BIOMD0000000326
type: SBMLModel
reaction: 044905
parameter: 045059
species: 044723
reaction: 044816
reaction: 044847
parameter: 045072
parameter: 045146
parameter: 045084
species: 044793
species: 044752
parameter: 045161
species: 044770
parameter: 045173
species: 044800
area units: area
reaction: 044920
reaction: 044831
species: 044745
parameter: 045130
parameter: 045125
parameter: 045165
parameter: 045137
reaction: 044917
rule: 045020
reaction: 044828
species: 044747
species: 044797
species: 044740
species: 044776
rule: 045008
reaction: 044901
reaction: 044812
reaction: 044843
species: 044733
reaction: 044855
reaction: 044870
parameter: 045118
parameter: 045149
reaction: 044882
name: DellOrco2009_phototransduction
parameter: 045042
species: 044735
species: 044717
reaction: 044872
species: 044762
rule: 044988
parameter: 045046
rule: 044996
species: 044782
parameter: 045070
reaction: 044913
species: 044748
parameter: 045048
occurs in: http://identifiers.org/taxonomy/10090
reaction: 044836
reaction: 044867
parameter: 045061
species: 044757
parameter: 045135
parameter: 045054
parameter: 045150
reaction: 044896
rule: 044991
species: 044786
species: 044790
species: 044788
species: 044792
parameter: 045082
species: 044783
parameter: 045094
reaction: 044906
rule: 045031
reaction: 044817
reaction: 044848
rule: 045001
parameter: 045109
rule: 044990
parameter: 045162
parameter: 045174

044905
type: Reaction
is version of: GO:0043241
kinetic law: 784967
reversible: false
product: 784931
notes: One out of two PDE subunits is deactivated and one GTP is hydrolyzed
name: v_r23
product: 784955
product: 784943
reactant: 784919
fast: false

784931
type: SpeciesReference
stoichiometry: 1.0
species: 044722

044722
type: Species
initial concentration: 0.0
initial amount: NaN
has part: P27600
constant: false
has part: CHEBI:17552
has only substance units: false
name: Ga_GDP
is: SBO:0000296
in compartment: 044715
boundary condition: false

044715
type: Compartment
is version of: GO:0005829
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytosol

784955
type: SpeciesReference
stoichiometry: 1.0
species: 044798

044798
type: Species
name: RGS
has only substance units: false
initial amount: NaN
is: SBO:0000252
boundary condition: false
initial concentration: 3000000.0
constant: false
is version of: O54828
in compartment: 044715

784943
type: SpeciesReference
stoichiometry: 1.0
species: 044737

044737
type: Species
initial amount: NaN
constant: false
has part: CHEBI:15996
initial concentration: 0.0
in compartment: 044715
name: PDE_a_Ga_GTP
has part: P27600
is: SBO:0000296
boundary condition: false
has part: P09174
has only substance units: false

784919
type: SpeciesReference
stoichiometry: 1.0
species: 044800

044800
type: Species
has only substance units: false
initial amount: NaN
has part: CHEBI:15996
initial concentration: 0.0
has part: P27600
has part: P09174
has part: O54828
name: RGS_Ga_GTP_a_PDE_a_Ga_GTP
in compartment: 044715
constant: false
boundary condition: false
is: SBO:0000296

045059
type: Parameter
constant: true
value: 0.6
name: omega

044723
type: Species
initial amount: NaN
in compartment: 044715
boundary condition: false
constant: false
has part: P27600
name: Ga_GTP
has part: CHEBI:15996
is: SBO:0000296
has only substance units: false
initial concentration: 0.0

044816
type: Reaction
is version of: GO:0006461
reactant: 781889
reactant: 781877
notes: Rn and RK binding before phospohorylation occurs
reversible: true
product: 781901
fast: false
kinetic law: 781913
name: v_r2_6

781889
type: SpeciesReference
stoichiometry: 1.0
species: 044802

044802
type: Species
initial amount: NaN
name: RK
is version of: Q9WVL4
has only substance units: false
initial concentration: 10838.0
constant: false
boundary condition: false
is: SBO:0000252
in compartment: 044715

781877
type: SpeciesReference
stoichiometry: 1.0
species: 044790

044790
type: Species
constant: false
initial concentration: 0.0
is: SBO:0000252
boundary condition: false
initial amount: NaN
is version of: C02456
name: R6
in compartment: 044715
has only substance units: false

781901
type: SpeciesReference
stoichiometry: 1.0
species: 044797

044797
type: Species
constant: false
is: SBO:0000297
boundary condition: false
has part: Q9WVL4
has part: C02456
in compartment: 044715
name: R6_RKpre
has only substance units: false
initial amount: NaN
initial concentration: 0.0

044847
type: Reaction
kinetic law: 783036
product: 783024
reactant: 783012
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_0

783024
type: SpeciesReference
stoichiometry: 1.0
species: 044730

044730
type: Species
constant: false
initial amount: NaN
is version of: O35599
name: Ops
in compartment: 044715
is: SBO:0000252
boundary condition: false
has only substance units: false
initial concentration: 0.0

783012
type: SpeciesReference
stoichiometry: 1.0
species: 044740

044740
type: Species
is: SBO:0000252
boundary condition: false
initial concentration: 0.0
has only substance units: false
name: R0
has part: P15409
constant: false
in compartment: 044715
initial amount: NaN

045072
type: Parameter
constant: true
value: 7.0E-4
name: kRrecyc

045146
type: Parameter
constant: false
value: 0.0
name: kRK1_3

045084
type: Parameter
constant: true
value: 0.05
name: kGshutoff

044793
type: Species
has only substance units: false
has part: C02456
has part: CHEBI:15996
name: R6_G_GTP
boundary condition: false
initial concentration: 0.0
in compartment: 044715
is: SBO:0000296
constant: false
initial amount: NaN
has part: Q3U6B2

044752
type: Species
has part: Q9WVL4
constant: false
in compartment: 044715
has part: C02456
initial concentration: 0.0
name: R1_RKpost
is: SBO:0000297
has only substance units: false
initial amount: NaN
boundary condition: false

045161
type: Parameter
constant: false
value: 0.0
name: kG1_1

044770
type: Species
is: SBO:0000297
constant: false
has part: C02456
initial amount: NaN
in compartment: 044715
initial concentration: 0.0
has only substance units: false
has part: Q9WVL4
name: R3_RKpost
boundary condition: false

045173
type: Parameter
constant: false
value: 0.0
name: alfamax

044920
type: Reaction
kinetic law: 785486
modifier: 785474
modifier: 785462
reactant: 785450
notes: Hydrolysis by means of PDE
fast: false
reversible: false
name: v_r35

044726
type: Species
name: Ga_GTP_a_PDE_a_Ga_GTP
is: SBO:0000296
has part: P27600
has only substance units: false
has part: CHEBI:15996
initial concentration: 0.0
in compartment: 044715
boundary condition: false
initial amount: NaN
constant: false
has part: P09174

785450
type: SpeciesReference
stoichiometry: 1.0
species: 044805

044805
type: Species
constant: false
has only substance units: false
in compartment: 044715
initial concentration: 4.0
is: SBO:0000247
name: cGMP
boundary condition: false
initial amount: NaN
is version of: CHEBI:16356

044831
type: Reaction
kinetic law: 782421
fast: false
is version of: GO:0043241
reversible: false
name: v_r4_6
product: 782397
product: 782409
reactant: 782385
notes: Dissociation of Rn and RK

782397
type: SpeciesReference
stoichiometry: 1.0
species: 044790

782409
type: SpeciesReference
stoichiometry: 1.0
species: 044802

782385
type: SpeciesReference
stoichiometry: 1.0
species: 044796

044796
type: Species
has part: Q9WVL4
initial concentration: 0.0
has part: C02456
has only substance units: false
boundary condition: false
name: R6_RKpost
initial amount: NaN
in compartment: 044715
constant: false
is: SBO:0000297

