LOCUS       NZ_HG813243             4439 bp    DNA     circular CON 06-APR-2024
DEFINITION  Staphylococcus epidermidis PM221 plasmid 4, complete sequence.
ACCESSION   NZ_HG813243
VERSION     NZ_HG813243.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3139103
            Assembly: GCF_000751035.1
KEYWORDS    RefSeq; complete genome; complete replicon.
SOURCE      Staphylococcus epidermidis PM221
  ORGANISM  Staphylococcus epidermidis PM221
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1
  AUTHORS   Savijoki,K., Iivanainen,A., Siljamaki,P., Laine,P.K., Paulin,L.,
            Karonen,T., Pyorala,S., Kankainen,M., Nyman,T.A., Salomaki,T.,
            Koskinen,P., Holm,L., Simojoki,H., Taponen,S., Sukura,A.,
            Kalkkinen,N., Auvinen,P. and Varmanen,P.
  TITLE     Genomics and proteomics provide new insight into the commensal and
            pathogenic lifestyles of bovine and human-associated Staphylococcus
            epidermidis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4439)
  AUTHORS   Kammonen,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JAN-2014) Institute of Biotechnology, University of
            Helsinki, Viikinkaari 4, 00014, FINLAND
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000751035.1-RS_2024_04_06
            Annotation Date                   :: 04/06/2024 01:19:01
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,528
            CDSs (total)                      :: 2,444
            Genes (coding)                    :: 2,349
            CDSs (with protein)               :: 2,349
            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)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 67 of 95
            Pseudo Genes (incomplete)         :: 42 of 95
            Pseudo Genes (internal stop)      :: 28 of 95
            Pseudo Genes (multiple problems)  :: 34 of 95
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            HG813243.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4439
                     /organism="Staphylococcus epidermidis PM221"
                     /mol_type="genomic DNA"
                     /strain="PM221"
                     /db_xref="taxon:1449752"
                     /plasmid="4"
     gene            1..1242
                     /gene="mobV"
                     /locus_tag="SEB_RS11835"
                     /old_locus_tag="SEB_p402528"
     CDS             1..1242
                     /gene="mobV"
                     /locus_tag="SEB_RS11835"
                     /old_locus_tag="SEB_p402528"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000122374.1"
                     /translation="MSYSIVRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNANKQNFNNLIDEKIEQNYTGKRKIRTDAIKHIDGLITSDNDFFDNQTPEDTKQFF
                     EYAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKEVVGNKKALTAFQ
                     DRFNEHVKQRGYDLERGQSRQVTNAKHEQISQYKQKTEYHKQEYERESQKTDHIKQKND
                     KLMQEYQKSLNTLKKPINVPYEQETEKVGGLFSKEIQETGNVVISQKDFNEFQKQIKAA
                     QDISEDYEYIKSGRALDDKDKEIREKDDLLNKAVERIENADDNFNQLYENAKPLKENIE
                     IALKLLKILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQ
                     EQQKNQKRDRGMHL"
                     /name="mobV"
