Figure 3.

Structure-based sequence alignments and phylogenetic relatedness. (A) Organization of homologous RT domains in various IEP-related proteins. Conserved sequence motifs RT1–RT7 (purple) and IFDs (insertion in fingers domain, dark purple) are depicted. Insertions between RT1 and RT7 are designated as white spaces. The two catalytic aspartates are highlighted (red D's). (B) Phylogenetic tree showing evolutionary relatedness among proteins in panel A. The tree was constructed by the neighbor-joining method using structure-based sequence alignments. Copia and Ty1 RTs were added based on structure predictions as an out-group in the phylogenetic analysis.