LOCUS       NZ_CP093177             2585 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Staphylococcus epidermidis strain TMDU-137 plasmid p4, complete
            sequence.
ACCESSION   NZ_CP093177
VERSION     NZ_CP093177.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26515364
            Assembly: GCF_024204745.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2585)
  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  JOURNAL   Unpublished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 2585)
  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                   :: 249.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/20/2023 03:41:00
            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)                     :: 2,479
            CDSs (total)                      :: 2,395
            Genes (coding)                    :: 2,333
            CDSs (with protein)               :: 2,333
            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)              :: 62
            CDSs (without protein)            :: 62
            Pseudo Genes (ambiguous residues) :: 0 of 62
            Pseudo Genes (frameshifted)       :: 37 of 62
            Pseudo Genes (incomplete)         :: 33 of 62
            Pseudo Genes (internal stop)      :: 22 of 62
            Pseudo Genes (multiple problems)  :: 24 of 62
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093177.1.
            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..2585
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="TMDU-137"
                     /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="2015-03-09"
                     /collected_by="TMDU hospital staff"
     gene            9..932
                     /locus_tag="MNU44_RS12340"
                     /old_locus_tag="MNU44_12330"
     CDS             9..932
                     /locus_tag="MNU44_RS12340"
                     /old_locus_tag="MNU44_12330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002499696.1"
                     /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_002485596.1"
                     /translation="MDKYTEKKQRNQVFQKFIKRHVKEGQMDLIKECNTFLSFVADRTL
                     EKQKLHKSNLCKNRFCPVCSWRKARKDALGLSLMMQYIKQKEDKQFIFLTLTTPNVTVE
                     HLEDEIKNYNESFRRLSNRKHFKSIAKGYVRKLEITYNKKRDDYNPHFHVLIAVNKSYF
                     TDKRYYISQKEWLNLWRDVTGIDEITQVHVQKIKQNNNKELYEMAKYSGKDSDYLVNQK
                     VFDTFYKSLKGKQILVYSGLFKEARKKLKNGDLDYLKEVDPTEYIYQIFYHWNQKEYLA
                     SEIFDLTEEEKSRINHQMIDEIDEEK"
                     /name="protein rep"
     gene            complement(1764..2087)
                     /gene="qacC"
                     /locus_tag="MNU44_RS12345"
                     /old_locus_tag="MNU44_12335"
     ARG             complement(1768..2087)
                     /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(<2134..2229)
                     /locus_tag="MNU44_RS12350"
                     /old_locus_tag="MNU44_12340"
                     /pseudo=""
     CDS             complement(<2134..2229)
                     /locus_tag="MNU44_RS12350"
                     /old_locus_tag="MNU44_12340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001146389.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0022857 - transmembrane transporter
                     activity [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="SMR family transporter"
                     /name="SMR family transporter"
     ARG             complement(1765..2087)
                     /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          10..932
                     /name="rep_cluster_1281"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.675"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttataacat ggataagtat actgagaaga aacaaagaaa tcaagtattt cagaaattta
       61 ttaagcgaca tgtcaaagaa gggcaaatgg atttgataaa ggagtgcaat acattcttga
      121 gttttgtggc agatagaacg ttagagaaac agaaattgca taaatctaat ttgtgtaaaa
      181 atcgattttg tcctgtatgt tcatggcgaa aagcgagaaa agatgcgtta ggtttatcat
      241 tgatgatgca atatattaag caaaaagaag ataaacaatt catcttttta acacttacga
      301 caccaaatgt aacagttgag catttggaag atgaaataaa aaattataat gagtcgttta
      361 gacgattaag taatcgtaaa cattttaaat ctatagctaa aggttacgta agaaaattag
      421 aaattactta caacaaaaaa cgcgatgatt ataatccaca ttttcatgtt ttgattgctg
      481 ttaacaaatc gtattttaca gacaaacgat attatattag tcaaaaagaa tggctgaatt
      541 tatggcgaga tgtgactgga attgatgaaa tcacacaagt acatgttcaa aaaatcaaac
      601 agaacaacaa caaagaatta tacgaaatgg cgaagtattc tggtaaagat agcgattatt
      661 tagttaatca aaaagtgttc gatacatttt ataaatctct taagggaaaa caaattcttg
      721 tttattctgg actgtttaaa gaggcaagaa agaaattaaa aaatggagat ttagattatc
      781 ttaaagaagt agatccgaca gaatatattt atcaaatttt ttatcactgg aaccaaaaag
      841 aatacttagc gagtgaaatt tttgatttga ctgaagaaga aaaaagtaga attaatcatc
      901 aaatgattga tgaaattgac gaagaaaaat aaaaataaat tttcttaaac gttagcaaaa
      961 agctagcgtt tttttgttga aaatacgtta aaaatggctg ggtacaacct gggtacaaaa
     1021 cgcaaaaaat gcataccttt ttaaaatcgc tgtatccctt gaaatgtctg gcttcgccag
     1081 accatacatt tttaaatgta tgcaaatttc ccttatgctc ttacaaagaa tttagagcca
     1141 attcaaaatt ccgtgttttt ttgaaagaaa ttgcccctgc aggaactaaa aaagttgatg
     1201 attttttgag ccattttatg caaaatttta gtttgcatgt agatgggcag tgtttatttt
     1261 tttctgccca gtttgctaaa tttttaattt gcatataact gggcagtgtc taaaaaatta
     1321 gtcactggtt ttgctcaaat ttttgtttgt gaaattaaga tatatttatt tggctcatat
     1381 ttgcgtttta aaagcgtata tagactttta ggtataaaac tatatgattt acccctgaat
     1441 ctttaaaatg cccccttaaa attcaaataa aggcatataa aaataaaaag ccaacccaga
     1501 taaaatggat tggcttttta tttgcttttg cgaagtagat tataaaaaac tacttttaat
     1561 aagcacccta aatgtgatgt ctatattata acaagaacac gcatttatgc cgagaaaatt
     1621 tattgtgcgt tgagaagaac ccttaactaa acttgcagac gaatgtcggc atagcgtgag
     1681 ctattaagcc gaccattcga caagttttgg gattgttaag ggttccgagg ctcaacgtca
     1741 ataaagcaat tggaataaag caattaatgc gatgttccga aaatgtttaa cgaaactacg
     1801 ccgactatga ttaaaactat agatactata gttattagat ttatttgttc tttgaaaata
     1861 attattgaga ctacggttgt taagactaaa cctagtcccg cccaagttgc ataagttata
     1921 tttagtggta ggtgttgcat tgttttactt aaaaaataga aacaaattcc aaatgaaatt
     1981 attgttccta aggatggtat aaattttgaa aagccttctg aagatttaag aaatgcactt
     2041 ccaataactt cagtacttat ggctattatt aaataaatat aaggcatttt taactccttt
     2101 taattttcgt attttattta attttattct aaaggatggt ataaattttg aaaagccttc
     2161 tgaagattta agaaatgcac ttccaataac ttcagtactt atggctatta ttaaataaat
     2221 ataaggcatt tttaactcct tttaattttc gtattttatt taattttatt ctaagtattt
     2281 tttaattgta gtcttgtatt ttgagtgtca ttcgcgtggt atttttgtgg attgatggtt
     2341 tttgaaaggt ttttgaaacg agttgaaaac gagtttcttc ttgtcttgat actataggta
     2401 actattacaa gctataatag ttacccttaa tctgttggta tatctggttt cgagcataaa
     2461 aaaagttgct ttttcatacc tagtatagta gagtttatgg tgtccaagcc aaaactttac
     2521 aagaaaggag aaaaagcaac tttttttatg gcattagttt gtgtaaaact aagttgtttt
     2581 gttgt
//
