LOCUS       NZ_CP131672             3011 bp    DNA     circular CON 24-APR-2024
DEFINITION  Staphylococcus aureus strain 2004N07-109 plasmid p2004N07-109-2,
            complete sequence.
ACCESSION   NZ_CP131672
VERSION     NZ_CP131672.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766256
            Assembly: GCF_038430115.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3011)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Rapid Diagnostics and Real-time Genomic Surveillance System for
            Pathogens from Culture
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3011)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JUL-2023) 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                     :: 12-NOV-2018
            Assembly Method                   :: CCBGpipe v. 1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology :: Oxford Nanopore MinION and Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038430115.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 00:04:41
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,872
            CDSs (total)                      :: 2,790
            Genes (coding)                    :: 2,703
            CDSs (with protein)               :: 2,703
            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)              :: 87
            CDSs (without protein)            :: 87
            Pseudo Genes (ambiguous residues) :: 0 of 87
            Pseudo Genes (frameshifted)       :: 45 of 87
            Pseudo Genes (incomplete)         :: 38 of 87
            Pseudo Genes (internal stop)      :: 19 of 87
            Pseudo Genes (multiple problems)  :: 14 of 87
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131672.1.
            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..3011
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="2004N07-109"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="p2004N07-109-2"
                     /geo_loc_name="Taiwan"
                     /collection_date="2004"
                     /collected_by="NHRI"
     gene            join(2733..3011,1..717)
                     /locus_tag="Q7635_RS14345"
                     /old_locus_tag="Q7635_14340"
     CDS             join(2733..3011,1..717)
                     /locus_tag="Q7635_RS14345"
                     /old_locus_tag="Q7635_14340"
                     /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            complement(1700..2281)
                     /locus_tag="Q7635_RS14350"
                     /old_locus_tag="Q7635_14345"
     CDS             complement(1700..2281)
                     /locus_tag="Q7635_RS14350"
                     /old_locus_tag="Q7635_14345"
                     /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          788..952
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.398"
                     /coverage="100.0"
                     /evalue="1.13e-79"
     Typing          2..717
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.629"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaaaaata gttatcaagc tcaaaaagtg attgaagaag taattaagga aaagccaaaa
       61 gcacgttggt tgtttttaac actttcaacc aaaaatgcga tagatggaga tactttagaa
      121 caaagtttga agcatctaac taaagcattt gataggttga gtagatataa aaaggttaaa
      181 caaaatcttg ttggatttat gcgttcaaca gaagttaccg ttaataaaaa tgatggtagt
      241 tataatcagc atatgcacgt tttgttatgt gttgaaaatg catattttag aaaaaaagag
