Figure 3

A domain architecture and gene-neighborhood network showing the manifold functional connections of the HEPN domain. The graphs were rendered using the Cytoscape program [73]. The network is an ordered graph with the cyan edges representing the connection between adjacent domains combined in the same polypeptides and the gold edges representing the context in the gene neighborhood. (A) The “force-directed” network was derived using the spring-embedded layout utilizing the Kamada–Kawai algorithm, which works well for graphs with 50–100 nodes [74]. The natural clustering of the functional categories emerging from this algorithm is indicated with labels. (B) The nodes of the network arranged by function. (C) Condensed network, where the domain belonging to a given functional category has been collapsed into that category name. (D) A domain architecture graph of HEPN and the various N-terminal domains which co-occur with other defense-related domains, showing the interchangeability of HEPN and the defense-related domains.