044745
type: Species
in compartment: 044715
initial concentration: 0.0
is version of: Q9WVL4
is: SBO:0000297
constant: false
boundary condition: false
has only substance units: false
initial amount: NaN
is version of: P15409
name: R0_RKpre

045130
type: Parameter
constant: false
value: 0.0
name: premag

045125
type: Parameter
constant: true
value: 400.0
name: eT

045165
type: Parameter
constant: false
value: 0.0
name: kG1_4

045137
type: Parameter
constant: false
value: 0.0
name: preflash

044917
type: Reaction
kinetic law: 785402
modifier: 785390
product: 785377
notes: Influx of extracellular Ca2+ through cGMP-gated cation channels
fast: false
reversible: false
name: v_r33

785377
type: SpeciesReference
stoichiometry: 1.0
species: 044720

044720
type: Species
has only substance units: false
in compartment: 044715
boundary condition: false
constant: false
initial amount: NaN
initial concentration: 0.6
name: Ca2_free
is: SBO:0000247
is version of: CHEBI:29108
is version of: C00076

044828
type: Reaction
reactant: 782288
name: v_r4_4
product: 782300
reversible: false
product: 782312
notes: Dissociation of Rn and RK
fast: false
is version of: GO:0043241
kinetic law: 782324

782288
type: SpeciesReference
stoichiometry: 1.0
species: 044778

044778
type: Species
boundary condition: false
has part: C02456
name: R4_RKpost
has part: Q9WVL4
has only substance units: false
initial amount: NaN
initial concentration: 0.0
in compartment: 044715
constant: false
is: SBO:0000297

782300
type: SpeciesReference
stoichiometry: 1.0
species: 044772

044772
type: Species
in compartment: 044715
constant: false
name: R4
initial amount: NaN
boundary condition: false
has only substance units: false
initial concentration: 0.0
is version of: C02456
is: SBO:0000252

782312
type: SpeciesReference
stoichiometry: 1.0
species: 044802

044747
type: Species
constant: false
in compartment: 044715
has part: P20443
is: SBO:0000297
initial concentration: 0.0
initial amount: NaN
has only substance units: false
boundary condition: false
name: R1_Arr
has part: C02456

044776
type: Species
name: R4_G_GTP
has part: Q3U6B2
constant: false
boundary condition: false
initial concentration: 0.0
is: SBO:0000296
initial amount: NaN
has only substance units: false
has part: CHEBI:15996
in compartment: 044715
has part: C02456

044901
type: Reaction
reactant: 784786
reversible: false
is version of: GO:0006461
fast: false
kinetic law: 784823
product: 784811
notes: Here PDE has two Ga bound but only one active subunit
reactant: 784799
name: v_r20

784786
type: SpeciesReference
stoichiometry: 1.0
species: 044723

784811
type: SpeciesReference
stoichiometry: 1.0
species: 044725

044725
type: Species
constant: false
in compartment: 044715
boundary condition: false
is: SBO:0000296
has part: P27600
name: Ga_GTP_PDE_a_Ga_GTP
has part: P09174
has part: CHEBI:15996
initial concentration: 0.0
has only substance units: false
initial amount: NaN

784799
type: SpeciesReference
stoichiometry: 1.0
species: 044737

044812
type: Reaction
reactant: 781742
name: v_r2_3
fast: false
kinetic law: 781766
reactant: 781730
is version of: GO:0006461
notes: Rn and RK binding before phospohorylation occurs
reversible: true
product: 781754

781742
type: SpeciesReference
stoichiometry: 1.0
species: 044802

781730
type: SpeciesReference
stoichiometry: 1.0
species: 044763

044763
type: Species
in compartment: 044715
has only substance units: false
initial concentration: 0.0
initial amount: NaN
name: R3
is: SBO:0000252
constant: false
boundary condition: false
is version of: C02456

781754
type: SpeciesReference
stoichiometry: 1.0
species: 044771

044771
type: Species
has only substance units: false
is: SBO:0000297
has part: Q9WVL4
boundary condition: false
initial concentration: 0.0
constant: false
has part: C02456
name: R3_RKpre
in compartment: 044715
initial amount: NaN

044843
type: Reaction
fast: false
product: 782891
kinetic law: 782903
product: 782879
is version of: GO:0046155
name: v_r6_4
notes: Arrestin mediated R -> ops
reversible: false
reactant: 782867

782891
type: SpeciesReference
stoichiometry: 1.0
species: 044730

782879
type: SpeciesReference
stoichiometry: 1.0
species: 044717

044717
type: Species
boundary condition: false
constant: false
is version of: P20443
has only substance units: false
is: SBO:0000252
in compartment: 044715
name: Arr
initial amount: NaN
initial concentration: 3.13E7

782867
type: SpeciesReference
stoichiometry: 1.0
species: 044773

044773
type: Species
is: SBO:0000297
name: R4_Arr
in compartment: 044715
has part: P20443
has only substance units: false
constant: false
boundary condition: false
initial concentration: 0.0
initial amount: NaN
has part: C02456

044733
type: Species
has part: Q8CFY0
has part: O35599
has only substance units: false
in compartment: 044715
name: Ops_Gt
is: SBO:0000297
initial amount: NaN
boundary condition: false
initial concentration: 0.0
constant: false

044855
type: Reaction
kinetic law: 783253
product: 783241
reactant: 783228
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_6

783241
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783228
type: SpeciesReference
stoichiometry: 1.0
species: 044790

044870
type: Reaction
name: v_r13_6
is version of: GO:0006461
reactant: 783760
fast: false
notes: Rhodopsin and transducin binding
reactant: 783772
reversible: true
kinetic law: 783796
product: 783784

783760
type: SpeciesReference
stoichiometry: 1.0
species: 044728

044728
type: Species
initial amount: NaN
name: Gt
constant: false
in compartment: 044715
boundary condition: false
has only substance units: false
is: SBO:0000252
is version of: Q8CFY0
initial concentration: 3.6E8

783772
type: SpeciesReference
stoichiometry: 1.0
species: 044790

783784
type: SpeciesReference
stoichiometry: 1.0
species: 044795

044795
type: Species
initial amount: NaN
constant: false
is: SBO:0000297
name: R6_Gt
boundary condition: false
has part: C02456
in compartment: 044715
has part: Q8CFY0
has only substance units: false
initial concentration: 0.0

045118
type: Parameter
constant: true
value: 47.554
name: gammaCa

045149
type: Parameter
constant: false
value: 0.0
name: kRK1_5

044882
type: Reaction
kinetic law: 784157
product: 784145
reactant: 784133
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_2

784145
type: SpeciesReference
stoichiometry: 1.0
species: 044758

044758
type: Species
initial concentration: 0.0
has part: C02456
is: SBO:0000296
has part: Q3U6B2
boundary condition: false
constant: false
has part: CHEBI:15996
name: R2_G_GTP
has only substance units: false
in compartment: 044715
initial amount: NaN

784133
type: SpeciesReference
stoichiometry: 1.0
species: 044757

044757
type: Species
has part: Q3U6B2
boundary condition: false
has only substance units: false
initial amount: NaN
has part: C02456
in compartment: 044715
name: R2_G
initial concentration: 0.0
is: SBO:0000297
constant: false

045042
type: Parameter
constant: true
value: 1.335E7
name: PDEtot

044735
type: Species
boundary condition: false
has only substance units: false
initial amount: NaN
name: PDE
in compartment: 044715
constant: false
is: SBO:0000252
is version of: P09174
initial concentration: 1.335E7

044872
type: Reaction
kinetic law: 783868
product: 783856
reactant: 783844
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_1

