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type: SBMLModel
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reaction: 477236
species: 477174
occurs in: http://identifiers.org/taxonomy/40674
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length unit: length
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species: 477163
reaction: 477242
reaction: 477224
name: MM s2p2 - reg
species: 477205
name: F26BPc phosphatase
units def: 109895
function def: 477502
function def: 477530
name: Transketolase
name: Constant flux (reversible)
species: 477175
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parameter: 477544
species: 477184
species: 477171
reaction: 477209
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 .
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reaction: 477222
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name: MMlike s1p2 - reg + no p2 alone
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is described by: http://identifiers.org/pubmed/22001849
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function def: COPASI2
occurs in: http://identifiers.org/taxonomy/33090
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477201
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477544
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477209
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477250
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109944
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477237
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111142
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477547
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name: G6P

477218
type: Reaction
kinetic law: 110246
product: 110234
reactant: 110222
fast: false
reversible: false
name: RuBisCO (7)

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

110234
type: SpeciesReference
stoichiometry: 1.0
species: 477138

110222
type: SpeciesReference
stoichiometry: 1.0
species: 477136

477225
type: Reaction
kinetic law: 110636
modifier: 110623
product: 110611
reactant: 110599
reactant: 110586
fast: false
reversible: true
name: Aldolase (SBP)

477300
type: LocalParameter
is: SBO:0000009
value: 0.011364
name: Vm

477299
type: LocalParameter
is: SBO:0000009
value: 2.0129E-5
name: Kp1

477297
type: LocalParameter
is: SBO:0000009
value: 3.6393E-4
name: Ks2

477296
type: LocalParameter
is: SBO:0000009
value: 1.7677E-4
name: Ks1

477295
type: LocalParameter
is: SBO:0000009
value: 1.18815
name: q

110611
type: SpeciesReference
stoichiometry: 1.0
species: 477156

477156
type: Species
is version of: http://identifiers.org/pubchem.compound/164735
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.0E-4
initial amount: NaN
in compartment: 477128
name: SBP

110599
type: SpeciesReference
stoichiometry: 1.0
species: 477142

110586
type: SpeciesReference
stoichiometry: 1.0
species: 477154

477245
type: Reaction
kinetic law: 111568
product: 111556
product: 111544
reactant: 111532
fast: false
reversible: true
name: Sucrose phosphatase

477455
type: LocalParameter
value: 0.002191
name: Kp2

477454
type: LocalParameter
value: 0.01
name: Kp1

477398
type: LocalParameter
value: 5.354E-5
name: Ks1

477397
type: LocalParameter
value: 1.35286
name: q

477396
type: LocalParameter
value: 0.0010267
name: Vm

111556
type: SpeciesReference
stoichiometry: 1.0
species: 477205

111544
type: SpeciesReference
stoichiometry: 1.0
species: 477204

477204
type: Species
is version of: CHEBI:17992
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 477130
name: Succ

111532
type: SpeciesReference
stoichiometry: 1.0
species: 477202

477202
type: Species
is version of: http://identifiers.org/pubchem.compound/161554
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 477130
name: SucPc

477221
type: Reaction
kinetic law: 110392
modifier: 110380
modifier: 110368
product: 110356
reactant: 110344
fast: false
reversible: true
name: Aldolase (FBP)

477276
type: LocalParameter
is: SBO:0000009
value: 0.022727
name: Vm

477275
type: LocalParameter
is: SBO:0000009
value: 2.0129E-5
name: Kp1

477273
type: LocalParameter
is: SBO:0000009
value: 3.6393E-4
name: Ks2

477272
type: LocalParameter
is: SBO:0000009
value: 2.7035E-4
name: Ks1

477271
type: LocalParameter
is: SBO:0000009
value: 1.18815
name: q

110356
type: SpeciesReference
stoichiometry: 1.0
species: 477147

110344
type: SpeciesReference
stoichiometry: 2.0
species: 477142

477213
type: Reaction
kinetic law: 110102
product: 110090
product: 110078
reactant: 110066
fast: false
reversible: true
name: RuBisCO (5) - EP

477257
type: LocalParameter
is: SBO:0000009
value: 70000.0
name: k2

477256
type: LocalParameter
is: SBO:0000009
value: 6.0
name: k1

110090
type: SpeciesReference
stoichiometry: 1.0
species: 477132

110078
type: SpeciesReference
stoichiometry: 1.0
species: 477141

110066
type: SpeciesReference
stoichiometry: 1.0
species: 477138

477233
type: Reaction
product: 110961
kinetic law: 111010
modifier: 110985
reactant: 110937
name: AGPase
reversible: true
product: 110949
reactant: 110925
fast: false
modifier: 110997
modifier: 110973

