Fig. 4.

Global view of protein space via the motif network. The nodes represent the set of 8,219 identified motifs, colored by the SCOP class of the majority of their domains (see color legend; white represents cases where no SCOP class is the majority); edges connect between motifs that cooccur in a domain. The motif network was constructed using the set of alignments that are longer than 75 residues, with more than 25% sequence similarity, and less than 2.5 Å rmsd (Methods). We see that the alpha/beta (and the all-alpha) motifs are more common, more gregarious, and form the largest connected component.