arnold11
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000393) Biomodels notes: The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Zhu 2007) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 1.0 litre | |
| — | 0.001 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| chloroplast | chloroplast | 3.0 | 1.0 | |
| cytosol | cytosol | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| ADP | ADP | 0.82 | chloroplast (chloroplast) | ✔ | |
| ADPc | ADPc | 0.65 | cytosol (cytosol) | ✔ | |
| ATP | ATP | 0.68 | chloroplast (chloroplast) | ✘ | |
| ATPc | ATPc | 0.35 | cytosol (cytosol) | ✔ | |
| CO2 | CO2 | 0.009 | chloroplast (chloroplast) | ✔ | |
| DHAP | DHAP | 0.476190476190476 | chloroplast (chloroplast) | ✔ | |
| DHAPc | DHAPc | 2.19047619047619 | cytosol (cytosol) | ✔ | |
| DPGA | DPGA | 0.0011 | chloroplast (chloroplast) | ✘ | |
| E4P | E4P | 0.05 | chloroplast (chloroplast) | ✘ | |
| F26BPc | F26BPc | 0.0000078 | cytosol (cytosol) | ✘ | |
| F6P | F6P | 0.640764257004718 | chloroplast (chloroplast) | ✔ | |
| F6Pc | F6Pc | 1.68883505322742 | cytosol (cytosol) | ✔ | |
| FBP | FBP | 0.669999999999999 | chloroplast (chloroplast) | ✘ | |
| FBPc | FBPc | 2.0 | cytosol (cytosol) | ✘ | |
| G1P | G1P | 0.0854779518844294 | chloroplast (chloroplast) | ✔ | |
| G1Pc | G1Pc | 0.226844324349507 | cytosol (cytosol) | ✔ | |
| G6P | G6P | 1.47375779111085 | chloroplast (chloroplast) | ✔ | |
| G6Pc | G6Pc | 3.88432062242307 | cytosol (cytosol) | ✔ | |
| GAP | GAP | 0.0238095238095238 | chloroplast (chloroplast) | ✔ | |
| GAPc | GAPc | 0.109523809523809 | cytosol (cytosol) | ✔ | |
| GCA | GCA | 0.36 | chloroplast (chloroplast) | ✘ | |
| GCAc | GCAc | 0.36 | cytosol (cytosol) | ✘ | |
| GCEA | GCEA | 0.1812 | chloroplast (chloroplast) | ✘ | |
| GCEAc | GCEAc | 0.1812 | cytosol (cytosol) | ✘ | |
| GLUc | GLUc | 24.0 | cytosol (cytosol) | ✔ | |
| GLYc | GLYc | 1.8 | cytosol (cytosol) | ✘ | |
| GOAc | GOAc | 0.028 | cytosol (cytosol) | ✘ | |
| HPRc | HPRc | 0.0035 | chloroplast (chloroplast) | ✘ | |
| HeP | HeP | 2.2 | chloroplast (chloroplast) | ✘ | |
| HePc | HePc | 5.8 | cytosol (cytosol) | ✘ | |
| KGc | KGc | 0.4 | cytosol (cytosol) | ✔ | |
| NAD | NAD | 0.4 | cytosol (cytosol) | ✔ | |
| NADH | NADH | 0.47 | cytosol (cytosol) | ✔ | |
| NADP | NADP | 0.29 | chloroplast (chloroplast) | ✔ | |
| NADPH | NADPH | 0.21 | chloroplast (chloroplast) | ✔ | |
| O2 | O2 | 0.2646 | chloroplast (chloroplast) | ✔ | |
| PGA | PGA | 2.4 | chloroplast (chloroplast) | ✘ | |
