LOCUS       CP052961                2366 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD46-1 plasmid pHD46-1_2, complete
            sequence.
ACCESSION   CP052961
VERSION     CP052961.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732902
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                   :: 200x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:42:09
            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)                     :: 2,672
            CDSs (total)                      :: 2,591
            Genes (coding)                    :: 2,507
            CDSs (with protein)               :: 2,507
            Genes (RNA)                       :: 81
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 84
            CDSs (without protein)            :: 84
            Pseudo Genes (ambiguous residues) :: 0 of 84
            Pseudo Genes (frameshifted)       :: 42 of 84
            Pseudo Genes (incomplete)         :: 43 of 84
            Pseudo Genes (internal stop)      :: 28 of 84
            Pseudo Genes (multiple problems)  :: 22 of 84
            ##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="HD46-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD46-1_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            complement(join(2084..2366,1..194))
                     /locus_tag="HJI06_13355"
     CDS             complement(join(2084..2366,1..194))
                     /locus_tag="HJI06_13355"
                     /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="QRJ12665.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     gene            complement(642..1376)
                     /gene="erm(C)"
                     /locus_tag="HJI06_13360"
     ARG             complement(646..1376)
                     /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"
     ARG             complement(643..1376)
                     /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="99.59"
                     /coverage="100.0"
     Typing          complement(2..194)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.15e-96"
     Typing          complement(2085..2366)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.859"
                     /coverage="99.0"
                     /evalue="3.7e-74"
ORIGIN
        1 aggatatagt taacgatttt aagttttttt ccgccaatca tatctaacat acttattaat
       61 tgcactatat atgcctttac gaagttacca gacgtttgtt tacggtataa cttgtctacc
      121 tctatgactt ctccactttc ttcgtctatg agcctctgag agcctttata gactgttcca
      181 tatctttctt tcatcttttt ctcactcctt attttaaact attctaacta tatcataact
      241 gttctaaaaa aaaaagaaca tttgttaaaa gaaattagaa caaaatgagt gaaaaattag
      301 aacaaacaaa ttccttataa accttatcat ctcaacctat attaagattt tacctagttg
      361 aatcttcttt tctatataaa gcgtcggagc atatcagggg gttatctaac gtaaatgcta
      421 cccttcggct cgctttcgct cggcattgac gtcagatact gcaccccctg aacccccatg
      481 ctccaacagc aaaaaggaaa ctttttgctg cttttccgac gcttattcgc ttcgctcata
      541 tttatataga aaagaagtga atgcgcaaaa gacataatcg attcacaaaa aataggtaca
      601 cgaaaaacaa gttaagggat gcagtttatg catcccttaa cttacttatt aaataattta
      661 tagctattga aaagagataa gaattgttca aagctaatat tgtttaaatc gtcaattcct
      721 gcatgtttta aggaattgtt aaattgattt tttgtaaata ttttcttgta ttctttgtta
      781 acccatttca taacgaaata attatacttc tgtttatctt tgtgtgatat tcttgatttt
      841 tttctattta atctgataag tgagctattc actttaggtt taggatgaaa atattctctt
      901 ggaaccatac ttaatataga aatatcaact tctgccatta aaaataatgc caatgagcgt
      961 tttgtattta ataatctttt agcaaacccg tattccacga ttaaataaat ctcatcagct
     1021 atactatcaa aaacaatttt gcgtattata tccgtactta tgttataagg tatattacca
     1081 aatattttat aggattggtt tttaggaaat ttaaactgca atatatcctt gtttaaaact
     1141 tggaaattat cgtgatcaac aagtttattt tctgtagttt tgcataattt atggtctatt
     1201 tcaatggcag ttacgaaatt acacctctgt actaattcaa gggtaaaatg cccttttcct
     1261 gagccgattt caaagatatt atcatgttca tttaatctta tatttgtcat tattttatct
     1321 atattatgtt ttgaagtaat aaagttttga ctgtgtttta tatttttctc gttcattata
     1381 accctcttta ttttttcctc cttataaaat tagtataatt atagcacgag ctctgataaa
     1441 tatgaacatg atgagtgatc gttaaattta tactgcaatc tgatgcgatt attgaataaa
     1501 agatatgaga gatttatcta gtttcttttt ttacaagaaa aaagaaagtt cttaaaggtt
     1561 ttatactttt ggtcgtagag cacacggttt aacgacttaa ttacgaagta aataagtcta
     1621 gtgtgttaga ctttaatgtt tttttaaggc attagtgcat ttaagcgtca gagcatggct
     1681 ttatgccgag aaaactattg gttggaatgg cgtgtgtgtt agccaaagct ttggcgagtt
     1741 ggttgggggt ttcatgggat taatcccatg aaagtaccaa ctcaacaaca cactaacgcc
     1801 tgttggttcc aaccaatagg aaattggaat aagcaattag tataatgaga gtataatgtt
     1861 ggtataacgt tagtataatg atgctttttt tcattatatt ttttatgtac tttaaacctg
     1921 cacgcttatg tgaattagaa aaagcttaat cgcatttcat agattgacct cccaataaca
     1981 ccacgtagtt attgggaggt caatctattt catttgcgtt aagcttttga tctacattaa
     2041 gcgtgcaggt tttttgtcta tttgtagacg attttatgtt atactagtcc ttgaaagaat
     2101 aataatcaga taatgcattt tcttgttttt catttgcctc ttgctcaaag ttcccaaatt
     2161 cgagtaagag gtatttttgt ttttggtcgt cgcctctcat tagtagttca gggtttaaca
     2221 ttaatactcc agtttttctt tttataatat ttccttcttc taagatttta agtgttgtta
     2281 ttactgtttg tagacttgtt cctgtagctt ttgctatttc tcttgttgta gctatcattg
     2341 tattgttact taagtggaca ttatct
//
