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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