FIG 2 .

Phylogeny estimation of P-type type IV secretion systems (P-T4SSs). Phylogeny was estimated from concatenated alignments of five components (VirB4 and VirB8 to VirB11), except for rvhB-II, which contains homologs to VirB4, VirB8, and VirB9 only (see the text for further details on alignment and data set construction). ML-based phylogeny was estimated with RAxML on the unmasked alignment (LG + gamma + Ι). Branch support was assessed with 1,000 bootstrap pseudoreplications. A tree with specific bootstrap values, as well as additional phylogenies estimated from alternative alignments/models/optimality criteria, is provided in Text S1 in the supplemental material. The tree was rooted with four P-T4SSs from species of Epsilonproteobacteria. rvh-I and rvh-II T4SSs are in light and dark gray, respectively. The Bartonella vir, vbh, and trw T4SSs are colored different shades of green. Red stars depict sequences used to generate VirB8 structures in this study; blue stars depict sequences previously used to determine VirB8 structures. Plasmid-encoded T4SSs are depicted with open circles, with plasmid names provided. NCBI GenBank accession numbers for all proteins are provided in Text S1 in the supplemental material.