LOCUS       NZ_CP129368             2473 bp    DNA     circular CON 19-JUL-2023
DEFINITION  Staphylococcus epidermidis strain CKFA-393 plasmid pCKFA393-3,
            complete sequence.
ACCESSION   NZ_CP129368
VERSION     NZ_CP129368.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36269254
            Assembly: GCF_030435915.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2473)
  AUTHORS   Lee,G.Y. and Yang,S.-J.
  TITLE     Genome sequence of a SCCmec V carrying S. epidermidis isolate
            recovered from a broiler
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2473)
  AUTHORS   Lee,G.Y. and Yang,S.-J.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUL-2023) Department of veterinary microbiology, Seoul
            National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South
            Korea
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Prokka v. v1.14.6
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 484.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/14/2023 15:50:09
            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)                     :: 2,329
            CDSs (total)                      :: 2,245
            Genes (coding)                    :: 2,191
            CDSs (with protein)               :: 2,191
            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)              :: 54
            CDSs (without protein)            :: 54
            Pseudo Genes (ambiguous residues) :: 0 of 54
            Pseudo Genes (frameshifted)       :: 30 of 54
            Pseudo Genes (incomplete)         :: 34 of 54
            Pseudo Genes (internal stop)      :: 16 of 54
            Pseudo Genes (multiple problems)  :: 20 of 54
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP129368.1.
            Bacteria and source DNA available from Seoul National University.
            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="CKFA-393"
                     /isolation_source="cloaca"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:1282"
                     /plasmid="pCKFA393-3"
                     /geo_loc_name="South Korea: Gyeongsang"
                     /lat_lon="35.4 N 128.9 E"
                     /collection_date="2019-05-19"
                     /collected_by="Chung-Ang University"
     gene            join(2471..2473,1..474)
                     /locus_tag="QYE85_RS11635"
     CDS             join(2471..2473,1..474)
                     /locus_tag="QYE85_RS11635"
                     /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"
     gene            1169..1228
                     /gene="ermCL"
                     /locus_tag="QYE85_RS11640"
     CDS             1169..1228
                     /gene="ermCL"
                     /locus_tag="QYE85_RS11640"
                     /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            1289..2023
                     /gene="erm(C)"
                     /locus_tag="QYE85_RS11645"
     ARG             1290..2020
                     /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"
     ARG             1290..2023
                     /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          2..484
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.588"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaagaaagat atggaacagt ctataaaggc tctcagaggc tcatagacga agaaagtgga
       61 gaagtcatag aggtagacaa gttataccgt aaacaaacgt ctggtaactt cgtaaaggca
      121 tatatagtgc aattaataag tatgttagat atgattggcg gaaaaaaact taaaatcgtt
      181 aactatatcc tagataatgt ccacttaagt aacaatacaa tgatagctac aacaagagaa
      241 atagcaaaag ctacaggaac aagtctacaa acagtaataa caacacttaa aatcttagaa
      301 gaaggaaata ttataaaaag aaaaactgga gtattaatgt taaaccctga actactaatg
      361 agaggcgacg accaaaaaca aaaatacctc ttactcgaat ttgggaactt tgagcaagag
      421 gcaaatgaaa aacaagaaaa tgcattatct gattattatt ctttcaagga ctagtataac
      481 ataaaatcgt ctacaaatag acaaaaaacc tgcacgctta atgtagatca aaagcttaac
      541 gcaaatgaaa tagattgacc tcccaataac accacgtagt tattgggagg tcaatctatg
      601 aaatgcgatt aagctttttc taattcacat aagcgtgcag gtttaaagta cataaaaaat
      661 ataatgaaaa aaagcatcat tatactaacg ttataccaac attatactct cattatacta
      721 attgcttatt ccaatttcct attggttgga accaacaggc gttagtgtgt tgttgagttg
      781 gtactttcat gggattaatc ccatgaaacc cccaaccaac tcgccaaagc tttggctaac
      841 acacacgcca ttccaaccaa tagttttctc ggcataaagc catgctctga cgcttaaatg
      901 cactaatgcc ttaaaaaaac attaaagtct aacacactag acttatttac ttcgtaatta
      961 agtcgttaaa ccgtgtgctc tacgaccaaa agtataaaac ctttaagaac tttctttttt
     1021 cttgtaaaaa aagaaactag ataaatctct catatctttt attcaataat cgcatcagat
     1081 tgcagtataa atttaacgat cactcatcat gttcatattt atcagagctc gtgctataat
     1141 tatactaatt ttataaggag gaaaaaatat gggcattttt agtatttttg taatcagcac
     1201 agttcattat caaccaaaca aaaaataagt ggttataatg aatcgttaat aagcaaaatt
     1261 cattataacc aaattaaaga gggttataat gaacgagaaa aatataaaac acagtcaaaa
     1321 ctttattact tcaaaacata atatagataa aataatgaca aatataagat taaatgaaca
     1381 tgataatatc tttgaaatcg gctcaggaaa agggcatttt acccttgaat tagtacagag
     1441 gtgtaatttc gtaactgcca ttgaaataga ccataaatta tgcaaaacta cagaaaataa
     1501 acttgttgat cacgataatt tccaagtttt aaacaaggat atattgcagt ttaaatttcc
     1561 taaaaaccaa tcctataaaa tatttggtaa tataccttat aacataagta cggatataat
     1621 acgcaaaatt gtttttgata gtatagctga tgagatttat ttaatcgtgg aatacgggtt
     1681 tgctaaaaga ttattaaata caaaacgctc attggcatta tttttaatgg cagaagttga
     1741 tatttctata ttaagtatgg ttccaagaga atattttcat cctaaaccta aagtgaatag
     1801 ctcacttatc agattaaata gaaaaaaatc aagaatatca cacaaagata aacagaagta
     1861 taattatttc gttatgaaat gggttaacaa agaatacaag aaaatattta caaaaaatca
     1921 atttaacaat tccttaaaac atgcaggaat tgacgattta aacaatatta gctttgaaca
     1981 attcttatct cttttcaata gctataaatt atttaataag taagttaagg gatgcataaa
     2041 ctgcatccct taacttgttt ttcgtgtacc tattttttgt gaatcgatta tgtcttttgc
     2101 gcattcactt cttttctata taaatatgag cgaagcgaat aagcgtcgga aaagcagcaa
     2161 aaagtttcct ttttgctgtt ggagcatggg ggttcagggg gtgcagtatc tgacgtcaat
     2221 gccgagcgaa agcgagccga agggtagcat ttacgttaga taaccccctg atatgctccg
     2281 acgctttata tagaaaagaa gattcaacta ggtaaaatct taatataggt tgagatgata
     2341 aggtttataa ggaatttgtt tgttctaatt tttcactcat tttgttctaa tttcttttaa
     2401 caaatgttct ttttttttta gaacagttat gatatagtta gaatagttta aaataaggag
     2461 tgagaaaaag atg
//