783856
type: SpeciesReference
stoichiometry: 1.0
species: 044748

044748
type: Species
has part: Q3U6B2
boundary condition: false
has part: C02456
initial concentration: 0.0
has only substance units: false
name: R1_G
is: SBO:0000297
initial amount: NaN
in compartment: 044715
constant: false

783844
type: SpeciesReference
stoichiometry: 1.0
species: 044751

044751
type: Species
is: SBO:0000297
has only substance units: false
name: R1_Gt
in compartment: 044715
initial amount: NaN
initial concentration: 0.0
constant: false
has part: Q8CFY0
boundary condition: false
has part: C02456

044762
type: Species
is: SBO:0000297
has only substance units: false
name: R2_RKpre
boundary condition: false
initial amount: NaN
in compartment: 044715
constant: false
initial concentration: 0.0
has part: Q9WVL4
has part: C02456

045046
type: Parameter
constant: true
value: 3000000.0
name: RGStot

044782
type: Species
name: R5_Arr
initial concentration: 0.0
has part: P20443
has only substance units: false
is: SBO:0000297
constant: false
boundary condition: false
initial amount: NaN
in compartment: 044715
has part: C02456

045070
type: Parameter
constant: true
value: 0.0445091
name: kA3

044913
type: Reaction
is version of: GO:0050254
kinetic law: 785304
fast: false
notes: RK inhibition by Rec_2Ca (Rec_wCa2 is determined using QSSA and not directly)
reactant: 785268
reversible: true
product: 785280
modifier: 785292
name: v_r30

785268
type: SpeciesReference
stoichiometry: 1.0
species: 044802

785280
type: SpeciesReference
stoichiometry: 1.0
species: 044803

044803
type: Species
has only substance units: false
in compartment: 044715
boundary condition: false
constant: false
name: Rec_wCa2_RK
is: SBO:0000296
initial concentration: 4204560.0
has part: Q9WVL4
has part: CHEBI:29108
has part: P34057
initial amount: NaN

045048
type: Parameter
constant: true
value: 0.0
name: flashBG

044836
type: Reaction
kinetic law: 782614
product: 782601
reversible: true
is version of: GO:0006461
notes: Binding of activated R to Arrestin
name: v_r5_4
reactant: 782577
fast: false
reactant: 782589

782601
type: SpeciesReference
stoichiometry: 1.0
species: 044773

782577
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782589
type: SpeciesReference
stoichiometry: 1.0
species: 044772

044867
type: Reaction
notes: Rhodopsin and transducin binding
reversible: true
reactant: 783675
kinetic law: 783700
fast: false
is version of: GO:0006461
reactant: 783663
name: v_r13_4
product: 783688

783675
type: SpeciesReference
stoichiometry: 1.0
species: 044772

783663
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783688
type: SpeciesReference
stoichiometry: 1.0
species: 044777

044777
type: Species
name: R4_Gt
is: SBO:0000297
initial concentration: 0.0
in compartment: 044715
has part: C02456
has part: Q8CFY0
has only substance units: false
initial amount: NaN
boundary condition: false
constant: false

045061
type: Parameter
constant: true
value: 10838.0
name: RKdark

045135
type: Parameter
constant: false
value: 0.0
name: del

045054
type: Parameter
constant: true
value: 0.001
name: flashDur

045150
type: Parameter
constant: false
value: 0.0
name: kRK1_6

044896
type: Reaction
product: 784629
reactant: 784605
is version of: GO:0043241
name: v_r16_6
kinetic law: 784641
product: 784617
reversible: false
fast: false
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP

784629
type: SpeciesReference
stoichiometry: 1.0
species: 044790

784605
type: SpeciesReference
stoichiometry: 1.0
species: 044793

784617
type: SpeciesReference
stoichiometry: 1.0
species: 044721

044721
type: Species
constant: false
initial amount: NaN
is: SBO:0000296
in compartment: 044715
has part: CHEBI:15996
initial concentration: 0.0
boundary condition: false
name: G_GTP
has part: Q3U6B2
has only substance units: false

044786
type: Species
constant: false
has only substance units: false
initial amount: NaN
in compartment: 044715
has part: Q8CFY0
has part: C02456
is: SBO:0000297
name: R5_Gt
initial concentration: 0.0
boundary condition: false

044788
type: Species
name: R5_RKpre
constant: false
is: SBO:0000297
has part: C02456
boundary condition: false
has only substance units: false
has part: Q9WVL4
initial concentration: 0.0
in compartment: 044715
initial amount: NaN

044792
type: Species
is: SBO:0000297
boundary condition: false
initial amount: NaN
in compartment: 044715
constant: false
name: R6_G
initial concentration: 0.0
has only substance units: false
has part: C02456
has part: Q3U6B2

045082
type: Parameter
constant: true
value: 200.0
name: kG7

044783
type: Species
initial amount: NaN
has part: Q3U6B2
has only substance units: false
initial concentration: 0.0
is: SBO:0000297
boundary condition: false
in compartment: 044715
constant: false
has part: C02456
name: R5_G

045094
type: Parameter
constant: true
value: 1.57E-7
name: kRGS1

044906
type: Reaction
fast: false
reactant: 784991
reactant: 784979
notes: RGS binds to a PDE-Ga complex with one active subunit to form a complex. Here we assume that the association rate constant is the same as in v_r22
name: v_r24
is version of: GO:0006461
product: 785003
reversible: false
kinetic law: 785015

784991
type: SpeciesReference
stoichiometry: 1.0
species: 044798

784979
type: SpeciesReference
stoichiometry: 1.0
species: 044737

785003
type: SpeciesReference
stoichiometry: 1.0
species: 044801

044801
type: Species
is: SBO:0000296
has part: CHEBI:15996
initial concentration: 0.0
initial amount: NaN
has part: P09174
has only substance units: false
in compartment: 044715
boundary condition: false
has part: P27600
constant: false
has part: O54828
name: RGS_PDE_a_Ga_GTP

044817
type: Reaction
kinetic law: 781949
product: 781937
reactant: 781925
notes: Phosphorylation of Rn to Rn+1. In these reactions ATP (left) and ADP (right) are included in the rate constants
is version of: GO:0016310
fast: false
reversible: false
name: v_r3_0

781937
type: SpeciesReference
stoichiometry: 1.0
species: 044752

781925
type: SpeciesReference
stoichiometry: 1.0
species: 044745

044848
type: Reaction
kinetic law: 783072
product: 783060
reactant: 783048
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_1

783060
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783048
type: SpeciesReference
stoichiometry: 1.0
species: 044746

044746
type: Species
in compartment: 044715
initial concentration: 0.0
name: R1
boundary condition: false
constant: false
is version of: C02456
has only substance units: false
is: SBO:0000252
initial amount: NaN

045109
type: Parameter
constant: true
value: 4.3E-4
name: betasub

045162
type: Parameter
constant: false
value: 0.0
name: kG1_2

045174
type: Parameter
constant: false
value: 0.0
name: J

044820
type: Reaction
kinetic law: 782021
product: 782009
reactant: 781997
notes: Phosphorylation of Rn to Rn+1. In these reactions ATP (left) and ADP (right) are included in the rate constants
is version of: GO:0016310
fast: false
reversible: false
name: v_r3_2

782009
type: SpeciesReference
stoichiometry: 1.0
species: 044770

781997
type: SpeciesReference
stoichiometry: 1.0
species: 044762

044832
type: Reaction
kinetic law: 782469
is version of: GO:0006461
notes: Binding of activated R to Arrestin
reactant: 782433
fast: false
reactant: 782445
name: v_r5_1
product: 782457
reversible: true

782433
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782445
type: SpeciesReference
stoichiometry: 1.0
species: 044746

