Table 1. The current FOAM database is made of 73 969 HMMs designed to target 2870 different Kos.
| #HMM | #KO | #hmm/KO | |
|---|---|---|---|
| 01_Fermentation | 1342.5 | 173 | 7.76 |
| 02_Homoacetogenesis | 336 | 118 | 2.85 |
| 03_Superpathway of thiosulfate metabolism | 36 | 7 | 5.14 |
| 04_Utililization of sugar, conversion of pentose to EMP pathway intermediates | 100.5 | 14 | 7.18 |
| 05_Fatty acid oxidation | 1179.5 | 41 | 28.77 |
| 06_Amino acid utilization biosynthesis metabolism | 7773 | 805 | 9.66 |
| 07_Nucleic acid metabolism | 2734 | 288 | 9.49 |
| 08_Hydrocarbon degradation | 1415.5 | 85 | 16.65 |
| 09_Carbohydrate Active enzyme (CAZy) | 2305.5 | 305 | 7.56 |
| 10_TCA cycle | 478.5 | 35 | 13.67 |
| 11_Nitrogen cycle | 217.5 | 52 | 4.18 |
| 12_Transporters | 0.5 | 543 | 0.00 |
| 13_Hydrogen metabolism | 194.5 | 16 | 12.16 |
| 14_Methanogenesis | 524.5 | 57 | 9.20 |
| 15_Methylotrophy | 238 | 69 | 3.45 |
| 16_Embden Meyerhof-Parnos (EMP) | 209 | 35 | 5.97 |
| 17_Gluconeogenesis | 258 | 28 | 9.21 |
| 18_Sulfur metabolism | 35.5 | 33 | 1.08 |
| 19_Synthesis of saccharides and deriviatives | 2015.5 | 419 | 4.81 |
| 20_Polymers hydrolysis | 2740 | 358 | 7.65 |
| 21_Cellular response to stress | 11647 | 825 | 14.12 |
| Total: 35781 | Different KOs: 2870 |
On average, an HMM is made from an alignment of 81 peptide sequences and about 26 HMMs are built per KO. The file size is ∼7 GB.