| Pathway | #Steps | #Present | #Specific |
|---|
| L-leucine biosynthesis | 6 | 6 | 6 |
| L-tyrosine biosynthesis I | 3 | 3 | 3 |
| L-threonine biosynthesis | 2 | 2 | 2 |
| L-glutamate biosynthesis I | 2 | 2 | 2 |
| L-glutamate biosynthesis IV | 1 | 1 | 1 |
| L-glutamate biosynthesis III | 1 | 1 | 1 |
| L-glutamine degradation I | 1 | 1 | 1 |
| L-glutamine degradation II | 1 | 1 | 1 |
| 3-(4-hydroxyphenyl)pyruvate biosynthesis | 1 | 1 | 1 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 15 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 6 |
| L-ornithine biosynthesis I | 5 | 5 | 4 |
| L-arginine biosynthesis I (via L-ornithine) | 9 | 9 | 7 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 10 |
| L-valine biosynthesis | 4 | 4 | 3 |
| 3-methylbutanol biosynthesis (engineered) | 7 | 6 | 5 |
| superpathway of L-threonine biosynthesis | 6 | 6 | 4 |
| L-phenylalanine biosynthesis I | 3 | 3 | 2 |
| L-homoserine biosynthesis | 3 | 3 | 2 |
| ammonia assimilation cycle III | 3 | 3 | 2 |
| L-serine biosynthesis I | 3 | 3 | 2 |
| L-arginine biosynthesis III (via N-acetyl-L-citrulline) | 9 | 8 | 6 |
| L-methionine degradation II | 3 | 2 | 2 |
| nitric oxide biosynthesis II (mammals) | 3 | 2 | 2 |
| L-arginine biosynthesis II (acetyl cycle) | 10 | 9 | 6 |
| urea cycle | 5 | 3 | 3 |
| L-glutamate and L-glutamine biosynthesis | 7 | 5 | 4 |
| L-threonine degradation I | 6 | 6 | 3 |
| superpathway of L-serine and glycine biosynthesis I | 4 | 4 | 2 |
| CO2 fixation into oxaloacetate (anaplerotic) | 2 | 2 | 1 |
| L-alanine biosynthesis I | 2 | 2 | 1 |
| ammonia assimilation cycle I | 2 | 2 | 1 |
| L-tyrosine biosynthesis III | 4 | 3 | 2 |
| canavanine biosynthesis | 4 | 2 | 2 |
| L-tyrosine degradation II | 2 | 1 | 1 |
| L-threonine degradation V | 2 | 1 | 1 |
| atromentin biosynthesis | 2 | 1 | 1 |
| L-isoleucine biosynthesis III | 7 | 4 | 3 |
| superpathway of arginine and polyamine biosynthesis | 17 | 16 | 7 |
| pyruvate fermentation to isobutanol (engineered) | 5 | 4 | 2 |
| superpathway of L-homoserine and L-methionine biosynthesis | 8 | 8 | 3 |
| L-isoleucine biosynthesis II | 8 | 4 | 3 |
| superpathway of S-adenosyl-L-methionine biosynthesis | 9 | 9 | 3 |
| superpathway of L-methionine biosynthesis (transsulfuration) | 9 | 9 | 3 |
| ppGpp metabolism | 6 | 6 | 2 |
| L-citrulline degradation | 3 | 3 | 1 |
| superpathway of L-threonine metabolism | 18 | 16 | 6 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 5 |
| L-methionine biosynthesis II | 6 | 5 | 2 |
| superpathway of L-citrulline metabolism | 12 | 8 | 4 |
| L-isoleucine biosynthesis IV | 6 | 4 | 2 |
| L-isoleucine biosynthesis V | 3 | 2 | 1 |
| superpathway of ammonia assimilation (plants) | 3 | 2 | 1 |
| L-phenylalanine degradation II (anaerobic) | 3 | 2 | 1 |
| L-leucine degradation III | 3 | 2 | 1 |
| L-isoleucine degradation II | 3 | 2 | 1 |
| L-cysteine biosynthesis IX (Trichomonas vaginalis) | 3 | 2 | 1 |
| S-adenosyl-L-methionine salvage II | 3 | 2 | 1 |
| L-valine degradation II | 3 | 2 | 1 |
| L-arginine biosynthesis IV (archaea) | 9 | 4 | 3 |
| aliphatic glucosinolate biosynthesis, side chain elongation cycle | 30 | 10 | 10 |
| L-isoleucine degradation III (oxidative Stickland reaction) | 3 | 1 | 1 |
| L-valine degradation III (oxidative Stickland reaction) | 3 | 1 | 1 |
| L-leucine degradation V (oxidative Stickland reaction) | 3 | 1 | 1 |
| L-tyrosine degradation IV (to 4-methylphenol) | 3 | 1 | 1 |
| superpathway of L-tyrosine biosynthesis | 10 | 10 | 3 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I | 18 | 18 | 5 |
| S-adenosyl-L-methionine salvage I | 4 | 4 | 1 |
| superpathway of L-alanine biosynthesis | 4 | 4 | 1 |
| phosphopantothenate biosynthesis I | 4 | 4 | 1 |
| superpathway of L-methionine biosynthesis (by sulfhydrylation) | 12 | 10 | 3 |
| L-citrulline biosynthesis | 8 | 6 | 2 |
| dipicolinate biosynthesis | 4 | 3 | 1 |
| L-arginine degradation V (arginine deiminase pathway) | 4 | 3 | 1 |
| L-tyrosine degradation III | 4 | 2 | 1 |
| L-methionine biosynthesis IV | 4 | 2 | 1 |
| L-methionine biosynthesis III | 4 | 2 | 1 |
| L-phenylalanine degradation III | 4 | 2 | 1 |
| L-tyrosine biosynthesis II | 4 | 2 | 1 |
| L-phenylalanine biosynthesis II | 4 | 2 | 1 |
