LOCUS       CP052983                2366 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD25-1 plasmid pHD25-1_2, complete
            sequence.
ACCESSION   CP052983
VERSION     CP052983.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732892
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                   :: 149x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:53:36
            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)                     :: 2,626
            CDSs (total)                      :: 2,545
            Genes (coding)                    :: 2,466
            CDSs (with protein)               :: 2,466
            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)              :: 79
            CDSs (without protein)            :: 79
            Pseudo Genes (ambiguous residues) :: 0 of 79
            Pseudo Genes (frameshifted)       :: 35 of 79
            Pseudo Genes (incomplete)         :: 38 of 79
            Pseudo Genes (internal stop)      :: 30 of 79
            Pseudo Genes (multiple problems)  :: 18 of 79
            ##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="HD25-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD25-1_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            <1..361
                     /locus_tag="HJH96_13120"
     CDS             <1..361
                     /locus_tag="HJH96_13120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011282421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(B)"
                     /protein_id="QRJ31053.1"
                     /translation="IVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVN
                     SSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISF
                     EQFLSLFNSYKLFNK"
                     /name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(B)"
     gene            809..1285
                     /locus_tag="HJH96_13125"
     CDS             809..1285
                     /locus_tag="HJH96_13125"
                     /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="QRJ31054.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     gene            1993..>2366
                     /locus_tag="HJH96_13130"
     CDS             1993..>2366
                     /locus_tag="HJH96_13130"
                     /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="methyltransferase domain-containing protein"
                     /protein_id="QRJ31055.1"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFT
                     LELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPY
                     NISTDIIRKIVFDSIADEIY"
                     /name="methyltransferase domain-containing protein"
     ARG             1994..2364
                     /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="50.82"
     ARG             3..361
                     /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="99.16"
                     /coverage="48.77"
     Typing          810..1295
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatcgtggaa tacgggtttg ctaaaagatt attaaataca aaacgctcat tggcattatt
       61 tttaatggca gaagttgata tttctatatt aagtatggtt ccaagagaat attttcatcc
      121 taaacctaaa gtgaatagct cacttatcag attaaataga aaaaaatcaa gaatatcaca
      181 caaagataaa cagaagtata attatttcgt tatgaaatgg gttaacaaag aatacaagaa
      241 aatatttaca aaaaatcaat ttaacaattc cttaaaacat gcaggaattg acgatttaaa
      301 caatattagc tttgaacaat tcttatctct tttcaatagc tataaattat ttaataagta
      361 agttaaggga tgcataaact gcatccctta acttgttttt cgtgtaccta ttttttgtga
      421 atcgattatg tcttttgcgc attcacttct tttctatata aatatgagcg aagcgaataa
      481 gcgtcggaaa agcagcaaaa agtttccttt ttgctgttgg agcatggggg ttcagggggt
      541 gcagtatctg acgtcaatgc cgagcgaaag cgagccgaag ggtagcattt acgttagata
      601 accccctgat atgctccgac gctttatata gaaaagaaga ttcaactagg taaaatctta
      661 atataggttg agatgataag gtttataagg aatttgtttg ttctaatttt tcactcattt
      721 tgttctaatt tcttttaaca aatgttcttt tttttttaga acagttatga tatagttaga
      781 atagtttaaa ataaggagtg agaaaaagat gaaagaaaga tatggaacag tctataaagg
      841 ctctcagagg ctcatagacg aagaaagtgg agaagtcata gaggtagaca agttataccg
      901 taaacaaacg tctggtaact tcgtaaaggc atatatagtg caattaataa gtatgttaga
      961 tatgattggc ggaaaaaaac ttaaaatcgt taactatatc ctagataatg tccacttaag
     1021 taacaataca atgatagcta caacaagaga aatagcaaaa gctacaggaa caagtctaca
     1081 aacagtaata acaacactta aaatcttaga agaaggaaat attataaaaa gaaaaactgg
     1141 agtattaatg ttaaaccctg aactactaat gagaggcgac gaccaaaaac aaaaatacct
     1201 cttactcgaa tttgggaact ttgagcaaga ggcaaatgaa aaacaagaaa atgcattatc
     1261 tgattattat tctttcaagg actagtataa cataaaatcg tctacaaata gacaaaaaac
     1321 ctgcacgctt aatgtagatc aaaagcttaa cgcaaatgaa atagattgac ctcccaataa
     1381 ctacgtggtg ttattgggag gtcaatctat gaaatgcgat taagcttttt ctaattcaca
     1441 taagcgtgca ggtttaaagt acataaaaaa tataatgaaa aaaagcatca ttatactaac
     1501 gttataccaa cattatactc tcattatact aattgcttat tccaatttcc tattggttgg
     1561 aaccaacagg cgttagtgtg ttgttgagtt ggtactttca tgggattaat cccatgaaac
     1621 ccccaaccaa ctcgccaaag ctttggctaa cacacacgcc attccaacca atagttttct
     1681 cggcataaag ccatgctctg acgcttaaat gcactaatgc cttaaaaaaa cattaaagtc
     1741 taacacacta gacttattta cttcgtaatt aagtcgttaa accgtgtgct ctacgaccaa
     1801 aagtataaaa cctttaagaa ctttcttttt tcttgtaaaa aaagaaacta gataaatctc
     1861 tcatatcttt tattcaataa tcgcatcaga ttgcagtata aatttaacga tcactcatca
     1921 tgttcatatt tatcagagct cgtgctataa ttatactaat tttataagga ggaaaaaata
     1981 aagagggtta taatgaacga gaaaaatata aaacacagtc aaaactttat tacttcaaaa
     2041 cataatatag ataaaataat gacaaatata agattaaatg aacatgataa tatctttgaa
     2101 atcggctcag gaaaagggca ttttaccctt gaattagtac agaggtgtaa tttcgtaact
     2161 gccattgaaa tagaccataa attatgcaaa actacagaaa ataaacttgt tgatcacgat
     2221 aatttccaag ttttaaacaa ggatatattg cagtttaaat ttcctaaaaa ccaatcctat
     2281 aaaatatttg gtaatatacc ttataacata agtacggata taatacgcaa aattgttttt
     2341 gatagtatag ctgatgagat ttattt
//
