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value: 0.11
type: LocalParameter

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value: 365.806
type: LocalParameter

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value: 97.264
type: LocalParameter

773290
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value: 0.06
type: LocalParameter

772879
units: metaid_0000084
value: 6.0
type: LocalParameter

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species: metaid_0000017
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774107
units: dimensionless
value: 6.9E-5
type: LocalParameter

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value: 0.21
type: LocalParameter

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kind: SECOND
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species: metaid_0000042
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773422
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value: 0.003
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type: LocalParameter

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units: dimensionless
value: 1.9
type: LocalParameter

772807
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value: 0.314
type: LocalParameter

773710
units: metaid_0000072
value: 0.53
type: LocalParameter

metaid_0000030
is homolog to: REACT 1602
reversible: true
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is: R01070
type: Reaction
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kinetic law: 773084
name: Aldolase
product: 773071
reactant: 773058

773578
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value: 0.04
type: LocalParameter

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value: 5.12
type: Parameter

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value: 1.1918
type: LocalParameter

metaid_0000071
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metaid_0000090
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value: 0.045
name: TPI eq constant
type: Parameter

774143
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type: LocalParameter

metaid_0000031
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type: Reaction
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reactant: 773182
product: 773194
name: Glyceraldehyde 3-phosphate dehydrogenase

773254
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value: 0.17
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value: 810.0
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value: 0.23
type: LocalParameter

metaid_0000051
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units: metaid_0000072
value: 0.1
type: Parameter

metaid_0000070
unit: 772471
name: millimole
type: SBMLUnitsDef

772471
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772966
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species: metaid_0000042
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BIOMD0000000064
species: metaid_0000076
species: metaid_0000079
species: metaid_0000024
reaction: metaid_0000037
name: Teusink2000_Glycolysis
type: SBMLModel
parameter: metaid_0000064
reaction: metaid_0000036
function def: metaid_0000180
rule: metaid_0000082
compartment: metaid_0000003
units def: metaid_0000070
species: metaid_0000061
volume units: metaid_0000323
reaction: metaid_0000041
units def: metaid_0000072
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notes: Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Teusink,B et al.: Eur J Biochem 2000 Sep;267(17):5313-29. The model reproduces the steady-state fluxes and metabolite concentrations of the branched model as given in Table 4 of the paper. It is derived from the model on JWS online, but has the ATP consumption in the succinate branch with the same stoichiometrie as in the publication. The model was successfully tested on copasi v.4.4(build 26). For Vmax values, please note that there is a conversion factor of approx. 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol). The equilibrium constant for the ADH reaction in the paper is given for the reverse reaction (Keq = 1.45*10 4 ). The value used in this model is for the forward reaction: 1/Keq = 6.9*10 -5 . Vmax parameters values used (in [mM/min] except VmGLT): VmGLT 97.264 mmol/min VmGLK 226.45 VmPGI 339.667 VmPFK 182.903 VmALD 322.258 VmGAPDH_f 1184.52 VmGAPDH_r 6549.68 VmPGK 1306.45 VmPGM 2525.81 VmENO 365.806 VmPYK 1088.71 VmPDC 174.194 VmG3PDH 70.15 The result of the G6P steady state concentration (marked in red) differs slightly from the one given in table 4. of the publication Results for steady state: orig. article this model Fluxes[mM/min] Glucose 88 88 Ethanol 129 129 Glycogen 6 6 Trehalose 4.8 4.8 (G6P flux through trehalose branch) Glycerol 18.2 18.2 Succinate 3.6 3.6 Conc.[mM] G6P 1.07 1.03 F6P 0.11 0.11 F1,6P 0.6 0.6 DHAP 0.74 0.74 3PGA 0.36 0.36 2PGA 0.04 0.04 PEP 0.07 0.07 PYR 8.52 8.52 AcAld 0.17 0.17 ATP 2.51 2.51 ADP 1.29 1.29 AMP 0.3 0.3 NAD 1.55 1.55 NADH 0.04 0.04 Authors of the publication also mentioned a few misprints in the original article: in the kinetic law for ADH : the species a should denote NAD and b Ethanol the last term in the equation should read bpq /( K ib K iq K p ) in the kinetic law for PFK : R = 1 + λ 1 + λ 2 + g r λ 1 λ 2 equation L should read: L = L0*(..) 2 *(..) 2 *(..) …
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units def: metaid_0000084
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name: R_PFK
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value: 3200.0
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value: 0.5
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metaid_0000058
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value: 0.0845
type: Parameter

