LOCUS       NZ_CP113014             6859 bp    DNA     linear   CON 14-JAN-2024
DEFINITION  Staphylococcus aureus strain Zed plasmid unnamed3.
ACCESSION   NZ_CP113014
VERSION     NZ_CP113014.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31523632
            Assembly: GCF_026625265.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 6859)
  AUTHORS   Huang,Y.-T. and Liu,P.-Y.
  TITLE     Whole genome sequencing of methicillin-resistant Staphylococcus
            aureus
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6859)
  AUTHORS   Huang,Y.-T. and Liu,P.-Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-OCT-2022) Computer Science and Information
            Engineering, National Chung Cheng University, No.168, Sec. 1,
            University Rd., Min-Hsiung Township, Chia-yi County 621, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: flye v. 2.8.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 180x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/14/2024 02:53:22
            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)                     :: 3,154
            CDSs (total)                      :: 3,074
            Genes (coding)                    :: 2,965
            CDSs (with protein)               :: 2,965
            Genes (RNA)                       :: 80
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 62 of 109
            Pseudo Genes (incomplete)         :: 47 of 109
            Pseudo Genes (internal stop)      :: 21 of 109
            Pseudo Genes (multiple problems)  :: 20 of 109
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP113014.1.
            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..6859
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="Zed"
                     /isolation_source="environmental"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed3"
                     /geo_loc_name="Taiwan"
                     /lat_lon="24.23321 N 120.9417 E"
                     /collection_date="2022-06-01"
                     /collected_by="Po-Yu Liu"
     gene            <1..109
                     /locus_tag="OS078_RS00140"
                     /pseudo=""
     CDS             <1..109
                     /locus_tag="OS078_RS00140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001105942.1"
                     /note="frameshifted; incomplete; too short partial abutting
                     assembly gap; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=3
                     /transl_table=11
                     /product="IS6 family transposase"
                     /name="IS6 family transposase"
     gene            complement(475..821)
                     /locus_tag="OS078_RS00145"
                     /pseudo=""
     CDS             complement(475..821)
                     /locus_tag="OS078_RS00145"
                     /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="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="metalloregulator ArsR/SmtB family transcription
                     factor"
                     /name="metalloregulator ArsR/SmtB family transcription
                     factor"
     gene            complement(840..1456)
                     /gene="cadD"
                     /locus_tag="OS078_RS00150"
                     /pseudo=""
     CDS             complement(840..1456)
                     /gene="cadD"
                     /locus_tag="OS078_RS00150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017465246.1"
                     /note="frameshifted; 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            complement(1637..1759)
                     /locus_tag="OS078_RS00155"
     CDS             complement(1637..1759)
                     /locus_tag="OS078_RS00155"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000466482.1"
                     /translation="MFFYEDDDFDEMEEKYDYHEDKKIDDAFMPRKFIDVEKNP"
                     /name="hypothetical protein"
     gene            complement(1840..2028)
                     /locus_tag="OS078_RS00160"
     CDS             complement(1840..2028)
                     /locus_tag="OS078_RS00160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001030803.1"
