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Model repository

Models

+ Miyoshi et al. 2007
+ Plyusnina et al. (in prep.)
+ Hertel et al. 2013
+ Jablonsky et al. 2014
+ Clark et al. 2014 (in progress)
+ Fridlyand et al. 1995
o Grimaud et al. 2014
o E-cyano team 2017, clock & C-N metabolism
o Müller et al. 2019

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E-cyano team 2017, clock & C-N metabolism

Integrated model made by connecting the Miyoshi model and the Grimaud model.

Annotations
Components
Reactions
Parameters
Simulation
Analysis
Experiments
+model: e-cyano team 2017, clock & C-N metabolism
The Grimaud model describes carbon-nitrogen metabolism. An important role in the model is held by nitrogenase, an enzyme responsible for catalysing nitrogen fixation. Nitrogenase activity is in the Grimaud model represented by a simple condition that keeps its activity turned on during a specific time period while turning it off for the rest of the day. In the real world, this condition is probably affected by the circadian clock mechanism as it has been shown that almost all genes in cyanobacteria are regulated by the circadian clock.Therefore, in the integrated model of circadian clock and carbon-nitrogen metabolism, nitrogenase activity si modelled by the circadian clock from the Miyoshi model. This connection if backed up by results showing correlation between concentration of KaiB4 in the Miyoshi model and nitrogenase activity indirectly though concentration of dissolved O2.

model: e-cyano team 2017, clock & C-N metabolism
+publication: Šalagovič 2017

Šalagovič, Jakub. Computational analysis and model integration of biorhythmic systems. Brno, 2017. Master's thesis. Masaryk University, Faculty of Informatics. Thesis supervisor David Šafránek.


