LOCUS       CP052947                3145 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD75-1 plasmid pHD75-1_6, complete
            sequence.
ACCESSION   CP052947
VERSION     CP052947.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732907
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3145)
  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 3145)
  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                   :: 146x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 14:36:52
            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)                     :: 2,526
            CDSs (total)                      :: 2,442
            Genes (coding)                    :: 2,393
            CDSs (with protein)               :: 2,393
            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)              :: 49
            CDSs (without protein)            :: 49
            Pseudo Genes (ambiguous residues) :: 0 of 49
            Pseudo Genes (frameshifted)       :: 36 of 49
            Pseudo Genes (incomplete)         :: 19 of 49
            Pseudo Genes (internal stop)      :: 21 of 49
            Pseudo Genes (multiple problems)  :: 19 of 49
            ##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..3145
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD75-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD75-1_6"
                     /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            complement(367..798)
                     /locus_tag="HJI11_12610"
     CDS             complement(367..798)
                     /locus_tag="HJI11_12610"
                     /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="QRJ01009.1"
                     /translation="MAGYKLGTDTIYRGTTWVQSQFVGVQPGYKTQKMHTFLKSLYPLK
                     CLASPDHTFLNVCKFPLCSYKEFRANSKFRVFLKEIAPAGTKKVDDFLSHFMQNFSLHV
                     DGQCLKISQLVLLKICDVKSKYIYLALICVLSAYIEFWI"
                     /name="hypothetical protein"
     gene            complement(860..1783)
                     /locus_tag="HJI11_12615"
     CDS             complement(860..1783)
                     /locus_tag="HJI11_12615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002499696.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QRJ01010.1"
                     /translation="MDKYTEKKQRNQVFQKFIKRHVKEGQMDLIKECNTFLSFVADRTL
                     EKQKLHKSNLCKNRFCPVCSWRKARKDALGLSLMMQYIKQKEDKQFIFLTLTTPNVTVE
                     HLEDEIKNYNESFRRLSNRKHFKSIAKGYVRKLEITYNKKRDDYNPHFHVLIAVNKSYF
                     TDKRYYISQKEWLNLWRDVTGIDEITQVHVQKIKQNNNKELYEMAKYSGKDSDYLVNQK
                     VFDTFYKSLKGKQILVYSGLFKEARKKLKNGDLDYLKEVDPTEYIYQIFYHWNQKEYLA
                     SEIFDLTEEEKSRINHQMIDEIDEEK"
                     /name="protein rep"
     gene            2148..2327
                     /locus_tag="HJI11_12620"
     CDS             2148..2327
                     /locus_tag="HJI11_12620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497268.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QRJ01011.1"
                     /translation="MPYIYLIIAISTEVIGSAFLKSSEGFSKFIPSFRIKLNKIRKLKG
                     VKNALYLFNNSHKY"
                     /name="hypothetical protein"
     gene            2290..2613
                     /gene="qacC"
                     /locus_tag="HJI11_12625"
     ARG             2291..2610
                     /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"
     gene            complement(2855..3043)
                     /locus_tag="HJI11_12630"
     CDS             complement(2855..3043)
                     /locus_tag="HJI11_12630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000147241.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QRJ01013.1"
                     /translation="MTALKIILMLCISAMVGDFVLVIFESMPINIWVARFIGGVGASLS
                     ALLFAYLFIFKDKKQRQ"
                     /name="hypothetical protein"
     ARG             2291..2613
                     /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          complement(861..1783)