metaid_0000029
is homolog to: REACT 736
kinetic law: 773032
product: 772979
modifier: 772992
reactant: 772953
modifier: 773005
reactant: 772966
name: Phosphofructokinase
reversible: false
type: Reaction
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fast: false
is: R00756
is: http://identifiers.org/ec-code/2.7.1.11

774204
stoichiometry: 1.0
species: metaid_0000017
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metaid_0000042
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has part: C00002
has part: CHEBI:16761
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initial amount: NaN
name: High energy phosphates
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initial concentration: 6.31

metaid_0000019
is: C01083
is: CHEBI:27082
in compartment: metaid_0000075
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initial concentration: 0.0
name: Trehalose
boundary condition: true
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773590
units: dimensionless
value: 6.7
type: LocalParameter

metaid_0000003
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constant: true
size: 1.0
spatial dimensions: 3.0
type: Compartment

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species: metaid_0000010
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772903
stoichiometry: 1.0
species: metaid_0000042
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metaid_0000028
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product: 772915
reactant: 772903
reactant: 772891
is version of: GO:0005992
fast: false
reversible: false
name: Trehalose 6-phosphate synthase
type: Reaction

metaid_0000059
constant: true
units: metaid_0000072
value: 0.0995
type: Parameter

773855
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species: metaid_0000016
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773939
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species: metaid_0000004
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774155
units: metaid_0000072
value: 1.11
type: LocalParameter

773194
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000018
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name: Glycogen
boundary condition: true
is: CHEBI:28087
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is: C00182
initial amount: NaN
constant: false
type: Species

773266
units: metaid_0000084
value: 6549.8
type: LocalParameter

773891
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

773326
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

metaid_0000054
constant: true
units: metaid_0000072
value: 0.71
type: Parameter

metaid_0000056
constant: true
units: dimensionless
value: 100.0
type: Parameter

metaid_0000040
product: 774216
reactant: 774191
is version of: http://identifiers.org/ec-code/1.1.1.8
product: 774228
kinetic law: 774240
reactant: 774204
type: Reaction
fast: false
reversible: false
name: Glycerol 3-phosphate dehydrogenase

metaid_0000017
name: NADH
initial concentration: 0.39
has only substance units: false
in compartment: metaid_0000075
is: C00004
is: CHEBI:16908
initial amount: NaN
type: Species
boundary condition: false
constant: false

metaid_0000080
constant: true
units: dimensionless
value: 0.45
name: AK eq constant
type: Parameter

metaid_0000016
in compartment: metaid_0000075
initial concentration: 1.2
type: Species
name: NAD
has only substance units: false
is: CHEBI:15846
constant: false
initial amount: NaN
boundary condition: false
is: C00003

772495
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scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

773434
units: metaid_0000072
value: 0.2
type: LocalParameter

773927
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

metaid_0000041
kinetic law: 774348
modifier: 774336
reactant: 774324
is version of: GO:0016887
is version of: http://identifiers.org/ec-code/3.6.1.3
fast: false
reversible: true
name: ATPase activity
type: Reaction

774167
units: metaid_0000072
value: 1.1
type: LocalParameter

metaid_0000055
constant: true
units: dimensionless
value: 0.66
type: Parameter

773867
stoichiometry: 4.0
species: metaid_0000042
type: SpeciesReference

773278
units: metaid_0000072
value: 0.0098
type: LocalParameter

metaid_0000057
constant: true
units: metaid_0000072
value: 0.65
type: Parameter

773158
units: metaid_0000072
value: 10.0
type: LocalParameter

774252
units: metaid_0000084
value: 70.15
type: LocalParameter

772621
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000035
fast: false
kinetic law: 773674
product: 773626
type: Reaction
product: 773638
is: R00200
is homolog to: REACT 1911
is: http://identifiers.org/ec-code/2.7.1.40
reversible: true
reactant: 773614
modifier: 773650
name: Pyruvate kinase
modifier: 773662

