Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment |
reaction21
Unnamed compartment
|
MassAction | PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (0.5 * B_kd * F_B_binding)[s-1] |
|
cAMP_Unnamed_compartment+PKA_A_B_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment |
reaction17
Unnamed compartment
|
MassAction | cAMP_Unnamed_compartment+PKA_A_B_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_A_B_C_Unnamed_compartment) - (Kr * PKA_BB_A_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (F9 * F5 * B_kd * F_B_binding)[s-1] |
|
PKA_BB_A_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment |
reaction8
Unnamed compartment
|
MassAction | PKA_BB_A_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_BB_A_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_AA_BB_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (2.0 * A2_kd * F_A_binding)[s-1] |
|
PKA_A_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C2 |
r5
Unnamed compartment
|
MassAction | PKA_A_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C2 |
|
|
reaction rate (J): (((Kf * PKA_A_B_C_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_A_C2))[uM.s-1]
forward rate constant (Kf): C_kr3[s-1.uM-1] reverse rate constant (Kr): (F2 * C_kd2 * C_kr3 * F4)[s-1] |
|
cAMP_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_A_B_Unnamed_compartment |
reaction7
Unnamed compartment
|
MassAction | cAMP_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_A_B_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_Unnamed_compartment) - (Kr * PKA_A_B_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (A_kd * F_A_binding)[s-1] |
|
C_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment |
r1
Unnamed compartment
|
MassAction | C_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * C_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_B_C2_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): C_kr2[s-1.uM-1] reverse rate constant (Kr): (C_kd2 * C_kr2 * F2)[s-1] |
|
cAMP_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_BB_A_Unnamed_compartment |
reaction22
Unnamed compartment
|
MassAction | cAMP_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_BB_A_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_A_B_Unnamed_compartment) - (Kr * PKA_BB_A_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (F9 * B_kd * F_B_binding)[s-1] |
|
PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_B |
r7
Unnamed compartment
|
MassAction | PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_B |
|
|
reaction rate (J): (((Kf * PKA_B_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_B))[uM.s-1]
forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (2.0 * B_kd * F_B_binding)[s-1] |
|
PKA_Unnamed_compartment+C_Unnamed_compartmentPKA_C_Unnamed_compartment |
reaction5
Unnamed compartment
|
MassAction | PKA_Unnamed_compartment+C_Unnamed_compartmentPKA_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): (2.0 * C_kr1)[s-1.uM-1] reverse rate constant (Kr): (C_kr1 * C_kd)[s-1] |
|
PKA_2C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_C2_Unnamed_compartment |
reaction11
Unnamed compartment
|
MassAction | PKA_2C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_C2_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_2C_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_C2_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): (2.0 * F_B_binding)[s-1.uM-1] reverse rate constant (Kr): (F1 * F2 * B_kd * F_B_binding)[s-1] |
|
PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2 |
r6
Unnamed compartment
|
MassAction | PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2 |
|
|
reaction rate (J): (((Kf * PKA_B_C2_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_A_C2))[uM.s-1]
forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (F3 * F4 * A_kd * F_A_binding)[s-1] |
|
PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment |
r2
Unnamed compartment
|
MassAction | PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_B_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): C_kr2[s-1.uM-1] reverse rate constant (Kr): (F1 * C_kr2 * C_kd)[s-1] |
|
PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment |
reaction0
Unnamed compartment
|
MassAction | PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_C_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_2C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): C_kr1[s-1.uM-1] reverse rate constant (Kr): (2.0 * C_kd2 * C_kr1)[s-1] |
|
PKA_AA_BB_Unnamed_compartment+C_Unnamed_compartmentPKA_AA_BB_C |
r0
Unnamed compartment
|
MassAction | PKA_AA_BB_Unnamed_compartment+C_Unnamed_compartmentPKA_AA_BB_C |
|
|
reaction rate (J): (((Kf * PKA_AA_BB_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_AA_BB_C))[uM.s-1]
forward rate constant (Kf): (2.0 * C_kr5)[s-1.uM-1] reverse rate constant (Kr): (F1 * F7 * C_kd * C_kr5 * F3 * F5)[s-1] |
|
cAMP_Unnamed_compartment+PKA_C_Unnamed_compartmentPKA_B_C_Unnamed_compartment |
reaction6
Unnamed compartment
|
MassAction | cAMP_Unnamed_compartment+PKA_C_Unnamed_compartmentPKA_B_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_C_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (F1 * B_kd * F_B_binding)[s-1] |
|
PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment |
r3
Unnamed compartment
|
MassAction | PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_BB_A_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_BB_A_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): C_kr4[s-1.uM-1] reverse rate constant (Kr): (F1 * C_kd * C_kr4 * F3 * F5)[s-1] |
|
cAMP_Unnamed_compartment+PKA_BB_A_C_Unnamed_compartmentPKA_AA_BB_C |
r4
Unnamed compartment
|
MassAction | cAMP_Unnamed_compartment+PKA_BB_A_C_Unnamed_compartmentPKA_AA_BB_C |
|
|
reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_BB_A_C_Unnamed_compartment) - (Kr * PKA_AA_BB_C))[uM.s-1]
forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (F7 * A2_kd * F_A_binding)[s-1] |
|
C_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment |
reaction4
Unnamed compartment
|