| PGAc | PGAc | 0.0 | cytosol (cytosol) | ✘ | |
| PGCA | PGCA | 0.0029 | chloroplast (chloroplast) | ✘ | |
| PeP | PeP | 0.25 | chloroplast (chloroplast) | ✘ | |
| Pi | Pi | 1.4749 | chloroplast (chloroplast) | ✔ | |
| PiPic | PiPic | 0.00000140022767958214 | cytosol (cytosol) | ✔ | |
| PiTc | PiTc | 4.0999844 | cytosol (cytosol) | ✔ | |
| Pic | Pic | 4.09998299977232 | cytosol (cytosol) | ✔ | |
| R5P | R5P | 0.125186846038864 | chloroplast (chloroplast) | ✔ | |
| Ru5P | Ru5P | 0.0500747384155456 | chloroplast (chloroplast) | ✔ | |
| RuBP | RuBP | 2.0 | chloroplast (chloroplast) | ✘ | |
| S7P | S7P | 2.0 | chloroplast (chloroplast) | ✘ | |
| SBP | SBP | 0.3 | chloroplast (chloroplast) | ✘ | |
| SERc | SERc | 7.5 | cytosol (cytosol) | ✘ | |
| SucPc | SucPc | 0.0 | cytosol (cytosol) | ✘ | |
| Succ | Succ | 0.0 | cytosol (cytosol) | ✘ | |
| TP | TP | 0.5 | chloroplast (chloroplast) | ✘ | |
| TPc | TPc | 2.3 | cytosol (cytosol) | ✘ | |
| UDPGc | UDPGc | 0.57 | cytosol (cytosol) | ✘ | |
| UDPc | UDPc | 0.18 | cytosol (cytosol) | ✔ | |
| UTPc | UTPc | 0.75 | cytosol (cytosol) | ✔ | |
| X5P | X5P | 0.0747384155455904 | chloroplast (chloroplast) | ✔ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| AGPase | AGPase | HeP + ATP > ∅ chloroplast * function_10(Vm, G1P, ATP, K1, K2, ADP, KR1, Pi, KA1, PGA, KA2, F6P, KA3, FBP) | |||
| ATP_S | ATP synthetase | ADP + Pi = ATP chloroplast * function_4(ADP, Pi, ATP, q, Ks1, Ks2, Kp1, Vm) | |||
| F26BPc_P | F26BPc phosphatase | F26BPc > HePc + Pic cytosol * function_16(Vm, F26BPc, Pic, Kr1, F6Pc, Kr2, Ks1) | |||
| F6P_TK | F6P transketolase | HeP + TP = E4P + PeP chloroplast * function_6(Vm, F6P, GAP, X5P, E4P, Ks1, Ks2, X5P, Kr1, E4P, Kr2, q) | |||
| F6Pc_K | F6Pc kinase | HePc + ATPc = F26BPc + ADPc cytosol * function_15(Vm, F6Pc, ATPc, F26BPc, ADPc, q, Ks1, F26BPc, Kr1, DHAPc, Kr2, Ks2, ADPc, Kr3) | |||
| FBP_A | FBP aldolase | {2.0}TP = FBP chloroplast * function_4(GAP, DHAP, FBP, q, Ks1, Ks2, Kp1, Vm) | |||
| FBPase | FBPase | FBP = HeP + Pi chloroplast * function_5(Vm, FBP, F6P, Pi, q, Ks1, F6P, Kr1, Pi, Kr2) | |||
| FBPc_A | FBPc aldolase | {2.0}TPc = FBPc cytosol * function_4(GAPc, DHAPc, FBPc, q, Ks1, Ks2, Kp1, Vm) | |||
| FBPcase | FBPcase | FBPc = HePc + Pic cytosol * function_12(FBPc, F6Pc, Pic, q, K52a, Kp1, Kp2, Vm) | |||
| GAP_DH | GAP dehydrogenase | DPGA + NADPH > TP + NADP chloroplast * function_3(Vm, DPGA, NADPH, K1, K2) | |||
| GCAc_Ox | GCAc oxidase | GCAc > GOAc cytosol * function_17(GCAc, Km, V) | |||