782457
type: SpeciesReference
stoichiometry: 1.0
species: 044747

045131
type: Parameter
constant: false
value: 0.0
name: mag

044890
type: Reaction
name: v_r16_1
product: 784374
product: 784386
fast: false
reactant: 784362
reversible: false
is version of: GO:0043241
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP
kinetic law: 784398

784374
type: SpeciesReference
stoichiometry: 1.0
species: 044721

784386
type: SpeciesReference
stoichiometry: 1.0
species: 044746

784362
type: SpeciesReference
stoichiometry: 1.0
species: 044750

044750
type: Species
constant: false
has part: Q3U6B2
initial concentration: 0.0
name: R1_G_GTP
has part: C02456
has only substance units: false
boundary condition: false
is: SBO:0000296
in compartment: 044715
initial amount: NaN
has part: CHEBI:15996

045138
type: Parameter
constant: false
value: 0.0
name: testflash

045050
type: Parameter
constant: true
value: 0.001
name: flash0Dur

044918
type: Reaction
kinetic law: 785438
modifier: 785426
product: 785414
notes: Synthesis by means of Guanylyl cyclase
fast: false
reversible: false
name: v_r34

785414
type: SpeciesReference
stoichiometry: 1.0
species: 044805

045066
type: Parameter
constant: true
value: 0.81323
name: omega_arr

045097
type: Parameter
constant: true
value: 9.68777
name: kRec3

044732
type: Species
has part: CHEBI:15996
in compartment: 044715
has only substance units: false
initial concentration: 0.0
has part: O35599
boundary condition: false
constant: false
has part: Q3U6B2
initial amount: NaN
name: Ops_G_GTP
is: SBO:0000296

044861
type: Reaction
kinetic law: 783457
product: 783445
reactant: 783433
notes: Similarly to Firsov et al. (2006) we consider the rate of Rho regeneration from Ops + 11cis_ret combination as a first order kinetics with the rate constant kRecyc implicitely including 11cis_ret concentration. See paper for details.
is version of: GO:0016063
fast: false
reversible: false
name: v_r12

783445
type: SpeciesReference
stoichiometry: 1.0
species: 044738

044738
type: Species
name: R
in compartment: 044715
has only substance units: false
is version of: P15409
initial concentration: 3.6E9
boundary condition: false
initial amount: NaN
constant: false
is: SBO:0000252

783433
type: SpeciesReference
stoichiometry: 1.0
species: 044730

045090
type: Parameter
constant: true
value: 1.49834E-9
name: kP3

044902
type: Reaction
kinetic law: 784859
product: 784847
reactant: 784835
notes: Here PDE has two Ga bound and both its subunits are active
is version of: GO:0031334
fast: false
reversible: false
name: v_r21

784847
type: SpeciesReference
stoichiometry: 1.0
species: 044726

784835
type: SpeciesReference
stoichiometry: 1.0
species: 044725

044813
type: Reaction
kinetic law: 781817
name: v_r2_4
reactant: 781791
product: 781804
reversible: true
reactant: 781779
fast: false
notes: Rn and RK binding before phospohorylation occurs
is version of: GO:0006461

781791
type: SpeciesReference
stoichiometry: 1.0
species: 044802

781804
type: SpeciesReference
stoichiometry: 1.0
species: 044780

044780
type: Species
initial amount: NaN
has only substance units: false
has part: Q9WVL4
name: R4_RKpre
boundary condition: false
is: SBO:0000297
in compartment: 044715
constant: false
has part: C02456
initial concentration: 0.0

781779
type: SpeciesReference
stoichiometry: 1.0
species: 044772

045112
type: Parameter
constant: true
value: 29.7778
name: Jdark

045143
type: Parameter
constant: false
value: 0.0
name: kRK1_1

044856
type: Reaction
reversible: true
reactant: 783265
reactant: 783277
kinetic law: 783301
product: 783289
notes: We assume the reverse reaction to occur with the same rate as v_r13_*
name: v_r8
is version of: GO:0006461
fast: false

783265
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783277
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783289
type: SpeciesReference
stoichiometry: 1.0
species: 044733

044871
type: Reaction
kinetic law: 783832
product: 783820
reactant: 783808
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_0

783820
type: SpeciesReference
stoichiometry: 1.0
species: 044741

044741
type: Species
in compartment: 044715
name: R0_G
has only substance units: false
boundary condition: false
constant: false
initial concentration: 0.0
initial amount: NaN
has part: Q3U6B2
has part: P15409
is: SBO:0000297

783808
type: SpeciesReference
stoichiometry: 1.0
species: 044743

044743
type: Species
initial concentration: 0.0
constant: false
in compartment: 044715
is: SBO:0000297
name: R0_Gt
has only substance units: false
boundary condition: false
has part: P15409
has part: Q8CFY0
initial amount: NaN

044781
type: Species
has only substance units: false
in compartment: 044715
initial concentration: 0.0
is version of: C02456
is: SBO:0000252
constant: false
boundary condition: false
name: R5
initial amount: NaN

045119
type: Parameter
constant: true
value: 0.6
name: Ca2dark

045043
type: Parameter
constant: true
value: 3.6E8
name: Gtot

045078
type: Parameter
constant: true
value: 600.0
name: kG4_GDP

044873
type: Reaction
kinetic law: 783904
product: 783892
reactant: 783880
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_2

783892
type: SpeciesReference
stoichiometry: 1.0
species: 044757

783880
type: SpeciesReference
stoichiometry: 1.0
species: 044760

044760
type: Species
boundary condition: false
in compartment: 044715
is: SBO:0000297
has part: Q8CFY0
name: R2_Gt
initial concentration: 0.0
initial amount: NaN
constant: false
has part: C02456
has only substance units: false

044756
type: Species
initial amount: NaN
has part: P20443
name: R2_Arr
boundary condition: false
is: SBO:0000297
has only substance units: false
in compartment: 044715
constant: false
has part: C02456
initial concentration: 0.0

044885
type: Reaction
kinetic law: 784229
product: 784217
reactant: 784205
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_4

784217
type: SpeciesReference
stoichiometry: 1.0
species: 044776

784205
type: SpeciesReference
stoichiometry: 1.0
species: 044775

044775
type: Species
boundary condition: false
initial concentration: 0.0
has part: C02456
is: SBO:0000297
in compartment: 044715
constant: false
initial amount: NaN
has only substance units: false
name: R4_G
has part: Q3U6B2

045170
type: Parameter
constant: false
value: 0.0
name: E

045047
type: Parameter
constant: true
value: 3.13E7
name: ArrTot

044785
type: Species
initial amount: NaN
has part: CHEBI:15996
has part: C02456
in compartment: 044715
name: R5_G_GTP
initial concentration: 0.0
has only substance units: false
has part: Q3U6B2
constant: false
boundary condition: false
is: SBO:0000296

045071
type: Parameter
constant: true
value: 6.1172E-13
name: kOps

044825
type: Reaction
product: 782155
name: v_r4_1
reversible: false
fast: false
reactant: 782142
kinetic law: 782180
notes: Dissociation of Rn and RK
is version of: GO:0043241
product: 782168

782155
type: SpeciesReference
stoichiometry: 1.0
species: 044746

782142
type: SpeciesReference
stoichiometry: 1.0
species: 044752

782168
type: SpeciesReference
stoichiometry: 1.0
species: 044802

045124
type: Parameter
constant: true
value: 1.9094
name: k2

044837
type: Reaction
name: v_r5_5
reversible: true
fast: false
notes: Binding of activated R to Arrestin
kinetic law: 782662
is version of: GO:0006461
product: 782650
reactant: 782626
reactant: 782638

782650
type: SpeciesReference
stoichiometry: 1.0
species: 044782

782626
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782638
type: SpeciesReference
stoichiometry: 1.0
species: 044781