110961
type: SpeciesReference
stoichiometry: 1.0
species: 477171

477337
type: LocalParameter
value: 0.01951
name: Kp2

477336
type: LocalParameter
value: 5.3013E-4
name: Kp1

477334
type: LocalParameter
value: 1.1023E-4
name: Ks2

477333
type: LocalParameter
value: 0.0010398
name: Ks1

477331
type: LocalParameter
value: 0.11059
name: q

477330
type: LocalParameter
value: 0.00113636
name: Vm

110937
type: SpeciesReference
stoichiometry: 1.0
species: 477166

110949
type: SpeciesReference
stoichiometry: 1.0
species: 477165

110925
type: SpeciesReference
stoichiometry: 1.0
species: 477148

477153
type: Species
is version of: http://identifiers.org/pubchem.compound/65533
constant: false
boundary condition: true
has only substance units: false
initial concentration: 7.33034781579417E-4
initial amount: NaN
in compartment: 477128
name: G1P

477228
type: Reaction
fast: false
modifier: 110733
modifier: 110781
reactant: 110708
modifier: 110745
name: Transketolase (S7P)
product: 110720
reversible: true
modifier: 110769
modifier: 110757
reactant: 110696
kinetic law: 110793

110708
type: SpeciesReference
stoichiometry: 1.0
species: 477142

110720
type: SpeciesReference
stoichiometry: 2.0
species: 477159

110696
type: SpeciesReference
stoichiometry: 1.0
species: 477157

477318
type: LocalParameter
value: 9.0464E-5
name: K2s2

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

477315
type: LocalParameter
value: 1.7677E-4
name: K2s1

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

477312
type: LocalParameter
value: 1.1438E-4
name: K2

477310
type: LocalParameter
value: 6.1349E-4
name: K1

477309
type: LocalParameter
value: 0.99996
name: q

477308
type: LocalParameter
value: 0.0821023
name: Vm

477248
type: Reaction
modifier: 111748
modifier: 111724
kinetic law: 111772
modifier: 111736
reactant: 111676
product: 111700
modifier: 111712
modifier: 111760
product: 111688
fast: false
name: F26BPc phosphatase
reversible: false

477471
type: LocalParameter
value: 1.0E-4
name: Kr4

477469
type: LocalParameter
value: 0.001
name: Kr3

477468
type: LocalParameter
value: 0.002
name: Kr1

477465
type: LocalParameter
value: 1.0E-9
name: Ks1

477464
type: LocalParameter
value: 2.05284E-10
name: Vm

111676
type: SpeciesReference
stoichiometry: 1.0
species: 477187

111700
type: SpeciesReference
stoichiometry: 1.0
species: 477205

111688
type: SpeciesReference
stoichiometry: 1.0
species: 477189

477178
type: Species
is version of: CHEBI:25523
constant: true
boundary condition: true
has only substance units: false
initial concentration: 2.9E-4
initial amount: NaN
in compartment: 477128
name: NADP

477243
type: Reaction
modifier: 111508
product: 111484
product: 111472
product: 111460
reactant: 111436
reversible: true
reactant: 111448
name: Sucrose synthase
kinetic law: 111520
fast: false
modifier: 111496

111484
type: SpeciesReference
stoichiometry: 1.0
species: 477208

477208
type: Species
is version of: CHEBI:15378
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.158489318357816
initial amount: NaN
in compartment: 477130
name: Hc

111472
type: SpeciesReference
stoichiometry: 1.0
species: 477202

111460
type: SpeciesReference
stoichiometry: 1.0
species: 477198

111436
type: SpeciesReference
stoichiometry: 1.0
species: 477189

111448
type: SpeciesReference
stoichiometry: 1.0
species: 477195

477395
type: LocalParameter
value: 0.00164329
name: Kr12

477393
type: LocalParameter
value: 3.74778E-4
name: Kp2

477392
type: LocalParameter
value: 6.42157E-4
name: Kp1

477390
type: LocalParameter
value: 1.10717E-4
name: Ks2

477389
type: LocalParameter
value: 0.00920241
name: Kr11

477387
type: LocalParameter
value: 2.78407E-4
name: Ks1

477386
type: LocalParameter
value: 1.00012
name: q

477385
type: LocalParameter
value: 7.38636E-5
name: Vm

477231
type: Reaction
kinetic law: 110913
product: 110901
reactant: 110889
reactant: 110877
fast: false
reversible: true
name: ATP synthase

