Culturing: Bifido_ML2, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
| Pathway | #Steps | #Present | #Specific |
|---|
| L-tryptophan biosynthesis | 6 | 6 | 6 |
| L-aspartate biosynthesis | 1 | 1 | 1 |
| L-alanine biosynthesis II | 1 | 1 | 1 |
| L-alanine degradation III | 1 | 1 | 1 |
| L-aspartate degradation I | 1 | 1 | 1 |
| L-glutamine degradation I | 1 | 1 | 1 |
| 3-(4-hydroxyphenyl)pyruvate biosynthesis | 1 | 1 | 1 |
| L-histidine biosynthesis | 10 | 10 | 9 |
| L-valine biosynthesis | 4 | 4 | 3 |
| L-leucine biosynthesis | 6 | 6 | 4 |
| L-phenylalanine biosynthesis I | 3 | 3 | 2 |
| L-isoleucine biosynthesis II | 8 | 6 | 5 |
| pyruvate fermentation to isobutanol (engineered) | 5 | 4 | 3 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 10 |
| 3-methylbutanol biosynthesis (engineered) | 7 | 6 | 4 |
| superpathway of aromatic amino acid biosynthesis | 18 | 18 | 9 |
| superpathway of L-alanine biosynthesis | 4 | 4 | 2 |
| L-phenylalanine biosynthesis III (cytosolic, plants) | 2 | 2 | 1 |
| L-alanine biosynthesis I | 2 | 2 | 1 |
| L-cysteine biosynthesis III (from L-homocysteine) | 2 | 2 | 1 |
| L-glutamate biosynthesis I | 2 | 2 | 1 |
| L-glutamate degradation II | 2 | 2 | 1 |
| pyruvate fermentation to (R)-acetoin II | 2 | 2 | 1 |
| hydrogen sulfide biosynthesis II (mammalian) | 6 | 4 | 3 |
| L-isoleucine biosynthesis IV | 6 | 4 | 3 |
| L-alanine degradation V (oxidative Stickland reaction) | 2 | 1 | 1 |
| 4-aminobenzoate biosynthesis I | 2 | 1 | 1 |
| malate/L-aspartate shuttle pathway | 2 | 1 | 1 |
| L-tyrosine degradation II | 2 | 1 | 1 |
| L-tryptophan degradation IV (via indole-3-lactate) | 2 | 1 | 1 |
| atromentin biosynthesis | 2 | 1 | 1 |
| superpathway of L-tryptophan biosynthesis | 13 | 13 | 6 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 3 |
| L-isoleucine biosynthesis III | 7 | 4 | 3 |
| C4 photosynthetic carbon assimilation cycle, NAD-ME type | 11 | 6 | 4 |
| ammonia assimilation cycle III | 3 | 3 | 1 |
| L-tyrosine biosynthesis I | 3 | 3 | 1 |
| pyruvate fermentation to (S)-acetoin | 3 | 2 | 1 |
| pyruvate fermentation to (R)-acetoin I | 3 | 2 | 1 |
| nitric oxide biosynthesis II (mammals) | 3 | 2 | 1 |
| aliphatic glucosinolate biosynthesis, side chain elongation cycle | 30 | 10 | 10 |
| (R)-cysteate degradation | 3 | 1 | 1 |
| L-asparagine degradation III (mammalian) | 3 | 1 | 1 |
| L-tyrosine degradation IV (to 4-methylphenol) | 3 | 1 | 1 |
| sulfolactate degradation III | 3 | 1 | 1 |
| pyruvate fermentation to acetate and alanine | 3 | 1 | 1 |
| taurine biosynthesis III | 3 | 1 | 1 |
| L-phenylalanine degradation II (anaerobic) | 3 | 1 | 1 |
| L-alanine degradation II (to D-lactate) | 3 | 1 | 1 |
| indole-3-acetate biosynthesis VI (bacteria) | 3 | 1 | 1 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 4 |
| UTP and CTP dephosphorylation I | 7 | 5 | 2 |
| anaerobic energy metabolism (invertebrates, cytosol) | 7 | 4 | 2 |
| C4 photosynthetic carbon assimilation cycle, PEPCK type | 14 | 6 | 4 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 4 | 1 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 4 | 1 |
| homocysteine and cysteine interconversion | 4 | 3 | 1 |
| guanosine ribonucleotides de novo biosynthesis | 4 | 3 | 1 |
| L-tyrosine degradation III | 4 | 2 | 1 |
| L-phenylalanine degradation III | 4 | 2 | 1 |
| phosphopantothenate biosynthesis I | 4 | 2 | 1 |
| canavanine biosynthesis | 4 | 2 | 1 |
| superpathway of L-aspartate and L-asparagine biosynthesis | 4 | 2 | 1 |
| phosphopantothenate biosynthesis III (archaea) | 4 | 1 | 1 |
| L-tryptophan degradation VIII (to tryptophol) | 4 | 1 | 1 |
| acridone alkaloid biosynthesis | 4 | 1 | 1 |
| superpathway of histidine, purine, and pyrimidine biosynthesis | 46 | 39 | 10 |
| superpathway of L-phenylalanine biosynthesis | 10 | 10 | 2 |
| superpathway of L-cysteine biosynthesis (mammalian) | 5 | 3 | 1 |
| urea cycle | 5 | 3 | 1 |
| superpathway of (R,R)-butanediol biosynthesis | 5 | 3 | 1 |
| trans-4-hydroxy-L-proline degradation I | 5 | 2 | 1 |
