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507158
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507144
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145191
stoichiometry: 1.0
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506912
is version of: CHEBI:13389
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507045
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507031
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507117
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506850
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506926
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reactant: 143000
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507196
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506953
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507103
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507157
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507143
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145323
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145143
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506993
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506965
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507185
is: SBO:0000009
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506964
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506851
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507118
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507104
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507195
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507257
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145009
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506966
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507033
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506914
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507059
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BIOMD0000000393
rule: 507209
rule: 507199
name: MM s1 + reg 2*n
species: 506918
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reaction: 506926
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function def: 507256
species: 506854
function def: 507236
name: MM s1p2 - reg
species: 506915
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 .
parameter: 507257
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length unit: length
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species: 506902
type: SBMLModel
species: 506871
function def: 507228
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reaction: 506929
name: Competitive inhibition (irr)
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function def: 507255
parameter: 507267
species: 506868
species: 506890
name: MMlike s2p2 + reg 2*c
function def: 507244
species: 506922
reaction: 506965
parameter: 507259
species: 506907
name: starch synthase - Pettersson
reaction: 506946
species: 506852
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reaction: 506934
species: 506904
function def: 507247
reaction: 506928
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name: MMlike s2p2 + reg 1*c
rule: 507201
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species: 506891
species: 506920
curated: true
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species: 506887
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parameter: 507265
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reaction: 506938
rule: 507227
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506924
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modifier: 142892
modifier: 142856
product: 142844
modifier: 142880
name: RuBisCO - CO2
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fast: false
reversible: false
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144241
stoichiometry: 1.0
species: 506906
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507105
is: SBO:0000009
value: 50.0
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507258
is: SBO:0000009
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name: cP
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507043
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value: 15.0
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507155
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145335
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507145
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value: 6.0
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145155
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506991
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506867
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143374
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is: SBO:0000009
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507032
is: SBO:0000009
value: 2.5
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506915
is part of: CHEBI:17234
constant: true
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507269
is: SBO:0000009
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name: K52a
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507058
is: SBO:0000009
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506952
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name: F26BPc phosphatase
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506925
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507259
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constant: true
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144253
stoichiometry: 1.0
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506968
type: Reaction
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name: GCEA dehydrogenase
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506936
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144853
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507021
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506958
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name: GPT - GCA
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506978
is: SBO:0000009
value: 30.1408
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507041
is: SBO:0000009
value: 0.3
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145083
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507107
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145107
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type: SpeciesReference

507266
is: SBO:0000009
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name: Wc*min
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506999
is: SBO:0000009
value: 0.1
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144505
stoichiometry: 1.0
species: 506904
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506916
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name: KGc
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506969
kinetic law: 145383
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reversible: true
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product: 145359
product: 145347
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reactant: 145335
name: GLUc:GOAc aminotransferase

144289
stoichiometry: 1.0
species: 506903
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507147
is: SBO:0000009
value: 0.22
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506937
kinetic law: 143674
product: 143662
reactant: 143650
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fast: false
reversible: true
name: ATP synthetase
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506997
is: SBO:0000009
value: 12.0
name: Kr2
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507109
is: SBO:0000009
value: 0.555034
name: Vm
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506979
is: SBO:0000009
value: 0.24
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507040
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507189
is: SBO:0000009
value: 2.0
name: Kr1
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506998
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value: 3.12207
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143807
stoichiometry: 1.0
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507267
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name: Wo*min
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506989
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507167
is: SBO:0000009
value: 0.21
name: Ks1
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144865
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species: 506878
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506996
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value: 0.7
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506938
reversible: false
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modifier: 143710
name: AGPase
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reactant: 143686
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507139
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506975
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506956
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modifier: 144733
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name: GPT - GCEAc
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507129
is: SBO:0000027
value: 5.0
name: Km
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506948
modifier: 144361
reactant: 144289
modifier: 144337
modifier: 144397
product: 144313
name: SucPc synthase
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kinetic law: 144409
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product: 144325
modifier: 144385
fast: false
reversible: true
reactant: 144301

507188
is: SBO:0000009
value: 1.7
name: Ks1
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144517
stoichiometry: 1.0
species: 506922
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506928
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product: 143084
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506918
is: CHEBI:43474
constant: false
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506976
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145095
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506995
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507149
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value: 0.2
name: Km
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507159
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506957
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modifier: 144781
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506949
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506908
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143205
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507179
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506919
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constant: false
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initial concentration: 4.0999844
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name: PiTc
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506977
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506929
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507169
is: SBO:0000009
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144661
stoichiometry: 1.0
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507265
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507187
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143638
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143217
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143795
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506871
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506907
is: CHEBI:16308
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506973
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506849
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506983
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506859
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507137
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506906
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506860
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143987
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506899
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506984
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143157
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145021
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143229
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506888
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144685
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506985
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initial concentration: 7.8E-6
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ORG:
  orgname: Max-Planck-Institute of Molecular Plant Physiology
n:
  given: Anne
  family: Arnold

143999
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144325
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506854
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507113
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143518
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W3 CDTF: Mon Oct 24 12:17:58 BST 2011

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507037
is: SBO:0000009
value: 5.734
name: q
type: LocalParameter

507055
is: SBO:0000009
value: 0.74
name: KA
type: LocalParameter

507069
is: SBO:0000009
value: 0.25
name: KR2
type: LocalParameter

506910
is version of: http://identifiers.org/pubchem.compound/6133
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.75
initial amount: NaN
in compartment: 506845
name: UTPc
type: Species

507172
is: SBO:0000009
value: 1.45611
name: V
type: LocalParameter

143338
stoichiometry: 1.0
species: 506862
type: SpeciesReference

144445
stoichiometry: 1.0
species: 506918
type: SpeciesReference

507047
is: SBO:0000009
value: 0.08
name: K1
type: LocalParameter

143554
stoichiometry: 1.0
species: 506872
type: SpeciesReference

507094
is: SBO:0000009
value: 0.11
name: Kp2
type: LocalParameter

507027
is: SBO:0000009
value: 0.05
name: Ks1
type: LocalParameter

507152
is: SBO:0000009
value: 0.22
name: Ki
type: LocalParameter

507142
is: SBO:0000009
value: 5.0
name: V
type: LocalParameter

144709
stoichiometry: 1.0
species: 506891
type: SpeciesReference

507089
is: SBO:0000009
value: 0.31
name: q
type: LocalParameter

507075
is: SBO:0000009
value: 0.63
name: KR1
type: LocalParameter

507017
is: SBO:0000009
value: 3.12207
name: Vm
type: LocalParameter

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