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Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

Figure 3

Sequence similarity networks are useful tools for exploration of the kinase superfamily.

Two ways of coloring the same network of 513 human kinase domains are shown. The network is thresholded at a BLAST E-value of 1×10−25. The worst edges displayed correspond to a median of 29% identity over alignments of 260 residues. A. Network colored by kinase class. B. Network colored by the presence of a catalytic Lys in the “VAIK” motif: Each of the 513 sequences was aligned to a sequence model of the kinase domain, and the identity of the residue at the catalytic Lys position is mapped to the network. *Note that MAP2K1 and MAP2K2 registered a Lys to Arg substitution due to a sequence alignment error. The other labeled kinases truly do not contain a homologous catalytic K, but only the WNK kinases have been shown to have kinase activity. See Table II for statistics.

Figure 3