LOCUS       NZ_CP013618             3048 bp    DNA     circular CON 03-MAR-2024
DEFINITION  Staphylococcus aureus strain RIVM1295 plasmid pRIVM1295-2, complete
            sequence.
ACCESSION   NZ_CP013618
VERSION     NZ_CP013618.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04325935
            Assembly: GCF_001465635.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3048)
  AUTHORS   Bosch,T., Witteveen,S., Haenen,A., Landman,F. and Schouls,L.M.
  TITLE     Next-Generation Sequencing Confirms Presumed Nosocomial Transmission
            of Livestock-Associated Methicillin-Resistant Staphylococcus aureus
            in the Netherlands
  JOURNAL   Appl Environ Microbiol 82 (14), 4081-4089 (2016)
   PUBMED   27129960
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3048)
  AUTHORS   Witteveen,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-DEC-2015) Laboratory for Infectious Diseases &
            Screening, National Institute for Public Health & the Environment
            (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The
            Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: CLC Genomics Workbench v. version 8.5.1
            Sequencing Technology             :: 454; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/03/2024 08:02:28
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,742
            CDSs (total)                      :: 2,660
            Genes (coding)                    :: 2,566
            CDSs (with protein)               :: 2,566
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 49 of 94
            Pseudo Genes (incomplete)         :: 38 of 94
            Pseudo Genes (internal stop)      :: 28 of 94
            Pseudo Genes (multiple problems)  :: 17 of 94
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP013618.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3048
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM1295"
                     /isolation_source="unavailable"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pRIVM1295-2"
                     /geo_loc_name="Netherlands: Bilthoven"
                     /lat_lon="52.13 N 5.210 E"
                     /collection_date="2009-03-26"
                     /collected_by="Dutch National Institute for Public Health
                     and the Environment (RIVM)"
     gene            complement(244..1248)
                     /locus_tag="AUC48_RS13895"
                     /old_locus_tag="AUC48_13885"
     CDS             complement(244..1248)
                     /locus_tag="AUC48_RS13895"
                     /old_locus_tag="AUC48_13885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_078099054.1"
                     /translation="MQYNTTKCIDENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVVKEKPTARWLFLTLSTKNAIDGDHLEQSLKHMSKAFNKLKMYTKVKKNLVGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQVEWVDLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDEKNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            complement(1431..2252)
                     /locus_tag="AUC48_RS13900"
                     /old_locus_tag="AUC48_13890"
     CDS             complement(1431..2252)
                     /locus_tag="AUC48_RS13900"
                     /old_locus_tag="AUC48_13890"
                     /inference="COORDINATES: protein motif:HMM:NF025217.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative RNA methyltransferase"
                     /protein_id="WP_049948317.1"
                     /translation="MFFKCSICDEKLKRGYKTLACENNHTFDIAKEGYSNLISGHKKSK
                     YDKKLFIARRELNDSSNLYSILISKIIEIIKKYEIKTKNNVIDVGTGEGYILNEISKTF
                     LGENEFLGIDIAKEGVKKAAKSYKNINWLVADLADIPVMNGNVDFLINVLSPSNYDEFK
                     RVLDKEGKLIKIIPNSDYLKEIRNIVFSNHKNKDYDNSEVIDLFEANFNKIEMIDISYK
                     VKLNKEELNKLLDMTPLTWNLSDVEKEGIIKKNLSEITMSFKVLVGGFKTS"
                     /name="putative RNA methyltransferase"
