LOCUS       CP052972                2241 bp    DNA     circular BCT 10-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD33-1 plasmid pHD33-1_1, complete
            sequence.
ACCESSION   CP052972
VERSION     CP052972.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732897
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                   :: 219x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:30:35
            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)                     :: 2,457
            CDSs (total)                      :: 2,373
            Genes (coding)                    :: 2,294
            CDSs (with protein)               :: 2,294
            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)              :: 79
            CDSs (without protein)            :: 79
            Pseudo Genes (ambiguous residues) :: 0 of 79
            Pseudo Genes (frameshifted)       :: 38 of 79
            Pseudo Genes (incomplete)         :: 39 of 79
            Pseudo Genes (internal stop)      :: 21 of 79
            Pseudo Genes (multiple problems)  :: 16 of 79
            ##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="HD33-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD33-1_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(1994..2241,1..751)
                     /locus_tag="HJI01_12275"
     CDS             complement(join(1994..2241,1..751))
                     /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="QRL13741.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            1079..1402
                     /gene="qacC"
                     /locus_tag="HJI01_12280"
     ARG             1080..1399
                     /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             1080..1402
                     /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..751)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.867"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1989..2176)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.889"
                     /coverage="100.0"
                     /evalue="4.86e-59"
ORIGIN
        1 ttaaataatc ggacgactta accgagtatt ttgatgtctc tttaattgca gcttgtatat
       61 ctttatcgcc ttttttattc ggcttaattg ctttgatatt tgcgactggt ttgtaatcaa
      121 cttgaagagc tttttgccat aaattgatcc actcttcttg cgttatataa ttctcttttt
      181 ttctgaaata agcattttca acacacaata aaacgtgcat atgttgatta taacttccgt
      241 catttttgtt aactgtaact tcagttgaac gcataaaacc gattaaattc tttttaactt
      301 ttgcatacat ttttaacttg ttaaaagctt tcgacatata ttttaaactc tgttctaaat
      361 gctcaccatc tatcgcattt tttgttgaaa gtgttaagaa taaccaacgt gcttttggct
      421 tttctttaac cactgcttca atgacttttt gagcttgata actatttttc attgaacgcc
      481 tccaattaca aaccggacat aatttagact tacaaaacca tgttttataa agttttaaat
      541 acccttcatc agtcggctta aattctaaga cgttaccaca ttgcttcacg ttaaaagcct
      601 ttttaatttt taaaatttct agtatatctg cataacttac attgtcgatt ttcttttctc
      661 tccatgggcg ttgtgtccca cttttagtca tatctttcaa tgtttcatta tcttgatttt
      721 cgtctatata ttttgtagta ttatattgca tataaaaaga cctccagttt tgatttagat
      781 tcgacacctt aatcatataa ctggggtttt tttatgtcaa ttttttcttt cacgctaaaa
      841 aaacaacaca aatgttgtca taccaacgtt tttaaaacat tttaattctt tgagttattt
      901 ctatatagta tcaagacaag aagaaactcg ttttcaactc gtttcaaaaa cctttcaaaa
      961 accatcaatc cacaaaaata ccacgcgaat gacactcaaa atacaagact acaattaaaa
     1021 aatactttac aattaaaaaa tacttagaat aaaatacgaa aattaaaagg agctaaaaat
     1081 gccttatatt tatttaataa tagccataag tactgaagtt attggaagtg catttcttaa
     1141 atcttcagaa ggcttttcaa aatttatacc atccttagga acaataattt catttggaat
     1201 ttgtttctat tttttaagta aaacaatgca acacctacca ctaaatataa cttatgcaac
     1261 ttgggcggga ctaggtttag tcttaacaac cgtagtctca ataattattt tcaaagaaca
     1321 aataaatcta ataactatag tatctatagt tttaatcata gtcggcgtag tttcgttaaa
     1381 cattttcgga acatcgcatt aattgcttta ttccaattgc tttattgacg ttgagcctcg
     1441 gaacccttaa caatcccaaa acttgtcgaa tggtcggctt aatagctcac gctatgccga
     1501 cattcgtctc caagtttagt taagggttct tctcaacatc aataaatttt ctcggcataa
     1561 atgctgtgtt ataattaaaa ttcctttctt gatctatttt tcactgataa cacctaaata
     1621 ttaaaacagt gcatataaga gctaccaaaa tttttaaggg tagctcttta ttttttgttc
     1681 aaacatttat tcaaaatcag aataccttta tttttaattt taaggggtca ttttaaagaa
     1741 ttaagggtta tttatatagt tttataccta aaaacctaaa tcggctctta aaacgcaaat
     1801 gagagccaaa taaaaataat tgcttttcac aaacaaaaat ttgagcaaaa ccagtgtcga
     1861 attttttaga cactgcccat ttacatgcaa atttaaaaat tagcataaaa aatgggcaac
     1921 catgccggtt gaacgctata gttcctgcag gggcaaaaaa gcataaaaaa acgctagctt
     1981 tgataagcta acgttacaaa ttttttaaga aataattttg tttttcaaaa ttccaaatgg
     2041 ccgtaattga atgggctttt tgttcttctt cagtcgtttt ttcttcatcg ctcgtttgaa
     2101 ttaaattacc ttcttcggca tcgtctaaat ttaaaagttt atgtttttgt ttaagtaaac
     2161 caccgtaact taacatacgt tttctgtata aaccttgttc taaatcttga acaatttctg
     2221 cgtctttttc atggtttcct g
//
