Additional file 2: of KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome

Alignment of IFT25 with permutated KIAA0556 repeat sequences. When aligned using HHpred, a significant part of the Chlamydomonas IFT25 N-terminus was unmatched with human KIAA0556 and significant sequence remained at the C-terminus of the repeats, suggesting a circular permutation relationship between the repeats and IFT25. Shown is a HHpred alignment of IFT25 orthologues with permutated repeat sequences (r1–4) from KIAA0556 orthologues, which results in improved sequence matches. In each permutated repeat sequence, 30–40 amino acids from the beginning of each repeat have been added to the end of the same repeat (denoted by red box) using manual editing. The precise number of amino acids transposed in this way was calculated by iterative comparison. Alignment was edited manually to improve gapped regions and other minor adjustments. Attributes of the amino acids are coloured using ClustalX colour schemes. light blue = hydrophobic; cyan = aromatic; green = polar; red = positive charge; magenta = negative charge; orange = glycine; light green = proline. Positions are only coloured if 25 % or more of the residues share a given property. Secondary structures of IFT25 are shown in the first row; arrows (yellow) denote beta strands; cylinder (blue) denotes helical structure. (JPG 1555 kb