Difference between revisions of "Team:NCKU Tainan/Model"
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| − | + | Parameters of CO<sub>2</sub> bypass pathway | |
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| − | + | Parameters of PPP pathway | |
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Revision as of 15:28, 20 September 2018
Model
Achievement
Purpose
CO2 uptake
| CO2 uptake | Kf | Kr | |||||
|---|---|---|---|---|---|---|---|
| R1 | $${[CO_2]_{air} \rightarrow [CO_2]_uptake}$$ | 9.23E-04 | 4.78E-04 | ||||
| R2 | $${[CO_2]_{uptake} + [H_2O] \rightarrow [H_2CO_3]}$$ | 0.062 | 23.7 | ||||
| R3 | $${[H_2CO_3] \rightarrow [H^+] + [HCO_3^-]}$$ | 8000000 | 4.7E10 | ||||
| R4 | $${[HCO_3^-] \rightarrow [H^+] + [CO_3^{2-}]}$$ | 3 | 5E10 | ||||
| R5 | $${[H^+] + [HCO_3^-] \longleftrightarrow [H_2O] + [CO_2]_{uptake}}$$ | Vmax | Km | ||||
| 0.47333 | 0.0062 | ||||||
CO2 Metabolism
| E4P | erythrose-4-phosphate |
| F6P | fructose-6-phosphate |
| FBP | fructose-1,6-bisphosphate |
| G6P | glucose-6-phosphate |
| GAP | glyceraldehyde-3-phosphate |
| PEP | phosphoenol pyruvate |
| PYR | pyruvate |
| R5P | ribose-5-phosphate |
| Ru5P | ribulose-5-phosphate |
| S7P | sedoheptulose-7-phosphate |
| X5P | xylulose-5-phosphate |
| 6PG | 6-phosphogluconate |
| DHAP | Dihydroxyacetone phosphate |
| 3PG | 3-Phosphoglyceric acid |
| RuBP | ribulose-1,5-bisphosphate |
| PRK | Phosphoribulokinase |
| Rubisco | Ribulose-1,5-bisphosphate carboxylase/ oxygenase |
| AcCoA | Acetyl-CoA |
| CIT | Citrate |
| ICIT | Isocitrate |
| AKG | Alpha-ketoglutarate |
| SUCCoA | Succinyl-CoA |
| SUCC | Succinate |
| FUM | Fumarate |
| MAL | Malate |
| OAA | Oxaloacetic acid |
| GOX | Glyoxylate |
Pathway
| CO2 bypass pathway | Vmax (1/S) | KM (mM) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A1 | $${Xylose \rightarrow Xylulose}$$ $${Xylulose + ATP \rightarrow X5P}$$ | 0.02456 | 124.55879 | ||||||||||
| A2 | $${X5P \rightarrow Ru5P}$$ | 0.08 | 12.5 | ||||||||||
| A3 | $${Ru5P \xrightarrow{PRK} RuBP}$$ | 225.81858 | 0.27 | ||||||||||
| A4 | $${RuBP + CO_2 \xrightarrow{RuBisCO} 3PG}$$ | Vmax | Krubp | KCO2 | |||||||||
| 333.33 | 53 | 2.7 | |||||||||||
| Pentose Phosphate Pathway | Vmax (1/S) | KM (mM) | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B1 | $${Ru5P \rightarrow R5P}$$ | 0.13672 | 12.5 | |||||||||||||||||||||
| B2 | $${X5P + R5P \rightarrow S7P + GAP}$$ | |||||||||||||||||||||||
| $${X5P \rightarrow S7P}$$ | 58.27 | 4.96E-09 | ||||||||||||||||||||||
| $${X5P \rightarrow GAP}$$ | 58.27 | 48 | ||||||||||||||||||||||
| $${R5P \rightarrow S7P}$$ | 58.27 | 0.008 | ||||||||||||||||||||||
| $${R5P \rightarrow GAP}$$ | 58.27 | 3.05E-07 | ||||||||||||||||||||||
| B3 | $${S7P + GAP \rightarrow F6P + E4P}$$ | |||||||||||||||||||||||
| $${S7P \rightarrow E4P}$$ | 58.27 | 2.524 | ||||||||||||||||||||||
| $${S7P \rightarrow F6P}$$ | 58.27 | 6.10E-09 | ||||||||||||||||||||||
| $${GAP \rightarrow E4P}$$ | 58.27 | 1.73E-07 | ||||||||||||||||||||||
