BIOMD0000000245
type: SBMLModel
parameter: 106529
parameter: 106506
reaction: 106456
is described by: http://identifiers.org/pubmed/11434967
reaction: 106462
parameter: 106503
substance units: 845151
rule: 106485
reaction: 106449
compartment: 106421
species: 106426
reaction: 106457
units def: 845284
reaction: 106446
species: 106541
parameter: 106511
reaction: 106458
parameter: 106532
species: 106432
parameter: 106501
is: MODEL1003250000
species: 106433
parameter: 106512
parameter: 106509
parameter: 106518
parameter: 106489
units def: 845247
parameter: 106524
rule: 106486
reaction: 106451
reaction: 106442
parameter: 106536
rule: 106483
parameter: 106527
parameter: 106498
parameter: 106504
reaction: 106454
species: 106429
units def: 845223
parameter: 106521
parameter: 106539
rule: 106484
area units: metaid_0000005
parameter: 106507
species: 106436
parameter: 106533
units def: 845320
reaction: 106447
reaction: 106438
species: 106424
reaction: 106459
occurs in: http://identifiers.org/taxonomy/4932
parameter: 106493
parameter: 106513
units def: 845368
parameter: 106534
has version: GO:0006099
parameter: 106496
parameter: 106491
parameter: 106502
reaction: 106452
parameter: 106537
species: 106431
volume units: 845199
compartment: 106422
parameter: 106516
rule: 106480
reaction: 106443
species: 106428
length unit: length
has version: sce00020
units def: 845151
rule: 106482
reaction: 106448
parameter: 106528
parameter: 106499
time units: 845175
parameter: 106519
notes: This the model from the article: A biochemically structured model for Saccharomyces cerevisiae. Lei F, Rotbøll M, Jørgensen SB. J Biotechnol. 2001 Jul 12;88(3):205-21. PMID: 11434967 ,DOI: 10.1016/S0168-1656(01)00269-3 Abstract: A biochemically structured model for the aerobic growth of Saccharomyces cerevisiae on glucose and ethanol is presented. The model focuses on the pyruvate and acetaldehyde branch points where overflow metabolism occurs when the growth changes from oxidative to oxido-reductive. The model is designed to describe the onset of aerobic alcoholic fermentation during steady-state as well as under dynamical conditions, by triggering an increase in the glycolytic flux using a key signalling component which is assumed to be closely related to acetaldehyde. An investigation of the modelled process dynamics in a continuous cultivation revealed multiple steady states in a region of dilution rates around the transition between oxidative and oxido-reductive growth. A bifurcation analysis using the two external variables, the dilution rate, D, and the inlet concentration of glucose, S(f), as parameters, showed that a fold bifurcation occurs close to the critical dilution rate resulting in multiple steady-states. The region of dilution rates within which multiple steady states may occur depends strongly on the substrate feed concentration. Consequently a single steady state may prevail at low feed concentrations, whereas multiple steady states may occur over a relatively wide range of dilution rates at higher feed concentrations. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Pub…

106529
type: Parameter
constant: true
units: 845247
value: 13.0

845247
type: SBMLUnitsDef
unit: 845272
unit: 845260
name: gram per liter

845272
type: SBMLUnit
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scale: 0
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kind: LITRE

845260
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exponent: 1.0
scale: 0
multipler: 1.0
kind: GRAM

106506
type: Parameter
constant: true
units: 845320
value: 5.81

845320
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unit: 845344
unit: 845332
name: gram per liter per hour

845356
type: SBMLUnit
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scale: 0
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kind: SECOND

845344
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kind: LITRE

845332
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106456
type: Reaction
kinetic law: 846248
reactant: 846236
is: SBO:0000185
fast: false
reversible: false
name: Acetate outflow

846236
type: SpeciesReference
stoichiometry: 1.0
species: 106427

106427
type: Species
boundary condition: false
name: Acetate
in compartment: 106421
initial amount: NaN
initial concentration: 0.0
is: CHEBI:40480
is: C00033
is: SBO:0000247
has only substance units: false
constant: false

106421
type: Compartment
is version of: GO:0005576
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: environment

106462
type: Reaction
kinetic law: 846368
reactant: 846356
is: SBO:0000185
fast: false
reversible: false
name: AcDH BM outflow

