LOCUS       NZ_CP093169             2241 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Staphylococcus epidermidis strain TMDU-41 plasmid p4, complete
            sequence.
ACCESSION   NZ_CP093169
VERSION     NZ_CP093169.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26514226
            Assembly: GCF_024204705.1
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  JOURNAL   Unpublished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 (07-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 Date                     :: 2020
            Assembly Method :: Unicycler hybrid assembley v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 283.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/20/2023 03:49:39
            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)                     :: 2,351
            CDSs (total)                      :: 2,267
            Genes (coding)                    :: 2,215
            CDSs (with protein)               :: 2,215
            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)              :: 52
            CDSs (without protein)            :: 52
            Pseudo Genes (ambiguous residues) :: 0 of 52
            Pseudo Genes (frameshifted)       :: 34 of 52
            Pseudo Genes (incomplete)         :: 30 of 52
            Pseudo Genes (internal stop)      :: 18 of 52
            Pseudo Genes (multiple problems)  :: 23 of 52
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093169.1.
            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="TMDU-41"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="p4"
                     /geo_loc_name="Japan"
                     /lat_lon="35.701735 N 139.7642509 E"
                     /collection_date="2015-01-21"
                     /collected_by="TMDU hospital staff"
     gene            complement(join(1283..2241,1..40))
                     /locus_tag="MNU56_RS11715"
                     /old_locus_tag="MNU56_11700"
     CDS             complement(join(1283..2241,1..40))
                     /locus_tag="MNU56_RS11715"
                     /old_locus_tag="MNU56_11700"
                     /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            368..691
                     /gene="qacC"
                     /locus_tag="MNU56_RS11720"
                     /old_locus_tag="MNU56_11705"
     ARG             369..688
                     /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             369..691
                     /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(1284..2241)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.896"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttgattttc gtctatatat tttgtagtat tatattgcat ataaaaagac ctccagtttt
       61 gatttagatt cgacacctta atcatataac tggggttttt ttatgtcaat tttttctttc
      121 acgctaaaaa aacaacacaa atgttgtcat accaacgttt ttaaaacatt ttaattcttt
      181 gagttatttc tatatagtat caagacaaga agaaactcgt tttcaactcg tttcaaaaac
      241 ctttcaaaaa ccatcaatcc acaaaaatac cacgcgaatg acactcaaaa tacaagacta
      301 caattaaaaa atactttaca attaaaaaat acttagaata aaatacgaaa attaaaagga
      361 gctaaaaatg ccttatattt atttaataat agccataagt actgaagtta ttggaagtgc
      421 atttcttaaa tcttcagaag gcttttcaaa atttatacca tccttaggaa caataatttc
      481 atttggaatt tgtttctatt ttttaagtaa aacaatgcaa cacctaccac taaatataac
      541 ttatgcaact tgggcgggac taggtttagt cttaacaacc gtagtctcaa taattatttt
      601 caaagaacaa ataaatctaa taactatagt atctatagtt ttaatcatag tcggcgtagt
      661 ttcgttaaac attttcggaa catcgcatta attgctttat tccaattgct ttattgacgt
      721 tgagcctcgg aacccttaac aatcccaaaa cttgtcgaat ggtcggctta atagctcacg
      781 ctatgccgac attcgtctcc aagtttagtt aagggttctt ctcaacatca ataaattttc
      841 tcggcataaa tgctgtgtta taattaaaat tcctttcttg atctattttt cactgataac
      901 acctaaatat taaaacagtg catataagag ctaccaaaat ttttaagggt agctctttat
      961 tttttgttca aacatttatt caaaatcaga atacctttat ttttaatttt aaggggtcat
     1021 tttaaagaat taagggttat ttatatagtt ttatacctaa aaacctaaat cggctcttaa
     1081 aacgcaaatg agagccaaat aaaaataatt gcttttcaca aacaaaaatt tgagcaaaac
     1141 cagtgtcgaa ttttttagac actgcccatt tacatgcaaa tttaaaaatt agcataaaaa
     1201 atgggcaacc atgccggttg aacgctatag ttcctgcagg ggcaaaaaag cataaaaaaa
     1261 cgctagcttt gataagctaa cgttacaaat tttttaagaa ataattttgt ttttcaaaat
     1321 tccaaatggc cgtaattgaa tgggcttttt gttcttcttc agtcgttttt tcttcatcgc
     1381 tcgtttgaat taaattacct tcttcggcat cgtctaaatt taaaagttta tgtttttgtt
     1441 taagtaaacc accgtaactt aacatacgtt ttctgtataa accttgttct aaatcttgaa
     1501 caatttctgc gtctttttca tggtttcctg ttaaataatc ggacgactta accgagtatt
     1561 ttgatgtctc tttaattgca gcttgtatat ctttatcgcc ttttttattc ggcttaattg
     1621 ctttgatatt tgcgactggt ttgtaatcaa cttgaagagc tttttgccat aaattgatcc
     1681 actcttcttg cgttatataa ttctcttttt ttctgaaata agcattttca acacacaata
     1741 aaacgtgcat atgttgatta taacttccgt catttttgtt aactgtaact tcagttgaac
     1801 gcataaaacc gattaaattc tttttaactt ttgcatacat ttttaacttg ttaaaagctt
     1861 tcgacatata ttttaaactc tgttctaaat gctcaccatc tatcgcattt tttgttgaaa
     1921 gtgttaagaa taaccaacgt gcttttggct tttctttaac cactgcttca atgacttttt
     1981 gagcttgata actatttttc attgaacgcc tccaattaca aaccggacat aatttagact
     2041 tacaaaacca tgttttataa agttttaaat acccttcatc agtcggctta aattctaaga
     2101 cgttaccaca ttgcttcacg ttaaaagcct ttttaatttt taaaatttct agtatatctg
     2161 cataacttac attgtcgatt ttcttttctc tccatgggcg ttgtgtccca cttttagtca
     2221 tatctttcaa tgtttcatta t
//
