LOCUS       NZ_CP062472             6486 bp    DNA     circular CON 23-DEC-2023
DEFINITION  Staphylococcus aureus strain MRSA - AMRF 3 plasmid pKH18, complete
            sequence.
ACCESSION   NZ_CP062472
VERSION     NZ_CP062472.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11974902
            Assembly: GCF_015220695.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 6486)
  AUTHORS   Devarajan,B., Rudhra,O., Rajapandian,S., Prajna,V.N. and Prajna,L.
  TITLE     Complete Genome Sequencing of MRSA Ocular Isolates from the Patients
            with Eye Diseases
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6486)
  AUTHORS   Devarajan,B., Rudhra,O., Rajapandian,S., Prajna,V.N. and Prajna,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-SEP-2020) Bioinformatics, Aravind Medical Research
            Foundation, 1,Anna nagar, Madurai, Tamil Nadu 625 020, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 1.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 178.11x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/23/2023 19:36:01
            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)                     :: 2,819
            CDSs (total)                      :: 2,735
            Genes (coding)                    :: 2,594
            CDSs (with protein)               :: 2,594
            Genes (RNA)                       :: 84
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 89 of 141
            Pseudo Genes (incomplete)         :: 38 of 141
            Pseudo Genes (internal stop)      :: 33 of 141
            Pseudo Genes (multiple problems)  :: 18 of 141
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062472.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..6486
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="MRSA - AMRF 3"
                     /isolation_source="eye"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pKH18"
                     /geo_loc_name="India:Madurai"
                     /lat_lon="9.93 N 78.12 E"
                     /collected_by="Aravind eye hospital"
     gene            <2..457
                     /gene="cadD"
                     /locus_tag="ILP75_RS13945"
                     /old_locus_tag="ILP75_13945"
                     /pseudo=""
     CDS             <2..457
                     /gene="cadD"
                     /locus_tag="ILP75_RS13945"
                     /old_locus_tag="ILP75_13945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017465246.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cadmium resistance transporter CadD"
                     /name="cadD"
     gene            476..823
                     /locus_tag="ILP75_RS13950"
                     /old_locus_tag="ILP75_13950"
     CDS             476..823
                     /locus_tag="ILP75_RS13950"
                     /old_locus_tag="ILP75_13950"
                     /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            1014..2009
                     /locus_tag="ILP75_RS13955"
                     /old_locus_tag="ILP75_13955"
     CDS             1014..2009
                     /locus_tag="ILP75_RS13955"
                     /old_locus_tag="ILP75_13955"
