In the BLAST comparisons presented here each protein in the Chlamydia trachomatis proteome is used as a query against the entire Treponema pallidum proteome and vice versa. For each protein the best match to a protein in the other proteome is recorded. "Best match" depends on the E-value, which is a measure of the probablility that the observed level of similarity between two compared proteins could be due to chance alone. Thus, an E-value approaching 0 means there is "zero probability" the protein's goodness-of-match to another protein can be attributed to chance. Examples of matches with excellent and marginal E-values are here.
W-H Li in his book Molecular Evolution (Sinauer Associates, Inc. Sunderland, Massachusetts) gives a succinct definition of orthologous and paralogous genes: "Two genes are said to be paralogous if they are derived from a duplication event, but orthologous if they are derived from a speciation event." Further details here.
We have produced a map of orthologous proteins in the C. trachomatis and T. pallidum proteomes. Comparisons showing orthologous regions contain depictions of groups of orthologous pairs that appear to have been conserved together. This comparison helps to resolve what structural changes have occurred in one genome relative to the other. In addition, this analysis reveals how similar the two genomes appear to be overall.