units: dimensionless
value: 0.0

472299
type: LocalParameter
value: 0.0

472107
type: LocalParameter
units: dimensionless
value: -Infinity

472159
type: LocalParameter
units: dimensionless
value: Infinity

472193
type: LocalParameter
units: dimensionless
value: 0.0

471857
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid cell
name: FADH2

472205
type: LocalParameter
units: dimensionless
value: Infinity

472343
type: LocalParameter
units: dimensionless
value: Infinity

471898
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid cell
name: P2G

472054
type: LocalParameter
units: dimensionless
value: 0.0

472272
type: LocalParameter
units: dimensionless
value: 0.0

472187
type: LocalParameter
units: dimensionless
value: 0.0

472101
type: LocalParameter
units: dimensionless
value: -Infinity

472219
type: LocalParameter
units: dimensionless
value: Infinity

472068
type: LocalParameter
units: dimensionless
value: 0.0

472047
type: LocalParameter
units: dimensionless
value: 0.0

472265
type: LocalParameter
units: dimensionless
value: 0.0

471877
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid cell
name: MAL

472094
type: LocalParameter
value: -0.6667

472333
type: LocalParameter
value: 0.0

472248
type: LocalParameter
units: dimensionless
value: 0.0

472209
type: LocalParameter
value: 0.1333

472224
type: LocalParameter
units: dimensionless
value: -Infinity

471924
type: Species
constant: false
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid cell
name: CO2

472058
type: LocalParameter
value: 0.0

472276
type: LocalParameter
units: dimensionless
value: 0.0

472126
type: LocalParameter
units: dimensionless
value: Infinity

472230
type: LocalParameter
value: 0.0

472244
type: LocalParameter
units: dimensionless
value: -Infinity

472119
type: LocalParameter
units: dimensionless
value: 0.0

472163
type: LocalParameter
value: 13.81

471839
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid cell
name: ACCOAcyt

472336
type: LocalParameter
units: dimensionless
value: Infinity

471958
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YGR254W OR YHR174W) PROTEIN_ASSOCIATION:(ENO1 OR ENO2)
fast: false
reversible: true
name: enolase

472038
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION: PROTEIN_ASSOCIATION:
fast: false
reversible: false
name: ATP maintenance flux

471954
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YCR012W PROTEIN_ASSOCIATION:PGK1
fast: false
reversible: true
name: 3-phosphogycerate kinase

472036
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION: PROTEIN_ASSOCIATION:
fast: false
reversible: false
name: electronic chain: reoxidation of FADH

471952
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YJL052W OR YJR009C OR YGR192C) PROTEIN_ASSOCIATION:(TDH1 OR TDH2 OR TDH3)
fast: false
reversible: true
name: glyceraldehyde-3-phosphate dehydrogenase

471966
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YIL053W OR YER062C) PROTEIN_ASSOCIATION:(GPP1 OR GPP2)
fast: false
reversible: false
name: glycerol phosphatase

472016
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YPL262W PROTEIN_ASSOCIATION:FUM1
fast: false
reversible: true
name: fumarate hydratase

471964
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YPL061W PROTEIN_ASSOCIATION:ALD6
fast: false
reversible: true
name: aldehyde dehydrogenase (NADPcyt- dependent)

472020
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YKL029C PROTEIN_ASSOCIATION:MAE1
fast: false
reversible: false
name: malic enzyme

471938
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YBR020W OR YMR105C OR YBR018C) PROTEIN_ASSOCIATION:(GAL1 OR GAL5 OR GAL7)
fast: false
reversible: false
name: galactokinase

472002
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YNL037C OR YOR136W) PROTEIN_ASSOCIATION:(IDH1 OR IDH2)
fast: false
reversible: false
name: isocitrate dehydrogenase (NADmit- dependent)

472000
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YLR304C PROTEIN_ASSOCIATION:ACO1
fast: false
reversible: true
name: aconitate synthetase

471980
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YKR097W PROTEIN_ASSOCIATION:PCK1
fast: false
reversible: false
name: phosphoenolpyruvate carboxykinase

472008
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YIL125W OR YDR148C) PROTEIN_ASSOCIATION:(KGD1 OR KGD2)
fast: false
reversible: false
name: alpha-ketogluterate dehydrogenase

471998
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YNR001C OR YPR001W) PROTEIN_ASSOCIATION:(CIT1 OR CIT3)
fast: false
reversible: false
name: citrate synthase (cytosolic)

472014
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YJR051W PROTEIN_ASSOCIATION:OSM1
fast: false
reversible: false
name: fumarate reductase

471994
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YLR354C PROTEIN_ASSOCIATION:TAL1
fast: false
reversible: true
name: transaldolase

471992
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YPR074C OR YBR117C) PROTEIN_ASSOCIATION:(TKL1 OR TKL2)
fast: false
reversible: true
name: transketolase

472026
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YCR005C PROTEIN_ASSOCIATION:CIT2
fast: false
reversible: false
name: citrate synthase (mitochondrial)

471978
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YGL062W OR YBR218C) PROTEIN_ASSOCIATION:(PYC1 OR PYC2)
fast: false
reversible: false
name: pyruvate carboxylase

472028
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YER065C PROTEIN_ASSOCIATION:ICL1
fast: false
reversible: false
name: isocitrate lyase

472034
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION: PROTEIN_ASSOCIATION:
fast: false
reversible: false
name: electronic chain: reoxidation of NADH

471950
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YDR050C PROTEIN_ASSOCIATION:TPI1
fast: false
reversible: true
name: triosephosphate isomerase

