LOCUS       NZ_CP084011             2507 bp    DNA     circular CON 09-NOV-2023
DEFINITION  Staphylococcus epidermidis strain NBRC 113846 plasmid unnamed3,
            complete sequence.
ACCESSION   NZ_CP084011
VERSION     NZ_CP084011.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21163584
            Assembly: GCF_020181395.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2507)
  AUTHORS   Tourlousse,D.M., Narita,K., Miura,T., Furukawa,M., Shimamura,M.,
            Sekiguchi,Y. and Kawasaki,H.
  TITLE     Characterization and demonstration of mock communities as control
            reagents for accurate human microbiome community measurements
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2507)
  AUTHORS   Tourlousse,D.M., Narita,K., Miura,T., Furukawa,M., Shimamura,M.,
            Sekiguchi,Y. and Kawasaki,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2021) Biomedical Research Institute, National
            Institute of Advanced Industrial Science and Technology, Biomedical
            Research Institute, AIST Tsukuba Central 6, 1-1-1 Higashi, Tsukuba,
            Ibaraki 305-8566, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Flye v. 2.8.3; Racon v. 1.4.20; Medaka v. 1.2.2;
            Pilon v. 1.23
            Assembly Name                     :: Sepi_113846
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 362.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/09/2023 06:58:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,399
            CDSs (total)                      :: 2,315
            Genes (coding)                    :: 2,253
            CDSs (with protein)               :: 2,253
            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)       :: 36 of 62
            Pseudo Genes (incomplete)         :: 32 of 62
            Pseudo Genes (internal stop)      :: 25 of 62
            Pseudo Genes (multiple problems)  :: 25 of 62
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084011.1.
            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..2507
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="NBRC 113846"
                     /isolation_source="human skin"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="unnamed3"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            join(2284..2507,1..100)
                     /gene="qacC"
                     /locus_tag="LCR03_RS11940"
                     /old_locus_tag="LCR03_11940"
     CDS             join(2284..2507,1..100)
                     /gene="qacC"
                     /locus_tag="LCR03_RS11940"
                     /old_locus_tag="LCR03_11940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001146389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /protein_id="WP_001146389.1"
                     /translation="MPYIYLIIAISTEVIGSAFLKSSEGFSKFIPSLGTIISFGICFYF
                     LSKTMQHLPLNITYATWAGLGLVLTTVVSIIIFKEQINLITIVSIVLIIVGVVSLNIFG
                     TSH"
                     /name="qacC"
     gene            complement(566..934)
                     /locus_tag="LCR03_RS11945"
                     /old_locus_tag="LCR03_11945"
     CDS             complement(566..934)
                     /locus_tag="LCR03_RS11945"
                     /old_locus_tag="LCR03_11945"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_053023411.1"
                     /translation="MAGYKLGTDTIYRGTTWVQSQFVGVQPGYKTQKMHTFLKSLYPLK
                     CLASPDHTFLNVCKFPLCSYKEFRANSKFRVFLKEIAPAGTKKVDDFLSHFMQNFSLHV
                     DGQCLFFSAQFAKFLICI"
                     /name="hypothetical protein"
     gene            complement(996..1919)
                     /locus_tag="LCR03_RS11950"
                     /old_locus_tag="LCR03_11950"
