| ORF | name | Annotation |
| Rv0106 | Rv0106 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0280 | PPE3 | PPE FAMILY PROTEIN |
| Rv0287 | esxG | ESAT-6 LIKE PROTEIN ESXG (CONSERVED HYPOTHETICAL PROTEIN TB9.8) |
| Rv0287 | esxG | ESAT-6 LIKE PROTEIN ESXG (CONSERVED HYPOTHETICAL PROTEIN TB9.8) |
| Rv0289 | Rv0289 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv0291 | mycP3 | PROBABLE MEMBRANE-ANCHORED MYCOSIN MYCP3 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-3) |
| Rv0292 | Rv0292 | PROBABLE CONSERVED TRANSMEMBRANE PROTEIN |
| Rv0490 | senX3 | PUTATIVE TWO COMPONENT SENSOR HISTIDINE KINASE SENX3 |
| Rv0675 | echA5 | PROBABLE ENOYL-CoA HYDRATASE ECHA5 (ENOYL HYDRASE) (UNSATURATED ACYL-CoA HYDRATASE) (CROTONASE) |
| Rv1035c | Rv1035c | PROBABLE TRANSPOSASE (FRAGMENT) |
| Rv1130 | Rv1130 | CONSERVED HYPOTHETICAL PROTEIN |
| Rv1131 | gltA1 | PROBABLE CITRATE SYNTHASE I GLTA1 |
| Rv1523 | Rv1523 | Probable methyltransferase |
| Rv1593c | Rv1593c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv2159c | Rv2159c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv2840c | Rv2840c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv2873 | mpt83 | CELL SURFACE LIPOPROTEIN MPT83 (LIPOPROTEIN P23) |
| Rv2909c | rpsP | PROBABLE 30S RIBOSOMAL PROTEIN S16 RPSP |
| Rv2933 | ppsC | PHENOLPTHIOCEROL SYNTHESIS TYPE-I POLYKETIDE SYNTHASE PPSC |
| Rv3019c | esxR | SECRETED ESAT-6 LIKE PROTEIN ESXR (TB10.3) (ESAT-6 LIKE PROTEIN 9) |
| Rv3020c | esxS | ESAT-6 LIKE PROTEIN ESXS |
| Rv3063 | cstA | PROBABLE CARBON STARVATION PROTEIN A HOMOLOG CSTA |
| Rv3161c | Rv3161c | POSSIBLE DIOXYGENASE |
| Rv3246c | mtrA | TWO COMPONENT SENSORY TRANSDUCTION TRANSCRIPTIONAL REGULATORY PROTEIN MTRA |
| Rv3462c | infA | PROBABLE TRANSLATION INITIATION FACTOR IF-1 INFA |
| Rv3462c | infA | PROBABLE TRANSLATION INITIATION FACTOR IF-1 INFA |
| Rv1839c | Rv1839c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv2004c | Rv2004c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv2028c | Rv2028c | CONSERVED HYPOTHETICAL PROTEIN |
| Rv2029c | pfkB | Probable phosphofructokinase PfkB (PHOSPHOHEXOKINASE) |
| Rv2031c | hspX | HEAT SHOCK PROTEIN HSPX (ALPHA-CRSTALLIN HOMOLOG) (14 kDa ANTIGEN) (HSP16.3) |
| Rv2056c | rpsN2 | Probable ribosomal protein S14 RpsN2 |
| Rv2058c | rpmB2 | Probable 50S ribosomal protein L28 RpmB2 |
| Rv2069 | sigC | PROBABLE RNA POLYMERASE SIGMA FACTOR, ECF SUBFAMILY, SIGC |