**3.4.2 Analysis of the sigma factor proteins in subfamily B**

From the analysis of the sigma factor class of paralogs in GroupB (Figure 11), we infer that duplication events followed by divergence resulted in the 2 groups of sigma factor subfamilies (marked as B1 and B2 in Figure 11). The sigma factor proteins in each of the subfamilies have significantly diverged after gene duplication. For the two sigma proteins (sigK and sigL) in one of the subfamilies (Figure 12), sigK was identified to have no orthologs in *M, avium, M paratuberculosis* or *M. leprae*, and sigL was noted to have no orthologs in *M. leprae*. These results are inconsistent with the published reports of Manganelli *et al*, 2003. For the other subfamily of sigma proteins (sigC and sigD) on the phylogenetic tree (Figure 12), we did not identify orthologs for sigC in *M. paratuberculosis* or sigD in *M. leprae*.
