FIG 4 .

Putative horizontal transfer of inteins. (A) Evidence of common ancestry among phage and mycobacterial inteins. Phylogenetic analysis (ML) of class 3 mycobacteriophage/mycobacterial inteins (left) and their ATPase-containing exteins (right), excluding RecB. The intein tree shows two examples of supported clustering (red), including mycobacteriophage TerL1-c/e and mycobacterial DnaB-b inteins, indicating a common ancestor. The exteins group independently from their inteins. Inteins were aligned based on splicing blocks; exteins were aligned based on the ATPase domain. Full trees for class 1 and 3 inteins are in Fig. S2 in the supplemental material. (B) Putative horizontal transfer of TdS inteins. Phylogenetic analyses of TdS inteins (left) and TdS proteins (right), some with inteins. Incongruence in clustering of the two trees implies horizontal intein transfer (red). The presence of an intein is indicated by its insertion site a or c. For both panels, trees are unrooted and values for significant external nodes higher than 75% are shown. Scale indicates the number of substitutions per site. Genus abbreviations are as follows: M, Mycobacterium; S, Streptomyces; K, Kitasatospora; Rh, Rhodococcus; N, Nocardia; Mi, Microbacterium; G, Gordonia.