                     /translation="MNKDTMLDKGYVIATILNVFFLLGLIFISHLENLYILIPYVILMG
                     INAIYLVVKVMNFKKNN"
                     /name="hypothetical protein"
     gene            complement(2606..2752)
                     /locus_tag="OS078_RS00165"
     CDS             complement(2606..2752)
                     /locus_tag="OS078_RS00165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001092934.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001092935.1"
                     /translation="MNTKILTGMTGSSLERKINNFINDNQIEVIDIKFSSSVFYFGVMI
                     IYK"
                     /name="hypothetical protein"
     gene            complement(2757..>3056)
                     /locus_tag="OS078_RS00170"
                     /pseudo=""
     CDS             complement(2757..>3056)
                     /locus_tag="OS078_RS00170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001568503.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="frameshifted; 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="protein rep"
                     /name="protein rep"
     gene            complement(3076..4019)
                     /locus_tag="OS078_RS00175"
                     /pseudo=""
     CDS             complement(3076..4019)
                     /locus_tag="OS078_RS00175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001829877.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiator protein A"
                     /name="replication initiator protein A"
     gene            4462..5232
                     /locus_tag="OS078_RS00180"
     CDS             4462..5232
                     /locus_tag="OS078_RS00180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001813127.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="WP_000848988.1"
                     /translation="MKTIKMVADELNVTKQTIVNNAKNLNISFKKENGINYINDNDCLK
                     IIEKITKKERTMQNKESIKKERFNENTAEFEKHIYNNSNGFESLKTKVNELEKQIEIFE
                     TRAKNDEKYIENLTKQLDQQNSNVNTLNKLLENQQILALESNKKIQKLENQLEEERQLN
                     YSFDTATNDRQSINPQEATFTEEYQNSNQQQKKIQPIEAELNHKGITKAKKDDSSNEDV
                     LKRDDKLSEEIESGPEDREVETPKKGFWSRLFGS"
                     /name="DUF536 domain-containing protein"
     gene            complement(5546..6106)
                     /locus_tag="OS078_RS00185"
     CDS             complement(5546..6106)
                     /locus_tag="OS078_RS00185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001077893.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001077893.1"
                     /translation="MNRADIFKIFDVELNITIFLGALVATFIYFISYMNNVNELITLCL
                     TLAFPAYLLKISRSFEVILLEEKIKNSKIKICDKDRIEREILVKKNLIDELLFPNRVIK
                     KYTLTILIYSIGIIILLLLCNMLSYGIGENVNFIWRLLACYVTSVTVIIVALIIMIMIF
                     DLIIGLLLNFQIFLKNKKYDDFL"
                     /name="hypothetical protein"
     gene            complement(6314..>6859)
                     /locus_tag="OS078_RS00190"
                     /pseudo=""
     CDS             complement(6314..>6859)
                     /locus_tag="OS078_RS00190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000622778.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="QacA/B family quaternary ammonium compound efflux
                     MFS transporter"
                     /name="QacA/B family quaternary ammonium compound efflux
                     MFS transporter"
     ARG             complement(6315..6859)
                     /name="qacA"
                     /gene="qacA"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.45"
                     /coverage="35.21"
     Typing          complement(2768..2946)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.222"
                     /coverage="95.0"
                     /evalue="3.73e-65"
     Typing          complement(3077..4019)
                     /name="rep_cluster_1215"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.365"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatacacagg cattgaatgt atttatggac tatataaaag aaccgcagat ctcttcagat
       61 ctacgggttt tcgccatgcc gtgtaattag catcatgcta gctagttaat acaaagtatt
      121 actttaaaca taaggttaga cacttatttt ttaactttgc aacagaacct tacattatct