| GCEA_DH | GCEA dehydrogenase | HPRc + NADH = GCEAc + NAD function_21(Vm, HPRc, NADH, GCEAc, NAD, q, Ks1, HPRc, Kr1) | |||
| GCEA_K | GCEA kinase | ATP + GCEA = PGA + ADP chloroplast * function_20(Vm, ATP, GCEA, PGA, ADP, q, Ks1, PGA, Kr1, Ks2) | |||
| GLUcGOAc_AT | GLUc:GOAc aminotransferase | GLUc + GOAc = KGc + GLYc cytosol * function_20(Vm, GLUc, GOAc, KGc, GLYc, q, Ks1, GLYc, Kr1, Ks2) | |||
| GLYc_DC | GLYc decarboxylase | {2.0}GLYc > SERc cytosol * function_22(Vm, GLYc, Ks1, SERc, Kr1) | |||
| GPT_GCA | GPT - GCA | GCA > GCAc function_18(GCA, GCEA, Km, V, Ki) | |||
| GPT_GCAc | GPT - GCAc | GCAc > GCA function_18(GCAc, GCEAc, Km, V, Ki) | |||
| GPT_GCEA | GPT - GCEA | GCEA > GCEAc function_18(GCEA, GCA, Km, V, Ki) | |||
| GPT_GCEAc | GPT - GCEAc | GCEAc > GCEA function_18(GCEAc, GCAc, Km, V, Ki) | |||
| PGA_K | PGA kinase | PGA + ATP > DPGA + ADP chloroplast * function_2(Vm, PGA, ATP, Ks1, Ks2, ADP, Kr1) | |||
| PGAc_Deg | PGAc degradation | PGAc > ∅ cytosol * function_17(PGAc, Km, V) | |||
| PGCA_P | PGCA phosphatase | PGCA > GCA chloroplast * function_19(Vm, PGCA, Ks1, GCA, Kr1, Pi, Kr2) | |||
| Ru5P_K | Ru5P kinase | PeP + ATP = RuBP + ADP chloroplast * function_9(Vm, Ru5P, ATP, RuBP, ADP, q, Ks1, PGA, Kr1, RuBP, Kr2, Pi, Kr3, ADP, Kr41, Ks2, Kr42) | |||
| RuBisCO_CO2 | RuBisCO - CO2 | RuBP > {2.0}PGA chloroplast * function_1(Wc_min, RuBP, K, PGA, KR1, FBP, KR2, SBP, KR3, Pi, KR4, NADPH, KR5) | |||
| RuBisCO_O2 | RuBisC0 - O2 | RuBP > PGA + PGCA chloroplast * function_1(Wo_min, RuBP, K, PGA, KR1, FBP, KR2, SBP, KR3, Pi, KR4, NADPH, KR5) | |||
| S7P_TK | S7P transketolase | TP + S7P = {2.0}PeP chloroplast * function_6(Vm, GAP, S7P, X5P, R5P, Ks1, Ks2, X5P, Kr1, R5P, Kr2, q) | |||
| SBP_A | SBP aldolase | TP + E4P = SBP chloroplast * function_7(Vm, DHAP, E4P, SBP, q, Ks1, Ks2) | |||
| SBPase | SBPase | SBP = S7P + Pi chloroplast * function_8(Vm, SBP, S7P, Pi, q, Ks1, Pi, Kr1) | |||
| SERcGOAc_AT | SERc:GOAc aminotransferase | SERc + GOAc = HPRc + GLYc function_20(Vm, SERc, GOAc, HPRc, GLYc, q, Ks1, GLYc, Kr1, Ks2) | |||
| SucPc_P | SucPc phosphatase | SucPc = Succ + Pic cytosol * function_8(Vm, SucPc, Succ, Pic, q, Ks1, Succ, Kr1) | |||
| SucPc_S | SucPc synthase | HePc + UDPGc = SucPc + UDPc cytosol * function_14(Vm, F6Pc, UDPGc, SucPc, UDPc, q, Ks1, FBPc, Kr1, Ks2, UDPc, Kr2, SucPc, Kr3, Succ, Kr4, Pic, Kr5) | |||
| Succ_Deg | Succ degradation | Succ > ∅ cytosol * function_17(Succ, Km, V) | |||
