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type: SBMLModel
species: metaid F16bP
notes: A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures AM Martins, D Camacho, J Shuman, W Sha, P Mendes, V Shulaev, Current Genomics 2004 5:649-663 This is a model of yeast glycolysis and glycerol synthesis for high medium glucose concentration. It was constructed by joining the glycolysis model of Teusink et al. (2000) Eur J Biochem 267, 5313, modified by Pritchard and Kell (2002) Eur. J. Biochem. 269, 3894, with the glycerol synthesis model of Crownright et al. (2002) Appl. Env. Microbiol. 68, 4448. Glycerol transport was added as a first order reaction with parameters that comply with empirical data on internal/external glycerol ratios. Curation notes The model provided by the authors is available from http://www.mcisb.org/resources/models/martins04_original.xml . It contains one error: the kinetic law of glycerol 3-phosphate dehydrogenase has denominator of the form (1+NADH/Kdhap+NAD/Kg3p)*(1+DHAP/Knadh+G3P/Knad) rather than (1+DHAP/Kdhap+G3P/Kg3p)*(1+NADH/Knadh+NAD/Knad). This has now been corrected; steady states of the original model may be resolved by exchanging the order of substrates and products in COPASI . Some other cosmetic changes (e.g minutes to seconds) have also been carried out. 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, …
is described by: http://identifiers.org/doi/10.2174/1389202043348643
units def: 151876
function def: 151754
species: metaid P3G
name: reversible michaelis-menten: ordered bi-bi
reaction: metaid ATPase
reaction: metaid HXT
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function def: 151802
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species: metaid EtOH
function def: 151778
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species: metaid succinate
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function def: 151827
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reaction: metaid HXK
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time units: 033055
name: irreversible michaelis-menten: one noncompeting couple
reaction: metaid GPP
reaction: metaid PGM
name: Martins2004_Yeast_Glycolysis_GlycerolSynthesis
function def: 151814
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reaction: metaid ADH
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metaid GLY
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metaid EtOH
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metaid succinate
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metaid PGK
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reactant: 153094
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metaid BPG
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153094
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153130
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153214
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153202
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153190
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153178
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153166
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153154
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153118
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metaid HXK
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152238
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152310
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152298
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152262
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metaid PDC
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kinetic law: 153612
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153648
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153636
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153624
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value: 14.2966666666667

153588
type: SpeciesReference
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metaid AcAld
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name: acetaldehyde
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metaid PYR
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name: pyruvate
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153600
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species: metaid CO2

metaid CO2
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initial concentration: 1.0

metaid GPP
type: Reaction
reversible: false
kinetic law: 154482
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reactant: 154446
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fast: false
product: 154470

154530
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value: 1.0

154518
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154506
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value: 3.5

154494
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value: 1.73333333333333

154458
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metaid iP
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metaid PGM
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name: phosphoglyceromutase
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153251
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metaid P2G
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153323
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value: 1.0

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value: 0.19

153287
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value: 1.2

153275
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value: 43.0833333333333

153238
type: SpeciesReference
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species: metaid P3G

metaid succinate branch
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product: 154398
name: succinate branch
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reactant: 154386
kinetic law: 154422
fast: false
reversible: false
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154398
type: SpeciesReference
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species: metaid NADH

metaid NADH
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154386
type: SpeciesReference
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species: metaid NAD

metaid NAD
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154434
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154373
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metaid GPD
type: Reaction
is: SBO:0000176
product: 154047
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is: http://identifiers.org/ec-code/1.1.1.94
name: glycerol 3-phosphate dehydrogenase
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reactant: 154011
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154155
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154179
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value: 0.023

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154143
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species: metaid NADH

154035
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species: metaid G3P

154011
type: SpeciesReference
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species: metaid DHAP

metaid DHAP
type: Species
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initial concentration: 2.5253634682754
name: dihydroxyacetone phosphate
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boundary condition: false
has only substance units: false

metaid ADH
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reactant: 153685
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is version of: http://identifiers.org/ec-code/1.1.1.1
reversible: true
reactant: 153673
is: R00754
name: alcohol dehydrogenase
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product: 153697
product: 153709
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153685
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species: metaid NAD

