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.