TABLE 3.
Size, position, and integration sites of all 19 prophages (P) and six prophage-like elements (PLE) within sample 194195.
| Prophage detected by PHASTER | Gene 5’ to prophage | Gene 3’ to prophage | Size (bp) | Position |
| P1 | cpxPb | fieF | 31,356 | 237,188–268,544 |
| P2a | zur | aphA | 19,508 | 433,909–453,417 |
| PLE1 | leuX | Hypotheticalb | 9,862 | 678,235–688,097 |
| PLE2 | intAb | nanM | 33,695 | 688,557–722,252 |
| P3a | tRNA-Thr (cgt) | prgR | 54,474 | 1,128,970–1,183,444 |
| P4 | ybhCb | ybhB | 38,693 | 1,751,265–1,789,958 |
| P5 | yccAb | tRNA-Ser (tga) | 49,561 | 2,021,966–2,071,527 |
| PLE3 | ycdU | tRNA-Ser (gga) | 85,778 | 2,170,090–2,255,868 |
| P6a | potC | potB | 48,949 | 2,342,248–2,391,197 |
| P7 | potA | caeBb | 65,659 | 2,393,794–2,459,453 |
| P8a | ompW | ispE | 79,722 | 2,544,993–2,624,715 |
| P9a | ompW | trpA | 98,899 | 2,675,966–2,774,865 |
| P10a | ttcA | rspR | 101,788 | 2,877,961–2,979,749 |
| P11 | ompN | rspAb | 45,568 | 3,160,400–3,205,968 |
| P12 | yecAb | tRNA-Leu (taa) | 20,043 | 3,542,644–3,562,687 |
| P13 | yodB | tRNA-Ser (cga)b | 43,687 | 3,617,610–3,661,297 |
| PLE4 | cobU | Hypothetical | 13,348 | 3,684,489–3,697,837 |
| P14 (stx2c) | yeeW | sbcBb | 60,586 | 3,698,735–3,759,321 |
| P15a | yehV | mlrAb | 52,982 | 3,900,672–3,953,654 |
| P16 (stx2a) | yfcV | argWb | 74,662 | 4,190,350–4,265,012 |
| P17 | argWb | lacY | 8,233 | 4,265,444–4,273,677 |
| P18 | ssrA | alpAb | 20,904 | 4,549,827–4,570,731 |
| PLE5 | tRNA-Phe (gaa) | pitB | 23,331 | 4,924,934–4,948,265 |
| P19 | yicCb | yicC | 15,440 | 5,631,805–5,647,245 |
| PLE6 (LEE) | selC | yicL | 43,021 | 5,665,860–5,708,881 |
ARefers to prophages that appear to be compound prophages (i.e., two or more prophages that are sequential or one phage integrated inside another, with intact integrase genes). BRefers to the end in which the Integrase gene (intA) is located.