Sequence alignment of different RNase H domains. The RNases H from human origin, E. coli, XMRV, MoMLV, B. haludorans, HIV-1 and PFV are shown. The numbers represent the amino acid numbers of the corresponding full length enzymes. The alignment was performed with the program CLC Protein Workbench 5 (version 5.3). The arrows and boxes below indicate the secondary structures determined for PFV RNase H; α-helices are shown in blue, β-strands in gray. The active site residues are highlighted in bright green; the cysteines (C654, C709) of PFV RNase H are marked in yellow. The C-helices and basic loops of the enzymes are highlighted in magenta and orange, respectively.