Navigation
To browse the projects in the ontology view use either the graphical scheme below or the navigation panel on the left. The root level is displayed after clicking on the Projects button in the main menu bar at the top of the screen. For switching to model view, click on the project name in the navigation tree.
The central feature of the ontology view is the graphical scheme representing the projection of the project to respective biological structures. The graphical scheme is active, the individual model parts implemented in the project are emphasized yellow when moving the mouse over them. After clicking on any implemented part, the scheme is zoomed in. The description panel at the bottom contains all the detailed information relevant for the currently focused project level.
Annotations Tab
All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.
Components Tab
The Components Tab displays all the model species (state variables) relevant for the currently focused project level. Annotation data for particular components are accessible after clicking on the requested component header.
Reactions Tab
Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.
Parameters Tab
All quantitative parameters are managed under Parameters Tab. Constants are separated from algebraically evaluated parameters.
Simulation Tab
Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of parameters and initial conditions is listed in respective folders. Folder Options contains parameters of the simulation algorithm.
Heme f
“Oxidized state of haem f of cytochrome b6/f. It accepts one electron from reduced plastoquinone (through iron-sulphur cluster, Rieske center, placed in cytochrome b6/f too) at the lumenal side of thylakoid membrane thus participating in/allowing the linear electron transport.”
f
“Reduced state of haem f of cytochrome b6/f. It donates the electron to plastocyanine molecule in lumen thus participating in/allowing the linear electron transport.”
f-
Model states corresponding to the currently selected level:
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
Initial value: 1
Simulation type: reaction
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Simulation type: reaction
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”
Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c-/f- * Pc+-kbF*bL-/bH.c-/f * Pc
Product: bL-/bH.c-/f, Pc
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c/f--kbct*Fd * bL-/bH.c-/f-
Product: Fd, bL-/bH.c-/f-
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c-/f--kbct*Fd * bL-/bH.c2-/f-
Product: Fd, bL-/bH.c2-/f-
| Kinetic rate constant | Value |
|---|
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”
Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c-/f-"kbL,F"*PQ * bL-/bH.c-/f-
Product: PQ, bL-/bH.c-/f-
| Kinetic rate constant | Value |
|---|
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”
Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c-/f--"k(HC)L"*bL/bH.c2-/f-
Product: bL/bH.c2-/f-
| Kinetic rate constant | Value |
|---|
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”
Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c/f- * Pc+-kbF*bL-/bH.c/f * Pc
Product: bL-/bH.c/f, Pc
| Kinetic rate constant | Value |
|---|
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”
Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL-/bH.c2-/f--"kb(HC)"*PQH * bL-/bH.c/f-
Product: PQH, bL-/bH.c/f-
| Kinetic rate constant | Value |
|---|
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”
Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c/f-"kbL,F"*PQ * bL-/bH.c/f-
Product: PQ, bL-/bH.c/f-
| Kinetic rate constant | Value |
|---|
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”
Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c/f--"k(HC)L"*bL/bH.c-/f-
Product: bL/bH.c-/f-
| Kinetic rate constant | Value |
|---|
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”
Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c2-/f- * Pc+-kbF*bL-/bH.c2-/f * Pc
Product: bL-/bH.c2-/f, Pc
| Kinetic rate constant | Value |
|---|
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”
Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c2-/f-"kbL,F"*PQ * bL-/bH.c2-/f-
Product: PQ, bL-/bH.c2-/f-
| Kinetic rate constant | Value |
|---|
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”
Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c-/f- * Pc+-kbF*bL/bH.c-/f * Pc
Product: bL/bH.c-/f, Pc
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c/f--kbct*Fd * bL/bH.c-/f-
Product: Fd, bL/bH.c-/f-
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c-/f--kbct*Fd * bL/bH.c2-/f-
Product: Fd, bL/bH.c2-/f-
| Kinetic rate constant | Value |
|---|
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”
Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c/f- * Pc+-kbF*bL/bH.c/f * Pc
Product: bL/bH.c/f, Pc
| Kinetic rate constant | Value |
|---|
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”
Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL/bH.c2-/f--"kb(HC)"*PQH * bL/bH.c/f-
Product: PQH, bL/bH.c/f-
| Kinetic rate constant | Value |
|---|
