Figure 1.

RTs identified in eubacterial, archaeal and phage genomes. RTs were classified based on limited phylogenetic analyses, BLAST scores and sequence examination for synapomorphies. The number of RTs per group is indicated in parentheses and by triangle size. Domain structures are depicted in black (alignable with group II introns), gray (uncertain alignment) and white (lack of alignability). Additional domains, including domains of unknown function (DUFs), are in light gray squares, with parentheses indicating that some members lack the domain. In this figure, the designation of an extension as a DUF indicates that the amino acid sequence is conserved within the group. Groups corresponding to lineages in Kojima and Kanehisa (38) are as follows: G2L1 [H1, H2, H3 in (38)]; G2L2, (H4); UG1 (F1); UG3 (G); UG5 (F2); UG6 (E); UG8 (G); UG9 (D); retrons (A); and DGRs (B, C).