Figure 3

Alignments of sequences at the C-terminus integrase. Group A elements possess a CR motif with several strongly conserved amino acid residues near the N-terminus. These residues are not present in Beetle1, Beetle2 or SilL1, but are well conserved in the grass species elements (see bottom part of the alignment). The numbers between two aligned blocks specify the number of amino acid residues not shown. No putative targeting domain (PTD) is encoded by group B elements. The type II chromodomain of group C elements shares sequence similarity with Tekay, Galadriel and Reina clade members. The dotted line above each alignment marks a region conserved among all plant chromoviruses. The arrow shows the portion of the integrase lying within the 3' long terminal repeat(LTR). Asterisks indicate stop codons at the end of each open reading frame. A highly conserved GPY/F motif [36, 37] is indicated by a black trapezoid above the beginning of each alignment.