     gene            1769..2713
                     /locus_tag="SEB_RS11840"
                     /old_locus_tag="SEB_p402529"
     CDS             1769..2713
                     /locus_tag="SEB_RS11840"
                     /old_locus_tag="SEB_p402529"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_000277654.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKQERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     VDLTDLMKSTLKANEKQLQKQIDFWQHEFKFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2875..4254
                     /gene="tet(K)"
                     /locus_tag="SEB_RS11845"
                     /old_locus_tag="SEB_p402530"
     ARG             2876..4251
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="99.78"
                     /coverage="100.0"
     Typing          1770..2713
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1239
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcttatt ccattgttag agtttcaaaa gttaaatctg gaacaaatac aacgggcata
       61 caaaaacatg ttcaaagaga aaataataat tatgaaaatg aagatataga ccatagtaaa
      121 acttacttaa attatgattt ggtaaatgct aataaacaga attttaataa cttgattgat
      181 gaaaaaatcg aacagaatta tacaggcaaa agaaaaatta gaacagacgc gattaaacac
      241 attgatggtt taattacatc agacaatgat ttctttgata atcaaacgcc agaagataca
      301 aagcagtttt ttgaatatgc taaagagttt ttagaacaag aatacggtaa agataattta
      361 ttatatgcaa cagttcacat ggacgaaaaa acaccacata tgcattatgg cgttgttcca
      421 ataactgatg atggtcgttt aagtgctaaa gaagttgtag gtaataaaaa agctttaaca
      481 gcgtttcaag atagatttaa tgagcatgtt aaacaacgag gatatgattt agaacgtggg
      541 caatcaagac aagtaacaaa tgctaaacat gagcaaataa gtcagtataa acaaaaaaca
      601 gaatatcata agcaagaata tgaacgtgag agccaaaaaa cagaccatat aaagcaaaag
      661 aacgataaat taatgcaaga gtaccaaaaa tcgttaaata cgcttaaaaa gcctataaat
      721 gttccgtatg agcaagaaac tgaaaaagta ggtggtttat ttagcaaaga aatacaagaa
      781 actggaaatg ttgtaataag ccaaaaagat ttcaatgaat ttcagaaaca gataaaagct
      841 gctcaagata tttcggaaga ttacgagtat ataaagtctg gtagagcctt agatgataaa
      901 gataaggaaa tacgagagaa agatgattta ttaaataaag cagttgagcg tattgaaaac
      961 gcagacgata attttaacca actttacgaa aatgcaaagc cacttaaaga gaatatagaa
     1021 atagcgttaa agcttttaaa aatcttacta aaagagttag aacgagtttt aggaagaaat
     1081 acctttgcgg aaagagttaa taagttaaca gaagatgaac caaaactaaa tggtttagca
     1141 ggaaacttag ataaaaaaat gaatccagaa ttatattcag aacaggaaca gcaacaagaa
     1201 caacaaaaga atcaaaaacg agatagaggt atgcacttat agaacatgca tttatgccga
     1261 gaaaacttat tggttggaat gggctatgtg ttagctaact tgttagcgag ttggttggac
     1321 ttgaattggg attaatccca agaaagtacc aactcaacaa cacataaagc cctgtaggtt
     1381 ccgaccaata aggaaattgg aataaagcaa taaaaggagt tgaagaaatg aaattcagag
     1441 aagcctttga gaattttata acaagtaagt atgtacttgg tgttttagta gttttaactg
     1501 tttaccagat aatacaaatg cttaaataaa aaaagacttg atctgattag accaagtctt
     1561 ttgatagtgt tatattaata acaaaataaa aaggagtcgc tcacgccctg accaaagttt
     1621 gtgaacgaca tcattcaaag aaaaaaacac tgagttgttt ttataatctt gtatatttag
     1681 atattaaacg atatttaaat atacatcaag atatatattt gggtgagcga ttccttaaac
     1741 gaaattgaga ttaaggagtc gattttttat gtataaaaac aatcatgcaa atcattcaaa
     1801 tcatttggaa aatcacgatt tagacaattt ttctaaaacc ggctactcta atagccggtt
