Fig. 3. Sequence comparison of NIMU and its higher eukaryotic homologues with the telomere end-binding protein (TEBP) subunits and ß of ciliated protozoa. Multiple sequences alignments were obtained using the 3D-PSSM program [(Kelley et al., 2000) online at http://www.sbg.bio.ic.ac.uk/servers/3dpssm/] where amino acids are placed into the following conserved groups based on secondary structure predictions: LIVM, PSTAG, QNEHDRK, CW, FY, followed by minor manual adjustment. The mammalian and plant sequences were manually aligned to the TEBPß. TEBPa, telomere end binding protein subunit; TEBPb, telomere end binding protein ß subunit. The organisms are abbreviated as follows: An, Aspergillus nidulans; At, Arabidopsis thaliana (accession no. NM_120714.1); Hs, Homo sapiens (Baumann and Cech, 2001); Mc, Moneuplotes crassus (Wang et al., 1992); Mf, Macaca fascicularis (accession no. AB066545.1); Mm, Mus musculus (accession no. NM_133931.1); Nc, Neurospora crassa (accession no. CAC28643.1); On, Oxytricha nova (Gray et al., 1991; Hicke et al., 1990); Ot, Oxytricha trifallax (Prescott et al., 1998; DuBois and Prescott, 1997); Sl, Stylonychia lemnae (accession no. AAF87600); Sm, Stylonychia mytilis (Fang and Cech, 1991); Sp, Schizosaccharomyces pombe (Baumann and Cech, 2001). (A) Domain structure of the three most highly conserved regions of homology between the NIMU/Pot1 proteins and the TEBP and ß subunits of protozoa. The positions of oligonucleotide/oligosaccharide-binding (OB) folds of O. nova TEBP and ß are indicated by black lines below the domain structures. Two strong regions of homology (black and cross hatched boxes) were identified between the NIMU/Pot1proteins and the TEBP subunits corresponding to regions overlapping the first two OB folds. A third region of homology (white box) was found between the NIMU/Pot1 proteins and the TEBPß subunits which overlap with the OB fold of TEBPß. (B,C) Multiple sequence alignments of the two subunit domains (black and cross hatched boxes in A). Starting and ending amino acid numbers are shown. Residues conserved in at least four sequences (including both ciliate and non-ciliate sequences) are shown as white letters shaded in black. Residues conserved in at least four of the non-ciliate sequences and representing at least two kingdoms are shown as black letters shaded in grey. (D) Multiple sequence alignment of the ß subunit domain (white box in A). Shading as in C. An asterisk indicates the L536Q mutation in nimU24. Sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession numbers AJ567920 (nimU genomic DNA) and AJ567922 (nimU cDNA).