LOCUS       NZ_CP029168             4203 bp    DNA     circular CON 01-DEC-2023
DEFINITION  Staphylococcus aureus strain PTDrAP2 plasmid pPTDrAP2a, complete
            sequence.
ACCESSION   NZ_CP029168
VERSION     NZ_CP029168.1
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 4203)
  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  JOURNAL   Unpublished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 4203)
  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
            CP029168.1.
            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..4203
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="PTDrAP2"
                     /isolation_source="Pig nares"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:1280"
                     /plasmid="pPTDrAP2a"
                     /geo_loc_name="Australia"
                     /lat_lon="35 S 147 E"
                     /collection_date="2015-08-12"
     gene            1..600
                     /locus_tag="DD562_RS00005"
                     /old_locus_tag="DD562_00005"
     CDS             1..600
                     /locus_tag="DD562_RS00005"
                     /old_locus_tag="DD562_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012816703.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_012816703.1"
                     /translation="MSENVIKETENKKNSRGRNWTFVLYPESAKAEWLEYLKELHIQFV
                     VSPLHDRDTDTEGRMKKEHYHILVMYEGNKSYEQIKIITEELNATIPQIAGSVKGLVRY
                     MLHMDDPNKFKYQKEDMIVYGGVDVDELLKKTTTDRYKLIKEMIEFIDEQGIVEFKSLM
                     DYAMKFKFDDWFPLLCDNSAYVIQEYIKSNRYKSDR"
                     /name="replication protein"
     gene            complement(747..1481)
                     /gene="erm(C)"
                     /locus_tag="DD562_RS00010"
                     /old_locus_tag="DD562_00010"
     ARG             complement(751..1481)
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1526..1585)
                     /gene="ermCL"
                     /locus_tag="DD562_RS14910"
     CDS             complement(1526..1585)
                     /gene="ermCL"
                     /locus_tag="DD562_RS14910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methylase leader peptide ErmCL"
                     /protein_id="WP_002503927.1"
                     /translation="MGIFSIFVINTVHYQPNKK"
                     /name="ermCL"
     gene            1878..3068
                     /gene="mobV"
                     /locus_tag="DD562_RS00020"
                     /old_locus_tag="DD562_00020"
     CDS             1878..3068
                     /gene="mobV"
                     /locus_tag="DD562_RS00020"
                     /old_locus_tag="DD562_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011178348.1"
                     /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="MobV family relaxase"
                     /protein_id="WP_031917739.1"
                     /translation="MSYSILRVERVKGSGNTKGLQKHNQRENNNYNNKDIRHEDTHKNY
                     DLIHEKNVDYNQLISDKIDSNYTGNRKIRKDAIRHVEGIITSDEKFFNRLSEEETHQFF
                     KDSLDFAKQEYGEENILYATVHLDEKVPHMHFGFVPLTDDGRLSAKEKLGNKKAMTELQ
                     DRFNHHVNSRGYGLERGTAKQVSEREHKHIDKFKKDTQFHKQELQTVKSDLKKLDSQLN
                     AHISDLRVTSDFEYENEVEVKKGLFKAGEKLETGRKVISAEEFERIQRTVIAASNIVDD
                     YEKIRETDFFKENEELKSKNLKYAAFSIETNKENEKLKKENEEYKELFTKYQKLTRGLY
                     TTLRDSFQGFDKVYDNISNKLQQNDKTAVFGKFMDFVKEEVREQERTKQRDIDIER"
                     /name="mobV"
     gene            3248..3757
