Table 5.
Sequence of all donor sites for tprK variable regions in treponemal species and subspecies studied here
| Region and site | Sequence | Strain(s)d |
|---|---|---|
| V1 DSs | ||
| DS7 | GGGCATTGCATCTGAAACTGGTGGCGCCGGAGCCCTCA | All strains |
| DS15 | GGGGGCATTGCATCCGTGGTGGCGCCATCAAGCA | Nichols Gen, UW104, UW126, Street14, Sea81-4 |
| GGGGCATTGCATCCGTGGTGGCGCCATCAAGCA | Nichols Sea, Chicago, Dal-1 | |
| GGGGGCATTGCATCCGATGGTGGCACCATCAAGCA | Cuniculi A, Gauthier, Iraq B, CDC2, Samoa D, Fribourg-Blanc | |
| DS20 | GGGGCTTGCATCTGAAAAAAATGGTGGCGCCCAACCCCTCAAGCAc | Nichols Sea, Chicago, Dal-1 |
| GGGGCATTGCATCTGAAAAAAATGGTGGCGCCCAACCCCTCAAGCAc | Gauthier, Iraq B, Samoa D, Fribourg-Blanc, Sea81-4, CDC2, UW104, UW126, Street14, Nichols Gen | |
| DS29 | CTGGGGCATTGCATATGAAAATGGTGGCGCCCAACCCCTCAAGCAb,c | All strains |
| DS37 | GGGGCATTGCATCCGAAGATGGTAGCGCCGGAAACCTCAAGCATGGAb | All strains |
| GGGCATTGCATCCGAAGATGGTAGCGCCGGAAACCTCAAGCATGGAb | Cuniculi A | |
| V2 DSs | ||
| DS8 | ACCGACTGGGAGGGCAAAGACAGTCAGGGCAAGGCCCCAGCAGGAACTTCCAGCAC | Cuniculi A |
| ACCGACTGGGAGGGCAAAGACAATCAGGGCAAGGCCCCAGCAGGAACTCCCAGCAC | Iraq B | |
| ACCGACTGGGAGGGCAAAGACAGTCAGGGCAAGGCCCCAGCAGGAACTCCCAGCACGTA | All others | |
| DS16 | ACTGGGAGGGCAAAGACAGCAAGGGCGTCGCCCAAGCAGGAGCAAACCACAGCA | Gauthier, CDC2 |
| ACTGGGAGGGCAAAGACAGCAAGGGCGTCGTCCAAGCAGGAGCAAACCACAGCA | All others | |
| DS21 | CTAACACCGACTGGGAGGGCAAACCAAACGGCAACGTCCCAGCAGGAGTAACCCCCAGCAc | All strains |
| DS30 | ACACCGACTGGGAGGGCAAGTCAAACACGGGCGCCCCAGCAGCAGGb,c | All strains |
| DS38 | GGGAGGGCAAGTCAAACACGGGCGCCGCCCGAGCAGGAAGAAACCACCGCb | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc |
| GGGAGGGCAAGTCAAACACGGGCGCCGCCCGAGCAGGAAGAAACCACAGCb | All others | |
| DS45 | ACATCAACTTCCCGGTGTATGGGGGTGTCTTGCACGCATCGCAGGCTb | All strains |
| V3 DSs | ||
| DS3.1a | TACAATTCCACGCTTTCTGGCGACTATGCCCTACCCCGAGCCCCAGCCCCAATCCTA | Cuniculi A |
| DS3 | TAGCGGCTATGCCGCAGCCCCAGCCATCAACTTCCCGGT | Cuniculi A |
| TAGCAGCTATGCCACAGCCCGAGCCGGAGCCGACATCAACTTCCCGGT | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc | |
| TAGCGGCTATGCCACAGCCCGAGCCGGAGCCGACATCAACTTCCCGGT | All others | |
| DS10 | CCCGAGCCCTACCCGCAGCCGCAGCCGCAGTCAACAACGACATCTTAT | Cuniculi A |
| CCCGAGCCCTACCCGCAGCCGCAGCCGCAGCCGCAGTCAACAACGACATCTTAT | All others | |
| DS12 | CCCCAAGCCCAAGCCGCAGCCAACATCAACTTCCCGGTATGGA | Cuniculi A |
| CCCCAAGCCCCAGCCGCAGCCAACATCAACTTCCCGGTATGGA | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc | |
| CCCCAAGCCCCAGCCGCAGCCAACATCAACTTCCCGGTATGGG | All others | |
| DS18 | GCCCGAGCCGCAGCCCCAGCCGGAGCCAACGACATCTCAT | Cuniculi A |
| GCCCGAGCCCGAGCCGGAGCCGCAGTGCCAGCCGCAGCCGACGACATCTTAT | All others | |
| DS24 | AACTCCACACTGTCTAGCGGCTATGCCCAAGCAGCCGGAGCCGCAGCCCAc | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc, Sea81-4 |
| AACTCCACACTGTCTAGCGGCTATGCCCAAGCAGCCGGAGCCGCAGCCGGAGTCCCAGCCCTACCCGGAGCCGCAGCCCAc | All others | |
| DS26 | AGCCCCAGCCCCAGCCCCAGCCCCAGCCAACAACGCCATCTTATGGGA | Nichols Gen, Nichols Sea, Chicago, Dal-1 |
| AGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCAACAACGCCATCTTATGGGA | Sea81-4 | |
| GCCCTGGCCCGAGCCCGACCCCCAGCCCCAGCCAACAACGCCATCTTATGGGA | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc, UW104, UW126 | |
| AGCCCTGGCCGGAGCCCTACCCCGAGCCCCAGACATCTTATGGGA | Cuniculi A | |
| DS32 | CCCCAGCCCAACCCCCAGCCAACATCTTATGGGb,c | All strains |
| DS34 | GCCCAAGCCCGAGCCCTGGCAGCCGGb,c | All strains |
| DS41 | GCCCTACCCCCAGCCGCAGCCCCAGCCAATGACATCTTATGGGb | Cuniculi A |
| GCCCAACCCCCAGCCGTAGCCCCAGCCAATGACATCTTATGGGAb | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc | |
| GCCCAACTCCCAGCCGTAGCCCCAGCCAATGACATCTTATGGGAb | All others | |
| DS43 | TCCACGCTTTCTGGCGACTATGCCCGACCCGGAGCCGCAGCCGb | Cuniculi A |
| TCCACACTTTCTGGCGACTATGCCCGAGCCGCAGCCGCAGCCGb | Sea81-4 | |
| TCCACGCTTTCTGGCGACTATGCCCGAGCCGCAGCCGCAGCCGb | All others | |
| DS55e | TGCTGCTCCTACGAAGTGGAAGGCAGGATATTGTGGGTAT | Nichols Sea, Dal-1 |
| V4 DSs | ||
| DS6 | TGGGGCATAAGAAAAACGGAGCGAATGGCGACATAGGCGCAGA | All strains |
| DS14 | CGTGGGGCGTAAGAAAGACGGAGCGCAGGGCAATGGCGTAGGCGC | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc |
| CGTGGGGCGTAAGAAAGACGGAGCGCAGGGCACCGTAGGCGC | All others | |
| DS36 | CAGACGTGGGGCATAAGAAAGAGAATGCAGCGAACGTCAATGGCACCGTb | All strains |
| DS36.1 | CAGACGTGGGGCATAAGAGAAACGTCCGAGCCCAAGCCCAAGCCGCAGATGCGTT | Cuniculi A |
| DS47 | CGTGGGGCATAAGAAAAACGCAGCTCCCGATGGCATAGGCGCCTCACGCGCb | All strains |
| V5 DSs | ||
| DS3.2a | TTCCCGGTGTGGGACGTCCGCCCGCATCGAAGGCCAGCAATGTGTTTAAAGATGTCTTTCTCACCGATACCACACCCATGCGGACGCACGACGGTGCAG | Cuniculi A |
| DS5 | CGCATCGAAGGCCAGCAATGTGTTTATAGACGTCTTTCTCACCAATGCCATGGACATGCAG ACGCACGACTG | Cuniculi A |
| CGCATCGGAGGCCAGCAATGTGTTTAAAGACGTCTTTCTCACCAATGCCATGGACATGCAG ACGCACGACTG | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc | |
| CGCATCGAAGGCCAGCAATGTGTTTAAAGACGTCTTTCTCACCAATGCCATGGACATGCAG ACGCACGACTG | All others | |
| DS13 | CGCAGGCCAGCAATGTATTTCAGGGAGTATTTCTCAACATGGCCATGACCGCACACGACTG | All strains |
