LOCUS       NZ_CP080565             3332 bp    DNA     circular CON 14-SEP-2023
DEFINITION  Staphylococcus aureus strain HL16278 plasmid pHL16278, complete
            sequence.
ACCESSION   NZ_CP080565
VERSION     NZ_CP080565.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17301230
            Assembly: GCF_019551355.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3332)
  AUTHORS   Kim,J.-M., Chung,S.H. and Kim,J.-S.
  TITLE     Whole genome sequence of MRSA HL16278
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3332)
  AUTHORS   Kim,J.-M., Chung,S.H. and Kim,J.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JUL-2021) Laboratory Medicine, Hallym University
            College of Medicine, 150 Seongan-ro, Gangdong-gu, Seoul 05355, South
            Korea
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-APR-2020
            Assembly Method                   :: SPAdes v. 3.14.0
            Assembly Name                     :: HL16278
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 817x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/14/2023 05:19:40
            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)                     :: 2,725
            CDSs (total)                      :: 2,646
            Genes (coding)                    :: 2,578
            CDSs (with protein)               :: 2,578
            Genes (RNA)                       :: 79
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 68
            CDSs (without protein)            :: 68
            Pseudo Genes (ambiguous residues) :: 0 of 68
            Pseudo Genes (frameshifted)       :: 33 of 68
            Pseudo Genes (incomplete)         :: 33 of 68
            Pseudo Genes (internal stop)      :: 16 of 68
            Pseudo Genes (multiple problems)  :: 13 of 68
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080565.1.
            Annotation performed at Hallym University College of Medicine on
            July 30, 2021 using the NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP) version 2021-01-11.build5132.  Annotation modified by
            submitter.
            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..3332
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="HL16278"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pHL16278"
                     /geo_loc_name="South Korea:Seoul"
                     /lat_lon="37.5362 N 127.1354 E"
                     /collection_date="2014"
                     /collected_by="Kandong Sacred Hospital"
     gene            1..618
                     /gene="cadD"
                     /locus_tag="JMO07_RS13520"
                     /old_locus_tag="JMO07_002710"
     ARG             2..615
                     /name="cadD"
                     /gene="cadD"
                     /gene_name="cadmium resistance transporter CadD"
                     /tool="amrfinderplus"
                     /drug_class="CADMIUM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            637..984
                     /locus_tag="JMO07_RS13525"
                     /old_locus_tag="JMO07_002711"
     CDS             637..984
                     /locus_tag="JMO07_RS13525"
                     /old_locus_tag="JMO07_002711"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020366422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="metalloregulator ArsR/SmtB family transcription
                     factor"
                     /protein_id="WP_000119690.1"
                     /translation="MSYENTCDVICVHEDKVNNALSFLEDDKSKKLLNILEKICDEKKL
                     KIILSLIKEDELCVCDISLILKMSVASTSHHLRLLYKNEVLDFYKDGKMAYYFIKDDEI
                     REFFSKNHEGF"
                     /name="metalloregulator ArsR/SmtB family transcription
                     factor"
     gene            1175..2170
                     /locus_tag="JMO07_RS13530"
                     /old_locus_tag="JMO07_002712"
     CDS             1175..2170
                     /locus_tag="JMO07_RS13530"
                     /old_locus_tag="JMO07_002712"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199887.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANIKAI
                     KPNKKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     Typing          1176..2170
