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Figure 1 | BMC Bioinformatics

Figure 1

From: The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold

Figure 1

Multiple sequence alignment of representative proteins containing the PAM domain. Of the original set, only sequences with less than 80% identity to each other are shown. The borders of the domain have been assigned taking into account the results of the sequence alignments from PSI-BLAST [17] and the structural alignments from 3D-Jury [23]. Sequences are grouped by phylogenetic relationships, as explained in the legend to Fig. 2. For each sequence, the species, the domain starting and ending residues and the database accession number are reported. The consensus in 70% of the sequences is below the alignment; h, l, p and + indicate hydrophobic, aliphatic, polar, and positive residues, respectively. Hydrophobic residues are highlighted in blue, aliphatic residues in cyan, polar residues in green, positive residues in red and other conserved residues in yellow. The secondary structure predictions using PHD [24], PsiPred [25] and SAM-T99 [26] are reported. For PHD, the upper cases indicate elements predicted with expected average accuracy >82%, and lower cases those predicted with expected average accuracy <82%. The consensus among the three methods is indicated in red. The secondary structure elements of the Sec17 3D structure (1QQE) [27], taken as a representative of the TPR-like structural superfamily, are shown as red cylinders (α-helices: α5–α13). Abbreviations: Ag; Anopheles gambiae; At: Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cs, Ciona savignyi; Dm, Drosophila melanogaster; Hs, Homo sapiens; Nc, Neurospora crassa; Nt: Nicotiana tabacum; Pf, Plasmodium falciparum; Py, Plasmodium yoelii; Sc, saccharomyces cerevisiae; Sp: Schizosaccharomices pombae; Tb, Trypanosoma brucei, Ec, Encephalitozoon cuniculi, H, helix.

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