Sequence alignments of ribonuclease H (RNH) and josephin-related cysteine protease (JCP). Residues conserved among all sequences are red, and residues conserved among Dualen elements are yellow. Catalytic residues are indicated by asterisks. (A) Alignment of RNH. Six Dualen elements and representatives of five clades of recently branched non-LTR retrotransposons, six groups of LTR retroelements, and cellular RNH were aligned. (B) Alignment of JCP and josephin. Five Dualen elements and representatives of the ataxin-3 family and the josephin family were aligned. Catalytic residues of distant cysteine proteases (the human USP18, the human UCH-L1, and foot-and-mouth disease virus leader protease (FMDV_LeadP)) are also shown. Residues conserved among ataxin-3 and josephin, but not among JCP of Dualen elements are green.
