begin name
bray2
end name

begin reactions
motorr1 {1.0}M + {1.0}Yp = {1.0}MYp
motorr2 {1.0}MYp + {1.0}Yp = {1.0}MYpYp
motorr3 {1.0}MYpYp + {1.0}Yp = {1.0}MYpYpYp
motorr4 {1.0}MYpYpYp + {1.0}Yp = {1.0}MYpYpYpYp
phosphorylationr1 {1.0}A = {1.0}Ap
phosphorylationr10 {1.0}Bp = {1.0}B
phosphorylationr2 {1.0}A = {1.0}Ap
phosphorylationr3 {1.0}A = {1.0}Ap
phosphorylationr4 {1.0}TaspWA + {1.0}Yp = {1.0}TaspWA + {1.0}Y
phosphorylationr5 {1.0}Ap + {1.0}Y = {1.0}A + {1.0}Yp
phosphorylationr6 {1.0}Y = {1.0}Yp
phosphorylationr7 {1.0}Yp = {1.0}Y
phosphorylationr8 {1.0}Yp + {1.0}Z = {1.0}Y + {1.0}Z
phosphorylationr9 {1.0}Ap + {1.0}B = {1.0}A + {1.0}Bp
reaction1 {1.0}TA + {1.0}$asp = {1.0}TaspA
reaction2 {1.0}TW + {1.0}$asp = {1.0}TaspW
reaction3 {1.0}TWA + {1.0}$asp = {1.0}TaspWA
regulatoryr1 {1.0}T + {1.0}$asp = {1.0}Tasp
regulatoryr10 {1.0}Tasp + {1.0}A = {1.0}TaspA
regulatoryr11 {1.0}TaspW + {1.0}A = {1.0}TaspWA
regulatoryr12 {1.0}TaspA + {1.0}W = {1.0}TaspWA
regulatoryr13 {1.0}Tasp + {1.0}WA = {1.0}TaspWA
regulatoryr14 {1.0}Tni + {1.0}W = {1.0}TniW
regulatoryr15 {1.0}Tni + {1.0}A = {1.0}TniA
regulatoryr16 {1.0}TniW + {1.0}A = {1.0}TniWA
regulatoryr17 {1.0}TniA + {1.0}W = {1.0}TniWA
regulatoryr18 {1.0}Tni + {1.0}WA = {1.0}TniWA
regulatoryr2 {1.0}T + {1.0}$ni = {1.0}Tni
regulatoryr3 {1.0}T + {1.0}W = {1.0}TW
regulatoryr4 {1.0}T + {1.0}A = {1.0}TA
regulatoryr5 {1.0}W + {1.0}A = {1.0}WA
regulatoryr6 {1.0}TW + {1.0}A = {1.0}TWA
regulatoryr7 {1.0}TA + {1.0}W = {1.0}TWA
regulatoryr8 {1.0}T + {1.0}WA = {1.0}TWA
regulatoryr9 {1.0}Tasp + {1.0}W = {1.0}TaspW
end reactions

