Figure 1
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 subfamilies 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 superfamily is shown below the alignment [54]. Alpha-helices and beta-strands are indicated by green cylinders and arrows, respectively. 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 cerevisiae. 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 represent sequence insertions that are not included.