Figure 3

Amino acid sequence alignments for the RNase HI domains. RNase HI protein sequences were derived from the bacillales and lactobacillales listed in Additional File 2 and were aligned by using the Clustal method. Arrows and rectangles indicate beta-strands and alpha-helices, respectively. The upper and lower secondary structures were generated on the basis of the RNase HI domains of E. coli [33] and B. halodurans [29]. Dark and light shadings indicate highly conserved and similar amino acid residues, respectively. Asterisks denote amino acid residues that are involved in the catalytic function of RNase HI. The boxed region below the label for alpha-helix 3 forms a basic protrusion handle in the E. coli RNase HI structure. The combinations of RNase H genes are represented to the right of the sequences (see the text for details). The symbols ^† and ^§ indicate active and inactive RNase H, respectively.