Table 3 |
|||
|
Comparison of tricarboxylic acid and glyoxylate cycle reactions in Arabidopsis reconstructions. |
|||
|
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. |
|||
|
Radrich et al. BMC Systems Biology 2010 4:114 doi:10.1186/1752-0509-4-114 |
|||