772891
stoichiometry: 2.0
species: metaid_0000005
type: SpeciesReference

metaid_0000077
name: ADP concentration
in compartment: metaid_0000075
initial concentration: NaN
is: C00008
initial amount: NaN
boundary condition: false
is: CHEBI:16761
has only substance units: false
type: Species
constant: false

773831
units: metaid_0000072
value: 4.33
type: LocalParameter

metaid_0000006
type: Species
in compartment: metaid_0000075
constant: false
is: C05345
boundary condition: false
name: Fructose 6 Phosphate
is: CHEBI:15946
has only substance units: false
initial concentration: 0.62
initial amount: NaN

773386
units: metaid_0000072
value: 0.53
type: LocalParameter

772843
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

773170
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

773506
units: dimensionless
value: 0.19
type: LocalParameter

773458
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000025
reversible: true
modifier: 772647
kinetic law: 772659
modifier: 772634
reactant: 772609
fast: false
is: R00299
reactant: 772596
type: Reaction
product: 772621
name: Hexokinase
is: http://identifiers.org/ec-code/2.7.1.2
is homolog to: REACT 1318

773110
units: metaid_0000072
value: 0.3
type: LocalParameter

773482
units: metaid_0000084
value: 2525.81
type: LocalParameter

773746
units: metaid_0000072
value: 1.5
type: LocalParameter

773698
units: metaid_0000072
value: 0.14
type: LocalParameter

metaid_0000007
name: Fructose-1,6 bisphosphate
initial concentration: 5.51
is: C00354
has only substance units: false
is: CHEBI:16905
in compartment: metaid_0000075
boundary condition: false
initial amount: NaN
type: Species
constant: false

metaid_0000076
in compartment: metaid_0000075
initial amount: NaN
name: ATP concentration
initial concentration: NaN
has only substance units: false
is: C00002
type: Species
is: CHEBI:15422
boundary condition: false
constant: false

metaid_0000034
kinetic law: 773554
type: Reaction
product: 773542
is: R00658
name: Enolase
reactant: 773530
reversible: true
is homolog to: REACT 1400
is: http://identifiers.org/ec-code/4.2.1.11
fast: false

772707
units: dimensionless
value: 3800.0
type: LocalParameter

773071
stoichiometry: 2.0
species: metaid_0000008
type: SpeciesReference

metaid_0000086
unit: 772583
unit: 772570
name: mmolepermin
type: SBMLUnitsDef

774264
units: metaid_0000072
value: 0.4
type: LocalParameter

metaid_0000024
initial amount: NaN
initial concentration: 0.15
boundary condition: true
is: CHEBI:17754
type: Species
name: Glycerol
is: C00116
has only substance units: false
constant: false
in compartment: metaid_0000075

773302
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

774324
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

metaid_0000014
is: C00084
type: Species
constant: false
has only substance units: false
initial amount: NaN
is: CHEBI:15343
in compartment: metaid_0000075
initial concentration: 0.17
name: Acetaldehyde
boundary condition: false

773058
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

773843
stoichiometry: 2.0
species: metaid_0000014
type: SpeciesReference

773374
units: metaid_0000084
value: 1306.45
type: LocalParameter

metaid_0000033
name: Phosphoglycerate mutase
is: R01518
is homolog to: REACT 576
type: Reaction
reactant: 773446
fast: false
product: 773458
is: http://identifiers.org/ec-code/5.4.2.1
reversible: true
kinetic law: 773470

772831
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

773182
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000079
has part: C00020
type: Species
initial concentration: 4.1
boundary condition: false
initial amount: NaN
has part: CHEBI:16027
name: sum of AXP conc
has only substance units: false
has part: CHEBI:16761
has part: CHEBI:15422
constant: true
in compartment: metaid_0000075
has part: C00002
has part: C00008