     CDS             complement(996..1919)
                     /locus_tag="LCR03_RS11950"
                     /old_locus_tag="LCR03_11950"
                     /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"
     ARG             2285..2505
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="74.32"
                     /coverage="69.16"
     Typing          complement(997..1919)
                     /name="rep_cluster_1281"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.675"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aattattttc aaagaacaaa taaatctaat aactatagta tctatagttt taatcatagt
       61 cggcgtagtt tcgttaaaca ttttcggaac atcgcattaa ttgctttatt ccaattgctt
      121 tattgacgtt gagcctcgga acccttaaca atcccaaaac ttgtcgaatg gtcggcttaa
      181 tagctcacgc tatgccgaca ttcgtctgca agtttagtta agggttcttc tcaacgcaca
      241 ataaattttc tcggcataaa tgcgtgttct tgttataata tagacatcac atttagggtg
      301 cttattaaaa gtagtttttt ataatctact tcgcaaaagc aaataaaaag ccaatccatt
      361 ttatctgggt tggcttttta tttttatatg cctttatttg aattttaagg gggcatttta
      421 aagattcagg ggtaaatcat atagttttat acctaaaagt ctatatacgc ttttaaaacg
      481 caaatatgag ccaaataaat atatcttaat ttcacaaaca aaaatttgag caaaaccagt
      541 gactaatttt ttagacactg cccagttata tgcaaattaa aaatttagca aactgggcag
      601 aaaaaaataa acactgccca tctacatgca aactaaaatt ttgcataaaa tggctcaaaa
      661 aatcatcaac ttttttagtt cctgcagggg caatttcttt caaaaaaaca cggaattttg
      721 aattggctct aaattctttg taagagcata agggaaattt gcatacattt aaaaatgtat
      781 ggtctggcga agccagacat ttcaagggat acagcgattt taaaaaggta tgcatttttt
      841 gcgttttgta cccaggttgt acccctacaa attgcgattg tacccaggtt gtacccctat
      901 atattgtgtc tgtacccagt ttgtacccag ccatttttaa cgtattttca acaaaaaaac
      961 gctagctttt tgctaacgtt taagaaaatt tatttttatt tttcttcgtc aatttcatca
     1021 atcatttgat gattaattct acttttttct tcttcagtca aatcaaaaat ttcactcgct
     1081 aagtattctt tttggttcca gtgataaaaa atttgataaa tatattctgt cggatctact
     1141 tctttaagat aatctaaatc tccatttttt aatttctttc ttgcctcttt aaacagtcca
     1201 gaataaacaa gaatttgttt tcccttaaga gatttataaa atgtatcgaa cactttttga
     1261 ttaactaaat aatcgctatc tttaccagaa tacttcgcca tttcgtataa ttctttgttg
     1321 ttgttctgtt tgattttttg aacatgtact tgtgtgattt catcaattcc agtcacatct
     1381 cgccataaat tcagccattc tttttgacta atataatatc gtttgtctgt aaaatacgat
     1441 ttgttaacag caatcaaaac atgaaaatgt ggattataat catcgcgttt tttgttgtaa
     1501 gtaatttcta attttcttac gtaaccttta gctatagatt taaaatgttt acgattactt
     1561 aatcgtctaa acgactcatt ataatttttt atttcatctt ccaaatgctc aactgttaca
     1621 tttggtgtcg taagtgttaa aaagatgaat tgtttatctt ctttttgctt aatatattgc
     1681 atcatcaatg ataaacctaa cgcatctttt ctcgcttttc gccatgaaca tacaggacaa
     1741 aatcgatttt tacacaaatt agatttatgc aatttctgtt tctctaacgt tctatctgcc
     1801 acaaaactca agaatgtatt gcactccttt atcaaatcca tttgcccttc tttgacatgt
     1861 cgcttaataa atttctgaaa tacttgattt ctttgtttct tctcagtata cttatccatg
     1921 ttataacaca acaaaacaac ttagttttac acaaactaat gccataaaaa aagttgcttt
     1981 ttctcctttc ttgtaaagtt ttggcttgga caccataaac tctactatac taggtatgaa
     2041 aaagcaactt tttttatgct cgaaaccaga tataccaaca gattaagggt aactattata
     2101 gcttgtaata gttacctata gtatcaagac aagaagaaac tcgttttcaa ctcgtttcaa
     2161 aaacctttca aaaaccatca atccacaaaa ataccacgcg aatgacactc aaaatacaag
     2221 actacaatta aaaaatactt agaataaaat taaataaaat acgaaaatta aaaggagtta
     2281 aaaatgcctt atatttattt aataatagcc ataagtactg aagttattgg aagtgcattt
     2341 cttaaatctt cagaaggctt ttcaaaattt ataccatcct taggaacaat aatttcattt
     2401 ggaatttgtt tctatttttt aagtaaaaca atgcaacacc taccactaaa tataacttat
     2461 gcaacttggg cgggactagg tttagtctta acaaccgtag tctcaat
//
