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In contrast, the ParC gene gain site originates from a gene duplication from the ancestral GyrA gene.
We estimate the statistical support for a GGGPS gene gain site by considering a hypergeometric distribution model (sampling without replacement), that is, a "Two Urn" model.
Statistical support for the ParC gene gain site, on the left side of the graph, is even stronger than that for the GGGPS site.
Hence, there is even stronger statistical support (PCum < 10−) for the ParC gene gain site being on the left side of the rooted ring than there is for placing the GGGPS gene gain site on the right side of the rooted ring.
Accordingly, there is no statistical support on the left side of the graph in figure 2 A for a GGGPS gene gain site, because the cumulative probability for the two-sided test is PCum < 3.9502 × 10−.
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Second, to complement the result from HDX and gain site-specific information about the dimer interface, we selected amino acids for alanine substitution that are predicted to make significant energetic contributions to SecA dimerization based on alternative dimer interfaces.
The seven remaining rooted trees (not shown) require four gene gain sites and one or more gene loss sites.
This rooted ring most parsimoniously explains the phylogenetic distributions of the GGGPS and ParC genes using four gene gain sites, including the two gene gain sites at the root for HisF and GyrA, and no gene loss sites.
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