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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

From: Staphylococci phages display vast genomic diversity and evolutionary relationships

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)
  1. a An alternative integrase nomenclature system is provided as in Goerke et al. 2009 (29)
  2. 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
  3. 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
  4. 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