Urea cycle (3D)

Citrate cycle (3D)

Gluconeogenesis (3D)

Catabolism of proline, histidine, arginine, glutamate and glutamine (steps 1.4.1.2 and 2.6.1.13)
3D (steps 1.4.1.2 and 2.6.1.13)

Catabolism of tryptophan and lysine (steps 1.5.1.7 and 2.6.1.39)
3D (steps 1.5.1.7 and 2.6.1.39)

Catabolism of threonine, tryptophan, glycine, proline, arginine, cysteine and serine (steps 2.6.1.2 and 2.6.1.1)
3D (steps 2.6.1.2 and 2.6.1.1)

Catabolism of phenylalanine, tyrosine and leucine (steps 2.6.1.42 and 2.6.1.5)
3D (steps 2.6.1.42 and 2.6.1.5)

Catabolism of isoleucine, leucine and tryptophan (steps 2.6.1.2; 2.6.1.42 Catabolism of isoleucine and 2.6.1.42 Catabolism of leucine)
3D (steps 2.6.1.2; 2.6.1.42 Catabolism of isoleucine and 2.6.1.42 Catabolism of leucine)

Catabolism of aspartate and asparagine (3D)

Catabolism of methionine, threonine, isoleucine and valine (3D)

Synthesis of aspartate, methionine, lysine and threonine (steps 2.6.1.1 and 2.6.1.17)
3D (steps 2.6.1.1 and 2.6.1.17)

Synthesis of valine, alanine, isoleucine and leucine (steps 2.6.1.42 Catabolism of isoleucine and valine and 2.6.1.42 Catabolism of leucine)
3D (steps 2.6.1.42 Catabolism of isoleucine and valine and 2.6.1.42 Catabolism of leucine)

Synthesis of phenylalanine and tyrosine (3D)

Synthesis of serine, glycine and cysteine (3D)

Synthesis of histidine (3D)

Synthesis of glutamine, arginine, glutamate and proline (steps 1.4.1.2 and 2.6.1.11)
3D (steps 1.4.1.2 and 2.6.1.11)

Ascorbate and aldarate metabolism (Kyoto University)

Ubiquinone biosynthesis (Kyoto University)

Glyoxylate and dicarboxylate metabolism (Kyoto University)

Butanoate metabolism (Kyoto University)

C5-Branched dibasic acid metabolism (Kyoto University)

Reductive carboxylate cycle (CO2 fixation) (Kyoto University)

Vitamin B6 metabolism (Kyoto University)

And the transamination reactions: