LOCUS       NZ_CP093204             6585 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Staphylococcus epidermidis strain TSM-31 plasmid p2, complete
            sequence.
ACCESSION   NZ_CP093204
VERSION     NZ_CP093204.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26520624
            Assembly: GCF_024204885.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 6585)
  AUTHORS   Saito,R., Ayibieke,A. and Yamada,K.
  TITLE     bloodstream S. epidermidis isolates from two Hospitals in Tokyo
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6585)
  AUTHORS   Saito,R., Ayibieke,A. and Yamada,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAR-2022) Molecular Microbiology, Tokyo Medical and
            Dental University, 1-5-45 yushima, Bunkyo-ku, Tokyo 113-8510, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Unicycler hybrid assembley v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 557.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/20/2023 03:40:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,379
            CDSs (total)                      :: 2,295
            Genes (coding)                    :: 2,235
            CDSs (with protein)               :: 2,235
            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)              :: 60
            CDSs (without protein)            :: 60
            Pseudo Genes (ambiguous residues) :: 0 of 60
            Pseudo Genes (frameshifted)       :: 37 of 60
            Pseudo Genes (incomplete)         :: 30 of 60
            Pseudo Genes (internal stop)      :: 23 of 60
            Pseudo Genes (multiple problems)  :: 23 of 60
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093204.1.
            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..6585
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="TSM-31"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="p2"
                     /geo_loc_name="Japan"
                     /lat_lon="35.75322977 N 139.70093331 E"
                     /collection_date="2012-04-19"
                     /collected_by="Toshima hospital staff"
     gene            complement(join(5710..6585,1..135))
                     /locus_tag="MNU47_RS11865"
                     /old_locus_tag="MNU47_11855"
     CDS             complement(join(5710..6585,1..135))
                     /locus_tag="MNU47_RS11865"
                     /old_locus_tag="MNU47_11855"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_002498904.1"
                     /translation="MATTKLSATKSTSRAINYAEKRAVEKSGLNCDVDYAKSSFKAARE
                     LYGKTDGNQGHVIIQSFQPGEVTPEQCNQLGLALAEKLVPNHQVAVYTHADTNHVHNHI
                     VLNSIDLNTGKKFNNNKQALRDVRAFNDEVCRAQGLSVPEKDTARLRYTQTEKAIADPN
                     TTSTAQYSWKDDIREAIDQSTATNMEEFQKHLNQHGITIERVTPKSITYRHLAENKKVR
                     GRKLGEDYNKGGIQHGFERQIQRRQQQKHKSDTNFQPKRSTSNRHESTERDTGVTQSDW
                     DQFAQDTNELERRRQAAESARLVDEKARRDREKRVREKPTSRPIINIDRDHGLEL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(301..687)
                     /gene="mobC"
                     /locus_tag="MNU47_RS11870"
                     /old_locus_tag="MNU47_11860"
     CDS             complement(301..687)
                     /gene="mobC"
                     /locus_tag="MNU47_RS11870"
