Figure 7

Alignment of OrfAB sequences from IS 3 -family sub-groups correlated with secondary structure data of IS 2. Sequences in descending order, IS861 (IS150 subgroup), IS3, IS911 (IS3 subgroup), IS2, IS407 and IS51 were aligned using the ClustalW2 multiple sequence alignment tool [50]. Coordinates above the sequences are those of IS2. Amino acid groups are color coded as follows: Red - acidic residues; blue - basic residues; green - non-polar hydrophobics; cyan - aromatics (Y and F); dark green - tryptophan; gray - proline; light purple - amides; blue-gray - small polar; aquamarine - small non-polar; ochre - glycine; magenta - histidine and brown - cysteine. Secondary structure elements (green cylinders for α helices and red arrows for β strands) for IS2 were determined by the Protein Structure Prediction Protocol (see Figure 8) and are shown above the sequences for the N-terminus of the protein as B α1-3 (putative binding domain), the putative leucine zipper-like domain and the middle interval (elements M α1-7). In the C-terminal half of the sequences, elements of a putative catalytic active site motif are identified as C β 1-5 and C α 1-6. IS: insertion sequence.