BIOMD0000000086
type: SBMLModel
reaction: metaid_0000025
reaction: metaid_0000045
species: metaid_0000014
species: metaid_0000008
rule: metaid_0000023
reaction: metaid_0000035
is version of: GO:0008277
reaction: metaid_0000034
reaction: metaid_0000041
species: metaid_0000018
area units: metaid_0000005
volume units: metaid_0000004
curated: true
species: metaid_0000022
occurs in: http://identifiers.org/taxonomy/131567
reaction: metaid_0000026
reaction: metaid_0000043
rule: metaid_0000024
species: metaid_0000012
species: metaid_0000015
species: metaid_0000006
reaction: metaid_0000044
species: metaid_0000009
modified:
  W3 CDTF: Thu Jul 05 15:49:52 BST 2012
created:
  W3 CDTF: Wed Nov 29 17:40:19 GMT 2006
compartment: metaid_0000005
reaction: metaid_0000047
species: metaid_0000019
reaction: metaid_0000040
time units: metaid_0000007
species: metaid_0000020
reaction: metaid_0000048
notes: This model is according to the paper Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction by Bornheimer et al 2004.The figure 3 is reproduced by Copasi 4.0.19 (development) .It is three-dimensional logarithmic plots show the output of simulations of Z and v at various concentrations of R and GAP. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
reaction: metaid_0000029
reaction: metaid_0000033
species: metaid_0000010
species: metaid_0000013
reaction: metaid_0000042
reaction: metaid_0000032
species: metaid_0000007
reaction: metaid_0000039
parameter: metaid_0000003
species: metaid_0000016
creator:
  ORG:
    orgname: University of Oxford
  n:
    given: Enuo
    family: He
reaction: metaid_0000038
parameter: metaid_0000004
is: MODEL4822989369
species: metaid_0000017
reaction: metaid_0000037
is described by: http://identifiers.org/pubmed/15520372
species: metaid_0000021
length unit: length
reaction: metaid_0000046
reaction: metaid_0000036
reaction: metaid_0000027
reaction: metaid_0000031
name: Bornheimer2004_GTPaseCycle
species: metaid_0000011
substance units: metaid_0000020
reaction: metaid_0000030
reaction: metaid_0000028

metaid_0000025
type: Reaction
kinetic law: 177656
product: 177644
reactant: 177632
reactant: 177620
is version of: GO:0005515
fast: false
reversible: true
name: G protein binding GAP

177680
type: LocalParameter
value: 8.0

177668
type: LocalParameter
value: 8780000.0

177644
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000008
type: Species
name: GA
has only substance units: false
initial concentration: 0.0
has part: GO:0005834
constant: false
in compartment: metaid_0000005
has part: IPR000342
boundary condition: false
initial amount: NaN

metaid_0000005
type: Compartment
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

177632
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

metaid_0000006
type: Species
initial amount: NaN
has only substance units: false
is version of: IPR000342
initial concentration: 0.0
notes: GAP
in compartment: metaid_0000005
name: A
constant: false
boundary condition: false

177620
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000007
type: Species
boundary condition: false
initial concentration: 1.0E-8
is: GO:0005834
name: G
constant: false
in compartment: metaid_0000005
initial amount: NaN
has only substance units: false
notes: inactive G protein

metaid_0000045
type: Reaction
fast: false
name: RG*AT hydrolysis
has version: REACT 348
product: 179091
product: 179103
is version of: GO:0003924
kinetic law: 179116
reactant: 179079
reversible: true

179091
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

metaid_0000022
type: Species
initial concentration: 0.0
name: RGAD
has part: CHEBI:17552
boundary condition: false
initial amount: NaN
in compartment: metaid_0000005
has part: IPR000342
has only substance units: false
has part: GO:0005834
has part: GO:0043235
constant: false

179103
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

metaid_0000013
type: Species
is: CHEBI:18367
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0044
initial amount: NaN
in compartment: metaid_0000005
name: Pi

179140
type: LocalParameter
value: 0.00297

179128
type: LocalParameter
value: 25.0

179079
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

metaid_0000021
type: Species
has part: CHEBI:15996
initial concentration: 0.0
initial amount: NaN
has only substance units: false
boundary condition: false
has part: GO:0043235
has part: GO:0005834
in compartment: metaid_0000005
has part: IPR000342
name: RG*AT
constant: false

metaid_0000014
type: Species
is: CHEBI:17552
notes: GDP
constant: false
initial concentration: 1.49E-4
is: C00035
in compartment: metaid_0000005
has only substance units: false
initial amount: NaN
boundary condition: false
name: D

metaid_0000023
notes: The [Gtot]=the initial value of [G]=10e-9 M

metaid_0000035
type: Reaction
has version: REACT 348
is version of: GO:0003924
product: 178378
fast: false
name: RG*T hydrolysis
kinetic law: 178390
reversible: true
reactant: 178354
product: 178366

