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. 2010 Dec 29;5(12):e15713. doi: 10.1371/journal.pone.0015713

Table 4. Genome regions with changes specific to individual strains of T. p. pallidum (Nichols, SS14, DAL-1 and Mexico A), of T. p. pertenue strains (Samoa D, CDC-2 and Gauthier), and the Fribourg-Blanc isolate.

TPI interval/affected IGR or gene(s)/(coordinates according to the Nichols genome [25]) Strain(s) Detected indel Putative gene function or sequence similarity Characterization of hypothetical protein/predicted cellular localizationa GenBank accession no.
TPI5B TP0067 (73405–73707) Samoa D deletion (303 bp) gene coding for conserved hypothetical protein TPR domain, bacterial cytoplasm HM151365 Samoa D
TPI13 IGR TP0135–TP0136 (156488–156551) Nicholsb insertion (64 bp) - -
TPI13 TP0136 (157949–158017) DAL-1 insertion (58 bp) resulting in frameshift mutation, 67 nt in this region remained gene coding for fibronectin binding protein [28], (452 aa) HM585255 DAL-1
TPI21A TP0259 (270357–270365) Gauthier deletion (9 bp) gene coding for hypothetical protein LysM domain, bacterial inner membrane HM151366 Gauthier
TPI42A TP0548 (591799–591846) Fribourg-Blanc deletion (48 bp) gene coding for hypothetical protein HM585227 Fribourg-Blanc
TPI49 TP0629 (686998–687299) Gauthier deletion (302 bp) resulting in frameshift mutation gene coding for hypothetical protein (151 aa) bacterial cytoplasm, signal sequence present in Nichols HM151367 Gauthier
TPI55 IGR TP0696–TP0697 (764890–765321) Fribourg-Blanc insertion of repetitive sequence (430 bp) - HM151369 Fribourg-Blanc
TPI65B TP0858 (935500–935578) Gauthier continuous deletion (79 bp) resulting in frameshift mutation and small indels gene coding for hypothetical protein (385 aa) signal sequence, UPF0164 domain, bacterial inner membrane HM151368 Gauthier
a

The following algorithms were used for identification of sequence motifs and for prediction of cellular organization: SignalP, LipoP, CDD, Pfam, PSORT, and InterProScan.

b

In the GenBank-deposited Nichols genome sequence, an insertion of 64 bp is included. All other investigated strains including subpopulation of the Nichols strain, have shorter version of this IGR.