Table 1.
Recombination Events in Treponema pallidum Detected Using PIM with the NIC-Mapped Data Set.
| Gene_Event | Start | End | Size (bp) | SNPs | Origin | Receptor | Function (UniProt) |
|---|---|---|---|---|---|---|---|
| TP0136_1 | 158,092 | 158,104 | 13 | 4 | TPE | SW6 | Adhesin allowing binding to fibronectin |
| TP0136_2 | 158,138 | 158,149 | 12 | 4 | Seattle 81-4 | SW6 | |
| TP0136_3 | 158,149 | 158,167 | 19 | 3 | TPE | Seattle 81-4 | |
| TP0136_4 | 158,271 | 158,336 | 66 | 6 | TPE | Nichols clade | |
| TP0136_5 | 158,346 | 158,364 | 18 | 7 | TEN | Nichols clade | |
| TP0136_6 | 158,915 | 158,976 | 62 | 3 | TPE-TEN | Nichols clade | |
| TP0136_7 | 159,312 | 159,323 | 12 | 5 | TPE-TEN | Nichols clade | |
| TP0164 | 187,064 | 187,177 | 113 | 4 | TPE-TEN | NE20, SEA86 cluster | troB, iron/zinc/manganeseABC superfamily ATP-binding cassette transporter, ABC protein |
| TP0179 | 198,040 | 198,428 | 391 | 9 | TPE-TEN | Nichols clade | Hypothetical protein |
| TP0326 | 347,027 | 347,956 | 929 | 32 | TEN | SS14 clade excluding Mexico A | β-barrel assembly machinery A (BamA) ortholog and rare outer membrane protein |
| TP0462 | 492,772 | 493,605 | 834 | 43 | TPE-TEN | NE20, SEA86 cluster | Hypothetical protein |
| TP0488 | 522,981 | 523,620 | 640 | 41 | TEN | Mexico A | Mcp2, methyl-accepting chemotaxis protein |
| TP0515 | 555,872 | 557,771 | 1,900 | 17 | TPE-TEN | Nichols clade | LptD homolog |
| TP0548 | 593,563 | 594,215 | 653 | 45 | TPE-TEN | Nichols clade | OMP—FadL family |
| TP0558 | 606,171 | 606,591 | 421 | 4 | TPE-TEN | SS14 clade | NiCoT family nickel–cobalt transporter, high affinity |
| TP0865_1 | 945,224 | 945,542 | 319 | 13 | TPE-TEN | NE20, SEA86 cluster | OMP—FadL family |
| TP0865_2 | 945,224 | 945,542 | 319 | 13 | TPE-TEN | Seattle 81-4 | As above |
| TP0865_3 | 945,830 | 946,298 | 469 | 18 | TEN | NE20, SEA86 cluster | As above |
| TP0865_4 | 945,830 | 946,298 | 469 | 18 | TEN | Seattle 81-4 | As above |
| TP0967 | 1,051,257 | 1,052,302 | 1,046 | 15 | TPE-TEN | Seattle 81-4 | TolC-homolog |
| TP0968 | 1,052,414 | 1,053,617 | 1,204 | 22 | TEN | Seattle 81-4 | TolC-homolog |
Note.—For each recombination event (denoted as gene_event), we report the start and end positions of the event (coordinates according to the Nichols strain), its size in base pairs, the number of SNPs detected in the event, the donor (origin) cluster/strain, the recipient (receptor) cluster/strain (supplementary figs. 1–12, Supplementary Material online, for additional details), and the functional significance of the gene according to UniProt.