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110041
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is: http://identifiers.org/pubchem.compound/122357
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110465
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477386
value: 1.00012
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ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

111034
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477553
is: SBO:0000009
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value: 2.10226E-5
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value: 7.38636E-5
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477142
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110416
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109908
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477541
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477150
is: CHEBI:15946
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111142
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111676
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477178
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110356
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477361
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value: 5.0E-4
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477557
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value: 7.386364E-5
name: V28
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BIOMD0000000392
parameter: 477541
type: SBMLModel
reaction: 477236
species: 477174
occurs in: http://identifiers.org/taxonomy/40674
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length unit: length
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reaction: 477224
name: MM s2p2 - reg
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name: F26BPc phosphatase
units def: 109895
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name: Transketolase
name: Constant flux (reversible)
species: 477175
species: 477136
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rule: 477480
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species: 477184
species: 477171
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reaction: 477237
notes: This model is from the article: A quantitative comparison of Calvin–Benson cycle models Anne Arnold, Zoran Nikoloski Trends in Plant Science 2011 Oct 14. 22001849 , Abstract: The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering. Note: Model of the Calvin cycle and the related end-product pathways to starch and sucrose synthesis by Laisk et al. (2006, DOI:10.1007/s11120-006-9109-1 ) and the personally provided implementation to Laisk et al. (2009, DOI:10.1007/978-1-4020-9237-4_13 ). A reduced version of the published model is implemented (light-dependent reactions are taken out). The parameter values are widely taken from Laisk et al. (1989,[click here for PDF] ). The initial metabolite values are chosen from the data set of Zhu et al. (2007,DOI:10.1104/pp.107.103713 ). A detailed description of all modifications is given in the model described by Arnold and Nikoloski (2011,PMID:22001849 .
volume units: 109871
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curated: true
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name: F6Pc kinase
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reaction: 477240
reaction: 477222
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name: cyt. FBPase
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units def: 109871
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name: MMlike s1p2 - reg + no p2 alone
species: 477187
is described by: http://identifiers.org/pubmed/22001849
rule: 477494
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name: MM s2p2 + reg 1*x,1*a
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function def: 477537
function def: COPASI2
occurs in: http://identifiers.org/taxonomy/33090
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parameter: 477550
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477278
is: SBO:0000009
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477177
is version of: CHEBI:16474
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name: NADPH
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111058
stoichiometry: 1.0
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477376
value: 0.0018624
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477374
value: 6.5319E-5
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477213
kinetic law: 110102
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110078
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477227
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477289
is: SBO:0000009
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477544
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value: 0.001
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477166
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name: ATP
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477365
value: 3.74778E-4
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110344
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110672
stoichiometry: 1.0
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477373
value: 1.1065E-6
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477249
is: SBO:0000009
value: 50000.0
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111688
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477239
kinetic law: 111276
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477363
value: 2.78407E-4
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477228
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modifier: 110733
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name: Transketolase (S7P)
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477545
is: SBO:0000196
constant: true
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477165
is version of: http://identifiers.org/pubchem.compound/16500
constant: false
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477175
is version of: CHEBI:15379
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name: O2
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477208
is version of: CHEBI:15378
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110258
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477210
kinetic law: 110005
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reversible: false
name: RuBisCO (2) - V(CO2)
type: Reaction

477268
is: SBO:0000009
value: 5.3013E-4
name: Kp2
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477234
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name: Starch synthase
type: Reaction

477253
is: SBO:0000009
value: 6.0
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477248
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kinetic law: 111772
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reversible: false

477267
is: SBO:0000009
value: 2.7035E-4
name: Kp1
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110720
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477221
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477233
product: 110961
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477222
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477252
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value: 300000.0
name: k1
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477212
kinetic law: 110054
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109944
stoichiometry: 1.0
species: 477133
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477256
is: SBO:0000009
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109981
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477236
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111700
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477246
name: F6Pc kinase
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477265
is: SBO:0000009
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109932
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species: 477132
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477224
type: Reaction
modifier: 110538
product: 110502
kinetic law: 110574
name: Transketolase (F6P)
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477245
kinetic law: 111568
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fast: false
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name: Sucrose phosphatase
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477264
is: SBO:0000009
value: 0.0011122
name: Ks1
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111604
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109920
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477243
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reversible: true
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name: Sucrose synthase
kinetic law: 111520
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110889
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109993
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111592
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477257
is: SBO:0000009
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477307
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477242
name: UGPase
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111532
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477130
constant: true
size: 1.0
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name: cytosol
type: Compartment

477231
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110877
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477308
value: 0.0821023
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110138
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477259
is: SBO:0000009
value: 3030.3
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477230
fast: false
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name: Ru5P kinase
reactant: 110817
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modifier: 110853
product: 110829
kinetic law: 110865

110477
stoichiometry: 1.0
species: 477142
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477240
reactant: 111288
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name: cyt. FBPase
kinetic law: 111350
fast: false
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reversible: true
product: 111300
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477309
value: 0.99996
name: q
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477550
is: SBO:0000196
constant: true
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name: PiTc
type: Parameter

