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. 2008 Sep 12;4(9):e1000174. doi: 10.1371/journal.pcbi.1000174

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Riley et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) PE/PPE operon pairs are identified. (B) Protein sequences of PE/PPE operon pairs are aligned to the known PE/PPE structure [13]. (C) Phylogenetic distance matrices for operon pairs are generated from the multiple alignments. (D) Coevolution of all genomewide PE/PPE pairs is evaluated by comparing distance vectors of length 14, consisting of the sequence distances between each protein and its 14 homologs in the PE or PPE reference matrix. (E) Coevolution correlations are further processed to generate predicted PE/PPE complexes.