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BIOMD0000000391
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reaction: metaid_0000053
occurs in: http://identifiers.org/taxonomy/33090
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species: metaid_0000032
name: MM s1 + reg 5*c (RuBisCO)
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 pathway to starch synthesis by Poolman et al. (2000, DOI:10.1093/jexbot/51.suppl_1.319 ). The parameter values are widely taken from Pettersson and Ryde-Pettersson (1988,DOI:10.1111/j.1432-1033.1988.tb14242.x ) and Poolman (1999,[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 .
reaction: metaid_0000045
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creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
created:
  W3 CDTF: Fri Sep 16 15:50:04 BST 2011
units def: metaid_0000011
modified:
  W3 CDTF: Fri Apr 20 20:50:00 BST 2012
type: SBMLModel
is: MODEL1109270007
species: metaid_0000027
species: metaid_0000024
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name: Arnold2011_Poolman2000_CalvinCycle_Starch
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name: MM s1 + reg 2*c (FBPase)
species: metaid_0000015
name: starch synthase
curated: true
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is: GO:0019253
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length unit: length
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name: MM s2 + reg 3*c-s1,1*m-s2 (Ru5P kinase)
species: metaid_0000020
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name: MM s1 + reg 1*c (SBPase, starch phos)
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creator:
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    orgname: EMBL-EBI
  n:
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    family: Chelliah
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name: MM s2 - reg (ATP synth)
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time units: 949038
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name: MM s1 + reg A,3*c (TPT)
is described by: http://identifiers.org/pubmed/22001849

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is version of: CHEBI:15946
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notes: Poolman (1999)
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metaid_0000012
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notes: changed velocity in accordance with the authors: (...)/(G1P+Km1)((1+[ADP]/Ki)([ATP]+Km2*(...)))
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089894
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is version of: http://identifiers.org/pubchem.compound/668

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constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.47375779111085
initial amount: NaN
in compartment: metaid_0000012
name: G6P
type: Species

448394
is: SBO:0000009
value: 4.0
name: KR3
type: LocalParameter

448355
is: SBO:0000009
value: 0.84
name: KR1
type: LocalParameter

metaid_0000047
kinetic law: 090340
product: 090328
product: 090316
reactant: 090304
reactant: 090292
fast: false
reversible: true
name: S7P transketolase
type: Reaction

448388
is: SBO:0000009
value: 1000.0
name: Vm
type: LocalParameter

090184
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

089918
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

448374
is: SBO:0000009
value: 12.0
name: KR2
type: LocalParameter

448365
is: SBO:0000009
value: 31.25
name: k2
type: LocalParameter

448432
is: SBO:0000009
value: 0.63
name: KR1
type: LocalParameter

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

given: Zoran
family: Nikoloski