      181 attttctttt ctctccatgg gcgttgtttt ccacttttcg tcatatcttt taacgtttta
      241 ttatcttgat tttcggttat acttctagta gtattatatt gcatataaaa agaactccag
      301 tattgattta gattagacac cttaatcata ttactggagt ttttttatgt caaattttat
      361 tttccccaag caaaacagta tgaaacgccg tcatatcaac gcttcaaaag gattttagaa
      421 aagaacgtta tttctatata gtatcaagac aagaagaaac tcgtttcact cgtttcaaaa
      481 accctcatga tttttagaga aaaacctctt attccatcgt ctttaataaa ataatatgcc
      541 atcttttcca tctttataaa aatcaagtac ctcattttta tataaaagcc ttaaatgatg
      601 tgaagttgaa gcaacactca ttttcaatat caaagaaata tcacaaacac acaactcatc
      661 ttctttaatc aaagataata tgattttcaa tttcttctca tcacaaattt tttctaaaat
      721 gttaagtaat ttcttagatt tatcatcttc taaaaactta aagcattgtt aactttatcc
      781 tcatgtacac agatcacatc acaagtattt tcataactca tataaaatca caccctaaat
      841 taaaatataa atcctaaaat tgtttgaata gtgtcatttt caataataat aaataaacct
      901 aaagctatat aaataatagc cataatccaa cgactaaatt tctcaacaat ttctccaatt
      961 cctgggatat tagctaattt ttgtgcagta aacaccaaga agaaaattaa aattaaaaag
     1021 acaaacagag taagtaataa attagtaaca cttaatgtca caaaatacgg aacaaataaa
     1081 ccaatattat cggcgccaca acttgctatc gtaacaattg caaccgtacc aactaattta
     1141 gacaatcctt tttcattcag ttctttttta gctctctttt ctccttcaca atcacataaa
     1201 tagccacttt aattccaaga taaattggta ttaaacccaa taaacctaat atccacttct
     1261 ctgaaacata atttaataca aaagctaaaa acaaactaac taatattaaa ataatagacc
     1321 ctaaatattg accaatataa atatctctat attctttttt agtctttgct ctagcaaaaa
     1381 atattaataa aattactaat aaatcaaatg ctgtagcaat ataaagaata gcagcagtga
     1441 caaccgtttg aatcatacat acacctcatt caaaaatatt tttgaatgta ttataactaa
     1501 tatttttaaa taatcatagg tgctttattc caattgcttt attgacgttg agcctcggaa
     1561 cccctaacaa tcccaaaact tgtcgaatgg tcggcttaat agctcacgct atgccgacat
     1621 tcgtcttcaa gtttagttaa gggttcttct caacatcaat aaattttctc ggcataaatg
     1681 cgtcgtctat ttttttatct tcatgataat catatttttc ttccatctcg tcaaaatcat
     1741 catcttcata gaaaaacaaa aagtaagcaa caacaccaat aggaataaaa aatagtgtga
     1801 aaacaagaag aaactcgttt caaaatcccc tcaaatattc taattattct ttttgaaatt
     1861 cataacttta acaaccaaat aaatagcatt tattcccatc aaaataacat acggaattaa
     1921 tatatataaa ttttccaaat gagatataaa aattaatcca agtaaaaaga aaacatttaa
     1981 aatagttgct ataacgtaac ctttatctaa cattgtgtct ttattcaaaa taaaaactcc
     2041 ttttaaaaaa aaactttatc acaagactta ctcaaattat aaataccttt attttgaatt
     2101 ttaagggggt attttaaaga tttaggggta aatcatatag ttttctatct aaaacctata
     2161 taatctctta aaacgcaaat atgaaccaaa tacatatatg ctattttcaa aaacaaaatt
     2221 ttaaataaaa ccaatgacta tttttttaaa cactgcccat ttacatgcaa attaaaagtt
     2281 agcataaaat cctttaaaac ttccccccat gtttttctaa attcctgcaa gacatttttt
     2341 atcaaaatcg agaattttta ttttttctct aagaacccgt aactccgtaa gagcataagg
     2401 gaaatttgac cccatgtata catggggtat ctggcaaagc cagacaattc aaagcttcaa
     2461 caatattttt atgtggggtc ataaaaagct tatgtcacac ttttgtgaca caatatattg
     2521 catttgtcac aaaaataagc cagtactttt ttataaaaac agtaaaaaaa gacatcagtc
     2581 atcactaatg tcttaaactc tttaattatt tataaataat cattacccca aaataaaata
     2641 cagaacttga aaacttaata tcaatgactt cgatttggtt atcattaata aaattattga
     2701 tttttcgttc taaagaactt ccagtcattc cagttaaaat tttagtgttc atatttttaa
     2761 ctccttaaat tttttaaata ataattttgc tttttcgaaa ttccaaattg ctgtaatcga
     2821 atgtgctttt tcttcttcgt ctgtcgtttt atcttcatca cttgtattaa tcaaattacc
     2881 atcttcggca tcgtctaagt ttaaaatttt atgcttttct ttaagtaatc caccataact
     2941 taacatacgt tttcgataca aaccttttct agatcactta aaatttcttg atttttttcg
     3001 tcgtcatcag ttaaaaagtc agatgattta acggaatatt ttgatgtctc tttgattgtt
     3061 ataaaatcat ttgaattatt gattaaagat attatattgt ttcatgtttt tacggcgcat
     3121 ataaagggca tgtgtttctt caagttcagc tttaatggat tgcattaaat aaccttgcat
     3181 agcttcaacg gtttcattct tttgtagcaa catcgcttta aaacgtttca atacacttac
     3241 aatttcaaac tcaacatctt ctaaacgata ataagtatca tgtgaagtat taaatgactt
     3301 tttccctttg agtaatacgc ttttaataat ccgaatttct ctaatttcaa atttacttaa
     3361 atagtcttga agttgttgtg gcaattcttc gagtacttgg aacttaaggg cgtcattatt
     3421 aaattcagtt ttttgatgat ttgtatgatt cgaatgatga ttattattta ttaaagtatt
     3481 agatataata tcattcatat catacgtatc attatcccca ttttctatat aattagtatt