| TPT_DHAP | TPT - DHAP | TP > TPc function_11(Vm, DHAP, KA, Pic, K, Pi, KR1, PGA, KR2, GAP, KR3) | |||
| TPT_GAP | TPT - GAP | TP > TPc function_11(Vm, GAP, KA, Pic, K, Pi, KR1, PGA, KR2, DHAP, KR3) | |||
| TPT_PGA | TPT - PGA | PGA > PGAc function_11(Vm, PGA, KA, Pic, K, Pi, KR1, GAP, KR2, DHAP, KR3) | |||
| UGPase | UGPase | HePc + UTPc = UDPGc + PiPic cytosol * function_13(G1Pc, UTPc, UDPGc, PiPic, q, Ks1, Ks2, Kp1, Kp2, Vm) |
| Id | Value | |
|---|---|---|
| E | 1.456965457 | |
| K52a | 0.00277857142857143 | |
| Wc_min | 0.76667245633627 | |
| Wo_min | 0.280229143229506 | |
| cA | 1.5 | |
| cAc | 1.0 | |
| cNc | 0.87 | |
| cP | 15.0 | |
| cPc | 15.0 | |
| cUc | 1.5 |
| Id | Value | Reaction | |
|---|---|---|---|
| K | 0.02 | RuBisCO_CO2 (RuBisCO - CO2) | |
| KR1 | 0.84 | RuBisCO_CO2 (RuBisCO - CO2) | |
| KR2 | 0.04 | RuBisCO_CO2 (RuBisCO - CO2) | |
| KR3 | 0.075 | RuBisCO_CO2 (RuBisCO - CO2) | |
| KR4 | 0.9 | RuBisCO_CO2 (RuBisCO - CO2) | |
| KR5 | 0.07 | RuBisCO_CO2 (RuBisCO - CO2) | |
| Vm | 30.1408 | PGA_K (PGA kinase) | |
| Ks1 | 0.24 | PGA_K (PGA kinase) | |
| Ks2 | 0.39 | PGA_K (PGA kinase) | |
| Kr1 | 0.23 | PGA_K (PGA kinase) | |
| Vm | 4.03948 | GAP_DH (GAP dehydrogenase) | |
| K1 | 0.004 | GAP_DH (GAP dehydrogenase) | |
| K2 | 0.1 | GAP_DH (GAP dehydrogenase) | |
| q | 7.1 | FBP_A (FBP aldolase) | |
| Ks1 | 0.3 | FBP_A (FBP aldolase) | |
| Ks2 | 0.4 | FBP_A (FBP aldolase) | |
| Kp1 | 0.02 | FBP_A (FBP aldolase) | |
| Vm | 1.21889 | FBP_A (FBP aldolase) | |
| Vm | 0.72626 | FBPase (FBPase) | |
| q | 666000.0 | FBPase (FBPase) | |
| Ks1 | 0.033 | FBPase (FBPase) | |
| Kr1 | 0.7 | FBPase (FBPase) | |
| Kr2 | 12.0 | FBPase (FBPase) | |
| Vm | 3.12207 | F6P_TK (F6P transketolase) | |
| Ks1 | 0.1 | F6P_TK (F6P transketolase) | |
| Ks2 | 0.1 | F6P_TK (F6P transketolase) | |
| Kr1 | 0.1 | F6P_TK (F6P transketolase) | |
| Kr2 | 0.1 | F6P_TK (F6P transketolase) | |
| q | 10.0 | F6P_TK (F6P transketolase) | |
| Vm | 1.21889 | SBP_A (SBP aldolase) | |
| q | 1.017 | SBP_A (SBP aldolase) | |
| Ks1 | 0.4 | SBP_A (SBP aldolase) | |
| Ks2 | 0.2 | SBP_A (SBP aldolase) | |
| Vm | 0.324191 | SBPase (SBPase) | |
| q | 666000.0 | SBPase (SBPase) | |
| Ks1 | 0.05 | SBPase (SBPase) | |
| Kr1 | 12.0 | SBPase (SBPase) | |
| Vm | 3.12207 | S7P_TK (S7P transketolase) | |
| Ks1 | 0.072 | S7P_TK (S7P transketolase) | |
| Ks2 | 0.46 | S7P_TK (S7P transketolase) | |
| Kr1 | 0.1 | S7P_TK (S7P transketolase) | |
| Kr2 | 1.5 | S7P_TK (S7P transketolase) | |
| q | 1.17647 | S7P_TK (S7P transketolase) | |
