LOCUS       CP052957                2491 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD47-1 plasmid pHD47-1_2, complete
            sequence.
ACCESSION   CP052957
VERSION     CP052957.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732903
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2491)
  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 2491)
  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..2491
                     /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_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(46..234)
                     /locus_tag="HJI07_12565"
     CDS             complement(46..234)
                     /locus_tag="HJI07_12565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002440614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CsbD family protein"
                     /protein_id="QRJ10156.1"
                     /translation="MSEEKFEQAKGNIKETIGDATDNKDLKAEGKGDKASGKAKEVVDD
                     VKDKANDLIDKVKGDKN"
                     /name="CsbD family protein"
     gene            complement(948..1892)
                     /locus_tag="HJI07_12570"
     CDS             complement(948..1892)
                     /locus_tag="HJI07_12570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002440612.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QRJ10157.1"
                     /translation="MSRKEQEIHSKQSTLQEVTNYTSTGYSNSRLGVHSVHPQNPKLSF
                     DAMTIVGNLSRDNAQKLSSFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIINYMEDDGFTRIDLAFDFEDDLSNYYAMTDKAVK
                     KTVFYGRDGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVMSDHLWRVEIELKRDMV
                     DYWNDCFNDLHILKPDWTSPEKLNEQAMVYMLIHEEDKWGELNKRTKYKYKNLIKEISP
                     VDLTELMKSTLRENEKQLQKQIEFWQTKGKKLF"
                     /name="replication initiation protein"
     Typing          complement(974..1796)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.204"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 cccaagtatg ctacataata atacttaaga cgttttaatt tttatttagt ttttatctcc
       61 tttaacttta tcaatcaagt cattagcttt atctttaaca tcatctacta cttctttggc
      121 tttaccagaa gctttatctc ctttaccttc tgcttttaaa tccttattat cagtagcatc
      181 tccaatagtc tctttgatat ttccttttgc ttgttcgaat ttttcttcgc tcattttcta
      241 ttcctcctaa ataatcaatg tctacaatac aattctatta ttcaaatacc ctttttaaaa
      301 gtgaaatcat atcctttttt atcccatgca ttaaaccttg tattatccca tgtatacaaa
      361 atgatttatg tattactcct tttcatttag aatatcaaaa actatcctac agatagacta
      421 ctcaaaaaat gagtagtctt tttattttgc attttaagcc ctttctagga catttaatca
      481 ttccacgtat aaaaatgact aaaaactttt tttgttcaac agagaggcta taaatcattt
      541 taaaatttat ttctcaacac tttcagaaaa aaatatgttt ttttatttta attatccttc
      601 tcaataaaaa gctaaaacct gaaaaaaata ggtgtataat gtaactttta tattttaaaa
      661 tattttaaaa gagcataaga ggaatcctac acagaaatgt ctccgtatgt agccattcgg
      721 tagccgtttc tgtgcaaaat attgatttga cagtgtcaaa tgggattcct atttatgcga
      781 taaaaattgt tatatgactc ccgaacgact acacaaaagc taccgaatag ctacccaaaa
      841 tcaaaaatga ctcccaaatg gctacataaa atcaaaaata gctcccaaat agctcccttt
      901 ttatggagcc atttgggagc taaaagggag tcaaatggta gccattttta aaatagcttc
      961 ttaccttttg tctgccaaaa ttctatttgc ttttgtaatt gtttttcatt ttctcttaaa
     1021 gtcgatttca ttaattccgt taaatcaact ggagatattt ctttaattaa atttttatat
     1081 ttatatttag ttcttttatt caattctccc catttgtctt cttcatgaat taacatgtaa
     1141 accattgctt gttcatttaa tttttctggc gaagtccaat ctggtttcaa gatatgtaaa
     1201 tcattaaaac aatcattcca gtaatccacc atatctcttt taagttcaat ttctacacgc
     1261 cataagtgat cagacataac ttcgacatct gcgttatctt tacgttcttg ttttttgtta
     1321 taaattctaa taaatctatc actatcacga acgccaaaat attttgtttc tggtttcccg
     1381 tcacgaccat aaaatacagt tttcttaact gctttatcag tcattgcata ataattactt
     1441 aaatcatctt caaaatcaaa agctaaatct attcttgtaa aaccgtcatc ttccatgtag
     1501 ttgataatgt tttgttttaa ccaaagcatt tcttcatgcg taagtttatt cggattaaat
     1561 tcaacacgca tattacgtct atcccatgta tctgctttta ctttgtcgta ttcgatataa
     1621 actttttcct gcagtgcttt agctttaaat ttcgtttgta gtatatccca aagtcgaatt
     1681 tgtggttcga tactcataaa tgacgatagc ttttgagcgt tgtcacgact gagatttcca
     1741 actattgtca tagcgtcaaa acttaattta ggattttgtg ggtgcacaga atgcactcct
     1801 aaccggctat tagagtatcc ggttgaggtg taatttgtaa cttcttgtaa tgtgctttgc
     1861 tttgaatgaa tttcttgctc ttttctactc ataaaaaatc gactccttaa tttaatttaa
     1921 gaagtcgccc acccgaatat ttatcttgat gtatatttaa atatcgttta gtatttaaat
     1981 atacaaattc ataaaaaaca actcatgttt tctttttgga ttgtcgttca caaactttgg
     2041 tcggtgggtg agcgacttct ttttatttgt ttattaatat aacactatca aaaggcttgg
     2101 tctaatcaga tcaagtcttt tttagtacca aaacttatta cataatcaaa aattaatttt
     2161 ctttagataa tttatattgc ttgtaagcat aataaactat aaatgactgt actactactt
     2221 gtgcaaaaga taatgctata cgaatgcttt tcttagtttt ctcactcatt ttcttcaact
     2281 ccttttgttg ctttattcca attgctttat tgacgttgag cctcggaacc cttaacaatc
     2341 cctaaacttg tcgaatcgtc ggcttaatag ctcacgctat gccgacattc gtctccaagt
     2401 ttagttaagg gttcttctca acatcaataa attttctcgg cataaatgcg tgtcttatta
     2461 tttattttta ttcactttaa ataaaaaacg t
//
