LOCUS       CP052958                2312 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD47-1 plasmid pHD47-1_3, complete
            sequence.
ACCESSION   CP052958
VERSION     CP052958.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732903
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2312)
  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 2312)
  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                   :: 142x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:43:08
            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)                     :: 2,516
            CDSs (total)                      :: 2,435
            Genes (coding)                    :: 2,358
            CDSs (with protein)               :: 2,358
            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)              :: 77
            CDSs (without protein)            :: 77
            Pseudo Genes (ambiguous residues) :: 0 of 77
            Pseudo Genes (frameshifted)       :: 42 of 77
            Pseudo Genes (incomplete)         :: 30 of 77
            Pseudo Genes (internal stop)      :: 29 of 77
            Pseudo Genes (multiple problems)  :: 19 of 77
            ##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..2312
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD47-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD47-1_3"
                     /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(2061..2312,1..225))
                     /locus_tag="HJI07_12575"
     CDS             complement(join(2061..2312,1..225))
                     /locus_tag="HJI07_12575"
                     /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="QRJ10158.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     gene            complement(673..1407)
                     /gene="erm(C)"
                     /locus_tag="HJI07_12580"
     ARG             complement(677..1407)
                     /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(674..1407)
                     /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..225)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.26e-113"
     Typing          complement(2106..2312)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="98.0"
                     /evalue="3.26e-104"
ORIGIN
        1 cattgtattg ttacttaagt ggacattatc taggatatag ttaacgattt taagtttttt
       61 tccgccaatc atatctaaca tacttattaa ttgcactata tatgccttta cgaagttacc
      121 agacgtttgt ttacggtata acttgtctac ctctatgact tctccacttt cttcgtctat
      181 gagcctctga gagcctttat agactgttcc atatctttct ttcatctttt tctcactcct
      241 tattttaaac tattctaact atatcataac tgttctaaaa aaaaaagaac atttgttaaa
      301 agaaattaga acaaaatgag tgaaaaatta gaacaaacaa attccttata aaccttatca
      361 tctcaaccta tattaagatt ttacctagtt gaatcttctt ttctatataa agcgtcggag
      421 catatcaggg ggttatctaa cgtaaatgct acccttcggc tcgctttcgc tcggcattga
      481 cgtcagatac tgcaccccct gaacccccat gctccaacag caaaaaggaa actttttgct
      541 gcttttccga cgcttattcg cttcgctcat atttatatag aaaagaagtg aatgcgcaaa
      601 agacataatc gattcacaaa aaataggtac acgaaaaaca agttaaggga tgcagtttat
      661 gcatccctta acttacttat taaataattt atagctattg aaaagagata agaattgttc
      721 aaagctaata ttgtttaaat cgtcaattcc tgcatgtttt aaggaattgt taaattgatt
      781 ttttgtaaat attttcttgt attctttgtt aacccatttc ataacgaaat aattatactt
      841 ctgtttatct ttgtgtgata ttcttgattt ttttctattt aatctgataa gtgagctatt
      901 cactttaggt ttaggatgaa aatattctct tggaaccata cttaatatag aaatatcaac
      961 ttctgccatt aaaaataatg ccaatgagcg ttttgtattt aataatcttt tagcaaaccc
     1021 gtattccacg attaaataaa tctcatcagc tatactatca aaaacaattt tgcgtattat
     1081 atccgtactt atgttataag gtatattacc aaatatttta taggattggt ttttaggaaa
     1141 tttaaactgc aatatatcct tgtttaaaac ttggaaatta tcgtgatcaa caagtttatt
     1201 ttctgtagtt ttgcataatt tatggtctat ttcaatggca gttacgaaat tacacctctg
     1261 tactaattca agggtaaaat gcccttttcc tgagccgatt tcaaagatat tatcatgttc
     1321 atttaatctt atatttgtca ttattttatc tatattatgt tttgaagtaa taaagttttg
     1381 actgtgtttt atatttttct cgttcattat aaccctcttt attttttcct ccttataaaa
     1441 ttagtataat tatagcacga gctctgataa atatgaacat gatgagtgat cgttaaattt
     1501 atactgcaat ctgatgcgat tattgaataa aagatatgag agatttatct agtttctttt
     1561 tttacaagaa aaaagaaagt tcttaaaggt tttatacttt tggtcgtaga gcacacggtt
     1621 taacgactta attacgaagt aaataagtct agtgtgttag actttaatgt ttttttaagg
     1681 cattagtgca tttaagcgtc agagcatggc tttatgccga gaaaactatt ggttggaatg
     1741 gcgtgtgtgt tagccaaagc tttggcgagt tggttggggg tttcatggga ttaatcccat
     1801 gaaagtacca actcaacaac acactaacgc ctgttggttc caaccaatag gaaattggaa
     1861 taagcaatta gtataatgag agtataatgt tggtataacg ttagtataat gatgcttttt
     1921 ttcattatat tttttatgta ctttaaacct gcacgcttat gtgaattaga aaaagcttaa
     1981 tctatttcat ttgcgttaag cttttgatct acattaagcg tgcaggtttt ttgtctattt
     2041 gtagacgatt ttatgttata ctagtccttg aaagaataat aatcagataa tgcattttct
     2101 tgtttttcat ttgcctcttg ctcaaagttc ccaaattcga gtaagaggta tttttgtttt
     2161 tggtcgtcgc ctctcattag tagttcaggg tttaacatta atactccagt ttttcttttt
     2221 ataatatttc cttcttctaa gattttaagt gttgttatta ctgtttgtag acttgttcct
     2281 gtagcttttg ctatttctct tgttgtagct at
//