| Vm | 10.8348 | Ru5P_K (Ru5P kinase) | |
| q | 6846.0 | Ru5P_K (Ru5P kinase) | |
| Ks1 | 0.05 | Ru5P_K (Ru5P kinase) | |
| Kr1 | 2.0 | Ru5P_K (Ru5P kinase) | |
| Kr2 | 0.7 | Ru5P_K (Ru5P kinase) | |
| Kr3 | 4.0 | Ru5P_K (Ru5P kinase) | |
| Kr41 | 2.5 | Ru5P_K (Ru5P kinase) | |
| Ks2 | 0.059 | Ru5P_K (Ru5P kinase) | |
| Kr42 | 0.4 | Ru5P_K (Ru5P kinase) | |
| q | 5.734 | ATP_S (ATP synthetase) | |
| Ks1 | 0.014 | ATP_S (ATP synthetase) | |
| Ks2 | 0.3 | ATP_S (ATP synthetase) | |
| Kp1 | 0.3 | ATP_S (ATP synthetase) | |
| Vm | 15.0 | ATP_S (ATP synthetase) | |
| Vm | 0.266843 | AGPase (AGPase) | |
| K1 | 0.08 | AGPase (AGPase) | |
| K2 | 0.08 | AGPase (AGPase) | |
| KR1 | 10.0 | AGPase (AGPase) | |
| KA1 | 0.1 | AGPase (AGPase) | |
| KA2 | 0.02 | AGPase (AGPase) | |
| KA3 | 0.02 | AGPase (AGPase) | |
| Vm | 1.24333 | TPT_PGA (TPT - PGA) | |
| KA | 0.74 | TPT_PGA (TPT - PGA) | |
| K | 0.25 | TPT_PGA (TPT - PGA) | |
| KR1 | 0.63 | TPT_PGA (TPT - PGA) | |
| KR2 | 0.075 | TPT_PGA (TPT - PGA) | |
| KR3 | 0.077 | TPT_PGA (TPT - PGA) | |
| Vm | 1.24333 | TPT_GAP (TPT - GAP) | |
| KA | 0.74 | TPT_GAP (TPT - GAP) | |
| K | 0.075 | TPT_GAP (TPT - GAP) | |
| KR1 | 0.63 | TPT_GAP (TPT - GAP) | |
| KR2 | 0.25 | TPT_GAP (TPT - GAP) | |
| KR3 | 0.077 | TPT_GAP (TPT - GAP) | |
| Vm | 1.24333 | TPT_DHAP (TPT - DHAP) | |
| KA | 0.74 | TPT_DHAP (TPT - DHAP) | |
| K | 0.077 | TPT_DHAP (TPT - DHAP) | |
| KR1 | 0.63 | TPT_DHAP (TPT - DHAP) | |
| KR2 | 0.25 | TPT_DHAP (TPT - DHAP) | |
| KR3 | 0.075 | TPT_DHAP (TPT - DHAP) | |
| q | 12.0 | FBPc_A (FBPc aldolase) | |
| Ks1 | 0.3 | FBPc_A (FBPc aldolase) | |
| Ks2 | 0.4 | FBPc_A (FBPc aldolase) | |
| Kp1 | 0.02 | FBPc_A (FBPc aldolase) | |
| Vm | 0.107377 | FBPc_A (FBPc aldolase) | |
| q | 6663.0 | FBPcase (FBPcase) | |
| Kp1 | 0.7 | FBPcase (FBPcase) | |
| Kp2 | 12.0 | FBPcase (FBPcase) | |
| Vm | 0.063979 | FBPcase (FBPcase) | |
| q | 0.31 | UGPase (UGPase) | |
| Ks1 | 0.14 | UGPase (UGPase) | |
| Ks2 | 0.1 | UGPase (UGPase) | |
| Kp1 | 0.12 | UGPase (UGPase) | |
| Kp2 | 0.11 | UGPase (UGPase) | |
| Vm | 0.115403 | UGPase (UGPase) | |
| Vm | 0.0555034 | SucPc_S (SucPc synthase) | |
| q | 10.0 | SucPc_S (SucPc synthase) | |
| Ks1 | 0.8 | SucPc_S (SucPc synthase) | |
| Kr1 | 0.8 | SucPc_S (SucPc synthase) | |
| Ks2 | 2.4 | SucPc_S (SucPc synthase) | |
| Kr2 | 0.7 | SucPc_S (SucPc synthase) | |
| Kr3 | 0.4 | SucPc_S (SucPc synthase) | |
| Kr4 | 50.0 | SucPc_S (SucPc synthase) | |