477329
type: LocalParameter
value: 0.0284091
name: Vm

477328
type: LocalParameter
value: 3.1612E-4
name: Ks2

477327
type: LocalParameter
value: 3.1808E-4
name: Ks1

110901
type: SpeciesReference
stoichiometry: 1.0
species: 477166

110889
type: SpeciesReference
stoichiometry: 1.0
species: 477169

110877
type: SpeciesReference
stoichiometry: 1.0
species: 477168

477227
type: Reaction
kinetic law: 110684
product: 110672
product: 110660
reactant: 110648
fast: false
reversible: true
name: SBPase

477307
type: LocalParameter
value: 0.006744
name: Kp2

477305
type: LocalParameter
value: 1.5597E-5
name: Kp1

477304
type: LocalParameter
value: 1.2713E-5
name: Ks1

477302
type: LocalParameter
value: 0.77294
name: q

477301
type: LocalParameter
value: 0.00568182
name: Vm

110672
type: SpeciesReference
stoichiometry: 1.0
species: 477169

110660
type: SpeciesReference
stoichiometry: 1.0
species: 477157

110648
type: SpeciesReference
stoichiometry: 1.0
species: 477156

477215
type: Reaction
kinetic law: 110126
reactant: 110114
fast: false
reversible: true
name: RuBisCO (5) - EOP

110114
type: SpeciesReference
stoichiometry: 1.0
species: 477139

477139
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.966E-4
initial amount: NaN
in compartment: 477128
name: EOP

477556
type: Parameter
is: SBO:0000009
constant: false
value: -0.00532314322950372
name: W4

477230
type: Reaction
fast: false
reversible: true
name: Ru5P kinase
reactant: 110817
reactant: 110805
product: 110841
modifier: 110853
product: 110829
kinetic law: 110865

110817
type: SpeciesReference
stoichiometry: 1.0
species: 477166

110805
type: SpeciesReference
stoichiometry: 1.0
species: 477159

110841
type: SpeciesReference
stoichiometry: 1.0
species: 477168

110829
type: SpeciesReference
stoichiometry: 1.0
species: 477131

477326
type: LocalParameter
value: 0.568182
name: Vm

477324
type: LocalParameter
value: 9.11825E-5
name: Kp2

477323
type: LocalParameter
value: 9.95868E-5
name: Kp1

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

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

477319
type: LocalParameter
value: 1.05289
name: q

477212
type: Reaction
kinetic law: 110054
product: 110041
product: 110029
reactant: 110017
fast: false
reversible: true
name: RuBisCO (4)

477255
type: LocalParameter
is: SBO:0000009
value: 0.0
name: k2

477253
type: LocalParameter
is: SBO:0000009
value: 6.0
name: k1

110041
type: SpeciesReference
stoichiometry: 1.0
species: 477138

110029
type: SpeciesReference
stoichiometry: 1.0
species: 477141

110017
type: SpeciesReference
stoichiometry: 1.0
species: 477135

477551
type: Parameter
is: SBO:0000009
constant: true
value: 2.22786254125735E12
name: q12

ORG:
  orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
n:
  given: Zoran
  family: Nikoloski

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

477172
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0891250931577478
initial amount: NaN
in compartment: 477128
name: H

477542
type: Parameter
is: SBO:0000196
constant: true
value: 0.0015
name: ADT

477177
type: Species
is version of: CHEBI:16474
constant: true
boundary condition: true
has only substance units: false
initial concentration: 2.1E-4
initial amount: NaN
in compartment: 477128
name: NADPH

477553
type: Parameter
is: SBO:0000009
constant: true
value: 224014.808032967
name: Kp12

477239
type: Reaction
kinetic law: 111276
modifier: 111264
modifier: 111252
product: 111239
reactant: 111227
fast: false
reversible: true
name: cyt. Aldolase (FBP)

477368
type: LocalParameter
value: 0.00568182
name: Vm

477366
type: LocalParameter
value: 2.10226E-5
name: Kp1

477365
type: LocalParameter
value: 3.74778E-4
name: Ks2

477363
type: LocalParameter
value: 2.78407E-4
name: Ks1

477362
type: LocalParameter
value: 1.00224
name: q

111239
type: SpeciesReference
stoichiometry: 1.0
species: 477186

111227
type: SpeciesReference
stoichiometry: 2.0
species: 477181

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

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

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