LOCUS       NZ_CP029169             4213 bp    DNA     circular CON 01-DEC-2023
DEFINITION  Staphylococcus aureus strain PTDrAP2 plasmid pPTDrAP2b, complete
            sequence.
ACCESSION   NZ_CP029169
VERSION     NZ_CP029169.1
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 4213)
  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  JOURNAL   Unpublished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 4213)
  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
            CP029169.1.
            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..4213
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="PTDrAP2"
                     /isolation_source="Pig nares"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:1280"
                     /plasmid="pPTDrAP2b"
                     /geo_loc_name="Australia"
                     /lat_lon="35 S 147 E"
                     /collection_date="2015-08-12"
     gene            join(4118..4213,1..879)
                     /locus_tag="DD562_RS00035"
                     /old_locus_tag="DD562_00035"
     CDS             join(4118..4213,1..879)
                     /locus_tag="DD562_RS00035"
                     /old_locus_tag="DD562_00035"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002326821.1"
                     /translation="MSKRGTIVNEWEKLNRISNRRLKYQSLTLPLKMQWSIDRITIVGK
                     LKENIYYHTPNDVLILNFEQLMRLNEGNGYLKAVGNNGWQLLDQHEENIAYIEILKFHE
                     GKGRIDFNPNKINQFLSGSMKNFIHDLFLEPHFSRADIACDIVDIPDDFVSQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKIVPPEITTWWRLELQLRRG
                     KATDWHEMVHESLDSFASPHYFPPNTKVTERIMVKGLLYDHSEWGNLAKNTKKKYRDLL
                     KQESQNDELTNHLRESFAESADDLKRELDTWLQGLDVTEVGAE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            876..1295
                     /locus_tag="DD562_RS00040"
                     /old_locus_tag="DD562_00040"
     CDS             876..1295
                     /locus_tag="DD562_RS00040"
                     /old_locus_tag="DD562_00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_109028158.1"
                     /translation="MSNPVEKMTIKNLADELGVSKNTVRNQLVNSGFDLAQYKENGIIM
                     LDKELIGVARSIYRSKSDQLTGQLPVNNTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            1304..1678
                     /locus_tag="DD562_RS00045"
                     /old_locus_tag="DD562_00045"
     CDS             1304..1678
                     /locus_tag="DD562_RS00045"
                     /old_locus_tag="DD562_00045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_109028159.1"
                     /translation="MDKIDLREETVDRIELMYERLAYYLNLPDEDNYSEMLERIMDVLD
                     YLNLPDEDNYSEMLERIMDVLNSVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKL
                     MSHVMQLNQISVINSKKKEM"
                     /name="hypothetical protein"
     gene            1682..2044
                     /locus_tag="DD562_RS00050"
                     /old_locus_tag="DD562_00050"
     CDS             1682..2044
                     /locus_tag="DD562_RS00050"
                     /old_locus_tag="DD562_00050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            2265..3671
                     /locus_tag="DD562_RS00055"
                     /old_locus_tag="DD562_00055"
     CDS             2265..3671
                     /locus_tag="DD562_RS00055"
                     /old_locus_tag="DD562_00055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002333830.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          2..876
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.658"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2266..3668
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcagtggt caattgaccg aattaccata gtcggaaaac tgaaagaaaa tatttattat
       61 cacactccaa atgatgtgtt gattttaaat tttgaacagc ttatgcgttt gaacgaaggc
      121 aatggttatt taaaagctgt tgggaataat gggtggcaat tattagacca acacgaggaa
      181 aatatagctt atattgagat tcttaaattt catgaaggaa aagggcggat tgactttaat
      241 cctaataaaa tcaatcaatt tttatcaggt tccatgaaaa atttcattca tgatttattt
      301 ctagaacctc atttttcacg tgcggatatt gcttgcgata ttgtagatat tcccgatgac
      361 tttgttagtc agtatcgtgt agttgatcct gtgtctttta aaccaattta tgggcgttct
      421 ggtaagttag aaacggcata ttggggtagt cgtgccagtg aacgacaaat tcgaatgtac
      481 aataaaaaat tggaacaaga aagaaaacgt aaaattgttc cgccggaaat aacgacatgg
      541 tggcgactag aattgcagtt acgaagggga aaagcaactg attggcatga gatggttcat
      601 gaaagtttgg atagctttgc tagtccacat tattttccgc caaatactaa agttactgaa
