LOCUS       NZ_CP102969             6154 bp    DNA     linear   CON 02-JUL-2023
DEFINITION  Staphylococcus aureus strain 13-G-52 plasmid p13-G-52.
ACCESSION   NZ_CP102969
VERSION     NZ_CP102969.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30370429
            Assembly: GCF_024741635.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 6154)
  AUTHORS   Monecke,S., Roberts,M.C., Braun,S.D., Diezel,C., Muller,E.,
            Reinicke,M., Linde,J., Joshi,P.R., Paudel,S., Acharya,M.,
            Chalise,M.K., Fessler,A.T., Hotzel,H., Khanal,L., Koju,N.P.,
            Schwarz,S., Kyes,R.C. and Ehricht,R.
  TITLE     Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild
            and Captive Macaques
  JOURNAL   Int J Mol Sci 23 (19), 11225 (2022)
   PUBMED   36232529
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6154)
  AUTHORS   Braun,S.D., Diezel,C., Reinicke,M., Linde,J. and Monecke,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-AUG-2022) Optisch-Molekulare Diagnostik und
            Systemtechnologien, Leibniz Institute of Photonic Technology (IPHT),
            Philosophenweg 7, Jena 07743, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. v2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 136x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/02/2023 09:52:29
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,669
            CDSs (total)                      :: 2,587
            Genes (coding)                    :: 2,524
            CDSs (with protein)               :: 2,524
            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)              :: 63
            CDSs (without protein)            :: 63
            Pseudo Genes (ambiguous residues) :: 0 of 63
            Pseudo Genes (frameshifted)       :: 37 of 63
            Pseudo Genes (incomplete)         :: 31 of 63
            Pseudo Genes (internal stop)      :: 15 of 63
            Pseudo Genes (multiple problems)  :: 18 of 63
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP102969.1.
            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/
FEATURES             Location/Qualifiers
     source          1..6154
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="13-G-52"
                     /isolation_source="Wild animal"
                     /host="Macaca mulatta"
                     /db_xref="taxon:1280"
                     /plasmid="p13-G-52"
                     /geo_loc_name="Nepal: Gokarna"
                     /collection_date="2019"
                     /genotype="ST7691"
     gene            460..1077
                     /gene="cadD"
                     /locus_tag="NW965_RS13325"
                     /old_locus_tag="NW965_13320"
     CDS             460..1077
                     /gene="cadD"
                     /locus_tag="NW965_RS13325"
                     /old_locus_tag="NW965_13320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017465246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cadmium resistance transporter CadD"
                     /protein_id="WP_000616816.1"
                     /translation="MIQTVVAAAVLYIATAVDLLVILLIFFARAKTRKEYRDIYVGQYL
                     GSIILILVSLFLAFVLNYVPEKWILGLLGLIPIYLGIKVAIYDDCEGEKRAKKELNEKG
                     LSKLVGTVAIVTIASCGADNIGLFVPYFVTLSVTNLLLTLFVFLILIFFLVFTAQKLAN
                     IPGIGEIVEKFSRWIMAIIYIALGLFIIIENDTIQTILGFIF"
                     /name="cadD"
     gene            1096..1443
                     /locus_tag="NW965_RS13330"
                     /old_locus_tag="NW965_13325"
     CDS             1096..1443
                     /locus_tag="NW965_RS13330"
