Fig 6.

Sequences related to XisH and XisI. The trees include all sequences annotated as XisH, XisI, or fdxN excision-control proteins in IMG/ER (as of August 2012). A neighbor-joining tree was first constructed with all the inferred amino acid sequences, and the database was then divided into XisH- and XisI-like sequences. BOGUAY ORFs found adjacent to each other are indicated by boldface numbers; see Table S4 in the supplemental material for details. There is one additional putative partial XisI gene and 4 partial or split XisH genes in the BOGUAY genome. Phylogenetic analyses were conducted in MEGA5 (10), with sequences aligned by MUSCLE (11). Evolutionary histories were inferred by neighbor joining (76) with 500 bootstrap replicates (77). Evolutionary distances were computed by the Poisson correction method (78) and are in units of amino acid substitutions per site. All ambiguous positions were removed for each sequence pair. For XisH, the analysis involved 114 amino acid sequences, and there were 330 positions in the final data set. For XisI, 171 amino acid sequences and 260 positions were used. The scale bar represents amino acid changes per position. RAxML and Bayesian analyses gave similar groupings (not shown).