Relationship between the E-value threshold and numbers of unique proteins in pairs of isolates. For a given comparison, these graphs denote the number of proteins in the first isolate (e.g. Pseudomonas putida GB-1) that are not found in the second isolate (e.g. Pseudomonas putida KT2440). The relationship between pairs of isolates is: (A) same species; (B) same genus but different species; and (C) different genera. As an E-value threshold of 10-13 was ultimately chosen for our analyses, a vertical line corresponding to this E-value is indicated on each graph.