LOCUS       NZ_CP093207             2241 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Staphylococcus epidermidis strain TSM-36 plasmid p2, complete
            sequence.
ACCESSION   NZ_CP093207
VERSION     NZ_CP093207.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26520678
            Assembly: GCF_024204925.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2241)
  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  JOURNAL   Unpublished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 2241)
  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                   :: 742.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/20/2023 03:46:41
            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)                     :: 2,490
            CDSs (total)                      :: 2,404
            Genes (coding)                    :: 2,347
            CDSs (with protein)               :: 2,347
            Genes (RNA)                       :: 86
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 63
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 57
            CDSs (without protein)            :: 57
            Pseudo Genes (ambiguous residues) :: 0 of 57
            Pseudo Genes (frameshifted)       :: 37 of 57
            Pseudo Genes (incomplete)         :: 34 of 57
            Pseudo Genes (internal stop)      :: 19 of 57
            Pseudo Genes (multiple problems)  :: 25 of 57
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093207.1.
            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..2241
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="TSM-36"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="p2"
                     /geo_loc_name="Japan"
                     /lat_lon="35.75322977 N 139.70093331 E"
                     /collection_date="2012-09-28"
                     /collected_by="Toshima hospital staff"
     gene            complement(join(1503..2241,1..260))
                     /locus_tag="MNU43_RS12425"
                     /old_locus_tag="MNU43_12410"
     CDS             complement(join(1503..2241,1..260))
                     /locus_tag="MNU43_RS12425"
                     /old_locus_tag="MNU43_12410"
                     /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"
     gene            588..911
                     /gene="qacC"
                     /locus_tag="MNU43_RS12430"
                     /old_locus_tag="MNU43_12415"
     ARG             589..908
                     /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"
     ARG             589..911
                     /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(2..260)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.077"
                     /coverage="100.0"
                     /evalue="3.99e-81"
     Typing          complement(1504..2241)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.865"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 accggacata atttagactt acaaaaccat gttttataaa gttttaaata cccttcatca
       61 gtcggcttaa attctaagac gttaccacat tgcttcacgt taaaagcctt tttaattttt
      121 aaaatttcta gtatatctgc ataacttaca ttgtcgattt tcttttctct ccatgggcgt
      181 tgtgtcccac ttttagtcat atctttcaat gtttcattat cttgattttc gtctatatat
      241 tttgtagtat tatattgcat ataaaaagac ctccagtttt gatttagatt cgacacctta
      301 atcatataac tggggttttt ttatgtcaat tttttctttc acgctaaaaa aacaacacaa
      361 atgttgtcat accaacgttt ttaaaacatt ttaattcttt gagttatttc tatatagtat
      421 caagacaaga agaaactcgt tttcaactcg tttcaaaaac ctttcaaaaa ccatcaatcc
      481 acaaaaatac cacgcgaatg acactcaaaa tacaagacta caattaaaaa atactttaca
      541 attaaaaaat acttagaata aaatacgaaa attaaaagga gctaaaaatg ccttatattt
      601 atttaataat agccataagt actgaagtta ttggaagtgc atttcttaaa tcttcagaag
      661 gcttttcaaa atttatacca tccttaggaa caataatttc atttggaatt tgtttctatt
      721 ttttaagtaa aacaatgcaa cacctaccac taaatataac ttatgcaact tgggcgggac
      781 taggtttagt cttaacaacc gtagtctcaa taattatttt caaagaacaa ataaatctaa
      841 taactatagt atctatagtt ttaatcatag tcggcgtagt ttcgttaaac attttcggaa
      901 catcgcatta attgctttat tccaattgct ttattgacgt tgagcctcgg aacccttaac
      961 aatcccaaaa cttgtcgaat ggtcggctta atagctcacg ctatgccgac attcgtctcc
     1021 aagtttagtt aagggttctt ctcaacatca ataaattttc tcggcataaa tgctgtgtta
     1081 taattaaaat tcctttcttg atctattttt cactgataac acctaaatat taaaacagtg
     1141 catataagag ctaccaaaat ttttaagggt agctctttat tttttgttca aacatttatt
     1201 caaaatcaga atacctttat ttttaatttt aaggggtcat tttaaagaat taagggttat
     1261 ttatatagtt ttatacctaa aaacctaaat cggctcttaa aacgcaaatg agagccaaat
     1321 aaaaataatt gcttttcaca aacaaaaatt tgagcaaaac cagtgtcgaa ttttttagac
     1381 actgcccatt tacatgcaaa tttaaaaatt agcataaaaa atgggcaacc atgccggttg
     1441 aacgctatag ttcctgcagg ggcaaaaaag cataaaaaaa cgctagcttt gataagctaa
     1501 cgttacaaat tttttaagaa ataattttgt ttttcaaaat tccaaatggc cgtaattgaa
     1561 tgggcttttt gttcttcttc agtcgttttt tcttcatcgc tcgtttgaat taaattacct
     1621 tcttcggcat cgtctaaatt taaaagttta tgtttttgtt taagtaaacc accgtaactt
     1681 aacatacgtt ttctgtataa accttgttct aaatcttgaa caatttctgc gtctttttca
     1741 tggtttcctg ttaaataatc ggacgactta accgagtatt ttgatgtctc tttaattgca
     1801 gcttgtatat ctttatcgcc ttttttattc ggcttaattg ctttgatatt tgcgactggt
     1861 ttgtaatcaa cttgaagagc tttttgccat aaattgatcc actcttcttg cgttatataa
     1921 ttctcttttt ttctgaaata agcattttca acacacaata aaacgtgcat atgttgatta
     1981 taacttccgt catttttgtt aactgtaact tcagttgaac gcataaaacc gattaaattc
     2041 tttttaactt ttgcatacat ttttaacttg ttaaaagctt tcgacatata ttttaaactc
     2101 tgttctaaat gctcaccatc tatcgcattt tttgttgaaa gtgttaagaa taaccaacgt
     2161 gcttttggct tttctttaac cactgcttca atgacttttt gagcttgata actatttttc
     2221 attgaacgcc tccaattaca a
//