477344
value: 9.3583E-5
name: Ks
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477457
value: 1.02614E-7
name: Vm
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477354
value: 8.9213E-4
name: Ks
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477353
value: 0.0568182
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477181
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constant: false
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name: TPc
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111484
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477305
value: 1.5597E-5
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111580
stoichiometry: 1.0
species: 477189
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477315
value: 1.7677E-4
name: K2s1
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477135
constant: false
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477133
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477468
value: 0.002
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110114
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477355
value: 9.3583E-5
name: Kr1
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110017
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477304
value: 1.2713E-5
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111399
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477192
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477132
is: SBO:0000009
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477455
value: 0.002191
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477469
value: 0.001
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110805
stoichiometry: 1.0
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477341
value: 2.12052E-4
name: Ks1
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477193
is version of: http://identifiers.org/pubchem.compound/65533
constant: false
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477131
is: CHEBI:16710
constant: false
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name: RuBP
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477343
value: 0.0568182
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477357
value: 9.8597E-5
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109969
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477302
value: 0.77294
name: q
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477342
value: 6.36157E-4
name: Kp1
type: LocalParameter

477180
is version of: CHEBI:17050
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 477130
name: PGAc
type: Species

110029
stoichiometry: 1.0
species: 477141
type: SpeciesReference

477316
value: 5.407E-4
name: K2r1
type: LocalParameter

110150
stoichiometry: 1.0
species: 477175
type: SpeciesReference

477262
is: SBO:0000009
value: 0.0170455
name: Vm
type: LocalParameter

111374
stoichiometry: 1.0
species: 477196
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110817
stoichiometry: 1.0
species: 477166
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477139
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.966E-4
initial amount: NaN
in compartment: 477128
name: EOP
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477301
value: 0.00568182
name: Vm
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110696
stoichiometry: 1.0
species: 477157
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111288
stoichiometry: 1.0
species: 477186
type: SpeciesReference

477330
value: 0.00113636
name: Vm
type: LocalParameter

477320
value: 3.63934E-5
name: Ks1
type: LocalParameter

477321
value: 5.5117E-4
name: Ks2
type: LocalParameter

477138
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.045E-4
initial amount: NaN
in compartment: 477128
name: EP
type: Species

477310
value: 6.1349E-4
name: K1
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477300
is: SBO:0000009
value: 0.011364
name: Vm
type: LocalParameter

477350
value: 5.4107E-4
name: Kr3
type: LocalParameter

477260
is: SBO:0000009
value: 3.0
name: k1
type: LocalParameter

477331
value: 0.11059
name: q
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477250
is: SBO:0000009
value: 0.9
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type: LocalParameter

110490
stoichiometry: 1.0
species: 477154
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110162
stoichiometry: 0.5
species: 477166
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111472
stoichiometry: 1.0
species: 477202
type: SpeciesReference

477313
value: 2.7035E-4
name: K1s2
type: LocalParameter

110090
stoichiometry: 1.0
species: 477132
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110829
stoichiometry: 1.0
species: 477131
type: SpeciesReference

477291
is: SBO:0000009
value: 5.407E-4
name: K2s1
type: LocalParameter

110841
stoichiometry: 1.0
species: 477168
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111387
stoichiometry: 1.0
species: 477195
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111239
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species: 477186
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477136
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initial concentration: 3.206E-4
initial amount: NaN
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name: EPG
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477312
value: 1.1438E-4
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477333
value: 0.0010398
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111460
stoichiometry: 1.0
species: 477198
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477190
is version of: CHEBI:15946
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.00193356926724116
initial amount: NaN
in compartment: 477130
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477352
value: 9.4837E-5
name: Kr4
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110307
stoichiometry: 1.0
species: 477169
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477334
value: 1.1023E-4
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type: LocalParameter

110174
stoichiometry: 1.0
species: 477136
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477288
is: SBO:0000009
value: 1.1438E-4
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477199
is version of: CHEBI:15422
constant: true
boundary condition: true
has only substance units: false
initial concentration: 3.6E-4
initial amount: NaN
in compartment: 477130
name: ATPc
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477148
is version of: CHEBI:15965
constant: false
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has only substance units: false
initial concentration: 0.0022
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name: HeP
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477324
value: 9.11825E-5
name: Kp2
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110234
stoichiometry: 1.0
species: 477138
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477168
is version of: CHEBI:16761
constant: false
boundary condition: true
has only substance units: false
initial concentration: 8.2E-4
initial amount: NaN
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name: ADP
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111227
stoichiometry: 2.0
species: 477181
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477371
value: 2.2129E-5
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477273
is: SBO:0000009
value: 3.6393E-4
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type: LocalParameter

477392
value: 6.42157E-4
name: Kp1
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477292
is: SBO:0000009
value: 1.7677E-4
name: K2r1
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110586
stoichiometry: 1.0
species: 477154
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477128
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast
type: Compartment

