metaid C PHE
is: CHEBI:28044
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: phenylalanine
type: Species

424169
units: 178882
value: 3.24
type: LocalParameter

178919
exponent: -1.0
scale: 0
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kind: SECOND
type: SBMLUnit

424162
units: 178846
value: 1.848
type: LocalParameter

424122
product: 178967
fast: false
kinetic law: 178991
reactant: 178931
reversible: false
product: 178955
type: Reaction
modifier: 178979
name: G6PDH
reactant: 178943

179232
stoichiometry: 1.0
species: metaid C F6P
type: SpeciesReference

178895
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

424141
kinetic law: 179436
reactant: 179424
fast: false
reversible: false
name: u6PG
type: Reaction

178931
stoichiometry: 1.0
species: metaid C G6P
type: SpeciesReference

424159
units: 178846
value: 0.33
type: LocalParameter

metaid C TYR
is: CHEBI:18186
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: tyrosine
type: Species

178858
exponent: 1.0
scale: -3
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kind: MOLE
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424172
units: 178882
value: 10.5
type: LocalParameter

179376
stoichiometry: 1.0
species: metaid C S7P
type: SpeciesReference

179148
stoichiometry: 1.0
species: metaid C S7P
type: SpeciesReference

metaid C MgATP
is: CHEBI:30617
constant: false
boundary condition: true
has only substance units: false
initial concentration: 2.3
initial amount: NaN
in compartment: metaid CV
name: MgATP
type: Species

424178
units: 178882
value: 3.0
type: LocalParameter

179027
stoichiometry: 1.0
species: metaid C NADPH
type: SpeciesReference

424153
kinetic law: 179532
reactant: 179520
fast: false
reversible: false
name: uS7P
type: Reaction

metaid C F6P
is: CHEBI:15946
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.17
initial amount: NaN
in compartment: metaid CV
name: fructose 6-phosphate
type: Species

179015
stoichiometry: 1.0
species: metaid C NADP
type: SpeciesReference

metaid C GAP
is: CHEBI:17138
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.064
initial amount: NaN
in compartment: metaid CV
name: glyceraldehyde 3-phosphate
type: Species

424163
units: 178846
value: 0.109
type: LocalParameter

179172
stoichiometry: 1.0
species: metaid C Ru5P
type: SpeciesReference

424123
name: 6PGDH
type: Reaction
reactant: 179015
fast: false
product: 179040
modifier: 179052
kinetic law: 179064
reversible: false
product: 179027
reactant: 179003

metaid C NADPH
is: CHEBI:16474
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.16
initial amount: NaN
in compartment: metaid CV
name: NADPH
type: Species

metaid C NADP
is: CHEBI:18009
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.17
initial amount: NaN
in compartment: metaid CV
name: NADP+
type: Species

179400
stoichiometry: 1.0
species: metaid C F6P
type: SpeciesReference

424158
units: 178846
value: 0.116
type: LocalParameter

424173
units: 178846
value: 0.009
type: LocalParameter

424150
kinetic law: 179508
reactant: 179496
fast: false
reversible: false
name: uX5P
type: Reaction

179040
stoichiometry: 1.0
species: metaid C Ru5P
type: SpeciesReference

424124
kinetic law: 179100
product: 179088
reactant: 179076
fast: false
reversible: false
name: R5PI
type: Reaction

424170
units: 178882
value: 0.85
type: LocalParameter

178907
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

424167
units: 178882
value: 0.57
type: LocalParameter

179472
stoichiometry: 1.0
species: metaid C R5P
type: SpeciesReference

179388
stoichiometry: 1.0
species: metaid C E4P
type: SpeciesReference

178809
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

179136
stoichiometry: 1.0
species: metaid C GAP
type: SpeciesReference

metaid C X5P
is: CHEBI:16332
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.041
initial amount: NaN
in compartment: metaid CV
name: xylulose 5-phosphate
type: Species

178821
unit: 178833
name: per second
type: SBMLUnitsDef

179220
stoichiometry: 1.0
species: metaid C X5P
type: SpeciesReference

424147
kinetic law: 179484
reactant: 179472
fast: false
reversible: false
name: uR5P
type: Reaction

metaid C 6PG
is: CHEBI:16863
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.25
initial amount: NaN
in compartment: metaid CV
name: 6-phosphogluconate
type: Species

