LOCUS       CP052987                2241 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD04-1 plasmid pHD04-1_2, complete
            sequence.
ACCESSION   CP052987
VERSION     CP052987.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732890
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2241)
  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 2241)
  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                   :: 244x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 13:47:01
            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)                     :: 2,485
            CDSs (total)                      :: 2,401
            Genes (coding)                    :: 2,322
            CDSs (with protein)               :: 2,322
            Genes (RNA)                       :: 84
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (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)       :: 40 of 79
            Pseudo Genes (incomplete)         :: 39 of 79
            Pseudo Genes (internal stop)      :: 25 of 79
            Pseudo Genes (multiple problems)  :: 20 of 79
            CRISPR Arrays                     :: 2
            ##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..2241
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD04-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD04-1_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            join(1434..2241,1..191)
                     /locus_tag="HJH94_12425"
     CDS             join(1434..2241,1..191)
                     /locus_tag="HJH94_12425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QRI81669.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            complement(783..1106)
                     /gene="qacC"
                     /locus_tag="HJH94_12420"
     ARG             complement(787..1106)
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(784..1106)
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="71.96"
                     /coverage="100.0"
     Typing          10..197
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.889"
                     /coverage="100.0"
                     /evalue="4.86e-59"
     Typing          1435..2241
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.876"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaaaacgtat gttaagttac ggtggtttac ttaaacaaaa acataaactt ttaaatttag
       61 acgatgccga agaaggtaat ttaattcaaa cgagcgatga agaaaaaacg actgaagaag
      121 aacaaaaagc ccattcaatt acggccattt ggaattttga aaaacaaaat tatttcttaa
      181 aaaatttgta acgttagctt atcaaagcta gcgttttttt atgctttttt gcccctgcag
      241 gaactatagc gttcaaccgg catggttgcc cattttttat gctaattttt aaatttgcat
      301 gtaaatgggc agtgtctaaa aaattcgaca ctggttttgc tcaaattttt gtttgtgaaa
      361 agcaattatt tttatttggc tctcatttgc gttttaagag ccgatttagg tttttaggta
      421 taaaactata taaataaccc ttaattcttt aaaatgaccc cttaaaatta aaaataaagg
      481 tattctgatt ttgaataaat gtttgaacaa aaaataaaga gctaccctta aaaattttgg
      541 tagctcttat atgcactgtt ttaatattta ggtgttatca gtgaaaaata gatcaagaaa
      601 ggaattttaa ttataacaca gcatttatgc cgagaaaatt tattgatgtt gagaagaacc
      661 cttaactaaa cttggagacg aatgtcggca tagcgtgagc tattaagccg accattcgac
      721 aagttttggg attgttaagg gttccgaggc tcaacgtcaa taaagcaatt ggaataaagc
      781 aattaatgcg atgttccgaa aatgtttaac gaaactacgc cgactatgat taaaactata
      841 gatactatag ttattagatt tatttgttct ttgaaaataa ttattgagac tacggttgtt
      901 aagactaaac ctagtcccgc ccaagttgca taagttatat ttagtggtag gtgttgcatt
      961 gttttactta aaaaatagaa acaaattcca aatgaaatta ttgttcctaa ggatggtata
     1021 aattttgaaa agccttctga agatttaaga aatgcacttc caataacttc agtacttatg
     1081 gctattatta aataaatata aggcattttt agctcctttt aattttcgta ttttattcta
     1141 agtatttttt aattgtaaag tattttttaa ttgtagtctt gtattttgag tgtcattcgc
     1201 gtggtatttt tgtggattga tggtttttga aaggtttttg aaacgagttg aaaacgagtt
     1261 tcttcttgtc ttgatactat atagaaataa ctcaaagaat taaaatgttt taaaaacgtt
     1321 ggtatgacaa catttgtgtt gtttttttag cgtgaaagaa aaaattgaca taaaaaaacc
     1381 ccagttatat gattaaggtg tcgaatctaa atcaaaactg gaggtctttt tatatgcaat
     1441 ataatactac aaaatatata gacgaaaatc aagataatga aacattgaaa gatatgacta
     1501 aaagtgggac acaacgccca tggagagaaa agaaaatcga caatgtaagt tatgcagata
     1561 tactagaaat tttaaaaatt aaaaaggctt ttaacgtgaa gcaatgtggt aacgtcttag
     1621 aatttaagcc gactgatgaa gggtatttaa aactttataa aacatggttt tgtaagtcta
     1681 aattatgtcc ggtttgtaat tggaggcgtt caatgaaaaa tagttatcaa gctcaaaaag
     1741 tcattgaagc agtggttaaa gaaaagccaa aagcacgttg gttattctta acactttcaa
     1801 caaaaaatgc gatagatggt gagcatttag aacagagttt aaaatatatg tcgaaagctt
     1861 ttaacaagtt aaaaatgtat gcaaaagtta aaaagaattt aatcggtttt atgcgttcaa
     1921 ctgaagttac agttaacaaa aatgacggaa gttataatca acatatgcac gttttattgt
     1981 gtgttgaaaa tgcttatttc agaaaaaaag agaattatat aacgcaagaa gagtggatca
     2041 atttatggca aaaagctctt caagttgatt acaaaccagt cgcaaatatc aaagcaatta
     2101 agccgaataa aaaaggcgat aaagatatac aagctgcaat taaagagaca tcaaaatact
     2161 cggttaagtc gtccgattat ttaacaggaa accatgaaaa agacgcagaa attgttcaag
     2221 atttagaaca aggtttatac a
//
