TABLE 3.
Integration sites of phi3 phages and bacteriophage classification
| Isolate no. | Integration site | GenBank accession no.a | attB site (5′– 3′)b | Bacteriophage classificationc |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Phage genome size (bp) | Integrase | Genetic control | Replication module | Transcription module | Morphogenesis subtype | Amidase | Phage type | ||||
| 1439 | hlb | TGTATCCGAATTGG | 42,460 | Sa3 | ant4b | dnaD1a | dut3 | Fa | ami3 | Sa3int-ant4b-dnaD1a-dut3-Fa-ami3 | |
| LA86 | Pyruvate oxidase (SAPIG2589) | AM990992.1f | TGTATCCAAAATGG | 41,927 | Sa3 | ant4a | dnaD1b | dut2 | Fa | ami3 | Sa3int-ant4a-dnaD1b-dut2-Fa-ami3 |
| LA115 | hlb | TGTATCCAAACTGG | 41,335 | Sa3 | ant1a | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant1a-dnaD1b-dut1-Fa-ami3 | |
| LA208 | hlb | TGTATCCAAACTGG | 42,292 | Sa3 | ant4a | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant4a-dnaD1b-dut1-Fa-ami3 | |
| 3949 | Phage StauST398-5 | KC595279.1f | TGTATCCAACCAGG | 44,003 | Sa3 | ant4b | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant4b-dnaD1b-dut1-Fa-ami3 |
| LA232 | hlb | TGTATCCAAACTGG | 43,254 | Sa3 | ant4b | dnaD1b | dut2 | Fa | ami3 | Sa3int-ant4b-dnaD1b-dut2-Fa-ami3 | |
| 4623 | hlb | TGTATCCAAACTGG | 43,456 | Sa3 | ant4b | dnaD1b | dut2 | Fa | ami3 | Sa3int-ant4b-dnaD1b-dut2-Fa-ami3 | |
| LA272 | ilvB (SAPIG2093) | AM990992.1e | TGTATCCAAACTGG | 41,228 | Sa3 | NT | dnaD1b | dut3 | Fa | ami3 | Sa3int-dnaD1b-dut3-Fa-ami3 |
| LA281 | Between SAPIG0723 and SAPIG0724d | AM990992.1e | TGTATCCAAACTGT | 43,946 | Sa3 | ant4a | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant4a-dnaD1b-dut1-Fa-ami3 |
| 5235 | Between SAPIG0723 and SAPIG0724d | AM990992.1e | TGTATCCTTACTGT | 41,849 | Sa3 | NT | dnaC1 | dut1 | Fa | ami3 | Sa3int-dnaC1-dut1-Fa-ami3 |
| LA290 | hlb | TGTATCCGAATTGG | 43,453 | Sa3 | ant4b | dnaD1a | dut3 | Fa | ami3 | Sa3int-ant4b-dnaD1a-dut3-Fa-ami3 | |
| LA293 | hlb | TGTATCCGAATTGG | 43,543 | Sa3 | ant1a | dnaD1b | dut2 | Fa | ami3 | Sa3int-ant1a-dnaD1b-dut2-Fa-ami3 | |
| LA301 | hlb | TGTATCCGAATTGG | 42,458 | Sa3 | ant4b | dnaD1a | dut3 | Fa | ami3 | Sa3int-ant4b-dnaD1a-dut3-Fa-ami3 | |
| 5418 | hlb | TGTATCCGAATTGG | 42,458 | Sa3 | ant4b | dnaD1a | dut3 | Fa | ami3 | Sa3int-ant4b-dnaD1a-dut3-Fa-ami3 | |
| LA305 | hlb | TGTATCCAAACTGG | 40,712 | Sa3 | ant4a | dnaC1 | dut3 | Fa | ami3 | Sa3int-ant4a-dnaC1-dut3-Fa-ami3 | |
| LA309 | hlb | TGTATCCGAATTGG | 43,331 | Sa3 | ant4a | dnaD1a | dut3 | Fa | ami3 | Sa3int-ant4a-dnaD1a-dut3-Fa-ami3 | |
| LA343 | hlb | TGTATCCGAATTGG | 40,746 | Sa3 | ant4b | dnaD1a | dut1 | Fa | ami3 | Sa3int-ant4b-dnaD1a-dut1-Fa-ami3 | |
| LA388 | hlb | TGTATCCGAATTGG | 42,310 | Sa3 | ant1a | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant1a-dnaD1b-dut1-Fa-ami3 | |
| LA415 | hlb | TGTATCCGAATTGG | 41,810 | Sa3 | ant1a | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant1a-dnaD1b-dut1-Fa-ami3 | |
| LA436 | Alanine racemase (SAPIG2238) | AM990992.1e | TGTATCCAATCTGG | 43,263 | Sa3 | ant4a | dnaD1b | dut1 | Fa | ami3 | Sa3int-ant4a-dnaD1b-dut1-Fa-ami3 |
| LA562 | hlb | TGTATCCGAATTGG | 40,747 | Sa3 | ant4b | dnaD1a | dut1 | Fa | ami3 | Sa3int-ant4b-dnaD1a-dut1-Fa-ami3 | |
a
GenBank accession numbers correspond to genes used for alignment in WGS data.
b
Nucleotides differing from the original attB site of phage phi3 are underlined (24).
c
Classification of bacteriophage modules according to Kahánková et al. (41). NT, nontypeable.
d
SAPIG0723 encodes a nucleoside transporter protein; SAPIG0724 is the yxkD gene.
e
S. aureus ST398 (GenBank accession no. NC_017333.1) (20).
f
S. aureus phage StauST398-5pro (GenBank accession no. KC595279.1) (16).