| Kr5 | 11.0 | SucPc_S (SucPc synthase) | |
| Vm | 0.555034 | SucPc_P (SucPc phosphatase) | |
| q | 780.0 | SucPc_P (SucPc phosphatase) | |
| Ks1 | 0.35 | SucPc_P (SucPc phosphatase) | |
| Kr1 | 80.0 | SucPc_P (SucPc phosphatase) | |
| Vm | 0.100915 | F6Pc_K (F6Pc kinase) | |
| q | 590.0 | F6Pc_K (F6Pc kinase) | |
| Ks1 | 0.5 | F6Pc_K (F6Pc kinase) | |
| Kr1 | 0.021 | F6Pc_K (F6Pc kinase) | |
| Kr2 | 0.7 | F6Pc_K (F6Pc kinase) | |
| Ks2 | 0.5 | F6Pc_K (F6Pc kinase) | |
| Kr3 | 0.16 | F6Pc_K (F6Pc kinase) | |
| Vm | 0.0168192 | F26BPc_P (F26BPc phosphatase) | |
| Kr1 | 0.5 | F26BPc_P (F26BPc phosphatase) | |
| Kr2 | 0.1 | F26BPc_P (F26BPc phosphatase) | |
| Ks1 | 0.032 | F26BPc_P (F26BPc phosphatase) | |
| Km | 5.0 | Succ_Deg (Succ degradation) | |
| V | 2.0 | Succ_Deg (Succ degradation) | |
| Km | 1.0 | PGAc_Deg (PGAc degradation) | |
| V | 0.5 | PGAc_Deg (PGAc degradation) | |
| Km | 0.39 | GPT_GCEAc (GPT - GCEAc) | |
| V | 5.0 | GPT_GCEAc (GPT - GCEAc) | |
| Ki | 0.28 | GPT_GCEAc (GPT - GCEAc) | |
| Km | 0.39 | GPT_GCEA (GPT - GCEA) | |
| V | 5.0 | GPT_GCEA (GPT - GCEA) | |
| Ki | 0.28 | GPT_GCEA (GPT - GCEA) | |
| Km | 0.2 | GPT_GCA (GPT - GCA) | |
| V | 6.0 | GPT_GCA (GPT - GCA) | |
| Ki | 0.22 | GPT_GCA (GPT - GCA) | |
| Km | 0.2 | GPT_GCAc (GPT - GCAc) | |
| V | 6.0 | GPT_GCAc (GPT - GCAc) | |
| Ki | 0.22 | GPT_GCAc (GPT - GCAc) | |
| K | 0.02 | RuBisCO_O2 (RuBisC0 - O2) | |
| KR1 | 0.84 | RuBisCO_O2 (RuBisC0 - O2) | |
| KR2 | 0.04 | RuBisCO_O2 (RuBisC0 - O2) | |
| KR3 | 0.075 | RuBisCO_O2 (RuBisC0 - O2) | |
| KR4 | 0.9 | RuBisCO_O2 (RuBisC0 - O2) | |
| KR5 | 0.07 | RuBisCO_O2 (RuBisC0 - O2) | |
| Vm | 52.4199 | PGCA_P (PGCA phosphatase) | |
| Ks1 | 0.026 | PGCA_P (PGCA phosphatase) | |
| Kr1 | 94.0 | PGCA_P (PGCA phosphatase) | |
| Kr2 | 2.55 | PGCA_P (PGCA phosphatase) | |
| Vm | 5.71579 | GCEA_K (GCEA kinase) | |
| q | 300.0 | GCEA_K (GCEA kinase) | |
| Ks1 | 0.21 | GCEA_K (GCEA kinase) | |
| Kr1 | 0.36 | GCEA_K (GCEA kinase) | |
| Ks2 | 0.25 | GCEA_K (GCEA kinase) | |
| Km | 0.1 | GCAc_Ox (GCAc oxidase) | |
| V | 1.45611 | GCAc_Ox (GCAc oxidase) | |
| Vm | 3.30619 | SERcGOAc_AT (SERc:GOAc aminotransferase) | |
| q | 0.24 | SERcGOAc_AT (SERc:GOAc aminotransferase) | |
| Ks1 | 2.7 | SERcGOAc_AT (SERc:GOAc aminotransferase) | |
| Kr1 | 33.0 | SERcGOAc_AT (SERc:GOAc aminotransferase) | |
| Ks2 | 0.15 | SERcGOAc_AT (SERc:GOAc aminotransferase) | |
| Vm | 10.0098 | GCEA_DH (GCEA dehydrogenase) | |
| q | 250000.0 | GCEA_DH (GCEA dehydrogenase) | |