      661 cggattatgg tgaaaggttt gctttatgat cattctgagt ggggaaatct agctaagaat
      721 acaaagaaaa aatacaggga tttgttgaag caagaaagtc aaaatgatga attgacgaat
      781 catttgcgag agtcatttgc ggaatcggca gacgatttga aacgagaatt agatacatgg
      841 ctccaaggac ttgatgtaac ggaagtaggt gctgaatgag taatccagta gaaaaaatga
      901 ccataaaaaa tcttgctgac gaattgggtg tatcgaaaaa tacagtgcgc aatcaactgg
      961 tcaattcagg gtttgacctt gctcagtata aagaaaatgg cattatcatg ctagataaag
     1021 agttgattgg tgttgctcgg tcaatttatc ggtcaaaaag tgatcaattg actggtcaat
     1081 taccggtcaa taacacaggc agtgattttc ctttagaaaa agagaatgag tttttgcgtg
     1141 atcaattagc tgagaaggac aaacatattt ctgaattaac agaaatgatt cgtgatcaac
     1201 aaaaattgac cctgcttcag caacaaaaaa acgatcagtt gttactagaa aatcaagaat
     1261 taaaaaatcg aaaatggtgg caattctgga agtgaggtgt gacatggata aaattgattt
     1321 gagagaagaa acagtcgata gaattgaatt gatgtatgaa cggttagcgt attatttgaa
     1381 tttgccggat gaagataatt atagtgaaat gcttgaacga attatggatg ttcttgatta
     1441 tttgaatttg ccggatgaag ataattatag tgaaatgctt gaacgaatta tggatgttct
     1501 caactcggtt atcaatgctg atttagcaaa atcttcagtt ttgactaatg aatttgttca
     1561 taagcattta gcgcaaacaa ctgatgaatc agaaaaagaa ttttggttga aattaatgag
     1621 tcatgttatg cagttaaacc aaatttccgt tattaattcc aaaaaaaagg agatgtagtt
     1681 tatgggaatg actttagcag atattaaagc gcaagaagaa aaattaaaaa aagaacaagc
     1741 gaaacttcgc caacagaaaa aacgcttgat tgagaaagaa aatgctgcaa tgggcaaggc
     1801 tcttcgcaag cgttttgggt ttgaaacttt tgctgatttt gagcggtggc tatcgtcgat
     1861 ttctgacgat cagcaacacg aaaaatcagt ggataatgag tggcttgctg atgaaaaatc
     1921 agcgccaagc gaacgagatt atcccgatga atctgacggc ttattcggag tgataccgaa
     1981 taagaaaagt cagatgagtg agagtaaatt tacgtcaata tttaatgacg tgaatttacg
     2041 ataagcgatt attttgcgtg aagcaaaata aagcgtaaaa ggagttgaga gcgtgacacg
     2101 ctttcggctc cttttttcgt tgtcacttgt gacagcgaat accctcggag agcatttgga
     2161 attgtgacag ccatgtcaca attaggaaaa tgttactctt tgacaaagag taacagaaag
     2221 gtttacactc tttttattag cgacagccga aggagggttt taacttgggg ttcagtattt
     2281 cgttcaaaaa gggaacaaag aatacaagca tttctcataa taatcgtgag ttaactgata
     2341 gccaaaaaat caatgactgg cataagcata ttgatttcac aaaatcggat gaaaatatct
     2401 atttagaaca aacaaatatt cgtgaaaaat atgaagaatt attcggtgaa gccgtagaaa
     2461 aatataatgc aaagcagaaa agagccgata gaaaaatcga ggactattta gcaaaggttc
     2521 gcaaggataa aaaattggaa ccacagcgag aatttatcgt gcaaattggt actcttgatg
     2581 attttcgtac tactcgtgat gatggttctt ctactggcat atcggaacaa caagcagaac
     2641 aaaatcgagt gattgccaac aaaattttag ttgagtattt caaagaattt aaagaacgga
     2701 atcctaattt atccgtctac aatgctgtta ttcataatga cgaagtaagt ccgcacctgc
     2761 atttgaatat tgttcctgtt gctgaagggt ataaacgggg tgttcaaaag caaccaagtt
     2821 ttaacaaagc cttgcaacag cagggtttac gagcagataa agagaatggt cgagtgattt
     2881 ggaataattt taggaatcag gaagttgagt caattgaacg tttgatggca gattttggtt
     2941 gggagcgtga gttagtcggt actaacaaaa tcaaagatgt tcacgaatat aaagaaatca
     3001 tgagcgagat ttcagaattg cgtcaaacgg ccgtaaaaga gcgtgagagc gtttctgatg
     3061 agttgaggta tatttctagg caaagagaag aaaatgagcg agaaaaggct ctggtggctt
     3121 ctgagagagt gaagattgaa gaagagaaga aaaatatgct gaatgtaaaa aaagagatgg
     3181 cggtcatttt ccaaaaagat attgttcctt tagaaagttt caagaggctt cctgatggtt
     3241 cgtatcattt atctgggaat gattttgttg atttgtatca acgagctacg agagcaacaa
     3301 atgccaagag aaatgctgat aacatgagtg agcaatattt acagatgctt gagcaaaata
     3361 cagaattaaa tgagtatgta gctacattgg aagaagagcg tcatttgtct ggtagaaaac
     3421 aattagcaga tttacaagtg gaaaataaaa agctgaaaga agaaaatcgc tctttacgcc
     3481 agcgtttaga gcgattaaaa aacgcatttc aaaaatcgat cactcgtttg tctatccgtt
     3541 ttggtcttgc agaaaaggat atggggcttt ctgaggaatt agaagtgtta gagcaggaga
     3601 aaaccttatt ttatcgtcaa aacgtctcac agcgtaaatt agagcgttct gaagatgaga
     3661 tcgagtggta gttacgatgt gcagtcaacg gtaccggagg cggtttgtgc cgaggataag
     3721 gagttgacgg ctaaaccact agcctattaa gctgacattt gctaaaaaat ggccagtcca
     3781 ttttttggcc aacctagcgt tagcgaagtt tgggggcgcc cttttcaaag ggtgcggttt
     3841 tattttttgg atatttgcat agctaaagag aagtgctatt attgagttag caaacaaatg
     3901 aactgaaaaa agagtaaaaa aatagtcgag caacgctacc aacgttctcg acctttacgg
     3961 aaactaatcg cactagctcc gtaacttctt aatcattata cgaatatttt tagatttctt
     4021 caagactaga gattttttgg taatgaattt ttaagagtta cgtgaacttt tgaaaattct
     4081 ttccagaagt ctctttttct ttgaggagga acaaaatttg agtaaacgtg gcacgatcgt
     4141 gaatgagtgg gaaaaactta accgcatttc taacaggcgg ttaaagtatc aaagtttgac
     4201 ccttccctta aaa
//