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value: 1.1

153782
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153770
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value: 14492.7536231884

153806
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value: 0.031

153842
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value: 90.0

153733
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value: 111.334973497906

153794
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value: 0.11

153745
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value: 17.0

153758
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value: 0.92

153854
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value: 1.0

153818
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152008
type: SBMLUnitsDef
unit: 152045
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name: per mM squared per second

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152020
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metaid GAP
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initial amount: NaN
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initial concentration: 0.11363434103666
has only substance units: false
name: glyceraldehyde 3-phosphate
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in compartment: metaid cell
is: CHEBI:29052

metaid PEP
type: Species
is: SBO:0000247
is: CHEBI:18021
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initial concentration: 0.07545658303681
has only substance units: false
boundary condition: false
name: phosphoenolpyruvate
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initial amount: NaN

metaid PYK
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is version of: GO:0004743
reactant: 153431
is: R00200
name: pyruvate kinase
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product: 153467
product: 153455
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reversible: true

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153455
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value: 1.0

153552
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value: 1.5

153540
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value: 21.0

153528
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value: 6500.0

153516
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value: 0.53

153504
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value: 0.14

153492
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value: 16.6666666666667

153443
type: SpeciesReference
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species: metaid PEP

metaid trehalose branch
type: Reaction
fast: false
product: 154323
kinetic law: 154348
product: 154335
is version of: GO:0005992
reactant: 154299
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name: trehalose branch
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value: 0.00270304936782

154335
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species: metaid trehalose

metaid trehalose
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name: trehalose
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boundary condition: true
initial amount: NaN
constant: true
is: CHEBI:16551
initial concentration: 0.0
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is: C01083

154299
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154311
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species: metaid G6P

151960
type: SBMLUnitsDef
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unit: 151984
unit: 151972
name: per mM per second

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kind: SECOND

151984
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kind: LITRE

151972
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multipler: 1.0
kind: MOLE

metaid glycogen branch
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reactant: 154227
kinetic law: 154275
product: 154251
product: 154263
fast: false
reversible: false
reactant: 154239
name: glycogen branch
is: SBO:0000176
is version of: GO:0005978

154227
type: SpeciesReference
stoichiometry: 1.0
species: metaid ATP

154287
type: LocalParameter
units: 151960
value: 0.01649685493243

154251
type: SpeciesReference
stoichiometry: 1.0
species: metaid ADP

154263
type: SpeciesReference
stoichiometry: 1.0
species: metaid glycogen

metaid glycogen
type: Species
constant: true
name: glycogen
is: SBO:0000247
initial amount: NaN
is: C00182
in compartment: metaid cell
has only substance units: false
boundary condition: true
initial concentration: 0.0
is: CHEBI:28087

154239
type: SpeciesReference
stoichiometry: 1.0
species: metaid G6P

metaid ENO
type: Reaction
kinetic law: 153359
reactant: 153335
name: enolase
is version of: GO:0004634
is version of: http://identifiers.org/ec-code/4.2.1.11
is: R00658
product: 153347
fast: false
reversible: true
is: SBO:0000176

153419
type: LocalParameter
units: dimensionless
value: 1.0

153407
type: LocalParameter
units: 151876
value: 0.5

153395
type: LocalParameter
units: dimensionless
value: 6.7

153383
type: LocalParameter
units: 151876
value: 0.04

153371
type: LocalParameter
units: 151912
value: 3.36

153335
type: SpeciesReference
stoichiometry: 1.0
species: metaid P2G

153347
type: SpeciesReference
stoichiometry: 1.0
species: metaid PEP

metaid PGI
type: Reaction
product: 152395
kinetic law: 152407
reversible: true
is: R00771
is: SBO:0000176
fast: false
reactant: 152383
is version of: GO:0004347
is version of: http://identifiers.org/ec-code/5.3.1.9
name: phosphoglucose isomerase

