LOCUS       NZ_CP093178             2473 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Staphylococcus epidermidis strain TMDU-137 plasmid p5, complete
            sequence.
ACCESSION   NZ_CP093178
VERSION     NZ_CP093178.1
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 2473)
  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  JOURNAL   Unpublished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 2473)
  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
            CP093178.1.
            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..2473
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="TMDU-137"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="p5"
                     /geo_loc_name="Japan"
                     /lat_lon="35.701735 N 139.7642509 E"
                     /collection_date="2015-03-09"
                     /collected_by="TMDU hospital staff"
     gene            5..64
                     /gene="ermCL"
                     /locus_tag="MNU44_RS12355"
                     /old_locus_tag="MNU44_12345"
     CDS             5..64
                     /gene="ermCL"
                     /locus_tag="MNU44_RS12355"
                     /old_locus_tag="MNU44_12345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methylase leader peptide ErmCL"
                     /protein_id="WP_002497446.1"
                     /translation="MGIFSIFVISTVHYQPNKK"
                     /name="ermCL"
     gene            125..859
                     /gene="erm(C)"
                     /locus_tag="MNU44_RS12360"
                     /old_locus_tag="MNU44_12350"
     ARG             126..856
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1307..1783
                     /locus_tag="MNU44_RS12365"
                     /old_locus_tag="MNU44_12355"
     CDS             1307..1783
                     /locus_tag="MNU44_RS12365"
                     /old_locus_tag="MNU44_12355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000664727.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     ARG             126..859
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          1308..1793
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaatatgggc atttttagta tttttgtaat cagcacagtt cattatcaac caaacaaaaa
       61 ataagtggtt ataatgaatc gttaataagc aaaattcatt ataaccaaat taaagagggt
      121 tataatgaac gagaaaaata taaaacacag tcaaaacttt attacttcaa aacataatat
      181 agataaaata atgacaaata taagattaaa tgaacatgat aatatctttg aaatcggctc
      241 aggaaaaggg cattttaccc ttgaattagt acagaggtgt aatttcgtaa ctgccattga
      301 aatagaccat aaattatgca aaactacaga aaataaactt gttgatcacg ataatttcca
      361 agttttaaac aaggatatat tgcagtttaa atttcctaaa aaccaatcct ataaaatatt
      421 tggtaatata ccttataaca taagtacgga tataatacgc aaaattgttt ttgatagtat
      481 agctgatgag atttatttaa tcgtggaata cgggtttgct aaaagattat taaatacaaa
      541 acgctcattg gcattatttt taatggcaga agttgatatt tctatattaa gtatggttcc
      601 aagagaatat tttcatccta aacctaaagt gaatagctca cttatcagat taaatagaaa
      661 aaaatcaaga atatcacaca aagataaaca gaagtataat tatttcgtta tgaaatgggt
      721 taacaaagaa tacaagaaaa tatttacaaa aaatcaattt aacaattcct taaaacatgc
      781 aggaattgac gatttaaaca atattagctt tgaacaattc ttatctcttt tcaatagcta
      841 taaattattt aataagtaag ttaagggatg cataaactgc atcccttaac ttgtttttcg
      901 tgtacctatt ttttgtgaat cgattatgtc ttttgcgcat tcacttcttt tctatataaa
      961 tatgagcgaa gcgaataagc gtcggaaaag cagcaaaaag tttccttttt gctgttggag
     1021 catgggggtt cagggggtgc agtatctgac gtcaatgccg agcgaaagcg agccgaaggg
     1081 tagcatttac gttagataac cccctgatat gctccgacgc tttatataga aaagaagatt
     1141 caactaggta aaatcttaat ataggttgag atgataaggt ttataaggaa tttgtttgtt
     1201 ctaatttttc actcattttg ttctaatttc ttttaacaaa tgttcttttt tttttagaac
     1261 agttatgata tagttagaat agtttaaaat aaggagtgag aaaaagatga aagaaagata
     1321 tggaacagtc tataaaggct ctcagaggct catagacgaa gaaagtggag aagtcataga
     1381 ggtagacaag ttataccgta aacaaacgtc tggtaacttc gtaaaggcat atatagtgca
     1441 attaataagt atgttagata tgattggcgg aaaaaaactt aaaatcgtta actatatcct
     1501 agataatgtc cacttaagta acaatacaat gatagctaca acaagagaaa tagcaaaagc
     1561 tacaggaaca agtctacaaa cagtaataac aacacttaaa atcttagaag aaggaaatat
     1621 tataaaaaga aaaactggag tattaatgtt aaaccctgaa ctactaatga gaggcgacga
     1681 ccaaaaacaa aaatacctct tactcgaatt tgggaacttt gagcaagagg caaatgaaaa
     1741 acaagaaaat gcattatctg attattattc tttcaaggac tagtataaca taaaatcgtc
     1801 tacaaataga caaaaaacct gcacgcttaa tgtagatcaa aagcttaacg caaatgaaat
     1861 agattgacct cccaataaca ccacgtagtt attgggaggt caatctatga aatgcgatta
     1921 agctttttct aattcacata agcgtgcagg tttaaagtac ataaaaaata taatgaaaaa
     1981 aagcatcatt atactaacgt tataccaaca ttatactctc attatactaa ttgcttattc
     2041 caatttccta ttggttggaa ccaacaggcg ttagtgtgtt gttgagttgg tactttcatg
     2101 ggattaatcc catgaaaccc ccaaccaact cgccaaagct ttggctaaca cacacgccat
     2161 tccaaccaat agttttctcg gcataaagcc atgctctgac gcttaaatgc actaatgcct
     2221 taaaaaaaca ttaaagtcta acacactaga cttatttact tcgtaattaa gtcgttaaac
     2281 cgtgtgctct acgaccaaaa gtataaaacc tttaagaact ttcttttttc ttgtaaaaaa
     2341 agaaactaga taaatctctc atatctttta ttcaataatc gcatcagatt gcagtataaa
     2401 tttaacgatc actcatcatg ttcatattta tcagagctcg tgctataatt atactaattt
     2461 tataaggagg aaa
//
