Figure 3

Graph representation of pair-wise sequence similarities for known ubiquitin-like domains plus SD1 and SD2 domains. SD1 and SD2 domains cluster with SUMO proteins. The graph was generated using CLANS [22] and shows all pairwise interactions based on HSP P-values calculated using all-against-all BLASTP. The sequence file used as an input is available on the homepage [11]. Analysis of a more extensive assembly of ubiquitin-fold proteins [45] leads to the same conclusion, but a less well readable graph (not shown). AGP8 – autophagy 8 like proteins, AGP12 – autophagy 12 like proteins, URM1 – ubiquitin related modifier 1, UBP6 - Ubiquitin-specific processing protease 6, RUB1 – Related to ubiquitin 1.