044868
type: Reaction
is version of: GO:0006461
reversible: true
reactant: 783724
name: v_r13_5
reactant: 783712
kinetic law: 783748
notes: Rhodopsin and transducin binding
fast: false
product: 783736

783724
type: SpeciesReference
stoichiometry: 1.0
species: 044781

783712
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783736
type: SpeciesReference
stoichiometry: 1.0
species: 044786

044787
type: Species
initial concentration: 0.0
boundary condition: false
has part: C02456
is: SBO:0000297
in compartment: 044715
constant: false
initial amount: NaN
has part: Q9WVL4
has only substance units: false
name: R5_RKpost

045055
type: Parameter
constant: true
value: 0.0
name: flashMag

044897
type: Reaction
fast: false
reactant: 784653
kinetic law: 784689
product: 784665
is version of: GO:0007201
product: 784677
name: v_r17
reversible: false
notes: Dissociation of trimeric Gt into alpha and beta-gamma subunits

784653
type: SpeciesReference
stoichiometry: 1.0
species: 044721

784665
type: SpeciesReference
stoichiometry: 1.0
species: 044723

784677
type: SpeciesReference
stoichiometry: 1.0
species: 044727

044727
type: Species
constant: false
initial amount: NaN
initial concentration: 0.0
is: SBO:0000297
has only substance units: false
in compartment: 044715
name: Gbg
boundary condition: false
is version of: GO:0031680

045113
type: Parameter
constant: true
value: 96485.3415
name: F

044840
type: Reaction
reversible: false
reactant: 782722
product: 782734
name: v_r6_1
notes: Arrestin mediated R -> ops
product: 782747
kinetic law: 782759
fast: false
is version of: GO:0046155

782722
type: SpeciesReference
stoichiometry: 1.0
species: 044747

782734
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782747
type: SpeciesReference
stoichiometry: 1.0
species: 044730

045106
type: Parameter
constant: true
value: 2.5
name: m

044852
type: Reaction
kinetic law: 783180
product: 783168
reactant: 783156
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_4

783168
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783156
type: SpeciesReference
stoichiometry: 1.0
species: 044772

045115
type: Parameter
constant: true
value: 4.0
name: cGMPdark

045083
type: Parameter
constant: true
value: 2.0
name: kGrecyc

045155
type: Parameter
constant: false
value: 0.0
name: kA1_3

045095
type: Parameter
constant: true
value: 256.07
name: kRGS2

044907
type: Reaction
fast: false
name: v_r25
product: 785063
reactant: 785027
product: 785039
notes: The PDE subunit is deactivated and GTP is hydrolyzed. Here we assume that the deactivation/dissociation rate constant is the same as in v_r23
product: 785051
kinetic law: 785075
is version of: GO:0043241
reversible: false

785063
type: SpeciesReference
stoichiometry: 1.0
species: 044798

785027
type: SpeciesReference
stoichiometry: 1.0
species: 044801

785039
type: SpeciesReference
stoichiometry: 1.0
species: 044722

785051
type: SpeciesReference
stoichiometry: 1.0
species: 044735

044818
type: Reaction
kinetic law: 781985
product: 781973
reactant: 781961
notes: Phosphorylation of Rn to Rn+1. In these reactions ATP (left) and ADP (right) are included in the rate constants
is version of: GO:0016310
fast: false
reversible: false
name: v_r3_1

781973
type: SpeciesReference
stoichiometry: 1.0
species: 044761

044761
type: Species
is: SBO:0000297
boundary condition: false
has part: Q9WVL4
initial amount: NaN
constant: false
in compartment: 044715
has part: C02456
has only substance units: false
name: R2_RKpost
initial concentration: 0.0

781961
type: SpeciesReference
stoichiometry: 1.0
species: 044753

044753
type: Species
initial amount: NaN
name: R1_RKpre
has only substance units: false
constant: false
in compartment: 044715
initial concentration: 0.0
has part: Q9WVL4
boundary condition: false
has part: C02456
is: SBO:0000297

045074
type: Parameter
constant: true
value: 3.0586111111E-5
name: kG1_0

045086
type: Parameter
constant: true
value: 0.0549715
name: kP1

044768
type: Species
has part: Q8CFY0
has part: C02456
in compartment: 044715
has only substance units: false
initial amount: NaN
name: R3_Gt
boundary condition: false
initial concentration: 0.0
is: SBO:0000297
constant: false

044910
type: Reaction
fast: false
kinetic law: 785171
product: 785159
reactant: 785135
name: v_r27
product: 785147
notes: Inactivation of the aPDEa complex by Ga's GTPase capability; here we assume that the same rate constant as above applies
is version of: GO:0043241
reversible: false

785159
type: SpeciesReference
stoichiometry: 1.0
species: 044737

785135
type: SpeciesReference
stoichiometry: 1.0
species: 044726

785147
type: SpeciesReference
stoichiometry: 1.0
species: 044722

044821
type: Reaction
kinetic law: 782057
product: 782045
reactant: 782033
notes: Phosphorylation of Rn to Rn+1. In these reactions ATP (left) and ADP (right) are included in the rate constants
is version of: GO:0016310
fast: false
reversible: false
name: v_r3_3

782045
type: SpeciesReference
stoichiometry: 1.0
species: 044778

782033
type: SpeciesReference
stoichiometry: 1.0
species: 044771

044833
type: Reaction
name: v_r5_2
product: 782505
is version of: GO:0006461
reversible: true
reactant: 782493
reactant: 782481
fast: false
kinetic law: 782517
notes: Binding of activated R to Arrestin

782505
type: SpeciesReference
stoichiometry: 1.0
species: 044756

782493
type: SpeciesReference
stoichiometry: 1.0
species: 044755

044755
type: Species
has only substance units: false
constant: false
boundary condition: false
is version of: C02456
name: R2
is: SBO:0000252
initial amount: NaN
in compartment: 044715
initial concentration: 0.0

782481
type: SpeciesReference
stoichiometry: 1.0
species: 044717

W3 CDTF: Fri Apr 01 13:40:49 BST 2011

044876
type: Reaction
kinetic law: 783976
product: 783964
reactant: 783952
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_4

783964
type: SpeciesReference
stoichiometry: 1.0
species: 044775

783952
type: SpeciesReference
stoichiometry: 1.0
species: 044777

045127
type: Parameter
constant: true
value: 0.0238
name: ktherm

044891
type: Reaction
kinetic law: 784446
is version of: GO:0043241
product: 784434
reactant: 784410
name: v_r16_2
fast: false
product: 784422
reversible: false
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP

784434
type: SpeciesReference
stoichiometry: 1.0
species: 044755

784410
type: SpeciesReference
stoichiometry: 1.0
species: 044758

784422
type: SpeciesReference
stoichiometry: 1.0
species: 044721

044860
type: Reaction
reactant: 783385
kinetic law: 783421
fast: false
notes: Ops_G_GTP dissociation to Ops and G_GTP, here G_GTP is the Gt heterotrimer with bound GTP. We assume the same kinetics as in reactions v_r16_*
reversible: false
product: 783409
name: v_r11
is version of: GO:0043241
product: 783397

783385
type: SpeciesReference
stoichiometry: 1.0
species: 044732

783409
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783397
type: SpeciesReference
stoichiometry: 1.0
species: 044721

045167
type: Parameter
constant: false
value: 0.0
name: kG1_5

045051
type: Parameter
constant: true
value: 0.0
name: flash0Mag

045067
type: Parameter
constant: true
value: 6.0918E-10
name: kArr

045098
type: Parameter
constant: true
value: 0.610084
name: kRec4

044850
type: Reaction
kinetic law: 783108
product: 783096
reactant: 783084
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_2

783096
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783084
type: SpeciesReference
stoichiometry: 1.0
species: 044755