| DS13.1 | TATTTCGCATCGAAGGCCAGCAATGTGTTTAAAGATGTCTTTCTCGCTAGAAACATGGACAT GCAGACGCACGACTGTGCTACTTATATCAA | Cuniculi A |
| DS28 | AGCAATGTATTTCAGGGTGTCTTTCTCACCACACCCATGCAGAAGGACGACTGb | All strains |
| DS35 | TATTCGGGGGAGTATTTCTCACCAATAACATGCTGCAGCACGACTGb | All strains |
| DS46 | AGCAATGTATTCGAGGGAGTATTTCTCACCACACCCATGCGGACGCACGACATb | Cuniculi A |
| AGTAATGTATTTCAGGGTGTCTTTCTCACCGATACCACACCCATGCGGACGCACGACATb | All others | |
| DS48 | CGCATCGAAGGCCAGCAATGTATTTCAGGGTGTCTTTCTCGCTCGAAACATAGCCATGCG AGAGCACGACTGb,c | Samoa D |
| CGCATCGAAGGCCAGCAATGTATTTCAGGGTGTCTTTCTCGCTAGAAACATAGCCATGCGA GAGCACGACTGb,c | Gauthier, Iraq B, CDC2, Fribourg-Blanc | |
| CGCATCGAAGGCCAGCAATGTATTCGAGGGAGTATTTCTCGCTAGAAACATAGCCATGCGA GAGCACGACTGb,c | All others | |
| V6 DSs | ||
| DS1a | AAGCCCTACCCCCAGCCATTTACTTCCC | All strains |
| DS4 | CCCCAGCCATCAACTTCCCGGTGT | Cuniculi A |
| AGCCCGAGCCGGAGCCGACATCAACTTCCCGGTGT | All others | |
| DS11f | CGTACATGCCCGTCCACTACAAGGTCCTGACCGGACCCCAAGCCCAAGCCGCAGc | Cuniculi A |
| CGTACATGCCCGTCCACTACACGGTCCTGACCGGACCCCAAGCCCCAGCCGCAGc | All strains | |
| DS19f | CGTACATGCCTGTCCATTACAAAGTCCTAAAAGCCCACGCCCGAGCCCCAGCCGACATCCA CTTCCCGGTGTc | All strains |
| DS23f | GCCCGAGCCGTACCCCCAGCCCGAGTTGACATCTACTTCTCGGc | All strains |
| DS25f | CGTACGTACATGCCCGTCCATTGGAAAGCCCCAGCCCCAGCCCCAGCCCCAGCCAACAACGC CATCTTATGGGA | Nichols Gen, Nichols Sea, Chicago, Dal-1 |
| CGTACGTACATGCCCGTCCATTGGAAAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCAACAACGCCATCTTATGGGA | Sea81-4 | |
| CGTACGTACATGCCCGTCCATTGGAAAGCCCTGGCCCGAGCCCGACCCCCAGCCCCAGCCAACAACGCCATCTTATGGGA | Gauthier, Iraq B, Samoa D, CDC2, Street14, Fribourg-Blanc | |
| TGTACATGCCCGTCCATTGGAAAGCCCTGGCCGGAGCCCTACCCCGAGCC | Cuniculi A | |
| DS33 | TGCCCGTCCACGCCCAAGCCCGAGCCCTGGCAGCCGGAGTCCCACCCGGAGCCCCTG ATAb,c | All strains |
| DS40f | GAGAACGGCATGCCCGTCCATTGGAACGTCAGCGTACAGTCCCACGCCCGAGCCCTACCCCCAGCCGCAGCCCCAGCCAATGACATCb | Cuniculi A |
| CATGCCCGTCTATTACTTCGCAGCCCGAGCCCAACCCCCAGCCGTAGCCCCAGCCAATGACATCTb | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc | |
| CATGCCCGTCTATTACTTCGCAGCCCGAGCCCAACTCCCAGCCGTAGCCCCAGCCAATGACATCTb | All others | |
| DS42f | CGTACATGCCCGTCCATTGGAACGCCTTCACCCAAGCCCGAGCCCTGCCCGGAGCCCCAGTCCCAGCCATTTACTTCCCGGTb | Cuniculi A |
| CGTACATGCCCGTCCATTGGAACGCCTTCACCCAAGCCCGAGCCCTGCCCGGAGCCCCAGTCCCAGCCATCTACTTCCCGGTb | All others | |
| DS44f | GCCCGAGCCGCAGCCGCAGCCGGGGCTGGAGTCGACATCAACTTCCCGGTGTATGGb,c | All strains |
| DS50 | AAAACCCGAGCCCTACCCGCAGCCGCAGCCGCAGCCGCAGTCAACAACGACATCTc | All strains |