                     /old_locus_tag="NW965_13325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020366422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="metalloregulator ArsR/SmtB family transcription
                     factor"
                     /protein_id="WP_000119690.1"
                     /translation="MSYENTCDVICVHEDKVNNALSFLEDDKSKKLLNILEKICDEKKL
                     KIILSLIKEDELCVCDISLILKMSVASTSHHLRLLYKNEVLDFYKDGKMAYYFIKDDEI
                     REFFSKNHEGF"
                     /name="metalloregulator ArsR/SmtB family transcription
                     factor"
     gene            1634..2629
                     /locus_tag="NW965_RS13335"
                     /old_locus_tag="NW965_13330"
     CDS             1634..2629
                     /locus_tag="NW965_RS13335"
                     /old_locus_tag="NW965_13330"
                     /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_001199887.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANIKAI
                     KPNKKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     ARG             3793..4406
                     /name="cadD"
                     /gene="cadD"
                     /gene_name="cadmium resistance transporter CadD"
                     /tool="amrfinderplus"
                     /drug_class="CADMIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             461..1074
                     /name="cadD"
                     /gene="cadD"
                     /gene_name="cadmium resistance transporter CadD"
                     /tool="amrfinderplus"
                     /drug_class="CADMIUM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            4428..4775
                     /locus_tag="NW965_RS13345"
                     /old_locus_tag="NW965_13340"
     CDS             4428..4775
                     /locus_tag="NW965_RS13345"
                     /old_locus_tag="NW965_13340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020366422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="metalloregulator ArsR/SmtB family transcription
                     factor"
                     /protein_id="WP_000119690.1"
                     /translation="MSYENTCDVICVHEDKVNNALSFLEDDKSKKLLNILEKICDEKKL
                     KIILSLIKEDELCVCDISLILKMSVASTSHHLRLLYKNEVLDFYKDGKMAYYFIKDDEI
                     REFFSKNHEGF"
                     /name="metalloregulator ArsR/SmtB family transcription
                     factor"
     gene            4966..5961
                     /locus_tag="NW965_RS13350"
                     /old_locus_tag="NW965_13345"
     CDS             4966..5961
                     /locus_tag="NW965_RS13350"
                     /old_locus_tag="NW965_13345"
                     /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_001199887.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANIKAI
                     KPNKKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     Typing          1635..2629
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4967..5961
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccttacggga tttaactaga ttataacgac gaaaaacaga cctgtaaagc aataacaatt
       61 aggtctacca ggtagataaa gtgtacaaag tagaaccgaa aaagttattt attttgaaga
      121 tttttcgtag atataatttg ctaataaact tcctaaaact gaataaagaa aaatagttaa
      181 actcatgtaa tcactccata attctgaagt gtctccatgt ctacgcatag acacgcattt
      241 atgccgagaa aatttattgt gcgttgagaa gaacccttaa ctaaacttgc agacgaatgt
      301 cggcatagcg tgagctatta agccgaccat tcgacaagtt ttgggattgt taagggttcc
      361 gaggctcaac gtcaataaag caattggaat aaagcaccta tgattattta aaaatataag
