Function and Evolution of the Homeodomain. The structure of the homeodomain bound to DNA is shown as ribbon models. The location of the repressor domain is shown in orange, the nuclear localization signal in red, critical hydrophobic residues of the nuclear export signal in blue and positive sites in yellow. Only side chains of amino acids that make base contacts are shown. (C) Sequence logo of the Hox-gene homeodomain and surrounding amino acids. The overall height of the stacked amino acids indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino acid at that position. The location of the homeodmain is shown above the logo. The location of protein-protein interaction regions are shown in blue (note that only some sites, not all sites, in blue actually participate in protein-protein interactions), sequence motifs are shown in light gray and the location of helices in dark gray. Sites identified under directional selection after cluster duplication are shown with an asterik (*). Sites with known functional information are shown: G, characteristic paralog-group residue; S, site that assists in binding site discrimination between paralog groups; B, site that makes base contacts; H, site that is part of the hydrophobic core; P, site that contacts the phosphate backbone; E, location of leucine and isoleucine residues critical for the nuclear export signal.