Conserved Dlx motifs. Alignment of representative sequences, beneath each alignment is a sequence logo corresponding to the alignment of all Dlx sequences used to generate the phylogenetic tree in Fig 1. The overall height of each column corresponds to the overall sequence conservation at that position, and the height of each letter corresponds to the overall frequency of that amino acid. Sequence logos were created using Weblogo . A. Homeodomain alignment of representative Dlx genes. B. Conserved residues upstream of the homeodomain. Note the shared gap in CtDlxa, CtDlxb and PlaDlxa (underlined) C. The SKSAFME motif, located close to the N-terminus of the protein. A similar motif can be found in the same location in BfMsx. D. The YPY motif. E and F. Two conserved tryptophan residues are found downstream of the homeodomain, the first is generally followed by an aspartic acid, and the second by a tyrosine. G. Hydrophobic terminal motif, at or near the C-terminal of the protein. Species abbreviations are as follows: Branchiostoma floridae (Bf), Caenorhabditis elegans (Ce), Ciona intestinalis (Ci), Drosophila melanogaster (Dm), Lottia gigantea (Lg), Mus musculus (Mm), Nematostella vectensis (Nv), Trichoplax adhaerens (Tad).