Table 2. Genome regions showing variability in most of investigated strains of T. p. pallidum (Nichols, SS14, DAL-1 and Mexico A), T. p. pertenue strains (Samoa D, CDC-2 and Gauthier), and in the Fribourg-Blanc isolate.
| TPI interval/affected IGR or gene(s)/(coordinates following the Nichols genome [25]) | Strain(s) | Detected indel | Total no. of repetitions | Putative gene function or sequence similarity | Characterization of hypothetical protein/predicted cellular localizationa | GenBank accession no. | |
| TPI12A IGR TP0126–TP0127 (148526–148527) | Nicholsb, DAL-1, | insertion (1204 bp) | tprK-like sequence in tprD 3′ flanking region | HM585242, HM585259 Nichols HM585255 DAL-1 | |||
| SS14, Mexico A | insertion (1255 bp) | HM585243 SS14 HM585256, HM585257 Mexico A | |||||
| Samoa D, Gauthier, CDC-2, Fribourg-Blanc | insertion (1269 bp) | HM151364 Samoa D HM585245 Gauthier HM585244 CDC-2 HM585258 Fribourg-Blanc | |||||
| TPI32B TP0433–TP0434 (461079–461499) | Nichols | insertion/deletion of repetitive sequences (60 bp per repetition) | insertion of 7 repetitions | 14c | fusion of TP0433 and TP0434 to arp gene | - | |
| DAL-1 | insertion of 7 repetitions | 14 | HM585240 DAL-1 | ||||
| Mexico A | insertion of 9 repetitions | 16 | HM585249 Mexico A | ||||
| SS14 | insertion of 7 repetitions | 14 | - | ||||
| Samoa D | insertion of 5 repetitions | 12 | HM585237 Samoa D | ||||
| Gauthier | insertion of 3 repetitions | 10 | HM585239 Gauthier | ||||
| CDC-2 | deletion of 3 repetitions | 4 | HM585238 CDC-2 | ||||
| Fribourg-BlancΔ | insertion of 8 repetition | 15 | - | ||||
| TPI34aa TP0470 (497265–497688) | Nichols | insertion/deletion of repetitive sequences (24 bp per repetition) | - | 17d | gene encoding conserved hypothetical protein | signal sequence, bacterial inner membrane | - |
| DAL-1Δ | insertion of 10 repetitions | 27 | - | ||||
| Mexico AΔ | insertion of 9 repetitions | 26 | - | ||||
| SS14 | deletion of 7 repetitions | 10 | - | ||||
| Samoa D | deletion of 5 repetitions | 12 | HM585241 Samoa D | ||||
| GauthierΔ | insertion of 8 repetitions | 25 | - | ||||
| CDC-2Δ | insertion of 20 repetitions | 37 | - | ||||
| Fribourg-BlancΔ | insertion of 5 repetitions | 22 | - | ||||
| TPI71A-C TP0967 (1050281–1050282) | Mexico A, SS14 | insertion (9 bp) | gene encoding hypothetical protein | bacterial cytoplasm | HM151373 Mexico A | ||
| Samoa D | deletion (6 bp) | HM151370 Samoa D | |||||
| Gauthier, CDC-2, Fribourg-Blanc | insertion (12 bp) | HM151371 Gauthier HM151372 CDC-2 HM585251 Fribourg-Blanc |
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 Nichols genome, insertion of 1204 bp exists only in its subpopulation [22].
c
In the published Nichols genome sequence [25], only 7 tandem repetitions have been described in this region probably as a result of incorrect automated computer assembly. The correct number of repetitions in the Nichols strain is 14.
d
In this region, the T. p. pallidum strains contain additional incomplete repetition (16 bp in length), T. p. pertenue strains have the same incomplete repetition of 18 bp length.
Δ
The number of repetitions was estimated from PCR products visualized on agarose gels.