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compartments.net
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compartments.net
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substanceUnits("Number");
begin parameters
1 nEndo 5 # Constant
2 vol_EC 20.0 # Constant
3 vol_CP 4.0 # Constant
4 vol_NU 1.0 # Constant
5 vol_EN 0.5 # ConstantExpression
6 sa_PM 0.4 # Constant
7 sa_NM 0.1 # Constant
8 sa_EM 0.05 # ConstantExpression
9 eff_width 1.0 # Constant
10 L0 1000 # Constant
11 R0 200 # Constant
12 TF0 200 # Constant
13 DNA0 2 # Constant
14 Im0 40 # Constant
15 NP0 4 # Constant
16 kp_LR 0.1 # Constant
17 km_LR 1.0 # Constant
18 kp_LL 0.1 # Constant
19 km_LL 1.0 # Constant
20 k_R_endo 1.0 # Constant
21 k_recycle 0.1 # Constant
22 k_R_transphos 1.0 # Constant
23 k_R_dephos 0.1 # Constant
24 kp_R_TF 0.1 # Constant
25 km_R_TF 0.1 # Constant
26 kp_R_TFp 0.1 # Constant
27 km_R_TFp 10.0 # Constant
28 k_TF_transphos 1.0 # Constant
29 k_TF_dephos 1.0 # Constant
30 kp_TF_TF 0.1 # Constant
31 km_TF_TF 1.0 # Constant
32 kp_TF_p1 0.1 # Constant
33 km_TF_p1 1.0 # Constant
34 k_transcribe 1.0 # Constant
35 k_translate 1.0 # Constant
36 k_mRNA_to_CP 1.0 # Constant
37 k_mRNA_deg 1.0 # Constant
38 k_P_deg 0.1 # Constant
39 k_Im_bind_CP 0.1 # Constant
40 k_Im_unbind_CP 0.1 # Constant
41 k_Im_bind_NU 0.1 # Constant
42 k_Im_unbind_NU 10.0 # Constant
43 k_Im_enters_NP 0.1 # Constant
44 k_Im_exits_NP 1.0 # Constant
45 k_Im_cross_NP 1.0 # Constant
46 kp_P1_p2 0.1 # Constant
47 km_P1_p2 1.0 # Constant
end parameters
begin compartments
EC 3 vol_EC
PM 2 sa_PM*eff_width EC
CP 3 vol_CP PM
NM 2 sa_NM*eff_width CP
NU 3 vol_NU NM
EM 2 sa_EM*eff_width CP
EN 3 vol_EN EM
end compartments
begin molecule types
1 DNA(p1,p2)
2 Im(fg,cargo)
3 L(r,d)
4 NP(fg)
5 P1(im,dna)
6 P2()
7 R(l,tf~Y~pY)
8 Sink()
9 TF(r,d~Y~pY,dna,im)
10 mRNA1()
11 mRNA2()
end molecule types
begin observables
1 Molecules Tot_L L()
2 Molecules Tot_R R()
3 Molecules Tot_TF TF()
4 Molecules Tot_DNA DNA()
5 Molecules Tot_mRNA1 mRNA1()
6 Molecules Tot_mRNA2 mRNA2()
7 Molecules Tot_P1 P1()
8 Molecules Tot_P2 P2()
9 Molecules Tot_NP NP()
10 Molecules Tot_Im Im()
end observables
begin species
1 @EC::L(d,r) L0
2 @PM::R(l,tf~Y) R0
3 @CP::TF(d~Y,dna,im,r) TF0
4 @NU::DNA(p1,p2) DNA0
5 @CP::Im(cargo,fg) Im0
6 @NM::NP(fg) NP0
7 @CP::$Sink() 0
8 @PM::L(d,r!1)@EC.R(l!1,tf~Y) 0
9 @EC::L(d!1,r).L(d!1,r) 0
10 @NM::Im(cargo,fg!1)@CP.NP(fg!1) 0
11 @PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~Y) 0
12 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~Y) 0
13 @NM::Im(cargo,fg!1)@NU.NP(fg!1) 0
14 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~Y) 0
15 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~pY) 0
16 @NU::Im(cargo,fg) 0
17 @EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~Y) 0
18 @EM::R(l,tf~Y) 0