178378
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

178414
type: LocalParameter
value: 2.22E-9

178402
type: LocalParameter
value: 0.013

178354
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000016
type: Species
initial concentration: 0.0
has part: GO:0005834
name: RG*T
in compartment: metaid_0000005
has part: GO:0043235
initial amount: NaN
constant: false
has part: CHEBI:15996
boundary condition: false
has only substance units: false

178366
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

metaid_0000019
type: Species
has part: GO:0005834
constant: false
has part: CHEBI:17552
has part: GO:0043235
boundary condition: false
initial concentration: 0.0
in compartment: metaid_0000005
initial amount: NaN
name: RGD
has only substance units: false

metaid_0000034
type: Reaction
is version of: GO:0005102
reactant: 178294
reactant: 178282
fast: false
is version of: GO:0001664
name: GD binding Receptor
kinetic law: 178318
product: 178306
reversible: true

178294
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000010
type: Species
has version: IPR000337
notes: Receptor
is version of: GO:0043235
initial concentration: 1.0E-6
boundary condition: false
constant: false
initial amount: NaN
in compartment: metaid_0000005
has only substance units: false
name: R

178282
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000012
type: Species
has only substance units: false
name: GD
constant: false
boundary condition: false
initial amount: NaN
initial concentration: 0.0
has part: CHEBI:17552
in compartment: metaid_0000005
has part: GO:0005834

178342
type: LocalParameter
value: 0.00227

178330
type: LocalParameter
value: 9.47E7

178306
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

metaid_0000041
type: Reaction
reactant: 178788
reactant: 178800
name: GA binding Receptor
product: 178812
is version of: GO:0005102
reversible: true
kinetic law: 178824
is version of: GO:0001664
fast: false

178788
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

178800
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

178812
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

metaid_0000020
type: Species
constant: false
in compartment: metaid_0000005
initial amount: NaN
has only substance units: false
has part: IPR000342
has part: GO:0043235
has part: GO:0005834
name: RGA
initial concentration: 0.0
boundary condition: false

178849
type: LocalParameter
value: 5.43E-5

178837
type: LocalParameter
value: 2.28E7

metaid_0000018
type: Species
constant: false
name: GAD
has part: CHEBI:17552
boundary condition: false
has only substance units: false
has part: IPR000342
initial concentration: 0.0
in compartment: metaid_0000005
initial amount: NaN
has part: GO:0005834

metaid_0000026
type: Reaction
is version of: GO:0005515
product: 177716
fast: false
reversible: true
reactant: 177692
is version of: GO:0005525
name: G protein binding GTP
kinetic law: 177728
reactant: 177704

177716
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000011
type: Species
has only substance units: false
has part: GO:0005834
has part: CHEBI:15996
name: G*T
boundary condition: false
initial concentration: 0.0
constant: false
notes: active G protein
in compartment: metaid_0000005
initial amount: NaN

177692
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

177753
type: LocalParameter
value: 8.38E-6

177741
type: LocalParameter
value: 529000.0

177704
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000009
type: Species
has only substance units: false
boundary condition: false
is: C00044
constant: false
initial concentration: 4.68E-4
initial amount: NaN
is: CHEBI:15996
notes: GTP
in compartment: metaid_0000005
name: T

metaid_0000043
type: Reaction
reactant: 178946
fast: false
is version of: GO:0001664
product: 178958
reactant: 178934
name: G*AT binding Receptor
kinetic law: 178970
reversible: true
is version of: GO:0005102

178946
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

178958
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

178934
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

metaid_0000017
type: Species
boundary condition: false
initial concentration: 0.0
constant: false
in compartment: metaid_0000005
has part: IPR000342
name: G*AT
has only substance units: false
has part: CHEBI:15996
initial amount: NaN
has part: GO:0005834

178994
type: LocalParameter
value: 0.0433

178982
type: LocalParameter
value: 6200000.0

metaid_0000024
notes: The [Gtot]=the initial value of [G]=10e-9 M

metaid_0000015
type: Species
initial amount: NaN
has only substance units: false
name: RG
constant: false
in compartment: metaid_0000005
has part: GO:0005834
has part: GO:0043235
boundary condition: false
initial concentration: 0.0

metaid_0000044
type: Reaction
kinetic law: 179042
product: 179030
reactant: 179018
reactant: 179006
is version of: GO:0032403
fast: false
reversible: true
name: RG*T binding GAP

179067
type: LocalParameter
value: 0.478

179055
type: LocalParameter
value: 6300000.0

179030
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

179018
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

179006
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000047
type: Reaction
reactant: 179224
kinetic law: 179260
fast: false
is version of: GO:0001664
product: 179248
reversible: true
reactant: 179236
is version of: GO:0005102
name: GAD binding Receptor

179224
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

179284
type: LocalParameter
value: 0.00421

179272
type: LocalParameter
value: 4.94E7

179248
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

179236
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000040
type: Reaction
kinetic law: 178752
product: 178740
reactant: 178728
reactant: 178716
is version of: GO:0032403
fast: false
reversible: true
name: RG binding GAP