                     /old_locus_tag="MNU47_11860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011117491.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_011117491.1"
                     /translation="MSEQNTFVASDETVGRNRKPNRKAPKQISFRVSESEYLKLQQSAE
                     TLNMSVPAFVKKKAQGARLVAPKLDQATRQSVAKDLSMLGANANQIAKYCNQHQHEAPN
                     YEALERNISELRERLDEIWNMIQK"
                     /name="mobC"
     gene            complement(1023..1823)
                     /locus_tag="MNU47_RS11875"
                     /old_locus_tag="MNU47_11865"
     CDS             complement(1023..1823)
                     /locus_tag="MNU47_RS11875"
                     /old_locus_tag="MNU47_11865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002498218.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ABC transporter permease"
                     /protein_id="WP_002498218.1"
                     /translation="MKSSLFILKEHFNNLYLMKRLAQFEMKISNKNNYLGTAWELINPS
                     IQIFMYWFIFGLGFRNNRTVENIPFIFWLIVGISMWFFVNQGILNGTKAVTSKYKQVAK
                     MNFPLSILSSYIVLSKFYTHVLLLILIMLICALNGYYPTIYTLQLLIFIPYTLLLTMTI
                     TLLTSTLAVIIRDIQMLMQALMRIIFFISSILYLPTNALVLKVIQFNPIYFIAESYRAA
                     ILYQNWFFITHWKLSLYNLAFLLITFVLGSILHVKYREQFADFL"
                     /name="ABC transporter permease"
     gene            complement(1919..2113)
                     /locus_tag="MNU47_RS11880"
                     /old_locus_tag="MNU47_11870"
     CDS             complement(1919..2113)
                     /locus_tag="MNU47_RS11880"
                     /old_locus_tag="MNU47_11870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002485716.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002447414.1"
                     /translation="MKKISKLLIAFSLVTTLSYASASTGFMNDNSHEAFAKSKKKKHKG
                     NGNKHNCFPVGNSEFCTTP"
                     /name="hypothetical protein"
     gene            2847..3452
                     /locus_tag="MNU47_RS11885"
                     /old_locus_tag="MNU47_11875"
     CDS             2847..3452
                     /locus_tag="MNU47_RS11885"
                     /old_locus_tag="MNU47_11875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001076470.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_002498907.1"
                     /translation="MNKSKVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGEEVSSETL
                     KSVSNALDVTVNELFESISSSDKEEEIMEISKEQQKQFNYRKNELFTIKLITFSFIFVF
                     LGLFGIFVGELNGLEQNIYRIIWIFALFLSLAIMYYFLNVFISKKLDKKYPMTIGMKNR
                     NRKNEPVKNGWDFMARYWWIVFPIGGFLSWLIPELTGK"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3500..4357)
                     /locus_tag="MNU47_RS11890"
                     /old_locus_tag="MNU47_11880"
     CDS             complement(3500..4357)
                     /locus_tag="MNU47_RS11890"
                     /old_locus_tag="MNU47_11880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002458658.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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="RepB family plasmid replication initiator
                     protein"
                     /protein_id="WP_002498908.1"