W3 CDTF: Tue Apr 19 15:28:57 BST 2011

044862
type: Reaction
name: v_r13_0
reactant: 783469
product: 783493
is version of: GO:0006461
reversible: true
notes: Rhodopsin and transducin binding
fast: false
kinetic law: 783505
reactant: 783481

783469
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783493
type: SpeciesReference
stoichiometry: 1.0
species: 044743

783481
type: SpeciesReference
stoichiometry: 1.0
species: 044740

045140
type: Parameter
constant: false
value: 0.0
name: stimulus

044742
type: Species
boundary condition: false
is: SBO:0000296
has part: CHEBI:15996
initial concentration: 0.0
has part: Q3U6B2
constant: false
has only substance units: false
has part: P15409
initial amount: NaN
name: R0_G_GTP
in compartment: 044715

045091
type: Parameter
constant: true
value: 21.0881
name: kP4

044903
type: Reaction
reactant: 784883
is version of: GO:0006461
name: v_r22
reactant: 784871
product: 784895
reversible: false
kinetic law: 784907
fast: false
notes: RGS binds to a PDE-Ga complex with both active subunits to form a complex

784883
type: SpeciesReference
stoichiometry: 1.0
species: 044798

784871
type: SpeciesReference
stoichiometry: 1.0
species: 044726

784895
type: SpeciesReference
stoichiometry: 1.0
species: 044800

044845
type: Reaction
product: 782939
is version of: GO:0046155
name: v_r6_5
reversible: false
reactant: 782915
product: 782927
notes: Arrestin mediated R -> ops
kinetic law: 782951
fast: false

782939
type: SpeciesReference
stoichiometry: 1.0
species: 044730

782915
type: SpeciesReference
stoichiometry: 1.0
species: 044782

782927
type: SpeciesReference
stoichiometry: 1.0
species: 044717

045144
type: Parameter
constant: false
value: 0.0
name: kRK1_2

044857
type: Reaction
kinetic law: 783337
product: 783325
reactant: 783313
notes: GDP dissociation from Ops_Gt, GDP is taken into account in the rate constant. Here we assume the same kinetics as in reactions v_r14_*
fast: false
reversible: true
name: v_r9

783325
type: SpeciesReference
stoichiometry: 1.0
species: 044731

044731
type: Species
has part: O35599
boundary condition: false
has part: Q3U6B2
name: Ops_G
has only substance units: false
constant: false
in compartment: 044715
is: SBO:0000297
initial amount: NaN
initial concentration: 0.0

783313
type: SpeciesReference
stoichiometry: 1.0
species: 044733

044888
type: Reaction
is version of: GO:0043241
kinetic law: 784350
reversible: false
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP
name: v_r16_0
reactant: 784314
fast: false
product: 784338
product: 784326

784314
type: SpeciesReference
stoichiometry: 1.0
species: 044742

784338
type: SpeciesReference
stoichiometry: 1.0
species: 044740

784326
type: SpeciesReference
stoichiometry: 1.0
species: 044721

045079
type: Parameter
constant: true
value: 750.0
name: kG5_GTP

044791
type: Species
has part: C02456
has part: P20443
boundary condition: false
in compartment: 044715
initial concentration: 0.0
is: SBO:0000297
initial amount: NaN
constant: false
name: R6_Arr
has only substance units: false

044886
type: Reaction
kinetic law: 784265
product: 784253
reactant: 784241
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_5

784253
type: SpeciesReference
stoichiometry: 1.0
species: 044785

784241
type: SpeciesReference
stoichiometry: 1.0
species: 044783

045171
type: Parameter
constant: false
value: 0.0
name: Rec_wCa2

044766
type: Species
is: SBO:0000297
initial concentration: 0.0
has part: Q3U6B2
has only substance units: false
initial amount: NaN
boundary condition: false
has part: C02456
name: R3_G
in compartment: 044715
constant: false

044915
type: Reaction
kinetic law: 785340
product: 785328
reactant: 785316
notes: Ca2+ association and dissociation from intracellular buffers, with total concentration eT
is version of: GO:0006816
fast: false
reversible: true
name: v_r31

785328
type: SpeciesReference
stoichiometry: 1.0
species: 044718

044718
type: Species
in compartment: 044715
is version of: C00076
name: Ca2_buff
has only substance units: false
is: SBO:0000247
boundary condition: false
is version of: CHEBI:29108
initial amount: NaN
initial concentration: 42.857
constant: false

785316
type: SpeciesReference
stoichiometry: 1.0
species: 044720

044826
type: Reaction
name: v_r4_2
product: 782204
notes: Dissociation of Rn and RK
is version of: GO:0043241
reversible: false
fast: false
reactant: 782192
product: 782216
kinetic law: 782228

782204
type: SpeciesReference
stoichiometry: 1.0
species: 044755

782192
type: SpeciesReference
stoichiometry: 1.0
species: 044761

782216
type: SpeciesReference
stoichiometry: 1.0
species: 044802

044838
type: Reaction
reactant: 782674
kinetic law: 782710
reversible: true
reactant: 782686
name: v_r5_6
is version of: GO:0006461
notes: Binding of activated R to Arrestin
fast: false
product: 782698

782674
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782686
type: SpeciesReference
stoichiometry: 1.0
species: 044790

782698
type: SpeciesReference
stoichiometry: 1.0
species: 044791

045063
type: Parameter
constant: true
value: 400.0
name: kRK3_ATP

045152
type: Parameter
constant: false
value: 0.0
name: kA1_1

044898
type: Reaction
product: 784726
fast: false
reactant: 784702
notes: PDE activation. Here we have the following assumptions on the effector 1) Each PDE subunit may bind Ga_Gtp and become active independently from the other one and with no cooperativity, 2) A PDE hetero-tetramer can hence bind up to 2 different Ga_GTP and thus it works with its in vivo kcat (the reversible reaction is assumed to be possibly present but in this model its rate is set to zero)
name: v_r18
kinetic law: 784738
reactant: 784714
reversible: true
is version of: GO:0006461

784726
type: SpeciesReference
stoichiometry: 1.0
species: 044736

044736
type: Species
has only substance units: false
initial amount: NaN
boundary condition: false
has part: CHEBI:15996
has part: P09174
initial concentration: 0.0
name: PDE_Ga_GTP
constant: false
has part: P27600
is: SBO:0000296
in compartment: 044715

784702
type: SpeciesReference
stoichiometry: 1.0
species: 044723

784714
type: SpeciesReference
stoichiometry: 1.0
species: 044735

045100
type: Parameter
constant: true
value: 0.425272
name: Kp

044810
type: Reaction
reactant: 781644
name: v_r2_1
fast: false
is version of: GO:0006461
reversible: true
reactant: 781632
kinetic law: 781669
notes: Rn and RK binding before phospohorylation occurs
product: 781657

781644
type: SpeciesReference
stoichiometry: 1.0
species: 044802

781632
type: SpeciesReference
stoichiometry: 1.0
species: 044746

781657
type: SpeciesReference
stoichiometry: 1.0
species: 044753

044841
type: Reaction
kinetic law: 782807
is version of: GO:0046155
reactant: 782771
notes: Arrestin mediated R -> ops
name: v_r6_2
fast: false
product: 782795
product: 782783
reversible: false

782771
type: SpeciesReference
stoichiometry: 1.0
species: 044756

782795
type: SpeciesReference
stoichiometry: 1.0
species: 044730

782783
type: SpeciesReference
stoichiometry: 1.0
species: 044717

045107
type: Parameter
constant: true
value: 1.2
name: betadark

044853
type: Reaction
kinetic law: 783216
product: 783204
reactant: 783192
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_5

783204
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783192
type: SpeciesReference
stoichiometry: 1.0
species: 044781

