LOCUS       CP052946                3733 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD75-1 plasmid pHD75-1_5, complete
            sequence.
ACCESSION   CP052946
VERSION     CP052946.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732907
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3733)
  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 3733)
  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                   :: 146x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 14:36:52
            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)                     :: 2,526
            CDSs (total)                      :: 2,442
            Genes (coding)                    :: 2,393
            CDSs (with protein)               :: 2,393
            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)              :: 49
            CDSs (without protein)            :: 49
            Pseudo Genes (ambiguous residues) :: 0 of 49
            Pseudo Genes (frameshifted)       :: 36 of 49
            Pseudo Genes (incomplete)         :: 19 of 49
            Pseudo Genes (internal stop)      :: 21 of 49
            Pseudo Genes (multiple problems)  :: 19 of 49
            ##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..3733
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD75-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD75-1_5"
                     /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(3127..3733,1..338))
                     /locus_tag="HJI11_12595"
     CDS             complement(join(3127..3733,1..338))
                     /locus_tag="HJI11_12595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017722130.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QRJ01006.1"
                     /translation="MSKKAEEIQSKQSSEYENLNFSKTGYSNSRLNRHTMYTPEPKLSF
                     DAMTIVGNLNKNNAHKLSEFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEYDLSDYYAMTDKSVK
                     KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADIKIMSEHLWRVEIELKRDMV
                     DYWNDCFNDLHILQPDWKTIERTSDRAMVFMLLNDEEEWGKLERRTKNKYKKLIKEISL
                     IDLTDLMKSTLKANEKQLQKQIDFWQREFRFWK"
                     /name="replication initiation protein"
     gene            complement(863..2080)
                     /locus_tag="HJI11_12600"
     CDS             complement(863..2080)
                     /locus_tag="HJI11_12600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination enzyme"
                     /protein_id="QRJ01007.1"
                     /translation="MSYSIIRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNEYNQNFNNLIDEKIEQNYTGKRKIRTDAVKHVDGLITSDKEFFDNQTPEDTKQFF
                     EHAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKQVVGNKKALTEFQ
                     DRFNEYVNQRGYDLERGQSRQVTNAKHEQMSQYKQKTEYYKQEYERESQKTDEIKQKND
                     KLVREYQKSLNALKKPINVPYEKETKTVGGLFNKETQETGNVVIRQEDFNAFQKQIEAA
                     QSITDDYEYIKSDKALNDLKSENNELKQENENLRNDKSELRRHFKKEHAQNKHLKDLIN
                     YLRRLLEKLEKTLGRKNYIDLINGMTENNDKDRKIALTFDKEMHPEKYQEQEQQEEVKK
                     DRGRGR"
                     /name="plasmid recombination enzyme"
     gene            complement(2345..2992)
                     /locus_tag="HJI11_12605"
     CDS             complement(2345..2992)
                     /locus_tag="HJI11_12605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000143686.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type A-8 chloramphenicol O-acetyltransferase"
                     /protein_id="QRJ01008.1"
                     /translation="MTFNIINLETWDRKEYFNHYFNQQTTYSVTKEFDITLLKSMIKNK
                     GYELYPALIYTIVNIINQNKVFRTGINSEGNLGYWDKLNPLYTVFNKETEKFSNIWTES
                     NVSFNSFYNSYKSDLLEYKDKNEMFPKKPIPENTVPISMIPWIDFSSFNLNIGNNSRFL
                     LPIITIGKFYSKNNKIYLPVSLQVHHAVCDGYHVSLFMSEFQNIVDSVNEWI"
                     /name="type A-8 chloramphenicol O-acetyltransferase"
     ARG             complement(2349..2992)
                     /name="catA"
                     /gene="catA"
                     /gene_name="type A-8 chloramphenicol O-acetyltransferase"
                     /tool="amrfinderplus"
                     /drug_class="PHENICOL"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(2346..2992)
                     /name="catA8"
                     /gene="catA8"
                     /gene_name="chloramphenicol acetyltransferase (CAT)"
                     /tool="rgi"
                     /drug_class="phenicol antibiotic"
                     /identity="99.53"
                     /coverage="100.0"
     Typing          complement(2..338)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.929"
                     /coverage="100.0"
                     /evalue="1.85e-164"
     Typing          complement(3154..3733)
