Shown is a ClustalW alignment (left) and corresponding tree diagram of the 'YPWM' region for a subset of vertebrate and invertebrate Hox proteins. The YPWM motif is the Hox peptide that interacts with the Hox cofactor Exd, and consequently positions nearby residues that would otherwise be disordered. For the Hox protein Scr, these additional YPWM-associated residues insert into a particularly narrow region of the DNA minor groove. The fact that other Hox paralogs have equally well conserved residues surrounding the YPWM motif (as this figure shows) suggests that what we observed for Scr may be generally true for other Hox-cofactor-DNA interactions. See Joshi et. al., 2007 for more information.

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