      421 ttataataca ttcaaaaata tttttgaatg aggtgtatta tgattcaaac ggttgttgct
      481 gctgctgttc tttatattgc tacagcagtt gatttattag taattttatt aatatttttt
      541 gctagagcaa agactagaaa agaatataga gatatttatg ttggtcaata tttagggtct
      601 attattttaa tattagttag tttgttttta gcttttgtat taaattatgt tccagaaaag
      661 tggatattag gtttattggg tttaatacca atttatcttg gaattaaagt ggctatttat
      721 gatgattgtg aaggagaaaa gagagctaaa aaagaattga atgaaaaagg attgtctaaa
      781 ttagttggta cggttgcaat tgttacgata gcaagttgtg gcgccgataa tattggttta
      841 tttgttccgt attttgtgac attaagtgtt actaatttat tacttactct gtttgtcttt
      901 ttaattttaa ttttcttctt ggtgtttact gcacaaaaat tagctaatat cccaggaatt
      961 ggagaaattg ttgagaaatt tagtcgttgg attatggcta tcatttatat agctttaggt
     1021 ttatttatta ttattgaaaa tgacactatt caaacaattt taggatttat attttaattt
     1081 agggtgtgat tttatatgag ttatgaaaat acttgtgatg tgatctgtgt acatgaggat
     1141 aaagttaaca atgctttaag ttttttagaa gatgataaat ctaagaaatt acttaacatt
     1201 ttagaaaaaa tttgtgatga gaagaaattg aaaatcatat tatctttgat taaagaagat
     1261 gagttgtgtg tttgtgatat ttctttgata ttgaaaatga gtgttgcttc aacttcacat
     1321 catttaaggc ttttatataa aaatgaggta cttgattttt ataaagatgg aaagatggca
     1381 tattatttta ttaaagacga tgaaataaga gagtttttct ctaaaaatca tgagggtttt
     1441 tgaaacgagt gaaacgagtt tcttcttgtc ttgatactat atagaaataa ctcgatttta
     1501 tatatacagc tgtaactgtt gatattacag cgtttaaacg tgtttttgtg cgtgaaagga
     1561 aaatttgaca ataaaaaacc ccagttatat tattaaggtg tcgaatctta aataatactg
     1621 ggggtctttt tatatgcaat ataatactac tagaagtata accgaaaatc aagataataa
     1681 aacgttaaaa gatatgacga aaagtgggaa acaacgccca tggagagaaa agaaaataga
     1741 taatgtaagc tatgcagata tactagaaat tttaaaaatc aaaaaggctt ttaatgtaaa
     1801 acaatgtggt aatattttag aatttaagcc aactgatgaa ggttatttga agttacataa
     1861 gacatggttt tgtaaatcaa aattatgtcc ggtttgtaat tggagacgtg ctatgaaaaa
     1921 tagttatcaa gctcaaaaag tgattgaaga agtaattaag gaaaagccaa aagcacgttg
     1981 gttgttttta acactttcaa caaaaaatgc gatagatgga gatactttag aacaaagttt
     2041 gaagcatcta actaaagcat ttgataggtt gagtagatat aaaaaggtta aacaaaatct
     2101 tgttggattt atgcgttcaa cagaagttac cgttaataaa aatgacggta gttataatca
     2161 gcatatgcac gttttgttat gtgttgaaaa tgcatatttt agaaaaaaag agaattatat
     2221 aactcaagaa gaatgggtta atttatggca aagagcattg caagttgatt atcgacctgt
     2281 tgctaatatt aaagcgatca aaccaaataa aaaaggcgat aaagatattg aatctgcaat
     2341 caaagagacc tcaaaatatt cggttaaatc atctgatttt ttaactgatg atgatgaaaa
     2401 aaatcaagaa attgtaagtg atttagaaaa aggtttgtat cgaaagcgta tgttaagtta
     2461 tggtggattg ctgaaacaaa agcataaaat tttaaactta gacgatgctg aagatggaaa
     2521 tttgattaat acaagtgatg aagataaaac aacagatgaa gaagaaaagg cacattcgat
     2581 tacggcaatt tggaattttg aaaagcaaaa ttattattta aggcattagt gataactgat
     2641 gtcttttttt attacttttt tgtaaaaaag tgctgtctta tttttgtgac aaattctgta
     2701 tgtagtgtca caaaactgtg acaaacgcaa tatattgtgt cacaaaagtg tgacatttcg
     2761 tctttttatg cccccatgca aaaagatcga cgaagtcttg aaatatctgg ctttgccaga
     2821 tacctcatct atagatgggg tcatattttc cttatgctct tacggagttc ttagagaaaa
     2881 attgaaattt ctcgattttt gataaaaacg ccctgcagga atttagaaaa acatggggaa
     2941 gttttaaaga attttatgct catttttaat ttgcatgtaa atgggcagtg tctaaaaaac
     3001 tcgacactgg ttttactcga attttagttt gtgaaattaa gatatattta tttggctcat
     3061 atttgcgttt taaaagttta tgtaggtttt taggtataaa actatatgat ttacccataa
     3121 atctttaaaa tgacctctta aaattcaaaa taaaggcatt taaaaattaa caaaataaaa
     3181 aagctactag caaaaaacta gtagcttttg tcttgatgta gtattaattt ttatatctgc
     3241 gccacaacgc cgatttctta aaacgaatat aaaaaatcga cgaaggtcga ttatggtttt
