⊟Summary[edit | edit source]
- pan ID?: SAUPAN001246000
- symbol?: int1
- synonym:
- description?: site-specific integrase
- site-specific integrase
- bacteriophage integrase
- phiSLT ORF401-like protein, integrase
- prophage L54a, integrase
- pathogenicity island protein, integrase
- phage integrase
- phage integrase family protein
descriptions from strain specific annotations:
- strand?: +
- coordinates?: 1533433..1602641
- synteny block?: BlockID0007570
- occurrence?: in 24% of 34 strains
int2 (intφSa2) : lipoprotein-converting prophage site-specific integrase Sa2int [1]
This prophage integrase catalyzes insertion of prophages at the consensus attB sequence mawtwwrywyrTCRTCRTwwtrwkat within tandem DUF1672 lipoprotein paralogues typically located between ribU and srrB. Sa2int prophages typically carry the Panton-Valentine leukocidin toxins and can increase the virulence of their host strains. This integrase can also catalyze insertion into degenerate sites resembling the consensus attB sequence within such genes as lacG and sea.
NOTE : automated annotation programs can often misannotate intφSa2 (int2) as intφSa6 (int6) or vice versa (SACOL0318 is int6). intφSa6 is a distinct class of integrase that integrates prophage within gehB, at the consensus attB sequence: gtatctggcaagttaaaccaATYWTACAAGGRTGGGATcatgtcgattttatyggtgt. In addition to more reliable alignment-based methods, an easy way to discriminate between the two is by size - Sa1int is typically 350 AA whereas Sa6int is typically 401 AA.
⊟Orthologs[edit | edit source]
⊟Genome Viewer[edit | edit source]
| COL | |
| NCTC8325 | |
| USA300_FPR3757 |
⊟Alignments[edit | edit source]
- alignment of orthologues: CLUSTAL format alignment by MAFFT L-INS-i (v7.307)
COL MWFEKFKNKNNETKYRYYEKYKDPYTDKWKRVSVVLNKNTKQSQKEAMFRLEEKIKEKLN
NCTC8325 MWIEKFKNKNNETKYRYYEKYKDPYTDKWKRVSVVLNKNTKQSQKEAMFRLEEKIKEKLN
USA300_FPR3757 MWIEKFKNKNNETKYRYYEKYKDPYTDKWKRVSVVLNKNTKQSQKEAMFRLEEKIKEKLN
**:*********************************************************
COL NKSSSELKTLTFHALLDEWLEYHIKTSGFKVTTLDNLKTRIKNIKKNSSQNLLLNKIDTK
NCTC8325 NKSSSELKTLTFHALLDEWLEYHIKTSGSKLTTLNNIKIRIKNIKRYCSENLLLNKLDTK
USA300_FPR3757 NKSSSELKTLTFHALLDEWLEYHIKTSGSKLTTLNNIKIRIRNIKRYSSENLLLNKLDTK
**************************** *:***:*:* **:***: .*:******:***
COL YMQTFINELSNVYSANQVKRQLGHMKEAIKYAVKFYNYPNEHILNSVTLPKKSKTIEDIE
NCTC8325 YMQIFINKLSDIYSQNQVTRQLGDMKGAIKYAVKFYNYPNEYLLTNVKIPKRRKTIEDIE
USA300_FPR3757 YMQIFINKLSDIYSQNQVTRQLGDMKGAIKYAVKFYNYPNEYLLTNVKIPKRRKTIEDIE
*** ***:**::** ***.****.** **************::*..*.:**: *******
COL KEEAKMYNYLEMEQVIQIRDFILNDNNMQYRARILVAGAVEVQALTGMRIGELLALQVKD
NCTC8325 KDESKMYNYLEMNQVLQIRDHILNDNKLQKRNRILIASILEVQALTGMRIGELQALQEKD
USA300_FPR3757 KDESKMYNYLEMNQVLQIRDHILNDNKLHKRNRILIASILEVQALTGMRIGELQALQEKD
*:*:********:**:****.*****::: * ***:*. :************* *** **
COL VDLKNKTIDINGTIHRIKCNAGFGHKDTTKTAGSKRKIAINSRIANVLKKIMLENKKMQQ
NCTC8325 IDLLNKTINITGTIHRIKYEKGFGYKDTTKTISSKRSISINSRTVEIFKKIILENKMLKR
USA300_FPR3757 IDLLNKTINITGTIHRIKYEEGFGYKDTTKTISSKRSISINSRTVEIFKKIILENKMLKR
:** ****:*.******* : ***:****** .***.*:**** .:::***:**** :::
COL WEPSYVDRGFIFTTCQGNPMQGSRINKRLSSAAESLNINKKVTTHTLRHTHISLLAEMNI
NCTC8325 WNSSYVDRGFIFTTKKGNPLCNNQIAGVLKKTTKALNMNKKVTTHTFRHTHITLLVEMNV
USA300_FPR3757 WNSSYVDRGFIFTTKKGNPLCNNQIAGVLKKTTKALNMNKKVTTHTFRHTHITLLVEMNV
*:.*********** :***: ..:* *..::::**:********:*****:**.***:
COL SLKAIMKRVGHTDEKTTIKVYTHVTEKMDRELEQKLEKLVY
NCTC8325 SLKAIMKRVGHVDEKTTIRIYTHVTEKMDRELTQKLENIPS
USA300_FPR3757 SLKAIMKRVGHVDEKTTIRIYTHVTEKMDRELTQKLENIPS
***********.******::************ ****::
- ↑ Christiane Goerke, Roman Pantucek, Silva Holtfreter, Berit Schulte, Manuel Zink, Dorothee Grumann, Barbara M Bröker, Jiri Doskar, Christiane Wolz
Diversity of prophages in dominant Staphylococcus aureus clonal lineages.
J Bacteriol: 2009, 191(11);3462-8
[PubMed:19329640] [WorldCat.org] [DOI] (I p)E Boakes, A M Kearns, M Ganner, C Perry, R L Hill, M J Ellington
Distinct bacteriophages encoding Panton-Valentine leukocidin (PVL) among international methicillin-resistant Staphylococcus aureus clones harboring PVL.
J Clin Microbiol: 2011, 49(2);684-92
[PubMed:21106787] [WorldCat.org] [DOI] (I p)Douglas R Deutsch, Bryan Utter, Kathleen J Verratti, Heike Sichtig, Luke J Tallon, Vincent A Fischetti
Extra-Chromosomal DNA Sequencing Reveals Episomal Prophages Capable of Impacting Virulence Factor Expression in Staphylococcus aureus.
Front Microbiol: 2018, 9;1406
[PubMed:30013526] [WorldCat.org] [DOI] (P e)Geoffrey W Coombs, Sarah L Baines, Benjamin P Howden, Krister M Swenson, Frances G O'Brien
Diversity of bacteriophages encoding Panton-Valentine leukocidin in temporally and geographically related Staphylococcus aureus.
PLoS One: 2020, 15(2);e0228676
[PubMed:32040487] [WorldCat.org] [DOI] (I e)