| spermidine biosynthesis II | 4 | 2 | 1 |
| phosphopantothenate biosynthesis III (archaea) | 4 | 2 | 1 |
| 4-hydroxy-3-prenylbenzoate biosynthesis | 4 | 1 | 1 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 1 | 1 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 1 | 1 |
| superpathway of aromatic amino acid biosynthesis | 18 | 18 | 4 |
| superpathway of sulfate assimilation and cysteine biosynthesis | 9 | 9 | 2 |
| hypoglycin biosynthesis | 14 | 4 | 3 |
| superpathway of L-phenylalanine biosynthesis | 10 | 10 | 2 |
| L-methionine biosynthesis I | 5 | 5 | 1 |
| aspartate superpathway | 25 | 24 | 5 |
| L-arginine degradation XIII (reductive Stickland reaction) | 5 | 3 | 1 |
| seleno-amino acid biosynthesis (plants) | 5 | 3 | 1 |
| superpathway of plastoquinol biosynthesis | 5 | 2 | 1 |
| ectoine biosynthesis | 5 | 2 | 1 |
| L-tyrosine degradation I | 5 | 2 | 1 |
| superpathway of L-phenylalanine and L-tyrosine biosynthesis | 5 | 2 | 1 |
| 4-hydroxybenzoate biosynthesis I (eukaryotes) | 5 | 1 | 1 |
| L-leucine degradation IV (reductive Stickland reaction) | 5 | 1 | 1 |
| L-phenylalanine degradation VI (reductive Stickland reaction) | 5 | 1 | 1 |
| L-tyrosine degradation V (reductive Stickland reaction) | 5 | 1 | 1 |
| L-isoleucine degradation I | 6 | 4 | 1 |
| L-leucine degradation I | 6 | 2 | 1 |
| norspermidine biosynthesis | 6 | 2 | 1 |
| L-arginine degradation XIV (oxidative Stickland reaction) | 6 | 1 | 1 |
| folate transformations I | 13 | 9 | 2 |
| pyridoxal 5'-phosphate biosynthesis I | 7 | 7 | 1 |
| L-lysine biosynthesis VI | 7 | 6 | 1 |
| L-lysine biosynthesis III | 7 | 6 | 1 |
| C4 photosynthetic carbon assimilation cycle, NADP-ME type | 7 | 4 | 1 |
| 3-dehydroquinate biosynthesis II (archaea) | 7 | 3 | 1 |
| cremeomycin biosynthesis | 7 | 2 | 1 |
| L-glutamate degradation XI (reductive Stickland reaction) | 7 | 2 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 7 | 1 |
| nitrogen remobilization from senescing leaves | 8 | 5 | 1 |
| L-valine degradation I | 8 | 4 | 1 |
| grixazone biosynthesis | 8 | 2 | 1 |
| butanol and isobutanol biosynthesis (engineered) | 8 | 2 | 1 |
| superpathway of polyamine biosynthesis III | 8 | 2 | 1 |
| folate transformations III (E. coli) | 9 | 9 | 1 |
| superpathway of coenzyme A biosynthesis I (bacteria) | 9 | 9 | 1 |
| L-lysine biosynthesis I | 9 | 9 | 1 |
| L-lysine biosynthesis II | 9 | 6 | 1 |
| L-phenylalanine degradation IV (mammalian, via side chain) | 9 | 4 | 1 |
| L-histidine biosynthesis | 10 | 10 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 6 | 1 |
| L-glutamate degradation V (via hydroxyglutarate) | 10 | 5 | 1 |
| reductive acetyl coenzyme A pathway I (homoacetogenic bacteria) | 10 | 3 | 1 |
| rosmarinic acid biosynthesis I | 10 | 1 | 1 |
| bacilysin biosynthesis | 10 | 1 | 1 |
| folate transformations II (plants) | 11 | 10 | 1 |
| C4 photosynthetic carbon assimilation cycle, NAD-ME type | 11 | 8 | 1 |
| (S)-reticuline biosynthesis I | 11 | 1 | 1 |
| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage | 12 | 11 | 1 |
| chorismate biosynthesis II (archaea) | 12 | 8 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 8 | 1 |
| 2,5-xylenol and 3,5-xylenol degradation | 13 | 1 | 1 |
| C4 photosynthetic carbon assimilation cycle, PEPCK type | 14 | 9 | 1 |
| superpathway of rosmarinic acid biosynthesis | 14 | 2 | 1 |
| superpathway of chorismate metabolism | 59 | 54 | 4 |
| salinosporamide A biosynthesis | 15 | 3 | 1 |
| cyclosporin A biosynthesis | 15 | 2 | 1 |
| mixed acid fermentation | 16 | 16 | 1 |
| gluconeogenesis II (Methanobacterium thermoautotrophicum) | 18 | 9 | 1 |
| superpathway of seleno-compound metabolism | 19 | 6 | 1 |
| superpathway of novobiocin biosynthesis | 19 | 4 | 1 |
| ethene biosynthesis V (engineered) | 25 | 18 | 1 |
| platensimycin biosynthesis | 26 | 6 | 1 |
| anaerobic aromatic compound degradation (Thauera aromatica) | 27 | 2 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 22 | 2 |
| odd iso-branched-chain fatty acid biosynthesis | 34 | 24 | 1 |
| even iso-branched-chain fatty acid biosynthesis | 34 | 24 | 1 |
| anteiso-branched-chain fatty acid biosynthesis | 34 | 24 | 1 |
| superpathway of histidine, purine, and pyrimidine biosynthesis | 46 | 46 | 1 |