LOCUS       NZ_AP024317             3909 bp    DNA     circular CON 23-SEP-2023
DEFINITION  Staphylococcus aureus strain BDH17 plasmid pBDH17-2, complete
            sequence.
ACCESSION   NZ_AP024317
VERSION     NZ_AP024317.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00269944
            Assembly: GCF_019669345.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1
  AUTHORS   Nakaminami,H., Kim,E.S., Kaneko,H., Yokomori,S., Moon,S.M.,
            Song,K.H., Jung,J., Park,J.S. and Kim,H.B.
  TITLE     Comparative genomics analysis for a human variant of CC398 (ST1232)
            methicillin-resistant Staphylococcus aureus isolated in Korea and
            Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3909)
  AUTHORS   Kaneko,H. and Nakaminami,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JAN-2021) Contact:Hiroshi Kaneko Tokyo University of
            Pharmacy and Life Sciences, Department of Microbiology; Horinouchi
            1432-1, Hachioji, Tokyo 192-0392, Japan URL
            :https://www.toyaku.ac.jp/
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Coverage                   :: 1932x
            Sequencing Technology             :: MGI DNBSEQ; ONT GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/23/2023 03:29:38
            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)                     :: 2,784
            CDSs (total)                      :: 2,702
            Genes (coding)                    :: 2,618
            CDSs (with protein)               :: 2,618
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 84
            CDSs (without protein)            :: 84
            Pseudo Genes (ambiguous residues) :: 0 of 84
            Pseudo Genes (frameshifted)       :: 42 of 84
            Pseudo Genes (incomplete)         :: 38 of 84
            Pseudo Genes (internal stop)      :: 26 of 84
            Pseudo Genes (multiple problems)  :: 18 of 84
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP024317.1.
            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..3909
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="BDH17"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pBDH17-2"
                     /geo_loc_name="South Korea"
                     /collection_date="2019"
                     /genotype="ST1232"
     gene            join(3104..3909,1..463)
                     /gene="mobV"
                     /locus_tag="K5602_RS13795"
     CDS             join(3104..3909,1..463)
                     /gene="mobV"
                     /locus_tag="K5602_RS13795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000331753.1"
                     /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_031824442.1"
                     /translation="MAYSIIRVAKVKSKTNTKGIQKHVQRQNKNYENMDIDLEKSYLNY
                     DLVNDSPIDYNQKIEEKIEQNYNGKRKIRKDAVKHIDGLITSGNEFFKNQTLEETKQFF
                     EHAKTFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITEDGRLSAKEVLGNKKALTEFQ
                     DRFNEHINSCGYDLSRGITRGVTPRRHEQISRYKNLTDYHKEEYEHESRKLDRIKQESE
                     EVMEQYQNALDVLKKPINVPYELETEKVGGLFNKETQETGNVVIDKNEFDLLQEQVKAS
                     QLITDDYEYIKSGKALKDFEKKNKRLEDRLLDEQIKNGKVIDKYNDLVDSYNNLLEQNQ
                     EKEKELNRSYKLFNNVFKLIKGVMKEETYHSLINHIDNHLESSKMRETMIVDDNDEQFF
                     KKKYQRHEPEIIFEDERDDGYTL"
                     /name="mobV"
     gene            985..1929
                     /locus_tag="K5602_RS13800"
                     /old_locus_tag="BDH17TP_26190"
     CDS             985..1929
                     /locus_tag="K5602_RS13800"
