BIOMD0000000063
type: SBMLModel
parameter: 560641
occurs in: http://identifiers.org/taxonomy/4932
curated: true
is version of: GO:0006113
reaction: metaid_0000018
parameter: metaid_0100014
species: metaid_0000005
volume units: metaid_0000323
reaction: metaid_0000021
reaction: metaid_0000014
reaction: metaid_0000020
species: metaid_0000010
species: metaid_0000012
species: metaid_0000008
is homolog to: REACT 723
is: MODEL6624154196
species: metaid_0000004
rule: 560639
creator:
  ORG:
    orgname: Stellenbosh University
  n:
    given: Jacky L
    family: Snoep
reaction: metaid_0000019
length unit: length
is described by: 0141-0229(90)90033-M
units def: metaid_0000025
compartment: metaid_0000022
modified:
  W3 CDTF: Wed May 16 11:21:43 BST 2012
parameter: 560650
parameter: metaid_0200014
notes: This a model from the article: Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae Jorge L. Galazzo and James E. Bailey Enzyme and Microbial Technology Volume 12, Issue 3, 1990, Pages 162-172. DOI: 10.1016/0141-0229(90)90033-M Abstract: Measurements of rates of glucose uptake and of glycerol and ethanol formation combined with knowledge of the metabolic pathways involved in S. cerevisiae were employed to obtain in vivo rates of reaction catalysed by pathway enzymes for suspended and alginate-entrapped cells at pH 4.5 and 5.5. Intracellular concentrations of substrates and effectors for most key pathway enzymes were estimated from in vivo phosphorus-31 nuclear magnetic resonance measurements. These data show the validity in vivo of kinetic models previously proposed for phosphofructokinase and pyruvate kinase based on in vitro studies. Kinetic representations of hexokinase, glycogen synthetase, and glyceraldehyde 3-phosphate dehydrogenase, which incorporate major regulatory properties of these enzymes, are all consistent with the in vivo data. This detailed model of pathway kinetics and these data on intracellular metabolite concentrations allow evaluation of flux-control coefficients for all key enzymes involved in glucose catabolism under the four different cell environments examined. This analysis indicates that alginate entrapment increases the glucose uptake rate and shifts the step most influencing ethanol production from glucose uptake to phosphofructokinase. The rate of ATP utilization in these nongrowing cells strongly limits ethanol production at pH 5.5 but is relatively insignificant at pH 4.5. SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS Run this model online at http://jjj.biochem.sun.ac.za To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144 . . . . . . Biomodels Curation:…
species: metaid_0000007
reaction: metaid_0000015
creator:
  ORG:
    orgname: California Institute of Technology
  n:
    given: Harish
    family: Dharuri
units def: 755917
units def: metaid_0000023
created:
  W3 CDTF: Sun Aug 13 20:32:16 BST 2006
units def: metaid_0000027
reaction: metaid_0000016
units def: metaid_0000026
is: sce00010
parameter: 560644
compartment: metaid_0000003
parameter: 560647
species: metaid_0000006
species: metaid_0000011
species: metaid_0000013
area units: area
time units: 755917
substance units: metaid_0000023
name: Galazzo1990_FermentationPathwayKinetics
reaction: metaid_0000017
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
rule: 560636

560641
type: Parameter
constant: true
units: metaid_0000026
value: 14.31
name: Trehalose and Glycogen formation_Vm3

metaid_0000026
type: SBMLUnitsDef
unit: 755990
unit: 755978
unit: 755966
name: mM per minute

755990
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

755978
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

755966
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid_0000018
type: Reaction
kinetic law: 756246
has part: http://identifiers.org/ec-code/2.7.2.3
has part: R01015
has part: http://identifiers.org/ec-code/4.2.1.11
has part: R01061
name: GAPD
has part: http://identifiers.org/ec-code/5.4.2.1
has part: http://identifiers.org/ec-code/1.2.1.12
has part: http://identifiers.org/ec-code/5.3.1.1
has part: http://identifiers.org/ec-code/4.1.2.13
reversible: true
has part: R01512
has part: R00658
product: 756234
has part: R01070
fast: false
has part: R01518
product: 756222
reactant: 756209

560568
type: LocalParameter
units: metaid_0000025
value: 2.5

metaid_0000025
type: SBMLUnitsDef
unit: 755954
unit: 755942
name: milliMolar

755954
type: SBMLUnit
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scale: 0
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kind: LITRE

