LOCUS       NZ_CP039450             3011 bp    DNA     circular CON 17-OCT-2023
DEFINITION  Staphylococcus aureus strain VGC1 plasmid pVGC1_2, complete
            sequence.
ACCESSION   NZ_CP039450
VERSION     NZ_CP039450.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11431687
            Assembly: GCF_008330045.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3011)
  AUTHORS   Fu,P.-K., Hsu,Y.-C., Hsu,P.-C., Liou,C.-H., Kuo,S.-C. and Yang
            Lauderdale,T.-L.
  TITLE     Methicillin-resistant Staphylococcus aureus Bacteriophage as a
            Virulence Factor that Elevates IL-6 and Shields MRSA from Being
            Phagocytized
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3011)
  AUTHORS   Chen,F.-J., Wu,H.-C. and Liao,Y.-C.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-APR-2019) National Institute of Infectious Diseases
            and Vaccinology, National Health Research Institutes, No. 35, Keyan
            Road, Zhunan Town, Miaoli County 350, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 26-MAR-2019
            Assembly Method                   :: Canu v. 1.6; Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 445.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/17/2023 02:01:55
            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)                     :: 2,891
            CDSs (total)                      :: 2,809
            Genes (coding)                    :: 2,726
            CDSs (with protein)               :: 2,726
            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)              :: 83
            CDSs (without protein)            :: 83
            Pseudo Genes (ambiguous residues) :: 0 of 83
            Pseudo Genes (frameshifted)       :: 37 of 83
            Pseudo Genes (incomplete)         :: 44 of 83
            Pseudo Genes (internal stop)      :: 14 of 83
            Pseudo Genes (multiple problems)  :: 11 of 83
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039450.1.
            Bacteria and source DNA available from Feng-Jui Chen.
            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..3011
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="VGC1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pVGC1_2"
                     /geo_loc_name="Taiwan: Taichung"
                     /lat_lon="24.186048 N 120.604496 E"
                     /collection_date="2013-04"
                     /collected_by="Pin-Kuei Fu"
                     /genotype="ST59"
     gene            complement(646..1641)
                     /locus_tag="E8M03_RS14650"
                     /old_locus_tag="E8M03_14810"
     CDS             complement(646..1641)
                     /locus_tag="E8M03_RS14650"
                     /old_locus_tag="E8M03_14810"
                     /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_001199895.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAYNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQKALQVDYRPVANIKAI
                     KPNQKGDKDIESAIKETSKYSVKSSDFLTDNDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKITDEEAKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     gene            2093..2674
                     /locus_tag="E8M03_RS14655"
                     /old_locus_tag="E8M03_14815"
     CDS             2093..2674
                     /locus_tag="E8M03_RS14655"
                     /old_locus_tag="E8M03_14815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991701.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000991701.1"
                     /translation="MNAIQKSVSLRKVLVISLSFLTILSMVLNFNFKEAQAQNKNNIAD
                     KNIETLNEKEIEKELDYIYGKIIVLDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKNSSISPRAVGGNYKNSNDCFYSEVLNSYGELLTGNIIAAVFDDVKAKNIKSAAKKL
                     ARIGIKGNLAGIAATMVSKDVQCTLKYGWF"
                     /name="hypothetical protein"
     Typing          complement(412..576)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.398"
                     /coverage="100.0"
                     /evalue="1.13e-79"
     Typing          complement(647..1641)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.687"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgtttaatt aagatttttt atttttcgtt atccaagagg cgcatttaca tacttaaaaa
       61 tgcgtcgagc taaaaccaaa atttacgtgt aataatcgaa tatacttatt ttgcatttta
      121 agggggtatt tagaacgaac tttaaaaata tatagtttta tacctgtatt atcttatttg
      181 tttcttaaaa cgcaaatatg agccaaataa atatattctg attttataat caaaaatttt
      241 ttataatcaa aaattcgatc aaacccagtg tcgatttttc ggacactgcc catttacatg
      301 caaattaaaa attagcataa aatcctttaa aacttccccc atgtttttct aaattcctgc
      361 agggcgcttt ttatcaaaaa tcgagaattt ttattttttc tctaagaact ccgtaagagc
      421 ataaggagaa tttgctatca ttcaaaaatg ataggtctgg caaagccaga cattccaagg
      481 gttttaagta attttaaagt gatatcataa aaagctgtag tgtcacactt ttgtgacaca
      541 atatattgcg tttgtcacag ttttgtgaca ctacatacag catttgtcac aaaaataaga
      601 cagtactttt ttacaaaaaa tcaataaaaa agacatcagt catcactaat gtcttaaata
      661 ataattttgt ttttcaaaat tccaaattgc cgtaattgaa tgtgcttttg cttcttcatc
      721 tgttatttta tcttcatcac ttgtattaat taaattacca tcttcagcat cgtctaagtt
      781 taaaatttta tgcttttgtt taagcaatcc accataactt aacatacgtt ttcgatataa
      841 acctttttct aaatcactta caatttcttg atttttttcg tcattgtcag ttaaaaaatc
      901 agatgactta accgaatatt ttgatgtctc tttgattgcc gattcaatat ctttatcgcc
      961 tttttgatta ggtttaattg ctttaatatt tgcaacaggt cgataatcaa cttgtaatgc
     1021 tttttgccat aaattaaccc attcttcttg agttatataa ttctcttttt ttctaaaata
     1081 tgcattttca acacataaca aaacgtgcat atgctgatta taactaccat catttttatt
     1141 aacggtaact tctgttgaac gcataaatcc aacaagattt tgtttaacct ttttatatct
     1201 actcaaccta tcaaatgctt tagttagatg cttcaaactt tgttctaaag tatctccatc
     1261 tatcgcattt ttggttgaaa gtgttaaaaa caaccaacgt gcttttggct tttccttaat
     1321 tacttcttca atcacttttt gagcttgata actatttttc atagcacgcc tccaattaca
     1381 aactggacat agctttgatt tacaaaacca cgtcttatgt aatttcaaat aaccttcatc
     1441 ggtcggcttg aattctaaga cgttaccaca ttgttttacg ttataagcct tttttatttt
     1501 taaaatttca agtatatctg catagcttac attatctatt ttcttttctc tccatgggcg
     1561 ttgtttccca cttttcgtca tatcttttaa cgttttatta tcttgatttt cggttatact
     1621 tctagtagta ttatattgca tataaaaaga cccccagtat tatttaagat tcgacacctt
     1681 aataatataa ctggggtttt ttattgtcaa attttccttt cacgcacaaa aacacgttta
     1741 aacgctgtaa tatcaacagt tacagctata tatataaaat cgagttattt ctatatagta
     1801 tcaagacaag aagaaactcg ttttcaactc gtttcaaaaa caatctattt ctttttctct
     1861 ttatagccct ctaaacctaa ataaatcaat gtgaaaacca acgaataaat aaagctttct
     1921 aaaaagtcaa aaggattatt aaataaaatc gaattaacaa aattaaatat taaaaatacg
     1981 gacaataaaa caattaaaaa ataaataaac ttattcatat taaactcctt tgtttttata
     2041 tgttaatatt atattggatt catttaaata acaaaacaag agggcattta taatgaatgc
     2101 aattcaaaaa agtgtatcac taagaaaagt tttagtaata tctttaagtt ttttaactat
     2161 actttcaatg gtcttgaatt ttaattttaa agaagctcaa gcccaaaaca aaaacaacat
     2221 cgcagataaa aacattgaaa ctttaaacga aaaagaaatc gaaaaagaac tagactacat
     2281 atatggcaaa attattgttt tagataaaga cggaaccgct aaagatgtta atctagaaaa
     2341 tgccaaatct agatatggat atgttcctga aggtttccaa aaactaaaga acgacataga
     2401 gaataaaaag aaaaatagct caatatcacc tagagcagtt ggtggaaact acaaaaatag
     2461 taatgactgt ttctattctg aagttttaaa ctcatatgga gaacttttaa ccggtaatat
     2521 aatcgcagca gtttttgatg atgtaaaagc caaaaacata aagagtgcag caaaaaaatt
     2581 agccagaatt ggcataaaag gaaatttagc tggaattgca gctactatgg tttcaaagga
     2641 tgtacaatgt actctgaaat acggatggtt ctaaatatat aatttattcc aattgcttta
     2701 ttgacgttga gcctcggaac ccttaacaat ccctaaactt gtcgaatcgt cggcttaata
     2761 gctcacgcta tgccgacatt cgtcttcaag tttagttaag ggttcttctc aacatcaata
     2821 aattttctcg gcataaatgc atgtttgatt atgcgtgtaa ctatccctta aataaaacat
     2881 taattgtgca ctgatttact aattattatc ccttgctttc attcacacta taatcaacac
     2941 cttaattcta aacatctgaa gtaatcataa tttttaaacc taataaaatt cgtgactatc
     3001 ttagttaaac t
//