                     /locus_tag="DD562_RS00025"
                     /old_locus_tag="DD562_00025"
     CDS             3248..3757
                     /locus_tag="DD562_RS00025"
                     /old_locus_tag="DD562_00025"
                     /inference="COORDINATES: protein motif:HMM:NF016085.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF402 domain-containing protein"
                     /protein_id="WP_031915809.1"
                     /translation="MKELDILVYKYNNKLHYEWQTILIKENDNYVLVKGEIGRKLKHYT
                     KGKVFNCPLKSLEFFSLTEGFTVNIDISNSGDIEYYCNICLPSKFNLEEKNLSFIDLDL
                     DLIIDNKGHLKVIDEDEFILNSESMSYPKDIIDLTYKNLENLKKKIRNNEFPFDGFFEK
                     YIEEIK"
                     /name="DUF402 domain-containing protein"
     gene            3956..4123
                     /locus_tag="DD562_RS00030"
                     /old_locus_tag="DD562_00030"
     CDS             3956..4123
                     /locus_tag="DD562_RS00030"
                     /old_locus_tag="DD562_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006308237.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cop-6 protein"
                     /protein_id="WP_006308237.1"
                     /translation="MVVDRKEEKKVAVTLRLTTEENEILNRIKEKYNISKSDATGILIK
                     KYAKEEYGAF"
                     /name="cop-6 protein"
     ARG             complement(748..1481)
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="97.54"
                     /coverage="100.0"
     Typing          2..600
                     /name="Inc11"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.833"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1879..3065
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgaaa atgtaataaa agaaactgaa aacaagaaaa attcaagagg acgtaattgg
       61 acatttgttt tatatccaga atcagcaaaa gcagagtggt tagagtattt aaaagagtta
      121 cacattcaat ttgtagtgtc tccattacat gatagggata ctgatacaga aggtaggatg
      181 aaaaaagagc attatcatat tctagtgatg tatgagggta ataaatctta tgaacagata
      241 aaaataatta cagaagaatt gaatgcgact attccgcaga ttgcaggaag tgtgaaaggt
      301 cttgtgagat atatgcttca catggacgat cctaataaat ttaaatatca aaaagaagat
      361 atgatagttt atggcggtgt agatgttgat gaattattaa agaaaacaac aacagataga
      421 tataaattaa ttaaagaaat gattgagttt attgatgaac aaggaatcgt agaatttaag
      481 agtttaatgg attatgcaat gaagtttaaa tttgatgatt ggttcccgct tttatgtgat
      541 aactcggcgt atgttattca agaatatata aaatcaaatc ggtataaatc tgaccgatag
      601 attttgaatt taagagtgtc acaagacact cttttttcgc accagcgaaa actggtttaa
      661 gccgactgcg caaaagacat aatcgattca caaaaaatag gcacacgaaa aacaagttaa
      721 gggatgcagt ttatgcatcc cttaacttac ttattaaata atttatagct attgaaaaga
      781 gataagaatt gttcaaagct aatattgttt aaatcgtcaa ttcctgcatg ttttaaggaa
      841 ttgttaaatt gattttttgt aaatattttc ttgtattctt tgttaaccca tttcataacg
      901 aaataattat acttttgttt atctttgtgt gatattcttg atttttttct acttaatctg
      961 ataagtgagc tattcacttt aggtttagga tgaaaatatt ctcttggaac catacttaat
     1021 atagaaatat caacttctgc cattaaaagt aatgccaatg agcgttttgt atttaataat
     1081 cttttagcaa acccgtattc cacgattaaa taaatctcat tagctatact atcaaaaaca
     1141 attttgcgta ttatatccgt acttatgtta taaggtatat taccatatat tttataggat
     1201 tggtttttag gaaatttaaa ctgcaatata tccttgttta aaacttggaa attatcgtga
     1261 tcaacaagtt tattttctgt agttttgcat aatttatggt ctatttcaat ggcagttacg
     1321 aaattacacc tctttactaa ttcaagggta aaatggcctt ttcctgagcc gatttcaaag
     1381 atattatcat gttcatttaa tcttatattt gtcattattt tatctatatt atgttttgaa