      301 aattatataa ctcaagaaga atgggttaat ttatggcaaa aagcattaca agttgattat
      361 cgacctgttg caaatattaa agcaattaaa cctaatcaaa aaggcgataa agatattgaa
      421 tcggcaatca aagagacatc aaaatattcg gttaagtcat ctgatttttt aactgacaat
      481 gacgaaaaaa atcaagaaat tgtaagtgat ttagaaaaag gtttatatcg aaaacgtatg
      541 ttaagttatg gtggattgct taaacaaaag cataaaattt taaacttaga cgatgctgaa
      601 gatggtaatt taattaatac aagtgatgaa gataaaataa cagatgaaga agcaaaagca
      661 cattcaatta cggcaatttg gaattttgaa aaacaaaatt attatttaag acattagtga
      721 tgactgatgt cttttttatt gattttttgt aaaaaagtac tgtcttattt ttgtgacaaa
      781 tgctgtatgt agtgtcacaa aactgtgaca aacgcaatat attgtgtcac aaaagtgtga
      841 cactacagct ttttatgata tcactttaaa attacttaaa acccttggaa tgtctggctt
      901 tgccagacct atcatttttg aatgatagca aattctcctt atgctcttac ggagttctta
      961 gagaaaaatt aaaaattctc gatttttgat aaaaagcgcc ctgcaggaat ttagaaaaac
     1021 atgggggaag ttttaaagga ttttatgcta atttttaatt tgcatgtaaa tgggcagtgt
     1081 ccgaaaaatc gacactgggt ttgatcgaat ttttgattat aaaaaatttt tgattataaa
     1141 atcagaatat atttatttgg ctcatatttg cgttttaaga aacaaataag ataatacagg
     1201 tataaaacta tatattttta aagttcgttc taaatacccc cttaaaatgc aaaataagta
     1261 tattcgatta ttacacgtaa attttggttt tagctcgacg catttttaag tatgtaaatg
     1321 cgcctcttgg ataacgaaaa ataaaaaatc ttaattaaac agagtttaac taagatagtc
     1381 acgaatttta ttaggtttaa aaattatgat tacttcagat gtttagaatt aaggtgttga
     1441 ttatagtgtg aatgaaagca agggataata attagtaaat cagtgcacaa ttaatgtttt
     1501 atttaaggga tagttacacg cataatcaaa catgcattta tgccgagaaa atttattgat
     1561 gttgagaaga acccttaact aaacttgaag acgaatgtcg gcatagcgtg agctattaag
     1621 ccgacgattc gacaagttta gggattgtta agggttccga ggctcaacgt caataaagca
     1681 attggaataa attatatatt tagaaccatc cgtatttcag agtacattgt acatcctttg
     1741 aaaccatagt agctgcaatt ccagctaaat ttccttttat gccaattctg gctaattttt
     1801 ttgctgcact ctttatgttt ttggctttta catcatcaaa aactgctgcg attatattac
     1861 cggttaaaag ttctccatat gagtttaaaa cttcagaata gaaacagtca ttactatttt
     1921 tgtagtttcc accaactgct ctaggtgata ttgagctatt tttcttttta ttctctatgt
     1981 cgttctttag tttttggaaa ccttcaggaa catatccata tctagatttg gcattttcta
     2041 gattaacatc tttagcggtt ccgtctttat ctaaaacaat aattttgcca tatatgtagt
     2101 ctagttcttt ttcgatttct ttttcgttta aagtttcaat gtttttatct gcgatgttgt
     2161 ttttgttttg ggcttgagct tctttaaaat taaaattcaa gaccattgaa agtatagtta
     2221 aaaaacttaa agatattact aaaacttttc ttagtgatac acttttttga attgcattca
     2281 ttataaatgc ccccttgttt tgttatttaa atgaatccaa tataatatta acatataaaa
     2341 acaaaggagt ttaatatgaa taagtttatt tattttttaa ttgttttatt gtccgtattt
     2401 ttaatattta attttgttaa ttcgatttta tttaataatc cttttgactt tttagaaagc
     2461 tttatttatt cgttggtttt cacattgatt tatttaggtt tagagggcta taaagagaaa
     2521 aagaaataga ttgtttttga aacgagttga aaacgagttt cttcttgtct tgatactata
     2581 tagaaataac tcgattttat atatatagct gtaactgttg atattacagc gtttaaacgt
     2641 gtttttgtgc gtgaaaggaa aatttgacaa taaaaaaccc cagttatatt attaaggtgt
     2701 cgaatcttaa ataatactgg gggtcttttt atatgcaata taatactact agaagtataa
     2761 ccgaaaatca agataataaa acgttaaaag atatgacgaa aagtgggaaa caacgcccat
     2821 ggagagaaaa gaaaatagat aatgtaagct atgcagatat acttgaaatt ttaaaaataa
     2881 aaaaggctta taacgtaaaa caatgtggta acgtcttaga attcaagccg accgatgaag
     2941 gttatttgaa attacataag acgtggtttt gtaaatcaaa gctatgtcca gtttgtaatt
     3001 ggaggcgtgc t
//
