LOCUS       NZ_CP029171             2627 bp    DNA     circular CON 01-DEC-2023
DEFINITION  Staphylococcus aureus strain PTDrAP2 plasmid pPTDrAP2d, complete
            sequence.
ACCESSION   NZ_CP029171
VERSION     NZ_CP029171.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08999457
            Assembly: GCF_003111745.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2627)
  AUTHORS   Murphy,R.J.T., Loring,J., Ramsay,J.P., Coombs,G.W. and Abraham,S.
  TITLE     Draft genome sequence of ST398 Staphylococcus aureus strain PTDrAP2
            with mutant cfr allele isolated from Australian pigs
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2627)
  AUTHORS   Murphy,R.J.T., Loring,J., Ramsay,J.P., Coombs,G.W. and Abraham,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-APR-2018) School of Biomedical Sciences, Curtin
            University, Kent Street, Bentley, WA 6102, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-MAR-2018
            Assembly Method                   :: Canu v. 1.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 588.9x
            Sequencing Technology             :: PacBio; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/01/2023 05:40:09
            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)                     :: 2,860
            CDSs (total)                      :: 2,778
            Genes (coding)                    :: 2,676
            CDSs (with protein)               :: 2,676
            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)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 48 of 102
            Pseudo Genes (incomplete)         :: 52 of 102
            Pseudo Genes (internal stop)      :: 32 of 102
            Pseudo Genes (multiple problems)  :: 27 of 102
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP029171.1.
            Bacteria and source DNA available from Dr Joshua Ramsay, Curtin
            University.
            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..2627
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="PTDrAP2"
                     /isolation_source="Pig nares"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:1280"
                     /plasmid="pPTDrAP2d"
                     /geo_loc_name="Australia"
                     /lat_lon="35 S 147 E"
                     /collection_date="2015-08-12"
     gene            13..936
                     /locus_tag="DD562_RS00070"
                     /old_locus_tag="DD562_00070"
     CDS             13..936
                     /locus_tag="DD562_RS00070"
                     /old_locus_tag="DD562_00070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002499696.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_103894999.1"
                     /translation="MEKYTEKKQRNQVFQKFIKRHIGENQMNLVEDCNTFLSFVADKTL
                     EKQKLYKANSCKNRFCPVCAWRKARKDALGLSLMMQYIKQQQKKEFIFLTLTTPNVMSD
                     ELENEIKRYNNSFRKLIKRKKVDSVIKGYVRKLEITYNKKRDDYNPHFHVLIAVNKSYF
                     TDKRYYISQQEWLDLWRDVTGISEITQVQVQKIRQNNNKELYEMAKYSGKDSDYLINQK
                     VFDAFYKSLKGKQVLVYSGLFKEAKKKLKNGDLDYLKEIDPTEYIYQIFYIWKQKEYLA
                     SELYDLTEQEKREINHKMIDEIEEEQ"
                     /name="protein rep"
     gene            complement(1996..2319)
                     /gene="qacG"
                     /locus_tag="DD562_RS00080"
                     /old_locus_tag="DD562_00080"