                     /name="rep_cluster_1281"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.675"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatggtcggc ttaatagctc acgctatgcc gacattcgtc tgcaagttta gttaagggtt
       61 cttctcaaca tcaataaatt ttctcggcat aaatgcgtgt tctactcccc gaatttttat
      121 tcaaacaaca tgaaaatttg ataaatagct agtaccagca acacaacata tacatactta
      181 ttcgttaaaa aattctctaa tgcttctcta aatttcattt tttaacaact cctgttttct
      241 cataaattta tccactttca gtttttcttt taacaaactt tatcataact cttacaaaaa
      301 ttttgagtgc ctttattttt aattttaaag gggtattttg aagaaacact aaatatttac
      361 atagttttat atccaaaatt ctatataagc gcttaaaacg caaatgagag ccaaataaat
      421 atattttgat ttcacatcac aaatttttag caaaaccagt tgcgaaattt ttagacactg
      481 cccatctaca tgcaaactaa aattttgcat aaaatggctc aaaaaatcat caactttttt
      541 agttcctgca ggggcaattt ctttcaaaaa aacacggaat tttgaattgg ctctaaattc
      601 tttgtaagag cataagggaa atttgcatac atttaaaaat gtatggtctg gcgaagccag
      661 acatttcaag ggatacagcg attttaaaaa ggtatgcatt ttttgcgttt tgtacccagg
      721 ttgtacccct acaaattgcg attgtaccca ggttgtaccc ctatatattg tgtctgtacc
      781 cagtttgtac ccagccattt ttaacgtatt ttcaacaaaa aaacgctagc tttttgctaa
      841 cgtttaagaa aatttatttt tatttttctt cgtcaatttc atcaatcatt tgatgattaa
      901 ttctactttt ttcttcttca gtcaaatcaa aaatttcact cgctaagtat tctttttggt
      961 tccagtgata aaaaatttga taaatatatt ctgtcggatc tacttcttta agataatcta
     1021 aatctccatt ttttaatttc tttcttgcct ctttaaacag tccagaataa acaagaattt
     1081 gttttccctt aagagattta taaaatgtat cgaacacttt ttgattaact aaataatcgc
     1141 tatctttacc agaatacttc gccatttcgt ataattcttt gttgttgttc tgtttgattt
     1201 tttgaacatg tacttgtgtg atttcatcaa ttccagtcac atctcgccat aaattcagcc
     1261 attctttttg actaatataa tatcgtttgt ctgtaaaata cgatttgtta acagcaatca
     1321 aaacatgaaa atgtggatta taatcatcgc gttttttgtt gtaagtaatt tctaattttc
     1381 ttacgtaacc tttagctata gatttaaaat gtttacgatt acttaatcgt ctaaacgact
     1441 cattataatt ttttatttca tcttccaaat gctcaactgt tacatttggt gtcgtaagtg
     1501 ttaaaaagat gaattgttta tcttcttttt gcttaatata ttgcatcatc aatgataaac
     1561 ctaacgcatc ttttctcgct tttcgccatg aacatacagg acaaaatcga tttttacaca
     1621 aattagattt atgcaatttc tgtttctcta acgttctatc tgccacaaaa ctcaagaatg
     1681 tattgcactc ctttatcaaa tccatttgcc cttctttgac atgtcgctta ataaatttct
     1741 gaaatacttg atttctttgt ttcttctcag tatacttatc catgttataa cacaacaaaa
     1801 caacttagtt ttacacaaac taatgccata aaaaaagttg ctttttctcc tttcttgtaa
     1861 agttttggct tggacaccat aaactctact atactaggta tgaaaaagca acttttttta
     1921 tgctcgaaac cagatatacc aacagattaa gggtaactat tatagcttgt aatagttacc
     1981 tatagtatca agacaagaag aaactcgttt tcaactcgtt tcaaaaacct ttcaaaaacc
     2041 atcaatccac aaaaatacca cgcgaatgac actcaaaata caagactaca attaaaaaat
     2101 acttagaata aaattaaata aaatacgaaa attaaaagga gttaaaaatg ccttatattt
     2161 atttaataat agccataagt actgaagtta ttggaagtgc atttcttaaa tcttcagaag
     2221 gcttttcaaa atttatacca tcctttagaa taaaattaaa taaaatacga aaattaaaag
     2281 gagttaaaaa tgccttatat ttatttaata atagccataa gtactgaagt tattggaagt
     2341 gcatttctta aatcttcaga aggcttttca aaatttatac catccttagg aacaataatt
     2401 tcatttggaa tttgtttcta ttttttaagt aaaacaatgc aacacctacc actaaatata
     2461 acttatgcaa cttgggcggg actaggttta gtcttaacaa ccgtagtctc aataattatt
     2521 ttcaaagaac aaataaatct aataactata gtatctatag ttttaatcat agtcggcgta
     2581 gtttcgttaa acattttcgg aacatcgcat taattgcttt attccaattg ctttattgac
     2641 gttgagcctc ggaaccctta acaatcccaa aacttgtcga atggtcggct taatagctca
     2701 cgctatgccg acattcgtct gcaagtttag ttaagggttc ttctcaacgc acaataaatt
     2761 ttctcggcat aaatgcctgc tctacttttt gttcttactc actttgatag ccaaaaatgc
     2821 cattccaatg ttagcaacac tgaacatatt tgttttattg acgttgcttt ttatccttaa
     2881 aaataaataa gtaggcaaac aataaagctg ataaagaagc tcctactcct ccgataaatc
     2941 tagcaaccca gatattaatc ggcatacttt caaaaatcac taacacaaaa tctccgacca
     3001 tagcagaaat acataacatc aagataattt ttagagcagt cataaaatca ctcctttttt
     3061 cttaacacta ctaaaattat cgctttattc caattgcttt attgacgttg agcctcggaa
     3121 cccttaacaa tcccaaaact tgttg
//
