LOCUS       CP052954                2241 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD66-1 plasmid pHD66-1_1, complete
            sequence.
ACCESSION   CP052954
VERSION     CP052954.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732904
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2241)
  AUTHORS   Both,A., Huang,J., Qi,M., Lausmann,C., Weisselberg,S., Buttner,H.,
            Lezius,S., Failla,A.V., Christner,M., Stegger,M., Gehrke,T.,
            Baig,S., Citak,M., Alawi,M., Aepfelbacher,M. and Rohde,H.
  TITLE     Distinct clonal lineages and within-host diversification shape
            invasive Staphylococcus epidermidis populations
  JOURNAL   PLoS Pathog 17 (2), e1009304 (2021)
   PUBMED   33544760
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 2241)
  AUTHORS   Both,A., Huang,J., Qi,M., Lausmann,C., Weisselberg,S., Buettner,H.,
            Lezius,S., Failla,A.V., Christner,M., Stegger,M., Gehrke,T.,
            Baig,S., Citak,M., Alawi,M., Aepfelbacher,M. and Rohde,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-APR-2020) Institute of Medical Microbiology, Virology
            and Hygiene, University Medical Center Hamburg-Eppendorf,
            Martinistr. 52, Hamburg, Hamburg 20246, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 95x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:33:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 2,465
            CDSs (total)                      :: 2,381
            Genes (coding)                    :: 2,311
            CDSs (with protein)               :: 2,311
            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)              :: 70
            CDSs (without protein)            :: 70
            Pseudo Genes (ambiguous residues) :: 0 of 70
            Pseudo Genes (frameshifted)       :: 34 of 70
            Pseudo Genes (incomplete)         :: 35 of 70
            Pseudo Genes (internal stop)      :: 21 of 70
            Pseudo Genes (multiple problems)  :: 17 of 70
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..2241
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD66-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD66-1_1"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2018"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            join(1924..2241,1..681)
                     /locus_tag="HJI08_12320"
     CDS             join(1924..2241,1..681)
                     /locus_tag="HJI08_12320"
                     /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="QRJ07800.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            complement(1273..1596)
                     /gene="qacC"
                     /locus_tag="HJI08_12325"
     ARG             complement(1277..1596)
                     /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"
     ARG             complement(1274..1596)
                     /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          2..687
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.212"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1925..2241
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.45e-165"
ORIGIN
        1 gtggttaaag aaaagccaaa agcacgttgg ttattcttaa cactttcaac aaaaaatgcg
       61 atagatggtg agcatttaga acagagttta aaatatatgt cgaaagcttt taacaagtta
      121 aaaatgtatg caaaagttaa aaagaattta atcggtttta tgcgttcaac tgaagttaca
      181 gttaacaaaa atgacggaag ttataatcaa catatgcacg ttttattgtg tgttgaaaat
      241 gcttatttca gaaaaaaaga gaattatata acgcaagaag agtggatcaa tttatggcaa
      301 aaagctcttc aagttgatta caaaccagtc gcaaatatca aagcaattaa gccgaataaa
      361 aaaggcgata aagatataca agctgcaatt aaagagacat caaaatactc ggttaagtcg
      421 tccgattatt taacaggaaa ccatgaaaaa gacgcagaaa ttgttcaaga tttagaacaa
      481 ggtttataca gaaaacgtat gttaagttac ggtggtttac ttaaacaaaa acataaactt
      541 ttaaatttag acgatgccga agaaggtaat ttaattcaaa cgagcgatga agaaaaaacg
      601 actgaagaag aacaaaaagc ccattcaatt acggccattt ggaattttga aaaacaaaat
      661 tatttcttaa aaaatttgta acgttagctt atcaaagcta gcgttttttt atgctttttt
      721 gcccctgcag gaactatagc gttcaaccgg catggttgcc cattttttat gctaattttt
      781 aaatttgcat gtaaatgggc agtgtctaaa aaattcgaca ctggttttgc tcaaattttt
      841 gtttgtgaaa agcaattatt tttatttggc tctcatttgc gttttaagag ccgatttagg
      901 tttttaggta taaaactata taaataaccc ttaattcttt aaaatgaccc cttaaaatta
      961 aaaataaagg tattctgatt ttgaataaat gtttgaacaa aaaataaaga gctaccctta
     1021 aaaattttgg tagctcttat atgcactgtt ttaatattta ggtgttatca gtgaaaaata
     1081 gatcaagaaa ggaattttaa ttataacaca gcatttatgc cgagaaaatt tattgatgtt
     1141 gagaagaacc cttaactaaa cttggagacg aatgtcggca tagcgtgagc tattaagccg
     1201 accattcgac aagttttggg attgttaagg gttccgaggc tcaacgtcaa taaagcaatt
     1261 ggaataaagc aattaatgcg atgttccgaa aatgtttaac gaaactacgc cgactatgat
     1321 taaaactata gatactatag ttattagatt tatttgttct ttgaaaataa ttattgagac
     1381 tacggttgtt aagactaaac ctagtcccgc ccaagttgca taagttatat ttagtggtag
     1441 gtgttgcatt gttttactta aaaaatagaa acaaattcca aatgaaatta ttgttcctaa
     1501 ggatggtata aattttgaaa agccttctga agatttaaga aatgcacttc caataacttc
     1561 agtacttatg gctattatta aataaatata aggcattttt agctcctttt aattttcgta
     1621 ttttattcta agtatttttt aattgtaaag tattttttaa ttgtagtctt gtattttgag
     1681 tgtcattcgc gtggtatttt tgtggattga tggtttttga aaggtttttg aaacgagttg
     1741 aaaacgagtt tcttcttgtc ttgatactat atagaaataa ctcaaagaat taaaatgttt
     1801 taaaaacgtt ggtatgacaa catttgtgtt gtttttttag cgtgaaagaa aaaattgaca
     1861 taaaaaaacc ccagttatat gattaaggtg tcgaatctaa atcaaaactg gaggtctttt
     1921 tatatgcaat ataatactac aaaatatata gacgaaaatc aagataatga aacattgaaa
     1981 gatatgacta aaagtgggac acaacgccca tggagagaaa agaaaatcga caatgtaagt
     2041 tatgcagata tactagaaat tttaaaaatt aaaaaggctt ttaacgtgaa gcaatgtggt
     2101 aacgtcttag aatttaagcc gactgatgaa gggtatttaa aactttataa aacatggttt
     2161 tgtaagtcta aattatgtcc ggtttgtaat tggaggcgtt caatgaaaaa tagttatcaa
     2221 gctcaaaaag tcattgaagc a
//