| Ks1 | 0.09 | GCEA_DH (GCEA dehydrogenase) | |
| Kr1 | 12.0 | GCEA_DH (GCEA dehydrogenase) | |
| Vm | 2.74582 | GLUcGOAc_AT (GLUc:GOAc aminotransferase) | |
| q | 607.0 | GLUcGOAc_AT (GLUc:GOAc aminotransferase) | |
| Ks1 | 1.7 | GLUcGOAc_AT (GLUc:GOAc aminotransferase) | |
| Kr1 | 2.0 | GLUcGOAc_AT (GLUc:GOAc aminotransferase) | |
| Ks2 | 0.15 | GLUcGOAc_AT (GLUc:GOAc aminotransferase) | |
| Vm | 2.49475 | GLYc_DC (GLYc decarboxylase) | |
| Ks1 | 6.0 | GLYc_DC (GLYc decarboxylase) | |
| Kr1 | 4.0 | GLYc_DC (GLYc decarboxylase) |
| Definition | |
|---|---|
| Ru5P = PeP / (1.0 + 1.0 / 0.4 + 1.0 / 0.67) | |
| Pi = cP - 2.0 * (RuBP + DPGA + FBP + SBP) - (PGA + TP + HeP + E4P + S7P + PeP + ATP + PGCA) | |
| X5P = PeP / 0.67 / (1.0 + 1.0 / 0.4 + 1.0 / 0.67) | |
| G1P = HeP * 0.058 / (1.0 + 1.0 / 2.3 + 0.058) | |
| GAP = 0.05 * TP / (1.0 + 0.05) | |
| DHAP = TP / (1.0 + 0.05) | |
| G6P = HeP / (1.0 + 1.0 / 2.3 + 0.058) | |
| R5P = PeP / 0.4 / (1.0 + 1.0 / 0.4 + 1.0 / 0.67) | |
| K52a = 0.0025 * (1.0 + F26BPc / 7.000000e-05) | |
| ADPc = cAc - ATPc | |
| Wo_min = 0.24 * 2.913930914 * O2 / (O2 + 0.222 * (1.0 + CO2 / 0.0115)) * ((1.0 + RuBP / E - abs(1.0 - RuBP / E)) / 2.0) | |
| UDPc = cUc - UTPc - UDPGc | |
| DHAPc = TPc / (1.0 + 0.05) | |
| G1Pc = HePc * 0.0584 / (1.0 + 1.0 / 2.3 + 0.0584) | |
| Wc_min = 2.913930914 * CO2 / (CO2 + 0.0115 * (1.0 + O2 / 0.222)) * ((1.0 + RuBP / E - abs(1.0 - RuBP / E)) / 2.0) | |
| PiPic = PiTc - Pic | |
| Pic = 12000000.0 / 2.0 * (sqrt(1.0 + 4.0 * PiTc / 12000000.0) - 1.0) | |
| F6Pc = HePc / 2.3 / (1.0 + 1.0 / 2.3 + 0.0584) | |
| PiTc = cPc - 2.0 * (FBPc + F26BPc) - (PGAc + TPc + HePc + SucPc + ATPc + UTPc) | |
| GAPc = 0.05 * TPc / (1.0 + 0.05) | |
| G6Pc = HePc / (1.0 + 1.0 / 2.3 + 0.0584) | |
| ADP = cA - ATP | |
| F6P = HeP / 2.3 / (1.0 + 1.0 / 2.3 + 0.058) |
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| function_4(s1, s2, p1, q, Ks1, Ks2, Kp1, Vm) = Vm * (s1 * s2 - p1 / q) / (Ks1 * Ks2 * ((1 + s1 / Ks1) * (1 + s2 / Ks2) + p1 / Kp1)) | |
| function_6(Vm, s1, s2, p1, p2, Ks1, Ks2, r1, Kr1, r2, Kr2, q) = Vm * (s1 * s2 - p1 * p2 / q) / ((s1 + Ks1 * (1 + r1 / Kr1 + r2 / Kr2)) * (s2 + Ks2)) | |
| function_16(Vm, s1, r1, Kr1, r2, Kr2, Ks1) = Vm * s1 / ((s1 + Ks1) * (1 + r1 / Kr1) * (1 + r2 / Kr2)) | |
| function_5(Vm, s1, p1, p2, q, Ks1, r1, Kr1, r2, Kr2) = Vm * (s1 - p1 * p2 / q) / (s1 + Ks1 * (1 + r1 / Kr1 + r2 / Kr2)) | |
| function_17(substrate, Km, V) = V * substrate / (Km + substrate) | |
