LOCUS       CP053011                2241 bp    DNA     circular BCT 10-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD104-2 plasmid pHD104-2_4,
            complete sequence.
ACCESSION   CP053011
VERSION     CP053011.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14734458
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 (27-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                   :: 43x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 15:54:52
            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)                     :: 2,340
            CDSs (total)                      :: 2,269
            Genes (coding)                    :: 2,207
            CDSs (with protein)               :: 2,207
            Genes (RNA)                       :: 71
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 51
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 62
            CDSs (without protein)            :: 62
            Pseudo Genes (ambiguous residues) :: 0 of 62
            Pseudo Genes (frameshifted)       :: 41 of 62
            Pseudo Genes (incomplete)         :: 23 of 62
            Pseudo Genes (internal stop)      :: 24 of 62
            Pseudo Genes (multiple problems)  :: 20 of 62
            ##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="HD104-2"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD104-2_4"
                     /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(join(2044..2241,1..801))
                     /locus_tag="HKH64_11695"
     CDS             complement(join(2044..2241,1..801))
                     /locus_tag="HKH64_11695"
                     /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="QRL18158.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            1129..1452
                     /gene="qacC"
                     /locus_tag="HKH64_11700"
     ARG             1130..1449
                     /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             1130..1452
                     /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(2..801)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.875"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2039..2226)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.889"
                     /coverage="100.0"
                     /evalue="4.86e-59"
ORIGIN
        1 accttgttct aaatcttgaa caatttctgc gtctttttca tggtttcctg ttaaataatc
       61 ggacgactta accgagtatt ttgatgtctc tttaattgca gcttgtatat ctttatcgcc
      121 ttttttattc ggcttaattg ctttgatatt tgcgactggt ttgtaatcaa cttgaagagc
      181 tttttgccat aaattgatcc actcttcttg cgttatataa ttctcttttt ttctgaaata
      241 agcattttca acacacaata aaacgtgcat atgttgatta taacttccgt catttttgtt
      301 aactgtaact tcagttgaac gcataaaacc gattaaattc tttttaactt ttgcatacat
      361 ttttaacttg ttaaaagctt tcgacatata ttttaaactc tgttctaaat gctcaccatc
      421 tatcgcattt tttgttgaaa gtgttaagaa taaccaacgt gcttttggct tttctttaac
      481 cactgcttca atgacttttt gagcttgata actatttttc attgaacgcc tccaattaca
      541 aaccggacat aatttagact tacaaaacca tgttttataa agttttaaat acccttcatc
      601 agtcggctta aattctaaga cgttaccaca ttgcttcacg ttaaaagcct ttttaatttt
      661 taaaatttct agtatatctg cataacttac attgtcgatt ttcttttctc tccatgggcg
      721 ttgtgtccca cttttagtca tatctttcaa tgtttcatta tcttgatttt cgtctatata
      781 ttttgtagta ttatattgca tataaaaaga cctccagttt tgatttagat tcgacacctt
      841 aatcatataa ctggggtttt tttatgtcaa ttttttcttt cacgctaaaa aaacaacaca
      901 aatgttgtca taccaacgtt tttaaaacat tttaattctt tgagttattt ctatatagta
      961 tcaagacaag aagaaactcg ttttcaactc gtttcaaaaa cctttcaaaa accatcaatc
     1021 cacaaaaata ccacgcgaat gacactcaaa atacaagact acaattaaaa aatactttac
     1081 aattaaaaaa tacttagaat aaaatacgaa aattaaaagg agctaaaaat gccttatatt
     1141 tatttaataa tagccataag tactgaagtt attggaagtg catttcttaa atcttcagaa
     1201 ggcttttcaa aatttatacc atccttagga acaataattt catttggaat ttgtttctat
     1261 tttttaagta aaacaatgca acacctacca ctaaatataa cttatgcaac ttgggcggga
     1321 ctaggtttag tcttaacaac cgtagtctca ataattattt tcaaagaaca aataaatcta
     1381 ataactatag tatctatagt tttaatcata gtcggcgtag tttcgttaaa cattttcgga
     1441 acatcgcatt aattgcttta ttccaattgc tttattgacg ttgagcctcg gaacccttaa
     1501 caatcccaaa acttgtcgaa tggtcggctt aatagctcac gctatgccga cattcgtctc
     1561 caagtttagt taagggttct tctcaacatc aataaatttt ctcggcataa atgctgtgtt
     1621 ataattaaaa ttcctttctt gatctatttt tcactgataa cacctaaata ttaaaacagt
     1681 gcatataaga gctaccaaaa tttttaaggg tagctcttta ttttttgttc aaacatttat
     1741 tcaaaatcag aataccttta tttttaattt taaggggtca ttttaaagaa ttaagggtta
     1801 tttatatagt tttataccta aaaacctaaa tcggctctta aaacgcaaat gagagccaaa
     1861 taaaaataat tgcttttcac aaacaaaaat ttgagcaaaa ccagtgtcga attttttaga
     1921 cactgcccat ttacatgcaa atttaaaaat tagcataaaa aatgggcaac catgccggtt
     1981 gaacgctata gttcctgcag gggcaaaaaa gcataaaaaa acgctagctt tgataagcta
     2041 acgttacaaa ttttttaaga aataattttg tttttcaaaa ttccaaatgg ccgtaattga
     2101 atgggctttt tgttcttctt cagtcgtttt ttcttcatcg ctcgtttgaa ttaaattacc
     2161 ttcttcggca tcgtctaaat ttaaaagttt atgtttttgt ttaagtaaac caccgtaact
     2221 taacatacgt tttctgtata a
//