publication: Šalagovič 2017
Contains:
+cytosol
Initial expression: 1
Simulation type: fixed
+KaiC6
Initial expression: 340.8
Simulation type: reaction
+PPKaiC6
Initial expression: 921.3
Simulation type: reaction
+CPKaiC6
Initial expression: 1916.4
Simulation type: reaction
+KaiC
Initial expression: 1118.2
Simulation type: reaction
+PKaiC
Initial expression: 119.3
Simulation type: reaction
+KaiB4i
Initial expression: 3274
Simulation type: reaction
+KaiB4
Initial expression: 0.25
Simulation type: reaction
+KaiA2
Initial expression: 183.2
Simulation type: reaction
+KaiA
Initial expression: 10.5
Simulation type: reaction
+kaiA_mRNA
Initial expression: 2.9
Simulation type: reaction
+kaiBC_mRNA
Initial expression: 2.95
Simulation type: reaction
+KaiA2B4
Initial expression: 33.1
Simulation type: reaction
+Cr
Initial expression: 100
Simulation type: reaction
+Cf
Initial expression: 650
Simulation type: reaction
+Nr
Initial expression: 100
Simulation type: reaction
+Cnit
Initial expression: 0
Simulation type: reaction
+Nf
Initial expression: Cf*alpha3
Simulation type: assignment
+Ctot
Initial expression: Cf+Cr+Cnit
Simulation type: assignment
+Ntot
Initial expression: Nf+Nr
Simulation type: assignment
+t_
Initial expression: 0
Simulation type: reaction
+KaiB
Initial expression: 1042.7
Simulation type: reaction
+Cf input (Grimaud)
Equation: -> Cf
Modifiers: Cr, Cnit, Nr, Nf
Function: Cf input (Grimaud) (irreversible)
Reaction rate: r3*Cr*Nr/Nf+r7*Cnit
Kinetic rate constant Value
r3 0.025
r7 0.83
+Cf output (Grimaud)
Equation: Cf ->
Function: Cf output (Grimaud) (irreversible)
Reaction rate: (r4*phi+D_)*Cf
Kinetic rate constant Value
r4 0.00093
D_ 0.0083
phi KaiB4/cs
+Cnit input (Grimaud)
Equation: -> Cnit
Modifiers: Cf
Function: Cnit input (Grimaud) (irreversible)
Reaction rate: r4*phi*Cf
Kinetic rate constant Value
r4 0.00093
phi KaiB4/cs
+Cnit output (Grimaud)
Equation: Cnit ->
Function: Cnit output (Grimaud) (irreversible)
Reaction rate: (r7 + D_)*Cnit
Kinetic rate constant Value
r7 0.83
D_ 0.0083
+Cr input (Grimaud)
Equation: -> Cr
Modifiers: Cf
Function: Cr input (Grimaud) (irreversible)
Reaction rate: r2*(Ir/(Ir+Kl+I_*I_/Kil))*Cf
Kinetic rate constant Value
r2 0.275
Ir 130*exp(1)^(-1*((((t_+12) % 24)-12)^2)/(2*2^2))/3
Kil 4500
Kl 55.5
I_ 130/3/3
+Cr output (Grimaud)
Equation: Cr ->
Modifiers: Nr, Nf, Cnit, Cf
Function: Cr output (Grimaud) (irreversible)
Reaction rate: ((r3+r3*gamma3)*Nr/Nf + r5 + D_)*Cr + alpha1*r1*Cnit + lambda5*(r2*(Ir/(Ir+Kl+I_*I_/Kil))*Cf)/Cf*Cnit
Kinetic rate constant Value
r3 0.025
gamma3 0.4
r5 0.027
D_ 0.0083
r1 14.5
alpha1 1.9
lambda5 5200
r2 0.275
I_ 130/3/3
Kil 4500
Kl 55.5
Ir 130*exp(1)^(-1*((((t_+12) % 24)-12)^2)/(2*2^2))/3
+KaiA dimer and KaiB-active tetramer dissociation
Equation: KaiA2B4 -> KaiA2
Function: Mass Action (irreversible)
Reaction rate: k12*KaiA2B4
Kinetic rate constant Value
k12 0.08788
+KaiA dimer and KaiB-active tetramer formation
Equation: KaiB4 + KaiA2 -> KaiA2B4
Function: Mass action (two substrates) (reversible)
Reaction rate: k11*theta1*KaiB4*KaiA2
Kinetic rate constant Value
theta1 1
k11 0.0008756
+KaiA dimer dissociation
Equation: KaiA2 -> KaiA
Function: Mass Action (irreversible)
Reaction rate: k7*KaiA2
Kinetic rate constant Value
k7 0.162
+KaiA dimer formation
Equation: KaiA -> KaiA2
Function: Mass Action 2nd order (irreversible)
Reaction rate: k8*KaiA*KaiA
Kinetic rate constant Value
k8 0.268
+KaiA protein degradation
Equation: KaiA ->
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg1*KaiA*L_
Kinetic rate constant Value
kpdeg1 0.008
L_ ceil(Ir/100--0.0005)
+KaiA translation
Equation: -> KaiA
Modifiers: kaiA_mRNA
Function: Light dependend inflow (irreversible)
Reaction rate: ktl1*L_*kaiA_mRNA
Kinetic rate constant Value
ktl1 0.008239
L_ ceil(Ir/100--0.0005)
+KaiAmRNA degradation
Equation: kaiA_mRNA ->
Function: Mass Action (irreversible)
Reaction rate: kmdeg1*kaiA_mRNA
Kinetic rate constant Value
kmdeg1 0.133
+KaiB and KaiC translation
Equation: -> KaiB
Modifiers: kaiBC_mRNA
Function: Light dependend inflow (irreversible)
Reaction rate: ktl2*L_*kaiBC_mRNA
Kinetic rate constant Value
ktl2 170.1
L_ ceil(Ir/100--0.0005)
+KaiB protein degradation
Equation: KaiB ->
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg2*KaiB*L_
Kinetic rate constant Value
kpdeg2 0.49
L_ ceil(Ir/100--0.0005)
+KaiB tetramer complex activation
Equation: KaiB4i -> KaiB4
Modifiers: CPKaiC6
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat_b2*CPKaiC6*KaiB4i)/(Km_b2 + KaiB4i)
Kinetic rate constant Value
kcat_b2 0.346
Km_b2 66.75
+KaiB tetramer complex inactivation
Equation: KaiB4 -> KaiB4i
Modifiers: PPKaiC6
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat_b1*PPKaiC6*KaiB4)/(Km_b1 + KaiB4)
Kinetic rate constant Value
kcat_b1 2.423
Km_b1 0.602
+KaiB-active tetramer dissociation
Equation: KaiB4 -> KaiB
Function: Mass Action (irreversible)