19 @PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~pY) 0
20 @PM::R(l,tf~pY) 0
21 @EM::L(d,r!1)@EN.R(l!1,tf~Y) 0
22 @PM::L(d,r!1)@EC.R(l!1,tf~pY) 0
23 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~pY) 0
24 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY).R(l!3,tf~pY) 0
25 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~Y,dna,im,r!4)@CP 0
26 @EN::L(d!1,r).L(d!1,r) 0
27 @EN::L(d,r) 0
28 @EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~pY) 0
29 @EM::R(l,tf~pY) 0
30 @PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~pY!3).TF(d~Y,dna,im,r!3)@CP 0
31 @PM::R(l,tf~pY!1).TF(d~Y,dna,im,r!1)@CP 0
32 @EM::L(d,r!1)@EN.R(l!1,tf~pY) 0
33 @PM::L(d,r!1)@EC.R(l!1,tf~pY!2).TF(d~Y,dna,im,r!2)@CP 0
34 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY).R(l!3,tf~pY) 0
35 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~Y,dna,im,r!4)@CP 0
36 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~Y,dna,im,r!4)@CP 0
37 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~Y,dna,im,r!5)@CP 0
38 @EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~pY!3).TF(d~Y,dna,im,r!3)@CP 0
39 @EM::R(l,tf~pY!1).TF(d~Y,dna,im,r!1)@CP 0
40 @EM::L(d,r!1)@EN.R(l!1,tf~pY!2).TF(d~Y,dna,im,r!2)@CP 0
41 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~Y,dna,im,r!4)@CP 0
42 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~Y,dna,im,r!5)@CP 0
43 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP 0
44 @PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~pY!3).TF(d~pY,dna,im,r!3)@CP 0
45 @PM::R(l,tf~pY!1).TF(d~pY,dna,im,r!1)@CP 0
46 @PM::L(d,r!1)@EC.R(l!1,tf~pY!2).TF(d~pY,dna,im,r!2)@CP 0
47 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP 0
48 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~pY,dna,im,r!4)@CP 0
49 @CP::TF(d~pY,dna,im,r) 0
50 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~pY,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP 0
51 @PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~pY,dna,im,r!4)@CP 0
52 @EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~pY!3).TF(d~pY,dna,im,r!3)@CP 0
53 @EM::R(l,tf~pY!1).TF(d~pY,dna,im,r!1)@CP 0
54 @EM::L(d,r!1)@EN.R(l!1,tf~pY!2).TF(d~pY,dna,im,r!2)@CP 0
55 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~pY,dna,im,r!4)@CP 0
56 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~pY,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP 0
57 @EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~pY,dna,im,r!4)@CP 0
58 @CP::TF(d~pY!1,dna,im,r).TF(d~pY!1,dna,im,r) 0
59 @CP::Im(cargo!1!2,fg).TF(d~pY!3,dna,im!1,r).TF(d~pY!3,dna,im!2,r) 0
60 @NM::Im(cargo!1!2,fg!3)@CP.NP(fg!3).TF(d~pY!4,dna,im!1,r)@CP.TF(d~pY!4,dna,im!2,r)@CP 0
61 @NM::Im(cargo!1!2,fg!3)@NU.NP(fg!3).TF(d~pY!4,dna,im!1,r)@NU.TF(d~pY!4,dna,im!2,r)@NU 0
62 @NU::TF(d~pY!1,dna,im,r).TF(d~pY!1,dna,im,r) 0
