LOCUS       NZ_CP029170             3050 bp    DNA     circular CON 01-DEC-2023
DEFINITION  Staphylococcus aureus strain PTDrAP2 plasmid pPTDrAP2c, complete
            sequence.
ACCESSION   NZ_CP029170
VERSION     NZ_CP029170.1
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 3050)
  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  JOURNAL   Unpublished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 3050)
  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
            CP029170.1.
            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..3050
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="PTDrAP2"
                     /isolation_source="Pig nares"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:1280"
                     /plasmid="pPTDrAP2c"
                     /geo_loc_name="Australia"
                     /lat_lon="35 S 147 E"
                     /collection_date="2015-08-12"
     gene            13..936
                     /locus_tag="DD562_RS00060"
                     /old_locus_tag="DD562_00060"
     CDS             13..936
                     /locus_tag="DD562_RS00060"
                     /old_locus_tag="DD562_00060"
                     /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_109028160.1"
                     /translation="MEKYTEKKQRNQVFQKFIKRHIGENQMDLVEDCNTFLSFVADKTL
                     EKQKLYKANSCKNRFCPVCAWRKARKDALGLSLMMQYIKQEENKEFIFLTLTTPNVMSD
                     ELENEIKHYNNSFRKLIKRKKVDSVIKGYVRKLEVTYNKKRDDYNPHFHVLIAVNKSYF
                     KDTKSYISQKEWLNLWRDVTGISEITQVQVQKIRQNNNKELYEMAKYSGKDSDYLINQK
                     VFDAFYKSLKGKQVLVYSGLFKEAKKKLKNGDLDYLKEIDPTEYIYQIFYIWKQKEYLA
                     SELYDLTEQEKREINHKMIDEIEEEQ"
                     /name="protein rep"
     gene            2015..2836
                     /locus_tag="DD562_RS00065"
                     /old_locus_tag="DD562_00065"
     CDS             2015..2836
                     /locus_tag="DD562_RS00065"
                     /old_locus_tag="DD562_00065"
                     /inference="COORDINATES: protein motif:HMM:NF025217.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative RNA methyltransferase"
                     /protein_id="WP_049948317.1"
                     /translation="MFFKCSICDEKLKRGYKTLACENNHTFDIAKEGYSNLISGHKKSK
                     YDKKLFIARRELNDSSNLYSILISKIIEIIKKYEIKTKNNVIDVGTGEGYILNEISKTF
                     LGENEFLGIDIAKEGVKKAAKSYKNINWLVADLADIPVMNGNVDFLINVLSPSNYDEFK
                     RVLDKEGKLIKIIPNSDYLKEIRNIVFSNHKNKDYDNSEVIDLFEANFNKIEMIDISYK
                     VKLNKEELNKLLDMTPLTWNLSDVEKEGIIKKNLSEITMSFKVLVGGFKTS"
                     /name="putative RNA methyltransferase"
     Typing          2..936
                     /name="rep_cluster_1230"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.833"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          11..933
                     /name="MOBC"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="80.195"
                     /coverage="97.0"
                     /evalue="2.7700000000000003e-177"
ORIGIN
        1 atgtgttata acatggaaaa gtatactgag aaaaaacaaa gaaatcaagt atttcagaaa
       61 tttattaaac gtcatattgg agagaatcaa atggatttag ttgaagattg taatacattt
      121 ctgtcttttg tagctgataa aactttagaa aaacagaaat tatataaagc taattcttgt
      181 aaaaatcgat tttgtcctgt ctgcgcttgg agaaaagcta gaaaagatgc attgggttta
      241 tctttgatga tgcaatatat taagcaggag gaaaataagg agtttatctt tttaactttg
