Table 5. Genome regions showing frameshifts and/or major sequence changesa (MSC) of T. p. pallidum (SS14, DAL-1 and Mexico A), T. p. pertenue strains (Samoa D, CDC-2 and Gauthier), and the Fribourg-Blanc isolate when compared to the reference Nichols genome.
| Gene | Strain | Detected frameshift or MSC (position according to the Nichols genome [25]) | Protein change | Characterization of hypothetical protein/predicted cellular localizationb | GenBank accession no. |
| TP0126c | DAL-1 | 1 nt deletion resulting in frameshift mutation (148340) | truncated hypothetical protein TP0126 (from 291 to 227 aa) | signal sequence present, bacterial inner membrane or periplasmic space (DAL-1, Mexico A, Gauthier, CDC-2, Fribourg-Blanc), bacterial cytoplasm (Nichols, Samoa D) | HM585255 DAL-1 |
| Mexico A | HM585256 Mexico A | ||||
| Gauthier | HM585245 Gauthier | ||||
| CDC-2 | HM585244 CDC-2 | ||||
| Fribourg-Blanc | HM585258 Fribourg-Blanc | ||||
| TP0127 c | Mexico A | 1 nt deletion resulting in frameshift mutation (148945) | truncated hypothetical protein TP0127 (from 229 aa to 222 aa) | DUF2715 domain, bacterial inner membrane (Mexico A) | HM585256 Mexico A |
| DAL-1 | 2 nt deletion resulting in frameshift mutation (148944–148945) | truncated hypothetical protein TP0127 (from 229 aa to 126 aa) | HM585255 DAL-1 | ||
| SS14 | - | ||||
| Samoa D | HM151364 Samoa D | ||||
| Gauthier | HM585245 Gauthier | ||||
| CDC-2 | HM585244 CDC-2 | ||||
| Fribourg-Blanc | HM585258 Fribourg-Blanc | ||||
| TP0129 | Samoa D | 2 nt substitution (149875–149876) | premature stop codon resulting in 26-aa deletion at C-terminus of hypothetical protein TP0129 (from 158 to 132 aa) | bacterial cytoplasm | HM151364 Samoa D |
| Gauthier | HM585245 Gauthier | ||||
| CDC-2 | HM585244 CDC-2 | ||||
| Fribourg-Blanc | HM585258 Fribourg-Blanc | ||||
| TP0131 | Mexico A | MSC and small indels (151122–152890) | truncated TprD (TP0131) protein (from 598 aa to 596 aa) | HM585256 Mexico A | |
| Samoa D | HM151364 Samoa D | ||||
| CDC-2 | HM585244 CDC-2 | ||||
| Fribourg-Blanc | HM585258 Fribourg-Blanc | ||||
| TP0136 | DAL-1 | frameshift mutation (see Table 4) MSC and small indels (156887–158256) | truncated fibronectin binding protein TP0136 (from 495 aa to 452 aa) | HM585255 DAL-1 | |
| SS14 | (from 495 aa to 492 aa) | - | |||
| Mexico A | (from 495 aa to 492 aa) | HM585257 Mexico A | |||
| Samoa D | (from 495 aa to 470 aa) | HM151364 Samoa D | |||
| Gauthier | (from 495 aa to 470 aa) | HM585245 Gauthier | |||
| CDC-2 | (from 495 aa to 481 aa) | HM585244 CDC-2 | |||
| Fribourg-Blanc | (from 495 aa to 481 aa) | HM585258 Fribourg-Blanc | |||
| TP0315 | Samoa D | 1 nt deletion resulting in frameshift mutation, MSC (330506) | elongation of conserved hypothetical protein TP0315 at C-terminus (from 215 aa to 270 aa) | DUF2715 domain, bacterial inner membrane (T. p. pallidum strains), bacterial outer membrane or periplasmic space (T. p. pertenue strains) | HM585230 Samoa D |
| Gauthier | HM585231 Gauthier | ||||
| CDC-2 | HM585232 CDC-2 | ||||
| Fribourg-Blanc | HM585258 Fribourg-Blanc | ||||
| TP0548 | SS14 | MSC and small indels (591822–592917) | elongation of treponemal conserved hypothetical protein TP0548 (from 434 aa to 438 aa) | bacterial inner membrane | - |
| Mexico A | (from 434 aa to 438 aa) | HM585228 Mexico A | |||
| Samoa D | shortening of treponemal conserved hypothetical protein TP0548 (from 434 aa to 432 aa) | HM245777 Samoa D | |||
| Gauthier | (from 434 aa to 432 aa) | HM243496 Gauthier | |||
| CDC-2 | (from 434 aa to 432 aa) | HM243495 CDC-2 | |||
| Fribourg-Blanc | (from 434 aa to 418 aa) | HM585227 Fribourg-Blanc |
a
Major sequence changes were defined as continuous amino acid replacements comprising 10 or more residues or 15 and more dispersed amino acid replacements.
b
The following algorithms were used for identification of sequence motifs and for prediction of cellular organization: SignalP, LipoP, CDD, Pfam, PSORT, and InterProScan.
c
The reference Nichols strain was not resequenced in this region.