Figure 9.

Structural analysis of MAW and P-loop motif regions. The MAW and P-loop motifs are highly conserved parts of the RecA protein family found at E. coli homolog positions 40–65 and 66–73, respectively. Labels denote the locations of α-helix B and β-strand 1 from the E. coli RecA crystal structure. Sorting the ProfileGrid rows by various amino acid physical constants reveals structural patterns within the context of the entire MSA. (A) Sorting by decreasing helical propensity shows that residues which do not favor helical formation (circled) immediately follow a helix in the MAW motif. (B) Sorting by decreasing volume displays the pattern (blue lines) that large amino acids are flanked by residues smaller than threonine. Whereas these panels were generated from the spreadsheet output, the JProfileGrid software allows an interactive analysis by switching between residue properties and color schemes.