<i>RC1339/</i>APRc gene homologues from <i>Rickettsia</i> spp. display a striking pattern of sequence conservation among each other and retain structural similarity with other members of the retropepsin family.

<p>(A) Multi-alignment of deduced amino acid sequences of the putative retropepsin-like protease from representative species from all rickettsial taxonomic groups (spotted fever group, typhus group, transitional group and ancestral group). Sequences were aligned against RC1339/APRc sequence from <i>R. conorii</i> (NP_360976) using the ClustalW software <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004324#ppat.1004324-Thompson1" target="_blank">[69]</a>. Accession numbers and corresponding species are described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004324#ppat-1004324-t001" target="_blank">Table 1</a>. The predicted α-helical transmembrane domains are represented by cylinders and the box indicates the active site motif (DTG). (B) Structure-based alignment of the soluble catalytic domain of RC1339/APRc with HIV-1 (PDB 3hvp), EIAV (PDB 2fmb) and XMRV (PDB 3nr6) retropepsins and with DdI1 putative protease domain (PDB 2i1a), performed with PROMALS3D <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004324#ppat.1004324-Pei1" target="_blank">[71]</a>. The first line shows conservation indices for positions with a conservation index above 4. Consensus_ss represent consensus predicted secondary structures (alpha-helix: h; beta-strand: e). Sequences are colored according to predicted secondary structures (red: alpha-helix, blue: beta-strand). Red nines highlight the most conserved positions. Active site consensus motif Asp-Thr-Gly and hydrophobic-hydrophobic-Gly sequence are boxed.