MassAction | C_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * C_Unnamed_compartment) * PKA_A_B_Unnamed_compartment) - (Kr * PKA_A_B_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): C_kr3[s-1.uM-1] reverse rate constant (Kr): (F1 * C_kd * C_kr3 * F3)[s-1] |
|
PKA_B_B+cAMP_Unnamed_compartmentPKA_BB_A_Unnamed_compartment |
r8
Unnamed compartment
|
MassAction | PKA_B_B+cAMP_Unnamed_compartmentPKA_BB_A_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * PKA_B_B) * cAMP_Unnamed_compartment) - (Kr * PKA_BB_A_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): (2.0 * F_A_binding)[s-1.uM-1] reverse rate constant (Kr): (F9 * A_kd * F_A_binding)[s-1] |
|
cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment |
reaction18
Unnamed compartment
|
MassAction | cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment |
|
|
reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_A_B_C_Unnamed_compartment))[uM.s-1]
forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (F3 * A_kd * F_A_binding)[s-1] |
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
Unnamed compartment |
Compartment
(+) (-)
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
cAMP_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_B_B | Unnamed compartment | |
|
|
|
PKA_A_B_C_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_BB_A_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_B_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_B_C_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_BB_A_C_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_C_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_A_B_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_2C_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_AA_BB_C | Unnamed compartment | |
|
|
|
C_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_B_C2_Unnamed_compartment | Unnamed compartment | |
|
|
|
PKA_B_A_C2 | Unnamed compartment | |
|
|
|
PKA_AA_BB_Unnamed_compartment | Unnamed compartment | |
|
|
Name | Text Annotations | BioNetGen Definition |
---|
Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
test | Deterministic (ODE) Compartmental |
Application - test
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
cAMP_Unnamed_compartment | 0.0 [uM] | 0.0
[um2/s] PKA_B_B |
0.0
[uM]
|
0.0
[um2/s] | PKA_A_B_C_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_BB_A_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_B_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_B_C_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_BB_A_C_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_C_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_Unnamed_compartment |
0.011
[uM]
|
0.0
[um2/s] | PKA_A_B_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_2C_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_AA_BB_C |
0.0
[uM]
|
0.0
[um2/s] | C_Unnamed_compartment |
0.02
[uM]
|
0.0
[um2/s] | PKA_B_C2_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s] | PKA_B_A_C2 |
0.0
[uM]
|
0.0
[um2/s] | PKA_AA_BB_Unnamed_compartment |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
reaction21 | included |
reaction17 | included |
reaction8 | included |
r5 | included |
reaction7 | included |
r1 | included |
reaction22 | included |
r7 | included |
reaction5 | included |
reaction11 | included |
r6 | included |
r2 | included |
reaction0 | included |
r0 | included |
reaction6 | included |
r3 | included |
r4 | included |
reaction4 | included |
r8 | included |
reaction18 | included |
Name | End Time | Output Options |
---|---|---|
Simulation0 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Copy of Simulation0 | 500000.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
C_kr=.23 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
C_kr=23 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
C_kd=.0038 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
C_kd=.000038 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kf_A=.8 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kf_A=.008 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kr_A=.12 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kr_A=.0012 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kf_B=.82 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kf_B=.0082 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kr_B=.00221 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Kr_B=.0000221 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Copy of Kr_B=.0000221 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
F_B_binding=31.75 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
F_B_binding=.3175 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
B_factor=50 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
B_factor=.5 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
B_kd=.13 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
B_kd=.0013 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
A_kd=.3 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
A_kd=.003 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
F_A_binding=3 | 1200.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
F_A_binding=.03 | 2000.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
A_Factor=230 | 2000.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
A_Factor=2.3 | 2000.0 [s] |
KeepEvery 20 KeepAtMost 6000 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | Unnamed compartment |
Global Parameters
Name | Expression |
---|---|
F_B_binding | 0.0031[uM-1.s-1] |
|
|
B_kd | 6.59E-4[tbd] |
|
|
B_factor | 5.0[tbd] |
|
|
F_A_binding | 3.0[uM-1.s-1] |
|
|
A_kd | 0.00105[tbd] |
|
|
A_factor | 23.0[tbd] |
|
|
C_kr | 0.0023[s-1] |
|
|
C_kd | 2.52E-7[uM] |
|
|
Vm | 0.31[s-1] |
|
|
Kf_A | 0.08[1] |
|
|
Kr_A | 0.012[s-1] |
|
|
Kf_B | 0.082[1] |
|
|
Kr_B | 2.21E-4[s-1] |
|
|
B1_factor | 1.0[tbd] |
|
|
F1 | 1.0[tbd] |
|
|
F2 | 2310.0[tbd] |
|
|
F3 | 13.5[tbd] |
|
|
F4 | 206.0[tbd] |
|
|
C_kd2 | 1.4E-6[tbd] |
|
|
F5 | 275.0[tbd] |
|
|
C_kr1 | 1.0[uM-1.s-1] |
|
|
C_kr2 | 1.0[uM-1.s-1] |
|
|
C_kr3 | 1.0[uM-1.s-1] |
|
|
C_kr4 | 300.0[uM-1.s-1] |
|
|
C_kr5 | 1.0[uM-1.s-1] |
|
|
F6 | 1408.0[tbd] |
|
|
F7 | 1380.0[tbd] |
|
|
F9 | 1.97[tbd] |
|
|
A2_kd | 0.0057[uM] |
|
|