                     /translation="MSGETVVYKNDMNLVPLRKFNNTEVNLFFTLCNKLKDKGNLTVNV
                     PFEELKELSNYYSHDKKLFIQDLEKFYDKVFSLTYREETENVIRKFILFTKVEIYKDKE
                     YVAIGVNPDLEHIINSLTSNFTKFELKEMTHLKSTYSKHMFRILKQYKHTGYVKIKIDD
                     FRERLDIPNSYRMTNINQKVLAPIIKELGFIFNNLNINKIKAKKGRKIEWLEFTFDAEK
                     RIHNKRQPQMANIDKSRQYISREKTPRWLEERTYEKQIKNEYDPQLEKERKAFLKQLQL
                     DWED"
                     /name="RepB family plasmid replication initiator protein"
     gene            complement(5202..5807)
                     /locus_tag="MNU47_RS11895"
                     /old_locus_tag="MNU47_11885"
     CDS             complement(5202..5807)
                     /locus_tag="MNU47_RS11895"
                     /old_locus_tag="MNU47_11885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002440619.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_077431415.1"
                     /translation="MKRLEEIEKREYERNQRHDQLLTSIETTASNFNQATDFTQKRFIS
                     AARHYIERINNDNLKQDFHTAIQKELEDVKTDTQNVVKEVQNNQSELRQANNNYKKMID
                     ERMKSNAIVIKQYDQVIHRLTKGITAMFFIVALVMVAFLVISPLGDWLGVQHFYEWLNH
                     VLKTGHSAWRYFMLVFYLVPYILFGVLIYAILKAYERL"
                     /name="mobilization protein"
     Typing          659..897
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(3501..4324)
                     /name="rep_cluster_1256"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5714..6585)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcacgagcg gctttaaaac tagatttggc atagtccacg tcacaattta agccactttt
       61 ctcaacggca cgtttttcag cgtaattgat ggcccgtgat gttgatttag tcgcacttaa
      121 tttagttgtt gccattggta tcacgcgctt ttttcttttt atatgatata tataaatcaa
      181 tacctgtgat aaaagttaaa agtgaaaaac acaaaatcac cggaaattgt ggatcaaaga
      241 aaataaaata aaacaatatc attaaacaca tcacaaataa aatggcactt acaatcattt
      301 ttatttttgg atcatgttcc atatctcatc taacctttca cgtaattcac taatgttacg
      361 ttctaatgct tcgtagttcg gtgcttcgtg ttgatgttgg ttgcaatatt tcgcaatctg
      421 attggcattt gcacccaaca tacttaaatc tttagctacc gattgtcgcg ttgcttgatc
      481 caatttgggt gcgaccaatc gggcgccttg tgcctttttc ttaacgaacg caggaacact
      541 catatttaaa gtttcagctg attgttgtaa ctttaaatat tcggattcgc tcacacgaaa
      601 actaatttgt ttcggcgcct tacggttggg tttacggttt cgcccaacag tttcgtcgct
      661 agccacaaat gtgttttgtt cgctcattca atcccaccac gctttcttcg aaagataacg
      721 ccgttcttac atcttacttt atatgataaa gtaagattca tcaagtcgtt aagtggtttg
      781 gcaagcattg gctttgctag ccactaacgt ggcagacgcg cctgcttgtt gggggtaatc
      841 cccaagcccc ttatggattt tttctaacga aaaaatagtg gctaattgct agccactaaa
      901 ttcaaaacca tcaaaaccgc agcaaccaaa aatatttttg ctataattat taaacccaaa
      961 tgaaaaataa aattaaaaaa gaaatgagaa taagatcaaa aataatgttc tttatattct
     1021 gtttataaaa aatctgcaaa ttgttcacga tatttaacat gtaaaataga gcccaacaca
     1081 aaagtaatta aaaggaaagc aagattatat aaagatagtt tccaatgtgt tataaaaaac
     1141 caattttgat atagaattgc tgctctataa ctttcagcta taaaatagat aggattaaat
     1201 tgtataacct ttaaaactaa agcatttgtc ggtaaatata aaattgaaga tataaaaaat
     1261 attattctca taagagcttg cataagcatt tggatgtctc taataattac agctaatgtt
     1321 gaagttaata gtgttattgt cattgtcagt aacagagtgt aagggataaa aattaataat
     1381 tgtaatgtat atatagtagg gtaatatcca tttaaagcac atataagcat aattaaaata