     3541 atttaactca gtatcattag actgtgaatt tggaagttct tgaccactta aattacagtt
     3601 ctagaacttc caaattcatt gttctggaac tgtgaatttg gaagttcctt ggtaagactt
     3661 gcttcaatat cataatttgg ttttaataaa tataatctat ttggtttatt aaggccaaca
     3721 cgctcttgag ttaataaatt aaaatttact aactcttttt tcaattttat gattttttgt
     3781 tctccataac ctaagtactc gcacaaatgt ttattactga aaataaagta aatgttatta
     3841 tttctatcta cccattcatt ttggatggat aattcgaaac gatcttttaa taatgcatac
     3901 ataattttgg cttctgctga cattttctta aaatatgcat cttcgaacaa atatttagga
     3961 agttggtaaa atctttcagt ttttacttgt gataaattgt atttctcaaa attgggcata
     4021 ataaaaacct catttccact ttttggatag aggtaataaa acaattttta cgtaggttat
     4081 atgttttgta cttgcactta tatgattaga tatatataat acaagtatca aaaaattata
     4141 taaacagacg aatgcgaatc gttttattac cgagagtcga tgctacgcca atagtatcga
     4201 ctcttttaat attcacaaag taatattaac acttttaaga ttgtatataa agctttttaa
     4261 gtttagttga aagaacattg taactttaaa atgataaaat tcaccacttt agtacctaat
     4321 tagtcaccta tagaaggttt taacggctaa ttaggtacta aagtagtgaa ataggtagta
     4381 aatttagatg tcgaaagatg aaaaaatatt tgttaggtgg taaaatttag gtaccaattt
     4441 atgtacctaa ggatgaatgt tatgaaaact attaaaatgg ttgctgatga attgaatgta
     4501 actaaacaaa ctattgttaa taatgctaaa aacttaaata tatcttttaa aaaagaaaat
     4561 ggaattaatt atattaatga taatgattgt ttaaaaatta tagaaaagat cactaagaaa
     4621 gaaaggacaa tgcaaaataa agaatcaata aaaaaagaaa gatttaatga aaatactgca
     4681 gagtttgaaa agcatatata caataattca aatggttttg agtcattaaa aacaaaagta
     4741 aatgaattag aaaagcaaat agaaatcttt gaaactagag ctaaaaatga cgaaaaatat
     4801 attgagaatt taactaaaca actagatcaa caaaatagca atgttaatac attaaataaa
     4861 ctgttggaga atcaacaaat attagcttta gaaagtaata aaaagattca aaaactagaa
     4921 aaccaattag aagaagaaag acagcttaat tactcttttg atacagcgac taatgataga
     4981 caaagcatta atccgcaaga agcaactttt actgaagaat atcaaaatag caaccaacaa
     5041 caaaagaaaa tacaaccaat agaagcagaa ttaaatcata agggcataac taaagcgaaa
     5101 aaggatgaca gttcaaacga agacgtatta aagagagatg ataaactatc tgaagaaata
     5161 gagagtggac ctgaggacag ggaagtagaa acacctaaaa aggggttttg gagtcgtttg
     5221 tttggtagct aaaatattaa ttaggcacta aaagtttata acttttagtg ccttttatat
     5281 agtgagaact tctggtaatc atcagttatg ttaaactcta acaaaaacta aattatcaga
     5341 agaattatct agggtattaa acataggtaa atcaattttc tatcgccaat agtataaaca
     5401 tcatccatat taatctgaag atagctacat aatttttaac agcatagcct ttatttgtat
     5461 aaggcgccat aaactctatt aaatatggtt tgttttgagg tttctatgtt taatcattta
     5521 atttttcatt atataaatcg aataattata aaaagtcatc atacttttta ttttttaaaa
     5581 atatttgaaa atttaatagt aatccaatta taagatcaaa tatcattatc attataatca
     5641 aggcaactat aatcactgtg acactcgtta cataacaagc tagtaatctc cagataaaat
     5701 tgacattttc accaattcca taacttaaca tattacaaag tagtaaaaga ataataatac
     5761 ctatactgta aattaaaatt gtcagtgtat attttttaat aactctatta ggaaacaata
     5821 gttcatctat taggttcttt ttcaccagta tctctcgttc aattctatct ttgtcacaga
     5881 ttttgatttt actatttttt attttttcct ctaataaaat aacctcgaac gatctgctaa
     5941 tttttaataa atatgcagga aaagctaatg ttaagcataa tgtaattaat tcatttacat
     6001 tgttcatgta acttataaaa tagatgaaag ttgctactag tgctcctaaa aatatagtta
     6061 tattaagttc tacatcaaat attttaaaaa tatctgctct attcatcagt taatcatcct
     6121 ttcaaggttt attaatacta ataaattatt agatataggt atatcatatt attaatttaa
     6181 gaaattgtct tttataattt tattttctta ataaaaaaaa gtagaaccat ttaaaattaa
     6241 tggttctact ttttaactat tactaatttt aaaaataaac taatctacaa tatctaaaaa
     6301 tatatgttta gtactatttt tgtttagtta tatcaagtga tttgggaatt aacaaataga
     6361 caactattga aatgataatc atgataatcc cacctactaa agcagttgct acaaaagcat
     6421 cattaaatga tgttacagcc tcgtttgcaa gctgttttat ccccgtagct ttagctactt
     6481 cgacagcgcc cactacagat tcttcagcta catgagctaa atctccaact ataccttttg
     6541 atgaaaaaga tgaaatatct aaaaatacac gataaagcat agaagatagg ctaccaagta
     6601 ctgctacacc aaaaacattt ccaaggtcat acatagactc ttcaacagca gctgcattac
     6661 ctgcttttga tgtaggtgtt tctaacatta ttagagcaga tgcaactgct agtgaagcca
     6721 taccagctcc aactaaaatt aatgctaaag ccattataga atatgataat ggatgaccaa
     6781 agaaatacat aataaacatg ccaatggctg caattccaat tccggaaggt aacactattt
     6841 tcggtccaaa tcgcgccgc
//
