LOCUS       CP052970                2241 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD33-3 plasmid pHD33-3_1, complete
            sequence.
ACCESSION   CP052970
VERSION     CP052970.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732898
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                   :: 150x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:50:03
            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)                     :: 2,487
            CDSs (total)                      :: 2,403
            Genes (coding)                    :: 2,322
            CDSs (with protein)               :: 2,322
            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)              :: 81
            CDSs (without protein)            :: 81
            Pseudo Genes (ambiguous residues) :: 0 of 81
            Pseudo Genes (frameshifted)       :: 37 of 81
            Pseudo Genes (incomplete)         :: 43 of 81
            Pseudo Genes (internal stop)      :: 21 of 81
            Pseudo Genes (multiple problems)  :: 17 of 81
            ##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="HD33-3"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD33-3_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(2058..2241,1..140)
                     /gene="qacC"
                     /locus_tag="HJI02_12430"
     CDS             join(2058..2241,1..140)
                     /gene="qacC"
                     /locus_tag="HJI02_12430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001146389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /protein_id="QRJ21701.1"
                     /translation="MPYIYLIIAISTEVIGSAFLKSSEGFSKFIPSLGTIISFGICFYF
                     LSKTMQHLPLNITYATWAGLGLVLTTVVSIIIFKEQINLITIVSIVLIIVGVVSLNIFG
                     TSH"
                     /name="qacC"
     gene            complement(732..1730)
                     /locus_tag="HJI02_12435"
     CDS             complement(732..1730)
                     /locus_tag="HJI02_12435"
                     /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="QRJ21702.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     ARG             2059..2240
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="70.49"
                     /coverage="57.01"
     Typing          complement(733..1730)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gggcgggact aggtttagtc ttaacaaccg tagtctcaat aattattttc aaagaacaaa
       61 taaatctaat aactatagta tctatagttt taatcatagt cggcgtagtt tcgttaaaca
      121 ttttcggaac atcgcattaa ttgctttatt ccaattgctt tattgacgtt gagcctcgga
      181 acccttaaca atcccaaaac ttgtcgaatg gtcggcttaa tagctcacgc tatgccgaca
      241 ttcgtctcca agtttagtta agggttcttc tcaacatcaa taaattttct cggcataaat
      301 gctgtgttat aattaaaatt cctttcttga tctatttttc actgataaca cctaaatatt
      361 aaaacagtgc atataagagc taccaaaatt tttaagggta gctctttatt ttttgttcaa
      421 acatttattc aaaatcagaa tacctttatt tttaatttta aggggtcatt ttaaagaatt
      481 aagggttatt tatatagttt tatacctaaa aacctaaatc ggctcttaaa acgcaaatga
      541 gagccaaata aaaataattg cttttcacaa acaaaaattt gagcaaaacc agtgtcgaat
      601 tttttagaca ctgcccattt acatgcaaat ttaaaaatta gcataaaaaa tgggcaacca
      661 tgccggttga acgctatagt tcctgcaggg gcaaaaaagc ataaaaaaac gctagctttg
      721 ataagctaac gttacaaatt ttttaagaaa taattttgtt tttcaaaatt ccaaatggcc
      781 gtaattgaat gggctttttg ttcttcttca gtcgtttttt cttcatcgct cgtttgaatt
      841 aaattacctt cttcggcatc gtctaaattt aaaagtttat gtttttgttt aagtaaacca
      901 ccgtaactta acatacgttt tctgtataaa ccttgttcta aatcttgaac aatttctgcg
      961 tctttttcat ggtttcctgt taaataatcg gacgacttaa ccgagtattt tgatgtctct
     1021 ttaattgcag cttgtatatc tttatcgcct tttttattcg gcttaattgc tttgatattt
     1081 gcgactggtt tgtaatcaac ttgaagagct ttttgccata aattgatcca ctcttcttgc
     1141 gttatataat tctctttttt tctgaaataa gcattttcaa cacacaataa aacgtgcata
     1201 tgttgattat aacttccgtc atttttgtta actgtaactt cagttgaacg cataaaaccg
     1261 attaaattct ttttaacttt tgcatacatt tttaacttgt taaaagcttt cgacatatat
     1321 tttaaactct gttctaaatg ctcaccatct atcgcatttt ttgttgaaag tgttaagaat
     1381 aaccaacgtg cttttggctt ttctttaacc actgcttcaa tgactttttg agcttgataa
     1441 ctatttttca ttgaacgcct ccaattacaa accggacata atttagactt acaaaaccat
     1501 gttttataaa gttttaaata cccttcatca gtcggcttaa attctaagac gttaccacat
     1561 tgcttcacgt taaaagcctt tttaattttt aaaatttcta gtatatctgc ataacttaca
     1621 ttgtcgattt tcttttctct ccatgggcgt tgtgtcccac ttttagtcat atctttcaat
     1681 gtttcattat cttgattttc gtctatatat tttgtagtat tatattgcat ataaaaagac
     1741 ctccagtttt gatttagatt cgacacctta atcatataac tggggttttt ttatgtcaat
     1801 tttttctttc acgctaaaaa aacaacacaa atgttgtcat accaacgttt ttaaaacatt
     1861 ttaattcttt gagttatttc tatatagtat caagacaaga agaaactcgt tttcaactcg
     1921 tttcaaaaac ctttcaaaaa ccatcaatcc acaaaaatac cacgcgaatg acactcaaaa
     1981 tacaagacta caattaaaaa atactttaca attaaaaaat acttagaata aaatacgaaa
     2041 attaaaagga gctaaaaatg ccttatattt atttaataat agccataagt actgaagtta
     2101 ttggaagtgc atttcttaaa tcttcagaag gcttttcaaa atttatacca tccttaggaa
     2161 caataatttc atttggaatt tgtttctatt ttttaagtaa aacaatgcaa cacctaccac
     2221 taaatataac ttatgcaact t
//
