TABLE 3.

Characteristics of T. paraluiscuniculi tpr genes and predicted proteins

T. paraluiscuniculi Tpr	Closest Nichols strain homologe	Primer seta	ORF lengthb (bp)	Predicted size (kDa)	Signal peptidec	Predicted cellular locationd
TprG/I hybrid		tprG (sense), tprF (antisense)
Reading frame A	TprG (amino-terminal region)		777	27.7	U	IM
Reading frame B	Tprl (central and carboxyl-terminal regions)		1,344
Subfamily I
TprC		tprC
Reading frame A	TprD2e		591	21.4	C	P/OM
Reading frame B	TprD2		1,413
TprD		tprD
Reading frame A	TprD2		591	21.4	C	P/OM
Reading frame B	TprD2		1,413
Subfamily II
TprG1		tprE
Reading frame A	TprG		753	27.7	U	IM
Reading frame B		1,752
TprG2		tprJ
Reading frame A	TprG		753	27.7	U	IM
Reading frame B	TprG		1,752
Subfamily III
TprA	TprA	tprA	1,797	65.9	U	IM
TprB	TprB	tprB	1,935	69.5	N	Cy
TprH	TprH	tprH	2,082	76.0	N	Cy
TprKf	TprK	tprK	1,518	57.7	C	P/OMg
TprL	TprL	tprL	1,341	48.8	N	Cy

^aIndicates which tpr gene was targeted for amplification. In the Nichols strain of T. pallidum, each set recognizes the flanking regions of the gene indicated. Reading frames A and B indicate the two ORFs generated by the frameshift. No predictions (size, signal peptide, and cellular localization) are reported for the B ORFs due to the lack of evidence that these regions are actually transcribed or translated.

^bTotal length includes stop codon.

^cSignal peptide predicted by Psort (http://psort.nibb.ac.jp/). U, uncleavable; C, cleavable; N, none.

^dLocation of the predicted protein in the bacterial cell, predicted by Psort. OM, outer membrane; IM, inner membrane; P, periplasmic; Cy, cytoplasmic.

^eThe tprD2 allele is not present in the Nichols strain genome. However, it was reported in several strains of T. pallidum subsp. pallidum (8).

^fThe TprK 1.1 clone was used for this prediction.

^gPrediction made with the translational start site for Nichols TprK (4, 15) at position 26 of the sequence indicated as TprK-N in Fig. 7.