044767
type: Species
has part: CHEBI:15996
has only substance units: false
is: SBO:0000296
in compartment: 044715
initial amount: NaN
name: R3_G_GTP
has part: Q3U6B2
constant: false
boundary condition: false
initial concentration: 0.0
has part: C02456

045116
type: Parameter
constant: true
value: 3.0
name: ncg

044807
type: Reaction
kinetic law: 781571
product: 781559
reactant: 781547
is version of: GO:0070141
fast: false
reversible: false
name: v_r1

781559
type: SpeciesReference
stoichiometry: 1.0
species: 044740

781547
type: SpeciesReference
stoichiometry: 1.0
species: 044738

045156
type: Parameter
constant: false
value: 0.0
name: kA1_4

044880
type: Reaction
kinetic law: 784084
product: 784072
reactant: 784060
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_0

784072
type: SpeciesReference
stoichiometry: 1.0
species: 044742

784060
type: SpeciesReference
stoichiometry: 1.0
species: 044741

044908
type: Reaction
name: v_r26
kinetic law: 785123
product: 785099
reactant: 785087
notes: Inactivation of the PDEa complex by Ga's GTPase capability
is version of: GO:0006461
reversible: false
product: 785111
fast: false

785099
type: SpeciesReference
stoichiometry: 1.0
species: 044722

785087
type: SpeciesReference
stoichiometry: 1.0
species: 044737

785111
type: SpeciesReference
stoichiometry: 1.0
species: 044735

045075
type: Parameter
constant: true
value: 2250.34
name: kG2

045087
type: Parameter
constant: true
value: 0.0
name: kP1_rev

045158
type: Parameter
constant: false
value: 0.0
name: kA1_5

045164
type: Parameter
constant: false
value: 0.0
name: kG1_3

045176
type: Parameter
constant: false
value: 0.0
name: deltaJ

044911
type: Reaction
kinetic law: 785208
product: 785196
reactant: 785184
notes: Here we assume, according to Felber et al. (1996) that Gt may hydrolize GTP to GDP, and hence inactivate
is version of: GO:0006184
fast: false
reversible: false
name: v_r28

785196
type: SpeciesReference
stoichiometry: 1.0
species: 044722

785184
type: SpeciesReference
stoichiometry: 1.0
species: 044723

044822
type: Reaction
kinetic law: 782093
product: 782081
reactant: 782069
notes: Phosphorylation of Rn to Rn+1. In these reactions ATP (left) and ADP (right) are included in the rate constants
is version of: GO:0016310
fast: false
reversible: false
name: v_r3_4

782081
type: SpeciesReference
stoichiometry: 1.0
species: 044787

782069
type: SpeciesReference
stoichiometry: 1.0
species: 044780

045121
type: Parameter
constant: true
value: 0.01
name: Ca2_0

044865
type: Reaction
notes: Rhodopsin and transducin binding
reactant: 783566
reversible: true
product: 783590
reactant: 783578
kinetic law: 783602
name: v_r13_2
is version of: GO:0006461
fast: false

783566
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783590
type: SpeciesReference
stoichiometry: 1.0
species: 044760

783578
type: SpeciesReference
stoichiometry: 1.0
species: 044755

045133
type: Parameter
constant: false
value: 0.0
name: predur

044877
type: Reaction
kinetic law: 784012
product: 784000
reactant: 783988
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_5

784000
type: SpeciesReference
stoichiometry: 1.0
species: 044783

783988
type: SpeciesReference
stoichiometry: 1.0
species: 044786

045128
type: Parameter
constant: false
value: 0.0
name: background

045168
type: Parameter
constant: false
value: 0.0
name: kG1_6

044892
type: Reaction
reversible: false
reactant: 784458
is version of: GO:0043241
product: 784470
fast: false
kinetic law: 784496
name: v_r16_3
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP
product: 784483

784458
type: SpeciesReference
stoichiometry: 1.0
species: 044767

784470
type: SpeciesReference
stoichiometry: 1.0
species: 044721

784483
type: SpeciesReference
stoichiometry: 1.0
species: 044763

045052
type: Parameter
constant: true
value: 0.0
name: flashDel

044851
type: Reaction
kinetic law: 783144
product: 783132
reactant: 783120
notes: Thermal decay of R's catalytic active form MetaII. Rate constant from Xu et al. We assume that the rate constant is independent of the phosphorylation state. See Mitchell DC, Kibelbek J, Litman BJ. (Biochemistry, 1992) for further detail
is version of: GO:0046155
fast: false
reversible: false
name: v_r7_3

783132
type: SpeciesReference
stoichiometry: 1.0
species: 044730

783120
type: SpeciesReference
stoichiometry: 1.0
species: 044763

045101
type: Parameter
constant: true
value: 2.0
name: w

044863
type: Reaction
kinetic law: 783554
reactant: 783517
is version of: GO:0006461
reactant: 783529
product: 783542
fast: false
name: v_r13_1
reversible: true
notes: Rhodopsin and transducin binding

783517
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783529
type: SpeciesReference
stoichiometry: 1.0
species: 044746

783542
type: SpeciesReference
stoichiometry: 1.0
species: 044751

045056
type: Parameter
constant: true
value: 0.0
name: otherstimulus

045103
type: Parameter
constant: true
value: 1.0
name: Vcyto

045080
type: Parameter
constant: true
value: 2000.0
name: kG6

045092
type: Parameter
constant: true
value: 0.033
name: kPDEshutoff

044815
type: Reaction
reversible: true
is version of: GO:0006461
fast: false
reactant: 781841
product: 781853
notes: Rn and RK binding before phospohorylation occurs
name: v_r2_5
reactant: 781829
kinetic law: 781865

781841
type: SpeciesReference
stoichiometry: 1.0
species: 044802

781853
type: SpeciesReference
stoichiometry: 1.0
species: 044788

781829
type: SpeciesReference
stoichiometry: 1.0
species: 044781

044846
type: Reaction
notes: Arrestin mediated R -> ops
product: 782975
kinetic law: 782999
fast: false
is version of: GO:0046155
name: v_r6_6
product: 782987
reversible: false
reactant: 782963

782975
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782987
type: SpeciesReference
stoichiometry: 1.0
species: 044730

782963
type: SpeciesReference
stoichiometry: 1.0
species: 044791

044858
type: Reaction
kinetic law: 783373
product: 783361
reactant: 783349
notes: GTP binding to Ops_G, GDP is taken into account in the rate constant. We assume the same kinetics as in reactions v_r15_*
is version of: GO:0005525
fast: false
reversible: false
name: v_r10

783361
type: SpeciesReference
stoichiometry: 1.0
species: 044732

783349
type: SpeciesReference
stoichiometry: 1.0
species: 044731

044765
type: Species
initial amount: NaN
in compartment: 044715
initial concentration: 0.0
has only substance units: false
constant: false
has part: P20443
name: R3_Arr
boundary condition: false
has part: C02456
is: SBO:0000297

ORG:
  orgname: University of Oldenburg, Institute of Biology and Environmental Sciences
n:
  given: Daniele
  family: Dell'Orco

045147
type: Parameter
constant: false
value: 0.0
name: kRK1_4

044875
type: Reaction
kinetic law: 783940
product: 783928
reactant: 783916
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_3

783928
type: SpeciesReference
stoichiometry: 1.0
species: 044766

783916
type: SpeciesReference
stoichiometry: 1.0
species: 044768

044887
type: Reaction
kinetic law: 784302
product: 784290
reactant: 784277
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_6

784290
type: SpeciesReference
stoichiometry: 1.0
species: 044793

784277
type: SpeciesReference
stoichiometry: 1.0
species: 044792

044830
type: Reaction
kinetic law: 782373
notes: Dissociation of Rn and RK
reversible: false
reactant: 782336
product: 782348
product: 782361
is version of: GO:0043241
name: v_r4_5
fast: false