773518
units: metaid_0000072
value: 0.08
type: LocalParameter

772531
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

774011
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

774179
units: metaid_0000072
value: 90.0
type: LocalParameter

metaid_0000065
constant: true
units: dimensionless
value: 3.0
type: Parameter

774360
units: metaid_0000085
value: 33.7
type: LocalParameter

774191
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000027
name: Glycogen synthesis
is homolog to: REACT 1736
fast: false
kinetic law: 772867
reversible: false
product: 772855
type: Reaction
reactant: 772831
is version of: GO:0005978
reactant: 772843

metaid_0000085
unit: 772557
name: permin
type: SBMLUnitsDef

metaid_0000004
is: C00293
boundary condition: false
has only substance units: false
name: Glucose in Cytosol
constant: false
initial concentration: 0.087
is: CHEBI:17234
in compartment: metaid_0000075
type: Species
initial amount: NaN

metaid_0000013
is: CHEBI:15361
in compartment: metaid_0000075
type: Species
has only substance units: false
name: Pyruvate
initial concentration: 1.85
constant: false
initial amount: NaN
is: C00022
boundary condition: false

773122
units: dimensionless
value: 0.069
type: LocalParameter

metaid_0000078
initial amount: NaN
in compartment: metaid_0000075
initial concentration: NaN
is: CHEBI:16027
has only substance units: false
name: AMP concentration
type: Species
constant: false
is: C00020
boundary condition: false

metaid_0000032
is homolog to: REACT 1771
name: Phosphoglycerate kinase
modifier: 773350
modifier: 773338
kinetic law: 773362
reactant: 773302
is: R01512
product: 773326
type: Reaction
product: 773314
reversible: true
is: http://identifiers.org/ec-code/2.7.2.3
fast: false

773782
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

773097
units: metaid_0000084
value: 322.258
type: LocalParameter

773758
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000064
constant: true
units: metaid_0000072
value: 0.111
type: Parameter

773494
units: metaid_0000072
value: 1.2
type: LocalParameter

772719
units: metaid_0000072
value: 30.0
type: LocalParameter

773314
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000026
type: Reaction
reversible: true
kinetic law: 772769
is: http://identifiers.org/ec-code/5.3.1.9
name: Glucose-6-phosphate isomerase
is homolog to: REACT 116
reactant: 772743
is: R00771
product: 772756
fast: false

773530
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000012
constant: false
boundary condition: false
name: Phosphoenolpyruvate
is: C00074
initial amount: NaN
has only substance units: false
initial concentration: 0.07
type: Species
in compartment: metaid_0000075
is: CHEBI:18021

metaid_0000084
unit: 772544
unit: 772531
unit: 772519
name: mMpermin
type: SBMLUnitsDef

774276
units: metaid_0000072
value: 0.023
type: LocalParameter

metaid_0000005
in compartment: metaid_0000075
initial concentration: 2.45
boundary condition: false
is: C00668
name: Glucose 6 Phosphate
type: Species
is: CHEBI:17665
initial amount: NaN
has only substance units: false
constant: false

772695
units: metaid_0000072
value: 0.15
type: LocalParameter

772940
units: metaid_0000084
value: 2.4
type: LocalParameter

773134
units: metaid_0000072
value: 2.0
type: LocalParameter

metaid_0000063
constant: true
units: dimensionless
value: 0.397
type: Parameter

772557
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

774023
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

774083
units: metaid_0000072
value: 0.92
type: LocalParameter

metaid_0000039
product: 774035
product: 774047
is version of: R00746
kinetic law: 774059
fast: false
name: Alcohol dehydrogenase
reactant: 774011
is homolog to: REACT 799
is version of: http://identifiers.org/ec-code/1.1.1.2
reactant: 774023
reversible: true
type: Reaction

772915
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

metaid_0000011
is: C00631
type: Species
constant: false
initial concentration: 0.12
has only substance units: false
in compartment: metaid_0000075
initial amount: NaN
name: 2-phosphoglycerate
boundary condition: false
is: CHEBI:17835

metaid_0000021
is: CHEBI:30031
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000075
name: Succinate
type: Species

773806
units: metaid_0000084
value: 174.194
type: LocalParameter

774288
units: dimensionless
value: 4300.0
type: LocalParameter

773987
units: metaid_0000072
value: 1.0
type: LocalParameter

metaid_0000072
unit: 772507
unit: 772495
name: mM
type: SBMLUnitsDef

772683
units: metaid_0000072
value: 0.08
type: LocalParameter

772953
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

metaid_0000038
kinetic law: 773951
product: 773939
reactant: 773927
is homolog to: REACT 2092
is version of: GO:0046323
fast: false
reversible: true
name: Glucose transport
type: Reaction

