Figure 1

Architecture and consensus alignments of the eRF1/Dom34p family. A) A schematic representation of the domain architecture of eRF1 is shown along with B) an alignment of separate consensus sequences for paralogues of eRF1/Dom34p for eukaryotes and archaea. Fifty percent conservation consensus sequences were calculated using the Python program ConsensusFinder (G. Atkinson). Uppercase letters indicate amino acids conserved in > 50% of all examined sequences, and lowercase letters indicate a common amino acid substitution group conserved in > 50% of the sequences. A '.' denotes a position that is universally present but not conserved in sequence, and gaps are denoted by "-". Domains are indicated above the alignment with lines terminating in arrows. Other family-specific symbols are as follows: dashed grey box with filled circles below – location of Dom34p residues implicated in endonuclease activity [32, 35], filled grey box – eRF1 structural minidomains, open grey box – human eRF3 binding sites [11], dashed line – RNA binding site [30], "^" characters – putative NLS domain [56], and "~" characters – well conserved patches that fall outside previously reported functional motifs. The a/eRF1-specific insertion at positions 356–393 is shown in detail in additional file 4. Secondary structure is indicated below the alignment for human eRF1 (PDB accession code 1DT9, [91]) and S. cerevisae Dom34p (PDB accession code 2VGM, [32]). Blue arrows show β-sheets and red tubes show α-helices. Pale blocks within structural elements indicate positions in the alignment that are not present in the sequence of the protein from which the structure was determined.