begin rate equations
motorr1 = cell*function4motorr1[M[t], MYp[t], Yp[t], cell, ka, kappa]
motorr2 = cell*function4motorr2[MYp[t], MYpYp[t], Yp[t], alpha, cell, ka, kappa]
motorr3 = cell*function4motorr3[MYpYp[t], MYpYpYp[t], Yp[t], alpha, cell, ka, kappa]
motorr4 = cell*function4motorr4[MYpYpYp[t], MYpYpYpYp[t], Yp[t], alpha, cell, ka, kappa]
phosphorylationr1 = cell*Autophosphorylation[phosphorylationr1kcat, parameter2, A[t]]
phosphorylationr10 = cell*phosphorylationr10k1*Bp[t]
phosphorylationr2 = cell*ModAutophosphorylation[TWA[t], A[t], phosphorylationr2kcat, parameter2]
phosphorylationr3 = cell*ModAutophosphorylation[TniWA[t], A[t], phosphorylationr3kcat, parameter2]
phosphorylationr4 = cell*phosphorylationr4k1*TaspWA[t]*Yp[t]
phosphorylationr5 = cell*phosphorylationr5k1*Ap[t]*Y[t]
phosphorylationr6 = cell*Autophosphorylation[phosphorylationr6kcat, parameter2, Y[t]]
phosphorylationr7 = cell*phosphorylationr7k1*Yp[t]
phosphorylationr8 = cell*phosphorylationr8k1*Yp[t]*Z[t]
phosphorylationr9 = cell*phosphorylationr9k1*Ap[t]*B[t]
reaction1 = cell*(asp*reaction1k1*TA[t] - reaction1k2*TaspA[t])
reaction2 = cell*(-(reaction2k2*TaspW[t]) + asp*reaction2k1*TW[t])
reaction3 = cell*(-(reaction3k2*TaspWA[t]) + asp*reaction3k1*TWA[t])
regulatoryr1 = cell*(asp*regulatoryr1k1*T[t] - regulatoryr1k2*Tasp[t])
regulatoryr10 = cell*(regulatoryr10k1*A[t]*Tasp[t] - regulatoryr10k2*TaspA[t])
regulatoryr11 = cell*(regulatoryr11k1*A[t]*TaspW[t] - regulatoryr11k2*TaspWA[t])
regulatoryr12 = cell*(-(regulatoryr12k2*TaspWA[t]) + regulatoryr12k1*TaspA[t]*W[t])
regulatoryr13 = cell*(-(regulatoryr13k2*TaspWA[t]) + regulatoryr13k1*Tasp[t]*WA[t])
regulatoryr14 = cell*(-(regulatoryr14k2*TniW[t]) + regulatoryr14k1*Tni[t]*W[t])
regulatoryr15 = cell*(regulatoryr15k1*A[t]*Tni[t] - regulatoryr15k2*TniA[t])
regulatoryr16 = cell*(regulatoryr16k1*A[t]*TniW[t] - regulatoryr16k2*TniWA[t])
regulatoryr17 = cell*(-(regulatoryr17k2*TniWA[t]) + regulatoryr17k1*TniA[t]*W[t])
regulatoryr18 = cell*(-(regulatoryr18k2*TniWA[t]) + regulatoryr18k1*Tni[t]*WA[t])
regulatoryr2 = cell*(ni*regulatoryr2k1*T[t] - regulatoryr2k2*Tni[t])
regulatoryr3 = cell*(-(regulatoryr3k2*TW[t]) + regulatoryr3k1*T[t]*W[t])
regulatoryr4 = cell*(regulatoryr4k1*A[t]*T[t] - regulatoryr4k2*TA[t])
regulatoryr5 = cell*(regulatoryr5k1*A[t]*W[t] - regulatoryr5k2*WA[t])
regulatoryr6 = cell*(regulatoryr6k1*A[t]*TW[t] - regulatoryr6k2*TWA[t])
regulatoryr7 = cell*(-(regulatoryr7k2*TWA[t]) + regulatoryr7k1*TA[t]*W[t])
regulatoryr8 = cell*(-(regulatoryr8k2*TWA[t]) + regulatoryr8k1*T[t]*WA[t])
regulatoryr9 = cell*(-(regulatoryr9k2*TaspW[t]) + regulatoryr9k1*Tasp[t]*W[t])
end rate equations

begin parameters
alpha = 0.14
ka = 0.1
kappa = "2.25e-07"
parameter1 = "1e-07"
parameter3 = 0.0003
asp = 0.0
ni = 0.0
species1 = 0.1
phosphorylationr1kcat = 0.001
phosphorylationr2kcat = 75000.0
phosphorylationr3kcat = 200000.0
phosphorylationr4k1 = 100000000.0
phosphorylationr5k1 = 200000.0
phosphorylationr6kcat = 0.0
phosphorylationr7k1 = 0.037
phosphorylationr8k1 = 500000.0
phosphorylationr9k1 = 1000000.0
phosphorylationr10k1 = 1.0
regulatoryr1k1 = 1000000.0
regulatoryr1k2 = 1.0
regulatoryr2k1 = 1000.0
regulatoryr2k2 = 1.0
regulatoryr3k1 = 100000.0
regulatoryr3k2 = 1.0
regulatoryr4k1 = 10000.0
regulatoryr4k2 = 1.0
regulatoryr5k1 = 100000.0
regulatoryr5k2 = 1.0
regulatoryr6k1 = 400000.0
regulatoryr6k2 = 1.0
regulatoryr7k1 = 400000.0
regulatoryr7k2 = 1.0
regulatoryr8k1 = 400000.0
regulatoryr8k2 = 1.0
regulatoryr9k1 = 100000.0
regulatoryr9k2 = 1.0
regulatoryr10k1 = 10000.0
regulatoryr10k2 = 1.0
regulatoryr11k1 = 400000.0
regulatoryr11k2 = 1.0
regulatoryr12k1 = 400000.0
regulatoryr12k2 = 1.0
regulatoryr13k1 = 400000.0
regulatoryr13k2 = 1.0
regulatoryr14k1 = 0.1
regulatoryr14k2 = 1.0
regulatoryr15k1 = 0.01
regulatoryr15k2 = 1.0
regulatoryr16k1 = 0.4
regulatoryr16k2 = 1.0
regulatoryr17k1 = 0.4
regulatoryr17k2 = 1.0
regulatoryr18k1 = 0.4
regulatoryr18k2 = 1.0
reaction1k1 = 1000000.0
reaction1k2 = 1.0
reaction2k1 = 1000000.0
reaction2k2 = 1.0
reaction3k1 = 1000000.0
reaction3k2 = 1.0
cell = "1.41e-15"
end parameters

