Table 3.
Reaction | Radrich | Poolman | AraGEM |
---|---|---|---|
Succinate + Ubiquinone ↔ Fumarate + Ubiquinol | OK | OK | With FAD/FADH2 |
Fumarate + H2O ↔ Malate | OK | OK | OK |
Malate + NAD ↔ Oxaloacetate + NADH + H Malate + NADP ↔ Oxaloacetate + NADPH + H |
No H | Only with NAD/NADH | OK |
Oxaloacetate + ADP + Orthophosphate + Acetyl-CoA ↔ Citrate + ATP + CoA | OK | OK | OK |
Citrate ↔ cis-Aconitate + H2O | OK | No H2O | OK |
cis-Aconitate + H2O ↔ Isocitrate | OK | No H2O | OK |
Isocitrate ↔ Succinate + Glyoxylate | OK | OK | OK |
Glyoxylate + H2O +Acetyl-CoA ↔ Malate + CoA | OK | No H2O | OK |
Isocitrate + NAD ↔ 2-oxoglutarate + CO2 + NADH + H Isocitrate + NADP ↔ 2-oxoglutarate + CO2 + NADPH + H |
No H | Only with NAD/NADH; 2 H |
OK |
Isocitrate + NADP ↔ Oxalosuccinate + NADPH + H | No H | NA | NA |
Oxalosuccinate + NADP ↔ 2-oxoglutarate + CO2 + NADPH + H | No H | NA | NA |
2-oxoglutarate + CoA + NAD ↔ Succinyl-CoA + CO2 + NADH | OK | OK | With ferredoxin |
2-oxoglutarate + Thiamine-pyrophosphate ↔ 3-carboxy-1-hydroxypropyl-ThPP + Co2 | OK | NA | OK |
3-carboxy-1-hydroxypropyl-ThPP + Lipoamide-E ↔ Succinyldihydrolipoamide-E + Thiamine-pyrophosphate | OK | NA | OK |
Succinyldihydrolipoamide-E + CoA ↔ Succinyl-CoA + Dihydropiloamide-E | OK | NA | OK |
Succinyl-CoA + ADP + Orthophosphate ↔ Succinate + ATP + CoA Succinyl-CoA + GDP + Orthophosphate ↔ Succinate + GTP + CoA |
OK | OK | Only with ADP/ATP |
"Radrich" refers to this work, "Poolman" to the model by Poolman et al. [16] and "AraGEM" to the model by de Oliveira Dal'Molin et al. [17]. OK indicates that the reaction in the model is identical to the first column, NA that it is not included in the model; other differences are explicitly described.