                     /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"
     gene            3172..3789
                     /gene="cadD"
                     /locus_tag="ILP75_RS13960"
                     /old_locus_tag="ILP75_13960"
     ARG             3173..3786
                     /name="cadD"
                     /gene="cadD"
                     /gene_name="cadmium resistance transporter CadD"
                     /tool="amrfinderplus"
                     /drug_class="CADMIUM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            3808..4155
                     /locus_tag="ILP75_RS13965"
                     /old_locus_tag="ILP75_13965"
     CDS             3808..4155
                     /locus_tag="ILP75_RS13965"
                     /old_locus_tag="ILP75_13965"
                     /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            4343..5338
                     /locus_tag="ILP75_RS13970"
                     /old_locus_tag="ILP75_13970"
     CDS             4343..5338
                     /locus_tag="ILP75_RS13970"
                     /old_locus_tag="ILP75_13970"
                     /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          1015..2009
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4344..5338
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttgttttta gcttttgtat taaattatgt tccagaaaag tggatattag gtttattggg
       61 tttaatacca atttatcttg gaattaaagt ggctatttat gatgattgtg aaggagaaaa
      121 gagagctaaa aaagaattga atgaaaaagg attgtctaaa ttagttggta cggttgcaat
      181 tgttacgata gcaagttgtg gcgccgataa tattggttta tttgttccgt attttgtgac
      241 attaagtgtt actaatttat tacttactct gtttgtcttt ttaattttaa ttttcttctt
      301 ggtgtttact gcacaaaaat tagctaatat cccaggaatt ggagaaattg ttgagaaatt
      361 tagtcgttgg attatggcta tcatttatat agctttaggt ttatttatta ttattgaaaa
      421 tgacactatt caaacaattt taggatttat attttaattt agggtgtgat tttatatgag
      481 ttatgaaaat acttgtgatg tgatctgtgt acatgaggat aaagttaaca atgctttaag
      541 ttttttagaa gatgataaat ctaagaaatt acttaacatt ttagaaaaaa tttgtgatga
      601 gaagaaattg aaaatcatat tatctttgat taaagaagat gagttgtgtg tttgtgatat
      661 ttctttgata ttgaaaatga gtgttgcttc aacttcacat catttaaggc ttttatataa
      721 aaatgaggta cttgattttt ataaagatgg aaagatggca tattatttta ttaaagacga
      781 tgaaataaga gagtttttct ctaaaaatca tgagggtttt tgaaacgagt gaaacgagtt
      841 tcttcttgtc ttgatactat atagaaataa ctcgatttta tatatacagc tgtaactgtt
      901 gatattacag cgtttaaacg tgtttttgtg cgtgaaagga aaatttgaca ataaaaaacc
      961 ccagttatat tattaaggtg tcgaatctta aataatactg ggggtctttt tatatgcaat
     1021 ataatactac tagaagtata accgaaaatc aagataataa aacgttaaaa gatatgacga
     1081 aaagtgggaa acaacgccca tggagagaaa agaaaataga taatgtaagc tatgcagata
     1141 tactagaaat tttaaaaatc aaaaaggctt ttaatgtaaa acaatgtggt aatattttag
     1201 aatttaagcc aactgatgaa ggttatttga agttacataa gacatggttt tgtaaatcaa
     1261 aattatgtcc ggtttgtaat tggagacgtg ctatgaaaaa tagttatcaa gctcaaaaag
     1321 tgattgaaga agtaattaag gaaaagccaa aagcacgttg gttgttttta acactttcaa
     1381 caaaaaatgc gatagatgga gatactttag aacaaagttt gaagcatcta actaaagcat
     1441 ttgataggtt gagtagatat aaaaaggtta aacaaaatct tgttggattt atgcgttcaa
     1501 cagaagttac cgttaataaa aatgacggta gttataatca gcatatgcac gttttgttat
     1561 gtgttgaaaa tgcatatttt agaaaaaaag agaattatat aactcaagaa gaatgggtta
     1621 atttatggca aagagcattg caagttgatt atcgacctgt tgctaatatt aaagcgatca
     1681 aaccaaataa aaaaggcgat aaagatattg aatctgcaat caaagagacc tcaaaatatt
     1741 cggttaaatc atctgatttt ttaactgatg atgatgaaaa aaatcaagaa attgtaagtg
     1801 atttagaaaa aggtttgtat cgaaagcgta tgttaagtta tggtggattg ctgaaacaaa
     1861 agcataaaat tttaaactta gacgatgctg aagatggaaa tttgattaat acaagtgatg
     1921 aagataaaac aacagatgaa gaagaaaagg cacattcgat tacggcaatt tggaattttg
     1981 aaaagcaaaa ttattattta aggcattagt gataactgat gtcttttttt attacttttt
     2041 tgtaaaaaag tgctgtctta tttttgtgac aaattctgta tgtagtgtca caaaactgtg
     2101 acaaacgcaa tatattgtgt cacaaaagtg tgacatttcg tctttttatg cccccatgca
     2161 aaaagatcga cgaagtcttg aaatatctgg ctttgccaga tacctcatct atagatgggg
     2221 tcatattttc cttatgctct tacggagttc ttagagaaaa attgaaattt ctcgattttt
     2281 gataaaaacg ccctgcagga atttagaaaa acatggggaa gttttaaaga attttatgct
     2341 catttttaat ttgcatgtaa atgggcagtg tctaaaaaac tcgacactgg ttttactcga
     2401 attttagttt gtgaaattaa gatatattta tttggctcat atttgcgttt taaaagttta
     2461 tgtaggtttt taggtataaa actatatgat ttacccataa atctttaaaa tgacctctta
     2521 aaattcaaaa taaaggcatt taaaaattaa caaaataaaa aagctactag caaaaaacta
     2581 gtagcttttg tcttgatgta gtattaattt ttatatctgc gccacaacgc cgatttctta
     2641 aaacgaatat aaaaaatcga cgaaggtcga ttatggtttt tgcacgcgtt cttttagaac
     2701 gcataagtgc gcccttacgg gatttaacta gattataacg acgaaaaaca gacctgtaaa
     2761 gcaataacaa ttaggtctac caggtagata aagtgtacaa agtagaaccg aaaaagttat
     2821 ttattttgaa gatttttcgt agatataatt tgctaataaa cttcctaaaa ctgaataaag
     2881 aaaaatagtt aaactcatgt aatcactcca taattctgaa gtgtctccat gtctacgcat
     2941 agacacgcat ttatgccgag aaaatttatt gtgcgttgag aagaaccctt aactaaactt
     3001 gcagacgaat gtcggcatag cgtgagctat taagccgacc attcgacaag ttttgggatt
     3061 gttaagggtt ccgaggctca acgtcaataa agcaattgga ataaagcacc tatgattatt
     3121 taaaaatata agttataata cattcaaaaa tatttttgaa tgaggtgtat tatgattcaa
     3181 acggttgttg ctgctgctgt tctttatatt gctacagcag ttgatttatt agtaatttta
     3241 ttaatatttt ttgctagagc aaagactaga aaagaatata gagatattta tgttggtcaa
     3301 tatttagggt ctattatttt aatattagtt agtttgtttt tagcttttgt attaaattat
     3361 gttccagaaa agtggatatt aggtttattg ggtttaatac caatttatct tggaattaaa
     3421 gtggctattt atgatgattg tgaaggagaa aagagagcta aaaaagaatt gaatgaaaaa
     3481 ggattgtcta aattagttgg tacggttgca attgttacga tagcaagttg tggcgccgat
     3541 aatattggtt tatttgttcc gtattttgtg acattaagtg ttactaattt attacttact
     3601 ctgtttgtct ttttaatttt aattttcttc ttggtgttta ctgcacaaaa attagctaat
     3661 atcccaggaa ttggagaaat tgttgagaaa tttagtcgtt ggattatggc tatcatttat
     3721 atagctttag gtttatttat tattattgaa aatgacacta ttcaaacaat tttaggattt
     3781 atattttaat ttagggtgtg attttatatg agttatgaaa atacttgtga tgtgatctgt
     3841 gtacatgagg ataaagttaa caatgcttta agttttttag aagatgataa atctaagaaa
     3901 ttacttaaca ttttagaaaa aatttgtgat gagaagaaat tgaaaatcat attatctttg
     3961 attaaagaag atgagttgtg tgtttgtgat atttctttga tattgaaaat gagtgttgct
     4021 tcaacttcac atcatttaag gcttttatat aaaaatgagg tacttgattt ttataaagat
     4081 ggaaagatgg catattattt tattaaagac gatgaaataa gagagttttt ctctaaaaat
     4141 catgagggtt tttgaaacga gtgaaacgag tttcttcttg tcttgatact atatagaaat
     4201 aactcgattt tatatataca gctgtaactg ttgatattac agcgtttaaa cgtgttttgt
     4261 gcgtgaaagg aaaatttgac aataaaaccc cagttatatt attaaggtgt cgaatcttaa
     4321 ataatactgg gggtcttttt atatgcaata taatactact agaagtataa ccgaaaatca
     4381 agataataaa acgttaaaag atatgacgaa aagtgggaaa caacgcccat ggagagaaaa
     4441 gaaaatagat aatgtaagct atgcagatat actagaaatt ttaaaaatca aaaaggcttt
     4501 taatgtaaaa caatgtggta atattttaga atttaagcca actgatgaag gttatttgaa
     4561 gttacataag acatggtttt gtaaatcaaa attatgtccg gtttgtaatt ggagacgtgc
     4621 tatgaaaaat agttatcaag ctcaaaaagt gattgaagaa gtaattaagg aaaagccaaa
     4681 agcacgttgg ttgtttttaa cactttcaac aaaaaatgcg atagatggag atactttaga
     4741 acaaagtttg aagcatctaa ctaaagcatt tgataggttg agtagatata aaaaggttaa
     4801 acaaaatctt gttggattta tgcgttcaac agaagttacc gttaataaaa atgacggtag
     4861 ttataatcag catatgcacg ttttgttatg tgttgaaaat gcatatttta gaaaaaaaga
     4921 gaattatata actcaagaag aatgggttaa tttatggcaa agagcattgc aagttgatta
     4981 tcgacctgtt gctaatatta aagcgatcaa accaaataaa aaaggcgata aagatattga
     5041 atctgcaatc aaagagacct caaaatattc ggttaaatca tctgattttt taactgatga
     5101 tgatgaaaaa aatcaagaaa ttgtaagtga tttagaaaaa ggtttgtatc gaaagcgtat
     5161 gttaagttat ggtggattgc tgaaacaaaa gcataaaatt ttaaacttag acgatgctga
     5221 agatggaaat ttgattaata caagtgatga agataaaaca acagatgaag aagaaaaggc
     5281 acattcgatt acggcaattt ggaattttga aaagcaaaat tattatttaa ggcattagtg
     5341 ataactgatg tcttttttta ttactttttt gtaaaaaagt gctgtcttat ttttgtgaca
     5401 aattctgtat gtagtgtcac aaaactgtga caaacgcaat atattgtgtc acaaaagtgt
     5461 gacatttcgt ctttttatgc ccccatgcaa aaagatcgac gaagtcttga aatatctggc
     5521 tttgccagat acctcatcta tagatggggt catattttcc ttatgctctt acggagttct
     5581 tagagaaaaa ttgaaatttc tcgatttttg ataaaaacgc cctgcaggaa tttagaaaaa
     5641 catggggaag ttttaaagaa ttttatgctc atttttaatt tgcatgtaaa tgggcagtgt
     5701 ctaaaaaact cgacactggt tttactcgaa ttttagtttg tgaaattaag atatatttat
     5761 ttggctcata tttgcgtttt aaaagtttat gtaggttttt aggtataaaa ctatatgatt
     5821 tacccataaa tctttaaaat gacctcttaa aattcaaaat aaaggcattt aaaaattaac
     5881 aaaataaaaa agctactagc aaaaaactag tagcttttgt cttgatgtag tattaatttt
     5941 tatatctgcg ccacaacgcc gatttcttaa aacgaatata aaaaatcgac gaaggtcgat
     6001 tatggttttt gcacgcgttc ttttagaacg cataagtgcg cccttacggg atttaactag
     6061 attataacga cgaaaaacag acctgtaaag caataacaat taggtctacc aggtagataa
     6121 agtgtacaaa gtagaaccga aaaagttatt tattttgaag atttttcgta gatataattt
     6181 gctaataaac ttcctaaaac tgaataaaga aaaatagtta aactcatgta atcactccat
     6241 aattctgaag tgtctccatg tctacgcata gacacgcatt tatgccgaaa atttattgtg
     6301 cgttgagaag aacccttaac taaacttgca gacgaatgtc ggcatagcgt gagctattaa
     6361 gccgaccatt cgacaagttt tgggattgtt aagggttccg aggctcaacg tcaataaagc
     6421 aattggaata aagcacctat gattatttaa aaatataagt tataatacat tcaaaaaata
     6481 ttttga
//