846356
type: SpeciesReference
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species: 106433

106433
type: Species
is: SBO:0000241
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 106421
name: BM(AcDH)

106503
type: Parameter
constant: true
units: 845247
value: 2.0E-5

845151
type: SBMLUnitsDef
unit: 845163
name: gram

845163
type: SBMLUnit
exponent: 1.0
scale: 0
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kind: GRAM

106449
type: Reaction
modifier: 846067
kinetic law: 846103
fast: false
reactant: 846055
is version of: GO:0009056
name: active BM degradation
modifier: 846079
modifier: 846091
is: SBO:0000179
reversible: false

106431
type: Species
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.002
initial amount: NaN
in compartment: 106421
name: BM

846055
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species: 106432

106432
type: Species
is: SBO:0000241
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 106421
name: BM(active)

106424
type: Species
has only substance units: false
is: C00293
constant: false
in compartment: 106421
boundary condition: false
name: Glucose
is: CHEBI:17234
initial concentration: 15.0
initial amount: NaN
is: SBO:0000247

106429
type: Species
initial amount: NaN
constant: false
in compartment: 106421
initial concentration: 0.0
has only substance units: false
boundary condition: false
name: EtOH
is: C00469
is: CHEBI:16236
is: SBO:0000247

106426
type: Species
initial concentration: 0.0
has only substance units: false
constant: false
is: C00022
in compartment: 106421
is: CHEBI:15361
initial amount: NaN
boundary condition: false
name: Pyruvate
is: SBO:0000247

106457
type: Reaction
kinetic law: 846272
reactant: 846260
is: SBO:0000185
fast: false
reversible: false
name: Acetaldehyde outflow

846260
type: SpeciesReference
stoichiometry: 1.0
species: 106428

106428
type: Species
is: C00084
initial concentration: 0.0
is: SBO:0000247
boundary condition: false
initial amount: NaN
name: Acetaldehyde
constant: false
in compartment: 106421
is: CHEBI:15343
has only substance units: false

845284
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unit: 845308
unit: 845296
name: liter per gram

845308
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exponent: 1.0
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kind: LITRE

845296
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: GRAM

106446
type: Reaction
is: SBO:0000205
is version of: GO:0008283
product: 845863
kinetic law: 845887
product: 845851
reversible: false
is version of: GO:0016049
name: BM growth (gluc)
product: 845839
modifier: 845875
reactant: 845827
fast: false

845863
type: SpeciesReference
stoichiometry: 0.063
species: 106436

106436
type: Species
boundary condition: true
has only substance units: false
in compartment: 106421
constant: false
is: C00004
initial concentration: 0.0
name: Red. Equ. (NADH)
is: CHEBI:16908
is: SBO:0000247
initial amount: NaN

845851
type: SpeciesReference
stoichiometry: 0.127
species: 106434

106434
type: Species
constant: false
initial amount: NaN
name: CO2
is: CHEBI:16526
in compartment: 106421
boundary condition: true
is: C00011
has only substance units: false
is: SBO:0000247
initial concentration: 0.0

845839
type: SpeciesReference
stoichiometry: 0.732
species: 106431

845827
type: SpeciesReference
stoichiometry: 1.0
species: 106424

106541
type: Species
has version: C00293
has version: CHEBI:17234
initial concentration: 15.0
constant: false
in compartment: 106421
boundary condition: true
is: SBO:0000247
name: Glucose(feed)
initial amount: NaN
has only substance units: false

106511
type: Parameter
constant: true
units: 845320
value: 0.0104

106458
type: Reaction
kinetic law: 846296
reactant: 846284
is: SBO:0000185
fast: false
reversible: false
name: EtOH outflow

846284
type: SpeciesReference
stoichiometry: 1.0
species: 106429

106532
type: Parameter
constant: true
units: 845320
value: 0.00399

106501
type: Parameter
constant: true
units: 845284
value: 14.2

106512
type: Parameter
constant: true
units: 845247
value: 0.0102

106509
type: Parameter
constant: true
units: 845247
value: 2.64E-4

106518
type: Parameter
constant: true
units: 845247
value: 0.034

106489
type: Parameter
constant: false
units: 845368
value: 0.0

845368
type: SBMLUnitsDef
unit: 845404
unit: 845392
unit: 845380
name: mmole per gram BM per hour

