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species: species 20
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species 20
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type: Species
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initial amount: NaN
name: nadh
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type: LocalParameter

048030
value: 0.47
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048060
value: 225.0
type: LocalParameter

species 10
name: glucose
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type: Species
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047998
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048006
value: 0.1
type: LocalParameter

047984
value: 1.2
type: LocalParameter

species 21
has only substance units: false
initial concentration: 0.5
constant: false
name: bisphosphoglycerate
is: CHEBI:16001
type: Species
is: C00236
is: http://identifiers.org/cas/38168-82-0
initial amount: NaN
is: http://identifiers.org/pubchem.substance/3535
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species: species 12
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species 1
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initial concentration: 10.0
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initial amount: NaN
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name: pyruvate
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671653
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species: species 8
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vPGT
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product: 672113
reactant: 672101
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reversible: true
name: 3phosphoglycerate transport
type: Reaction

047966
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type: LocalParameter

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type: Reaction
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reactant: 672065
kinetic law: 672089
name: adenylate kinase glycosome
is version of: http://identifiers.org/ec-code/2.7.4.3
reversible: true
product: 672077
fast: false
is homolog to: REACT 643

671401
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species: species 16
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vGlyT
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product: 672209
reactant: 672197
is version of: GO:0015793
fast: false
reversible: true
name: glycerol transport
type: Reaction

671305
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species: species 14
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048088
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047956
value: 0.4
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048046
value: 3.83
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species 22
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name: glycerol3phosphate
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initial amount: NaN
initial concentration: 10.5208853981
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constant: false
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672053
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671245
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vGPO
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product: 671653
kinetic law: 671665
is version of: http://identifiers.org/ec-code/1.1.3.21
reactant: 671641
type: Reaction
name: glycerol3phosphate oxidase

048032
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value: 0.098
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047992
value: 720.9
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671641
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species: species 9
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671945
stoichiometry: 1.0
species: species 5
type: SpeciesReference

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is version of: http://identifiers.org/ec-code/5.3.1.1
type: Reaction
is version of: GO:0004807
reversible: true
fast: false
product: 671497
name: triosephosphate isomerase
reactant: 671485
is homolog to: REACT 775
is: R01015

species 3
name: atpc
initial amount: NaN
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is: C00002
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type: Species
has only substance units: false
is: http://identifiers.org/pubchem.substance/3304
is: http://identifiers.org/cas/56-65-5
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initial concentration: 0.341738611875
is: CHEBI:15422

species 23
is: C00197
initial amount: NaN
is: http://identifiers.org/pubchem.substance/3497
name: 3phosphoglycerate
is: CHEBI:17794
type: Species
constant: false
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in compartment: compartment 2
has only substance units: false
initial concentration: 0.0

vHK
reactant: 671257
fast: false
product: 671269
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is: R00299
reactant: 671245
is version of: GO:0004396
reversible: true
product: 671281
type: Reaction
kinetic law: 671293
name: hexokinase
is homolog to: REACT 1318

672149
stoichiometry: 1.0
species: species 8
type: SpeciesReference

species 13
name: ampg
constant: false
initial concentration: 4.24050185751
is: C00020
type: Species
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has only substance units: false
is: http://identifiers.org/pubchem.substance/3322
initial amount: NaN
is: http://identifiers.org/cas/61-19-8

vGK
product: 671909
product: 671897
name: glycerol kinase
is: R00847
is homolog to: REACT 724
reactant: 671885
is version of: http://identifiers.org/ec-code/2.7.1.30
kinetic law: 671921
is version of: GO:0004370
fast: false
reactant: 671872
reversible: true
type: Reaction

671897
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species: species 24
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672161
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species: species 9
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672065
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species: species 13
type: SpeciesReference

671365
stoichiometry: 1.0
species: species 16
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047968
value: 0.82
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671545
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species: species 21
type: SpeciesReference

047940
value: 108.9
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species 2
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is: CHEBI:16761
is: http://identifiers.org/pubchem.substance/3310
initial amount: NaN
is: http://identifiers.org/cas/20398-34-9
constant: false
boundary condition: false
is: C00008
type: Species
has only substance units: false
name: adpc
initial concentration: 1.31652277625

species 24
is: CHEBI:17754
name: glycerol
initial amount: NaN
is: http://identifiers.org/cas/56-81-5
boundary condition: false
in compartment: compartment 2
initial concentration: 0.0
type: Species
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constant: false
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is: http://identifiers.org/pubchem.substance/3416
has only substance units: false

