Repeated DNA sequences have been identified in a range of mycobacterial species and have been implicated in the increased virulence of some of these species, namely, Mycobacterium paratuberculosis and M. avium subsp. silvaticum. Here we present a case to suggest that the insertion sequences IS900 and IS902 encode a protein from a putative gene positioned on the complementary strand to their transposase genes. Based on amino acid homology analyses, this open reading frame (ORF2) could encode a transport protein. The ORF2 protein thus IS900 and IS902, may have a role in the increased pathogenicity of M. paratuberculosis and M. avium subsp. silvaticum from an M. avium background.