Reaction rate: k10*KaiB4
Kinetic rate constant Value
k10 0.0001615
+KaiB-active tetramer formation
Equation: KaiB -> KaiB4
Function: Mass Action 4th order (reversible)
Reaction rate: k9*KaiB*KaiB*KaiB*KaiB
Kinetic rate constant Value
k9 7.393e-17
+KaiC hexameric complex auto-phosphorylation
Equation: KaiC6 -> PPKaiC6
Function: Mass Action (irreversible)
Reaction rate: k21*KaiC6
Kinetic rate constant Value
k21 1.079e-08
+KaiC hexameric complex dissociation
Equation: KaiC6 -> KaiC
Function: Mass Action (irreversible)
Reaction rate: k1*KaiC6
Kinetic rate constant Value
k1 1.615
+KaiC hexameric complex formation
Equation: KaiC -> KaiC6
Function: Mass Action 6th order (reversible)
Reaction rate: k2*KaiC*KaiC*KaiC*KaiC*KaiC*KaiC
Kinetic rate constant Value
k2 2.039e-16
+KaiC hexameric complex phosphorylation
Equation: KaiC6 -> PPKaiC6
Modifiers: KaiA2
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat1*KaiA2*KaiC6)/(Km1 + KaiC6)
Kinetic rate constant Value
kcat1 0.539
Km1 602
+KaiC protein degradation
Equation: KaiC ->
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg3*KaiC*L_
Kinetic rate constant Value
kpdeg3 1.3
L_ ceil(Ir/100--0.0005)
+Nr input (Grimaud)
Equation: -> Nr
Modifiers: Cnit
Function: Nr input (Grimaud) (irreversible)
Reaction rate: 2*r1*Cnit
Kinetic rate constant Value
r1 14.5
+Nr output (Grimaud)
Equation: Nr ->
Modifiers: Cr, Cnit, Nf
Function: Nr ouutput (Grimaud) (irreversible)
Reaction rate: (alpha3*r3*Cr/Nf+lambda6*r1*Cnit/Nf + D_)*Nr
Kinetic rate constant Value
r1 14.5
r3 0.025
alpha3 0.155
lambda6 0.88
D_ 0.0083
+Time flow
Equation: -> t_
Function: Time flow (irreversible)
Reaction rate: theta1
Kinetic rate constant Value
theta1 1
+completely phosphorylated KaiC hexameric complex auto-dephosphorylation
Equation: CPKaiC6 -> PPKaiC6
Function: Mass Action (irreversible)
Reaction rate: k24*CPKaiC6
Kinetic rate constant Value
k24 1.079e-08
+completely phosphorylated KaiC hexameric complex dephosphorylation
Equation: CPKaiC6 -> PPKaiC6
Modifiers: KaiA2B4
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat4*KaiA2B4*CPKaiC6)/(Km4 + CPKaiC6)
Kinetic rate constant Value
kcat4 0.89
Km4 0.602
+completely phosphorylated KaiC hexameric complex dissociation
Equation: CPKaiC6 -> PKaiC
Function: Mass Action (irreversible)
Reaction rate: k5*CPKaiC6
Kinetic rate constant Value
k5 0.162
+completely phosphorylated KaiC hexameric complex formation
Equation: PKaiC -> CPKaiC6
Function: Mass Action 6th order (reversible)
Reaction rate: k6*PKaiC*PKaiC*PKaiC*PKaiC*PKaiC*PKaiC
Kinetic rate constant Value
k6 1.019e-10
+kaiA mRNA transcription
Equation: -> kaiA_mRNA
Modifiers: CPKaiC6, PPKaiC6
Function: Enzyme-modulated light-dependend transcription (irreversible)
Reaction rate: ka1*(kbts1*RNAP)/(1+kbts1*RNAP)*(CPKaiC6/PPKaiC6)*L_
Kinetic rate constant Value
ka1 10170000
kbts1 3.657e-12
RNAP 5000
L_ ceil(Ir/100--0.0005)
+kaiBC mRNA degradation
Equation: kaiBC_mRNA ->
Function: Mass Action (irreversible)
Reaction rate: kmdeg2*kaiBC_mRNA
Kinetic rate constant Value
kmdeg2 0.178
+kaiBC mRNA trascription
Equation: -> kaiBC_mRNA
Modifiers: CPKaiC6, PPKaiC6
Function: Enzyme-modulated light-dependend transcription (irreversible)
Reaction rate: ka2*(kbts2*RNAP)/(1+kbts2*RNAP)*(CPKaiC6/PPKaiC6)*L_
Kinetic rate constant Value
ka2 64580000
kbts2 1e-12
RNAP 5000
L_ ceil(Ir/100--0.0005)
+partially phosphorylated KaiC hexameric complex auto-dephosphorylation
Equation: PPKaiC6 -> KaiC6
Function: Mass Action (irreversible)
Reaction rate: k22*PPKaiC6
Kinetic rate constant Value
k22 1.079e-05
+partially phosphorylated KaiC hexameric complex auto-phosphorylation
Equation: PPKaiC6 -> CPKaiC6
Function: Mass Action (irreversible)
Reaction rate: k23*PPKaiC6
Kinetic rate constant Value
k23 1.079e-06
+partially phosphorylated KaiC hexameric complex dephosphorylation
Equation: PPKaiC6 -> KaiC6
Modifiers: KaiA2B4
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat2*KaiA2B4*PPKaiC6)/(Km2 + PPKaiC6)
Kinetic rate constant Value
kcat2 0.539
Km2 602
+partially phosphorylated KaiC hexameric complex dissociation
Equation: PPKaiC6 -> KaiC
Function: Mass Action (irreversible)
Reaction rate: k3*PPKaiC6
Kinetic rate constant Value
k3 0.0001615
+partially phosphorylated KaiC hexameric complex formation
Equation: KaiC + PKaiC -> PPKaiC6
Function: Specific hexamer formation (Myioshi) (reversible)
Reaction rate: k4*KaiC*KaiC*KaiC*PKaiC*PKaiC*PKaiC
Kinetic rate constant Value
k4 1.019e-14
+partially phosphorylated KaiC hexameric complex phosphorylation
Equation: PPKaiC6 -> CPKaiC6
Modifiers: KaiA2
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat3*KaiA2*PPKaiC6)/(Km3 + PPKaiC6)
Kinetic rate constant Value
kcat3 1.079
Km3 0.602
+phosphorylated KaiC protein degradation
Equation: PKaiC ->
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg4*PKaiC*L_
Kinetic rate constant Value
kpdeg4 0.2
L_ ceil(Ir/100--0.0005)

