TABLE 3.

Predicted candidate T. pallidum rare outer membrane proteins

Protein tag	Name	OM localization/β-barrel predictionsa							Signal sequence predictionsd
		Cello	Psort	TMBETADISC (PSSM profileb)	TMBETADISC (AACc)	Bomp	Hhomp	Predtmbb	Ymaxe (SignalP 3.0)	Sf (PrediSI)	Signal-CFg
Group 1
TP0326	BamA	+	+	+	+	+	+	+	0.831	1	+
TP0865	HPh	+	+	+	+	+	+	+	0.125	0.70	+
Group 2
TP0117	TprC/D	+	−	+	+	+	+	+	0.531	0.65	+
TP0620	TprI	+	−	+	+	+	+	+	0.531	0.65	+
TP0621	TprJ	+	+	+	+	−	+	+	0.691	0.72	+
TP0969	HP	+	+	+	+	−	+	+	0.205	0.37	+
Group 3
TP0316	TprF	+	−	+	+	−	+	+	0.518	0.65	+
TP1031	TprL	+	−	+	−	+	+	+	0.065	0	−
Group 4
TP0009	TprA	+	−	+	+	+	−	−	0.234	0.22	−
TP0011	TprB	+	−	+	−	−	+	+	0.324	0.477	+
TP0155	CHPi	+	+	+	+	−	−	−	0.13	0.7	+
TP0313	TprE	+	−	+	−	−	+	+	0.691	0.72	+
TP0325	CHP	+	−	−	+	+	+	−	0.218	0.47	+
TP0421	CHP	+	+	+	−	−	−	+	0.443	0.75	+
TP0548	HP	+	−	+	−	−	+	+	0.226	0.64	+
TP0729	HP	+	+	+	+	−	−	−	0.27	0.80	+
TP0855	HP	+	+	+	+	−	−	−	0.432	0.54	+
TP0858	HP	+	−	+	−	−	+	+	0.249	1	+
TP0897	TprK	+	−	+	−	−	+	+	0.75	0	−

^aProteins are grouped according to the number of programs that predict OM localization or β-barrel formation.

^bPosition-specific scoring matrix profiles.

^cAmino acid composition.

^dPredicted N-terminal sequences and cleavage sites are shown in Fig. S1 in the supplemental material.

^eYmax is a derivative of the C score combined with the S score, where the C score is the cleavage site score and the S score is the amino acid position score in the signal sequence (10). A Ymax score of >0.4 indicates a cleaved signal sequence.

^fThe score was calculated using the equation (59). A score of >0.5 indicates a cleaved signal sequence.

^gPresence (+) or absence (−) of a cleavable signal sequence.

^hHP, hypothetical protein.

ⁱCHP, conserved hypothetical protein.