Figure 2.

Alignments of NR2E DBDs. Annotated alignments of NR2E DBDs based on ClustalW multiple alignments as described in Methods. The reference sequence of the human retinoic acid receptor gamma subunit is shown at the top. The red box identifies the P box, which plays a critical role in DNA binding site specificity. The blue box identifies the D box, which functions in protein dimerization. Underlined amino acid positions identify points of contact between RAR/RXR heterodimers and DNA bases, and asterisks identify protein dimerization contacts in structural studies [46]. Color scheme distinguishes ecdysozoans (black), non-vertebrate deuterostomes (red), and vertebrates (blue). Vertical boxes identify amino acids common to a particular clade (TLL/TLX, PNR/FAX-1, Hr83/NHR239). Species abbreviations are given in Figure 1. The Brugia malayi sequence is derived from separate candidate coding sequences that have not been assembled into a gene model or confirmed as an expressed gene. The C-terminal portion of the predicted Pristionchus pacificus NHR-239 ortholog was not included since it aligned very poorly and it is unclear whether this reflects true divergence, incorrect gene assembly, or a pseudogene. It is also possible that the B. malayi ortholog shown here is actually a pseudogene, since it has not been confirmed by a cDNA.