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name: Trehalose and Glycogen formation_Vm3
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756258
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metaid_0000013
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name: Glucose outside the cell
initial amount: NaN
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metaid_0000008
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is: C00074
name: Phosphoenol pyruvate
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756173
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560568
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value: 2.5
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755954
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560635
units: metaid_0000027
value: 25.1
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BIOMD0000000063
parameter: 560641
occurs in: http://identifiers.org/taxonomy/4932
type: SBMLModel
curated: true
is version of: GO:0006113
reaction: metaid_0000018
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
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
created:
  W3 CDTF: Sun Aug 13 20:32:16 BST 2006
species: metaid_0000004
rule: 560639
reaction: metaid_0000019
length unit: length
is described by: 0141-0229(90)90033-M
units def: metaid_0000025
compartment: metaid_0000022
creator:
  ORG:
    orgname: Stellenbosh University
  n:
    given: Jacky L
    family: Snoep
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:…
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modified:
  W3 CDTF: Wed May 16 11:21:43 BST 2012
compartment: metaid_0000003
parameter: 560647
creator:
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    orgname: California Institute of Technology
  n:
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    family: Dharuri
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
rule: 560636

metaid_0000027
unit: 756002
name: minute_inverse
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560502
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value: 0.1
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560550
units: dimensionless
value: 0.18
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560580
units: dimensionless
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756380
stoichiometry: 1.0
species: metaid_0000005
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metaid_0000012
has part: C01083
name: Glycogen and Trehalose
type: Species
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constant: false
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has part: CHEBI:27082
initial concentration: 0.0
initial amount: NaN
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560650
constant: true
units: metaid_0000026
value: 68.5
name: Hexokinase_Vm2
type: Parameter

756124
stoichiometry: 1.0
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755917
unit: 755929
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560538
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756222
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metaid_0000026
unit: 755990
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name: mM per minute
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560634
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value: 1.14815E-7
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560598
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756027
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560520
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560628
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value: 1.58793E-4
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560577
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metaid_0000015
reversible: true
is homolog to: REACT 1318
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is: R00299
type: Reaction
reactant: 756063
kinetic law: 756099
product: 756087
fast: false
reactant: 756075
name: Hexokinase

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

560571
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value: 0.00793966
type: LocalParameter

560559
units: metaid_0000025
value: 3.0E-4
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560545
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value: 49.9
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metaid_0000025
unit: 755954
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755904
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560514
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756063
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755966
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560647
constant: true
units: metaid_0000025
value: 2.0
name: Trehalose and Glycogen formation_K3Gly
type: Parameter

756234
stoichiometry: 2.0
species: metaid_0000008
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metaid_0000014
is homolog to: REACT 2092
reversible: true
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reactant: 756015
product: 756027
is: GO:0046323
modifier: 756039
type: Reaction
name: Glucose in
kinetic law: 756051

560526
units: metaid_0000025
value: 0.06
type: LocalParameter

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

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

560616
units: dimensionless
value: 164.084
type: LocalParameter

755990
exponent: -1.0
scale: 0
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kind: SECOND
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756319
stoichiometry: 0.5
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756112
stoichiometry: 1.0
species: metaid_0000005
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560592
units: dimensionless
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560586
units: dimensionless
value: 0.01
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560565
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value: 1.1
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560532
units: dimensionless
value: 0.019
type: LocalParameter

560553
units: metaid_0000025
value: 1.91939
type: LocalParameter

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

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

metaid_0000023
unit: 755904
name: millimole
type: SBMLUnitsDef

560625
units: dimensionless
value: 1.0
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560631
units: dimensionless
value: 1.0
type: LocalParameter

756075
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

560604
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value: 0.00793966
type: LocalParameter

756331
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

560506
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value: 14.31
type: LocalParameter

560497
units: metaid_0000026
value: 68.5
type: LocalParameter

560583
units: dimensionless
value: 164.084
type: LocalParameter

560523
units: metaid_0000025
value: 1.0
type: LocalParameter

metaid_0000004
name: Glucose inside the cell
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is: C00293
initial concentration: 0.0345
has only substance units: false
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is: CHEBI:17234
boundary condition: false

756136
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

560544
units: dimensionless
value: 1.0
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metaid_0000016
reactant: 756112
is homolog to: REACT 1736
has part: GO:0005992
name: Trehalose and Glycogen formation
product: 756136
type: Reaction
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reversible: true
reactant: 756124
kinetic law: 756148
fast: false

560610
units: dimensionless
value: 0.1
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metaid_0000022
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: Cytoplasm
type: Compartment

metaid_0000005
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
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560644
constant: true
units: dimensionless
value: 8.25
name: Trehalose and Glycogen formation_n3
type: Parameter

756160
stoichiometry: 1.0
species: metaid_0000005
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560511
units: metaid_0000025
value: 2.0
type: LocalParameter

560574
units: metaid_0000025
value: 5.0
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560607
units: metaid_0000025
value: 5.0
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756282
stoichiometry: 1.0
species: metaid_0000011
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560505
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value: 0.0062
type: LocalParameter

560496
units: metaid_0000027
value: 3.7
type: LocalParameter

756002
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scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

560613
units: dimensionless
value: 1.0
type: LocalParameter

560518
units: metaid_0000026
value: 31.7
type: LocalParameter

metaid_0000006
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
type: Species

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

756087
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

metaid_0000019
product: 756270
type: Reaction
is version of: GO:0043458
fast: false
reversible: true
name: Pyruvate kinase
is: http://identifiers.org/ec-code/2.7.1.40
modifier: 756294
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reactant: 756258
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560541
units: dimensionless
value: 1.0
type: LocalParameter

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

560508
units: dimensionless
value: 8.25
type: LocalParameter

560535
units: metaid_0000025
value: 0.025
type: LocalParameter

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

560529
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value: 3342.0
type: LocalParameter

560602
units: metaid_0000026
value: 203.0
type: LocalParameter

756209
stoichiometry: 1.0
species: metaid_0000007
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560499
units: metaid_0000025
value: 0.11
type: LocalParameter

756015
stoichiometry: 1.0
species: metaid_0000013
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metaid_0000007
boundary condition: false
name: Fructose 1,6-phosphate
is: CHEBI:16905
initial amount: NaN
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initial concentration: 9.144
has only substance units: false
constant: false
is: C00354
type: Species

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

560589
units: metaid_0000025
value: 0.2
type: LocalParameter

metaid_0000018
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
type: Reaction
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

560619
units: dimensionless
value: 0.01
type: LocalParameter

560562
units: metaid_0000025
value: 1.5
type: LocalParameter

756185
stoichiometry: 1.0
species: metaid_0000007
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560622
units: metaid_0000025
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type: LocalParameter

560556
units: metaid_0000025
value: 0.0806142
type: LocalParameter

755942
exponent: 1.0
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kind: MOLE
type: SBMLUnit

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

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

560569
units: metaid_0000026
value: 3440.0
type: LocalParameter

560517
units: metaid_0000025
value: 1.1
type: LocalParameter

756270
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference