LOCUS       NZ_AP019722             4439 bp    DNA     circular CON 13-FEB-2024
DEFINITION  Staphylococcus epidermidis strain NBRC 100911 plasmid pSEP1,
            complete sequence.
ACCESSION   NZ_AP019722
VERSION     NZ_AP019722.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00169832
            Assembly: GCF_006742205.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1
  AUTHORS   Miura,T., Furukawa,M., Shimamura,M., Ohyama,Y., Yamazoe,A. and
            Kawasaki,H.
  TITLE     Complete genome sequence of Staphylococcus epidermidis NBRC 100911
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4439)
  AUTHORS   Miura,T., Furukawa,M., Shimamura,M., Ohyama,Y., Yamazoe,A. and
            Kawasaki,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2019) Contact:Director-General Biological Resource
            Center National Institute of Technology and Evaluation, Biological
            Resource Center, NBRC; 2-5-8 Kazusakamatari, Kisarazu, Chiba
            292-0818, Japan URL :https://www.nite.go.jp/en/nbrc/
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Coverage                   :: 2187x
            Sequencing Technology             :: Illumina HiSeq; ONT GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/13/2024 04:10:14
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,307
            CDSs (total)                      :: 2,223
            Genes (coding)                    :: 2,172
            CDSs (with protein)               :: 2,172
            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)              :: 51
            CDSs (without protein)            :: 51
            Pseudo Genes (ambiguous residues) :: 0 of 51
            Pseudo Genes (frameshifted)       :: 34 of 51
            Pseudo Genes (incomplete)         :: 30 of 51
            Pseudo Genes (internal stop)      :: 22 of 51
            Pseudo Genes (multiple problems)  :: 27 of 51
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP019722.1.
            Annotated at DFAST https://dfast.nig.ac.jp/
            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"
                     /mol_type="genomic DNA"
                     /strain="NBRC 100911"
                     /culture_collection="NBRC:100911"
                     /type_material="type strain of Staphylococcus epidermidis"
                     /db_xref="taxon:1282"
                     /plasmid="pSEP1"
     gene            complement(join(4250..4439,1..755))
                     /locus_tag="FNL83_RS11955"
     CDS             complement(join(4250..4439,1..755))
                     /locus_tag="FNL83_RS11955"
                     /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            complement(1282..2523)
                     /gene="mobV"
                     /locus_tag="FNL83_RS11960"
                     /old_locus_tag="Sep02g_22340"
     CDS             complement(1282..2523)
                     /gene="mobV"
                     /locus_tag="FNL83_RS11960"
                     /old_locus_tag="Sep02g_22340"
                     /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            complement(2709..4088)
                     /gene="tet(K)"
                     /locus_tag="FNL83_RS11965"
                     /old_locus_tag="Sep02g_22350"
     ARG             complement(2713..4088)
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2..755)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1286..2523)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaactattg ctctatccgc agtgcgttgg atagttttcc aatctggttg caagatatgt
       61 aaatcactaa agcaatcatt ccagtaatcc accatatctc ttttaagttc gatttctaca
      121 cgccataaat gttcagacat aacttcagca tctgcattat ctttacgttc ttgcttttta
      181 ttataaattc taataaatct attactatct ctcacgccaa aatattttgt ttctggctta
      241 ccattacgac cataaaaaat agttttctta actgctttat cagacattgc atagtagtca
      301 ctcaaatcat cttcaaaatc aaaggctaaa tctaatcttg taaaaccgtc atcttccatg
      361 tagcttatta tattttgttt taaccaaatc atttcatctc gtgtaagttt gtttggatta
      421 aattcaatac gcatattacg tctatcccaa ctatctgctt tcactttgtc atattcaata
      481 taaacttttt cttgaagtgc tttagcttta aactttgttt gaagaatatc ccaaagtctt
      541 atttggggct ctacactcat aaatttagaa agggcttgag cgttgtctcg gttgagattt
      601 ccaacgatcg tcattgcatc aaaacttaat tttggatcag atatgcacac agtatgtgcg
      661 tccaaccggc tattagagta gccggtttta gaaaaattgt ctaaatcgtg attttccaaa
      721 tgatttgaat gatttgcatg attgttttta tacataaaaa atcgactcct taatctcaat
      781 ttcgtttaag gaatcgctca cccaaatata tatcttgatg tatatttaaa tatcgtttaa
