<i>In silico</i>-prediction of the ComEA-DNA complex.

<p>(A) Protein sequence alignment of the two helix-hairpin-helix motifs (HhH1-2) of ComEA/ComE homologs from the indicated organisms (using the ComEA residue numbering). The sequence conservation is shown in tones of blue (dark blue = highly conserved). (B) 3D model of ComEA and its predicted DNA binding mode based on comparative modeling using the ComEA-related protein of <i>T. thermophilus</i> HB8 (PDB ID: 2DUY) as a template (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004066#pgen.1004066.s011" target="_blank">movie S1</a>). The non-sequence-specific DNA backbone phosphate interactions with K62 and K63 are shown (inset). (C) The electrostatic potential at the molecular surface of ComEA is reported within a ±160 k_BT/e range (negative values in red, positive values in blue).