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

Figure 2

Comparison of trees and networks: amine-binding GPCRs.

A. Neighbor-Joining tree describing the interrelationships of 42 amine-binding human GPCR domains. Sequences are labeled according to the common name for their class (e.g., the sequence labeled α1D is adrenoceptor α1D; see additional data file 5 for all sequence database identifiers). B. Sequence similarity network including the same 42 sequences as in (A). This network was thresholded at a BLAST E-value of 1×10−33: only edges associated with E-values more significant than 1×10−33 are included in the network. This network contains 324 edges; the worst edges displayed correspond to a median of 30% identity over an alignment length of 280 amino acids. See Table I for a quantitative comparison of the two representations. The sequences labeled (a) and (b) are discussed in the text.

Figure 2

doi: https://doi.org/10.1371/journal.pone.0004345.g002