Multiple alignments of amino acid and DNA sequences, including inserted DNA sequences.

<p>Each panel shows A–C) DNA polymerase III alpha chain; D–F) tRNA ribosyltransferase-isomerase; G–I) phenylalanyl-tRNA synthetase subunit beta; A, D, G) amino acid alignments; B, E, H) structure models; C, F, I) DNA alignments. Letters in alignments indicate green, typical RPE-4s; blue, typical RPE-6s; purple, typical RPE-7s; red, extended RPE-4 regions; black, boundary regions of genes with inserted DNA sequences. Amino acids encoded by inserted DNA sequences were shown by red balls in the protein structures. Gene sequences were extracted from each genome sequence; <i>Rickettsia japonica</i> (this work); <i>R. conorii</i>, AE006914 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071861#pone.0071861-Ogata1" target="_blank">[13]</a>; <i>R. felis</i>, CP000053 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071861#pone.0071861-Ogata5" target="_blank">[28]</a>; <i>R. prowazekii</i>, AJ235269 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071861#pone.0071861-Andersson1" target="_blank">[29]</a>; <i>R. typhi</i>, AE017197 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071861#pone.0071861-McLeod1" target="_blank">[30]</a>; <i>Acetobacter pasteurianus</i> IFO 3283-01, AP011121 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071861#pone.0071861-Azuma2" target="_blank">[47]</a>. Protein Data Bank Identifiers (PDB IDs) for amino acid sequences of <i>Escherichia coli</i> DNA polymerase III alpha chain, <i>Bacillus subtilis</i> tRNA ribosyltransferase-isomerase, and <i>Thermus thermophilus</i> phenylalanyl-tRNA synthetase subunit beta are 2hnhA, 1yy3A, and 1b70B, respectively. J) The highly conserved short sequence in e-RPEs were illustrated using a sequence LOGO format <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071861#pone.0071861-Crooks1" target="_blank">[33]</a>.