| DS51 | AACTCCACACTGTCTAGCGGCTATGCCCAAGCAGCCGGAGCCGCAGCCCAc | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc |
| AACTCCACACTGTCTAGCGGCTATGCCCAAGCAGCCGGAGCCGCAGCCGGAGTCCCAGCCCTACCCGGAGCCGCAGCCCAc | All others | |
| DS52 | CCCGAGCCCTACCCGCAGCCGCAGCCGCAGCCGCAGTCAACAACGACATCTTATc | All strains |
| DS53 | AAGCCCTACCCCCAGCCATTTACTTCCC | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc |
| V7 DSs | ||
| DS2a | CCCCCTGCTGCTCCTGGTACGAAGTGGAGCAAGGAATATTGTGGGTATTACG | Gauthier |
| CCCCCTGCTGCTCCTGCTACGAAGTGGAGCAAGGAATATTGTGGGTATTACG | All others | |
| DS2.1a | CCCGGTTGTAG | Cuniculi A |
| DS2.2a | GACGTGGAGCAAGGAATATTGTGGGTATTACGA | Cuniculi A |
| DS9 | GTACGGCGGTACGAACAAAAAGGCCACGCCCCCTGCTGCTCCTGCTGTTCCTACGAAGTGGAAGGCAGAATATTG | Cuniculi A |
| GTACGGCGGTACGAACAAAAAGGCCACGCCCCCTGCTGCTCCTGCTGCTCCTACGAAGTGGAAGGCAGAATATTG | All strains | |
| DS17 | GTACAGGCGGTACGAACAAAAAAGCTGCTGCTGCAGCCCCTGCTCCTGGTACGAAGTGGAGCA | Cuniculi A |
| GTACGGCGGTACGAACAAAAAAGCTGCTGCTGCAGCCCCTGCTCCTGGTACGAAGTGGAGCA | All strains | |
| DS22 | GTACGGCGGTACGAACAAGCAAGCTGCTGCGGTCTGCTCTTACGAAGc | All strains |
| DS27 | CCCCTGCTGCTGCAGTTCCTGGTACGAAGTc | All strains |
| DS31 | GCGGTACGAACAAGAAAAACGATGCTGCTCCTGGTGCAGTTCCTGGGGCGGTCCCTGGTGCAGTTCCTGGTGCTGCTGCTCTTACGAAGTGGAAGGCAGGATATTGTGGGTATb,c | UW126, Street14 |
| GCGGTACGAACAAGAAAAACGATGCTGCTCCTGGTGCGGTTCCTGGGGCGGTCCCTGGTGCAGTTCCTGGTGCTGCTGCTCTTACGAAGTGGAAGGCAGGATATTGTGGGTATb,c | UW104 | |
| GCGGTACGAACAAGAAAAACGATGCTGCTCCTACGAAGTGGAAGGCAGGATATTGTGG GTATc | All others | |
| DS39 | TGCTCCTGCTCTTACGAAGTGGAGCAAAGGATATTGTGGGTATTACGc | Cuniculi A |
| TGCTCCTGGTACGAAGTGGAGCAAGGGATATTGTGGGTATTACGc | Fribourg-Blanc | |
| TGCTCCTGGTACGAAGTGGAGCAAGGAATATTGTGGGTATTACGc | Gauthier, Iraq B, Samoa D, CDC2 | |
| TGCTCCTGCTACGAAGTGGAAGGCAGAATATTGTGGGTATTACGc | All others | |
| DS49 | GTACGGCGGTACGAACAAGCAAGCTGCTGCGGTc | All strains |
| DS54 | CCCCCTGCTGCTCCTGGTACGAAGTGGAGCAAGGAATATTGTGGGTATTACGA | Gauthier, Iraq B, Samoa D, CDC2, Fribourg-Blanc |
| DS56e | CCCCCAGCCCAACCCCCAGCCAA | Nichols Sea, Dal-1 |
a
DSs located in the TP0131 (tprD) 5′-flanking region.
b
DSs absent in the original T. pallidum subsp. pallidum Nichols strain genome sequence (19).
c
DSs absent in T. paraluiscuniculi (Cuniculi A strain).
d
Nichols Gen, published Nichols strain sequence (19); Nichols Sea, Nichols strain propagated in our laboratory.
e
These DSs are located in the Tp0136 insertion.
f
These DSs are also used to generate variability in V3.