Comparison of conserved sites among subfamilies.

<p>The alignment comprising reference sequences for each of the subfamilies was color coded to show sites of conservation. The linker sequence (black bar) is highlighted to show the separation of the N-terminal DNA binding domain from the C-terminal regulatory domain. Colored cells denote that a position is conserved <i>within</i> a given, individual subfamily (<5% sequence variability, consistent with our definition of conservation during co-evolution analysis, see Methods); white cells denote non-conserved positions within a subfamily or gaps in the reference sequence. The amino acid shown within each conserved cell is the consensus amino acid. Positions that are conserved in only one of the six subfamilies are highlighted in green, while those conserved in multiple subfamilies (two or more) are highlighted in magenta. In an alignment of representative sequences drawn from 34 LacI/GalR subfamilies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084398#pone.0084398-Tungtur2" target="_blank">[14]</a>, only three positions (asterisks; 10, 19 and 21) were conserved (as defined by 5% sequence variability). Only 5 additional positions were conserved (daggers; 16, 47, 49, 53 and 56) among more closely-related subfamilies that contain a functionally-important “YxPxxxAxxL” (YPAL) motif in the linker region <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084398#pone.0084398-Tungtur2" target="_blank">[14]</a>.