Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems
Figure 1
(Top Panel) The four major steps used to define the PHN-Families are shown. The blue-shaded boxes (left and lower right) indicate the automated steps of the algorithm that, starting from a set of protein sequences, lead to the PHN-Families definition: i) generation of the network, ii) partitioning of the network for various cutoff values, iii) selection of the optimal cutoff. Values specific to the system analyzed in this study are shown on a gray background within the three boxes. The tan box (upper right) summarizes the investigation of the network topology. Since the PHN structure does not change upon addition of new sequences, this step does not need to be repeated when the sequence dataset is updated.
(A,B) A graphical visualization ([31], see Protocol S1) of the PHN in proximity to the VirB1 proteins is shown. (A) shows the results before partitioning, and (B) shows the results after partitioning. Different colors indicate different PHN-Families.
doi:10.1371/journal.pcbi. 0020173.g001