047954
value: 12.0
type: LocalParameter

species 14
is: CHEBI:4170
type: Species
name: glucose6phosphate
is: C00668
has only substance units: false
initial amount: NaN
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initial concentration: 0.5
is: http://identifiers.org/pubchem.substance/3937
in compartment: compartment 2
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vPK
fast: false
is homolog to: REACT 1911
product: 671799
reactant: 671774
product: 671811
is version of: http://identifiers.org/ec-code/2.7.1.40
name: pyruvate kinase
reactant: 671787
is version of: GO:0004743
reversible: true
kinetic law: 671823
type: Reaction
is: R00200

047994
value: 0.15
type: LocalParameter

671281
stoichiometry: 1.0
species: species 12
type: SpeciesReference

047980
value: 0.067
type: LocalParameter

671981
stoichiometry: 1.0
species: species 4
type: SpeciesReference

species 25
initial amount: NaN
is: C00031
constant: true
type: Species
initial concentration: 5.0
name: glucose external
boundary condition: true
in compartment: compartment 3
has only substance units: false
is: CHEBI:4167

species 5
is: CHEBI:17835
initial concentration: 0.0
type: Species
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has only substance units: false
name: 2phosphoglycerate
initial amount: NaN
boundary condition: false
is: http://identifiers.org/pubchem.substance/3904
constant: false
is: C00631

species 11
initial amount: NaN
is: C00002
initial concentration: 0.240501857508
constant: false
boundary condition: false
is: http://identifiers.org/cas/56-65-5
type: Species
has only substance units: false
name: atpg
in compartment: compartment 2
is: CHEBI:15422
is: http://identifiers.org/pubchem.substance/3304

672137
stoichiometry: 1.0
species: species 22
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vAKc
fast: false
type: Reaction
kinetic law: 672041
name: adenylate kinase cytosol
reversible: true
is version of: http://identifiers.org/ec-code/2.7.4.3
product: 672029
reactant: 672017
reactant: 672005
is homolog to: REACT 643
is: R00127
is version of: GO:0004017

vALD
modifier: 671437
fast: false
type: Reaction
is version of: GO:0004332
name: aldolase
is homolog to: REACT 1602
product: 671413
reactant: 671401
reversible: true
is: R01070
is version of: http://identifiers.org/ec-code/4.1.2.13
product: 671425
kinetic law: 671473
modifier: 671449
modifier: 671461

671269
stoichiometry: 1.0
species: species 14
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671353
stoichiometry: 1.0
species: species 11
type: SpeciesReference

672077
stoichiometry: 2.0
species: species 12
type: SpeciesReference

047942
value: 1.0
type: LocalParameter

species 26
is version of: CHEBI:32816
initial amount: NaN
is version of: C00022
is version of: http://identifiers.org/pubchem.substance/3324
name: pyruvate external
is version of: http://identifiers.org/cas/127-17-3
constant: true
boundary condition: true
initial concentration: 0.0
in compartment: compartment 3
has only substance units: false
is version of: B00006
type: Species

species 4
name: phosphoenolpyruvate
is: http://identifiers.org/pubchem.substance/3374
in compartment: compartment 1
initial amount: NaN
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is: B00019
type: Species
boundary condition: false
has only substance units: false
is: http://identifiers.org/cas/138-08-9
initial concentration: 0.0

671197
exponent: 1.0
scale: -3
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kind: LITRE
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species 12
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type: Species
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is: CHEBI:16761
name: adpg
is: C00008
is: http://identifiers.org/pubchem.substance/3310
boundary condition: false
is: http://identifiers.org/cas/20398-34-9
initial amount: NaN
initial concentration: 1.51899628498
in compartment: compartment 2

671557
stoichiometry: 1.0
species: species 20
type: SpeciesReference

047952
value: 0.126
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672209
stoichiometry: 1.0
species: species 27
type: SpeciesReference

species 18
boundary condition: false
is: http://identifiers.org/cas/591-57-1
has only substance units: false
initial concentration: 2.5
name: glyceraldehyde3phosphate
is: http://identifiers.org/pubchem.substance/3418
in compartment: compartment 2
constant: false
type: Species
initial amount: NaN
is: CHEBI:29052
is: C00118

671173
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

048038
value: 2.5
type: LocalParameter

671836
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species: species 3
type: SpeciesReference

048028
value: 0.1
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species: species 19
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species 6
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constant: false
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is: http://identifiers.org/cas/61-19-8
type: Species
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initial concentration: 2.24173861188
initial amount: NaN
has only substance units: false
in compartment: compartment 1
is: http://identifiers.org/pubchem.substance/3322
name: ampc

vENO
type: Reaction
is version of: GO:0004634
product: 671981
reversible: true
kinetic law: 671993
name: enolase
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fast: false
is: R00658
reactant: 671969
is homolog to: REACT 1400