845404
type: SBMLUnit
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scale: 0
multipler: 1.0
kind: GRAM

845392
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND

845380
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

106524
type: Parameter
constant: true
units: 845320
value: 0.589

106451
type: Reaction
kinetic law: 846139
modifier: 846127
reactant: 846115
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Acdh degradation

846115
type: SpeciesReference
stoichiometry: 1.0
species: 106433

106442
type: Reaction
is version of: GO:0004029
is version of: http://identifiers.org/ec-code/1.2.1.3
is version of: R00710
product: 845645
kinetic law: 845681
modifier: 845657
fast: false
reversible: false
modifier: 845669
reactant: 845621
product: 845633
name: Acetald. dehydrogenase
is: SBO:0000200

845645
type: SpeciesReference
stoichiometry: 0.363
species: 106436

845621
type: SpeciesReference
stoichiometry: 1.0
species: 106428

845633
type: SpeciesReference
stoichiometry: 1.363
species: 106427

106536
type: Parameter
constant: true
units: 845320
value: 0.00339

106527
type: Parameter
constant: true
units: 845247
value: 1.0E-6

106498
type: Parameter
constant: true
units: 845320
value: 47.1

106504
type: Parameter
constant: true
units: 845284
value: 0.101

106454
type: Reaction
kinetic law: 846224
reactant: 846212
is: SBO:0000185
fast: false
reversible: false
name: Pyruvate outflow

846212
type: SpeciesReference
stoichiometry: 1.0
species: 106426

845223
type: SBMLUnitsDef
unit: 845235
name: per hour

845235
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND

106521
type: Parameter
constant: true
units: 845247
value: 0.057

106539
type: Parameter
constant: true
units: 845223
value: 0.1
name: Dilutionrate

106507
type: Parameter
constant: true
units: 845247
value: 5.0E-7

106533
type: Parameter
constant: true
units: 845320
value: 0.392

106447
type: Reaction
product: 845923
kinetic law: 845971
modifier: 845959
name: BM growth (acetate)
fast: false
product: 845911
is version of: GO:0016049
is: SBO:0000205
is version of: GO:0008283
modifier: 845947
reversible: false
reactant: 845899
product: 845935

845923
type: SpeciesReference
stoichiometry: 0.325
species: 106434

845911
type: SpeciesReference
stoichiometry: 0.619
species: 106431

845899
type: SpeciesReference
stoichiometry: 1.0
species: 106427

845935
type: SpeciesReference
stoichiometry: 0.214
species: 106436

106438
type: Reaction
reversible: false
name: glycolysis
modifier: 845465
fast: false
kinetic law: 845477
reactant: 845416
is: SBO:0000205
is: GO:0006096
modifier: 845453
product: 845428
product: 845440

845416
type: SpeciesReference
stoichiometry: 1.0
species: 106424

845428
type: SpeciesReference
stoichiometry: 0.978
species: 106426

845440
type: SpeciesReference
stoichiometry: 0.178
species: 106436

106459
type: Reaction
kinetic law: 846320
reactant: 846308
is: SBO:0000185
fast: false
reversible: false
name: active BM outflow

846308
type: SpeciesReference
stoichiometry: 1.0
species: 106432

106493
type: Parameter
constant: true
units: 845320
value: 0.584

106513
type: Parameter
constant: true
units: 845320
value: 0.775

106534
type: Parameter
constant: true
units: 845247
value: 0.0023

106496
type: Parameter
constant: true
units: 845320
value: 1.43

106491
type: Parameter
constant: false
units: dimensionless
value: 0.1
name: X_a

106502
type: Parameter
constant: true
units: 845320
value: 0.501

106452
type: Reaction
kinetic law: 846175
product: 846163
reactant: 846151
is: SBO:0000185
fast: false
reversible: false
name: Glucose inflow

846163
type: SpeciesReference
stoichiometry: 1.0
species: 106424

846151
type: SpeciesReference
stoichiometry: 1.0
species: 106541

106537
type: Parameter
constant: true
units: 845247
value: 0.0018

845199
type: SBMLUnitsDef
unit: 845211
name: liter

845211
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

106422
type: Compartment
is: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