     1861 ggacgcacat actgtgtgca tatctgatcc aaaattaagt tttgatgcaa tgacgatcgt
     1921 tggaaatctc aaccgagaca acgctcaagc cctttctaaa tttatgagtg tagagcccca
     1981 aataagactt tgggatattc ttcaaacaaa gtttaaagct aaagcacttc aagaaaaagt
     2041 ttatattgaa tatgacaaag tgaaagcaga tagttgggat agacgtaata tgcgtattga
     2101 atttaatcca aacaaactta cacgagatga aatgatttgg ttaaaacaaa atataataag
     2161 ctacatggaa gatgacggtt ttacaagatt agatttagcc tttgattttg aagatgattt
     2221 gagtgactac tatgcaatgt ctgataaagc agttaagaaa actatttttt atggtcgtaa
     2281 tggtaagcca gaaacaaaat attttggcgt gagagatagt aatagattta ttagaattta
     2341 taataaaaag caagaacgta aagataatgc agatgctgaa gttatgtctg aacatttatg
     2401 gcgtgtagaa atcgaactta aaagagatat ggtggattac tggaatgatt gctttagtga
     2461 tttacatatc ttgcaaccag attggaaaac tatccaacgc actgcggata gagcaatagt
     2521 ttttatgtta ttgagtgatg aagaagaatg gggaaagctt cacagaaatt ctagaacaaa
     2581 atataagaat ttgataaaag aaatttcgcc agtcgattta acggacttaa tgaaatcgac
     2641 tttaaaagcg aacgaaaaac aattgcaaaa acaaatcgat ttttggcaac atgaatttaa
     2701 attttggaaa tagtgtacat attaatatta ctgaacaaaa atgatatatt taaactattc
     2761 taatttagga ggattttttt atgaagtgtc tatttaaaaa tttggggaat ttatatgagg
     2821 tgaaagaata atttacccct ataaacttta gtcacctcaa gtaaagaggt aaaattgttt
     2881 agtttatata aaaaatttaa aggtttgttt tatagcgttt tattttggct ttgtattctt
     2941 tcatttttta gtgtattaaa tgaaatggtt ttaaatgttt ctttacctga tattgcaaat
     3001 cattttaata ctactcctgg aattacaaac tgggtaaaca ctgcatatat gttaactttt
     3061 tcgataggaa cagcagtata tggaaaatta tctgattata taaatataaa aaaattgtta
     3121 attattggta ttagtttgag ctgtcttggt tcattgattg cttttattgg tcacaatcac
     3181 ttttttattt tggtttttgg taggttagta caaggagtag gatctgctgc attcccttca
     3241 ctgattatgg tggttgtagc tagaaatatt acaagaaaaa aacaaggcaa agcctttggt
     3301 tttataggat caattgtagc tttaggtgaa gggttaggtc cttcaatagg gggaataata
     3361 gcacattata ttcattggtc ttacctactt atacttccta tgattacaat agtaactata
     3421 ccttttctta ttaaagtaat ggtacctggt aaatcaacaa aaaatacatt agatatcgta
     3481 ggtattgttt taatgtctat aagtattata tgttttatgt tatttacgac aaattataat
     3541 tggacttttt taatactctt cacaatcttt tttgtgattt ttattaaaca tatttcaaga
     3601 gtttctaacc cttttattaa tcctaaacta gggaaaaaca ttccgtttat gcttggtttg
     3661 ttttctggtg ggctaatatt ttctatagta gctggtttta tatcaatggt gccttatatg
     3721 atgaaaacta tttatcatgt aaatgtagcg acaataggta atagtgttat ttttcctgga
     3781 accatgagtg ttattgtttt tggttatttt ggtggttttt tagtggatag aaaaggatca
     3841 ttatttgttt ttattttagg atcattgtct atctctataa gttttttaac tattgcattt
     3901 tttgttgagt ttagtatgtg gttgactact tttatgttta tatttgttat gggcggatta
     3961 tcttttacta aaacagttat atcaaaaata gtatcaagta gtctttctga agaagaagtt
     4021 gcttctggaa tgagtttgct aaatttcaca agttttttat cagagggaac aggtatagca
     4081 attgtaggag gtttattgtc actacaattg attaatcgta aactagttct ggaatttata
     4141 aattattctt ctggagtgta tagtaatatt cttgtagcca tggctatcct tattatttta
     4201 tgttgtcttt tgacgattat tgtatttaaa cgttctgaaa agcagtttga atagttatat
     4261 tatattttgg tttagaacta tgagtggcta gcattttgcc actcattttt tgcgttagca
     4321 aaaacaggtt taagcctcgc agagcacacg tattaacgac ttattaaaaa taagtctagt
     4381 gtgttagact taaactatta aatacacatg aaacctttgt gcttaggagt gatttttat
//