671221
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species: species 10
type: SpeciesReference

048040
value: 0.114
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671605
stoichiometry: 1.0
species: species 19
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048068
value: 598.0
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048010
value: 0.28
type: LocalParameter

species 19
initial amount: NaN
is: http://identifiers.org/cas/53-84-9
boundary condition: false
in compartment: compartment 2
constant: false
is: http://identifiers.org/pubchem.substance/3305
name: nad
has only substance units: false
is: C00003
type: Species
is: CHEBI:15846
initial concentration: 2.0

048078
value: 0.442
type: LocalParameter

048000
value: 0.1
type: LocalParameter

672029
stoichiometry: 2.0
species: species 2
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BIOMD0000000211
parameter: metaid_0000070
reaction: vGT
reaction: vPGT
reaction: vPFK
species: species 12
parameter: metaid_0000071
name: Rate Law for atp utilisation
species: species 8
reaction: vPT
time units: metaid_0000067
species: species 21
species: species 22
name: Rate Law for pyruvate kinase
name: Henri-Michaelis-Menten (irreversible)
species: species 15
species: species 7
reaction: vGPDH
is: MODEL1511155915
compartment: compartment 2
reaction: vPGI
name: Rate Law for aldolase
area units: metaid_0000005
species: species 4
function def: metaid_0000056
name: Reversible Michaelis-Menten
name: Rate Law for hexokinase
function def: metaid_0000060
is version of: GO:0006096
species: species 25
species: species 11
species: species 3
length unit: length
species: species 26
reaction: vAU
parameter: metaid_0000072
notes: This model is from the article: Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei. Albert MA, Haanstra JR, Hannaert V, Van Roy J, Opperdoes FR, Bakker BM, Michels PA. J Biol Chem 2005 Aug 5;280(31):28306-15. 15955817 , Abstract: A mathematical model of glycolysis in bloodstream form Trypanosoma brucei was developed previously on the basis of all available enzyme kinetic data (Bakker, B. M., Michels, P. A. M., Opperdoes, F. R., and Westerhoff, H. V. (1997) J. Biol. Chem. 272, 3207-3215). The model predicted correctly the fluxes and cellular metabolite concentrations as measured in non-growing trypanosomes and the major contribution to the flux control exerted by the plasma membrane glucose transporter. Surprisingly, a large overcapacity was predicted for hexokinase (HXK), phosphofructokinase (PFK), and pyruvate kinase (PYK). Here, we present our further analysis of the control of glycolytic flux in bloodstream form T. brucei. First, the model was optimized and extended with recent information about the kinetics of enzymes and their activities as measured in lysates of in vitro cultured growing trypanosomes. Second, the concentrations of five glycolytic enzymes (HXK, PFK, phosphoglycerate mutase, enolase, and PYK) in trypanosomes were changed by RNA interference. The effects of the knockdown of these enzymes on the growth, activities, and levels of various enzymes and glycolytic flux were studied and compared with model predictions. Data thus obtained support the conclusion from the in silico analysis that HXK, PFK, and PYK are in excess, albeit less than predicted. Interestingly, depletion of PFK and enolase had an effect on the activity (but not, or to a lesser extent, expression) of some other glycolytic enzymes. Enzymes located both in the glycosomes (the peroxisome-like organelles harboring the first seven enzymes of the glycolytic pathway of trypanosomes) and in the cytosol were affected. These data suggest the…
reaction: vGlyT
reaction: vPK
species: species 10
parameter: metaid_0000073
reaction: vAKg
species: species 18
species: species 6
species: species 19
name: Rate Law for phosphoglycerate kinase
units def: metaid_0000067
reaction: vANTI
name: Rate Law for glyceraldehyde3phosphatedehydrogenase
occurs in: http://identifiers.org/taxonomy/5691
is: tbr00010
type: SBMLModel
species: species 20
function def: metaid_0000064
species: species 27
name: Albert2005_Glycolysis
compartment: compartment 3
name: Rate Law for adenylate kinase
function def: metaid_0000062
function def: metaid_0000061
function def: metaid_0000057
curated: true
is homolog to: REACT 1383
species: species 14
species: species 2
reaction: vPGM
name: Rate Law for phophofructokinase
reaction: vTPI
reaction: vENO
name: Rate Law for glucose transport
reaction: vGPO
units def: metaid_0000068
species: species 23
species: species 1
species: species 24
reaction: vGK
species: species 17
species: species 9
reaction: vHK
substance units: metaid_0000068
parameter: metaid_0000074

