Sequence alignment of the DNA binding domain (DBD) of TRs. There is a highly conserved motif found at the 3' end of A/B domain, termed the 'N-terminal signature sequence' (NTSS). In non-chordate TR homologues, it is PYIPSYMXXXGPEEP; while in chordate NTSS, three amino acids are deleted (represented by dashes) generating a sequence of GYIPYL(D/E)KE(P/Q/L). In the N-terminus of the DBD, a methionine at position 16 (highlighted in red) is non-chordate TR specific. In this position an isoleucine is conserved for all chordate TRs. Two amino acids (His and Pro for all species except Ciona) are inserted at positions 33–34 of the N-terminus of DBD in chordate TRs (highlighted in blue). An aspartic acid in vertebrate TRs at the 8th position of the T-box is highly conserved for vertebrate TRs, a glutamic acid at this position is conserved for other TRs (highlighted in red). Stars identify the conserved cysteine residues that comprise the zinc finger of the DBD. The conserved residues are highlighted in green. CiTR: Ciona intestinalis nuclear receptor 1, DpTR: water flea Daphnia pulex TR, hTRa: Human thyroid receptor alpha, hTRb: Human thyroid receptor beta, LgTR: owl limpet Lottia gigantean TR, SeTRa: turbellarian Schmidtea mediterranea TRα, SeTRb: S. mediterranea TRβ, SjTRα: blood fluke Schistosoma japonium TR alpha, SjTRβ: S. japonium TR beta, SmTRα: blood fluke S. mansoni TR alpha, SmTRβ: S. mansoni TR beta, SpTR: sea urchin Strongylocentrotu purpuratus TR. The accession numbers of the aligned human nuclear receptors can be found in Additional files 1 and 2.