LOCUS       NZ_CP093211             2242 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Staphylococcus epidermidis strain TSM-50 plasmid p1, complete
            sequence.
ACCESSION   NZ_CP093211
VERSION     NZ_CP093211.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26520718
            Assembly: GCF_024204965.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2242)
  AUTHORS   Saito,R., Ayibieke,A. and Yamada,K.
  TITLE     bloodstream S. epidermidis isolates from two Hospitals in Tokyo
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2242)
  AUTHORS   Saito,R., Ayibieke,A. and Yamada,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAR-2022) Molecular Microbiology, Tokyo Medical and
            Dental University, 1-5-45 yushima, Bunkyo-ku, Tokyo 113-8510, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Unicycler hybrid assembley v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 830.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/20/2023 03:33:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,366
            CDSs (total)                      :: 2,282
            Genes (coding)                    :: 2,226
            CDSs (with protein)               :: 2,226
            Genes (RNA)                       :: 84
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 56
            CDSs (without protein)            :: 56
            Pseudo Genes (ambiguous residues) :: 0 of 56
            Pseudo Genes (frameshifted)       :: 37 of 56
            Pseudo Genes (incomplete)         :: 32 of 56
            Pseudo Genes (internal stop)      :: 19 of 56
            Pseudo Genes (multiple problems)  :: 25 of 56
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093211.1.
            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..2242
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="TSM-50"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="p1"
                     /geo_loc_name="Japan"
                     /lat_lon="35.75322977 N 139.70093331 E"
                     /collection_date="2014-07-28"
                     /collected_by="Toshima hospital staff"
     gene            174..497
                     /gene="qacC"
                     /locus_tag="MNU50_RS11810"
                     /old_locus_tag="MNU50_11790"
     ARG             175..494
                     /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(1090..2088)
                     /locus_tag="MNU50_RS11815"
                     /old_locus_tag="MNU50_11795"
     CDS             complement(1090..2088)
                     /locus_tag="MNU50_RS11815"
                     /old_locus_tag="MNU50_11795"
                     /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             175..497
                     /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(1091..2088)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tagtatcaag acaagaagaa actcgttttc aactcgtttc aaaaaccttt caaaaaccat
       61 caatccacaa aaataccacg cgaatgacac tcaaaataca agactacaat taaaaaatac
      121 tttacaatta aaaaatactt agaataaaat acgaaaatta aaaggagcta aaaatgcctt
      181 atatttattt aataatagcc ataagtactg aagttattgg aagtgcattt cttaaatctt
      241 cagaaggctt ttcaaaattt ataccatcct taggaacaat aatttcattt ggaatttgtt
      301 tctatttttt aagtaaaaca atgcaacacc taccactaaa tataacttat gcaacttggg
      361 cgggactagg tttagtctta acaaccgtag tctcaataat tattttcaaa gaacaaataa
      421 atctaataac tatagtatct atagttttaa tcatagtcgg cgtagtttcg ttaaacattt
      481 tcggaacatc gcattaattg ctttattcca attgctttat tgacgttgag cctcggaacc
      541 cttaacaatc ccaaaacttg tcgaatggtc ggcttaatag ctcacgctat gccgacattc
      601 gtctccaagt ttagttaagg gttcttctca acatcaataa attttctcgg cataaatgct
      661 gtgttataat taaaattcct ttcttgatct atttttcact gataacacct aaatattaaa
      721 acagtgcata taagagctac caaaattttt aagggtagct ctttattttt tgttcaaaca
      781 tttattcaaa atcagaatac ctttattttt aattttaagg ggtcatttta aagaattaag
      841 ggttatttat atagttttat acctaaaaac ctaaatcggc tcttaaaacg caaatgagag
      901 ccaaataaaa ataattgctt ttcacaaaca aaaatttgag caaaaccagt gtcgaatttt
      961 ttagacactg gcccatttac atgcaaattt aaaaattagc ataaaaaatg ggcaaccatg
     1021 ccggttgaac gctatagttc ctgcaggggc aaaaaagcat aaaaaaacgc tagctttgat
     1081 aagctaacgt tacaaatttt ttaagaaata attttgtttt tcaaaattcc aaatggccgt
     1141 aattgaatgg gctttttgtt cttcttcagt cgttttttct tcatcgctcg tttgaattaa
     1201 attaccttct tcggcatcgt ctaaatttaa aagtttatgt ttttgtttaa gtaaaccacc
     1261 gtaacttaac atacgttttc tgtataaacc ttgttctaaa tcttgaacaa tttctgcgtc
     1321 tttttcatgg tttcctgtta aataatcgga cgacttaacc gagtattttg atgtctcttt
     1381 aattgcagct tgtatatctt tatcgccttt tttattcggc ttaattgctt tgatatttgc
     1441 gactggtttg taatcaactt gaagagcttt ttgccataaa ttgatccact cttcttgcgt
     1501 tatataattc tctttttttc tgaaataagc attttcaaca cacaataaaa cgtgcatatg
     1561 ttgattataa cttccgtcat ttttgttaac tgtaacttca gttgaacgca taaaaccgat
     1621 taaattcttt ttaacttttg catacatttt taacttgtta aaagctttcg acatatattt
     1681 taaactctgt tctaaatgct caccatctat cgcatttttt gttgaaagtg ttaagaataa
     1741 ccaacgtgct tttggctttt ctttaaccac tgcttcaatg actttttgag cttgataact
     1801 atttttcatt gaacgcctcc aattacaaac cggacataat ttagacttac aaaaccatgt
     1861 tttataaagt tttaaatacc cttcatcagt cggcttaaat tctaagacgt taccacattg
     1921 cttcacgtta aaagcctttt taatttttaa aatttctagt atatctgcat aacttacatt
     1981 gtcgattttc ttttctctcc atgggcgttg tgtcccactt ttagtcatat ctttcaatgt
     2041 ttcattatct tgattttcgt ctatatattt tgtagtatta tattgcatat aaaaagacct
     2101 ccagttttga tttagattcg acaccttaat catataactg gggttttttt atgtcaattt
     2161 tttctttcac gctaaaaaaa caacacaaat gttgtcatac caacgttttt aaaacatttt
     2221 aattctttga gttatttcta ta
//
