Fig. 3

Phylogenetic analysis of Bacterial and Archaeal NarJ, NarW, DmsD, TorD and YcdY sequences. A rooted BI phylogram of 324 protein sequences from 130 different Bacterial and Archaeal species was performed using the Crenarchaeal Vulcanisaeta distributa NarJ sequence as an outgroup. A total of 10 million generations were performed and posterior probability values (0–1) at each node of the dendrogram are shown to provide branch confidence. Species (including Genbank locus tag) are listed on the right of each branch and coloured according to its NarJ subfamily member annotation (NarJ blue; DmsD red; TorD green; YcdY pink). Clades (1–3) and subclades (lettered) of significance that are discussed in the results section are highlighted by coloured circles; NarJ (1), DmsD (2) and TorD (3). The coloured heatmap to the right of species labels indicates the operon association of the NarJ subfamily member (operon). Starred branches indicate NarJ subfamily sequences from E.coli. Branches with asterisks identify DmsD associated with an ynfEFGH operon and branches with diamonds indicate NarJ subfamily sequences with transposon/ integrase genes identified within the +/− 10 ORF region of the operon