755942
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

560550
type: LocalParameter
units: dimensionless
value: 0.18

560547
type: LocalParameter
units: metaid_0000025
value: 0.0025

560562
type: LocalParameter
units: metaid_0000025
value: 1.5

560553
type: LocalParameter
units: metaid_0000025
value: 1.91939

560545
type: LocalParameter
units: metaid_0000026
value: 49.9

560559
type: LocalParameter
units: metaid_0000025
value: 3.0E-4

560556
type: LocalParameter
units: metaid_0000025
value: 0.0806142

560565
type: LocalParameter
units: metaid_0000025
value: 1.1

756234
type: SpeciesReference
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species: metaid_0000008

metaid_0000008
type: Species
is: CHEBI:18021
initial amount: NaN
constant: false
has only substance units: false
initial concentration: 0.0095
boundary condition: false
is: C00074
name: Phosphoenol pyruvate
in compartment: metaid_0000022

metaid_0000022
type: Compartment
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: Cytoplasm

756222
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000005

metaid_0000005
type: Species
boundary condition: false
is: C00002
has only substance units: false
in compartment: metaid_0000022
initial concentration: 1.19
is: CHEBI:15422
initial amount: NaN
name: ATP
constant: false

756209
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000007
type: Species
boundary condition: false
name: Fructose 1,6-phosphate
is: CHEBI:16905
initial amount: NaN
in compartment: metaid_0000022
initial concentration: 9.144
has only substance units: false
constant: false
is: C00354

metaid_0100014
type: Parameter
constant: false
units: metaid_0000026
value: NaN
name: VappGly

metaid_0000021
type: Reaction
kinetic law: 756392
reactant: 756380
is version of: GO:0016887
is version of: http://identifiers.org/ec-code/3.6.1.3
fast: false
reversible: true
name: ATPase

560635
type: LocalParameter
units: metaid_0000027
value: 25.1

metaid_0000027
type: SBMLUnitsDef
unit: 756002
name: minute_inverse

756002
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

756380
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

metaid_0000014
type: Reaction
is homolog to: REACT 2092
reversible: true
fast: false
reactant: 756015
product: 756027
is: GO:0046323
modifier: 756039
name: Glucose in
kinetic law: 756051

756015
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

metaid_0000013
type: Species
in compartment: metaid_0000003
constant: false
has only substance units: false
name: Glucose outside the cell
initial amount: NaN
boundary condition: true
is: CHEBI:17234
is: C00293
initial concentration: 1.0

metaid_0000003
type: Compartment
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: Extracellular

756027
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000004
type: Species
name: Glucose inside the cell
initial amount: NaN
constant: false
is: C00293
initial concentration: 0.0345
has only substance units: false
in compartment: metaid_0000022
is: CHEBI:17234
boundary condition: false

metaid_0000006
type: Species
has only substance units: false
boundary condition: false
initial amount: NaN
is: CHEBI:17665
is: C00668
name: Glucose 6-phosphate
constant: false
initial concentration: 1.011
in compartment: metaid_0000022

560496
type: LocalParameter
units: metaid_0000027
value: 3.7

560493
type: LocalParameter
units: metaid_0000026
value: 19.7

metaid_0000020
type: Reaction
fast: false
reactant: 756319
product: 756331
reversible: true
name: Glycerol synthesis
kinetic law: 756367
modifier: 756343
is version of: GO:0006114
modifier: 756355

756319
type: SpeciesReference
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species: metaid_0000007

756331
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000010
type: Species
is: CHEBI:17754
constant: false
boundary condition: true
in compartment: metaid_0000022
initial concentration: 0.0
name: Glycerol
is: C00116
has only substance units: false
initial amount: NaN

560607
type: LocalParameter
units: metaid_0000025
value: 5.0

560625
type: LocalParameter
units: dimensionless
value: 1.0

560622
type: LocalParameter
units: metaid_0000025
value: 0.2

560631
type: LocalParameter
units: dimensionless
value: 1.0

560634
type: LocalParameter
units: dimensionless
value: 1.14815E-7

560613
type: LocalParameter
units: dimensionless
value: 1.0

560610
type: LocalParameter
units: dimensionless
value: 0.1

560604
type: LocalParameter
units: metaid_0000025
value: 0.00793966

560628
type: LocalParameter
units: dimensionless
value: 1.58793E-4

560616
type: LocalParameter
units: dimensionless
value: 164.084

560619
type: LocalParameter
units: dimensionless
value: 0.01

560602
type: LocalParameter
units: metaid_0000026
value: 203.0

metaid_0000012
type: Species
has part: C01083
name: Glycogen and Trehalose
has part: CHEBI:28087
constant: false
has only substance units: false
in compartment: metaid_0000022
has part: CHEBI:27082
initial concentration: 0.0
initial amount: NaN
has part: C00182
boundary condition: true

metaid_0000019
type: Reaction
product: 756270
is version of: GO:0043458
fast: false
reversible: true
name: Pyruvate kinase
is: http://identifiers.org/ec-code/2.7.1.40
modifier: 756294
kinetic law: 756306
reactant: 756258
product: 756282

