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Table 3 Comparison of tricarboxylic acid and glyoxylate cycle reactions in Arabidopsis reconstructions.

From: Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

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
  1. "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.