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”
Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c2-/f- * Pc+-kbF*bL/bH.c2-/f * Pc
Product: bL/bH.c2-/f, Pc
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c/f-kbct*Fd * bL-/bH.c-/f
Product: Fd, bL-/bH.c-/f
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c-/f-kbct*Fd * bL-/bH.c2-/f
Product: Fd, bL-/bH.c2-/f
| Kinetic rate constant | Value |
|---|
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”
Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c-/f-"k(HC)L"*bL/bH.c2-/f
Product: bL/bH.c2-/f
| Kinetic rate constant | Value |
|---|
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”
Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL-/bH.c2-/f-"kb(HC)"*PQH * bL-/bH.c/f
Product: PQH, bL-/bH.c/f
| Kinetic rate constant | Value |
|---|
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”
Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c/f-"k(HC)L"*bL/bH.c-/f
Product: bL/bH.c-/f
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c/f-kbct*Fd * bL/bH.c-/f
Product: Fd, bL/bH.c-/f
| Kinetic rate constant | Value |
|---|
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”
Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c-/f-kbct*Fd * bL/bH.c2-/f
Product: Fd, bL/bH.c2-/f
| Kinetic rate constant | Value |
|---|
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”
Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL/bH.c2-/f-"kb(HC)"*bL/bH.c/f * PQH
Product: bL/bH.c/f, PQH
| Kinetic rate constant | Value |
|---|
Constant quantities
Initial value: 7
Simulation type: fixed
Simulation type: fixed
Initial value: 20000
Simulation type: fixed
Simulation type: fixed
Initial value: 10000
Simulation type: fixed
Simulation type: fixed
Initial value: 3330
Simulation type: fixed
Simulation type: fixed
Initial value: 1000
Simulation type: fixed
Simulation type: fixed
Initial value: 0.01
Simulation type: fixed
Simulation type: fixed
Initial value: 3500
Simulation type: fixed
Simulation type: fixed
Initial value: 1750
Simulation type: fixed
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Simulation type: fixed
Initial value: 175
Simulation type: fixed
Simulation type: fixed
Initial value: 35
Simulation type: fixed
Simulation type: fixed
Initial value: 250
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Simulation type: fixed
Initial value: 5
Simulation type: fixed
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 250
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 5
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 220
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Simulation type: fixed
Initial value: 2300
Simulation type: fixed
Simulation type: fixed
Initial value: 200
Simulation type: fixed
Simulation type: fixed
Initial value: 4000
Simulation type: fixed
Simulation type: fixed
Assigned quantities
Initial expression: ((1-0.55)*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")/(1-0.55*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")))/(1+((1/45+(("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")*4/63))*"PQ"))
Simulation type: assignment
Simulation type: assignment
Initial expression: (1-0.55)*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")/(1-0.55*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-"))
Simulation type: assignment
Simulation type: assignment
Initial expression: 10^(-(2.16*10^(-7)*1590*"Pc+" + 2.16*10^(-7)*10300*("P700+/Fb"+"P700+/Fb-")))
Simulation type: assignment
Simulation type: assignment
| Name | Value |
|---|---|
| bL-/bH.c-/f | 0 |
| bL-/bH.c-/f- | 0 |
| bL-/bH.c/f | 0 |
| bL-/bH.c/f- | 0 |
| bL-/bH.c2-/f | 0 |
| bL-/bH.c2-/f- | 0 |
| bL/bH.c-/f | 0 |
| bL/bH.c-/f- | 0 |
| bL/bH.c/f | 1 |
| bL/bH.c/f- | 0 |
| bL/bH.c2-/f | 0 |
| bL/bH.c2-/f- | 0 |
| Fd | 3 |
| Fd- | 0 |
| FNRa | 0 |
| FNRa- | 0 |
| FNRa2- | 0 |
| FNRi | 3 |
| P680+/Qa-/N | 0 |
| P680+/Qa-/Qb | 0 |
| P680+/Qa-/Qb- | 0 |
| P680+/Qa-/Qb2- | 0 |
| P680+/Qa/Qb | 0 |
| P680+/Qa/Qb- | 0 |
| P680+/Qa/Qb2- | 0 |
| P680/Qa-/N | 0 |
| P680/Qa-/Qb | 0 |
| P680/Qa-/Qb- | 0 |
| P680/Qa-/Qb2- | 0 |
| P680/Qa/N | 0 |
| P680/Qa/Qb | 1 |
| P680/Qa/Qb- | 0 |
| P680/Qa/Qb2- | 0 |
| P700+/Fb | 0 |
| P700+/Fb- | 0 |
| P700/Fb | 1 |
| P700/Fb- | 0 |
| Pc | 3 |
| Pc+ | 0 |
| PQ | 2.5 |
| PQH | 2.5 |
| S0 | 0.25 |
| S1 | 0.75 |
| S2 | 0 |
| S3 | 0 |
Constant quantities
| Name | Value |
|---|---|
| k(HC)L | 7 |
| k01 | 20000 |
| k12 | 10000 |
| k23 | 3330 |
| k30 | 1000 |
| ka | 0.01 |
| kAB1 | 3500 |
| kAB2 | 1750 |
| kb(HC) | 10 |
| kBA1 | 175 |
| kBA2 | 35 |
| kbB | 250 |
| kbct | 100 |
| kbF | 10 |
| kbFd | 5 |
| kbL,F | 10 |
| kbR | 10 |
| kbX | 10 |
| kf(HC) | 100 |
| kfB | 250 |
| kfct | 100 |
| kfF | 100 |
| kfFd | 5 |
| kfL,F | 100 |
| kFNR | 220 |
| kfR | 100 |
| kfX | 100 |
| kL(HC) | 2300 |
| kL1 | 200 |
| kL2 | 4000 |
Assigned quantities
| Name | Value |
|---|---|
| Fq(t) | |
| Funq(t) | |
| I820 |
| Name | Value |
|---|---|
| Simulation end | 1 |
| Use log time scale | 1 |
| Multiplication of time scale | 1 |
| Simulation start | 0.000001 |
| Number of steps | 200 |
| Simulation tolerance | 0.01 |
| Label x-axis | time [s] |
Simulate Export sbml