                     /name="rep_cluster_1078"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.771"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(1587..2080)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.303"
                     /coverage="92.0"
                     /evalue="3.71e-98"
ORIGIN
        1 ttaaattcaa cacgcatatt acgtctatcc cacgtatctg cttttacttt gtcatattcg
       61 atataaactt tttcttgtag agctttagct ttaaatttag tttgtagtat atcccaaagt
      121 cgaatttgtg gctcgacact cataaattca gatagtttgt gagcattatt tttattaaga
      181 tttccaacaa tagtcatagc gtcaaaactt aattttggtt ccggggtgta catagtatgt
      241 cggtttaacc ggctattaga gtagccggtt ttagaaaaat ttaaattttc gtattctgaa
      301 ctttgttttg actgaatttc ttctgctttt ttactcataa aaaatcgact ccttaatttt
      361 taagaagtcg tccatccaat cgtcaaatgt aaatgttgaa gaataatcaa atatcgttta
      421 atatctaatt atacaaaaat tacaaataac ataatcagta tatttggtat ggtcgttcca
      481 caaactttgg tcggggagtg gacgacttct ttatttttat tttgttatta atataacact
      541 atcaaaagtc ttggtctatt tagatcaagg ctttttttag tttattgcat tattccaatt
      601 tccttatggt ttggaaccta cagggcttta tgtgttgttg tgttggtgtt tcattgggat
      661 taatcccaaa tcaaccccac ccaacacgct aatcaagtta gctaacacat agcccattcc
      721 aaacaataag ttttctcggc ataatagcgt gttataatat gcgatagtac gaccaataca
      781 agattgtatt tagttaaata ggctttgaat gaggtttaaa actgctgtta taacgtttag
      841 ggcgcttatt aacagtagtt ttttatcttc cacgtcctct atctttttta acttcttctt
      901 gttgttcctg ctcttgatat ttttctgggt gcatttcttt atcaaacgtt aatgctattt
      961 ttctatcttt atcattgttt tcagtcatac cgttaatcaa atcaatataa ttttttctac
     1021 ctaaagtttt ttctaacttc tctaataatc ttcttaaata atttataagg tcttttaggt
     1081 gtttattttg agcatgctct tttttaaaat gccttcttaa ttcactttta tcgtttctaa
     1141 gattttcatt ttcttgttta agctcattat tttcactttt aaggtcattt aaagctttat
     1201 ctgacttaat atactcataa tcatctgtaa ttgattgtgc tgcttctatt tgcttctgaa
     1261 aggcattaaa atcttcttgt cttattacaa catttccagt ttcttgtgtt tctttgttaa
     1321 ataaaccacc tactgtttta gtttctttct catacgggac atttataggc tttttaagag
     1381 catttaatga cttttggtac tctcgcacca atttatcgtt cttttgcttt atttcgtctg
     1441 ttttttggct ctcacgctca tattcttgct tataatattc tgttttctgt ttatactgac
     1501 tcatttgctc atgctttgca tttgtaactt gtctggattg cccacgttct aaatcatagc
     1561 cacgctgatt aacatattcg ttaaacctat cttgaaactc tgttaaagcc tttttattcc
     1621 ctacaacttg tttagcactt aatcgaccat catcagttat tggaactaca ccataatgca
     1681 tatgtggtgt tttctcgtcc atatgaactg ttgcatataa taaattatct ttaccgtatt
     1741 cttgttctaa aaattcttta gcatgttcaa aaaactgctt tgtatcttct ggtgtttgat
     1801 tatcaaaaaa ttctttgtct gatgtaatta aaccgtcaac gtgtttaact gcatccgttc
     1861 tgatttttct tttacctgta taattttgtt ctattttttc atcaatcaag ttattaaaat
     1921 tttggttata ttcgtttacc aaatcataat tcaaataagt tttactatgg tctatatctt
     1981 cattttcata attattattt tctctttgaa catgtttttg aataccagtt gtatttgttc
     2041 cagactttac ttttgaaact ctaataatgg aataagacat ataaaaatca ctcctaagca
     2101 caaaggtttc atgtgtattt aatagtttaa gtctaacata ctagacttat tttgcaataa
     2161 gtcgttaaac cgtatgctct gcgaggctaa aaccattttt tgtgcaagca caaaaaatgg
     2221 actgaacaag tcagtccata agttcaaaac caaattcaaa atcaaaatcc agcaaccaaa
     2281 aatggtggtt gctataaact tataaatatc ataattactt aagtttatga aagttatttt
     2341 agatttaaat ccattcattt acactatcaa ctatattttg aaattcactc ataaataatg
     2401 aaacatggta accatcacat accgcatgat gaacttgcaa tgagactggt aaatagatct
     2461 tattattctt actataaaat ttacctattg taataattgg caataggaat ctactattat
     2521 taccaatatt taaattaaat gaactaaaat caatccaagg aatcatcgaa ataggaactg
     2581 tgttttcagg tattggtttt ttaggaaaca tttcattttt atctttatat tcaagtaagt
     2641 cactcttata actattataa aaagaattaa aactaacatt tgattctgtc caaatgttag
     2701 aaaatttttc agtttcttta ttaaagactg tatataaagg gtttaattta tcccaataac
     2761 ccaaatttcc ctcactatta attcctgttc taaatacttt attttgattt ataatattta
     2821 caattgtata aatcaaagca ggatacagtt catatccttt attttttatc atacttttaa
     2881 gtaaagtgat atcaaattct ttagtaacac tgtaagttgt ttgttgattg aaataatgat
     2941 taaaatattc ttttctatcc caagtttcca aattaataat attaaaagtc atatataatt
     3001 ttcctcctaa atttcatctt atctctttgt atttaggagg aataatcctc tgattttttc
     3061 atatattgtg tcacctctta aacgttaatt atactaaagt aacattttgt ataaaacaaa
     3121 gttactttac ttccaaaatc taaattcacg ttgccaaaaa tcaatctgct tttgcaattg
     3181 tttttcgttc gcttttaaag tcgatttcat taaatcagtt aaatcaatta gagatatttc
     3241 tttaattaat tttttatatt tattcttagt acgtctttct aattttcccc attcttcttc
     3301 atcattcaac aacataaaaa ccattgctct atcagaagta cgttcgatag ttttccaatc
     3361 tggttgtaat atatgtaaat cattaaaaca atcgttccaa taatcaacca tatctctttt
     3421 taattcaatt tctacacgcc ataagtgttc agacataatt ttaatatctg cattatcttt
     3481 gcgttcctgt tttttattat aaattctaat aaatctatca ctgtcacgaa caccaaaata
     3541 tttcgtttct ggtttaccgt tacgaccata aaaaatagtt ttcttaactg atttatcagt
     3601 cattgcataa taatcactta aatcatattc aaaatcaaaa gctaaatcta atcttgtaaa
     3661 accatcgtct tccatgtagt cgataatgtt ttgttttaac caaagcattt cttcatgcgt
     3721 aagtttattt gga
//
