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PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159JSNZLGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

Summary[edit | edit source]

  • pan ID?: SAUPAN000107000
  • symbol?:
  • synonym:
  • description?: IS5/IS1182 family transposase

      descriptions from strain specific annotations:

    • IS5/IS1182 family transposase
    • IS1272, transposase
    • IS1272 transposase
    • ISSau3 transposase
    • putative transposase
    • transposase DDE domain protein
  • strand?: -
  • coordinates?: 125375..138638
  • synteny block?: BlockID0000850
  • occurrence?: in 29% of 34 strains

tnpIS1272 : IS1272mec transposase [1] [1]

Staphylococci containing the Staphylococcal Chromosomal Cassette-methicillin resistance elements (SCCmec) will often contain an IS1272mec transposase truncating the MecR1 signal transducer protein. This IS5/IS1182/ISSau3 family transposase then forms the boundary between "class B" mec elements and the J2 region, particularly in SCCmec type I, IV and VI strains and plays a significant role in SCCmec subtyping. With standardization of SCCmec nomenclature, IS1272mec has become the established name for this transposase in SCCmec elements, although alternative nomenclature including IS1181, IS1182, ISSau3 and ISSep1 and IS663 have been used. Formally, IS1182mec is the nomenclature given if the entire coding sequence is in frame while IS1272mec requires recoding by frameshift, although sequencing and assembly errors can make such distinctions challenging. Outside of SCCmec elements where these nuances are important for subtyping, the more generic "ISSau3" nomenclature is typically preferred.

Orthologs[edit | edit source]

    COL:
    N315:
    NCTC8325:
    Newman:
    USA300_FPR3757:
    04-02981:
    08BA02176:
    11819-97:
    MS7_0036
    6850:
    RSAU_000920
    71193:
    ECT-R 2:
    ED133:
    ED98:
    HO 5096 0412:
    SAEMRSA15_00330
    JH1:
    JH9:
    JKD6008:
    JKD6159:
    SAA6159_00034
    JSNZ:
    LGA251:
    M013:
    MRSA252:
    MSHR1132:
    SAMSHR1132_00350
    MSSA476:
    Mu3:
    Mu50:
    MW2:
    MW0034
    RF122:
    ST398:
    T0131:
    TCH60:
    HMPREF0772_10432
    TW20:
    USA300_TCH1516:
    USA300HOU_0034
    VC40:

Genome Viewer[edit | edit source]

COL
USA300_FPR3757

Alignments[edit | edit source]

  • alignment of orthologues:
    CLUSTAL format alignment by MAFFT L-INS-i (v7.307)


    COL             MMLKVILYAYTQSVFSGRKIEKMLNDSIRMMWLSQNQKPSYKTINQFRVNPKVDALLESL
    USA300_FPR3757  ----MILYAYTQSVFSGRKIEKMLNDSIRMMWLSQNQKPSYKTINQFRVNPKVDALLESL
                        :*******************************************************

    COL             FIQFYSQCVKQNLIDDKAIFIDGTKIEANANRYTFVWKKSIQNHESKMNEDSKALYHELV
    USA300_FPR3757  FIQFYSQCVKQNLIDDKAIFIDGTKIEANANRYTFVWKKSIQNHESKMNEDSKALYHELV
                    ************************************************************

    COL             TNKIIPEIKEDHDNELTKEEIDLIGSHLDKEIEDLNQHINNEKCTKTRKQIRLKRTKIKK
    USA300_FPR3757  TNKIIPEIKEDHDNELTKEEIDLIGSHLDKEIEDLNQHINNEKCTKTRKQIRLKRTKIKK
                    ************************************************************

    COL             YKKQINDYFERKYRYEFQKSILKDRNSYSKTDYDATFMRMKEDHMKNGQLKPGYNLQIAT
    USA300_FPR3757  YKKQINDYFERKYRYEFQKSILKDRNSYSKTDYDATFMRMKEDHMKNGQLKPGYNLQIAT
                    ************************************************************

    COL             NSQFVLSYNVYQNPTDTRTMIPFLNSIQETYGHLPEYIVADAGYGSESNYKAIIDDFNRT
    USA300_FPR3757  NSQFVLSYNVYQNPTDTRTMIPFLNSIQETYGHLPEYIVADAGYGSESNYKAIIDDFNRT
                    ************************************************************

    COL             PLITYGMFIKDKTKKYKSDIFNTQNWNYDEINDEFICPNNKRLGFKRYAYRHDKYGYKRD
    USA300_FPR3757  PLITYGMFIKDKTKKYKSDIFNTQNWNYDEINDEFICPNNKRLGFKRYAYRHDKYGYKRD
                    ************************************************************

    COL             FKLYECDDCSECPLKNQCMNFNSKTNKKIMKNYNWEYFKSQINKKLSEPETKNIYSQRKI
    USA300_FPR3757  FKLYECDDCSECPLKNQCMNFNSKTNKKIMKNYNWEYFKSQINKKLSEPETKNIYSQRKI
                    ************************************************************

    COL             DVEPVFGFMKAILGFTRMSVRGLNKVKRELGFVLMALNIRKVVAQRAENNQKIYKKDNFY
    USA300_FPR3757  DVEPVFGFMKAILGFTRMSVRGLNKVKRELGFVLMALNIRKVVAQRAENNQKIYKKDNFY
                    ************************************************************

    COL             IISIEIVFFHLSKNFMSRTHYDLFFYC
    USA300_FPR3757  IISIEIVFFHLSKNFMSRTHYDLFFYC
                    ***************************

  1. G L Archer, J A Thanassi, D M Niemeyer, M J Pucci
    Characterization of IS1272, an insertion sequence-like element from Staphylococcus haemolyticus.
    Antimicrob Agents Chemother: 1996, 40(4);924-9
    [PubMed:8849253] [WorldCat.org] [DOI] (P p)
    N Kobayashi, S Urasawa, N Uehara, N Watanabe
    Distribution of insertion sequence-like element IS1272 and its position relative to methicillin resistance genes in clinically important Staphylococci.
    Antimicrob Agents Chemother: 1999, 43(11);2780-2
    [PubMed:10543763] [WorldCat.org] [DOI] (P p)
    Liang Chen, José R Mediavilla, Duarte C Oliveira, Barbara M Willey, Herminia de Lencastre, Barry N Kreiswirth
    Multiplex real-time PCR for rapid Staphylococcal cassette chromosome mec typing.
    J Clin Microbiol: 2009, 47(11);3692-706
    [PubMed:19726600] [WorldCat.org] [DOI] (I p)