63 @NU::Im(cargo!1!2,fg).TF(d~pY!3,dna,im!1,r).TF(d~pY!3,dna,im!2,r) 0
64 @NU::TF(d~pY,dna,im,r) 0
65 @NU::DNA(p1!1!2,p2).TF(d~pY!3,dna!1,im,r).TF(d~pY!3,dna!2,im,r) 0
66 @NU::mRNA1() 0
67 @CP::mRNA1() 0
68 @CP::P1(dna,im) 0
69 @CP::Im(cargo!1,fg).P1(dna,im!1) 0
70 @NM::Im(cargo!1,fg!2)@CP.NP(fg!2).P1(dna,im!1)@CP 0
71 @NM::Im(cargo!1,fg!2)@NU.NP(fg!2).P1(dna,im!1)@NU 0
72 @NU::P1(dna,im) 0
73 @NU::Im(cargo!1,fg).P1(dna,im!1) 0
74 @NU::DNA(p1,p2!1).P1(dna!1,im) 0
75 @NU::DNA(p1!1!2,p2!3).P1(dna!3,im).TF(d~pY!4,dna!1,im,r).TF(d~pY!4,dna!2,im,r) 0
76 @NU::mRNA2() 0
77 @CP::mRNA2() 0
78 @CP::P2() 0
end species
begin reaction rules
Rule1: L(r) + R(l) <-> L(r!1).R(l!1) kp_LR, km_LR
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
Rule2: \
L(d) + L(d) <-> L(d!1).L(d!1) kp_LL, km_LL
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
Rule3: \
@PM::R().R() -> @EM::R().R() k_R_endo
# ChangeCompartment(0,PM,EM,1)
Rule4: \
@EM::R() -> @PM::R() k_recycle
# ChangeCompartment(0,EM,PM,1)
Rule5: \
@EN::L() -> @EC::L() k_recycle
# ChangeCompartment(0,EN,EC,0)
Rule6: \
R().R(tf~Y) -> R().R(tf~pY) k_R_transphos
# StateChange(0.1.0,Y->pY)
Rule7: \
R(tf~pY) -> R(tf~Y) k_R_dephos
# StateChange(0.0.0,pY->Y)
Rule8: \
R(tf~pY) + TF(d~Y,r) <-> R(tf~pY!1).TF(d~Y,r!1) kp_R_TF, km_R_TF
# Bind(0.0.0,0.1.1)
# Reverse
# Unbind(0.0.0,0.1.1)
Rule9: \
R(tf~pY) + TF(d~pY,r) <-> R(tf~pY!1).TF(d~pY,r!1) kp_R_TFp, km_R_TFp
# Bind(0.0.0,0.1.1)
# Reverse
# Unbind(0.0.0,0.1.1)
Rule10: \
TF().R().R().TF(d~Y) -> TF().R().R().TF(d~pY) k_TF_transphos
# StateChange(0.3.0,Y->pY)
Rule11: \
TF(d~pY)@CP -> TF(d~Y)@CP k_TF_dephos
# StateChange(0.0.0,pY->Y)
Rule12: \
TF(r,d~pY,dna) + TF(r,d~pY,dna) <-> TF(r,d~pY!1,dna).TF(r,d~pY!1,dna) kp_TF_TF, km_TF_TF
# Bind(0.0.1,0.1.1)
# Reverse
# Unbind(0.0.1,0.1.1)
Rule13: \
TF(dna,im).TF(dna,im) + DNA(p1) <-> TF(dna!1,im).TF(dna!2,im).DNA(p1!1!2) kp_TF_p1, km_TF_p1
# Bind(0.0.0,0.2.0)
# Bind(0.1.0,0.2.0)
# Reverse
# Unbind(0.0.0,0.2.0)
# Unbind(0.1.0,0.2.0)
Rule14: \
DNA(p1!+) -> DNA(p1!+) + mRNA1()@NU k_transcribe
# Add Species mRNA1()@NU
Rule15: \
DNA(p2!+) -> DNA(p2!+) + mRNA2()@NU k_transcribe
# Add Species mRNA2()@NU
Rule16: \
mRNA1()@NU -> mRNA1()@CP k_mRNA_to_CP
# ChangeCompartment(0.0,NU,CP,0)
Rule17: \
mRNA2()@NU -> mRNA2()@CP k_mRNA_to_CP
# ChangeCompartment(0.0,NU,CP,0)
Rule18: \
mRNA1()@CP -> mRNA1()@CP + P1(im,dna)@CP k_translate
# Add Species P1(im,dna)@CP
Rule19: \
mRNA2()@CP -> mRNA2()@CP + P2()@CP k_translate
# Add Species P2()@CP
Rule20: \
mRNA1() -> Sink()@CP k_mRNA_deg DeleteMolecules
# Delete Molecule mRNA1()
# Add Species Sink()@CP
Rule21: \
mRNA2() -> Sink()@CP k_mRNA_deg DeleteMolecules
# Delete Molecule mRNA2()
# Add Species Sink()@CP
Rule22: \
P1() -> Sink()@CP k_P_deg DeleteMolecules
# Delete Molecule P1()
# Add Species Sink()@CP
Rule23: \