Constant quantities

+r1
Initial expression: 14.5
Simulation type: fixed
+r2
Initial expression: 0.275
Simulation type: fixed
+r3
Initial expression: 0.025
Simulation type: fixed
+r4
Initial expression: 0.00093
Simulation type: fixed
+r5
Initial expression: 0.027
Simulation type: fixed
+r7
Initial expression: 0.83
Simulation type: fixed
+alpha1
Initial expression: 1.9
Simulation type: fixed
+alpha3
Initial expression: 0.155
Simulation type: fixed
+gamma3
Initial expression: 0.4
Simulation type: fixed
+lambda5
Initial expression: 5200
Simulation type: fixed
+lambda6
Initial expression: 0.88
Simulation type: fixed
+D_
Initial expression: 0.0083
Simulation type: fixed
+Kl
Initial expression: 55.5
Simulation type: fixed
+Kil
Initial expression: 4500
Simulation type: fixed
+k_
Initial expression: 0.27
Simulation type: fixed
+Kb
Initial expression: 0.08
Simulation type: fixed
+theta0
Initial expression: 0
Simulation type: fixed
+theta1
Initial expression: 1
Simulation type: fixed
+Tp
Initial expression: 7
Simulation type: fixed
+Tc
Initial expression: 24
Simulation type: fixed
+T_
Initial expression: 0.0001
Simulation type: fixed
+phase
Initial expression: 12
Simulation type: fixed
+k4
Initial expression: 1.019e-14
Simulation type: fixed
+k3
Initial expression: 0.0001615
Simulation type: fixed
+k2
Initial expression: 2.039e-16
Simulation type: fixed
+k5
Initial expression: 0.162
Simulation type: fixed
+k1
Initial expression: 1.615
Simulation type: fixed
+k6
Initial expression: 1.019e-10
Simulation type: fixed
+k7
Initial expression: 0.162
Simulation type: fixed
+k8
Initial expression: 0.268
Simulation type: fixed
+k9
Initial expression: 7.393e-17
Simulation type: fixed
+k10
Initial expression: 0.0001615
Simulation type: fixed
+k11
Initial expression: 0.0008756
Simulation type: fixed
+k12
Initial expression: 0.08788
Simulation type: fixed
+k21
Initial expression: 1.079e-08
Simulation type: fixed
+k22
Initial expression: 1.079e-05
Simulation type: fixed
+k23
Initial expression: 1.079e-06
Simulation type: fixed
+k24
Initial expression: 1.079e-08
Simulation type: fixed
+ka1
Initial expression: 10170000
Simulation type: fixed
+ka2
Initial expression: 64580000
Simulation type: fixed
+kcat1
Initial expression: 0.539
Simulation type: fixed
+kcat2
Initial expression: 0.539
Simulation type: fixed
+kcat3
Initial expression: 1.079
Simulation type: fixed
+kcat4
Initial expression: 0.89
Simulation type: fixed
+kcat_b1
Initial expression: 2.423
Simulation type: fixed
+kcat_b2
Initial expression: 0.346
Simulation type: fixed
+kmdeg1
Initial expression: 0.133
Simulation type: fixed
+kmdeg2
Initial expression: 0.178
Simulation type: fixed
+kpdeg1
Initial expression: 0.008
Simulation type: fixed
+kpdeg2
Initial expression: 0.49
Simulation type: fixed
+kpdeg3
Initial expression: 1.3
Simulation type: fixed
+kpdeg4
Initial expression: 0.2
Simulation type: fixed
+ktl1
Initial expression: 0.008239
Simulation type: fixed
+ktl2
Initial expression: 170.1
Simulation type: fixed
+kbts1
Initial expression: 3.657e-12
Simulation type: fixed
+kbts2
Initial expression: 1e-12
Simulation type: fixed
+Km1
Initial expression: 602
Simulation type: fixed
+Km2
Initial expression: 602
Simulation type: fixed
+Km3
Initial expression: 0.602
Simulation type: fixed
+Km4
Initial expression: 0.602
Simulation type: fixed
+Km_b1
Initial expression: 0.602
Simulation type: fixed
+Km_b2
Initial expression: 66.75
Simulation type: fixed
+RNAP
Initial expression: 5000
Simulation type: fixed
+c1
Initial expression: 0.9
Simulation type: fixed
+c2
Initial expression: 0.25
Simulation type: fixed
+c3
Initial expression: 0.2
Simulation type: fixed
+c4
Initial expression: 2000
Simulation type: fixed
+cs
Initial expression: 1500
Simulation type: fixed