     3301 tgcacgcgtt cttttagaac gcataagtgc gcccttacgg gatttaacta gattataacg
     3361 acgaaaaaca gacctgtaaa gcaataacaa ttaggtctac caggtagata aagtgtacaa
     3421 agtagaaccg aaaaagttat ttattttgaa gatttttcgt agatataatt tgctaataaa
     3481 cttcctaaaa ctgaataaag aaaaatagtt aaactcatgt aatcactcca taattctgaa
     3541 gtgtctccat gtctacgcat agacacgcat ttatgccgag aaaatttatt gtgcgttgag
     3601 aagaaccctt aactaaactt gcagacgaat gtcggcatag cgtgagctat taagccgacc
     3661 attcgacaag ttttgggatt gttaagggtt ccgaggctca acgtcaataa agcaattgga
     3721 ataaagcacc tatgattatt taaaaatata agttataata cattcaaaaa tatttttgaa
     3781 tgaggtgtat tatgattcaa acggttgttg ctgctgctgt tctttatatt gctacagcag
     3841 ttgatttatt agtaatttta ttaatatttt ttgctagagc aaagactaga aaagaatata
     3901 gagatattta tgttggtcaa tatttagggt ctattatttt aatattagtt agtttgtttt
     3961 tagcttttgt attaaattat gttccagaaa agtggatatt aggtttattg ggtttaatac
     4021 caatttatct tggaattaaa gtggctattt atgatgattg tgaaggagaa aagagagcta
     4081 aaaaagaatt gaatgaaaaa ggattgtcta aattagttgg tacggttgca attgttacga
     4141 tagcaagttg tggcgccgat aatattggtt tatttgttcc gtattttgtg acattaagtg
     4201 ttactaattt attacttact ctgtttgtct ttttaatttt aattttcttc ttggtgttta
     4261 ctgcacaaaa attagctaat atcccaggaa ttggagaaat tgttgagaaa tttagtcgtt
     4321 ggattatggc tatcatttat atagctttag gtttatttat tattattgaa aatgacacta
     4381 ttcaaacaat tttaggattt atattttaat ttagggtgtg attttatatg agttatgaaa
     4441 atacttgtga tgtgatctgt gtacatgagg ataaagttaa caatgcttta agttttttag
     4501 aagatgataa atctaagaaa ttacttaaca ttttagaaaa aatttgtgat gagaagaaat
     4561 tgaaaatcat attatctttg attaaagaag atgagttgtg tgtttgtgat atttctttga
     4621 tattgaaaat gagtgttgct tcaacttcac atcatttaag gcttttatat aaaaatgagg
     4681 tacttgattt ttataaagat ggaaagatgg catattattt tattaaagac gatgaaataa
     4741 gagagttttt ctctaaaaat catgagggtt tttgaaacga gtgaaacgag tttcttcttg
     4801 tcttgatact atatagaaat aactcgattt tatatataca gctgtaactg ttgatattac
     4861 agcgtttaaa cgtgtttttg tgcgtgaaag gaaaatttga caataaaaaa ccccagttat
     4921 attattaagg tgtcgaatct taaataatac tgggggtctt tttatatgca atataatact
     4981 actagaagta taaccgaaaa tcaagataat aaaacgttaa aagatatgac gaaaagtggg
     5041 aaacaacgcc catggagaga aaagaaaata gataatgtaa gctatgcaga tatactagaa
     5101 attttaaaaa tcaaaaaggc ttttaatgta aaacaatgtg gtaatatttt agaatttaag
     5161 ccaactgatg aaggttattt gaagttacat aagacatggt tttgtaaatc aaaattatgt
     5221 ccggtttgta attggagacg tgctatgaaa aatagttatc aagctcaaaa agtgattgaa
     5281 gaagtaatta aggaaaagcc aaaagcacgt tggttgtttt taacactttc aacaaaaaat
     5341 gcgatagatg gagatacttt agaacaaagt ttgaagcatc taactaaagc atttgatagg
     5401 ttgagtagat ataaaaaggt taaacaaaat cttgttggat ttatgcgttc aacagaagtt
     5461 accgttaata aaaatgacgg tagttataat cagcatatgc acgttttgtt atgtgttgaa
     5521 aatgcatatt ttagaaaaaa agagaattat ataactcaag aagaatgggt taatttatgg
     5581 caaagagcat tgcaagttga ttatcgacct gttgctaata ttaaagcgat caaaccaaat
     5641 aaaaaaggcg ataaagatat tgaatctgca atcaaagaga cctcaaaata ttcggttaaa
     5701 tcatctgatt ttttaactga tgatgatgaa aaaaatcaag aaattgtaag tgatttagaa
     5761 aaaggtttgt atcgaaagcg tatgttaagt tatggtggat tgctgaaaca aaagcataaa
     5821 attttaaact tagacgatgc tgaagatgga aatttgatta atacaagtga tgaagataaa
     5881 acaacagatg aagaagaaaa ggcacattcg attacggcaa tttggaattt tgaaaagcaa
     5941 aattattatt taaggcatta gtgataactg atgtcttttt ttattacttt tttgtaaaaa
     6001 agtgctgtct tatttttgtg acaaattctg tatgtagtgt cacaaaactg tgacaaacgc
     6061 aatatattgt gtcacaaaag tgtgacattt cgtcttttta tgcccccatg caaaaagatc
     6121 gacgaagtct tgaaatatct ggctttgcca gata
//
