TABLE 2.
Protein prediction in the 5th percentile
| Categorya | COG(s) | Gene(s) | Protein information |
|---|---|---|---|
| Cellular processes and signaling [D],[M],[N],[O],[T], [U],[V],[W],[Y],[Z] | D | relB, relG | Toxin-antitoxin (TA) group |
| M | rmlA | Carbohydrate biosynthesis | |
| M | ftsQ | Essential cell division protein | |
| M | mpt83 | Cell surface lipoprotein | |
| O | groES | Chaperonin GroES | |
| O | ahpE (64), bcpB | Peroxiredoxin (direct antioxidants) | |
| T | mtrA | Response regulator | |
| T | garA | Virulence and glutamate metabolism | |
| V, M | lipP, pimA | Role in lipid metabolism | |
| Information storage and processing [A],[B],[J],[K],[L] | J, K, L | tuf, trmD, greA, hupB, gatB | Information pathways |
| K | mazE9 | Antitoxin (TA group) | |
| K | whiB1, whiB2, mce3R | Transcriptional regulator | |
| K | cspB | Cold shock protein | |
| K | argR | Amino acid biosynthesis | |
| K | trcR | Regulatory proteins | |
| Metabolism [C],[E],[F],[G],[H],[I],[P],[Q] | C | fdxA, fdxC | Iron-sulfur proteins |
| C | ctaE | Probable cytochrome oxidase | |
| C | rubA | Probable rubredoxin | |
| C, E | atpA, nuoL, nuoK, pepQ | Intermediate metabolism and respiration | |
| E | metC, lysA, livN, ilvG | Amino acid transport and metabolism | |
| F | nrdI | Ribonucleotide reductase function | |
| F, G, H, I | ndkA, rpiB, nadD, thiC, dxR, gpm1 | Intermediate metabolism and respiration | |
| G, Q, I, P | lppZ, lpqC, papA4, desA2 | Role in lipid metabolism | |
| G, P | sugC, rfbE | ABC transporter | |
| H | dfrA, folE, folB | Involved in folate metabolism | |
| H | kdtB | Coenzyme A (CoA) biosynthesis | |
| H | mog, moaB2, moaB1, moaC2 (30) | Molybdopterin biosynthesis | |
| I | mbtN | Mycobactin biosynthesis | |
| P | cysH, cysQ (65) | Sulfate activation pathway | |
| P | corA | Transmembrane protein | |
| Poorly characterized [R],[S] | UC | vapB26, vapB44, vapB12, vapB9 | Antitoxin (TA group) |
| S | vapC33, vapC8, vapC7, vapC20 | Toxin (TA group) | |
| S | vapC5, vapC47, vapB30, vapB32 | TA group | |
| S | yfiH | Multicopper oxidase | |
| Unable to characterize (UC) | UC, S | wbbL1, nicT, arfB | Cell and cell wall-associated processes |
| UC | lsr2 | Nucleoid-associated protein Lsr2 | |
| UC | mazE7, mazE3 | Antitoxin (TA group) | |
| UC | mymT (37) | Metallothionein | |
| UC | aprA (66) | Acid and phagosome regulated protein | |
| UC | metS | Information pathways |
COG classification of proteins combined with information from Mycobrowser (18) and UniProt (19). Additional information from the literature, which cannot be found in these two databases, is individually cited within the table. Genes related to the metabolism of essential elements for M. tuberculosis survival, such as thiamine (e.g., thiC), and others related to cell envelope and active transport were also observed (e.g., sugC). Genes belonging to the TA family, as well as genes related to metal binding and antioxidant activity, are present in the 5th percentile. The majority of the TA genes are poorly characterized by COGs. The classification-involved proteins were encoded by genetically characterized genes with reference to H37Rv. Protein prediction for the noncharacterized genes can be found in Data Set S1 in the supplemental material.