179520
stoichiometry: 1.0
species: metaid C S7P
type: SpeciesReference

179184
stoichiometry: 1.0
species: metaid C X5P
type: SpeciesReference

424125
kinetic law: 179160
product: 179148
product: 179136
reactant: 179124
reactant: 179112
fast: false
reversible: false
name: TKL1
type: Reaction

179088
stoichiometry: 1.0
species: metaid C R5P
type: SpeciesReference

424166
units: 178846
value: 0.055
type: LocalParameter

179003
stoichiometry: 1.0
species: metaid C 6PG
type: SpeciesReference

424135
kinetic law: 179352
product: 179340
reactant: 179328
fast: false
reversible: false
name: RPPK
type: Reaction

179448
stoichiometry: 1.0
species: metaid C Ru5P
type: SpeciesReference

179304
stoichiometry: 1.0
species: metaid C TYR
type: SpeciesReference

179340
stoichiometry: 1.0
species: metaid C PRPP
type: SpeciesReference

178967
stoichiometry: 1.0
species: metaid C NADPH
type: SpeciesReference

179268
stoichiometry: 1.0
species: metaid C E4P
type: SpeciesReference

metaid C S7P
is: CHEBI:15721
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.082
initial amount: NaN
in compartment: metaid CV
name: sedoheptulose 7-phosphate
type: Species

178955
stoichiometry: 1.0
species: metaid C 6PG
type: SpeciesReference

179280
stoichiometry: 1.0
species: metaid C PHE
type: SpeciesReference

179424
stoichiometry: 1.0
species: metaid C 6PG
type: SpeciesReference

metaid CV
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: intracellular
type: Compartment

metaid C G6P
is: CHEBI:14314
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.9
initial amount: NaN
in compartment: metaid CV
name: glucose 6-phosphate
type: Species

179124
stoichiometry: 1.0
species: metaid C X5P
type: SpeciesReference

424132
kinetic law: 179316
product: 179304
product: 179292
product: 179280
reactant: 179268
fast: false
reversible: false
name: PKDHA
type: Reaction

424176
units: 178882
value: 0.003
type: LocalParameter

metaid C R5P
is: CHEBI:17797
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.118
initial amount: NaN
in compartment: metaid CV
name: ribose 5-phosphate
type: Species

178870
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
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metaid C PRPP
is: CHEBI:17111
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: phosphoribosylpyrophosphate
type: Species

178833
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

179328
stoichiometry: 1.0
species: metaid C R5P
type: SpeciesReference

424144
kinetic law: 179460
reactant: 179448
fast: false
reversible: false
name: uRu5P
type: Reaction

metaid C Ru5P
is: CHEBI:17363
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.033
initial amount: NaN
in compartment: metaid CV
name: ribulose 5-phosphate
type: Species