      841 tatctaaata tacaagatta taaaaacaac tcagtgtttt tttctttgaa tgatgtcgtt
      901 cacaaacttt ggtcagggcg tgagcgactc ctttttattt tgttattaat ataacactat
      961 caaaagactt ggtctaatca gatcaagtct ttttttattt aagcatttgt attatctggt
     1021 aaacagttaa aactactaaa acaccaagta catacttact tgttataaaa ttctcaaagg
     1081 cttctctgaa tttcatttct tcaactcctt ttattgcttt attccaattt ccttattggt
     1141 cggaacctac agggctttat gtgttgttga gttggtactt tcttgggatt aatcccaatt
     1201 caagtccaac caactcgcta acaagttagc taacacatag cccattccaa ccaataagtt
     1261 ttctcggcat aaatgcatgt tctataagtg catacctcta tctcgttttt gattcttttg
     1321 ttgttcttgt tgctgttcct gttctgaata taattctgga ttcatttttt tatctaagtt
     1381 tcctgctaaa ccatttagtt ttggttcatc ttctgttaac ttattaactc tttccgcaaa
     1441 ggtatttctt cctaaaactc gttctaactc ttttagtaag atttttaaaa gctttaacgc
     1501 tatttctata ttctctttaa gtggctttgc attttcgtaa agttggttaa aattatcgtc
     1561 tgcgttttca atacgctcaa ctgctttatt taataaatca tctttctctc gtatttcctt
     1621 atctttatca tctaaggctc taccagactt tatatactcg taatcttccg aaatatcttg
     1681 agcagctttt atctgtttct gaaattcatt gaaatctttt tggcttatta caacatttcc
     1741 agtttcttgt atttctttgc taaataaacc acctactttt tcagtttctt gctcatacgg
     1801 aacatttata ggctttttaa gcgtatttaa cgatttttgg tactcttgca ttaatttatc
     1861 gttcttttgc tttatatggt ctgttttttg gctctcacgt tcatattctt gcttatgata
     1921 ttctgttttt tgtttatact gacttatttg ctcatgttta gcatttgtta cttgtcttga
     1981 ttgcccacgt tctaaatcat atcctcgttg tttaacatgc tcattaaatc tatcttgaaa
     2041 cgctgttaaa gcttttttat tacctacaac ttctttagca cttaaacgac catcatcagt
     2101 tattggaaca acgccataat gcatatgtgg tgttttttcg tccatgtgaa ctgttgcata
     2161 taataaatta tctttaccgt attcttgttc taaaaactct ttagcatatt caaaaaactg
     2221 ctttgtatct tctggcgttt gattatcaaa gaaatcattg tctgatgtaa ttaaaccatc
     2281 aatgtgttta atcgcgtctg ttctaatttt tcttttgcct gtataattct gttcgatttt
     2341 ttcatcaatc aagttattaa aattctgttt attagcattt accaaatcat aatttaagta
     2401 agttttacta tggtctatat cttcattttc ataattatta ttttctcttt gaacatgttt
     2461 ttgtatgccc gttgtatttg ttccagattt aacttttgaa actctaacaa tggaataaga
     2521 catataaaaa tcactcctaa gcacaaaggt ttcatgtgta tttaatagtt taagtctaac
     2581 agactagact tatttttaat aagtcgttaa tacgtgtgct ctgcgaggct taaacctgtt
     2641 tttgctaacg caaaaaatga gtggcaaaat gctagccact catagttcta aaccaaaata
     2701 taatataact attcaaactg cttttcagaa cgtttaaata caataatcgt caaaagacaa
     2761 cataaaataa taaggatagc catggctaca agaatattac tatacactcc agaagaataa
     2821 tttataaatt ccagaactag tttacgatta atcaattgta gtgacaataa acctcctaca
     2881 attgctatac ctgttccctc tgataaaaaa cttgtgaaat ttagcaaact cattccagaa
     2941 gcaacttctt cttcagaaag actacttgat actatttttg atataactgt tttagtaaaa
     3001 gataatccgc ccataacaaa tataaacata aaagtagtca accacatact aaactcaaca
     3061 aaaaatgcaa tagttaaaaa acttatagag atagacaatg atcctaaaat aaaaacaaat
     3121 aatgatcctt ttctatccac taaaaaacca ccaaaataac caaaaacaat aacactcatg
     3181 gttccaggaa aaataacact attacctatt gtcgctacat ttacatgata aatagttttc
     3241 atcatataag gcaccattga tataaaacca gctactatag aaaatattag cccaccagaa
     3301 aacaaaccaa gcataaacgg aatgtttttc cctagtttag gattaataaa agggttagaa
     3361 actcttgaaa tatgtttaat aaaaatcaca aaaaagattg tgaagagtat taaaaaagtc
     3421 caattataat ttgtcgtaaa taacataaaa catataatac ttatagacat taaaacaata
     3481 cctacgatat ctaatgtatt ttttgttgat ttaccaggta ccattacttt aataagaaaa
     3541 ggtatagtta ctattgtaat cataggaagt ataagtaggt aagaccaatg aatataatgt
     3601 gctattattc cccctattga aggacctaac ccttcaccta aagctacaat tgatcctata
     3661 aaaccaaagg ctttgccttg tttttttctt gtaatatttc tagctacaac caccataatc
     3721 agtgaaggga atgcagcaga tcctactcct tgtactaacc taccaaaaat caaaataaaa
     3781 aagtgattgt gaccaataaa agcaatcaat gaaccaagac agctcaaact aataccaata
     3841 attaacaatt tttttatatt tatataatca gataattttc catatactgc tgttcctatc
     3901 gaaaaagtta acatatatgc agtgtttacc cagtttgtaa ttccaggagt agtattaaaa
     3961 tgatttgcaa tatcaggtaa agaaacattt aaaaccattt catttaatac actaaaaaat
     4021 gaaagaatac aaagccaaaa taaaacgcta taaaacaaac ctttaaattt tttatataaa
     4081 ctaaacaatt ttacctcttt acttgaggtg actaaagttt ataggggtaa attattcttt
     4141 cacctcatat aaattcccca aatttttaaa tagacacttc ataaaaaaat cctcctaaat
     4201 tagaatagtt taaatatatc atttttgttc agtaatatta atatgtacac tatttccaaa
     4261 atttaaattc atgttgccaa aaatcgattt gtttttgcaa ttgtttttcg ttcgctttta
     4321 aagtcgattt cattaagtcc gttaaatcga ctggcgaaat ttcttttatc aaattcttat
     4381 attttgttct agaatttctg tgaagctttc cccattcttc ttcatcactc aataacata
//
