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

Summary[edit | edit source]

  • pan ID?: SAUPAN001769000
  • symbol?:
  • synonym:
  • description?: phi-like protein

      descriptions from strain specific annotations:

    • phi-like protein
    • VRR-NUC domain-containing protein
    • phi phage protein
    • phi related protein
    • VRR-NUC
  • strand?: -
  • coordinates?: 2194938..2195251
  • synteny block?: BlockID0011680
  • occurrence?: in 41% of 34 strains

vrr (vrr-nuc) : prophage replication-repair nuclease-resolvase [1]

Most staphylococcal prophage replicate in two stages: unidirectional (theta) replication to form the initial replication bubble, followed by pausing, viral replication restart and transition into sigma replication which is recombination protein-dependent and allows generation of long genomic concatemers. This transition frequently results in duplex-DNA structures (Holliday junctions) that need to be resolved. Replication-repair nuclease-resolvases resolve duplex DNA allowing viral replication restart to continue. This nuclease-resolvase is vrr-nuc-like. Other paralogues may be RusA-like or DUF1064-like.

Orthologs[edit | edit source]

    COL:
    N315:
    NCTC8325:
    Newman:
    USA300_FPR3757:
    04-02981:
    08BA02176:
    C248_0344
    11819-97:
    MS7_1473
    6850:
    71193:
    ECT-R 2:
    ED133:
    ED98:
    HO 5096 0412:
    SAEMRSA15_13790
    JH1:
    SaurJH1_1074
    JH9:
    SaurJH9_1054
    JKD6008:
    JKD6159:
    SAA6159_01383
    JSNZ:
    LGA251:
    M013:
    MRSA252:
    SAR1524
    MSHR1132:
    MSSA476:
    SAS0927
    Mu3:
    Mu50:
    MW2:
    MW1406
    RF122:
    ST398:
    SAPIG0368
    T0131:
    TCH60:
    HMPREF0772_11685
    TW20:
    USA300_TCH1516:
    USA300HOU_1457
    VC40:

Genome Viewer[edit | edit source]

NCTC8325
USA300_FPR3757

Alignments[edit | edit source]

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


    NCTC8325        MKESTLEKYLVKEITKLNGLCLKWVAPGTRGVPDRIIIMPEGKTYFVEMKQEKGKLHPLQ
    USA300_FPR3757  MKESTLEKYLVKEISKLNGLCLKWVAPGTRGVPDRIIIMPEGKTYFVEMKQEKGKLHPLQ
                    **************:*********************************************

    NCTC8325        KYVHRQFENRDHKVYVLWNKEQVNTFIRMVGGTFGD
    USA300_FPR3757  KYVHRQFENRDHKVYVLWNKEQVNTFIRMVGGTFGD
                    ************************************

  1. Lisa N Kinch, Krzysztof Ginalski, Leszek Rychlewski, Nick V Grishin
    Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
    Nucleic Acids Res: 2005, 33(11);3598-605
    [PubMed:15972856] [WorldCat.org] [DOI] (I e)
    Mindaugas Laganeckas, Mindaugas Margelevicius, Ceslovas Venclovas
    Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.
    Nucleic Acids Res: 2011, 39(4);1187-96
    [PubMed:20961958] [WorldCat.org] [DOI] (I p)
    Ambra Lo Piano, María I Martínez-Jiménez, Lisa Zecchi, Silvia Ayora
    Recombination-dependent concatemeric viral DNA replication.
    Virus Res: 2011, 160(1-2);1-14
    [PubMed:21708194] [WorldCat.org] [DOI] (I p)
    Lisa Zecchi, Ambra Lo Piano, Yuki Suzuki, Cristina Cañas, Kunio Takeyasu, Silvia Ayora
    Characterization of the Holliday junction resolving enzyme encoded by the Bacillus subtilis bacteriophage SPP1.
    PLoS One: 2012, 7(10);e48440
    [PubMed:23119018] [WorldCat.org] [DOI] (I p)
    Simon Pennell, Anne-Cécile Déclais, Jiejin Li, Lesley F Haire, Wioletta Berg, José W Saldanha, Ian A Taylor, John Rouse, David M J Lilley, Stephen J Smerdon
    FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.
    Cell Rep: 2014, 8(1);84-93
    [PubMed:24981866] [WorldCat.org] [DOI] (I p)