Multiple sequence alignment of (a) transmembrane-containing segments in cystinosin (CTNS) homologs, (b) LITAF (lipopolysaccharide-induced tumor necrosis factor α factor) homologs, and (c) Myb-like repeats in timeless (TIM) homologs aligned against Xenopus laevis (Xl) B-Myb (GeneInfo: 6226654), presented using CHROMA (Goodstadt and Ponting 2001). (a) CTNS-like repeats are shown in pairs in the following order (amino acid numbers and GeneInfo codes): Homo sapiensCTNS (140–171 and 279–310: 4826682); H. sapiens SL15 (56–87 and 167–198: 4759110); Arabidopsis thaliana SL15 (44–75 and 156–187: 8885552); Saccharomyces cerevisiae Endoplasmic reticulum defect suppressor 1 (ERS1p), (18–49 and 168–199: 6319919);Drosophila melanogaster CG17119 (145–176 and 284–315: 7300949); and, D. melanogaster CG3792 (SL15) (51–82 and 162–193: 10728573). Missense mutations in cystinosin (Attard et al. 1999) are shown in red and are underlined. A YFPQA pentapeptide in cystinosin that when mutated resulted in protein targeting abnormalities (Cherqui et al. 2001), has been underlined. (b) Hydrophobic residues that are likely to insert into membranes are relatively ill-conserved and have been replaced in the alignment by their respective numbers. GeneInfo codes and amino acid limits are given following the alignment. (c) The following sequences are shown: D. melanogaster TIM (913–971: 6175063) 913–971;Rattus norvegicus TIM (816–873 and 883–937: 7514104) ;D. melanogaster TIM2 (824–883 and 896–950: 8133124);Caenorhabditis elegans Y75B8A.22 (970–1029, 1038–1099, and 1106–1168: 7510480); and, A. thaliana TIM (847–903 and 928–984: 10177105). The secondary structures known from the B-Myb crystal structure (PDB code 1MSE) are shown beneath the alignment together with the predicted (Rost and Sander 1993) secondary structures of the TIM repeats at expected accuracies of >82% (H) or >72% (h); H/h, helical structure. Species abbreviations used: At, A. thaliana; Ce, C. elegans; Dm, D. melanogaster; Hs, H. sapiens; Mm, Mus musculus; Pf, Plasmodium falciparum; Rn, R. norvegicus; and Sc, S. cerevisiae. (Figure continues on next page.)
