LOCUS       NZ_CP129378             2353 bp    DNA     circular CON 19-JUL-2023
DEFINITION  Staphylococcus epidermidis strain CSMH-411EB plasmid pCSME411-4,
            complete sequence.
ACCESSION   NZ_CP129378
VERSION     NZ_CP129378.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36269258
            Assembly: GCF_030435955.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2353)
  AUTHORS   Lee,G.Y. and Yang,S.-J.
  TITLE     Genome sequence of a S. epidermidis isolate recovered from a chicken
            meat
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2353)
  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                   :: 552.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/14/2023 15:52:38
            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)                     :: 2,412
            CDSs (total)                      :: 2,328
            Genes (coding)                    :: 2,267
            CDSs (with protein)               :: 2,267
            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)              :: 61
            CDSs (without protein)            :: 61
            Pseudo Genes (ambiguous residues) :: 0 of 61
            Pseudo Genes (frameshifted)       :: 38 of 61
            Pseudo Genes (incomplete)         :: 32 of 61
            Pseudo Genes (internal stop)      :: 25 of 61
            Pseudo Genes (multiple problems)  :: 24 of 61
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP129378.1.
            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..2353
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="CSMH-411EB"
                     /isolation_source="Chicken meats"
                     /db_xref="taxon:1282"
                     /plasmid="pCSME411-4"
                     /geo_loc_name="South Korea: Gyeonggi"
                     /lat_lon="37.2 N 126.9 E"
                     /collection_date="2019-06-01"
                     /collected_by="Chung-Ang University"
     gene            complement(join(2028..2353,1..679))
                     /locus_tag="QYE82_RS12055"
     CDS             complement(join(2028..2353,1..679))
                     /locus_tag="QYE82_RS12055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_020368559.1"
                     /translation="MQYNTTRYVDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVVKEKPKARWLFLTLSARNAIDGEHLEQSLKHMSKAFNKLKMYTKVKKNLIGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENSYFKNKANYITQEEWVTLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIRAAIKETSKYSVKSSDFLTDDDEKNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            897..1382
                     /gene="lnu(A)"
                     /locus_tag="QYE82_RS12060"
     ARG             898..1379
                     /name="lnu(A)"
                     /gene="lnu(A)"
                     /gene_name="lincosamide nucleotidyltransferase Lnu(A)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE"
                     /identity="99.38"
                     /coverage="100.0"
     ARG             898..1382
                     /name="lnuA"
                     /gene="lnuA"
                     /gene_name="lincosamide nucleotidyltransferase (LNU)"
                     /tool="rgi"
                     /drug_class="lincosamide antibiotic"
                     /identity="98.76"
                     /coverage="100.0"
     Typing          complement(6..679)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.706"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2029..2353)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.239"
                     /coverage="100.0"
                     /evalue="2e-154"
ORIGIN
        1 tttgatttgg tttgatcgct ttaatatttg ctactggtcg ataatttact tgtaatgctt
       61 tttgccataa agtaacccat tcttcttgag ttatataatt agctttattc ttaaaatagc
      121 tattttcaac acacaataaa acgtgcatat gttgattata actaccgtca tttttattaa
      181 ccgttacttc ggttgaacgt aaaaatccga ttaaattctt tttaactttt gtatacattt
      241 ttaatttatt aaaagcctta gacatatgct ttaaactttg ttctaaatgt tcaccgtcta
      301 ttgcatttcg tgctgatagc gtaagaaata accaacgtgc ttttggcttt tctttaacca
      361 cttcttcaat cactttttga gcttgataac tatttttcat agcacgcctc caattacaaa
      421 ctgggcataa ttttgattta caaaaccatg ttttatgtaa tttcaaataa ccttcatcag
      481 ttggcttgaa ctctaagacg ttaccacatt gttttacgtt aaaagccttt tttattttta
      541 aaatttctag tatatctgca taacttacat tatcaatttt cttctctctc catgggcgtt
      601 gtttcccact tttcgtcata tcttttaatg tttcattatc ttgattttcg tctacatatc
      661 tagtagtatt atattgcata taaaaagcct ccagttttga ttttgattcg acaccttaat
      721 catataactg gggttttttc atgtcaaatt ttctttcaac aacaaaaaca accaaaaata
      781 ctgttatatc aacattcaaa tgacttttta tatctttgag ttatttctat atagtatcaa
      841 gacaagaaga aactcgtttt caactcgttt caaattccca agttaggagg gataaaatga
      901 aaaataataa tgtaacagaa aaagaattat tttatatttt agatttattt gaacacatga
      961 aagtaactta ttggttagat ggtggctggg gggtagatgt attaactgga aaacaacaaa
     1021 gagaacacag agatatagat atagattttg acgctcaaca cactcaaaaa gttatacaaa
     1081 aattagaaga tataggatac aaaatagaag ttgattggat gccttcacgt atggaactta
     1141 agcatgaaga atatgggtat ttagatattc atcctataaa tctaaatgat gatggatcaa
     1201 ttacccaagc aaacccagaa ggtggtaatt atgttttcca aaatgactgg ttttcagaaa
     1261 ctaattacaa agatcgaaaa ataccatgta tttcaaaaga agctcaactt ctttttcatt
     1321 ctggttatga tttaacagaa aaagaccatt ttgatataaa aaatttaaaa tcaataacat
     1381 aattgcttta ttccaattgc tttattgacg ttgagcctcg gaacccttaa caatcccaaa
     1441 acttgtcgaa tggtcggctt aatagctcac gctatgccga cattcgtctg caagtttagt
     1501 taagggttct tctcaacatc aataaatttt ctcggcataa atgcgtgttc ttgctataat
     1561 atatcttaga aaaatagatt aaatagctta tcgactattt gcataaatgc tattacaaca
     1621 ttcagtgtca ccagcactaa tttgtaatag cattttttat ttttaaattt tcaaagatac
     1681 caaattttaa atacctttat tttgaattct aagggggcat tttaaagatt taagggtaaa
     1741 tcatatagtt ttatacctaa aaacctacac aagcttttaa aacgcaaata tgagccaaat
     1801 aaatatattc taattccaca aacaaaaatt tgagcaaaac cagtgactat tttttagaca
     1861 ctgcccagtt acatgcaaat taaaaatttg gcatgtactg gcaaaaaaat tcagacactg
     1921 cccatttacg cacaaaatta tttttcgcgt aaaaactggg taaccatgct ggttaatcct
     1981 atagttcccg caggggcaaa aaacataaaa aaacgctagc tttttagcta acgtttcaaa
     2041 tcttttaagt aataattttg tttttcaaaa ttccaaattg cagtaattga atgtgctttt
     2101 tcttcttcgt ctgttgtttt atcttcgtca cttgtattaa ttaaattgcc atcttcggca
     2161 tcatctaaat ttaaaatttt atgtttttgt ttaagcaaac caccataact caacatacgt
     2221 tttcgatata aacctttttc taaatcattt acaatttctt gatttttttc atcatcatca
     2281 gttaaaaaat cagatgactt aaccgaatat ttcgaggttt ctttgatagc tgctcgaata
     2341 tctttatcgc ctt
//
