| Pathway | #Steps | #Present | #Specific |
|---|
| L-glutamate biosynthesis I | 2 | 2 | 2 |
| L-malate degradation I | 1 | 1 | 1 |
| L-glutamine degradation I | 1 | 1 | 1 |
| L-alanine biosynthesis III | 1 | 1 | 1 |
| L-cysteine degradation IV | 1 | 1 | 1 |
| L-glutamine degradation II | 1 | 1 | 1 |
| ammonia assimilation cycle III | 3 | 3 | 2 |
| glyoxylate cycle | 6 | 6 | 3 |
| chitobiose degradation | 2 | 2 | 1 |
| ribose phosphorylation | 2 | 2 | 1 |
| polyphosphate metabolism | 2 | 2 | 1 |
| cytidylyl molybdenum cofactor sulfurylation | 2 | 1 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 7 | 3 |
| 2-deoxy-D-ribose degradation I | 3 | 3 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 11 | 4 |
| TCA cycle VI (Helicobacter) | 9 | 7 | 3 |
| TCA cycle V (2-oxoglutarate synthase) | 9 | 7 | 3 |
| TCA cycle II (plants and fungi) | 9 | 7 | 3 |
| TCA cycle IV (2-oxoglutarate decarboxylase) | 9 | 7 | 3 |
| TCA cycle VII (acetate-producers) | 9 | 6 | 3 |
| bis(guanylyl molybdopterin) cofactor sulfurylation | 3 | 1 | 1 |
| TCA cycle I (prokaryotic) | 10 | 9 | 3 |
| TCA cycle III (animals) | 10 | 8 | 3 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 11 | 4 |
| L-glutamate and L-glutamine biosynthesis | 7 | 5 | 2 |
| thiazole component of thiamine diphosphate biosynthesis II | 7 | 5 | 2 |
| C4 photosynthetic carbon assimilation cycle, NADP-ME type | 7 | 4 | 2 |
| reductive TCA cycle I | 11 | 8 | 3 |
| sucrose degradation IV (sucrose phosphorylase) | 4 | 4 | 1 |
| superpathway of L-alanine biosynthesis | 4 | 4 | 1 |
| reductive TCA cycle II | 12 | 8 | 3 |
| nitrogen remobilization from senescing leaves | 8 | 5 | 2 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 1 | 1 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 1 | 1 |
| tRNA-uridine 2-thiolation (mammalian mitochondria) | 4 | 1 | 1 |
| tRNA-uridine 2-thiolation (yeast mitochondria) | 4 | 1 | 1 |
| photosynthesis light reactions | 4 | 1 | 1 |
| NADPH to cytochrome c oxidase via plastocyanin (thylakoid membrane) | 4 | 1 | 1 |
| 2-methylcitrate cycle I | 5 | 5 | 1 |
| [2Fe-2S] iron-sulfur cluster biosynthesis | 10 | 4 | 2 |
| tRNA-uridine 2-thiolation (thermophilic bacteria) | 5 | 1 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 25 | 5 |
| mixed acid fermentation | 16 | 16 | 3 |
| superpathway of thiamine diphosphate biosynthesis II | 11 | 9 | 2 |
| molybdopterin biosynthesis | 6 | 6 | 1 |
| ppGpp metabolism | 6 | 6 | 1 |
| thiazole component of thiamine diphosphate biosynthesis I | 6 | 6 | 1 |
| TCA cycle VIII (Chlamydia) | 6 | 5 | 1 |
| 2-methylcitrate cycle II | 6 | 4 | 1 |
| superpathway of photosynthetic hydrogen production | 6 | 3 | 1 |
| methylgallate degradation | 6 | 2 | 1 |
| methylaspartate cycle | 19 | 9 | 3 |
| gluconeogenesis I | 13 | 13 | 2 |
| pyruvate fermentation to propanoate I | 7 | 5 | 1 |
| incomplete reductive TCA cycle | 7 | 5 | 1 |
| C4 photosynthetic carbon assimilation cycle, PEPCK type | 14 | 9 | 2 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 18 | 3 |
| L-citrulline biosynthesis | 8 | 6 | 1 |
| protocatechuate degradation I (meta-cleavage pathway) | 8 | 3 | 1 |
| tRNA-uridine 2-thiolation (cytoplasmic) | 8 | 1 | 1 |
| ethene biosynthesis V (engineered) | 25 | 18 | 3 |
| superpathway of thiamine diphosphate biosynthesis I | 10 | 10 | 1 |
| anaerobic energy metabolism (invertebrates, mitochondrial) | 10 | 7 | 1 |
| glycolysis V (Pyrococcus) | 10 | 7 | 1 |
| superpathway of vanillin and vanillate degradation | 10 | 3 | 1 |
| glycolysis II (from fructose 6-phosphate) | 11 | 11 | 1 |
| tRNA-uridine 2-thiolation and selenation (bacteria) | 11 | 7 | 1 |
| L-glutamate degradation VIII (to propanoate) | 11 | 5 | 1 |
| superpathway of L-citrulline metabolism | 12 | 8 | 1 |
| syringate degradation | 12 | 3 | 1 |
| glycolysis I (from glucose 6-phosphate) | 13 | 13 | 1 |
| (S)-lactate fermentation to propanoate, acetate and hydrogen | 13 | 10 | 1 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 17 | 1 |
| superpathway of anaerobic energy metabolism (invertebrates) | 17 | 12 | 1 |
| oxygenic photosynthesis | 17 | 11 | 1 |
| superpathway of hexitol degradation (bacteria) | 18 | 18 | 1 |
| gluconeogenesis II (Methanobacterium thermoautotrophicum) | 18 | 9 | 1 |
| hexitol fermentation to lactate, formate, ethanol and acetate | 19 | 19 | 1 |
| superpathway of anaerobic sucrose degradation | 19 | 17 | 1 |
| superpathway of N-acetylneuraminate degradation | 22 | 22 | 1 |
| photosynthetic 3-hydroxybutanoate biosynthesis (engineered) | 26 | 19 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 19 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 22 | 2 |