messiha3
Used for Table 7b in the manuscript.
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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 |
|---|
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| default | — | — | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| E4P | — | 0.029 | default | ✘ | |
| G6L | — | 0.1 | default | ✘ | |
| NADPH | — | 0.16 | default | ✘ | |
| P6G | — | 0.25 | default | ✘ | |
| R5P | — | 0.118 | default | ✘ | |
| Ru5P | — | 0.033 | default | ✘ | |
| S7P | — | 0.082 | default | ✘ | |
| X5P | — | 0.041 | default | ✘ |
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 | |
|---|---|---|---|---|---|
| v_E4Psink | — | E4P = ∅ E4Psinkk*E4P | |||
| v_GND | — | P6G = NADPH + Ru5P (GND1*kcatGND1*NADP*P6G)/(KnadpGND1*Kp6gGND1*(1 + NADP/KnadpGND1 + NADPH/KnadphGND1)*(1 + P6G/Kp6gGND1 + Ru5P/Kru5pGND1)) + (GND2*kcatGND2*NADP*P6G)/((1 + NADP/KnadpGND2 + NADPH/KnadphGND2)*(1 + P6G/Kp6gGND2 + Ru5P/Kru5pGND2)) | |||
| v_NADPHoxidase | — | NADPH = ∅ NADPHoxidasek*NADPH | |||
| v_R5Psink | — | R5P = ∅ R5Psinkk*R5P | |||
| v_RKI | — | Ru5P = R5P (RKI1*RKIkcat*(-(R5P/RKIKeq) + Ru5P))/(RKIKru5p*(1 + R5P/RKIKr5p + Ru5P/RKIKru5p)) | |||
| v_RPE | — | Ru5P = X5P (RPE1*RPEkcat*(Ru5P - X5P/RPEKeq))/(RPEKru5p*(1 + Ru5P/RPEKru5p + X5P/RPEKx5p)) | |||
| v_SOL | — | G6L = P6G (SOL3*SOLkcat*G6L)/(SOLKg6l*(1 + G6L/SOLKg6l + P6G/SOLKp6g)) | |||
| v_TAL | — | S7P = E4P (kcatTAL1*TAL1*(-((F6P*E4P)/TALKeq) + GAP*S7P))/((1 + F6P/Kf6pTAL1 + GAP/KgapTAL1)*KgapTAL1*Ks7pTAL1*(1 + E4P/Ke4pTAL1 + S7P/Ks7pTAL1)) + (NQM1*TALkcatNQM1*(-((F6P*E4P)/TALKeq) + GAP*S7P))/((1 + F6P/TALKf6pNQM1 + GAP/TALKgapNQM1)*TALKgapNQM1*TALKs7pNQM1*(1 + E4P/TALKe4pNQM1 + S7P/TALKs7pNQM1)) | |||
| v_TKLE4P | — | E4P + X5P = ∅ (TKL1*TKLE4Pkcat*(-((F6P*GAP)/TKLE4PKeq) + E4P*X5P))/(Ke4pTAL*Kx5pTAL*(1 + F6P/Kf6pTAL + E4P/Ke4pTAL + R5P/Kr5pTAL + S7P/Ks7pTAL)*(1 + GAP/KgapTAL + X5P/Kx5pTAL)) | |||
| v_TKLR5P | — | R5P + X5P = S7P (TKL1*TKLR5Pkcat*(-((GAP*S7P)/TKLR5PKeq) + R5P*X5P))/(Kr5pTAL*Kx5pTAL*(1 + F6P/Kf6pTAL + E4P/Ke4pTAL + R5P/Kr5pTAL + S7P/Ks7pTAL)*(1 + GAP/KgapTAL + X5P/Kx5pTAL)) | |||
| v_ZWF | — | ∅ = G6L + NADPH (G6P*NADP*ZWF1*ZWFkcat)/(ZWFKg6p*ZWFKnadp*(1 + G6P/ZWFKg6p + G6L/ZWFKg6l)*(1 + NADP/ZWFKnadp + NADPH/ZWFKnadph)) |
| Id | Value | |
|---|---|---|
| E4Psinkk | 0.01 | |
| EXTERNAL | 0.0 | |
| F6P | 0.325 | |
| G6P | 0.0 | |
| GAP | 0.067 | |
| GND1 | 0.013 | |
| GND2 | 0.003 | |
| Ke4pTAL | 0.946 | |
| Ke4pTAL1 | 0.362 | |
| Kf6pTAL | 1.1 | |
| Kf6pTAL1 | 1.44 | |
| KgapTAL | 0.1 | |
| KgapTAL1 | 0.272 | |
| KnadpGND1 | 0.094 | |
| KnadpGND2 | 0.094 | |
| KnadphGND1 | 0.055 | |
| KnadphGND2 | 0.055 | |
| Kp6gGND1 | 0.062 | |
| Kp6gGND2 | 0.115 | |
| Kr5pTAL | 0.235 | |
| Kru5pGND1 | 0.1 | |
| Kru5pGND2 | 0.1 | |
| Ks7pTAL | 0.15 | |
| Ks7pTAL1 | 0.786 | |
| Kx5pTAL | 0.67 | |
| NADP | 0.0 | |
| NADPHoxidasek | 100.0 | |
| NQM1 | 0.02 | |
| R5Psinkk | 0.01 | |
| RKI1 | 0.05 | |
| RKIKeq | 4.0 | |
| RKIKiru5p | 9.88 | |
| RKIKr5p | 5.7 | |
| RKIKru5p | 2.47 | |
| RKIkcat | 335.0 | |
| RPE1 | 0.03 | |
| RPEKeq | 1.4 | |
| RPEKru5p | 5.97 | |
| RPEKx5p | 7.7 | |
| RPEkcat | 4020.0 | |
| SOL3 | 0.0296 | |
| SOLKg6l | 0.8 | |
| SOLKp6g | 0.5 | |
| SOLkcat | 4.3 | |
| TAL1 | 0.144 | |
| TALKe4pNQM1 | 0.305 | |
| TALKeq | 1.05 | |
| TALKf6pNQM1 | 1.04 | |
| TALKgapNQM1 | 0.272 | |
| TALKs7pNQM1 | 0.786 | |
| TALkcatNQM1 | 0.694 | |
| TKL1 | 0.455 | |
| TKLE4PKeq | 10.0 | |
| TKLE4Pkcat | 47.1 | |
| TKLR5PKeq | 1.2 | |
| TKLR5Pkcat | 40.5 | |
| ZWF1 | 0.02 | |
| ZWFKg6l | 0.01 | |
| ZWFKg6p | 0.042 | |
| ZWFKnadp | 0.045 | |
| ZWFKnadph | 0.017 | |
| ZWFkcat | 189.0 | |
| cell | 1.0 | |
| kcatGND1 | 28.0 | |
| kcatGND2 | 27.3 | |
| kcatTAL1 | 0.694 | |
| sumNADP | 0.33 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| G6P = 0.9 | |
| NADP = sumNADP - NADPH |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|