Sequence alignment of the ligand binding domain (LBD) of S. mansoni TRα and SmTRβ. Alignment of sequences from Helices (H) 3–12 of the LBD domain of S. mansoni TRs (SmTRα and SmTRβ). Helices described in  are boxed. The autonomous activation domain (AF2-AD) is indicated. Numbers at the end of each line indicate residue positions in the original sequence, amino acids of CiTR 490–587 are not shown in the alignment. CiTR: Ciona intestinalis nuclear receptor 1, hTRa: Human thyroid receptor alpha, hTRb: Human thyroid receptor beta, SmTRa: blood fluke S. mansoni TR alpha, SmTRb: S. mansoni TR beta. The accession numbers of the aligned human nuclear receptors can be found in Additional file 2.