BMC Genomics 2008, 9:308 http://www.biomedcentral.com/1471-2164/9/308 FDiegnudrreog3ram and Domain Architecture for RAWUL domain containing proteins Dendrogram and Domain Architecture for RAWUL domain containing proteins. The sequences are named as described in Figure 1. Vitis vinifera (Vitvi) sequences were included to construct the dendrogram. The main families (PRC1 Ring and WDR48-p80) and subfamilies (Bmi1/Mel18 and Ring1A/B) are indicated by coloured dotted lines, as in Figure 1. Only a representative set of sequences was labelled. The scale bar shows the average number of amino acid substitutions per site (0.1). The main bootstrap values for PRC1 Ring family classification are indicated. Schematics of domain architecture are repre- sented with the localization of the RAWUL, Ring domains and WD40 repeats according to this analysis, Pfam [91] and REP web servers [92], respectively. The ubiquitin related proteins fall into two separate classes [62]. Ubq-like proteins (UBLs; eg, SUMO, NEDD8, etc.) that function as modifiers in a manner analogous to that of ubiquitin and exist either in a free form or attached covalently to other proteins by their C-termini, and the ubiquitin-domain proteins (UDPs) that bear domains related to ubiquitin but are otherwise unrelated in sequence to each other (i.e. parkin, Rad23, DSK2). In con- trast to the UBL modifiers, the UDPs are not conjugated to other proteins. RAWUL domain lacks the characteristic C-terminal digly- cine motif required for enzymatic conjugation of the Ubq domain to an acceptor lysine. Neither are conserved the three most common acceptor lysine residues involved in polyubiquitination (Figure 1, represented in ubiquitin Page 5 of 11 (page number not for citation purposes)