Table 1.
Staphylococcal cluster B phage integrases. The dataset includes 205 staphylococcal phages, of which 132 belong to the cluster B Siphoviridae. Phams related to integration functions and virulence determinants are represented to phage member, clusters and protein domains
| Pham | Function | Alternative nomenclaturea | Number of members | Domainsb | Conserved, accessory or unique pham |
|---|---|---|---|---|---|
| Integrases | |||||
| 148 | Y-Int | Sa3, Sa9, Sa10, Sa11 | 38 | pfam14659; pfam00589 | Conserved (B9); Accessory (B2, B3, B4, B5, B6, B7, B10); Unique (B8, B12, B14, B15, B16, B17) |
| 280 | Y-Int | Sa1, Sa5 | 27 | pfam14657; pfam14659; pfam00589 | Conserved (B1); Unique (B7); Accessory (B2, B3) |
| 288 | S-Int | Sa7, Se1, Se12 | 25 | pfam00239; pfam07508 | Accessory (B2, B3, B4); Unique (B6, B10, B11, B13) |
| 1656 | Y-Int | – | 1 | pfam14659; pfam00589 | Unique (B8) |
| 1661 | Y-Int | Sa2, Sa6 | 40 | pfam00589 | Accessory (B3, B5, B6, B7) |
| Virulence determinants | |||||
| 297 | virE | 1 | pfam05272 | Unique (B5) | |
| 529 | holin-like | 12 | pfam16935 | Accessory (B6, B7); Unique (B5) | |
| 555 | PVL (lukF-PV) | 26 | pfam07968 | Accessory (B5, B6, B7) | |
| 914 | scn | 17 | pfam11546 | Accessory (B6, B7); Unique (B3) | |
| 1259 | pemK | 10 | pfam02452 | Accessory (B2, B3); Unique (B5) | |
| 1270 | virE | 23 | pfam05272 | Accessory (B5); Unique (B15) | |
| 1322 | holin-like | 1 | pfam16935 | Unique (B6) | |
| 1460 | sak | 16 | pfam02821 | Accessory (B6, B7); Unique (B8) | |
| 1579 | mazF | 8 | pfam02452 | Accessory (B6) | |
| 1597 | hlb | 1 | Pfam03372 | Unique (B7) | |
| 1903 | eta | 5 | pfam13365 | Accessory (B3); Unique (B2) | |
| 1939 | PVL (lukS-PV) | 27 | pfam07968 | Accessory (B5, B6, B7) | |
| 2064 | sea | 7 | pfam01123; pfam02876 | Accessory (B6) | |
| 2122 | chp | 10 | pfam11434 | Accessory (B6, B7) | |
a An alternative integrase nomenclature system is provided as in Goerke et al. 2009 (29)
bPham descriptions: pfam14659: Phage integrase, N-terminal SAM-like domain; pfam00589: Phage integrase family; pfam14657: AP2-like DNA-binding integrase domain; pfam00239: Resolvase, N terminal domain; pfam07508: Recombinase; pfam02899: Phage integrase, N-terminal SAM-like domain; pfam13495: Phage integrase, N-terminal SAM-like domain; pfam01123: Staphylococcal/Streptococcal toxin, OB-fold domain; pfam02876: Staphylococcal/Streptococcal toxin, beta-grasp domain; pfam02821: Staphylokinase/Streptokinase family; pfam11434: Chemotaxis-inhibiting protein CHIPS; pfam11546: Staphylococcal complement inhibitor SCIN; pfam05272: Virulence-associated protein E; pfam16935: Putative Holin-like Toxin (Hol-Tox); pfam07968: Leukocidin /Hemolysin toxin family; pfam02452: PemK-like, MazF-like toxin of type II toxin-antitoxin system; pfam13365: Trypsin-like peptidase domain; pfam03372: Endonuclease/Exonuclease/phosphatase family
Acronyms of integrase and virulence genes: Y-Int and S-Int, integrase of tyrosine or serine type; virE, virulence-associated protein E; PVL, Panton-Valentine leucocidin, that is activated by two polypeptide-enconding genes (lukS-PV, lukF-PV); scn, staphylococcal complement inhibitor; pemK, endoribonuclease toxin PemK; sak, plasminogen activator staphylokinase; mazF, endoribonuclease toxin MazF; hlb, β-hemolysin; eta, exfoliative toxin A; sea, staphylococcal enterotoxin A; chp, chemotaxis inhibitory protein
Note: The holin-toxin gene is different from the holin gene that participates in the lytic cassette. For instance, in phage P954, gp20 is the holin-toxin, gp21 is the holing and gp22 is the endolysin