Table 2.
Paired genes present in both the PE and PPE multigene families.*
| Sub-Lineage** | Paired genes | Associated ESAT-6 (esx) gene cluster region*** | |
| (PE) | (PPE) | ||
| I | Rv3872 | Rv3873 | Situated in ESAT-6 (esx) gene cluster region 1 |
| II | Rv0285 | Rv0286 | Situated in ESAT-6 (esx) gene cluster region 3 |
| II | Rv3018A | Rv3018c | Duplicated from ESAT-6 (esx) gene cluster region 3 |
| II | Rv3022A | Rv3021/22c | Duplicated from ESAT-6 (esx) gene cluster region 3 |
| II | Rv1386 | Rv1387 | Associated with ESAT-6 (esx) gene cluster region 3 |
| III | Rv3893c | Rv3892c | Situated in ESAT-6 (esx) gene cluster region 2 |
| III | Rv2107 | Rv2108 | Associated with ESAT-6 (esx) gene cluster region 2 |
| III or IV | Rv2431c | Rv2430c | Associated with ESAT-6 (esx) gene cluster region 2 or 5 |
| IV | Rv1788/91 | Rv1787/89/90 | Situated in ESAT-6 (esx) gene cluster region 5 |
| IV | Rv3622c | Rv3621c | Duplicated from ESAT-6 (esx) gene cluster region 5 |
| IV | Rv1195 | Rv1196 | Duplicated from ESAT-6 (esx) gene cluster region 5 |
| IV | Rv1040c | Rv1039c | Duplicated from ESAT-6 (esx) gene cluster region 5 |
| IV | Rv1169c | Rv1168c | Associated with ESAT-6 (esx) gene cluster region 5 |
| IV | Rv1806 | Rv1801/2/7/8/9 | Associated with ESAT-6 (esx) gene cluster region 5 |
| IV | Rv3477 | Rv3478 | Associated with ESAT-6 (esx) gene cluster region 5 |
| IV | Rv2769c | Rv2768c/70c | Associated with ESAT-6 (esx) gene cluster region 5 |
| IV | Rv0916c | Rv0915c | Associated with ESAT-6 (esx) gene cluster region 5 |
* Although they are physically-separated, Rv3746c and Rv3739c seems to have been a pair associated with either ESAT-6 gene cluster region 1 or 3, which was disrupted by the insertion of a number of genes.
** See Figure 5 and 6 for definition of sublineages.
*** "Situated in" denotes genes situated within ESAT-6 (esx) gene cluster regions, "Duplicated from" denotes genes confirmed to be duplicated from ESAT-6 (esx) gene clusters due to the presence of ESAT-6 and CFP-10 genes immediately adjacent to them, "Associated with" denotes genes which are hypothesized to have been duplicated from ESAT-6 (esx) gene cluster regions, as they are very homologous to their paralogues within the clusters (see Figure 1).