152395
type: SpeciesReference
stoichiometry: 1.0
species: metaid F6P

metaid F6P
type: Species
name: fructose 6-phosphate
initial amount: NaN
is: C05345
boundary condition: false
is: SBO:0000247
in compartment: metaid cell
is: CHEBI:16084
initial concentration: 0.78186379960245
has only substance units: false
constant: false

152468
type: LocalParameter
units: dimensionless
value: 1.0

152455
type: LocalParameter
units: 151876
value: 0.3

152443
type: LocalParameter
units: dimensionless
value: 0.29

152431
type: LocalParameter
units: 151876
value: 1.4

152419
type: LocalParameter
units: 151912
value: 17.6

152383
type: SpeciesReference
stoichiometry: 1.0
species: metaid G6P

metaid ALD
type: Reaction
kinetic law: 152782
reversible: true
fast: false
is version of: GO:0004332
is: R01068
reactant: 152746
product: 152770
is: SBO:0000176
product: 152758
name: fructosebisphosphate aldolase
is version of: http://identifiers.org/ec-code/4.1.2.13

152866
type: LocalParameter
units: dimensionless
value: 1.0

152854
type: LocalParameter
units: 151876
value: 10.0

152842
type: LocalParameter
units: 151876
value: 2.4

152830
type: LocalParameter
units: 151876
value: 2.0

152818
type: LocalParameter
units: 151876
value: 0.069

152806
type: LocalParameter
units: 151876
value: 0.3

152794
type: LocalParameter
units: 151912
value: 1.57816666666667

152746
type: SpeciesReference
stoichiometry: 1.0
species: metaid F16bP

152770
type: SpeciesReference
stoichiometry: 1.0
species: metaid GAP

152758
type: SpeciesReference
stoichiometry: 1.0
species: metaid DHAP

metaid TPI
type: Reaction
is version of: http://identifiers.org/ec-code/5.3.1.1
is: SBO:0000176
is: R01015
is version of: GO:0004807
name: triosephosphate isomerase
reactant: 152878
fast: false
product: 152890
kinetic law: 152902
reversible: true

152878
type: SpeciesReference
stoichiometry: 1.0
species: metaid DHAP

152890
type: SpeciesReference
stoichiometry: 1.0
species: metaid GAP

152938
type: LocalParameter
units: dimensionless
value: 1.0

152926
type: LocalParameter
units: dimensionless
value: 0.045

152914
type: LocalParameter
units: 152057
value: 7500.0

metaid glycerol efflux
type: Reaction
kinetic law: 154566
product: 154554
reactant: 154542
is version of: GO:0015793
is: SBO:0000185
fast: false
reversible: true
name: glycerol efflux

154578
type: LocalParameter
units: 152057
value: 0.0013294597699

154554
type: SpeciesReference
stoichiometry: 1.0
species: metaid GLYx

metaid GLYx
type: Species
constant: true
initial concentration: 0.084
is: SBO:0000247
initial amount: NaN
is: CHEBI:17754
boundary condition: true
name: glycerol
has only substance units: false
is: C00116
in compartment: metaid extracellular

154542
type: SpeciesReference
stoichiometry: 1.0
species: metaid GLY

metaid F26bP
type: Species
name: fructose 2,6-bisphosphate
has only substance units: false
is: SBO:0000247
boundary condition: true
in compartment: metaid cell
is: C00665
constant: true
initial amount: NaN
initial concentration: 0.02
is: CHEBI:28602

metaid AMP
type: Species
name: AMP
has only substance units: false
initial amount: NaN
is: SBO:0000247
constant: false
boundary condition: false
is: C00020
in compartment: metaid cell
is: CHEBI:16027
initial concentration: 0.21389019849713

152081
type: SBMLUnitsDef
unit: 152093
name: mmol

152093
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

W3 CDTF: Fri Feb 03 11:24:50 GMT 2012

ORG:
  orgname: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
n:
  given: Diogo
  family: Camacho

metaid TDH
type: Reaction
product: 152986
kinetic law: 152998
reactant: 152950
name: glyceraldehyde phosphate dehydrogenase
is: SBO:0000176
reactant: 152962
reversible: true
is version of: http://identifiers.org/ec-code/1.2.1.12
is: R01061
product: 152974
fast: false
is version of: GO:0004365

