LOCUS       CP052996                2369 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD21-2 plasmid pHD21-2_2, complete
            sequence.
ACCESSION   CP052996
VERSION     CP052996.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14734464
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2369)
  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 2369)
  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 (27-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                   :: 134x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 15:23:15
            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)                     :: 2,649
            CDSs (total)                      :: 2,568
            Genes (coding)                    :: 2,493
            CDSs (with protein)               :: 2,493
            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)              :: 75
            CDSs (without protein)            :: 75
            Pseudo Genes (ambiguous residues) :: 0 of 75
            Pseudo Genes (frameshifted)       :: 41 of 75
            Pseudo Genes (incomplete)         :: 33 of 75
            Pseudo Genes (internal stop)      :: 24 of 75
            Pseudo Genes (multiple problems)  :: 17 of 75
            ##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..2369
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD21-2"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD21-2_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            join(1858..2369,1..223)
                     /gene="erm(C)"
                     /locus_tag="HKH70_13240"
     CDS             join(1858..2369,1..223)
                     /gene="erm(C)"
                     /locus_tag="HKH70_13240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011282421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /protein_id="QRJ43476.1"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFT
                     LELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPY
                     NISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYF
                     HPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGID
                     DLNNISFEQFLSLFNSYKLFNK"
                     /name="erm(C)"
     gene            671..1147
                     /locus_tag="HKH70_13245"
     CDS             671..1147
                     /locus_tag="HKH70_13245"
                     /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="QRJ43477.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     ARG             3..223
                     /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="100.0"
                     /coverage="29.92"
     ARG             1859..2367
                     /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="99.41"
                     /coverage="69.67"
     Typing          672..1157
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcacttatc agattaaata gaaaaaaatc aagaatatca cacaaagata aacagaagta
       61 taattatttc gttatgaaat gggttaacaa agaatacaag aaaatattta caaaaaatca
      121 atttaacaat tccttaaaac atgcaggaat tgacgattta aacaatatta gctttgaaca
      181 attcttatct cttttcaata gctataaatt atttaataag taagttaagg gatgcataaa
      241 ctgcatccct taacttgttt ttcgtgtacc tattttttgt gaatcgatta tgtcttttgc
      301 gcattcactt cttttctata taaatatgag cgaagcgaat aagcgtcgga aaagcagcaa
      361 aaagtttcct ttttgctgtt ggagcatggg ggttcagggg gtgcagtatc tgacgtcaat
      421 gccgagcgaa agcgagccga agggtagcat ttacgttaga taaccccctg atatgctccg
      481 acgctttata tagaaaagaa gattcaacta ggtaaaatct taatataggt tgagatgata
      541 aggtttataa ggaatttgtt tgttctaatt tttcactcat tttgttctaa tttcttttaa
      601 caaatgttct ttttttttta gaacagttat gatatagtta gaatagttta aaataaggag
      661 tgagaaaaag atgaaagaaa gatatggaac agtctataaa ggctctcaga ggctcataga
      721 cgaagaaagt ggagaagtca tagaggtaga caagttatac cgtaaacaaa cgtctggtaa
      781 cttcgtaaag gcatatatag tgcaattaat aagtatgtta gatatgattg gcggaaaaaa
      841 acttaaaatc gttaactata tcctagataa tgtccactta agtaacaata caatgatagc
      901 tacaacaaga gaaatagcaa aagctacagg aacaagtcta caaacagtaa taacaacact
      961 taaaatctta gaagaaggaa atattataaa aagaaaaact ggagtattaa tgttaaaccc
     1021 tgaactacta atgagaggcg acgaccaaaa acaaaaatac ctcttactcg aatttgggaa
     1081 ctttgagcaa gaggcaaatg aaaaacaaga aaatgcatta tctgattatt attctttcaa
     1141 ggactagtat aacataaaat cgtctacaaa tagacaaaaa acctgcacgc ttaatgtaga
     1201 tcaaaagctt aacgcaaatg aaatagattg acctcccaat aactacgtgg tgttattggg
     1261 aggtcaatct atgaaatgcg attaagcttt ttctaattca cataagcgtg caggtttaaa
     1321 gtacataaaa aatataatga aaaaaagcat cattatacta acgttatacc aacattatac
     1381 tctcattata ctaattgctt attccaattt cctattggtt ggaaccaaca ggcgttagtg
     1441 tgttgttgag ttggtacttt catgggatta atcccatgaa acccccaacc aactcgccaa
     1501 agctttggct aacacacacg ccattccaac caatagtttt ctcggcataa agccatgctc
     1561 tgacgcttaa atgcactaat gccttaaaaa aacattaaag tctaataaca cactagactt
     1621 atttacttcg taattaagtc gttaaaccgt gtgctctacg accaaaagta taaaaccttt
     1681 aagaactttc ttttttcttg taaaaaaaga aactagataa atctctcata tcttttattc
     1741 aataatcgca tcagattgca gtataaattt aacgatcact catcatgttc atatttatca
     1801 gagctcgtgc tataattata ctaattttat aaggaggaaa aaataaagag ggttataatg
     1861 aacgagaaaa atataaaaca cagtcaaaac tttattactt caaaacataa tatagataaa
     1921 ataatgacaa atataagatt aaatgaacat gataatatct ttgaaatcgg ctcaggaaaa
     1981 gggcatttta cccttgaatt agtacagagg tgtaatttcg taactgccat tgaaatagac
     2041 cataaattat gcaaaactac agaaaataaa cttgttgatc acgataattt ccaagtttta
     2101 aacaaggata tattgcagtt taaatttcct aaaaaccaat cctataaaat atttggtaat
     2161 ataccttata acataagtac ggatataata cgcaaaattg tttttgatag tatagctgat
     2221 gagatttatt taatcgtgga atacgggttt gctaaaagat tattaaatac aaaacgctca
     2281 ttggcattat ttttaatggc agaagttgat atttctatat taagtatggt tccaagagaa
     2341 tattttcatc ctaaacctaa agtgaatag
//