| function_18(substrate, Inhibitor, Km, V, Ki) = V * substrate / (Km + substrate + Km * Inhibitor / Ki) | |
| function_9(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, r2, Kr2, r3, Kr3, r4, Kr41, Ks2, Kr42) = Vm * (s1 * s2 - p1 * p2 / q) / ((s1 + Ks1 * (1 + r1 / Kr1 + r2 / Kr2 + r3 / Kr3)) * (s2 * (1 + r4 / Kr41) + Ks2 * (1 + r4 / Kr42))) | |
| function_12(s1, p1, p2, q, Ks1, Kp1, Kp2, Vm) = Vm * (s1 - p1 * p2 / q) / (Ks1 * (s1 / Ks1 + (1 + p1 / Kp1) * (1 + p2 / Kp2))) | |
| function_8(Vm, s1, p1, p2, q, Ks1, r1, Kr1) = Vm * (s1 - p1 * p2 / q) / (s1 + Ks1 * (1 + r1 / Kr1)) | |
| function_15(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, r2, Kr2, Ks2, r3, Kr3) = Vm * (s1 * s2 - p1 * p2 / q) / ((s1 + Ks1 * (1 + r1 / Kr1) * (1 + r2 / Kr2)) * (s2 + Ks2 * (1 + r3 / Kr3))) | |
| function_21(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1) = Vm * (s1 * s2 - p1 * p2 / q) / (s1 + Ks1 * (1 + r1 / Kr1)) | |
| function_14(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, Ks2, r2, Kr2, r3, Kr3, r4, Kr4, r5, Kr5) = Vm * (s1 * s2 - p1 * p2 / q) / ((s1 + Ks1 * (1 + r1 / Kr1)) * (s2 + Ks2 * (1 + r2 / Kr2) * (1 + r3 / Kr3) * (1 + r4 / Kr4) * (1 + r5 / Kr5))) | |
| function_22(Vm, s1, Ks1, r1, Kr1) = Vm * s1 / (s1 + Ks1 * (1 + r1 / Kr1)) | |
| function_3(Vm, s1, s2, K1, K2) = Vm * s1 * s2 / ((s1 + K1) * (s2 + K2)) | |
| function_1(Vm, S, K, R1, KR1, R2, KR2, R3, KR3, R4, KR4, R5, KR5) = Vm * S / (S + K * (1 + R1 / KR1 + R2 / KR2 + R3 / KR3 + R4 / KR4 + R5 / KR5)) | |
| function_20(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, Ks2) = Vm * (s1 * s2 - p1 * p2 / q) / ((s1 + Ks1 * (1 + r1 / Kr1)) * (s2 + Ks2)) | |
| function_11(Vm, S, KA, A, K, R1, KR1, R2, KR2, R3, KR3) = Vm * S / (S * (1 + KA / A) + K * (1 + (1 + KA / A) * (R1 / KR1 + R2 / KR2 + R3 / KR3))) | |
| function_7(Vm, s1, s2, p1, q, Ks1, Ks2) = Vm * (s1 * s2 - p1 / q) / ((s1 + Ks1) * (s2 + Ks2)) | |
| function_19(Vm, s1, Ks1, r1, Kr1, r2, Kr2) = Vm * s1 / (s1 + Ks1 * (1 + r1 / Kr1) * (1 + r2 / Kr2)) | |
| function_10(Vm, S1, S2, K1, K2, R1, KR1, R2, KA1, A1, KA2, A2, KA3, A3) = Vm * S1 * S2 / ((S1 + K1) * (1 + R1 / KR1) * (S2 + K2 * (1 + K2 * R2 / (KA1 * A1 + KA2 * A2 + KA3 * A3)))) | |
| function_2(Vm, s1, s2, Ks1, Ks2, r1, Kr1) = Vm * s1 * s2 / ((s1 + Ks1) * (s2 + Ks2 * (1 + r1 / Kr1))) | |
| function_13(s1, s2, p1, p2, q, Ks1, Ks2, Kp1, Kp2, Vm) = Vm * (s1 * s2 - p1 * p2 / q) / (Ks1 * Ks2 * ((1 + s1 / Ks1) * (1 + s2 / Ks2) + (1 + p1 / Kp1) * (1 + p2 / Kp2) - 1)) |
| Trigger | Assignments |
|---|