     ARG             complement(2000..2319)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacG"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2..936
                     /name="rep_cluster_1230"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtgttata acatggaaaa gtatactgag aaaaaacaaa gaaatcaagt atttcagaaa
       61 tttattaaac gtcatattgg agagaatcaa atgaatttag ttgaagattg taatacattt
      121 ctgtcttttg tagctgataa aactttagaa aaacagaaat tatataaagc taattcttgt
      181 aaaaatcgat tttgtcctgt ctgcgcttgg agaaaagcta gaaaagacgc gttgggttta
      241 tctttgatga tgcaatatat taagcagcaa cagaaaaaag aatttatctt tttaacttta
      301 actacaccta acgtaatgag tgatgaatta gaaaatgaaa taaaacgtta caataattct
      361 tttagaaaac ttataaaaag aaaaaaagta gatagtgtta taaagggata tgttcgtaag
      421 ttagagatta catataataa aaaaagagat gattataacc ctcattttca cgtgttaatt
      481 gcagtaaata aatcgtattt cacagataaa agatattata ttagccaaca agaatggtta
      541 gatttatggc gtgatgtaac aggtatttca gaaatcacac aagttcaagt tcaaaaaata
      601 agacaaaaca ataataaaga gttatatgaa atggctaagt attctggtaa agatagtgat
      661 tatttaataa atcaaaaagt atttgatgca ttctataaat cacttaaagg taaacaggta
      721 ttagtttatt caggattatt taaagaggct aaaaagaaat taaaaaatgg ggatttagat
      781 tacttaaaag aaattgatcc aaccgaatat atctatcaaa ttttttatat ttggaaacaa
      841 aaagagtatt tagctagtga actttatgac ttaacagaac aagaaaaaag agaaattaat
      901 cacaaaatga tagacgaaat cgaggaagaa caataacaaa atataagtgc taacagctga
      961 cctcccgata acaccatgta gttattggga ggtcagctgt tgaattatgc acgagtattt
     1021 taaaagttat tgtgatgacg acgataaacg attatcaaaa gtataatgtt aaaatacttt
     1081 attatactaa cgttatataa acattatact ttcgttatac aaattttaac cctgttagga
     1141 actataaaaa atcatgaaaa ttttaatttg catgtaaatg ggccagtgtc taaaaaaatc
     1201 gacactggat ttgctcaaat ttttgtttgt gaaaagtaat tacttttatt tggctctcat
     1261 ttgcgtttta agagccgata taggttttta ggtataaaac tatataaata acccctaatt
     1321 ctttaaaata accctttaaa attcaaaata aaggcataaa aaataaaagc tatctcaatt
     1381 ttgagatagc ttttttcttt cgtacggtct gtttattttt ctttcgacgc cgtatcgtcg
     1441 atggaattca aaaaagttat gggctataaa tctacatcac tttttcaaga atgtagtagc
     1501 aatattcaag acaaattaat ttttataact gctcggaata tctcaagccg tttctttaat
     1561 tttgaaataa aaaaatcgac ggaggtcgat tatggttttt gcacgcgttc tttttagaac
     1621 gcataagtgc gcccttacgg cccttacggg acccttacgg cccttacggg atttaactag
     1681 attataacga cgaaaatcag acctgtaaag cgataactat tgtgataaag tttgctaaaa
     1741 aggagattaa aaaaatgctt atatttttat ttattttggt ttgtggtctt ttaggttatt
     1801 ttttgattag tcgttctaaa aaagattaga cacgcattta tgccgagaaa atttattgat
     1861 gttgagaaga acccttaact aaacttgcag acgaatgtcg gcatagcgtg agctattaag
     1921 ccgaccattc gacaagtttt gggattgtta agggttccga ggctcaacgt caataaagca
     1981 attggaataa aataatcaat ggctttctcc aaatacattt aagagcacta cacctataac
     2041 aattaagcca atagaaatta tactaattaa attaacattt tctttaaaaa cgataactga
     2101 gattattgtt gttaatacta atcctagacc tgcccatgtt gcgtaagtta tatttaaggg
     2161 caaaaatttt attgttaaac ttaaaaaata aaagcaaatt ccaaacgaaa gtagtgtacc
     2221 taatgttggc cataactttg tgaaaccttc tgatgttttt aaaaaactag ttccgattat
     2281 ttctgttgca attgagataa ataaatataa ataatgcatt aagcttctcc tttaatttct
     2341 atttgatagc ttatatttta atatatatta agtgaaagaa aaatttttaa gatttgtatt
     2401 ttaaaacgag ttgaaaacga gtttcttctt gtcttgataa taagggtaac tattgccggc
     2461 gaggctagtt acccttaaag tgttgatatg actgttttca aacataaaaa aagttgcttt
     2521 ttcgtaccta ttaatgtatc gttttaaatg actagtaaaa aacatacata gaaaggggaa
     2581 aaagcaactt ttttattatc atagtttgtg aaaactaagt tgttttt
//