                     /old_locus_tag="BDH17TP_26190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017722130.1"
                     /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_058142602.1"
                     /translation="MIKKAEEIQTKQSLENENLNFSKTGYSNSRSDVPFMYTPHPKLSF
                     DAMTIVGNLNKNSAQKLSEFMSIDPQIRLWDILQTKFKAKALEERVYIEYDKVKADVWD
                     RRNMRVEFNPNKLSRKEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAISDKALK
                     KTVYYGTNGMPETKYFGVRESDRFIRIYNKKQERKDNADVEVTSEHLWRVEIELKRNMV
                     DYWNDCFSDLHILKPDYSTIENSSERHTIMALLFDESEWGKLERRKKYRMKKLMSEISP
                     IDLTELMKLTLKKNEKQLQRQIDFWQREFRFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2103..2231
                     /locus_tag="K5602_RS13945"
                     /old_locus_tag="BDH17TP_26200"
     CDS             2103..2231
                     /locus_tag="K5602_RS13945"
                     /old_locus_tag="BDH17TP_26200"
                     /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="hypothetical protein"
                     /protein_id="WP_257878031.1"
                     /translation="MDYRTKKSKEKVANMIEEIKNNPFEWVIDYDMFYKIEQQLLK"
                     /name="hypothetical protein"
     gene            2252..2749
                     /locus_tag="K5602_RS13805"
                     /old_locus_tag="BDH17TP_26210"
     CDS             2252..2749
                     /locus_tag="K5602_RS13805"
                     /old_locus_tag="BDH17TP_26210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009496511.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_058142601.1"
                     /translation="MKQLGTLYFFCGKMGAGKSTKSKQMASDKHAVLLSEDEWLSSLYP
                     NQIESFEDYLKFSAQIKPLVRKHVQNILSVGIDVVMDFPANTQKQREWFLDMVLDVNAN
                     HQLIFLNLNNEQCLRQIAQRRNEQPERADFDTEAVFTHVTNFFEAPEASEGLNILEFSG
                     KE"
                     /name="ATP-binding protein"
     Typing          986..1927
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.466"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3..460
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.039"
                     /coverage="99.0"
                     /evalue="5.4e-77"
     Typing          3045..3907
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.611"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgaatttgat ttattgcagg aacaagtaaa agcttctcaa ctcattactg atgattatga
       61 atatattaaa agcggaaagg ctttaaaaga ttttgagaaa aaaaacaaaa gattagaaga
      121 tagattatta gacgaacaga ttaaaaatgg aaaagtaata gataaataca atgatttagt
      181 ggatagttat aataatttat tggaacaaaa tcaagaaaaa gaaaaagagt taaaccgttc
      241 gtataaacta tttaacaatg tgtttaagtt gattaaaggt gtgatgaaag aagaaacata
      301 tcattcgttg attaaccata ttgataatca cttagaaagc tcaaaaatgc gagaaacaat
      361 gattgtagat gataacgatg aacaattctt taagaaaaaa tatcaaaggc atgaaccaga
      421 aattattttt gaagatgaac gagatgatgg ctacacttta taaagacgac gcatttatgc
      481 cgagaaaatt tattgtgcgt tgagaagaac ccttaactaa acttggagac gaatgtcggc
      541 atagcgtgag ctattaagcc gaccattcga caagttttgg gattgttaag ggttccgagg
      601 ctcaacgtca ataaagcaat tggaataaag caataaaagg agttgaagaa atgaaattta
      661 gagaagcttt tgagaatttt atagcaagta agtatgtact tggtgtttta gtagttttaa
      721 ctgtttacca gataatacaa atgcttaaat aaaaaaagac ctgatctgat tagaccaagt
      781 cttttgatag tgttatatta ataacaaaat aaaaagaagt cgctcactcc ctcgccaaag
      841 tttgtgatag cgacttacct agaaaaaaca ctaagttgtt tttttatatc ttgtatatct
      901 agatattaaa cgatataagt ttattcttca agatatatat tcgggtgagc gacttcttaa
      961 attaaattaa ggagttgttt ttttgtgatt aaaaaagcag aagaaattca gacaaaacaa
