Table 7.
Metabolic network model of P. putida KT2440
| Pathway | Reactions |
|---|---|
| Transport reactions | ‘→ GLY[e]’ ‘→ NH3[c]’ ‘→ SO4[c]’ ‘→ O2[c]’ ‘biomass[c] → ’ ‘FORMATE_ex[e] → ’ ‘MAL_ex[e] → ’ ‘SUCC_ex[e] → ’ ‘PHA[c] → ’ ‘ATPmaintenance[c] →’ ‘CO2[c] → ’ |
| Glycerol uptake and conversion to glycerone-phosphate | ‘GLY[e] → GLY[p]’ ‘GLY[p] → GLY[c]’ ‘GLY[c] + ATP[c → GLY-3P[c] + ADP[c]’ ‘GLY-3P[c] + NAD[c] ↔ DHAP[c] + NADH[c]’ |
| Pentose phosphate pathway | ‘G6P[c] + NADP[c] → 6-P-Gluconate[c] + NADPH[c]’ ‘6-P-Gluconate[c] + NADP[c] → RIB-5P[c] + CO2[c] + NADPH[c]’ ‘RIB-5P[c] ⟺ XYL-5P[c]’ ‘RIB-5P[c] ⟺ RIBO-5P[c]’ ‘S7P[c] + GAP[c] ⟺ RIBO-5P[c] + XYL-5P[c]’ ‘S7P[c] + GAP[c] ⟺ E4P[c] + F6P[c]’ ‘F6P[c] + GAP[c] ⟺ E4P[c] + XYL-5P[c]’ |
| Entner-Doudoroff pathway | ‘6-P-Gluconate[c] → KDPG[c]’ ‘KDPG[c] → GAP[c] + PYR[c]’ |
| Embden-Meyerhof-Parnas pathway | ‘G6P[c] ⟺ F6P[c]’ ‘FBP[c] → F6P[c]’ ‘FBP[c] ⟺ GAP[c] + DHAP[c]’ ‘DHAP[c] ⟺ GAP[c]’ ‘GAP[c] + NAD[c] ⟺ 13-PG[c] + NADH[c]’ ‘ADP[c] + 13-PG[c] ⟺ ATP[c] + 3-PG[c]’ ‘3-PG[c] ⟺ 2-PG[c]’ ‘2-PG[c] ⟺ PEP[c]’ ‘PEP[c] + ADP[c] → PYR[c] + ATP[c]’ ‘PYR[c] + NAD[c] → AcCoA[c] + NADH[c] + CO2[c]’ ‘PYR[c] + 2 ATP[c] → 2 ADP[c] + PEP[c]’ |
| Citric acid cycle | ‘AcCoA[c] + OAA[c] → CIT[c]’ ‘CIT[c] ↔ ICI[c]’ ‘ICI[c] + NADP[c] → AKG[c] + CO2[c] + NADPH[c]’ ‘AKG[c] + NAD[c] → SUCC-CoA[c] + NADH[c] + CO2[c]’ ‘SUCC-CoA[c] + ADP[c] ↔ SUCC[c] + ATP[c]’ ‘SUCC[c] + Q[c] ↔ FUM[c] + QH2[c]’ ‘FUM[c] ↔ MAL[c]’ ‘MAL[c] + NAD[c] ↔ OAA[c] + NADH[c]’ |
| Organic acid production | ‘MAL[c] → MAL_ex[e]’ ‘SUCC[c] → SUCC_ex[e]’ ‘FORMATE[c] → FORMATE_ex[e]’ |
| Glyoxylate metabolism | ‘ICI[c] → Glyoxy[c] + SUCC[c]’ ‘Glyoxy[c] + AcCoA[c] → MAL[c]’ |
| Amphibolic metabolism | ‘OAA[c] → PYR[c] + CO2[c]’ ‘PEP[c] + CO2[c] + ATP[c] → OAA[c] + ADP[c]’ ‘MAL[c] + NADP[c] → PYR[c] + NADPH[c] + CO2[c]’ |
| PHA production | ‘5 AcCoA[c] + 4 ATP[c] + 7 NADPH[c] → C10-PHA[c] + 4 ADP[c] + 7 NADP[c]’ ‘4 AcCoA[c] + 4 ATP[c] + 7 NADPH[c] → C8-PHA[c] + 4 ADP[c] + 7 NADP[c]’ ‘6 AcCoA[c] + 4 ATP[c] + 7 NADPH[c] → C12-PHA[c] + 4 ADP[c] + 7 NADP[c]’ ‘0.75 C10-PHA[c] + 0.17 C8-PHA[c] + 0.08 C12-PHA[c] → PHA[c]’ |
| Energy metabolism | ‘NADPH[c] + NAD[c] → NADP[c] + NADH[c]’ ‘(3) NADH[c] + (3) NADP[c] + ATP[c] → (3) NAD[c] + (3) NADPH[c] + ADP[c]’ ‘(0.5) O2[c] + NADH[c] + (1.33) ADP[c] → NAD[c] + (1.33) ATP[c]’ ‘(0.5) O2[c] + QH2[c] + (0.66) ADP[c] → Q[c] + (0.66) ATP[c]’ ‘ATP[c] → ADP[c] + ATPmaintenance[c]’ ‘SO4[c] + (3) NADPH[c] + (4) ATP[c] → H2S[c] + (3) NADP[c] + (4) ADP[c]’ |
| Biomass production | ‘(1.481) OAA[c] + (1.338) 3-PG[c] + (0.627) RIBO-5P[c] + (17.821) ATP[c] + (16.548) NADPH[c] + (6.965) NH3[c] + (3.548) NAD[c] + (2.930) AcCoA[c] + (2.861) PYR[c] + (1.078) AKG[c] + (0.361) E4P[c] + (0.72) PEP[c] + (0.233) H2S[c] + (0.072) F6P[c] + (0.206) G6P[c] + (0.129) GAP[c] → biomass[c] + (16.548) NADP[c] + (3.548) NADH[c] + (17.821) ADP[c] + (1.678) CO2[c]’ |