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Figure 4: Structure-derived multiple-sequence alignment and dendrogram of known and putative AraC/XylS-family transcription factors. (a) The structures were aligned with SALIGN [16] and a multiple sequence alignment was derived from equivalent residue positions. Secondary structure elements are given at the top. Residues marked with a gray-shaded box are engaged in DNA base interactions, those marked with an asterisk contact the DNA sugar-phosphate backbone, and a hash sign denotes residues of the hydrophobic core. Numbering scheme and annotations are according to MarA protein (PDB code: 1bl0). Colors are as in Figure 2. (b) Maximum likelihood dendrogram derived from the structure-based MSA in (a) generated with the software MEGA5 [20]. Distances in the dendrogram refer to the number of amino acid substitutions per site. Only structures with two HTH domains (omitting Ada) were included. (c) For comparison, a more concise view of the dendrogram in Figure 3 is given, showing only relevant proteins.