| 4-hydroxy-2(1H)-quinolone biosynthesis | 5 | 2 | 1 |
| L-tryptophan degradation XIII (reductive Stickland reaction) | 5 | 1 | 1 |
| L-tyrosine degradation V (reductive Stickland reaction) | 5 | 1 | 1 |
| L-phenylalanine degradation VI (reductive Stickland reaction) | 5 | 1 | 1 |
| superpathway of plastoquinol biosynthesis | 5 | 1 | 1 |
| L-tyrosine degradation I | 5 | 1 | 1 |
| 4-hydroxybenzoate biosynthesis I (eukaryotes) | 5 | 1 | 1 |
| superpathway of chorismate metabolism | 59 | 32 | 10 |
| superpathway of L-threonine biosynthesis | 6 | 6 | 1 |
| superpathway of L-threonine metabolism | 18 | 13 | 3 |
| superpathway of guanosine nucleotides de novo biosynthesis I | 6 | 4 | 1 |
| superpathway of L-cysteine biosynthesis (fungi) | 6 | 4 | 1 |
| superpathway of L-citrulline metabolism | 12 | 7 | 2 |
| TCA cycle VIII (Chlamydia) | 6 | 2 | 1 |
| superpathway of 2,3-butanediol biosynthesis | 6 | 2 | 1 |
| superpathway of sulfolactate degradation | 6 | 2 | 1 |
| coenzyme M biosynthesis II | 6 | 1 | 1 |
| L-alanine degradation VI (reductive Stickland reaction) | 6 | 1 | 1 |
| DIBOA-glucoside biosynthesis | 6 | 1 | 1 |
| L-glutamate and L-glutamine biosynthesis | 7 | 5 | 1 |
| pyrimidine deoxyribonucleotides de novo biosynthesis IV | 7 | 4 | 1 |
| superpathway of guanosine nucleotides de novo biosynthesis II | 8 | 5 | 1 |
| L-citrulline biosynthesis | 8 | 5 | 1 |
| pyrimidine deoxyribonucleotides biosynthesis from CTP | 8 | 4 | 1 |
| butanol and isobutanol biosynthesis (engineered) | 8 | 3 | 1 |
| superpathway of anaerobic energy metabolism (invertebrates) | 17 | 6 | 2 |
| L-arginine biosynthesis I (via L-ornithine) | 9 | 8 | 1 |
| L-arginine biosynthesis III (via N-acetyl-L-citrulline) | 9 | 7 | 1 |
| superpathway of L-methionine biosynthesis (transsulfuration) | 9 | 7 | 1 |
| pyrimidine deoxyribonucleotides de novo biosynthesis I | 9 | 6 | 1 |
| pyrimidine deoxyribonucleotides de novo biosynthesis III | 9 | 5 | 1 |
| superpathway of coenzyme A biosynthesis I (bacteria) | 9 | 4 | 1 |
| L-arginine biosynthesis IV (archaea) | 9 | 4 | 1 |
| superpathway of L-alanine fermentation (Stickland reaction) | 9 | 3 | 1 |
| chloramphenicol biosynthesis | 9 | 1 | 1 |
| L-phenylalanine degradation IV (mammalian, via side chain) | 9 | 1 | 1 |
| superpathway of L-tyrosine biosynthesis | 10 | 10 | 1 |
| L-arginine biosynthesis II (acetyl cycle) | 10 | 10 | 1 |
| superpathway of tetrahydrofolate biosynthesis | 10 | 7 | 1 |
| superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) | 10 | 4 | 1 |
| superpathway of quinolone and alkylquinolone biosynthesis | 10 | 2 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 2 | 1 |
| rosmarinic acid biosynthesis I | 10 | 1 | 1 |
| superpathway of candicidin biosynthesis | 11 | 2 | 1 |
| (S)-reticuline biosynthesis I | 11 | 1 | 1 |
| superpathway of tetrahydrofolate biosynthesis and salvage | 12 | 9 | 1 |
| superpathway of L-methionine biosynthesis (by sulfhydrylation) | 12 | 6 | 1 |
| indole-3-acetate biosynthesis II | 12 | 2 | 1 |
| folate transformations I | 13 | 4 | 1 |
| superpathway of benzoxazinoid glucosides biosynthesis | 13 | 1 | 1 |
| 2,5-xylenol and 3,5-xylenol degradation | 13 | 1 | 1 |
| superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) | 14 | 9 | 1 |
| superpathway of purine nucleotide salvage | 14 | 9 | 1 |
| superpathway of rosmarinic acid biosynthesis | 14 | 1 | 1 |
| superpathway of L-methionine salvage and degradation | 16 | 5 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 8 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I | 18 | 16 | 1 |
| superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis | 18 | 13 | 1 |
| superpathway of purine nucleotides de novo biosynthesis I | 21 | 18 | 1 |
| aspartate superpathway | 25 | 23 | 1 |
| superpathway of purine nucleotides de novo biosynthesis II | 26 | 21 | 1 |
| anaerobic aromatic compound degradation (Thauera aromatica) | 27 | 1 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 16 | 2 |