Alignment of CR fusion proteins orthologous to C.PvuII and R.PvuII. The PvuII system (top line) is unfused, and shown for comparison. Fully conserved positions or those conserved in 5/6 systems are shaded, and known functional regions (in PvuII) are in bold font (transcriptional activation, recognition helix of the helix-turn-helix motif, dimerization interfaces, Mg++-coordinating residues for REase catalysis (cat), and recognition of the methylated (CH3) base to prevent cleavage. Species sources are as described in the Figure 1 legend. At the lower right, the numbers indicate % amino acid identity (“Ident”) or similarity (“Pos”) for each RM system C or REase (“R”) portion to the corresponding PvuII polypeptide.