Figure 3

Co-occurrence clusters of ubiquitin. General Features: a) the top of the diagram is part of the HMM sequence profile of ubiquitin; b) the color shading blocks with legends immediately below mark the important amino acids and segments forming the important structure and function of the protein; c-d) the APCs discovered are represented by arrays of aligned amino acids; the color shaded columns correspond to the significant residues marked as in b); if the co-occurrences of patterns between APCs are frequent, the co-occurrence APCs are linked by an edge with weight representing co-occurrence score; treating APCs as vertices. A co-occurrence APC cluster is represented by a weighted graph linking co-occurring APC s; the important functional regions of the molecules as listed in Table 2 are highlighted in colored blocks specified by the legend. Specific Features: Note that APC 5 and APC 6 are not linked by co-occurrence since they belong to different taxonomical group and with different amino acids, Asp(D)24 and Glu(E)24, in the same column.