179076
stoichiometry: 1.0
species: metaid C Ru5P
type: SpeciesReference

179112
stoichiometry: 1.0
species: metaid C R5P
type: SpeciesReference

178797
unit: 178809
name: millimole
type: SBMLUnitsDef

MODEL1004070001
species: metaid C 6PG
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Holly
    family: Summersgill
reaction: 424135
species: metaid C TYR
reaction: 424122
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
is: http://identifiers.org/taxonomy/4932
rule: 424184
substance units: 178797
time units: 172336
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Edward
    family: Kent
units def: 178882
rule: 424186
species: metaid C PHE
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
name: Vaseghi1999_Pentose_PP_yeast
species: metaid C S7P
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
species: metaid C TRP
reaction: 424128
reaction: 424124
reaction: 424138
species: metaid C X5P
species: metaid C PRPP
species: metaid C R5P
species: metaid C NADP
reaction: 424123
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Holly
    family: Summersgill
is described by: http://identifiers.org/pubmed/10935926
parameter: 424189
units def: 178821
reaction: 424144
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
reaction: 424141
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Holly
    family: Summersgill
reaction: 424150
reaction: 424156
reaction: 424132
units def: 178797
species: metaid C Ru5P
units def: 178846
reaction: 424129
species: metaid C F6P
reaction: 424125
length unit: 335510
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
notes: Model as described in: In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae Vaseghi S, Baumeister A, Rizzi M, Reuss M. Metab Eng. 1999 Apr;1(2):128-40. PMID: 10935926 , doi: 10.1006/mben.1998.0110 ; Abstract: The in vivo dynamics of the pentose phosphate pathway has been studied with transient experiments in continuous culture of Saccharomyces cerevisiae. Rapid sampling was performed with a special sampling device after disturbing the steady state with a pulse of glucose. The time span of observation was 120 s after the pulse. During this short time period the dynamic effect of protein biosynthesis can be neglected. The metabolites of interest (glucose 6-phosphate, NADP, NADPH, 6-phosphogluconate, and MgATP2-) we determined with enzymatic assays and HPLC. The experimental observations were then used for the identification of kinetic rate equations and parameters under in vivo conditions. In accordance with results from in vitro studies the in vivo diagnosis supports an ordered Bi-Bi mechanism with noncompetitive inhibition by MgATP2- for the enzyme glucose-6-phosphate dehydrogenase. In the case of 6-phosphogluconate dehydrogenase an ordered Bi-Ter mechanism with a competitive inhibition by MgATP2- has been found. Because the MgATP2- concentration decreases abruptly after the pulse of glucose the inhibitory effect vanishes and the flux through the pentose phosphate pathway increases. This regulation phenomenon guarantees the balance of fluxes through glycolysis and pentose phosphate pathway during the dynamic time period. Typographical errors found and corrected from the original manuscript: rMax given for 6GPDH and 6PGDH are reversed (by solving their defining equations) Eq (52) should read C_NADPH(t) = 0.16 + ... (from Fig. 2) While the model is identical to the one described in the article, it cannot reproduce all time courses displayed in the article. The time courses for S7P and X5P differ from fig 5 and some of the reaction rates show s…
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Edward
    family: Kent
curated: false
created:
  W3 CDTF: Thu Apr 09 01:00:00 BST 2009
species: metaid C E4P
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Natalie
    family: Stanford
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Natalie
    family: Stanford
species: metaid C NADPH
reaction: 424153
species: metaid C MgATP
volume units: 950046
area units: area
rule: 424185
type: SBMLModel
species: metaid C G6P
species: metaid C GAP
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Edward
    family: Kent
rule: 424187
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Natalie
    family: Stanford
compartment: metaid CV
reaction: 424147

424160
units: 178846
value: 1.702
type: LocalParameter

178846
unit: 178870
unit: 178858
name: mM
type: SBMLUnitsDef

178943
stoichiometry: 1.0
species: metaid C NADP
type: SpeciesReference

179208
stoichiometry: 1.0
species: metaid C E4P
type: SpeciesReference

179496
stoichiometry: 1.0
species: metaid C X5P
type: SpeciesReference

179292
stoichiometry: 1.0
species: metaid C TRP
type: SpeciesReference

424138
kinetic law: 179412
product: 179400
product: 179388
reactant: 179376
reactant: 179364
fast: false
reversible: false
name: TAL
type: Reaction

424174
units: 178882
value: 0.004
type: LocalParameter

179544
stoichiometry: 1.0
species: metaid C E4P
type: SpeciesReference

424157
units: 178882
value: 0.654
type: LocalParameter

424128
kinetic law: 179196
product: 179184
reactant: 179172
fast: false
reversible: false
name: Ru5PE
type: Reaction

metaid C E4P
is: CHEBI:48153
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.029
initial amount: NaN
in compartment: metaid CV
name: erythrose 4-phosphate
type: Species

179364
stoichiometry: 1.0
species: metaid C GAP
type: SpeciesReference

424161
units: 178882
value: 44.19
type: LocalParameter

179244
stoichiometry: 1.0
species: metaid C GAP
type: SpeciesReference

178882
unit: 178919
unit: 178907
unit: 178895
name: mM per second
type: SBMLUnitsDef

metaid C TRP
is: CHEBI:27897
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: tryptophan
type: Species

424156
kinetic law: 179556
reactant: 179544
fast: false
reversible: false
name: uE4P
type: Reaction

424175
units: 178846
value: 0.009
type: LocalParameter

424189
constant: true
units: 178821
value: 2.77778E-5
name: specific growth rate
type: Parameter

424129
kinetic law: 179256
product: 179244
product: 179232
reactant: 179220
reactant: 179208
fast: false
reversible: false
name: TKL2
type: Reaction