Figure 5.

Sequence alignment of the EcoR124I HsdR and its homologs and the templates used for modelling the NTD, RecA-I and RecA-II subdomains. Similar amino acids are coloured according to the physico-chemical properties of their side-chains: negatively charged, red, positively charged, blue, polar, magenta, hydrophobic, green. Sequences are named according to nomenclature from REBASE or PDB codes. Numbers in parentheses indicate how many amino acid residues have been omitted for the sake of clarity. Amino acid residues of the NTD that are predicted to form a catalytic site and residues of the central domain that are predicted to be involved in ATP binding are indicated above the alignment by an asterisk (*). Putative DNA-binding residues are indicated by a hash mark (#). The secondary structure of the EcoR124I domains derived from the model using the DSSP program is shown above the EcoR124I sequence. Secondary structure of the templates: 1hh1 and 2db3 shown below the sequences. β-Strands are shown as arrows and helices are shown as cylinders.