047950
value: 0.116
type: LocalParameter

species 17
type: Species
is: CHEBI:16108
initial amount: NaN
in compartment: compartment 2
name: dihydroxyacetonephosphate
initial concentration: 8.47911460193
is: C00111
is: http://identifiers.org/pubchem.substance/3411
has only substance units: false
is: B00029
constant: false
boundary condition: false

vPFK
is homolog to: REACT 736
is: R00756
name: phophofructokinase
reversible: true
reactant: 671341
kinetic law: 671389
is version of: http://identifiers.org/ec-code/2.7.1.11
product: 671377
is version of: GO:0003872
reactant: 671353
fast: false
product: 671365
type: Reaction

species 27
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type: Species
is: B00032
name: glycerol external
boundary condition: true
is: CHEBI:17754
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is: http://identifiers.org/pubchem.substance/3416
is: http://identifiers.org/cas/56-81-5
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species 7
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is: http://identifiers.org/pubchem.substance/3497
initial amount: NaN
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is: CHEBI:17794
has only substance units: false
initial concentration: 0.0
is: CHEBI:16108
constant: false
name: 3phosphoglycerate cytosol

672113
stoichiometry: 1.0
species: species 7
type: SpeciesReference

047970
value: 0.026
type: LocalParameter

vGAPDH
kinetic law: 671569
product: 671545
type: Reaction
reactant: 671533
fast: false
reactant: 671521
product: 671557
is: R01061
is version of: GO:0043878
name: glyceraldehyde3phosphatedehydrogenase
is version of: http://identifiers.org/ec-code/1.2.1.12
reversible: true
is homolog to: REACT 1847

047990
value: 5696.01
type: LocalParameter

671799
stoichiometry: 1.0
species: species 1
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048050
value: 60.86
type: LocalParameter

671521
stoichiometry: 1.0
species: species 18
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048080
value: 1000000.0
type: LocalParameter

species 16
initial amount: NaN
boundary condition: false
is: C05378
is: CHEBI:28013
has only substance units: false
in compartment: compartment 2
initial concentration: 10.0
constant: false
is: http://identifiers.org/pubchem.substance/7752
type: Species
name: fructose16bisphosphate

048052
value: 0.44
type: LocalParameter

671848
stoichiometry: 1.0
species: species 2
type: SpeciesReference

048090
value: 1000000.0
type: LocalParameter

vGT
kinetic law: 671233
product: 671221
reactant: 671209
is version of: GO:0046323
is homolog to: REACT 2092
fast: false
reversible: true
name: glucose transport
type: Reaction

671185
exponent: 1.0
scale: -3
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kind: MOLE
type: SBMLUnit

671872
stoichiometry: 1.0
species: species 22
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048026
value: 0.003
type: LocalParameter

species 8
boundary condition: false
initial concentration: 2.23134594788
type: Species
is: CHEBI:16108
initial amount: NaN
is: C00111
is: http://identifiers.org/pubchem.substance/3411
has only substance units: false
name: dihydroxyacetonephosphate cytosol
constant: false
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is: B00029

048066
value: 0.24
type: LocalParameter

048012
value: 0.4
type: LocalParameter

672173
stoichiometry: 1.0
species: species 17
type: SpeciesReference

species 15
constant: false
is: http://identifiers.org/pubchem.substance/7723
type: Species
is: CHEBI:16084
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initial amount: NaN
has only substance units: false
is: C05345
name: fructose6phosphate
initial concentration: 0.5
boundary condition: false

vPGM
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is: R01518
is version of: GO:0004619
is homolog to: REACT 576
reversible: true
kinetic law: 671957
product: 671945
is version of: http://identifiers.org/ec-code/5.4.2.1
fast: false
name: phosphoglycerate mutase
type: Reaction

671209
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species: species 25
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671885
stoichiometry: 1.0
species: species 12
type: SpeciesReference

vGPDH
type: Reaction
is version of: http://identifiers.org/ec-code/3.1.3.21
kinetic law: 671629
is: R00841
is homolog to: REACT 1146
reactant: 671593
fast: false
reversible: true
product: 671605
name: glycerol3phosphatedehydrogenase
reactant: 671581
product: 671617
is version of: GO:0004367

species 9
initial amount: NaN
is: http://identifiers.org/cas/57-03-4
is: C00093
in compartment: compartment 1
is: http://identifiers.org/pubchem.substance/3393
initial concentration: 2.76865405212
boundary condition: false
name: glycerol3phosphate cytosol
is: CHEBI:15978
has only substance units: false
constant: false
type: Species