| $${GAP \rightarrow F6P}$$ | 58.27 | 8.23E-09 | ||||||||||||||||||||||
| B4 | $${E4P + X5P \rightarrow F6P + GAP}$$ | |||||||||||||||||||||||
| $${E4P \rightarrow F6P}$$ | 1 | 1 | ||||||||||||||||||||||
| $${E4P \rightarrow GAP}$$ | 5.827E-4 | 1.733E-7 | ||||||||||||||||||||||
| $${X5P \rightarrow F6P}$$ | 0.05827 | 1.733E-7 | ||||||||||||||||||||||
| $${X5P \rightarrow GAP}$$ | 0.005827 | 48.8 | ||||||||||||||||||||||
| B5 | $${FBP \rightarrow GAP}$$ | 135.425 | 4 | |||||||||||||||||||||
| B6 | $${DHAP \longleftrightarrow GAP}$$ | Vmf | Vmr | KmDHAP | KmGAP | |||||||||||||||||||
| 0.2394 | 0.24 | 0.812 | 0.245 | |||||||||||||||||||||
| B7 | $${FBP \rightarrow DHAP}$$ | 0.0001247 | 0.04 | |||||||||||||||||||||
| B8 | $${F6P + ATP \rightarrow FBP + ADP}$$ | 88.2533 | 0.017 | |||||||||||||||||||||
| B9 | $${F6P \rightarrow G6P}$$ | 88.2353 | 0.017 | |||||||||||||||||||||
| B10 | $${G6P + NADP^+ \rightarrow 6PG + NADPH}$$ | Vmax | KmG6P | KmNADP | ||||||||||||||||||||
| 11.736 | 0.12 | 0.0123 | ||||||||||||||||||||||
| B11 | $${6PG + NADP^+ \rightarrow Ru5P + NADPH}$$ | 1.0 | 0.044 | |||||||||||||||||||||
| B12 | $${GAP + NADP^+ + ADP \rightarrow 3PGA + NADPH + ATP}$$ | 0.4 | 0.013 | |||||||||||||||||||||
| B13 | $${3PGA \rightarrow PEP}$$ | 0.43478 | 0.23 | |||||||||||||||||||||
| B14 | $${PEP \rightarrow PYR}$$ | 0.23148 | 0.45 | |||||||||||||||||||||
| TCA cycle | Vmf (mM/min) | Vmr (mM/min) | Ks (mM) | Kp (mM) | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C1 | $${PEP + HCO_3^- + NAD^+ \rightarrow OAA + NADH}$$ | 1 | 1 | 1 | 1 | |||||||||||||||||||
| C2 | $${AcCoA \rightarrow CIT}$$ | 64.8 | 0.648 | 0.05 | 0.12 | |||||||||||||||||||
| C3 | $${CIT \rightarrow ICIT}$$ | 31.2 | 0.312 | 1.7 | 0.7 | |||||||||||||||||||
| C4 | $${ICIT + NADP^+ \rightarrow AKG + NADPH + CO_2}$$ | 10.2 | 0.102 | 0.03 | 0.3 | |||||||||||||||||||
| C5 | $${AKG + NAD^+ \rightarrow AKG + NADPH + CO_2}$$ | 57.344 | 0.57344 | 0.1 | 1.0 | |||||||||||||||||||
| C6 | $${SUCCoA + ADP \rightarrow SUCC + ATP}$$ | 6.54 | 0.0651 | 0.015 | 0.15 | |||||||||||||||||||
| C7 | $${SUCC + FAD \rightarrow FUM + FADH_2}$$ | 1.02 | 1.02 | 0.12 | 0.15 | |||||||||||||||||||
| C8 | $${FUM \rightarrow MAL}$$ | 887.7 | 87.7 | 0.25 | 2.38 | |||||||||||||||||||
| C9 | $${MAL + NAD^+ \rightarrow OAA + NADH}$$ | 184 | 184 | 0.833 | 0.0443 | |||||||||||||||||||
| C10 | $${OAA \rightarrow CIT}$$ | 64.8 | 0.648 | 0.012 | 0.12 | |||||||||||||||||||
| C11 | $${PYR \rightarrow NADH + AcCoA + CO_2}$$ | Vmax (1/s) | KM (mM) | |||||||||||||||||||||
| 0.00518 | 1.5 | |||||||||||||||||||||||
| C12 | $${ICIT \rightarrow GOX}$$ | 1.172 | 0.01172 | 0.145 | 0.13 | |||||||||||||||||||
| C13 | $${GOX \rightarrow MAL}$$ | 20 | 0.2 | 0.057 | 1.0 | |||||||||||||||||||
| C14 | $${ICIT \rightarrow SUCC + GOX}$$ | Vmf (mM/min) | Vmr (mM/min) | Kicit (mM) | Ksucc (mM) | Kgox (mM) | ||||||||||||||||||
| 1.172 | 0.012 | 0.145 | 0.59 | 0.13 | ||||||||||||||||||||