Assigned quantities

+KaiC_rel
Initial expression: KaiC/(KaiC+PKaiC)
Simulation type: assignment
+PKaiC_rel
Initial expression: PKaiC/(KaiC+PKaiC)
Simulation type: assignment
+tph
Initial expression: (t_+phase) % Tc
Simulation type: assignment
+Ir
Initial expression: 130*exp(1)^(-1*((((t_+12) % 24)-12)^2)/(2*2^2))/3
Simulation type: assignment
+I_
Initial expression: 130/3/3
Simulation type: assignment
+phi
Initial expression: KaiB4/cs
Simulation type: assignment
+L_
Initial expression: ceil(Ir/100--0.0005)
Simulation type: assignment
+Initial conditions
Name Value
cytosol 1
KaiC6 340.8
PPKaiC6 921.3
CPKaiC6 1916.4
KaiC 1118.2
PKaiC 119.3
KaiB4i 3274
KaiB4 0.25
KaiA2 183.2
KaiA 10.5
kaiA_mRNA 2.9
kaiBC_mRNA 2.95
KaiA2B4 33.1
Cr 100
Cf 650
Nr 100
Cnit 0
Nf Cf*alpha3
Ctot Cf+Cr+Cnit
Ntot Nf+Nr
t_ 0
KaiB 1042.7
+Parameters

Constant quantities

Name Value
r1 14.5
r2 0.275
r3 0.025
r4 0.00093
r5 0.027
r7 0.83
alpha1 1.9
alpha3 0.155
gamma3 0.4
lambda5 5200
lambda6 0.88
D_ 0.0083
Kl 55.5
Kil 4500
k_ 0.27
Kb 0.08
theta0 0
theta1 1
Tp 7
Tc 24
T_ 0.0001
phase 12
k4 1.019e-14
k3 0.0001615
k2 2.039e-16
k5 0.162
k1 1.615
k6 1.019e-10
k7 0.162
k8 0.268
k9 7.393e-17
k10 0.0001615
k11 0.0008756
k12 0.08788
k21 1.079e-08
k22 1.079e-05
k23 1.079e-06
k24 1.079e-08
ka1 10170000
ka2 64580000
kcat1 0.539
kcat2 0.539
kcat3 1.079
kcat4 0.89
kcat_b1 2.423
kcat_b2 0.346
kmdeg1 0.133
kmdeg2 0.178
kpdeg1 0.008
kpdeg2 0.49
kpdeg3 1.3
kpdeg4 0.2
ktl1 0.008239
ktl2 170.1
kbts1 3.657e-12
kbts2 1e-12
Km1 602
Km2 602
Km3 0.602
Km4 0.602
Km_b1 0.602
Km_b2 66.75
RNAP 5000
c1 0.9
c2 0.25
c3 0.2
c4 2000
cs 1500

Assigned quantities

Name Value
KaiC_rel KaiC/(KaiC+PKaiC)
PKaiC_rel PKaiC/(KaiC+PKaiC)
tph (t_+phase) % Tc
Ir 130*exp(1)^(-1*((((t_+12) % 24)-12)^2)/(2*2^2))/3
I_ 130/3/3
phi KaiB4/cs
L_ ceil(Ir/100--0.0005)
+Options
Name Value
Simulation Start 0  
Simulation End 150  
Number of Steps 1500  

Simulate   Export sbml

Conservation analysis

Conservation

Modes analysis

Modes

Matrix analysis

Matrix
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI