TABLE 2.

Predicted levels of nucleotide variability and purifying selective pressure for the candidate genes of class A and three sample genes of class B

Candidate class	ORF locus taga	Predicted product encoded by the locus	Nucleotide variation rateb	dN/dS ratio derived from best-fit model in PAML analysisc	Predicted level of purifying selectiond	Sequence data from the 15 additional Francisella strainse
A	FTL_0039	Hypothetical membrane protein	0.0123	NAf	Weaker	−
A	FTL_0102-FTL0101	Cl−:H+ antiporter	0.0188	0.4920	Weaker	+
A	FTL_0168	Hypothetical membrane protein	0.0044	NA	High	−
A	FTL_0180	Acyltransferase	0.0080	NA	Weaker	−
A	FTL_0391-FTL_0392	Pilus assembly protein pilA	0.0049	0.3095	High	+
A	FTL_0439_ORF1	Hypothetical protein	0.0040	NA	High	−
A	FTL_0439_ORF2	Hypothetical protein	0.0069	0.1037	Weaker	+
A	FTL_0806	Amino acid transporter family protein	0.0056	NA	Weaker	−
A	FTL_1066	Fumaryl acetoacetate hydrolase family protein	0.0027	0.0891	High	+
A	FTL_1141	3-Oxoacyl-(acyl carrier protein) synthase III	0.0039	0.3606	High	+
A	FTL_1246	Conserved hypothetical protein	0.0331	0.6701	Weaker	+
A	FTL_1517	Hypothetical protein	0.0082	NA	Weaker	−
A	FTL_1521	Chitinase family 18 protein	0.0406	NA	Weaker	−
A	FTL_1611	Glycosyltransferase, group 2 family protein	0.0031	0.1242	High	+
A	FTL_1773	Conserved hypothetical protein	0.0040	0.0615	High	+
A	FTL_1860	Phosphoribosylformylglycinamidine synthase	0.0079	0.0810	Weaker	+
B	FTL_0997a	Hypothetical protein	NA	0.0848	Weaker	+
B	FTL_1291-FTL_1292	Conserved hypothetical protein	NA	1.1930	Weaker	+
B	FTL_1697-FTL_1698	Metal ion transporter	NA	0.7753	Weaker	+

^aLocus tags from the published sequence NC_007880; when two ORFs resulted from the mutation, the locus tags for both are cited.

^bBased on the alignments of the ORFs from the five sequenced genomes and/or PAML analysis.

^cResults for all models are available in Table S2 in the supplemental material.

^dInferred from the nucleotide variation rate, relative to the rate values for genes known to be under purifying selection.

^e+, sequences available; −, no sequence available.

^fNA, not available.