     Typing          complement(245..1248)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.806"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atttatataa cttaaaaagt taaattgttt agctcatttt tttgttcatg accagtgggg
       61 aattttttag acactgccca tttatatgca aacttaaaag ttagcaaaat gggcaagaaa
      121 aaataaacac tgcccagtta catgcaaatt taaaaattaa catgaaaatt gggcaaccat
      181 gccggttgaa cgctatagtt cccgcagggg caaaaagaca taaaaaaaac gctagctttt
      241 aagctaacgt ttcaaatctt ttaagtaata attttgtttt tcaaaattcc aaattgccgt
      301 aattgaatgt gctttttctt cttcgtctgt tgttttatct tcgtcacttg tattaatcaa
      361 attgccatct tcggcatcgt ctaaatttaa aattttatgt ttttgtttaa gcaatccacc
      421 ataactcaac atacgttttc ggtataaacc tttttccaaa tcattcacga tttcttgatt
      481 tttttcgtca tcatcagtta aaaaatcaga tgacttaact gaatatttag aggtttcttt
      541 gatagctgct tgaatatctt tatcgccttt ttgatttggt ttgatcgctt taatatttgc
      601 tactggtcga taattaacct gtaatgcttt ttgccataaa tcaacccatt caacttgcgt
      661 aatgtagttt tctttttttc tgaaatacgc attttcaaca cacaataaaa cgtgcatatg
      721 ttgattataa ctaccgtcat ttttattaac tgttacttca gttgagcgta aaaaacccac
      781 caaattcttt ttaacttttg tatacatctt taatttatta aaagccttag acatgtgttt
      841 taaactttgt tctaagtggt caccgtctat tgcattttta gtcgataaag taagaaataa
      901 ccaacgagca gttggctttt ctttaaccac ttcttcaatc actttttgag cttgataact
      961 atttttcata gcacgcctcc aattacaaac tgggcataat tttgacttac aaaaccatgt
     1021 cttatgtaat ttcaaataac cttcatcagt tggcttgaat tctaagacgt taccacattg
     1081 ttttacgtta aaagcctttt taatttttaa gatttccagt atatctgcat aacttacatt
     1141 atctatcttc ttttctctcc atgggcgttg tttcccactt ttcgtcatat cttttaatgt
     1201 tttattatct tgattttcgt ctatacattt agtagtatta tattgcatat aaaaagacct
     1261 ccagtattga tttaagcgtc gtaacttaat catattactg gagctttttt atgtcaattt
     1321 tttctttcac gcacaaaaat acataaaaac actgtcatac caacgataaa gcaacttttt
     1381 atatctttga gttatttcta tatagtatca agacaagaag aaactcgttt tcaactcgtt
     1441 ttaaaaccac caaccaaaac cttaaaactc atcgtaattt cacttaagtt tttcttaatt
     1501 attccttctt tttctacgtc acttaaattc cacgttaaag gcgtcatatc aagtaattta
     1561 ttcaattctt ctttatttaa tttaacctta taactaatgt ctatcatttc aattttatta
     1621 aaattagctt caaataaatc tataacctca gaattatcat aatccttatt tttatgatta
     1681 ctaaagacta tattccttat ttcttttaaa taatcactat taggaattat ttttatcaat
     1741 ttcccctctt tatctagaac tcttttaaac tcatcataat tagaagggct aagcacatta
     1801 attaaaaagt ctacattccc attcataact ggtatatcag ctagatcagc aaccaaccaa
     1861 tttatatttt tatatgattt tgctgctttt tttacacctt cttttgcaat gtctatacct
     1921 aagaattcat tttcaccaag aaatgtttta ctaatttcat ttaaaatata accctcacca
     1981 gtaccaacat ctatcacatt atttttagtt ttaatctcat attttttaat aatttctatg
     2041 atttttgaaa ttaatatcga atacaaattg ctactatcat tcaattctct tctagcaata
     2101 aacaattttt tatcgtattt acttttttta tgccctgaaa ttaaattcga ataaccctct
     2161 tttgcaatat caaaagtatg gttattctca catgctaaag ttttataacc tctctttaat
     2221 ttttcatcac atatagaaca cttaaaaaac atattcacac ctccaatcaa ataattataa
     2281 ataacaaagt tgctttattc caattgcttt attgacgttg agcctcggaa cccttaacaa
     2341 tcccaaaact tgtcgaatgg tcggcttaat agctcacgct atgccgacat tcgtctgcaa
     2401 gtttagttaa gggttcttct caacatcaat aaattttctc ggcataaatg cgtgttcttt
     2461 tcttgtctgc ccagtagaca aagtagaccc aactgttatt gctttacagg tctatttttc
     2521 gtcgttataa tctagttaaa tcccgtaagg gcgcacttat gcgttctaaa aagaacgcgt
     2581 aaaaaaccat aatcgacctt cgtcaatttt tatcttagtt ttaaggaatc ggcgttgtgg
     2641 cgcagatata aaaattaata ctgcacgaac tagaatcgac gttgtagcgt agatataaaa
     2701 attaatacta catagaaatt taactaagat ttaagctact agttttttgc tagtagcttt
     2761 tttattttct taatttttaa atgcctttat tttgaatttt aagggggtat ttagagcaaa
     2821 ctctatattt atatattttt atacctgtat atttatatat gtttcttaaa acgcaaatat
     2881 gagcaaaata agggtacatc tttctgacat ttaacttgta ttcaaaagac atattactta
     2941 aattgctaaa gtcattttaa atacaatcac ttgtactttt taaacataag ccagaaaaac
     3001 gatatagctc ttttatatat ttttctaatt tgattggaac tccctaaa
//