178776
type: LocalParameter
value: 0.00572

178764
type: LocalParameter
value: 74300.0

178740
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

178728
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

178716
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

metaid_0000048
type: Reaction
kinetic law: 179332
product: 179320
product: 179308
reactant: 179296
is version of: GO:0043241
fast: false
reversible: true
name: RGAD dissociation

179356
type: LocalParameter
value: 2940.0

179344
type: LocalParameter
value: 2.75

179320
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

179308
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

179296
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

metaid_0000029
type: Reaction
kinetic law: 177956
product: 177943
product: 177931
reactant: 177918
is version of: GO:0043241
fast: false
reversible: true
name: GD dissociation

177980
type: LocalParameter
value: 62.3

177968
type: LocalParameter
value: 1.0E-4

177943
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

177931
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

177918
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000033
type: Reaction
kinetic law: 178246
product: 178234
reactant: 178222
reactant: 178209
is version of: GO:0032403
fast: false
reversible: true
name: GD binding GAP

178270
type: LocalParameter
value: 0.95

178258
type: LocalParameter
value: 64100.0

178234
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

178222
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

178209
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000042
type: Reaction
name: RGA binding GTP
reversible: true
reactant: 178861
reactant: 178873
kinetic law: 178897
product: 178885
is version of: GO:0032403
fast: false
is version of: GO:0005525

178861
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

178873
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

178922
type: LocalParameter
value: 0.00875

178909
type: LocalParameter
value: 1620000.0

178885
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

metaid_0000032
type: Reaction
kinetic law: 178172
product: 178160
reactant: 178148
reactant: 178136
is version of: GO:0032403
fast: false
reversible: true
name: G*T binding GAP

178197
type: LocalParameter
value: 0.0408

178185
type: LocalParameter
value: 386000.0

178160
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

178148
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

178136
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000039
type: Reaction
kinetic law: 178680
product: 178667
product: 178655
reactant: 178643
is version of: GO:0043241
fast: false
reversible: true
name: GAD dissociation

178704
type: LocalParameter
value: 3.83

178692
type: LocalParameter
value: 1.0E-4

178667
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

178655
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

178643
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

metaid_0000003
type: Parameter
notes: fractional activity of G proteins
constant: false
value: 0.0
name: Z

metaid_0000038
type: Reaction
name: G*AT hydrolysis
has version: REACT 348
is version of: GO:0003924
kinetic law: 178607
product: 178583
reversible: true
fast: false
product: 178595
reactant: 178571

178631
type: LocalParameter
value: 0.244

178619
type: LocalParameter
value: 25.0

178583
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

178595
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

178571
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

metaid_0000004
type: Parameter
notes: GTP hydrolytic rate
constant: false
value: 0.0
name: v

metaid_0000037
type: Reaction
kinetic law: 178534
fast: false
is version of: GO:0005515
is version of: GO:0005525
reversible: true
product: 178522
reactant: 178510
name: GA binding GTP
reactant: 178498

178559
type: LocalParameter
value: 8.32E-8

178546
type: LocalParameter
value: 44700.0

178522
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

178510
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

178498
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000046
type: Reaction
kinetic law: 179188
product: 179176
reactant: 179164
reactant: 179152
is version of: GO:0032403
fast: false
reversible: true
name: RGD binding GAP

179212
type: LocalParameter
value: 0.685

179200
type: LocalParameter
value: 13000.0

179176
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

179164
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

179152
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

metaid_0000036
type: Reaction
kinetic law: 178462
product: 178450
product: 178438
reactant: 178426
is version of: GO:0043241
fast: false
reversible: true
name: RGD dissociation

178486
type: LocalParameter
value: 1470000.0

178474
type: LocalParameter
value: 2.0

178450
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

178438
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

178426
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

metaid_0000027
type: Reaction
kinetic law: 177803
product: 177791
reactant: 177778
reactant: 177766
is version of: GO:0001664
fast: false
reversible: true
name: G binding Receptor

177829
type: LocalParameter
value: 0.0179

177816
type: LocalParameter
value: 6.36E8

177791
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

177778
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

177766
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000031
type: Reaction
is version of: GO:0005102
fast: false
is version of: GO:0001664
kinetic law: 178100
product: 178088
name: G*T binding Receptor
reactant: 178076
reactant: 178064
reversible: true

178124
type: LocalParameter
value: 1.28

178112
type: LocalParameter
value: 1.32E8

178088
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

178076
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

178064
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000030
type: Reaction
product: 178016
reversible: true
reactant: 177992
is version of: GO:0005525
kinetic law: 178028
is version of: GO:0032403
reactant: 178004
name: RG binding GTP
fast: false

178016
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

177992
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

178052
type: LocalParameter
value: 0.00468

178040
type: LocalParameter
value: 853000.0

178004
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000028
type: Reaction
reactant: 177841
product: 177866
product: 177854
is version of: GO:0003924
kinetic law: 177879
has version: REACT 348
reversible: true
name: G*T hydrolysis
fast: false

177841
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

177866
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

177854
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

177905
type: LocalParameter
value: 9.03E-7

177892
type: LocalParameter
value: 0.013