P2() -> Sink()@CP k_P_deg DeleteMolecules
# Delete Molecule P2()
# Add Species Sink()@CP
Rule24: \
TF(im,dna,r).TF(im,dna,r) + Im(cargo)@CP <-> TF(im!1,dna,r).TF(im!2,dna,r).Im(cargo!1!2)@CP k_Im_bind_CP, k_Im_unbind_CP
# Bind(0.0.0,0.2.0)
# Bind(0.1.0,0.2.0)
# Reverse
# Unbind(0.0.0,0.2.0)
# Unbind(0.1.0,0.2.0)
Rule25: \
TF(im,dna,r).TF(im,dna,r) + Im(cargo)@NU <-> TF(im!1,dna,r).TF(im!2,dna,r).Im(cargo!1!2)@NU k_Im_bind_NU, k_Im_unbind_NU
# Bind(0.0.0,0.2.0)
# Bind(0.1.0,0.2.0)
# Reverse
# Unbind(0.0.0,0.2.0)
# Unbind(0.1.0,0.2.0)
Rule26: \
P1(im,dna) + Im(cargo)@CP <-> P1(im!1,dna).Im(cargo!1)@CP k_Im_bind_CP, k_Im_unbind_CP
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
Rule27: \
P1(im,dna) + Im(cargo)@NU <-> P1(im!1,dna).Im(cargo!1)@NU k_Im_bind_NU, k_Im_unbind_NU
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
Rule28: \
Im(fg) + NP(fg) <-> Im(fg!1).NP(fg!1) k_Im_enters_NP, k_Im_exits_NP
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
Rule29: \
Im(fg!1)@CP.NP(fg!1) <-> Im(fg!1)@NU.NP(fg!1) k_Im_cross_NP, k_Im_cross_NP MoveConnected
# ChangeCompartment(0.0,CP,NU,0)
# Reverse
# ChangeCompartment(0.0,NU,CP,0)
Rule30: \
P1(im,dna) + DNA(p2) <-> P1(im,dna!1).DNA(p2!1) kp_P1_p2, km_P1_p2
# Bind(0.0.1,0.1.0)
# Reverse
# Unbind(0.0.1,0.1.0)
end reaction rules
begin reactions
1 1,2 8 0.05*kp_LR #1
2 1,1 9 0.025*kp_LL #Rule2
3 5,6 10 0.25*k_Im_enters_NP #Rule28
4 2,9 11 0.1*kp_LR #1
5 8 1,2 km_LR #1(reverse)
6 1,8 11 0.05*kp_LL #Rule2
7 8,8 12 1.25*kp_LL #Rule2
8 9 1,1 km_LL #Rule2(reverse)
9 10 5,6 k_Im_exits_NP #Rule28(reverse)
10 10 13 k_Im_cross_NP #Rule29
11 2,11 12 2.5*kp_LR #1
12 11 2,9 km_LR #1(reverse)
13 12 2,11 2*km_LR #1(reverse)
14 11 1,8 km_LL #Rule2(reverse)
15 12 8,8 km_LL #Rule2(reverse)
16 12 14 k_R_endo #Rule3
17 12 15 2*k_R_transphos #Rule6
18 13 6,16 k_Im_exits_NP #Rule28(reverse)
19 13 10 k_Im_cross_NP #Rule29(reverse)
20 14 17,18 2*km_LR #1(reverse)
21 15 2,19 km_LR #1(reverse)
22 15 11,20 km_LR #1(reverse)
23 14 21,21 km_LL #Rule2(reverse)
24 15 8,22 km_LL #Rule2(reverse)
25 15 23 k_R_endo #Rule3
26 14 12 k_recycle #Rule4
27 14 23 2*k_R_transphos #Rule6
28 15 24 k_R_transphos #Rule6
29 15 12 k_R_dephos #Rule7
30 3,15 25 0.25*kp_R_TF #Rule8
31 6,16 13 k_Im_enters_NP #Rule28
32 1,20 22 0.05*kp_LR #1
33 9,20 19 0.1*kp_LR #1
34 11,20 15 2.5*kp_LR #1
35 17,18 14 20*kp_LR #1
36 2,19 15 2.5*kp_LR #1
37 19,20 24 2.5*kp_LR #1
38 17 18,26 km_LR #1(reverse)
39 19 9,20 km_LR #1(reverse)
40 21 18,27 km_LR #1(reverse)
41 22 1,20 km_LR #1(reverse)
42 23 18,28 km_LR #1(reverse)
43 23 17,29 km_LR #1(reverse)
44 24 19,20 2*km_LR #1(reverse)
45 25 2,30 km_LR #1(reverse)
46 25 11,31 km_LR #1(reverse)
47 1,22 19 0.05*kp_LL #Rule2
48 8,22 15 2.5*kp_LL #Rule2
49 21,21 14 10*kp_LL #Rule2
50 22,22 24 1.25*kp_LL #Rule2
51 17 21,27 km_LL #Rule2(reverse)
