Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies
Figure 6
Domain shuffling in the enoyl-CoA hydratase family.
The displayed networks contain all 410 enoyl-CoA hydratases from the crotonase superfamily network in Fig. 5A. The network is thresholded at a BLAST E-value of 1×10−50; the worst edges displayed correspond to a median of 40% identity over alignments of 260 amino acids. A. Network nodes colored by sequence length and edges colored by alignment length. B. Network nodes colored by species kingdom (Fungi, Metazoa, Viridplantae) or superkingdom (Bacteria, Eukaryota, Archaea). The same archaebacterial bifunctional enzymes are marked with a dashed oval in both A and B. C. Representative domain structures for the three major classes of enoyl-CoA hydratase-containing sequences, with domains defined using PFAM HMMs[36].