      301 actacaccta atgtaatgag tgatgaatta gaaaatgaaa taaagcatta caataattct
      361 tttagaaaac ttataaaaag aaaaaaggta gatagtgtta taaagggata tgtccgcaag
      421 ttagaggtta catataataa aaaaagagat gattataacc cacattttca tgtgttgatt
      481 gcagtaaata aatcatattt taaagataca aaatcttata ttagtcaaaa agaatggttg
      541 aatttatggc gtgatgtaac aggtatttca gaaattacac aagttcaagt tcaaaaaata
      601 agacaaaata ataataaaga gttatatgaa atggctaagt attctggtaa agatagtgat
      661 tacttaataa atcaaaaagt atttgatgct ttttataaat cacttaaagg taaacaggta
      721 ttagtttatt caggattgtt taaagaggct aaaaagaaat taaaaaatgg ggatttagat
      781 tacttaaaag aaattgatcc aaccgaatat atttatcaaa ttttttatat ttggaaacaa
      841 aaagagtatt tagctagtga actttacgac ttaacagaac aagaaaaaag agaaattaat
      901 cacaaaatga tagacgaaat cgaggaagag caataacaaa atatgagtgc taacagctga
      961 cctcccgata acactatgta gttattggga ggtcagctgt tgaattatgc acgagtattt
     1021 taaaagttat tgtgatgacg acggtaaacg agcgctaaaa gtataatatt aaaagttttt
     1081 attatattaa ctttctacta acattatact tttgttatac aaattttaac cctgttagga
     1141 actataaaaa catgaaaatt ttaatttgca tgtaactggg cagtgtctaa aaaattcgca
     1201 ctggtcatga acaaaaaaat gagctaaata atttaacttt ttaagttata taaattttag
     1261 ggagttccaa tcaaattaga aaaatatata aaagagctat atcattttcc tggcttatgt
     1321 ttaaaaagta caagtgattg tatttaaaat gactttagca atttaagtaa tatgtcattt
     1381 gaatacaagt taaatgtcag aaagatgtac ccttattttg ctcatatttg cgttttaaga
     1441 aacatatata aatatacagg tataaacata tataaatata gagtttgctc taaatacccc
     1501 cttaaaattc aaaataaagg catttaaaaa ttaagaaaat aaaaaagcta ctagcaaaaa
     1561 actagtagct taaatcttag ttaaatttct atgtagtatt aatttttata tctgcgccac
     1621 aacgccgatt ccttaaaact aagataaaaa ttgacgaagg tcgattatgg ttttttacgc
     1681 gttcttttta gaacgcataa gtgcgccctt acgggccctt acgggattta actagattat
     1741 aacgacgaaa aatagacctg taaagcaata acagttgggt ctactttgtc tactggtcag
     1801 acaagaaaag aacacgcatt tatgccgaga aaatttattg atgttgagaa gaacccttaa
     1861 ctaaacttgc agacgaatgt cggcatagcg tgagctatta agccgaccat tcgacaagtt
     1921 ttgggattgt taagggttcc gaggctcaac gtcaataaag caattggaat aaagcaactt
     1981 tgttatttat aattatttga ttggaggtgt gaatatgttt tttaagtgtt ctatatgtga
     2041 tgaaaaatta aagagaggtt ataaaacttt agcatgtgag aataaccata cttttgatat
     2101 tgcaaaagag ggttattcga atttaatttc agggcataaa aaaagtaaat acgataaaaa
     2161 attgtttatt gctagaagag aattgaatga tagtagcaat ttgtattcga tattaatttc
     2221 aaaaatcata gaaattatta aaaaatatga gattaaaact aaaaataatg tgatagatgt
     2281 tggtactggt gagggttata ttttaaatga aattagtaaa acatttcttg gtgaaaatga
     2341 attcttaggt atagacattg caaaagaagg tgtaaaaaaa gcagcaaaat catataaaaa
     2401 tataaattgg ttggttgctg atctagctga tataccagtt atgaatggga atgtagactt
     2461 tttaattaat gtgcttagcc cttctaatta tgatgagttt aaaagagttc tagataaaga
     2521 ggggaaattg ataaaaataa ttcctaatag tgattattta aaagaaataa ggaatatagt
     2581 ctttagtaat cataaaaata aggattatga taattctgag gttatagatt tatttgaagc
     2641 taattttaat aaaattgaaa tgatagacat tagttataag gttaaattaa ataaagaaga
     2701 attgaataaa ttacttgata tgacgccttt aacgtggaat ttaagtgacg tagaaaaaga
     2761 aggaataatt aagaaaaact taagtgaaat tacgatgagt tttaaagttt tggttggtgg
     2821 ttttaaaacg agttgaaaac gagtttcttc ttgtcttgat aataagggta actattgccg
     2881 gcgaggctag ttacccttaa aatattgata tggccgcttt taaacgcaaa aaaagttgct
     2941 tttttcagca tactcatgta gtgttttagg tgtctaatca aaaacattat gagaaaggag
     3001 aaaaagcaac tttttttatt gtcatagttt gtgaaaacta agttgttttt
//