52 19 1,22 km_LL #Rule2(reverse)
53 23 21,32 km_LL #Rule2(reverse)
54 24 22,22 km_LL #Rule2(reverse)
55 25 8,33 km_LL #Rule2(reverse)
56 24 34 k_R_endo #Rule3
57 25 35 k_R_endo #Rule3
58 17 11 k_recycle #Rule4
59 18 2 k_recycle #Rule4
60 21 8 k_recycle #Rule4
61 23 15 k_recycle #Rule4
62 23 34 k_R_transphos #Rule6
63 25 36 k_R_transphos #Rule6
64 19 11 k_R_dephos #Rule7
65 20 2 k_R_dephos #Rule7
66 22 8 k_R_dephos #Rule7
67 23 14 k_R_dephos #Rule7
68 24 15 2*k_R_dephos #Rule7
69 3,19 30 0.25*kp_R_TF #Rule8
70 3,20 31 0.25*kp_R_TF #Rule8
71 3,22 33 0.25*kp_R_TF #Rule8
72 3,23 35 0.25*kp_R_TF #Rule8
73 3,24 36 0.5*kp_R_TF #Rule8
74 25 3,15 km_R_TF #Rule8(reverse)
75 1,31 33 0.05*kp_LR #1
76 9,31 30 0.1*kp_LR #1
77 11,31 25 2.5*kp_LR #1
78 17,29 23 20*kp_LR #1
79 19,31 36 2.5*kp_LR #1
80 18,26 17 4*kp_LR #1
81 26,29 28 4*kp_LR #1
82 18,27 21 2*kp_LR #1
83 27,29 32 2*kp_LR #1
84 18,28 23 20*kp_LR #1
85 28,29 34 20*kp_LR #1
86 2,30 25 2.5*kp_LR #1
87 20,30 36 2.5*kp_LR #1
88 30,31 37 2.5*kp_LR #1
89 28 26,29 km_LR #1(reverse)
90 30 9,31 km_LR #1(reverse)
91 32 27,29 km_LR #1(reverse)
92 33 1,31 km_LR #1(reverse)
93 34 28,29 2*km_LR #1(reverse)
94 35 18,38 km_LR #1(reverse)
95 35 17,39 km_LR #1(reverse)
96 36 20,30 km_LR #1(reverse)
97 36 19,31 km_LR #1(reverse)
98 1,33 30 0.05*kp_LL #Rule2
99 8,33 25 2.5*kp_LL #Rule2
100 21,27 17 2*kp_LL #Rule2
101 21,32 23 20*kp_LL #Rule2
102 22,33 36 2.5*kp_LL #Rule2
103 27,27 26 kp_LL #Rule2
104 27,32 28 2*kp_LL #Rule2
105 32,32 34 10*kp_LL #Rule2
106 33,33 37 1.25*kp_LL #Rule2
107 26 27,27 km_LL #Rule2(reverse)
108 28 27,32 km_LL #Rule2(reverse)
109 30 1,33 km_LL #Rule2(reverse)
110 34 32,32 km_LL #Rule2(reverse)
111 35 21,40 km_LL #Rule2(reverse)
112 36 22,33 km_LL #Rule2(reverse)
113 36 41 k_R_endo #Rule3
114 28 19 k_recycle #Rule4
115 29 20 k_recycle #Rule4
116 32 22 k_recycle #Rule4
117 34 24 k_recycle #Rule4
118 35 25 k_recycle #Rule4
119 26 9 k_recycle #Rule5
120 27 1 k_recycle #Rule5
121 35 41 k_R_transphos #Rule6
122 28 17 k_R_dephos #Rule7
123 29 18 k_R_dephos #Rule7
124 32 21 k_R_dephos #Rule7
125 34 23 2*k_R_dephos #Rule7
126 36 25 k_R_dephos #Rule7
127 3,28 38 0.25*kp_R_TF #Rule8
128 3,29 39 0.25*kp_R_TF #Rule8
129 3,32 40 0.25*kp_R_TF #Rule8
130 3,34 41 0.5*kp_R_TF #Rule8
131 3,36 37 0.25*kp_R_TF #Rule8
132 30 3,19 km_R_TF #Rule8(reverse)
133 31 3,20 km_R_TF #Rule8(reverse)
134 33 3,22 km_R_TF #Rule8(reverse)
135 35 3,23 km_R_TF #Rule8(reverse)
136 36 3,24 km_R_TF #Rule8(reverse)
137 17,39 35 20*kp_LR #1
138 26,39 38 4*kp_LR #1
139 27,39 40 2*kp_LR #1
140 28,39 41 20*kp_LR #1
141 18,38 35 20*kp_LR #1
142 29,38 41 20*kp_LR #1
143 38,39 42 20*kp_LR #1
144 37 30,31 2*km_LR #1(reverse)
145 38 26,39 km_LR #1(reverse)
146 40 27,39 km_LR #1(reverse)
147 41 29,38 km_LR #1(reverse)
148 41 28,39 km_LR #1(reverse)
149 21,40 35 20*kp_LL #Rule2