     1441 gtaataaagt tttgactgtg ttttatattt ttctcgttca ttataaccct ctttaatttg
     1501 cttattaacg attcattata accatttatt ttttgtttgg ttgataatga actgtgttga
     1561 ttacaaaaat actaaaaatg cccatatttt tccctcctta taaaattagt ataattatag
     1621 cacgagctct gataaatatg aacatgatga gtgatcgtta aatttatact gcaatcggat
     1681 gcgattattg aataaaagat atgagagatt tatctaattt cttttttctt gtaaaaaaag
     1741 aaagttctta aaggttttat agttttggtc gtagagcaca cggtttaacg acttaattac
     1801 gaagtaaata agtctagtgt gttagacttt atgaaatcta tatacgttta tatatattta
     1861 ttatccggag gtgtcgtatg tcttattcaa ttttaagagt ggaaagagtt aaaggatctg
     1921 gaaatacaaa aggacttcaa aagcataatc aaagagaaaa taataattat aataacaagg
     1981 atattaggca tgaagataca cataaaaatt atgatttaat acatgagaaa aatgtggatt
     2041 ataatcaatt gatttcagat aaaattgatt caaattatac aggtaatcgt aaaattcgta
     2101 aggatgctat tcgacatgtg gaaggaataa ttacgagtga tgaaaagttt tttaatagat
     2161 tgagtgaaga agaaacacat caatttttta aggatagttt ggattttgct aaacaggaat
     2221 atggcgaaga aaatatatta tatgcaactg ttcatctgga tgaaaaagta ccgcatatgc
     2281 actttggatt tgtacctctg acagatgacg gtagattatc tgcgaaagag aaattaggta
     2341 ataaaaaagc aatgactgaa ttacaggata gatttaatca tcatgttaat tctaggggtt
     2401 atggtttgga acgtggaact gctaagcaag tgtctgaacg agaacataaa catattgata
     2461 aattcaaaaa ggatactcag tttcataaac aggaattaca aacggttaaa agtgatctta
     2521 aaaagttaga tagccaatta aacgctcata taagcgattt aagagttact agcgattttg
     2581 agtatgagaa tgaggtagaa gtcaaaaagg gcttatttaa ggcaggagaa aagctggaaa
     2641 caggacgtaa ggttatttct gcggaggaat ttgaaagaat acagagaact gtgattgctg
     2701 ctagtaatat tgttgatgat tatgaaaaga ttagagaaac tgattttttt aaagaaaatg
     2761 aagaattaaa gagtaagaat ctaaagtatg ctgcgtttag tattgaaacg aataaagaga
     2821 atgagaaact caaaaaagag aatgaagagt ataaagagtt gtttactaag tatcagaaac
     2881 taacgagagg gctttataca acgcttagag atagctttca aggctttgac aaggtatatg
     2941 acaatatcag taataaactt caacaaaacg ataagacggc agtttttggg aagtttatgg
     3001 actttgtgaa agaggaagtg cgtgaacaag agcgaacaaa acaaagagat attgatattg
     3061 agaggtaacg tctgtttatg ccgagaaaac tttttggctt tgaaagtcct taacttatac
     3121 ttagagcgca agcgaagtaa tagcgatagc tattaacttt cgcttggtaa agctcttagg
     3181 attgttaagg acgcagcgta tcaaagccat aaaaggaaat tggaataaat gcaaaggtgg
     3241 agaagaaatg aaggagttag atattctagt ttataaatat aataataaat tacattatga
     3301 atggcagact atattgataa aagagaatga taattatgtt ttagtaaaag gggaaatcgg
     3361 aagaaaactg aaacattata ctaaagggaa agtgtttaat tgtccgttga aatctttaga
     3421 gttcttttct cttacagaag gttttacagt aaatattgat atttctaatt caggagatat
     3481 tgaatattac tgtaatattt gtttgccttc aaaatttaat ttagaagaaa aaaatttatc
     3541 atttattgat ttagatttgg atttaataat agataataaa ggtcatttaa aagtaattga
     3601 tgaagatgag tttatattaa attcagagag tatgtcttat ccaaaagata ttattgatct
     3661 aacttataaa aacttagaaa atttaaagaa aaaaataaga aataatgaat ttccttttga
     3721 tggttttttt gaaaaataca tagaagaaat taaataaatt ataagacctt tttaaaggtc
     3781 tttttttagt aagaaaaggg aggatatgag ggtgttttcc taggggggta ctacgacctc
     3841 ccccctaggt gtccattgtc cattgtccaa acaaataaat aaatattggg tttttaatgt
     3901 taaaaggttg ttttttatgt taaagtgaaa aaaacagatg ctgggaggta cagtgatggt
     3961 tgtagataga aaagaagaga aaaaagttgc tgttacttta agacttacaa cagaagaaaa
     4021 tgagatatta aatagaatca aagaaaaata taatattagc aaatcagatg caaccggtat
     4081 tctaataaaa aaatatgcaa aggaggaata cggtgcattt taaataaaaa aagatagaca
     4141 gcactggcat gctgcctatc tatgactaaa ttttgttaag tgtattagca ccgttattat
     4201 atc
//