756270
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

560574
type: LocalParameter
units: metaid_0000025
value: 5.0

560583
type: LocalParameter
units: dimensionless
value: 164.084

560589
type: LocalParameter
units: metaid_0000025
value: 0.2

560571
type: LocalParameter
units: metaid_0000025
value: 0.00793966

560598
type: LocalParameter
units: dimensionless
value: 1.0

560592
type: LocalParameter
units: dimensionless
value: 1.0

560577
type: LocalParameter
units: dimensionless
value: 0.1

560586
type: LocalParameter
units: dimensionless
value: 0.01

560595
type: LocalParameter
units: dimensionless
value: 1.58793E-4

560569
type: LocalParameter
units: metaid_0000026
value: 3440.0

560580
type: LocalParameter
units: dimensionless
value: 1.0

560601
type: LocalParameter
units: dimensionless
value: 1.14815E-7

756258
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

756282
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000011
type: Species
is: CHEBI:16236
name: Ethanol
is: C00469
has only substance units: false
in compartment: metaid_0000022
initial concentration: 0.0
initial amount: NaN
constant: false
boundary condition: true

560650
type: Parameter
constant: true
units: metaid_0000026
value: 68.5
name: Hexokinase_Vm2

metaid_0200014
type: Parameter
constant: false
units: dimensionless
value: NaN
name: VratioVmax_ATP

metaid_0000015
type: Reaction
reversible: true
is homolog to: REACT 1318
is: http://identifiers.org/ec-code/2.7.1.2
is: R00299
reactant: 756063
kinetic law: 756099
product: 756087
fast: false
reactant: 756075
name: Hexokinase

756063
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

560505
type: LocalParameter
units: metaid_0000025
value: 0.0062

560502
type: LocalParameter
units: metaid_0000025
value: 0.1

560499
type: LocalParameter
units: metaid_0000025
value: 0.11

560497
type: LocalParameter
units: metaid_0000026
value: 68.5

756087
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

756075
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

755917
type: SBMLUnitsDef
unit: 755929
name: minute

755929
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000023
type: SBMLUnitsDef
unit: 755904
name: millimole

755904
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid_0000016
type: Reaction
reactant: 756112
is homolog to: REACT 1736
has part: GO:0005992
name: Trehalose and Glycogen formation
product: 756136
has part: GO:0005978
reversible: true
reactant: 756124
kinetic law: 756148
fast: false

756112
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

756136
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

756124
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

560517
type: LocalParameter
units: metaid_0000025
value: 1.1

560514
type: LocalParameter
units: metaid_0000025
value: 1.0

560511
type: LocalParameter
units: metaid_0000025
value: 2.0

560508
type: LocalParameter
units: dimensionless
value: 8.25

560506
type: LocalParameter
units: metaid_0000026
value: 14.31

560644
type: Parameter
constant: true
units: dimensionless
value: 8.25
name: Trehalose and Glycogen formation_n3

560647
type: Parameter
constant: true
units: metaid_0000025
value: 2.0
name: Trehalose and Glycogen formation_K3Gly

metaid_0000017
type: Reaction
product: 756185
has part: R00756
fast: false
reactant: 756160
reversible: true
has part: R00771
name: Phosphofructokinase
kinetic law: 756197
has part: REACT 736
has part: REACT 1164
reactant: 756173

756185
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

756160
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

560526
type: LocalParameter
units: metaid_0000025
value: 0.06

560529
type: LocalParameter
units: dimensionless
value: 3342.0

560538
type: LocalParameter
units: dimensionless
value: 5.0E-4

560520
type: LocalParameter
units: dimensionless
value: 10.0

560523
type: LocalParameter
units: metaid_0000025
value: 1.0

560541
type: LocalParameter
units: dimensionless
value: 1.0

560518
type: LocalParameter
units: metaid_0000026
value: 31.7

560535
type: LocalParameter
units: metaid_0000025
value: 0.025

560532
type: LocalParameter
units: dimensionless
value: 0.019

560544
type: LocalParameter
units: dimensionless
value: 1.0

756173
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006