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name: MM s1 + reg 2*n
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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 and photorespiration by Zhu et al. (2007, DOI:10.1104/pp.107.103713 ) and the personally provided implementation. The parameter values are partly taken from Pettersson and Ryde-Pettersson (1988,DOI:10.1111/j.1432-1033.1988.tb14242.x ). 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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506932
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143338
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506862
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143326
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506860
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143314
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506966
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145203
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145215
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506888
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145179
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507175
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507174
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507173
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145191
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506919
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506954
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507135
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507133
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144685
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506880
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506916
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506948
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506911
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144289
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144313
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507101
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507100
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507096
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507103
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507097
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507105
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507104
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507099
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507107
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144325
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144301
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506876
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506936
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507027
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507025
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507032
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507033
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507031
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507028
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507035
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507029
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507024
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506867
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506870
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143542
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143530
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143554
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143518
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506912
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506969
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product: 145347
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name: GLUc:GOAc aminotransferase

507191
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507189
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507188
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507187
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507185
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145359
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145347
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145323
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145335
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W3 CDTF: Mon Oct 24 12:17:58 BST 2011

142796
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507266
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506953
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name: Succ degradation

507131
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507129
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144661
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506941
type: Reaction
reversible: false
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fast: false
kinetic law: 143975
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name: TPT - GAP
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reactant: 143879
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507070
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507069
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507067
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507066
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507065
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507063
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143879
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143891
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142820
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506961
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144901
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507159
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507158
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507157
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507155
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507154
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507153
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144913
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144925
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506968
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145251
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145263
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506914
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145287
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507183
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507181
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507180
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507179
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145275
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506933
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507016
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507015
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507013
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507012
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143398
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143386
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143374
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507269
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506956
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507140
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507139
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507137
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144721
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144709
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ORG:
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n:
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506960
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507152
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507151
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507149
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144865
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144853
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506937
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name: ATP synthetase

507043
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507041
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507040
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507039
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507037
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143662
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143650
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143638
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506925
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142952
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142964
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142927
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142940
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506982
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506981
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506979
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506978
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506958
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507147
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507145
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507144
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144817
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144805
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507263
type: Parameter
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506970
type: Reaction
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reactant: 145395
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name: GLYc decarboxylase

507196
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507195
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507193
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145407
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145395
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506942
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product: 143999
name: TPT - DHAP
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modifier: 144023
modifier: 144035

507077
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507076
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507075
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507073
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507072
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507071
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143987
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143999
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506962
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507164
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507163
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507161
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507160
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145021
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145009
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506930
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143217
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143205
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143241
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143229
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507005
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507003
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507002
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507001
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506999
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506998
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ORG:
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n:
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506950
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144481
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144505
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144493
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507122
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507119
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507118
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507114
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144517
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506924
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142832
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142844
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506977
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506976
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506975
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506973
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506972
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506971
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506957
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507143
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507142
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507141
type: LocalParameter
is: SBO:0000027
value: 0.39
name: Km

144769
type: SpeciesReference
stoichiometry: 1.0
species: 506891

144757
type: SpeciesReference
stoichiometry: 1.0
species: 506879

506856
type: Species
is version of: http://identifiers.org/pubchem.compound/439958
constant: false
boundary condition: true
has only substance units: false
initial concentration: 1.47375779111085
initial amount: NaN
in compartment: 506843
name: G6P

506882
type: Species
is version of: CHEBI:15279
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.2646
initial amount: NaN
in compartment: 506843
name: O2

507258
type: Parameter
is: SBO:0000009
constant: true
value: 15.0
name: cP

506945
type: Reaction
kinetic law: 144205
modifier: 144193
product: 144181
product: 144169
reactant: 144157
fast: false
reversible: true
name: FBPcase

507088
type: LocalParameter
is: SBO:0000009
value: 0.063979
name: Vm

507087
type: LocalParameter
is: SBO:0000009
value: 12.0
name: Kp2

507085
type: LocalParameter
is: SBO:0000009
value: 0.7
name: Kp1

507084
type: LocalParameter
is: SBO:0000009
value: 6663.0
name: q

144181
type: SpeciesReference
stoichiometry: 1.0
species: 506918

144169
type: SpeciesReference
stoichiometry: 1.0
species: 506903

144157
type: SpeciesReference
stoichiometry: 1.0
species: 506898

507261
type: Parameter
is: SBO:0000009
constant: true
value: 15.0
name: cPc

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

W3 CDTF: Fri Apr 20 20:50:41 BST 2012