782336
type: SpeciesReference
stoichiometry: 1.0
species: 044787

782348
type: SpeciesReference
stoichiometry: 1.0
species: 044781

782361
type: SpeciesReference
stoichiometry: 1.0
species: 044802

044916
type: Reaction
kinetic law: 785364
reactant: 785352
notes: Efflux of Ca2+ via the Na+/Ca2+ - K+ exchanger. Note that intracellular Ca2 cannot be lower than Ca2_0
fast: false
reversible: false
name: v_r32

785352
type: SpeciesReference
stoichiometry: 1.0
species: 044720

044827
type: Reaction
kinetic law: 782276
fast: false
product: 782264
reversible: false
reactant: 782240
name: v_r4_3
notes: Dissociation of Rn and RK
product: 782252
is version of: GO:0043241

782264
type: SpeciesReference
stoichiometry: 1.0
species: 044802

782240
type: SpeciesReference
stoichiometry: 1.0
species: 044770

782252
type: SpeciesReference
stoichiometry: 1.0
species: 044763

045064
type: Parameter
constant: true
value: 20.0
name: kRK4

045068
type: Parameter
constant: true
value: 0.00323198
name: kA2

044900
type: Reaction
kinetic law: 784774
product: 784762
reactant: 784750
is version of: GO:0031334
fast: false
reversible: false
name: v_r19

784762
type: SpeciesReference
stoichiometry: 1.0
species: 044737

784750
type: SpeciesReference
stoichiometry: 1.0
species: 044736

044811
type: Reaction
notes: Rn and RK binding before phospohorylation occurs
reactant: 781694
reversible: true
kinetic law: 781718
reactant: 781682
name: v_r2_2
product: 781706
fast: false
is version of: GO:0006461

781694
type: SpeciesReference
stoichiometry: 1.0
species: 044802

781682
type: SpeciesReference
stoichiometry: 1.0
species: 044755

781706
type: SpeciesReference
stoichiometry: 1.0
species: 044762

044842
type: Reaction
product: 782843
reactant: 782819
is version of: GO:0046155
product: 782831
reversible: false
kinetic law: 782855
name: v_r6_3
notes: Arrestin mediated R -> ops
fast: false

782843
type: SpeciesReference
stoichiometry: 1.0
species: 044730

782819
type: SpeciesReference
stoichiometry: 1.0
species: 044765

782831
type: SpeciesReference
stoichiometry: 1.0
species: 044717

045110
type: Parameter
constant: true
value: 0.2
name: fCa

045141
type: Parameter
constant: false
value: 0.0
name: numConcFactor

044808
type: Reaction
name: v_r2_0
notes: Rn and RK binding before phospohorylation occurs
reactant: 781595
reversible: true
product: 781608
fast: false
is version of: GO:0006461
kinetic law: 781620
reactant: 781583

781595
type: SpeciesReference
stoichiometry: 1.0
species: 044802

781608
type: SpeciesReference
stoichiometry: 1.0
species: 044745

781583
type: SpeciesReference
stoichiometry: 1.0
species: 044740

044881
type: Reaction
kinetic law: 784121
product: 784109
reactant: 784097
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_1

784109
type: SpeciesReference
stoichiometry: 1.0
species: 044750

784097
type: SpeciesReference
stoichiometry: 1.0
species: 044748

045041
type: Parameter
constant: true
value: 3.6E9
name: Rtot

045076
type: Parameter
constant: true
value: 2000.0
name: kG3

045088
type: Parameter
constant: true
value: 940.706
name: kP2

045159
type: Parameter
constant: false
value: 0.0
name: kA1_6

044883
type: Reaction
kinetic law: 784193
product: 784181
reactant: 784169
notes: GTP binding to Rn_G. GTP is taken into account in the rate constant. Here G is still a heterotrimer and GTP binds to such heterotrimer_R complex
is version of: GO:0005525
fast: false
reversible: false
name: v_r15_3

784181
type: SpeciesReference
stoichiometry: 1.0
species: 044767

784169
type: SpeciesReference
stoichiometry: 1.0
species: 044766

045045
type: Parameter
constant: true
value: 35.0
name: Rectot

044912
type: Reaction
fast: false
reactant: 785220
kinetic law: 785256
reactant: 785232
reversible: false
product: 785244
notes: Gt recycling... heterotrimer reconstitution
name: v_r29
is version of: GO:0032795

785220
type: SpeciesReference
stoichiometry: 1.0
species: 044722

785232
type: SpeciesReference
stoichiometry: 1.0
species: 044727

785244
type: SpeciesReference
stoichiometry: 1.0
species: 044728

044823
type: Reaction
kinetic law: 782130
product: 782118
reactant: 782106
notes: Phosphorylation of Rn to Rn+1. In these reactions ATP (left) and ADP (right) are included in the rate constants
is version of: GO:0016310
fast: false
reversible: false
name: v_r3_5

782118
type: SpeciesReference
stoichiometry: 1.0
species: 044796

782106
type: SpeciesReference
stoichiometry: 1.0
species: 044788

045122
type: Parameter
constant: true
value: 0.381529
name: k1

044835
type: Reaction
notes: Binding of activated R to Arrestin
name: v_r5_3
product: 782553
reactant: 782529
reversible: true
is version of: GO:0006461
fast: false
reactant: 782541
kinetic law: 782565

782553
type: SpeciesReference
stoichiometry: 1.0
species: 044765

782529
type: SpeciesReference
stoichiometry: 1.0
species: 044717

782541
type: SpeciesReference
stoichiometry: 1.0
species: 044763

044866
type: Reaction
reversible: true
reactant: 783626
name: v_r13_3
kinetic law: 783651
notes: Rhodopsin and transducin binding
is version of: GO:0006461
fast: false
reactant: 783614
product: 783639

783626
type: SpeciesReference
stoichiometry: 1.0
species: 044763

783614
type: SpeciesReference
stoichiometry: 1.0
species: 044728

783639
type: SpeciesReference
stoichiometry: 1.0
species: 044768

045060
type: Parameter
constant: true
value: 250.0
name: kRK2

045134
type: Parameter
constant: false
value: 0.0
name: dur

044878
type: Reaction
kinetic law: 784048
product: 784036
reactant: 784024
notes: GDP dissociation from Rn_Gt. GDP is taken into account in the rate constant
is version of: GO:0046154
fast: false
reversible: true
name: v_r14_6

784036
type: SpeciesReference
stoichiometry: 1.0
species: 044792

784024
type: SpeciesReference
stoichiometry: 1.0
species: 044795

044893
type: Reaction
is version of: GO:0043241
product: 784520
name: v_r16_4
reversible: false
fast: false
reactant: 784508
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP
kinetic law: 784545
product: 784533

784520
type: SpeciesReference
stoichiometry: 1.0
species: 044721

784508
type: SpeciesReference
stoichiometry: 1.0
species: 044776

784533
type: SpeciesReference
stoichiometry: 1.0
species: 044772

044895
type: Reaction
product: 784581
fast: false
notes: Rn_G_GTP dissociation to Rn and G_GTP. Here G_GTP is the Gt heterotrimer with bound GTP
name: v_r16_5
product: 784569
is version of: GO:0043241
kinetic law: 784593
reversible: false
reactant: 784557

784581
type: SpeciesReference
stoichiometry: 1.0
species: 044781

784569
type: SpeciesReference
stoichiometry: 1.0
species: 044721

784557
type: SpeciesReference
stoichiometry: 1.0
species: 044785

045057
type: Parameter
constant: true
value: 0.0076429599557114
name: kRK1_0

045104
type: Parameter
constant: true
value: 0.17
name: Kc

045153
type: Parameter
constant: false
value: 0.0
name: kA1_2

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