150 27,40 38 2*kp_LL #Rule2
151 32,40 41 20*kp_LL #Rule2
152 40,40 42 10*kp_LL #Rule2
153 37 33,33 km_LL #Rule2(reverse)
154 38 27,40 km_LL #Rule2(reverse)
155 41 32,40 km_LL #Rule2(reverse)
156 37 42 k_R_endo #Rule3
157 38 30 k_recycle #Rule4
158 39 31 k_recycle #Rule4
159 40 33 k_recycle #Rule4
160 41 36 k_recycle #Rule4
161 41 35 k_R_dephos #Rule7
162 3,41 42 0.25*kp_R_TF #Rule8
163 37 3,36 2*km_R_TF #Rule8(reverse)
164 38 3,28 km_R_TF #Rule8(reverse)
165 39 3,29 km_R_TF #Rule8(reverse)
166 40 3,32 km_R_TF #Rule8(reverse)
167 41 3,34 km_R_TF #Rule8(reverse)
168 37 43 2*k_TF_transphos #Rule10
169 42 38,39 2*km_LR #1(reverse)
170 43 31,44 km_LR #1(reverse)
171 43 30,45 km_LR #1(reverse)
172 42 40,40 km_LL #Rule2(reverse)
173 43 33,46 km_LL #Rule2(reverse)
174 43 47 k_R_endo #Rule3
175 42 37 k_recycle #Rule4
176 42 3,41 2*km_R_TF #Rule8(reverse)
177 43 3,48 km_R_TF #Rule8(reverse)
178 43 36,49 km_R_TFp #Rule9(reverse)
179 42 47 2*k_TF_transphos #Rule10
180 43 50 k_TF_transphos #Rule10
181 43 37 k_TF_dephos #Rule11
182 1,45 46 0.05*kp_LR #1
183 9,45 44 0.1*kp_LR #1
184 11,45 51 2.5*kp_LR #1
185 19,45 48 2.5*kp_LR #1
186 30,45 43 2.5*kp_LR #1
187 2,44 51 2.5*kp_LR #1
188 20,44 48 2.5*kp_LR #1
189 31,44 43 2.5*kp_LR #1
190 44,45 50 2.5*kp_LR #1
191 44 9,45 km_LR #1(reverse)
192 46 1,45 km_LR #1(reverse)
193 47 39,52 km_LR #1(reverse)
194 47 38,53 km_LR #1(reverse)
195 48 20,44 km_LR #1(reverse)
196 48 19,45 km_LR #1(reverse)
197 50 44,45 2*km_LR #1(reverse)
198 1,46 44 0.05*kp_LL #Rule2
199 8,46 51 2.5*kp_LL #Rule2
200 22,46 48 2.5*kp_LL #Rule2
201 33,46 43 2.5*kp_LL #Rule2
202 46,46 50 1.25*kp_LL #Rule2
203 44 1,46 km_LL #Rule2(reverse)
204 47 40,54 km_LL #Rule2(reverse)
205 48 22,46 km_LL #Rule2(reverse)
206 50 46,46 km_LL #Rule2(reverse)
207 48 55 k_R_endo #Rule3
208 50 56 k_R_endo #Rule3
209 47 43 k_recycle #Rule4
210 48 51 k_R_dephos #Rule7
211 3,48 43 0.25*kp_R_TF #Rule8
212 47 3,55 km_R_TF #Rule8(reverse)
213 15,49 51 0.25*kp_R_TFp #Rule9
214 19,49 44 0.25*kp_R_TFp #Rule9
215 20,49 45 0.25*kp_R_TFp #Rule9
216 22,49 46 0.25*kp_R_TFp #Rule9
217 23,49 57 0.25*kp_R_TFp #Rule9
218 24,49 48 0.5*kp_R_TFp #Rule9
219 28,49 52 0.25*kp_R_TFp #Rule9
220 29,49 53 0.25*kp_R_TFp #Rule9
221 32,49 54 0.25*kp_R_TFp #Rule9
222 34,49 55 0.5*kp_R_TFp #Rule9
223 36,49 43 0.25*kp_R_TFp #Rule9
224 41,49 47 0.25*kp_R_TFp #Rule9
225 48,49 50 0.25*kp_R_TFp #Rule9
226 44 19,49 km_R_TFp #Rule9(reverse)
227 45 20,49 km_R_TFp #Rule9(reverse)
228 46 22,49 km_R_TFp #Rule9(reverse)
229 47 41,49 km_R_TFp #Rule9(reverse)
230 48 24,49 km_R_TFp #Rule9(reverse)
231 50 48,49 2*km_R_TFp #Rule9(reverse)
232 47 56 k_TF_transphos #Rule10
233 44 30 k_TF_dephos #Rule11
234 45 31 k_TF_dephos #Rule11
235 46 33 k_TF_dephos #Rule11
236 47 42 k_TF_dephos #Rule11
237 48 36 k_TF_dephos #Rule11