472032
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YOL126C PROTEIN_ASSOCIATION:MDH2
fast: false
reversible: true
name: malate dehydrogenase (cytoplasmic)

472030
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YNL117W PROTEIN_ASSOCIATION:MLS1
fast: false
reversible: false
name: malate synthase

471962
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YDL022W OR YOL059W) PROTEIN_ASSOCIATION:(GPD1 OR GPD2)
fast: false
reversible: false
name: glycerol-3-phosphate dehydrogenase

471960
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YAL038W OR YOR347C) PROTEIN_ASSOCIATION:(PYK1 OR PYK2)
fast: false
reversible: false
name: pyruvate kinase

472040
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION: PROTEIN_ASSOCIATION:
fast: false
reversible: false
name: biomass formation

471936
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YCL040W OR YFR053C OR YGL253W) PROTEIN_ASSOCIATION:(GLK1 OR HXK1 OR HXK2)
fast: false
reversible: false
name: glucokinase, hexokinase

471948
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YKL060C PROTEIN_ASSOCIATION:FBA1
fast: false
reversible: true
name: aldolase

471946
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YLR377C PROTEIN_ASSOCIATION:FBP1
fast: false
reversible: false
name: fructose 1,6-biphosphatase

471944
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YGR240C OR YMR205C) PROTEIN_ASSOCIATION:(PFK1 OR PFK2)
fast: false
reversible: false
name: phosphofructokinase

471942
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YBR196C PROTEIN_ASSOCIATION:PGI1
fast: false
reversible: true
name: glucose-6-phosphate isomerase

471956
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YKL152C OR YDL021W OR YOL056W) PROTEIN_ASSOCIATION:(GPM1 OR GPM2 OR GPM3)
fast: false
reversible: true
name: phosphoglycerate mutase

472006
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YLR174W PROTEIN_ASSOCIATION:IDP2
fast: false
reversible: false
name: isocitrate dehydrogenase (NADPcyt- dependent)

472004
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YDL066W PROTEIN_ASSOCIATION:IDP1
fast: false
reversible: false
name: isocitrate dehydrogenase (NADPmit- dependent)

472012
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YKL148C OR YLL041C OR YKL141W) PROTEIN_ASSOCIATION:(SDH1 OR SDH2 OR SDH3)
fast: false
reversible: false
name: succinate dehydrogenase

472010
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YOR142W OR YGR244C) PROTEIN_ASSOCIATION:(LSC1 OR LSC2)
fast: false
reversible: true
name: succinate-CoA ligase

471990
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YJL121C PROTEIN_ASSOCIATION:RPE1
fast: false
reversible: true
name: ribulose-phosphate 3-epimerase

471968
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YLR044C OR YDR081C OR YLR134W) PROTEIN_ASSOCIATION:(PDC1 OR PDC2 OR PDC5)
fast: false
reversible: false
name: pyruvate decarboxylase

472018
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YKL085W PROTEIN_ASSOCIATION:MDH1
fast: false
reversible: true
name: malate dehydrogenase (mitochondrial)

472024
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION: PROTEIN_ASSOCIATION:
fast: false
reversible: false
name: reoxidation of cytosolic NADH to mitochondrial NADH

472022
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YML042W PROTEIN_ASSOCIATION:CAT2
fast: false
reversible: false
name: carnitine O-acetyltransferase

471976
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YER178W OR YNL071W OR YBR221C) PROTEIN_ASSOCIATION:(PDA1 OR PDA2 OR PDB1)
fast: false
reversible: false
name: pyruvate dehydrogenase

471974
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YAL054C OR YLR153C) PROTEIN_ASSOCIATION:(ACS1 OR ACS2)
fast: false
reversible: false
name: acetyl-coenzyme A synthetase

471972
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YOR374W PROTEIN_ASSOCIATION:ALD4
fast: false
reversible: false
name: aldehyde dehydrogenase (NADPmit- dependent)

471970
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YOL086C OR YGL256W) PROTEIN_ASSOCIATION:(ADH1 OR ADH4)
fast: false
reversible: false
name: alcohol dehydrogenase

471988
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YOR095C PROTEIN_ASSOCIATION:RKI1
fast: false
reversible: true
name: ribose 5-phosphate isomerase

471986
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YHR183W OR YGR256W) PROTEIN_ASSOCIATION:(GND1 OR GND2)
fast: false
reversible: false
name: phosphogluconate dehydrogenase

471984
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YNR034W OR YCR073W-A OR YHR163W OR YGR248W) PROTEIN_ASSOCIATION:(SOL1 OR SOL2 OR SOL3 OR SOL4)
fast: false
reversible: false
name: 6-phosphogluconolactonase

471982
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:YNL241C PROTEIN_ASSOCIATION:ZWF1
fast: false
reversible: false
name: glucose-6-phosphate dehydrogenase

471996
type: Reaction
kinetic law: MODEL1008240001#
product: MODEL1008240001#
reactant: MODEL1008240001#
notes: GENE_ASSOCIATION:(YPR074C OR YBR117C) PROTEIN_ASSOCIATION:(TKL1 OR TKL2)
fast: false
reversible: true
name: transketolase

ORG:
  orgname: University of Manchester
n:
  given: Olusegun
  family: Oshota

ORG:
  orgname: University of Manchester
n:
  given: Kieran
  family: Smallbone

W3 CDTF: Thu Jun 13 12:09:14 BST 2013

W3 CDTF: Mon Aug 16 01:00:00 BST 2010