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgattcaaa cggttgttgc tgctgctgtt ctttatattg ctacagcagt tgatttatta
       61 gtaattttat taatattttt tgctagagca aagactagaa aagaatatag agatatttat
      121 gttggtcaat atttagggtc tattatttta atattagtta gtttgttttt agcttttgta
      181 ttaaattatg ttccagaaaa gtggatatta ggtttattgg gtttaatacc aatttatctt
      241 ggaattaaag tggctattta tgatgattgt gaaggagaaa agagagctaa aaaagaattg
      301 aatgaaaaag gattgtctaa attagttggt acggttgcaa ttgttacgat agcaagttgt
      361 ggcgccgata atattggttt atttgttccg tattttgtga cattaagtgt tactaattta
      421 ttacttactc tgtttgtctt tttaatttta attttcttct tggtgtttac tgcacaaaaa
      481 ttagctaata tcccaggaat tggagaaatt gttgagaaat ttagtcgttg gattatggct
      541 atcatttata tagctttagg tttatttatt attattgaaa atgacactat tcaaacaatt
      601 ttaggattta tattttaatt tagggtgtga ttttatatga gttatgaaaa tacttgtgat
      661 gtgatctgtg tacatgagga taaagttaac aatgctttaa gttttttaga agatgataaa
      721 tctaagaaat tacttaacat tttagaaaaa atttgtgatg agaagaaatt gaaaatcata
      781 ttatctttga ttaaagaaga tgagttgtgt gtttgtgata tttctttgat attgaaaatg
      841 agtgttgctt caacttcaca tcatttaagg cttttatata aaaatgaggt acttgatttt
      901 tataaagatg gaaagatggc atattatttt attaaagacg atgaaataag agagtttttc
      961 tctaaaaatc atgagggttt ttgaaacgag tgaaacgagt ttcttcttgt cttgatacta
     1021 tatagaaata actcgatttt atatatacag ctgtaactgt tgatattaca gcgtttaaac
     1081 gtgtttttgt gcgtgaaagg aaaatttgac aataaaaaac cccagttata ttattaaggt
     1141 gtcgaatctt aaataatact gggggtcttt ttatatgcaa tataatacta ctagaagtat
     1201 aaccgaaaat caagataata aaacgttaaa agatatgacg aaaagtggga aacaacgccc
     1261 atggagagaa aagaaaatag ataatgtaag ctatgcagat atactagaaa ttttaaaaat
     1321 caaaaaggct tttaatgtaa aacaatgtgg taatatttta gaatttaagc caactgatga
     1381 aggttatttg aagttacata agacatggtt ttgtaaatca aaattatgtc cggtttgtaa
     1441 ttggagacgt gctatgaaaa atagttatca agctcaaaaa gtgattgaag aagtaattaa
     1501 ggaaaagcca aaagcacgtt ggttgttttt aacactttca acaaaaaatg cgatagatgg
     1561 agatacttta gaacaaagtt tgaagcatct aactaaagca tttgataggt tgagtagata
     1621 taaaaaggtt aaacaaaatc ttgttggatt tatgcgttca acagaagtta ccgttaataa
     1681 aaatgacggt agttataatc agcatatgca cgttttgtta tgtgttgaaa atgcatattt
     1741 tagaaaaaaa gagaattata taactcaaga agaatgggtt aatttatggc aaagagcatt
     1801 gcaagttgat tatcgacctg ttgctaatat taaagcgatc aaaccaaata aaaaaggcga
     1861 taaagatatt gaatctgcaa tcaaagagac ctcaaaatat tcggttaaat catctgattt
     1921 tttaactgat gatgatgaaa aaaatcaaga aattgtaagt gatttagaaa aaggtttgta
     1981 tcgaaagcgt atgttaagtt atggtggatt gctgaaacaa aagcataaaa ttttaaactt
     2041 agacgatgct gaagatggaa atttgattaa tacaagtgat gaagataaaa caacagatga
     2101 agaagaaaag gcacattcga ttacggcaat ttggaatttt gaaaagcaaa attattattt
     2161 aaggcattag tgataactga tgtctttttt tattactttt ttgtaaaaaa gtgctgtctt
     2221 atttttgtga caaattctgt atgtagtgtc acaaaactgt gacaaacgca atatattgtg
     2281 tcacaaaagt gtgacatttc gtctttttat gcccccatgc aaaaagatcg acgaagtctt
     2341 gaaatatctg gctttgccag atacctcatc tatagatggg gtcatatttt ccttatgctc
     2401 ttacggagtt cttagagaaa aattgaaatt tctcgatttt tgataaaaac gccctgcagg
     2461 aatttagaaa aacatgggga agttttaaag aattttatgc tcatttttaa tttgcatgta
     2521 aatgggcagt gtctaaaaaa ctcgacactg gttttactcg aattttagtt tgtgaaatta
     2581 agatatattt atttggctca tatttgcgtt ttaaaagttt atgtaggttt ttaggtataa
     2641 aactatatga tttacccata aatctttaaa atgacctctt aaaattcaaa ataaaggcat
     2701 ttaaaaatta acaaaataaa aaagctacta gcaaaaaact agtagctttt gtcttgatgt
     2761 agtattaatt tttatatctg cgccacaacg ccgatttctt aaaacgaata taaaaaatcg
     2821 acgaaggtcg attatggttt ttgcacgcgt tcttttagaa cgcataagtg cgcccttacg
     2881 ggatttaact agattataac gacgaaaaac agacctgtaa agcaataaca attaggtcta
     2941 ccaggtagat aaagtgtaca aagtagaacc gaaaaagtta tttattttga agatttttcg
     3001 tagatataat ttgctaataa acttcctaaa actgaataaa gaaaaatagt taaactcatg
     3061 taatcactcc ataattctga agtgtctcca tgtctacgca tagacacgca tttatgccga
     3121 gaaaatttat tgtgcgttga gaagaaccct taactaaact tgcagacgaa tgtcggcata
     3181 gcgtgagcta ttaagccgac cattcgacaa gttttgggat tgttaagggt tccgaggctc
     3241 aacgtcaata aagcaattgg aataaagcac ctatgattat ttaaaaatat aagttataat
     3301 acattcaaaa atatttttga atgaggtgta tt
//