477548
is: SBO:0000196
constant: true
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name: PiT
type: Parameter

111300
stoichiometry: 1.0
species: 477189
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110648
stoichiometry: 1.0
species: 477156
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477169
is: CHEBI:43474
constant: false
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has only substance units: false
initial concentration: 0.0109928959090909
initial amount: NaN
in compartment: 477128
name: Pi
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477286
is: SBO:0000009
value: 6.1349E-4
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110937
stoichiometry: 1.0
species: 477166
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477272
is: SBO:0000009
value: 2.7035E-4
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110186
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species: 477141
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477187
is version of: http://identifiers.org/pubchem.compound/105021
constant: false
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initial concentration: 7.8E-9
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111313
stoichiometry: 1.0
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477336
value: 5.3013E-4
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477295
is: SBO:0000009
value: 1.18815
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477460
value: 0.001
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110599
stoichiometry: 1.0
species: 477142
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477285
is: SBO:0000009
value: 0.99943
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109883
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
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477275
is: SBO:0000009
value: 2.0129E-5
name: Kp1
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477294
is: SBO:0000009
value: 9.0464E-5
name: K2s2
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477461
value: 0.001
name: Kr1
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477390
value: 1.10717E-4
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477337
value: 0.01951
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477323
value: 9.95868E-5
name: Kp1
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110925
stoichiometry: 1.0
species: 477148
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477284
is: SBO:0000009
value: 0.170455
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477360
value: 9.6372E-5
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110270
stoichiometry: 1.0
species: 477166
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111362
stoichiometry: 1.0
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477189
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constant: false
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has only substance units: false
initial concentration: 0.0058
initial amount: NaN
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name: HePc
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477370
value: 0.792367
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477381
value: 1.4393E-4
name: Kp1
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477328
value: 3.1612E-4
name: Ks2
type: LocalParameter

477195
is version of: http://identifiers.org/pubchem.compound/8629
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.7E-4
initial amount: NaN
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name: UDPGc
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477462
value: 0.0015
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477297
is: SBO:0000009
value: 3.6393E-4
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477338
value: 0.00284091
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477395
value: 0.00164329
name: Kr12
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477358
value: 5.4107E-4
name: Kp
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111155
stoichiometry: 1.0
species: 477180
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111448
stoichiometry: 1.0
species: 477195
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477283
is: SBO:0000009
value: 0.0017914
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110198
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species: 477168
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477145
is: CHEBI:16108
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has only substance units: false
initial concentration: 2.50091578940897E-4
initial amount: NaN
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name: DHAP
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477196
is version of: CHEBI:15713
constant: true
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initial concentration: 3.6E-4
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name: UTPc
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477382
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477339
value: 1.00326
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477296
is: SBO:0000009
value: 1.7677E-4
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477329
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477159
is version of: http://identifiers.org/pubchem.compound/1005
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has only substance units: false
initial concentration: 2.5E-4
initial amount: NaN
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name: PeP
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477186
is version of: CHEBI:16905
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initial concentration: 0.002
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110282
stoichiometry: 1.0
species: 477142
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477396
value: 0.0010267
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477464
value: 2.05284E-10
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477454
value: 0.01
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477349
value: 9.6372E-5
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477144
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477326
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110961
stoichiometry: 1.0
species: 477171
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477156
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constant: false
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has only substance units: false
initial concentration: 3.0E-4
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name: SBP
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477393
value: 3.74778E-4
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477183
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constant: false
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110611
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477465
value: 1.0E-9
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111436
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species: 477189
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477271
is: SBO:0000009
value: 1.18815
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110222
stoichiometry: 1.0
species: 477136
type: SpeciesReference

ORG:
  orgname: Max-Planck-Institute of Molecular Plant Physiology
n:
  given: Anne
  family: Arnold

477281
is: SBO:0000009
value: 6.3429E-5
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477346
value: 8.9213E-4
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477327
value: 3.1808E-4
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477384
value: 0.00410568
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477147
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has only substance units: false
initial concentration: 6.7E-4
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name: FBP
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477198
is version of: CHEBI:17659
constant: true
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initial concentration: 6.4E-4
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477157
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477184
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477270
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value: 0.0027397
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477299
is: SBO:0000009
value: 2.0129E-5
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110295
stoichiometry: 1.0
species: 477168
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477471
value: 1.0E-4
name: Kr4
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477347
value: 9.8597E-5
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477209
kinetic law: 109957
product: 109944
reactant: 109932
reactant: 109920
fast: false
reversible: true
name: RuBisCO (1)
type: Reaction

477280
is: SBO:0000009
value: 3.2842E-5
name: Ks1
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110949
stoichiometry: 1.0
species: 477165
type: SpeciesReference

W3 CDTF: Wed Oct 19 15:54:38 BST 2011

orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany

W3 CDTF: Fri Apr 20 20:50:23 BST 2012

given: Zoran
family: Nikoloski