Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems.

ABSTRACT: From the analysis of 251 prokaryotic genomes stored in public databases, the 761,260 deduced proteins were used to reconstruct a complete set of bacterial proteic families. Using the new Overlap algorithm, we have partitioned the Protein Homology Network (PHN), where the proteins are the nodes and the links represent homology relationships. The algorithm identifies the densely connected regions of the PHN that define the families of homologous proteins, here called PHN-Families, recognizing the phylogenetic relationships embedded in the network. By direct comparison with a manually curated dataset, we assessed that this classification algorithm generates data of quality similar to a human expert. Then, we explored the network to identify families involved in the assembly of Type III and Ty

SUBMITTER: Medini D 

PROVIDER: S-EPMC1676029 | biostudies-literature | 2006 Dec

REPOSITORIES: biostudies-literature