LOCUS       NZ_CP132364             2230 bp    DNA     circular CON 18-AUG-2023
DEFINITION  Staphylococcus aureus strain UNC_SA54 plasmid p1, complete sequence.
ACCESSION   NZ_CP132364
VERSION     NZ_CP132364.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36911164
            Assembly: GCF_030758835.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2230)
  AUTHORS   Franklin,T. and Wolfgang,M.
  TITLE     NIH Task A43 Option 2 - Murine Chronic Infection Model
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2230)
  AUTHORS   Franklin,T. and Wolfgang,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-AUG-2023) Genetics, University of North Carolina at
            Chapel Hill, 120 Mason Farm Road 5000 D, Genetic Medicine Building
            CB#7264, Chapel Hill, NC 27599, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/17/2023 14:17:04
            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)                     :: 2,821
            CDSs (total)                      :: 2,739
            Genes (coding)                    :: 2,651
            CDSs (with protein)               :: 2,651
            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)              :: 88
            CDSs (without protein)            :: 88
            Pseudo Genes (ambiguous residues) :: 0 of 88
            Pseudo Genes (frameshifted)       :: 50 of 88
            Pseudo Genes (incomplete)         :: 44 of 88
            Pseudo Genes (internal stop)      :: 28 of 88
            Pseudo Genes (multiple problems)  :: 32 of 88
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP132364.1.
            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..2230
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="UNC_SA54"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="p1"
                     /geo_loc_name="USA: Portland, Oregon"
                     /collection_date="2020-02-24"
     gene            265..588
                     /gene="qacC"
                     /locus_tag="RAM34_RS00005"
                     /old_locus_tag="RAM34_00005"
     ARG             266..585
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1180..2178)
                     /locus_tag="RAM34_RS00010"
                     /old_locus_tag="RAM34_00010"
     CDS             complement(1180..2178)
                     /locus_tag="RAM34_RS00010"
                     /old_locus_tag="RAM34_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001160226.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002505443.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     ARG             266..588
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="71.96"
                     /coverage="100.0"
     Typing          complement(1181..2178)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatcaatttt ttctttcacg ctaaaaaaac aacacaaatg ttgtcatacc aacgttttta
       61 aaacatttta attctttgag ttatttctat atagtatcaa gacaagaaga aactcgtttt
      121 caactcgttt caaaaacctt tcaaaaacca tcaatccaca aaaataccac gcgaatgaca
      181 ctcaaaatac aagactacaa ttaaaaaata ctttacaatt aaaaaatact tagaataaaa
      241 tacgaaaatt aaaaggagct aaaaatgcct tatatttatt taataatagc cataagtact
      301 gaagttattg gaagtgcatt tcttaaatct tcagaaggct tttcaaaatt tataccatcc
      361 ttaggaacaa taatttcatt tggaatttgt ttctattttt taagtaaaac aatgcaacac
      421 ctaccactaa atataactta tgcaacttgg gcgggactag gtttagtctt aacaaccgta
      481 gtctcaataa ttattttcaa agaacaaata aatctaataa ctatagtatc tatagtttta
      541 atcatagtcg gcgtagtttc gttaaacatt ttcggaacat cgcattaatt gctttattcc
      601 aattgcttta ttgacgttga gcctcggaac ccttaacaat cccaaaactt gtcgaatggt
      661 cggcttaata gctcacgcta tgccgacatt cgtctccaag tttagttaag ggttcttctc
      721 aacatcaata aattttctcg gcataaatgc tgtgttataa ttaaaattcc tttcttgatc
      781 tatttttcac tgataacacc taaatattaa aacagtgcat ataagagcta ccaaaatttt
      841 taagggtagc tctttatttt ttgttcaaac atttattcaa aatcagaata cctttatttt
      901 taattttaag gggtcatttt aaagaattaa gggttattta tatagtttta tacctaaaaa
      961 cctaaatcgg ctcttaaaac gcaaatgaga gccaaataaa aataattgct tttcacaaac
     1021 aaaaatttga gcaaaaccag tgtcgaattt tttagacact gcccatttac atgcaaattt
     1081 aaaaattagc ataaaaaatg ggcaaccatg ccggttgaac gctatagttc ctgcaggggc
     1141 aaaaaagcat aaaaaaacgc tagctttgat aagctaacgt tacaaatttt ttaagaaata
     1201 attttgtttt tcaaaattcc aaatggccgt aattgaatgg gctttttgtt cttcttcagt
     1261 cgttttttct tcatcgctcg tttgaattaa attaccttct tcggcatcgt ctaaatttaa
     1321 aagtttatgt ttttgtttaa gtaaaccacc gtaacttaac atacgttttc tgtataaacc
     1381 ttgttctaaa tcttgaacaa tttctgcgtc tttttcatgg tttcctgtta aataatcgga
     1441 cgacttaacc gagtattttg atgtctcttt aattgcagct tgtatatctt tatcgccttt
     1501 tttattcggc ttaattgctt tgatatttgc gactggtttg taatcaactt gaagagcttt
     1561 ttgccataaa ttgatccact cttcttgcgt tatataattc tctttttttc tgaaataagc
     1621 attttcaaca cacaataaaa cgtgcatatg ttgattataa cttccgtcat ttttgttaac
     1681 tgtaacttca gttgaacgca taaaaccgat taaattcttt ttaacttttg catacatttt
     1741 taacttgtta aaagctttcg acatatattt taaactctgt tctaaatgct caccatctat
     1801 cgcatttttt gttgaaagtg ttaagaataa ccaacgtgct tttggctttt ctttaaccac
     1861 tgcttcaatg actttttgag cttgataact atttttcatt gaacgcctcc aattacaaac
     1921 cggacataat ttagacttac aaaaccatgt tttataaagt tttaaatacc cttcatcagt
     1981 cggcttaaat tctaagacgt taccacattg cttcacgtta aaagcctttt taatttttaa
     2041 aatttctagt atatctgcat aacttacatt gtcgattttc ttttctctcc atgggcgttg
     2101 tgtcccactt ttagtcatat ctttcaatgt ttcattatct tgattttcgt ctatatattt
     2161 tgtagtatta tattgcatat aaaaagacct ccagttttga tttagattcg acaccttaat
     2221 catataactg
//