     1441 agcaataaca catgggtata aaatttactt aagacgatat aactagataa tatagataat
     1501 ggaaaattca ttttagctac ttgcttatat ttgctagtaa ctgcttttgt accatttaaa
     1561 ataccttgat tcacaaaaaa ccacatactt attcctacaa ttaaccaaaa aataaaaggt
     1621 atattctcaa cagttctatt atttctgaaa cctaaaccaa aaataaacca atacataaaa
     1681 atctgtattg aaggattaat taattcccat gctgttccca aataattatt tttgttagaa
     1741 attttcattt caaattgtgc taatcttttc attaaatata aattattaaa atgttctttt
     1801 aatataaaca aagatgattt cataacatta agttaccttt ctaagattat caatattata
     1861 aatgaaacct aaaaaaaagg taaagcaatt gtttattgct ttaccttttc tattttaatt
     1921 atggagttgt acaaaattca ctgtttccga ctgggaagca attatgtttg ttaccatttc
     1981 ctttatgttt tttcttttta gatttagcaa atgcttcatg agagttatca ttcataaaac
     2041 cagttgaagc acttgcatat gatagtgttg ttactaatga aaatgcaata agaagtttcg
     2101 agattttttt catttctacc cctccaaaat attaatttaa agtaaagata tcacaatttt
     2161 aagaaaaatc aagacgaaaa aaatataaat ttattaattg gttttagcat atatttttga
     2221 agagtaaaat atagaatttt ttaatattct attcaatttt acaaattata cgtattctat
     2281 acaaactaac tacctataat agttaattat gtcaactaac aataaaggct taaacgctgt
     2341 taaatcaacg tttaagcctt tgtcttgtga ttatcgttta ttcatctttt atacatcgtt
     2401 gttctcacgt gttttcattc tttttcatta agtgaacttt tgtatcttta ttcacaattt
     2461 cacgtgataa cacaccgttt taaattgtag ttttttgtta tactggaaaa gcacttccgt
     2521 gcacaaagga ggtgtcacat acaatgataa tcttgctatt tgtactagat aagctcattt
     2581 ttccaattat tgttggttat gttctttatc tattacaaca agagcataag taaaaagaaa
     2641 cccccagccg gcacgctggg ggttttcaca tacaatgata tatctgctat ttgttacttt
     2701 cagtatatcc tttcttatgc tttttgtaaa attagatata tactttcttt taagaatata
     2761 attttgaagt aactgtcgtt tcattgtcgc ccatctgtcg gcaatttttc gtgttcattt
     2821 ttttagttga ggagtagttt atgagtatga acaaatcaaa agttgcagaa attagaaaac
     2881 aaaaatcgtt aactcaagaa aatttagcag aaaaggctta tgtaacagta agaacaattc
     2941 aaagaatgga ggctggagaa gaagttagta gtgaaacact taaaagtgtc tcaaacgcat
     3001 tagatgtgac agtcaatgaa ctattcgaat ctatctcgtc ttctgataag gaggaggaaa
     3061 taatggaaat atctaaagaa caacaaaagc agtttaatta tcgtaaaaat gaacttttta
     3121 ctattaaatt aataacattt agttttattt ttgtgttttt aggactattt ggaatctttg
     3181 taggtgagtt aaacggttta gaacaaaata tttaccgcat catttggatt ttcgctttat
     3241 ttttgagctt agcaataatg tattattttt taaatgtttt tatttcaaaa aaattagata
     3301 aaaaatatcc tatgactatt ggaatgaaaa atagaaatag aaaaaatgaa cctgtaaaaa
     3361 atggctggga ttttatggct agatattggt ggattgtttt tcctattgga gggtttctaa
     3421 gttggctaat tcctgaatta acaggaaaat aaaatacaaa acaaaagatc tttagccccc
     3481 ttgctaaaga tcttttgttt taatcttccc agtctaattg aagttgtttt aaaaatgctt
     3541 ttcgctcttt ttctaattgt ggatcatatt cattttttat ttgtttttca taagtacgtt
     3601 cttctaacca tctcggcgtt ttttcccgac ttatatattg tcgtgactta tctatattcg
     3661 ccatttgtgg ctgtcgttta ttgtgaatgc gtttctcagc gtcaaaagta aactctaacc
     3721 attcaatttt acgtcctttt tttgccttta ttttattgat attaaggtta ttaaaaataa
     3781 agcctaattc tttaatgata ggggctaata ctttttgatt aatatttgtc atacggtaac
     3841 tattaggaat atccagccgt tctctaaaat catcaatttt aatttttaca tagccagtat
     3901 gtttatactg cttaagtatt ctgaacatat gcttagaata tgtagattta aggtgtgtca
     3961 tttctttaag ttcaaattta gtgaagttac tagttaatga attaataata tgttctaaat
