Figure 3.

An amino acid alignment of eRF1 D1. Abbreviations of the sequence names are listed in Table 2. Residues conserved among >70% of standard code eRF1s are shaded. Converged unvaried sites in ciliate eRF1s that are identified both in this study and the study by Lozupone et al. (23) are boxed with filled circles. Converged unvaried sites newly identified in this study are boxed. ‘Convergent’ sites identified only in the study of Lozupone et al. (23) are marked with open circles. The sequences labeled as nodes 1–3 are the ancestral ciliate sequences inferred for these nodes on the full-length topology (see Fig. 1A). The residue numbers are based on human eRF1 (GenBank accession no. U90176). Asterisks indicate partial sequences. Sites that were excluded from the computational analyses are indicated by open triangles. The amino acid residues in the ancestral ciliate eRF1s (nodes 1–3 in Fig. 1A) for these excluded sites are not available and are indicated by question marks.