238 49 3 k_TF_dephos #Rule11
239 50 43 2*k_TF_dephos #Rule11
240 49,49 58 0.125*kp_TF_TF #Rule12
241 17,53 57 20*kp_LR #1
242 26,53 52 4*kp_LR #1
243 27,53 54 2*kp_LR #1
244 28,53 55 20*kp_LR #1
245 38,53 47 20*kp_LR #1
246 18,52 57 20*kp_LR #1
247 29,52 55 20*kp_LR #1
248 39,52 47 20*kp_LR #1
249 52,53 56 20*kp_LR #1
250 51 2,44 km_LR #1(reverse)
251 51 11,45 km_LR #1(reverse)
252 52 26,53 km_LR #1(reverse)
253 54 27,53 km_LR #1(reverse)
254 55 29,52 km_LR #1(reverse)
255 55 28,53 km_LR #1(reverse)
256 56 52,53 2*km_LR #1(reverse)
257 57 18,52 km_LR #1(reverse)
258 57 17,53 km_LR #1(reverse)
259 21,54 57 20*kp_LL #Rule2
260 27,54 52 2*kp_LL #Rule2
261 32,54 55 20*kp_LL #Rule2
262 40,54 47 20*kp_LL #Rule2
263 54,54 56 10*kp_LL #Rule2
264 51 8,46 km_LL #Rule2(reverse)
265 52 27,54 km_LL #Rule2(reverse)
266 55 32,54 km_LL #Rule2(reverse)
267 56 54,54 km_LL #Rule2(reverse)
268 57 21,54 km_LL #Rule2(reverse)
269 51 57 k_R_endo #Rule3
270 52 44 k_recycle #Rule4
271 53 45 k_recycle #Rule4
272 54 46 k_recycle #Rule4
273 55 48 k_recycle #Rule4
274 56 50 k_recycle #Rule4
275 57 51 k_recycle #Rule4
276 51 48 k_R_transphos #Rule6
277 57 55 k_R_transphos #Rule6
278 55 57 k_R_dephos #Rule7
279 3,55 47 0.25*kp_R_TF #Rule8
280 49,55 56 0.25*kp_R_TFp #Rule9
281 51 15,49 km_R_TFp #Rule9(reverse)
282 52 28,49 km_R_TFp #Rule9(reverse)
283 53 29,49 km_R_TFp #Rule9(reverse)
284 54 32,49 km_R_TFp #Rule9(reverse)
285 55 34,49 km_R_TFp #Rule9(reverse)
286 56 49,55 2*km_R_TFp #Rule9(reverse)
287 57 23,49 km_R_TFp #Rule9(reverse)
288 51 25 k_TF_dephos #Rule11
289 52 38 k_TF_dephos #Rule11
290 53 39 k_TF_dephos #Rule11
291 54 40 k_TF_dephos #Rule11
292 55 41 k_TF_dephos #Rule11
293 56 47 2*k_TF_dephos #Rule11
294 57 35 k_TF_dephos #Rule11
295 58 49,49 km_TF_TF #Rule12(reverse)
296 5,58 59 0.25*k_Im_bind_CP #Rule24
297 10,58 60 0.25*k_Im_bind_CP #Rule24
298 59 5,58 k_Im_unbind_CP #Rule24(reverse)
299 60 10,58 k_Im_unbind_CP #Rule24(reverse)
300 6,59 60 0.25*k_Im_enters_NP #Rule28
301 60 6,59 k_Im_exits_NP #Rule28(reverse)
302 60 61 k_Im_cross_NP #Rule29
303 61 13,62 k_Im_unbind_NU #Rule25(reverse)
304 61 6,63 k_Im_exits_NP #Rule28(reverse)
305 61 60 k_Im_cross_NP #Rule29(reverse)
306 62 64,64 km_TF_TF #Rule12(reverse)
307 4,62 65 kp_TF_p1 #Rule13
308 13,62 61 k_Im_bind_NU #Rule25
309 16,62 63 k_Im_bind_NU #Rule25
310 63 16,62 k_Im_unbind_NU #Rule25(reverse)
311 6,63 61 k_Im_enters_NP #Rule28
312 64,64 62 0.5*kp_TF_TF #Rule12
313 65 4,62 km_TF_p1 #Rule13(reverse)
314 65 65,66 k_transcribe #Rule14
315 66 67 k_mRNA_to_CP #Rule16
316 66 7 k_mRNA_deg #Rule20
317 67 67,68 k_translate #Rule18
318 67 7 k_mRNA_deg #Rule20
319 68 7 k_P_deg #Rule22
320 5,68 69 0.25*k_Im_bind_CP #Rule26
321 10,68 70 0.25*k_Im_bind_CP #Rule26
322 69 5,7 k_P_deg #Rule22
323 70 7,10 k_P_deg #Rule22
324 69 5,68 k_Im_unbind_CP #Rule26(reverse)