671787
stoichiometry: 1.0
species: species 2
type: SpeciesReference

671933
stoichiometry: 1.0
species: species 7
type: SpeciesReference

048044
value: 200.0
type: LocalParameter

048034
value: 0.29
type: LocalParameter

671774
stoichiometry: 1.0
species: species 4
type: SpeciesReference

048054
value: 0.24
type: LocalParameter

048082
value: 1000000.0
type: LocalParameter

048024
value: 2862.0
type: LocalParameter

048074
value: 0.442
type: LocalParameter

671425
stoichiometry: 1.0
species: species 18
type: SpeciesReference

671377
stoichiometry: 1.0
species: species 12
type: SpeciesReference

048014
value: 2.0
type: LocalParameter

048004
value: 465.0
type: LocalParameter

compartment 3
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: extracellular
type: Compartment

671497
stoichiometry: 1.0
species: species 18
type: SpeciesReference

047948
value: 0.1
type: LocalParameter

048064
value: 0.054
type: LocalParameter

vPT
kinetic law: 671701
product: 671689
reactant: 671677
is version of: GO:0006849
is version of: GO:0050833
fast: false
reversible: false
name: pyruvate transport
type: Reaction

671677
stoichiometry: 1.0
species: species 1
type: SpeciesReference

vPGK
is homolog to: REACT 1186
kinetic law: 671762
name: phosphoglycerate kinase
fast: false
product: 671750
product: 671738
is version of: http://identifiers.org/ec-code/2.7.2.3
reversible: true
reactant: 671726
reactant: 671713
is version of: GO:0004618
type: Reaction
is: R01512

672005
stoichiometry: 1.0
species: species 3
type: SpeciesReference

047974
value: 560.0
type: LocalParameter

671811
stoichiometry: 1.0
species: species 3
type: SpeciesReference

047960
value: 1305.0
type: LocalParameter

671713
stoichiometry: 1.0
species: species 21
type: SpeciesReference

metaid_0000070
constant: true
value: 1.0
name: RaHXK
type: Parameter

048042
value: 50.0
type: LocalParameter

048036
value: 1020.0
type: LocalParameter

vAU
kinetic law: 671860
product: 671848
reactant: 671836
is version of: GO:0006200
fast: false
reversible: false
name: atp utilisation
type: Reaction

048056
value: 0.27
type: LocalParameter

672197
stoichiometry: 1.0
species: species 24
type: SpeciesReference

048022
value: 200.0
type: LocalParameter

671617
stoichiometry: 1.0
species: species 22
type: SpeciesReference

048002
value: 0.02
type: LocalParameter

048016
value: 1.7
type: LocalParameter

047988
value: 999.3
type: LocalParameter

671485
stoichiometry: 1.0
species: species 17
type: SpeciesReference

048076
value: 1000000.0
type: LocalParameter

048062
value: 495.0
type: LocalParameter

metaid_0000071
constant: true
value: 1.0
name: RaPFK
type: Parameter

compartment 1
is: GO:0005829
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytosol
type: Compartment

671413
stoichiometry: 1.0
species: species 17
type: SpeciesReference

671581
stoichiometry: 1.0
species: species 17
type: SpeciesReference

671689
stoichiometry: 1.0
species: species 26
type: SpeciesReference

vANTI
kinetic law: 672185
reactant: 672149
reversible: true
fast: false
is version of: GO:0015169
product: 672173
name: gly3p dhap antiporter
type: Reaction
reactant: 672137
product: 672161

ORG:
  orgname: Humboldt University Berlin
n:
  given: Marvin
  family: Schulz

vPGI
is homolog to: REACT 1164
type: Reaction
is version of: http://identifiers.org/ec-code/5.3.1.9
reactant: 671305
fast: false
reversible: true
kinetic law: 671329
is: R00771
is version of: GO:0004347
name: phosphoglycerate isomerase
product: 671317

672101
stoichiometry: 1.0
species: species 23
type: SpeciesReference

047972
value: 10.7
type: LocalParameter

048084
value: 1000000.0
type: LocalParameter

672017
stoichiometry: 1.0
species: species 6
type: SpeciesReference

compartment 2
is: GO:0020015
constant: true
size: 1.0
spatial dimensions: 3.0
name: glycosome
type: Compartment

047962
value: 1305.0
type: LocalParameter

metaid_0000072
constant: true
value: 1.0
name: RaPYK
type: Parameter

orgname: Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology, Belgium.

W3 CDTF: Tue Jan 27 14:07:41 GMT 2009

W3 CDTF: Tue May 15 22:59:43 BST 2012

given: Vijayalakshmi
family: Chelliah

n:
  given: Paul A. M.
  family: Michels

ORG:
  orgname: EMBL-EBI