| ORF | name | Annotation |
| Rv0108c | Rv0108c | HYPOTHETICAL PROTEIN |
| Rv0166 | fadD5 | PROBABLE FATTY-ACID-CoA LIGASE FADD5 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) |
| Rv0168 | yrbE1B | CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE1B |
| Rv0169 | mce1A | MCE-FAMILY PROTEIN MCE1A |
| Rv0171 | mce1C | MCE-FAMILY PROTEIN MCE1C |
| Rv0173 | lprK | POSSIBLE MCE-FAMILY LIPOPROTEIN LPRK (MCE-FAMILY LIPOPROTEIN MCE1E) |
| Rv0174 | mce1F | MCE-FAMILY PROTEIN MCE1F |
| Rv0178 | Rv0178 | PROBABLE CONSERVED MCE ASSOCIATED MEMBRANE PROTEIN |
| Rv0240 | Rv0240 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0276 | Rv0276 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0293c | Rv0293c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0408 | pta | PROBABLE PHOSPHATE ACETYLTRANSFERASE PTA (PHOSPHOTRANSACETYLASE) |
| Rv0518 | Rv0518 | POSSIBLE EXPORTED PROTEIN |
| Rv0527 | ccdA | POSSIBLE CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCDA |
| Rv0528 | Rv0528 | PROBABLE CONSERVED TRANSMEMBRANE PROTEIN |
| Rv0569 | Rv0569 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0676c | mmpL5 | PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL5 |
| Rv0694 | lldD1 | POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD1 |
| Rv0695 | Rv0695 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0696 | Rv0696 | PROBABLE MEMBRANE SUGAR TRANSFERASE |
| Rv0868c | moaD2 | PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D 2 MOAD2 (MOLYBDOPTERIN CONVERTING FACTOR SMALL SUBUNIT) (MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1) |
| Rv0936 | pstA2 | PHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTA2 |
| Rv1095 | phoH2 | PROBABLE PHOH-LIKE PROTEIN PHOH2 (PHOSPHATE STARVATION-INDUCIBLE PROTEIN PSIH) |
| Rv1216c | Rv1216c | PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN |
| Rv1217c | Rv1217c | PROBABLE TETRONASIN-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER |
| Rv1481 | Rv1481 | PROBABLE MEMBRANE PROTEIN |
| Rv1497 | lipL | PROBABLE ESTERASE LIPL |
| Rv1502 | Rv1502 | HYPOTHETICAL PROTEIN |
| Rv1547 | dnaE1 | PROBABLE DNA POLYMERASE III (ALPHA CHAIN) DNAE1 (DNA NUCLEOTIDYLTRANSFERASE) |
| Rv1613 | trpA | Probable tryptophan synthase, alpha subunit trpA |
| Rv1664 | pks9 | Probable polyketide synthase pks9 |
| Rv1738 | Rv1738 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv1813c | Rv1813c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv1815 | Rv1815 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv1816 | Rv1816 | POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN |
| Rv1883c | Rv1883c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv1884c | rpfC | PROBABLE RESUSCITATION-PROMOTING FACTOR RPFC |
| Rv2676c | Rv2676c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv3083 | Rv3083 | PROBABLE MONOOXYGENASE (HYDROXYLASE) |
| Rv3084 | lipR | PROBABLE ACETYL-HYDROLASE/ESTERASE LIPR |
| Rv3086 | adhD | PROBABLE ZINC-TYPE ALCOHOL DEHYDROGENASE ADHD (ALDEHYDE REDUCTASE) |
| Rv3131 | Rv3131 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv3145 | nuoA | PROBABLE NADH DEHYDROGENASE I (CHAIN A) NUOA (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN A) |
| Rv3146 | nuoB | PROBABLE NADH DEHYDROGENASE I (CHAIN B) NUOB (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN B) |
| Rv3147 | nuoC | PROBABLE NADH DEHYDROGENASE I (CHAIN C) NUOC (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN C) |
| Rv3148 | nuoD | PROBABLE NADH DEHYDROGENASE I (CHAIN D) NUOD (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN D) |
| Rv3149 | nuoE | PROBABLE NADH DEHYDROGENASE I (CHAIN E) NUOE (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN E) |
| Rv3150 | nuoF | PROBABLE NADH DEHYDROGENASE I (CHAIN F) NUOF (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN F) |
| Rv3152 | nuoH | PROBABLE NADH DEHYDROGENASE I (CHAIN H) NUOH (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN H) |
| Rv3153 | nuoI | PROBABLE NADH DEHYDROGENASE I (CHAIN I) NUOI (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN I) |
| Rv3154 | nuoJ | PROBABLE NADH DEHYDROGENASE I (CHAIN J) NUOJ (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN J) |
| Rv3155 | nuoK | PROBABLE NADH DEHYDROGENASE I (CHAIN K) NUOK (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN K) |
| Rv3156 | nuoL | PROBABLE NADH DEHYDROGENASE I (CHAIN L) NUOL (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN L) |
| Rv3157 | nuoM | PROBABLE NADH DEHYDROGENASE I (CHAIN M) NUOK (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN M) |
| Rv3158 | nuoN | PROBABLE NADH DEHYDROGENASE I (CHAIN N) NUON (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN N) |
| Rv3160c | Rv3160c | POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) |
| Rv3282 | Rv3282 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv3322c | Rv3322c | POSSIBLE METHYLTRANSFERASE |
| Rv3324c | moaC3 | PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN C 3 MOAC3 |
| Rv3477 | PE31 | PE FAMILY PROTEIN |
| Rv3496c | mce4D | MCE-FAMILY PROTEIN MCE4D |
| Rv3614c | Rv3614c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv3615c | Rv3615c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv3616c | Rv3616c | CONSERVED HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN |
| Rv3648c | cspA | PROBABLE COLD SHOCK PROTEIN A CSPA |
| Rv3680 | Rv3680 | PROBABLE ANION TRANSPORTER ATPASE |
| Rv3734c | Rv3734c | CONSERVED HYPOTHETICAL PROTEIN |