774216
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

772756
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

metaid_0000062
constant: true
units: metaid_0000072
value: 6.82E-4
type: Parameter

774300
units: metaid_0000072
value: 1.0
type: LocalParameter

772544
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

773722
units: dimensionless
value: 6500.0
type: LocalParameter

773770
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000010
boundary condition: false
type: Species
constant: false
is: C00197
has only substance units: false
initial concentration: 0.9
initial amount: NaN
is: CHEBI:17794
in compartment: metaid_0000075
name: 3-phosphoglycerate

metaid_0000020
initial concentration: 1.0
is: C00011
name: CO2
boundary condition: true
in compartment: metaid_0000075
initial amount: NaN
type: Species
constant: false
is: CHEBI:16526
has only substance units: false

772782
units: metaid_0000084
value: 339.677
type: LocalParameter

772743
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

773146
units: metaid_0000072
value: 2.4
type: LocalParameter

metaid_0000008
constant: false
in compartment: metaid_0000075
initial concentration: 0.96
has part: CHEBI:29052
has part: C00118
boundary condition: false
has part: CHEBI:16108
has part: C00111
initial amount: NaN
name: Triose-phosphate
has only substance units: false
type: Species

772979
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000061
in compartment: metaid_0000075
boundary condition: false
name: F2,6P
has only substance units: false
type: Species
initial amount: NaN
is: CHEBI:28602
is: C00665
constant: true
initial concentration: 0.02

metaid_0000075
is: GO:0005829
constant: true
size: 1.0
spatial dimensions: 3.0
type: Compartment

metaid_0000037
reversible: false
reactant: 773867
product: 773879
product: 773891
type: Reaction
reactant: 773843
kinetic law: 773903
name: Succinate synthesis
is version of: GO:0006105
reactant: 773855
fast: false

772855
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

773398
units: metaid_0000072
value: 0.3
type: LocalParameter

773230
units: metaid_0000084
value: 1184.52
type: LocalParameter

774035
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

774095
units: metaid_0000072
value: 17.0
type: LocalParameter

metaid_0000023
initial concentration: 50.0
boundary condition: true
type: Species
name: Ethanol
is: C00469
constant: false
is: CHEBI:16236
in compartment: metaid_0000075
has only substance units: false
initial amount: NaN

774312
units: metaid_0000072
value: 0.93
type: LocalParameter

773045
units: metaid_0000084
value: 182.903
type: LocalParameter

773206
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000060
constant: true
units: dimensionless
value: 0.0174
type: Parameter

metaid_0000009
is: CHEBI:16001
initial amount: NaN
in compartment: metaid_0000075
has only substance units: false
name: 1,3-bisphosphoglycerate
type: Species
is: C00236
constant: false
initial concentration: 0.0
boundary condition: false

772671
units: metaid_0000084
value: 226.452
type: LocalParameter

773999
units: metaid_0000072
value: 1.1918
type: LocalParameter

774228
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000036
name: Pyruvate decarboxylase
reversible: false
type: Reaction
product: 773770
fast: false
is: http://identifiers.org/ec-code/4.1.1.1
is: R00224
product: 773782
reactant: 773758
kinetic law: 773794

772794
units: metaid_0000072
value: 1.4
type: LocalParameter

773686
units: metaid_0000084
value: 1088.71
type: LocalParameter

773734
units: metaid_0000072
value: 21.0
type: LocalParameter

metaid_0000022
has only substance units: false
name: Extracellular Glucose
initial amount: NaN
boundary condition: true
type: Species
is: C00293
constant: false
initial concentration: 50.0
in compartment: metaid_0000003
is: CHEBI:17234

given: Lukas
family: Endler

orgname: EMBL-EBI

W3 CDTF: Tue Sep 16 15:00:06 BST 2008

given: Harish
family: Dharuri

W3 CDTF: Thu Jul 19 19:26:07 BST 2012

ORG:
  orgname: California Institute of Technology

orgname: Stellenbosh University

given: Jacky L
family: Snoep