     1021 agcttagaaa acgaaaactt aaatttttct aaaaccggat actctaatag ccggtcagat
     1081 gtaccattta tgtacacccc tcatccaaaa ttaagttttg atgctatgac aatcgttgga
     1141 aatcttaata aaaatagtgc acaaaaactt tctgaattta tgagtattga tccacaaata
     1201 aggctttggg atatactaca aactaaattt aaagctaagg cgcttgaaga aagagtctat
     1261 attgaatatg acaaagtaaa agcagatgta tgggatagac gtaacatgcg tgttgaattt
     1321 aatccaaata aactttcacg taaagaaatg ttgtggttaa aacaaaatat tatagactac
     1381 atggaagatg atggatttac aagattagat ttagcttttg attttgaaga tgatttaagt
     1441 gattattatg caatatcgga taaagcttta aagaaaacag tgtattacgg aacaaatggc
     1501 atgccagaaa ctaaatattt tggtgttcgt gaaagtgata gatttattag aatttataat
     1561 aaaaaacaag agcgtaaaga taatgctgat gttgaagtta catctgaaca tttatggcgt
     1621 gtagaaattg aactcaaaag aaatatggtt gattattgga atgattgttt tagtgattta
     1681 catattttga aaccagatta ttcaactatt gaaaattctt cagaacggca tacgattatg
     1741 gctttacttt ttgatgaaag tgaatgggga aaattagaac gcagaaaaaa atatagaatg
     1801 aaaaaactga tgagtgaaat ttctccgatt gatttaacag aattaatgaa attgacttta
     1861 aaaaagaatg aaaaacaatt acaaaggcaa attgattttt ggcaacgtga atttaggttt
     1921 tggaagtgag ataaaattta taatatctta aaaatataaa ttttcaggag gttctaattt
     1981 gaaaaaaagt agagattcaa gtttctgaag aaatattatt acgtgatgca attaatgatg
     2041 atattaatga ttatctagct gttccgttta ataaagaact tttagaaatg tatggctcta
     2101 gtatggatta tcgtactaag aagtctaaag aaaaagttgc aaatatgatt gaagaaatta
     2161 agaataatcc ttttgaatgg gttattgact acgacatgtt ttacaagata gagcagcaat
     2221 tactaaaata aacttggggg gttgaaaaaa tatgaaacaa ttggggacgc tatacttttt
     2281 ctgtgggaaa atgggtgcag gaaaatcaac taaatcaaaa caaatggcat cagataaaca
     2341 tgccgtacta ttatctgagg atgaatggct ttcatctctt tatcccaatc aaatcgaatc
     2401 atttgaggac tatctaaaat tttcagcgca gatcaagccg ttggtgagaa agcatgtcca
     2461 aaatatatta agtgtcggta tagatgtagt gatggatttc ccagctaaca ctcaaaagca
     2521 gcgtgaatgg tttttggata tggtgttaga tgtcaatgca aatcatcaac taattttcct
     2581 taatctaaat aacgagcaat gcctacgtca aattgcacaa aggcgtaacg aacaacccga
     2641 aagagcagat tttgatacgg aagcggtgtt tactcatgtt actaactttt ttgaagcacc
     2701 agaagcctcc gagggtttaa atattttaga gtttagtgga aaagaataac aagacgttca
     2761 acgcgacatt gcggcacact taaacaatag ggcgcgattg atgaataaaa gatacgagag
     2821 aatattctcg tgtcttttat tattgagtgg ttttgtccgt taaactaaaa aaccgaaagc
     2881 gtgctatttt tagttttgct gaggtggcag agggcaggtt tttttgttta cttttttctc
     2941 gcaaaaaaag taaggtctaa aaggttttac ggttttcgtt ggcactgcca acagcctcgc
     3001 agagcatacg gtttaatgac ttattacgaa gtaactaagt ctagtgtgtt atactttaat
     3061 aaataaagct acgcaaaaac atgtgcagtg gaggaatttt aatatggcgt attctattat
     3121 cagagttgct aaagtgaaat caaaaacgaa tacaaaaggc attcaaaaac atgtacaaag
     3181 acaaaataaa aattatgaaa atatggatat tgatttagaa aaatcatact taaattacga
     3241 tttagtcaat gatagtccga ttgattataa tcaaaaaatc gaagagaaaa ttgaacaaaa
     3301 ttataatggg aaacgcaaaa ttagaaaaga cgcagtaaaa catattgatg gtttaattac
     3361 atctggtaat gaatttttta aaaatcaaac acttgaagaa acaaagcagt tttttgaaca
     3421 tgctaaaacg tttttagaac aagagtatgg taaagataat ttattatatg caacagtgca
     3481 tatggacgaa aaaacacctc atatgcatta tggggtagtt ccgattacag aagatggtcg
     3541 attgagtgcg aaagaggttt taggtaataa aaaggcacta actgaatttc aagatagatt
     3601 taacgaacat atcaatagtt gtggttatga cttgagtaga ggtataacaa ggggcgttac
     3661 accgagacga catgagcaga taagtcgtta taaaaattta acagattatc acaaagaaga
     3721 atatgagcat gagagccgaa aattagaccg tataaagcaa gaaagcgaag aagtaatgga
     3781 acagtatcaa aatgctttag atgttctaaa aaagcctata aatgtcccat atgagcttga
     3841 aactgaaaaa gttggtggat tgtttaacaa agaaacacag gaaacaggta acgtcgttat
     3901 tgataaaaa
//