325 70 10,68 k_Im_unbind_CP #Rule26(reverse)
326 6,69 70 0.25*k_Im_enters_NP #Rule28
327 70 6,69 k_Im_exits_NP #Rule28(reverse)
328 70 71 k_Im_cross_NP #Rule29
329 71 7,13 k_P_deg #Rule22
330 71 13,72 k_Im_unbind_NU #Rule27(reverse)
331 71 6,73 k_Im_exits_NP #Rule28(reverse)
332 71 70 k_Im_cross_NP #Rule29(reverse)
333 72 7 k_P_deg #Rule22
334 73 7,16 k_P_deg #Rule22
335 13,72 71 k_Im_bind_NU #Rule27
336 16,72 73 k_Im_bind_NU #Rule27
337 73 16,72 k_Im_unbind_NU #Rule27(reverse)
338 6,73 71 k_Im_enters_NP #Rule28
339 4,72 74 kp_P1_p2 #Rule30
340 65,72 75 kp_P1_p2 #Rule30
341 62,74 75 kp_TF_p1 #Rule13
342 75 62,74 km_TF_p1 #Rule13(reverse)
343 75 66,75 k_transcribe #Rule14
344 74 74,76 k_transcribe #Rule15
345 75 75,76 k_transcribe #Rule15
346 74 4,7 k_P_deg #Rule22
347 75 7,65 k_P_deg #Rule22
348 74 4,72 km_P1_p2 #Rule30(reverse)
349 75 65,72 km_P1_p2 #Rule30(reverse)
350 76 77 k_mRNA_to_CP #Rule17
351 76 7 k_mRNA_deg #Rule21
352 77 77,78 k_translate #Rule19
353 77 7 k_mRNA_deg #Rule21
354 78 7 k_P_deg #Rule23
end reactions
begin groups
1 Tot_L 1,8,2*9,2*11,2*12,2*14,2*15,2*17,2*19,21,22,2*23,2*24,2*25,2*26,27,2*28,2*30,32,33,2*34,2*35,2*36,2*37,2*38,40,2*41,2*42,2*43,2*44,46,2*47,2*48,2*50,2*51,2*52,54,2*55,2*56,2*57
2 Tot_R 2,8,11,2*12,2*14,2*15,17,18,19,20,21,22,2*23,2*24,2*25,28,29,30,31,32,33,2*34,2*35,2*36,2*37,38,39,40,2*41,2*42,2*43,44,45,46,2*47,2*48,2*50,2*51,52,53,54,2*55,2*56,2*57
3 Tot_TF 3,25,30,31,33,35,36,2*37,38,39,40,41,2*42,2*43,44,45,46,2*47,48,49,2*50,51,52,53,54,55,2*56,57,2*58,2*59,2*60,2*61,2*62,2*63,64,2*65,2*75
4 Tot_DNA 4,65,74,75
5 Tot_mRNA1 66,67
6 Tot_mRNA2 76,77
7 Tot_P1 68,69,70,71,72,73,74,75
8 Tot_P2 78
9 Tot_NP 6,10,13,60,61,70,71
10 Tot_Im 5,10,13,16,59,60,61,63,69,70,71,73
11 L_Dimers_EC 9
12 L_Dimers_PM 11,12,15,19,24,25,30,36,37,43,44,48,50,51
13 L_Dimers_EN 26
14 L_Dimers_EM 14,17,23,28,34,35,38,41,42,47,52,55,56,57
15 L_Bound_PM 8,2*11,2*12,2*15,2*19,22,2*24,2*25,2*30,33,2*36,2*37,2*43,2*44,46,2*48,2*50,2*51
16 L_Bound_EM 2*14,2*17,21,2*23,2*28,32,2*34,2*35,2*38,40,2*41,2*42,2*47,2*52,54,2*55,2*56,2*57
17 R_Dimers_PM 12,15,24,25,36,37,43,48,50,51
18 R_Dimers_EM 14,23,34,35,41,42,47,55,56,57
19 Catalytic_R 15,19,20,22,23,2*24,25,28,29,30,31,32,33,2*34,35,2*36,2*37,38,39,40,2*41,2*42,2*43,44,45,46,2*47,2*48,2*50,51,52,53,54,2*55,2*56,57
20 Catalytic_TF 25,30,31,33,35,36,2*37,38,39,40,41,2*42,2*43,44,45,46,2*47,48,2*50,51,52,53,54,55,2*56,57
21 Phos_TF 43,44,45,46,47,48,49,2*50,51,52,53,54,55,2*56,57,2*58,2*59,2*60,2*61,2*62,2*63,64,2*65,2*75
22 TF_Dimer_CP 58,59,60
23 TF_Dimer_NU 61,62,63,65,75
24 Bound_prom1 65,75
25 Bound_prom2 74,75
26 P1_NU 71,72,73,74,75
27 P1_CP 68,69,70
28 Im_NU 13,16,61,63,71,73
29 Im_CP 5,10,59,60,69,70
30 Im_Cargo_NP 60,61,70,71
31 P1_NU_free 72
32 P1_NU_dna 74,75
33 CountSink 7
end groups