152986
type: SpeciesReference
stoichiometry: 1.0
species: metaid NADH

153082
type: LocalParameter
units: dimensionless
value: 0.00533412710225

153070
type: LocalParameter
units: dimensionless
value: 1.0

153058
type: LocalParameter
units: 151876
value: 0.06

153046
type: LocalParameter
units: 151876
value: 0.0098

153034
type: LocalParameter
units: 151876
value: 0.09

153022
type: LocalParameter
units: 151876
value: 0.21

153010
type: LocalParameter
units: 151912
value: 19.2

152950
type: SpeciesReference
stoichiometry: 1.0
species: metaid GAP

152962
type: SpeciesReference
stoichiometry: 1.0
species: metaid NAD

152974
type: SpeciesReference
stoichiometry: 1.0
species: metaid BPG

metaid PFK
type: Reaction
kinetic law: 152553
is: R00756
is version of: GO:0003872
is version of: http://identifiers.org/ec-code/2.7.1.11
fast: false
reactant: 152480
modifier: 152528
product: 152516
product: 152504
modifier: 152540
reactant: 152492
name: phosphofructokinase
is: SBO:0000176
reversible: false

152638
type: LocalParameter
units: 151876
value: 0.65

152589
type: LocalParameter
units: 151876
value: 0.1

152577
type: LocalParameter
units: dimensionless
value: 5.12

152698
type: LocalParameter
units: dimensionless
value: 0.397

152626
type: LocalParameter
units: dimensionless
value: 100.0

152686
type: LocalParameter
units: 151876
value: 6.82E-4

152565
type: LocalParameter
units: 151912
value: 1.83333333333333

152674
type: LocalParameter
units: dimensionless
value: 0.0174

152734
type: LocalParameter
units: dimensionless
value: 1.0

152601
type: LocalParameter
units: 151876
value: 0.71

152662
type: LocalParameter
units: 151876
value: 0.0995

152613
type: LocalParameter
units: dimensionless
value: 0.66

152722
type: LocalParameter
units: dimensionless
value: 3.0

152710
type: LocalParameter
units: 151876
value: 0.111

152650
type: LocalParameter
units: dimensionless
value: 0.0845

152480
type: SpeciesReference
stoichiometry: 1.0
species: metaid ATP

152516
type: SpeciesReference
stoichiometry: 1.0
species: metaid F16bP

152504
type: SpeciesReference
stoichiometry: 1.0
species: metaid ADP

152492
type: SpeciesReference
stoichiometry: 1.0
species: metaid F6P

metaid AK
type: Reaction
fast: false
is version of: http://identifiers.org/ec-code/2.7.4.3
reversible: true
is: R00127
is: SBO:0000176
reactant: 153926
product: 153938
product: 153950
name: adenylate kinase
is version of: GO:0004017
kinetic law: 153963

153926
type: SpeciesReference
stoichiometry: 2.0
species: metaid ADP

153938
type: SpeciesReference
stoichiometry: 1.0
species: metaid AMP

153950
type: SpeciesReference
stoichiometry: 1.0
species: metaid ATP

153999
type: LocalParameter
units: dimensionless
value: 1.0

153987
type: LocalParameter
units: dimensionless
value: 0.45

153975
type: LocalParameter
units: 151960
value: 0.75

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

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

ORG:
  orgname: University of Manchester
n:
  given: Pedro
  family: Mendes

W3 CDTF: Fri Feb 03 11:24:50 GMT 2012

ORG:
  orgname: University of Manchester
n:
  given: Pedro
  family: Mendes

W3 CDTF: Fri Sep 10 01:00:00 BST 2010

ORG:
  orgname: University of Manchester
n:
  given: Pedro
  family: Mendes

W3 CDTF: Fri Feb 03 11:24:50 GMT 2012

W3 CDTF: Fri Feb 03 11:24:50 GMT 2012

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