LOCUS       CP052952                2241 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD66-6 plasmid pHD66-6_1, complete
            sequence.
ACCESSION   CP052952
VERSION     CP052952.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732905
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                   :: 148x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:32:33
            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)                     :: 2,437
            CDSs (total)                      :: 2,356
            Genes (coding)                    :: 2,287
            CDSs (with protein)               :: 2,287
            Genes (RNA)                       :: 81
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 69
            CDSs (without protein)            :: 69
            Pseudo Genes (ambiguous residues) :: 0 of 69
            Pseudo Genes (frameshifted)       :: 34 of 69
            Pseudo Genes (incomplete)         :: 33 of 69
            Pseudo Genes (internal stop)      :: 21 of 69
            Pseudo Genes (multiple problems)  :: 16 of 69
            ##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="HD66-6"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD66-6_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(1509..2241,1..266)
                     /locus_tag="HJI09_12180"
     CDS             join(1509..2241,1..266)
                     /locus_tag="HJI09_12180"
                     /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="QRJ05489.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            complement(858..1181)
                     /gene="qacC"
                     /locus_tag="HJI09_12185"
     ARG             complement(862..1181)
                     /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(859..1181)
                     /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          85..272
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.889"
                     /coverage="100.0"
                     /evalue="4.86e-59"
     Typing          1510..2241
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.864"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtcgtccga ttatttaaca ggaaaccatg aaaaagacgc agaaattgtt caagatttag
       61 aacaaggttt atacagaaaa cgtatgttaa gttacggtgg tttacttaaa caaaaacata
      121 aacttttaaa tttagacgat gccgaagaag gtaatttaat tcaaacgagc gatgaagaaa
      181 aaacgactga agaagaacaa aaagcccatt caattacggc catttggaat tttgaaaaac
      241 aaaattattt cttaaaaaat ttgtaacgtt agcttatcaa agctagcgtt tttttatgct
      301 tttttgcccc tgcaggaact atagcgttca accggcatgg ttgcccattt tttatgctaa
      361 tttttaaatt tgcatgtaaa tgggcagtgt ctaaaaaatt cgacactggt tttgctcaaa
      421 tttttgtttg tgaaaagcaa ttatttttat ttggctctca tttgcgtttt aagagccgat
      481 ttaggttttt aggtataaaa ctatataaat aacccttaat tctttaaaat gaccccttaa
      541 aattaaaaat aaaggtattc tgattttgaa taaatgtttg aacaaaaaat aaagagctac
      601 ccttaaaaat tttggtagct cttatatgca ctgttttaat atttaggtgt tatcagtgaa
      661 aaatagatca agaaaggaat tttaattata acacagcatt tatgccgaga aaatttattg
      721 atgttgagaa gaacccttaa ctaaacttgg agacgaatgt cggcatagcg tgagctatta
      781 agccgaccat tcgacaagtt ttgggattgt taagggttcc gaggctcaac gtcaataaag
      841 caattggaat aaagcaatta atgcgatgtt ccgaaaatgt ttaacgaaac tacgccgact
      901 atgattaaaa ctatagatac tatagttatt agatttattt gttctttgaa aataattatt
      961 gagactacgg ttgttaagac taaacctagt cccgcccaag ttgcataagt tatatttagt
     1021 ggtaggtgtt gcattgtttt acttaaaaaa tagaaacaaa ttccaaatga aattattgtt
     1081 cctaaggatg gtataaattt tgaaaagcct tctgaagatt taagaaatgc acttccaata
     1141 acttcagtac ttatggctat tattaaataa atataaggca tttttagctc cttttaattt
     1201 tcgtatttta ttctaagtat tttttaattg taaagtattt tttaattgta gtcttgtatt
     1261 ttgagtgtca ttcgcgtggt atttttgtgg attgatggtt tttgaaaggt ttttgaaacg
     1321 agttgaaaac gagtttcttc ttgtcttgat actatataga aataactcaa agaattaaaa
     1381 tgttttaaaa acgttggtat gacaacattt gtgttgtttt tttagcgtga aagaaaaaat
     1441 tgacataaaa aaaccccagt tatatgatta aggtgtcgaa tctaaatcaa aactggaggt
     1501 ctttttatat gcaatataat actacaaaat atatagacga aaatcaagat aatgaaacat
     1561 tgaaagatat gactaaaagt gggacacaac gcccatggag agaaaagaaa atcgacaatg
     1621 taagttatgc agatatacta gaaattttaa aaattaaaaa ggcttttaac gtgaagcaat
     1681 gtggtaacgt cttagaattt aagccgactg atgaagggta tttaaaactt tataaaacat
     1741 ggttttgtaa gtctaaatta tgtccggttt gtaattggag gcgttcaatg aaaaatagtt
     1801 atcaagctca aaaagtcatt gaagcagtgg ttaaagaaaa gccaaaagca cgttggttat
     1861 tcttaacact ttcaacaaaa aatgcgatag atggtgagca tttagaacag agtttaaaat
     1921 atatgtcgaa agcttttaac aagttaaaaa tgtatgcaaa agttaaaaag aatttaatcg
     1981 gttttatgcg ttcaactgaa gttacagtta acaaaaatga cggaagttat aatcaacata
     2041 tgcacgtttt attgtgtgtt gaaaatgctt atttcagaaa aaaagagaat tatataacgc
     2101 aagaagagtg gatcaattta tggcaaaaag ctcttcaagt tgattacaaa ccagtcgcaa
     2161 atatcaaagc aattaagccg aataaaaaag gcgataaaga tatacaagct gcaattaaag
     2221 agacatcaaa atactcggtt a
//
