BMC Genomics 2008, 9:308 http://www.biomedcentral.com/1471-2164/9/308 RFeigpurerese1ntative multiple alignment of the RAWUL domain Representative multiple alignment of the RAWUL domain. The coloring scheme indicates average BLOSUM62 score (correlated to amino acid conservation) in each alignment column: red (greater than 1.8), violet (between 1.8 and 1) and light yellow (between 1 and 0.2). Residues that are part of the hydrofobic core of the Ubq fold [50] are indicated by green ovals above the alignment. The limits of the domains are indicated by the residue positions on each side. The main families and sub- families are indicated by coloured bars to the left of the alignment; green (PRC1), violet (WD48-p80), red (Bmi1/Mel18) and yellow (Ring1A/B). Structure based sequence alignment [86] of representative members of UBL superfamily were included: pdb_1gnu: human gamma-aminobutyric acid receptor type A receptor-associated protein (GABARAP) [84]; pdb_1m94: yeast Ubl modifier protein homologous to ubiquitin 1 (Hub1) [87]; pdb_1yqb: human ubiquilin 3 [88]; pdb_1mg8: Ubl domain from mouse Parkin protein [89]; pdb_1aar: bovine Ubiquitin [90]. Independent PHD secondary structure predictions [55] for PRC1 Ring and WDR48-p80 families are shown below the family sequences. Consensus secondary structure of the Ubiquitin super- family is shown below the alignment [54]. Alpha-helices and beta-strands are indicated by green cylinders and arrows, respec- tively. The sequences are named with their Uniprot identifications, and also, if necessary, with their common species name: Human, Homo sapiens; Drome, Drosophila melanogaster; Caeel, Caenorhabditis elegans; Arath, Arabidopsis thaliana; Orysj, Oryza sativa; Crypv, Cryptosporidium parvum; Schja, Schistosoma japonicum; Aspfu, Aspergillus fumigatus; Neucr, Neurospora crassa; Kluma, Kluyveromyces marxianus; Debha, Debaryomyces hansenii; Schpo, Schizosaccharomyces pombe; Yeast, Saccharomyces cerevi- siae. The "est" prefix identifies sequence corrections using consensus sequences manually reconstructed by assembling highly similar expressed sequence tags from identical species (conceptual translations). The numbers in blue within the alignment rep- resent sequence insertions that are not included. suggested to be related to endosome/lysosome traffic [50- 52]. The statistical significance of profile to profile compari- sons was evaluated in terms of an E-value. Significant E- values connected all these sequences and reciprocal searches produced convergent results (Figure 2). The Bmi1/Mel18 subfamily profile search finds the Ring1A/1B subfamily with a 3.2e-11 E-value and the global profile of the PRC1 Ring family (including both Bmi1/Mel18 and Ring1A/1B subfamilies) detected the WDR48-p80 and the Ubl families with E-values of 3.7e-10 and 4.7e-07, respec- tively. The RAWUL HMM profile of the WDR48 family have less capability to detect remote protein homologies and localize the ubiquitin family with poor statistical sig- nificance (with an E value of 0.21), although RAWUL Page 3 of 11 (page number not for citation purposes)