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. 2012 Aug;194(16):4208–4225. doi: 10.1128/JB.00863-12

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.