106516
type: Parameter
constant: true
units: 845284
value: 440.0

106443
type: Reaction
is: GO:0006099
modifier: 845730
product: 845705
kinetic law: 845755
reactant: 845693
modifier: 845743
fast: false
reversible: false
is: SBO:0000205
product: 845717
name: TCA (acetate)

845705
type: SpeciesReference
stoichiometry: 1.446
species: 106434

845693
type: SpeciesReference
stoichiometry: 1.0
species: 106427

845717
type: SpeciesReference
stoichiometry: 1.066
species: 106436

106448
type: Reaction
modifier: 846007
name: Acdh production
reactant: 845983
kinetic law: 846043
is: SBO:0000184
modifier: 846031
reversible: false
product: 845995
modifier: 846019
is version of: GO:0006412
fast: false

845983
type: SpeciesReference
stoichiometry: 1.0
species: 106432

845995
type: SpeciesReference
stoichiometry: 1.0
species: 106433

106528
type: Parameter
constant: true
units: 845320
value: 0.0751

106499
type: Parameter
constant: true
units: 845247
value: 0.12

845175
type: SBMLUnitsDef
unit: 845187
name: hours

845187
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND

106519
type: Parameter
constant: true
units: dimensionless
value: 0.0125

106522
type: Parameter
constant: true
units: 845320
value: 1.203

106508
type: Parameter
constant: true
units: 845320
value: 4.8

106439
type: Reaction
modifier: 845537
fast: false
product: 845513
reactant: 845489
kinetic law: 845549
is: GO:0006099
reversible: false
is: SBO:0000205
name: TCA (pyruvate)
modifier: 845525
product: 845501

845513
type: SpeciesReference
stoichiometry: 0.908
species: 106436

845489
type: SpeciesReference
stoichiometry: 1.0
species: 106426

845501
type: SpeciesReference
stoichiometry: 1.499
species: 106434

106531
type: Parameter
constant: true
units: 845284
value: 25.0

106514
type: Parameter
constant: true
units: 845247
value: 0.1

106441
type: Reaction
has version: http://identifiers.org/ec-code/1.2.4.1
modifier: 845597
reactant: 845561
name: Pyruvate Dehydrogenase
reversible: false
fast: false
is version of: GO:0004738
kinetic law: 845609
has version: http://identifiers.org/ec-code/2.3.1.12
product: 845585
product: 845573
is: SBO:0000200
is version of: R00209

845561
type: SpeciesReference
stoichiometry: 1.0
species: 106426

845585
type: SpeciesReference
stoichiometry: 0.33
species: 106434

845573
type: SpeciesReference
stoichiometry: 0.5
species: 106428

106526
type: Parameter
constant: true
units: 845320
value: 0.008

106497
type: Parameter
constant: true
units: 845247
value: 0.94

106492
type: Parameter
constant: false
units: dimensionless
value: 0.0075
name: X_AcDH

106517
type: Parameter
constant: true
units: 845320
value: 2.82

106488
type: Parameter
constant: false
units: 845368
value: 0.0

106453
type: Reaction
kinetic law: 846200
reactant: 846187
is: SBO:0000185
fast: false
reversible: false
name: Glucose outflow

846187
type: SpeciesReference
stoichiometry: 1.0
species: 106424

106444
type: Reaction
product: 845791
is version of: GO:0004022
reactant: 845767
kinetic law: 845815
is version of: http://identifiers.org/ec-code/1.1.1.1
reactant: 845779
fast: false
has version: R00754
name: ADH
is: SBO:0000200
modifier: 845803
reversible: true

845791
type: SpeciesReference
stoichiometry: 1.045
species: 106429

845767
type: SpeciesReference
stoichiometry: 1.0
species: 106428

845779
type: SpeciesReference
stoichiometry: 0.363
species: 106436

106461
type: Reaction
kinetic law: 846344
reactant: 846332
is: SBO:0000185
fast: false
reversible: false
name: BM outflow

846332
type: SpeciesReference
stoichiometry: 1.0
species: 106431

106538
type: Parameter
constant: true
units: 845320
value: 0.02

106523
type: Parameter
constant: true
units: 845247
value: 0.0101

106494
type: Parameter
constant: true
units: 845247
value: 0.0116

W3 CDTF: Thu Jun 03 11:40:01 BST 2010

W3 CDTF: Thu Mar 25 02:28:31 GMT 2010

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler