LOCUS       NZ_CP015175             3085 bp    DNA     circular CON 15-NOV-2023
DEFINITION  Staphylococcus aureus strain RIVM6519 plasmid pRIVM6519-2, complete
            sequence.
ACCESSION   NZ_CP015175
VERSION     NZ_CP015175.1
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 3085)
  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                   :: 7000
            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
            CP015175.1.
            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..3085
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM6519"
                     /isolation_source="unavailable"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pRIVM6519-2"
                     /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(609..1529)
                     /locus_tag="A5J11_RS14085"
                     /old_locus_tag="A5J11_14080"
     CDS             complement(609..1529)
                     /locus_tag="A5J11_RS14085"
                     /old_locus_tag="A5J11_14080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002445662.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_011274352.1"
                     /translation="MDKYTEKKQRNQVFQKFIERHVKEGQMDLIRECNTFLSFVSDKTL
                     EKQKLYKSNLCKNRFCPVCAWRKARKDALGLSLMMQYIKQKEDKQFIFLTLTTPNVTVE
                     HLEDEIKHYNESFRRLSNRKHFKSIAKGYVRKLEITYNKKRDDYNPHFHVLIAVNKSYF
                     TDKRYYISQKEWLELWRDVTGNQAITQVHVQKVKQNNNKELYEMAKYSGKDSDYLVNQK
                     VFDAFYKALKGKQVLVYSGLFKDARKKLKNGELDYLKESDPTEYIYQIFYVWNQKEYLA
                     SEIYDLTEEEKREVNNQMINEIEEE"
                     /name="protein rep"
     gene            1893..2216
                     /gene="qacC"
                     /locus_tag="A5J11_RS14090"
                     /old_locus_tag="A5J11_14085"
     ARG             1894..2213
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="99.07"
                     /coverage="100.0"
     gene            2427..2819
                     /locus_tag="A5J11_RS14095"
                     /old_locus_tag="A5J11_14090"
     CDS             2427..2819
                     /locus_tag="A5J11_RS14095"
                     /old_locus_tag="A5J11_14090"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_031824197.1"
                     /translation="MENTNNLFERLEILTKPENIETTFFIILKFIIFIIILMIGALIVL
                     GILNSRRNYNPEKIWNKRKIRTLKSEIGGGQEYYFRYWIWQRNKRKNILIALRDYSPYE
                     EYYPSQKWLKKDKSKLPFRREIWVIK"
                     /name="hypothetical protein"
     ARG             1894..2216
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="72.9"
                     /coverage="100.0"
     Typing          complement(610..1529)
                     /name="rep_cluster_1300"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tagctttttt atttttaaaa ttttaaatac ctttattttg aattttaagg gggcatttta
       61 aagatttagg ggtaattcat atagttttat gcctaaaaac ttatataagc tcttaaaacg
      121 caaatatgag ccaaatacaa aaccaccgaa aatttaccgc aaagttaagt gcaaacccct
      181 tttcgatttt aatcgcctta aatcaccata aagcctttca tatcaagtat tatagatttt
      241 cgaaatcact aaaagtggaa agcaaaatca ggtcaaaacc aagcacaaca gtgcttttca
      301 cgagttggat atcaactctt aattctgcac tacccctttt taactcaaaa agtgggttac
      361 cgaaaagggt ttgcacttta tcaaaatcgc ccactaattc aattcaaaat cacaacacct
      421 tttatgccga gaaaacttat tgtttggaat agattttgtg ttagctagat tcattctaga
      481 gagttggttg gtcttgattt gggattaatc ccaagaaagt accaactcaa caacacaata
      541 agccttgttg gttccaaacc ataaggcaaa ttggaataaa aaagacgcta gctttcgcta
      601 acgtcttttt actcttcttc aatttcgtta atcatttggt tgtttacttc tcgtttttct
      661 tcttcggtta agtcgtaaat ctcacttgct agatactctt tttgattcca cacataaaag
      721 atttggtaaa tatattctgt cggatcactt tctttgagat aatccaactc gccatttttt
      781 agctttttgc gtgcatcttt aaacaatcca gaatagacaa gtacctgttt gccttttaat
      841 gctttataaa atgcgtcgaa tactttttga ttaacgagat aatcgctatc tttaccggaa
      901 tatttagcca tttcataaag ttctttatta ttgttttgct taaccttttg aacatgaact
      961 tgtgtaatag cttgattacc tgtcacatca cgccatagtt caagccattc tttttggctt
     1021 atataatatc gcttatctgt aaaatatgat ttattaaccg caattaatac atgaaaatgt
     1081 ggattataat catcgcgttt tttgttataa gtgatttcta attttcttac gtaaccttta
     1141 gctatagatt taaagtgttt acgattactt aatcgtctaa acgactcatt ataatgtttt
     1201 atttcatctt ccaaatgctc aactgttaca tttggcgtcg taagtgttaa aaagatgaat
     1261 tgtttatctt ccttttgctt aatatattgc atcatcaatg ataaacctaa cgcatctttt
     1321 ctcgcttttc gccatgcaca tacaggacaa aatcgatttt tacacaaatt agatttatac
     1381 aatttctgtt tttctaacgt cttatctgac acaaaactca agaatgtatt acactccctt
     1441 atcaaatcca tttgtccttc tttgacatgt cgttcaataa atttctgaaa tacttgattt
     1501 ctttgtttct tctcagtata cttatccatg ttataacaca acaaaacaac ttagttttat
     1561 acaaactaat gccataaaaa agttgctttt tctcctttct tgtaaagttt tggcttggac
     1621 accataaact ctactatact aggtacgaaa aagcaacttt ttttgcgctc gaaaccagat
     1681 ataccaacag attaaaggta actatcgtag cttgtaatag ttacctatag tatcaagaca
     1741 agaagaaact cgttttcaac tcgtttcaaa aacctttcaa aaaccatcaa tccacaaaaa
     1801 taccacgcga atgacactca aaatacaaga ctacaattaa aaaatactta gaataaaatt
     1861 aaataaaata cgaaaattaa aaggagttaa aaatgcctta tatttattta ataatagcca
     1921 taagtactga agttattgga agtgcatttc ttaaatcttc agaaggcttt tcaaaattta
     1981 taccatcctt aggaacaata atttcatttg gaatttgttt ctatttttta agtaaaacaa
     2041 tgcaacacct accactaaat ataacttatg caacttgggc gggactaggt ttagtcttaa
     2101 caaccgtagt ctcaataatt attttcaaag aacaaataaa tctaataact atagtatcta
     2161 tagttttaat catagtcggc gtagttttgt taaacatttt cggaacatcg cattaattgc
     2221 tttattccaa ttgctttatt gacgttgagc ctcggaaccc ttaacaatcc caaaacttgt
     2281 cgaatggtcg gcttaatagc tcacgctatg ccgacattcg tctgcaagtt tagttaaggg
     2341 ttcttctcaa cgcacaataa attttctcgg cataaatgcg atataatcaa aaataagcaa
     2401 taaatactat ttcgaggtga tagtagttgg aaaacactaa taatctattc gaaagattag
     2461 aaatattaac aaaaccagaa aatatagaaa ctacattttt tattatcctt aaattcatta
     2521 tttttatcat cattctaatg ataggagcgt taatagtttt aggaatattg aatagcagaa
     2581 gaaattacaa ccctgaaaaa atttggaaca aaagaaaaat tcgcactctt aaatcagaaa
     2641 ttggcggagg acaggaatac tattttagat actggatctg gcaaagaaat aaaagaaaaa
     2701 atattctaat cgctttaaga gattactctc catatgaaga atattatcca agtcaaaaat
     2761 ggctaaaaaa agataaatct aaattaccat tccgaagaga aatatgggtt ataaaataac
     2821 taaccttctt actttacatg tctatttttc atcgttataa tctagttaaa tcccgtaagg
     2881 gcgcacttat gcgttctaaa aagaacgcgt gcaaaaacca taatcgacct tcgtcgattt
     2941 tttatcttag ttttaagtaa tcggcgttgt ggcgcagata caaaaattaa tactgcacga
     3001 atttgaatcg acgttgtagc gtagatataa aaattaatac tacatcaaaa tttaactaag
     3061 atttaagcta ctagtttttt gctag
//
