smallbone23
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000458) Biomodels notes: Table 6 and 7 that corresponds to the steady state concentrations of metabolites and steady state fluxes of reactions are reproduced as curation figure. The model was simulated using Copasi v4.8 (Build 35). 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 | |
|---|---|---|
| — | 0.001 mole | |
| — | 0.001 mole litre^(-1.0) | |
| — | 1.0 second^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| p3g | 3-phosphoglycerate | 2.36 | cell (cell) | ✔ | |
| php | phosphohydroxypyruvate | 0.6 | cell (cell) | ✘ | |
| pser | phosphoserine | 0.09 | cell (cell) | ✘ | |
| ser | serine | 4.9 | cell (cell) | ✔ | |
| serA | serA | 1.15 | cell (cell) | ✔ | |
| serB | serB | 0.25 | cell (cell) | ✔ | |
| serC | serC | 0.1 | cell (cell) | ✔ |
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 | |
|---|---|---|---|---|---|
| PDH | phosphoglycerate dehydrogenase | p3g = php cell * serA * kcatA * (p3g / KAp3g) / (1 + p3g / KAp3g + php / KAphp) / (1 + ser / KiAser) | |||
| PSA | phosphoserine aminotransferase | php = pser cell * serC * kcatC * (php / KCphp) / (1 + php / KCphp + pser / KCpser) | |||
| PSP | phosphoserine phosphatase | pser = ser cell * serB * kcatB * (pser / KBpser) / (1 + pser / KBpser + ser / KBser) |
| Id | Value |
|---|
| Id | Value | Reaction | |
|---|---|---|---|
| kcatA | 0.55 per s | PDH (phosphoglycerate dehydrogenase) | |
| KAp3g | 1.2 mM | PDH (phosphoglycerate dehydrogenase) | |
| KAphp | 0.0032 mM | PDH (phosphoglycerate dehydrogenase) | |
| KiAser | 0.0038 mM | PDH (phosphoglycerate dehydrogenase) | |
| kcatC | 1.75 per s | PSA (phosphoserine aminotransferase) | |
| KCphp | 0.0015 mM | PSA (phosphoserine aminotransferase) | |
| KCpser | 0.0017 mM | PSA (phosphoserine aminotransferase) | |
| kcatB | 1.43 per s | PSP (phosphoserine phosphatase) | |
| KBpser | 0.0015 mM | PSP (phosphoserine phosphatase) | |
| KBser | 0.15 mM | PSP (phosphoserine phosphatase) |
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