begin initial conditions
A[0] = Ai
Ap[0] = Api
B[0] = Bi
Bp[0] = Bpi
M[0] = Mi
MYp[0] = MYpi
MYpYp[0] = MYpYpi
MYpYpYp[0] = MYpYpYpi
MYpYpYpYp[0] = MYpYpYpYpi
T[0] = Ti
TA[0] = TAi
TW[0] = TWi
TWA[0] = TWAi
Tasp[0] = Taspi
TaspA[0] = TaspAi
TaspW[0] = TaspWi
TaspWA[0] = TaspWAi
Tni[0] = Tnii
TniA[0] = TniAi
TniW[0] = TniWi
TniWA[0] = TniWAi
W[0] = Wi
WA[0] = WAi
Y[0] = Yi
Yp[0] = Ypi
Z[0] = Zi
end initial conditions

begin initial values
Ai = 3e-06
Api = 3.48e-08
Bi = 1.93e-06
Bpi = 6.87e-08
Mi = 6.24e-09
MYpi = 7.77e-10
MYpYpi = 2.99e-10
MYpYpYpi = 3.78e-10
MYpYpYpYpi = 2.31e-09
Ti = 3.12e-06
TAi = 4.44e-07
TWi = 5.91e-07
TWAi = 8.47e-07
Taspi = 0.0
TaspAi = 0.0
TaspWi = 0.0
TaspWAi = 0.0
Tnii = 0.0
TniAi = 0.0
TniWi = 0.0
TniWAi = 0.0
Wi = 2.89e-06
WAi = 6.78e-07
Yi = 9.9e-06
Ypi = 7e-09
Zi = 2e-05
end initial values

begin assignment rules
parameter2 := species1/(parameter3 + species1)
Bias := (M[t] + MYp[t])/(M[t] + MYp[t] + MYpYp[t] + MYpYpYp[t] + MYpYpYpYp[t])
end assignment rules

begin function definitions
ModAutophosphorylation[M_,S_,kcat_,correction_] := correction*kcat*M*S
Autophosphorylation[kcat_,correction_,E_] := correction*E*kcat
function4motorr4[MYpYpYp_,MYpYpYpYp_,Yp_,alpha_,cell_,ka_,kappa_] := (ka*(-4*alpha^3*kappa*MYpYpYpYp + MYpYpYp*Yp))/cell
function4motorr3[MYpYp_,MYpYpYp_,Yp_,alpha_,cell_,ka_,kappa_] := (ka*((-3*alpha^2*kappa*MYpYpYp)/2 + MYpYp*Yp))/cell
function4motorr2[MYp_,MYpYp_,Yp_,alpha_,cell_,ka_,kappa_] := (ka*((-2*alpha*kappa*MYpYp)/3 + MYp*Yp))/cell
function4motorr1[M_,MYp_,Yp_,cell_,ka_,kappa_] := (ka*(-(kappa*MYp)/4 + M*Yp))/cell
end function definitions

begin events
event_1 = (t >= 5, {asp -> parameter1}, 0)
event_2 = (t >= 10, {asp -> 0}, 0)
end events

begin process annotations
end process annotations

begin species annotations
M http://identifiers.org/uniprot/P06974
T http://identifiers.org/uniprot/P07017
W http://identifiers.org/uniprot/P0A964
Z http://identifiers.org/uniprot/P0A9H9
asp http://identifiers.org/obo.chebi/CHEBI:35391
ni http://identifiers.org/obo.chebi/CHEBI:49786
species_1 http://identifiers.org/obo.chebi/CHEBI:15422
end species annotations

begin units
end units