LOCUS       NZ_CP015174             4264 bp    DNA     circular CON 15-NOV-2023
DEFINITION  Staphylococcus aureus strain RIVM6519 plasmid pRIVM6519-1, complete
            sequence.
ACCESSION   NZ_CP015174
VERSION     NZ_CP015174.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04590098
            Assembly: GCF_001618305.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4264)
  AUTHORS   Witteveen,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2016) Laboratory for Infectious Diseases &
            Screening, National Institute for Public Health & the Environment
            (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA,
            Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: CLC Genomics Workbench v. 8.5.1
            Genome Coverage                   :: 1000
            Sequencing Technology             :: Illumina; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/15/2023 04:40:14
            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)                     :: 2,772
            CDSs (total)                      :: 2,708
            Genes (coding)                    :: 2,634
            CDSs (with protein)               :: 2,634
            Genes (RNA)                       :: 64
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 44
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 74
            CDSs (without protein)            :: 74
            Pseudo Genes (ambiguous residues) :: 0 of 74
            Pseudo Genes (frameshifted)       :: 37 of 74
            Pseudo Genes (incomplete)         :: 35 of 74
            Pseudo Genes (internal stop)      :: 29 of 74
            Pseudo Genes (multiple problems)  :: 25 of 74
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP015174.1.
            Source DNA available from Thijs Bosch (Thijs.Bosch@rivm.nl).
            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..4264
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM6519"
                     /isolation_source="unavailable"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pRIVM6519-1"
                     /geo_loc_name="Netherlands: Bilthoven"
                     /lat_lon="52.13 N 5.210 E"
                     /collection_date="2012-12-20"
                     /collected_by="Dutch National Institute for Public Health
                     and the Environment (RIVM)"
     gene            complement(271..780)
                     /locus_tag="A5J11_RS14065"
                     /old_locus_tag="A5J11_14055"
     CDS             complement(271..780)
                     /locus_tag="A5J11_RS14065"
                     /old_locus_tag="A5J11_14055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002504405.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063125036.1"
                     /translation="MKKILSATIAGTLLATGVGSALNNPIAKAENVQKAETISQDVKSD
                     KQYQALSPESKESFRVIVESNNYNNQQQMQLLRDTGQTKGISENGTSDRGKIGITKKVV
                     KQAWKTLPPNIKKKIGTQSKFYGAVKTFDHFTDDIENGIYKKMKGFGLTNNEAWIATKA
                     ITLIIL"
                     /name="hypothetical protein"
     gene            complement(1054..1542)
                     /locus_tag="A5J11_RS14690"
     CDS             complement(1054..1542)
                     /locus_tag="A5J11_RS14690"
                     /inference="COORDINATES: protein motif:HMM:NF017542.3"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_078270799.1"
                     /translation="MTKERYGTVYKGKEMYVNQETGEVLEVDKIYRQQVQGNFVKAYIK
                     GLVMMLDVVGGSKLKVVNYLLDNLRLSDNKLIATTREIADNTKTSPTTVTDTLKTLENG
                     NVIKRRTGVIMLNPEILLRGDDNKHRHLLVEFEEFDRANEEQHAKVEYDSFKNNSDTL"
                     /name="replication/maintenance protein RepL"
     gene            2380..2718
                     /gene="mobC"
                     /locus_tag="A5J11_RS14075"
                     /old_locus_tag="A5J11_14070"
     CDS             2380..2718
                     /gene="mobC"
                     /locus_tag="A5J11_RS14075"
                     /old_locus_tag="A5J11_14070"
                     /inference="COORDINATES: protein motif:HMM:NF017524.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_063125037.1"
                     /translation="MVTENRRESKQIKFRVTQEEYERLEQMAETLNTSVPMLAKDATQK
                     KRIKAPLIDRQGAIEIAKELRAIGTNINQITRAVNTKELIDYDIGNALLDELGDLRNEM
                     GKLWQLLK"
                     /name="mobC"
     gene            2700..3809
                     /locus_tag="A5J11_RS14080"
                     /old_locus_tag="A5J11_14075"
     CDS             2700..3809
                     /locus_tag="A5J11_RS14080"
                     /old_locus_tag="A5J11_14075"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_063125038.1"
                     /translation="MAVIKISATKSLNRLISYAEKKAEVQSGVNVDDEFAKEQMKTTQM
                     IFNKNDGRQGYHLIQSFDPEDNITPEEANEIGQELAKEVAPDHEITIYTHTDRDHIHNH
                     ICINSVNMNTGKKFVNDRNKLYEMRNKSNELCQRYNLVNSSNKQAQIRYTQAERAIIEK
                     GQISWKDEIRQAIDKEKLNANSFDEFKDNMQENYGIEVKERGKNISFKHPDKKAFVRGK
                     TLGNAYEKGTINNELNRESERTEQQTQSDRPKQVVRTNERPRGTDKNVEKRADVTRIEH
                     YSRDNGDTQSVGQDTKPNHKGTKRNSKRERDFRRAFEKHNERTAELNGRADEELPDREQ
                     ENVRDNQADIGEDRAEPQLEIELDGPELQ"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          complement(1055..1542)
                     /name="rep_cluster_1944"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2701..3806
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcttttttat ttcttttatt gaacttataa atacaataaa cgataactat aattatggtt
       61 aataaatcaa aagacagagc aaatgcatca ctaaatgatt gttttaacca aagaaatctt
      121 attataaata ataaaaatga ttgtatgatt actgctataa agacattaat aacaggttta
      181 tcctttataa aattataaac aatgtaggaa ataactgaaa tagttattag gaacataaat
      241 atatgtggtg ccattaaagg cctcccttaa ttataaaatg attagtgtaa tggctttagt
      301 agctatccaa gcttcgttgt tagttaaacc aaaacctttc atttttttgt atataccatt
      361 ttctatatca tcagtaaagt ggtcgaaagt ttttacagca ccatagaatt tactttgtgt
      421 tccgattttc ttttttatat taggaggtaa tgttttccaa gcttgtttta caactttttt
      481 tgtaatacca attttcccac gatcagaagt tccattttca gaaatacctt ttgtttgacc
      541 tgtatctctg agtagttgca tctgttgttg attattatag ttattacttt caacaatgac
      601 tctgaaactt tctttagatt ctggtgataa agcttgatat tgcttgtcag attttacatc
      661 ttgagaaata gtttctgctt tctgtacatt ttcggcttta gcaataggat tatttaaagc
      721 acttccaaca cctgtagcta ataatgttcc agctattgta gcagataaaa tttttttcat
      781 tgtgtagaaa ctcctttatc aagatattct cccaaaaaca ttcccaaata taaaataaca
      841 aaaaaacaac gctttttata gtttattgta aaaaatgatt aagaattttt ataaatgtgt
      901 atcaaaatta aaataagatg agttttgata tacaaaaagc ttagccataa tagaccaagc
      961 tttttgttag tgttatatta ataacaaaat aaaaaaagaa gtcgcccact ccccaaccag
     1021 aattaagttt tgttactaac atgtcacgac atgttataat gtatctgagt tatttttaaa
     1081 gctatcatat tcaacttttg cgtgttgttc ttcatttgct ctgtcgaact cctcaaattc
     1141 tacaagcaaa tgtctatgct tattatcatc tccacgtaaa agtatttcag gatttagcat
     1201 aattacacca gttctacgct taatgacatt accgttttca agagttttta atgtgtctgt
     1261 tacagttgta ggactggttt ttgtattgtc tgcaatttct ctagtcgtgg ctataagttt
     1321 attgtctgat agtcgtaaat tatctaataa gtaattaacg acttttagct tactaccacc
     1381 tactacatct aacatcatta ctagtccttt aatatacgct ttaacaaagt ttccctgtac
     1441 ttgttgcctg tatatcttat ctacttctaa tacctctcct gtttcttgat taacatacat
     1501 ttctttacct ttgtatacag ttccatatct ttctttagtc atttaaatct aacctcctgt
     1561 tgttataaat tgaaacaaac gttacaaaaa tatagtaaca taaataccaa aaaaatagtt
     1621 ataaaatcga ttttgttaca gaaaactgtt acaaatatac cagaaaactg ttacaaacaa
     1681 attccttata aacattgtta tatcaaccta tattaagaat ttaagtagtt gaatcttctt
     1741 ttctatataa agcgtcggag catatcaggg ggttatctaa cgtaaatgct acccttcggc
     1801 tcgctttcgc tcggcattga cgtcagatac tgcaccccct gaacccccat gctccgacag
     1861 caaaaaggaa actttttgct gctcgtccga cgcttattca cttcgttcat attcatatag
     1921 aaaagaagtg aatgcgttaa tgcatttttg agtgaataat attttatact gtgagtgtta
     1981 acgagcagat cataaaatat atatgaacgc cgtttacggt atttcagtaa acggacatag
     2041 caaccacatt tttggttgct tgggttttgg tttttggaag tgtcaaaatg acacttcctt
     2101 tttgcgtcag caaaaacagg gggattgggg agcgccccaa caagtaggtg tatgggtacc
     2161 atacacgtat cttgccaaag ctctctcatc aatgctatga tgagaccgta aagttgttta
     2221 tttaattgtt gccgacaatt aaataattca acatacgggc gttttttagg gtggcgcaaa
     2281 tattaagcgc cagactaaaa acatgatagc tttagggggc aaatttgacg gcacattttt
     2341 gccgtcgccc cctaaacttg atgaagagag gtgcgattgt tggttacgga gaatagacga
     2401 gaaagcaagc aaataaagtt cagagtgacg caagaagaat acgagcgatt agaacaaatg
     2461 gcagaaacgt taaatacatc tgttccaatg cttgcgaaag atgcaacgca gaaaaaacgt
     2521 ataaaagcac cattgattga tagacaaggt gcaattgaaa ttgctaaaga gttaagagca
     2581 attggaacga atattaatca gattacaaga gcagtgaata caaaagaatt aattgattat
     2641 gacataggaa acgcactatt ggacgaatta ggcgatttaa gaaacgagat ggggaaacta
     2701 tggcagttat taaaataagc gctacaaagt ctttaaatag gcttatatcg tatgcagaaa
     2761 agaaagcaga agtgcaatca ggtgtaaatg tcgatgatga atttgcgaaa gagcagatga
     2821 aaacaacaca aatgatattt aataaaaacg acggacgaca gggttatcat ttaattcagt
     2881 cattcgatcc agaagataat atcacaccag aagaagccaa tgagataggt caagaattag
     2941 caaaagaagt tgcaccagac catgaaataa cgatttatac gcatacagat agagaccata
     3001 ttcataatca tatatgcata aatagtgtga atatgaatac agggaaaaaa tttgtgaatg
     3061 atagaaataa gctttatgaa atgcgtaata aaagtaatga gttatgccaa agatacaatt
     3121 tagttaattc tagcaacaaa caggcacaaa ttaggtacac acaggcagaa agagcaatca
     3181 tagaaaaagg tcaaatcagt tggaaagatg aaattagaca agcgattgat aaagaaaaat
     3241 taaatgcgaa tagctttgat gaatttaaag ataatatgca agagaactac ggtattgaag
     3301 ttaaggaacg tggaaagaat atcagtttca aacatcccga taaaaaagca tttgtgagag
     3361 gtaaaacttt aggcaatgct tacgagaaag gaacgataaa caatgagctt aacagagaga
     3421 gtgaacgaac agaacaacag acgcaatcag atagaccaaa acaagttgtt agaacaaatg
     3481 aaagacctag aggcacagat aagaacgttg agaaacgagc cgatgttact agaatcgagc
     3541 attactcaag agataacggc gatacacaaa gcgtcggaca agatactaaa ccaaatcaca
     3601 aaggcacaaa aagaaatagc aagcgagaac gagacttccg tagagcattt gaaaagcata
     3661 atgagcgcac tgcagaactt aatggacgag cagatgaaga acttccagac agagaacaag
     3721 aaaatgttag agacaatcaa gccgacattg gagaagatag agcagagcca caactcgaaa
     3781 ttgaactcga tggaccagaa cttcaatagc atggtttctc atattcgaca tacaagcaat
     3841 atgaataacc ttagaaacca tttaatcaat attgggggtt caagtatcct aacaacgata
     3901 ttagtcctta ttttgcattt tataggggtt atatgagcca tataaatgat taagcacgtt
     3961 ttatgccgag aaaatctatt tgtcgatgag agcccttaat tagactaaaa gcgccagcgg
     4021 tcggatagcg tcagctatca aatcgaccga tggacagctt taggattatt aaggagcgca
     4081 gaatcgtcga caaatagagg aattggaata atgcaatttt ttaatgaggt taaattttaa
     4141 ttaaagattt taaataatga ttagaaaaaa gataatagac atgaagaaag gagctaatct
     4201 aaaatagact agctccttta atatattctg gattaataaa ggataattac gtcaatttca
     4261 ctgt
//