     4021 ctggattaac accaatagcc acatactctt tatctttata aatttctact ttagtaaaaa
     4081 gaataaattt tctaataaca ttctcagttt cttctctata tgttaaagag aaaactttgt
     4141 catagaattt ttctaaatct tgaataaaaa gctttttatc atgactatag taattactta
     4201 attcttttaa ttcttcaaat ggcacattaa cagtcaaatt gcctttatct tttaatttat
     4261 tacacaaagt aaaaaataga ttaacttcag tattattaaa ttttctcagt ggaactaaat
     4321 tcatatcatt tttatatact actgtttctc cactcaacta actccactcc aatctaaaag
     4381 aaacctatat agaataaaga ttcctattaa ctttaattgt aaatacttat aatcactatg
     4441 ttataaacaa taataacata aagaaaccta atataaaaaa agtttcttta gtttaatgat
     4501 tggttgcctt tagtttaatg attggttgcc tttagtttaa tgattggttg cctttagttt
     4561 aatgattggt tgcctttaac atttcaaatc tattgtcact ctaaggatca aatgactcct
     4621 aaaaaggttt taaaaagatt tataaaaaga tattaaaaag ttcggggcaa tttgcccctc
     4681 acaaattcaa aagacaaaaa ggaaacccac cacatttgtg gtgggttttt attatttaaa
     4741 aaagtaataa gtgatataac tttaatgcat tattccaatt gctttattga cattgagcct
     4801 ctgaaccctt aataaaccct aaaactgtcg actcgtcggt ttcatagctc acactatccc
     4861 gacattcgtc gaaacagttt aattaagggt tcttctcaat gctcaataaa ttttctcggc
     4921 ataagcgcat gtgctattct tcattttcca tatcttttac aacctttaat atcggtgtga
     4981 ttagtaatga taaaataaat gctgattcta aaatcagaaa aatatttgtt ccttcaaaaa
     5041 atattaagtt gaccacatat ccaaaaagac aaaatacaat aaaaaaacaa ataaagtgaa
     5101 caatagaatt caaggcgagc actccttttt ggtttctacg ctattttaag cttgatatag
     5161 cttcttcatt aaacaaaagg taattttcta tttattttgt attaaagacg ctcatatgct
     5221 tttaaaatgg catatataag cactccaaat aaaatataag gtacaagata gaaaacaagc
     5281 atgaaataac gccatgctga atgccccgtt ttaagcacgt ggttcagcca ttcgtaaaaa
     5341 tgttggacgc ctaaccagtc acctaaggga cttataacta aaaaggcgac catcactaag
     5401 gcaacgataa aaaacatggc tgtgatgcct ttagttaaac gatgtatgac ttgatcatat
     5461 tgtttaatca ctattgcgtt gctcttcata cgttcatcaa tcattttttt ataattatta
     5521 ttggcttgtc gcagttcgga ttggttgttt tgaacttcct taactacgtt ttgtgtgtct
     5581 gttttgacat cttctaattc tttttgtata gctgtgtgaa aatcttgttt taaattatcg
     5641 ttattaatcc gttcaatata atgtcttgcc gcgcttataa aacgcttttg tgtgaagtct
     5701 gtggcttgat taaagttcga ggccgtggtc tcgatcgatg ttaataattg gtcgtgacgt
     5761 tggtttctct cgtactctct tttctcgatc tcttcgagcc ttttcatcaa caagtcttgc
     5821 tgattctgca gcttgtcggc gacgctcaag ctcatttgtg tcttgggcga attggtccca
     5881 atctgattga gtgacgcctg tatctcgttc agttgattca tgacggtttg aagttgatcg
     5941 ttttggctgg aagttcgtgt ctgatttatg tttttgttgt tgtcgtcgtt gtatttgtct
     6001 ttcaaagcca tgttggatgc ctcctttatt gtaatcttcg cccaatttac gcccgcgtac
     6061 ttttttattt tcagctaaat gccgataggt aatgcttttg ggggtaacac gttcaatcgt
     6121 aataccatgt tgattcagat gtttttgaaa ttcttccata tttgtcgctg ttgattggtc
     6181 aattgcctca cgtatgtcat ctttccatga gtattgtgct gtcgacgtcg tgttagggtc
     6241 ggcaatcgct ttttctgttt gggtgtaacg taagcgtgct gtgtctttct caggcacgct
     6301 caacccctgt gctcgacaaa cctcgtcgtt gaacgctctc acatcgcgta gggcttgttt
     6361 attattgtta aatttcttac ctgtattgag gtcaattgaa ttaagtacaa tatgattgtg
     6421 tacatggttt gtatctgcat gcgtatagac ggcgacttga tgattgggga cgagtttttc
     6481 agcaagcgct aatcctaatt ggttacattg ttcgggcgtc acttcgccag gttgaaacga
     6541 ttggataatg acatgccctt gattaccgtc tgttttgcca tacaa
//
