LOCUS       CP052950                2366 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD69-1 plasmid pHD69-1_2, complete
            sequence.
ACCESSION   CP052950
VERSION     CP052950.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732906
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2366)
  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 2366)
  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                   :: 67x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:30:47
            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)                     :: 2,339
            CDSs (total)                      :: 2,255
            Genes (coding)                    :: 2,190
            CDSs (with protein)               :: 2,190
            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)              :: 65
            CDSs (without protein)            :: 65
            Pseudo Genes (ambiguous residues) :: 0 of 65
            Pseudo Genes (frameshifted)       :: 40 of 65
            Pseudo Genes (incomplete)         :: 28 of 65
            Pseudo Genes (internal stop)      :: 20 of 65
            Pseudo Genes (multiple problems)  :: 19 of 65
            ##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..2366
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD69-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD69-1_2"
                     /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            503..1237
                     /gene="erm(C)"
                     /locus_tag="HJI10_11690"
     ARG             504..1234
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1685..2161
                     /locus_tag="HJI10_11695"
     CDS             1685..2161
                     /locus_tag="HJI10_11695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="QRJ03203.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     ARG             504..1237
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.18"
                     /coverage="100.0"
     Typing          1686..2171
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttatactaac gttataccaa cattatactc tcattatact aattgcttat tccaatttcc
       61 tattggttgg aaccaacagg cgttagtgtg ttgttgagtt ggtactttca tgggattaat
      121 cccatgaaac ccccaaccaa ctcgccaaag ctttggctaa cacacacgcc attccaacca
      181 atagttttct cggcataaag ccatgctctg acgcttaaat gcactaatgc cttaaaaaaa
      241 cattaaagtc taacacacta gacttattta cttcgtaatt aagtcgttaa accgtgtgct
      301 ctacgaccaa aagtataaaa cctttaagaa ctttcttttt tcttgtaaaa aaagaaacta
      361 gataaatctc tcatatcttt tattcaataa tcgcatcaga ttgcagtata aatttaacga
      421 tcactcatca tgttcatatt tatcagagct cgtgctataa ttatactaat tttataagga
      481 ggaaaaaata aagagggtta taatgaacga gaaaaatata aaacacagtc aaaactttat
      541 tacttcaaaa cataatatag ataaaataat gacaaatata agattaaatg aacatgataa
      601 tatctttgaa atcggctcag gaaaagggca ttttaccctt gaattagtac agaggtgtaa
      661 tttcgtaact gccattgaaa tagaccataa attatgcaaa actacagaaa ataaacttgt
      721 tgatcacgat aatttccaag ttttaaacaa ggatatattg cagtttaaat ttcctaaaaa
      781 ccaatcctat aaaatatttg gtaatatacc ttataacata agtacggata taatacgcaa
      841 aattgttttt gatagtatag ctgatgagat ttatttaatc gtggaatacg agtttgctaa
      901 aagattatta aatacaaaac gctcattggc attattttta atggcagaag ttgatatttc
      961 tatattaagt atggttccaa gagaatattt tcatcctaaa cctaaagtga atagctcact
     1021 tatcagatta aatagaaaaa aatcaagaat atcacacaaa gataaacaga agtataatta
     1081 tttcgttatg aaatgggtta acaaagaata caagaaaata tttacaaaaa atcaatttaa
     1141 caattcctta aaacatgcag gaattgacga tttaaacaat attagctttg aacaattctt
     1201 atctcttttc aatagctata aattatttaa taagtaagtt aagggatgca taaactgcat
     1261 cccttaactt gtttttcgtg tacctatttt ttgtgaatcg attatgtctt ttgcgcattc
     1321 acttcttttc tatataaata tgagcgaagc gaataagcgt cggaaaagca gcaaaaagtt
     1381 tcctttttgc tgttggagca tgggggttca gggggtgcag tatctgacgt caatgccgag
     1441 cgaaagcgag ccgaagggta gcatttacgt tagataaccc cctgatatgc tccgacgctt
     1501 tatatagaaa agaagattca actaggtaaa atcttaatat aggttgagat gataaggttt
     1561 ataaggaatt tgtttgttct aatttttcac tcattttgtt ctaatttctt ttaacaaatg
     1621 ttcttttttt tttagaacag ttatgatata gttagaatag tttaaaataa ggagtgagaa
     1681 aaagatgaaa gaaagatatg gaacagtcta taaaggctct cagaggctca tagacgaaga
     1741 aagtggagaa gtcatagagg tagacaagtt ataccgtaaa caaacgtctg gtaacttcgt
     1801 aaaggcatat atagtgcaat taataagtat gttagatatg attggcggaa aaaaacttaa
     1861 aatcgttaac tatatcctag ataatgtcca cttaagtaac aatacaatga tagctacaac
     1921 aagagaaata gcaaaagcta caggaacaag tctacaaaca gtaataacaa cacttaaaat
     1981 cttagaagaa ggaaatatta taaaaagaaa aactggagta ttaatgttaa accctgaact
     2041 actaatgaga ggcgacgacc aaaaacaaaa atacctctta ctcgaatttg ggaactttga
     2101 gcaagaggca aatgaaaaac aagaaaatgc attatctgat tattattctt tcaaggacta
     2161 gtataacata aaatcgtcta caaatagaca aaaaacctgc acgcttaatg tagatcaaaa
     2221 gcttaacgca aatgaaatag attgacctcc caataacacc acgtagttat tgggaggtca
     2281 atctatgaaa tgcgattaag ctttttctaa ttcacataag cgtgcaggtt taaagtacat
     2341 aaaaaatata atgaaaaaaa gcatca
//
