LOCUS       NZ_CP113013             6869 bp    DNA     linear   CON 14-JAN-2024
DEFINITION  Staphylococcus aureus strain Zed plasmid unnamed2.
ACCESSION   NZ_CP113013
VERSION     NZ_CP113013.1
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 6869)
  AUTHORS   Huang,Y.-T. and Liu,P.-Y.
  TITLE     Whole genome sequencing of methicillin-resistant Staphylococcus
            aureus
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6869)
  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
            CP113013.1.
            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..6869
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="Zed"
                     /isolation_source="environmental"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed2"
                     /geo_loc_name="Taiwan"
                     /lat_lon="24.23321 N 120.9417 E"
                     /collection_date="2022-06-01"
                     /collected_by="Po-Yu Liu"
     gene            <1..547
                     /locus_tag="OS078_RS00085"
                     /pseudo=""
     CDS             <1..547
                     /locus_tag="OS078_RS00085"
                     /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=2
                     /transl_table=11
                     /product="QacA/B family quaternary ammonium compound efflux
                     MFS transporter"
                     /name="QacA/B family quaternary ammonium compound efflux
                     MFS transporter"
     gene            752..1312
                     /locus_tag="OS078_RS00090"
     CDS             752..1312
                     /locus_tag="OS078_RS00090"
                     /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(1628..2398)
                     /locus_tag="OS078_RS00095"
     CDS             complement(1628..2398)
                     /locus_tag="OS078_RS00095"
                     /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            2842..3788
                     /locus_tag="OS078_RS00100"
                     /pseudo=""
     CDS             2842..3788
                     /locus_tag="OS078_RS00100"
                     /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            3918..4106
                     /locus_tag="OS078_RS00105"
     CDS             3918..4106
                     /locus_tag="OS078_RS00105"
                     /inference="COORDINATES: protein motif:HMM:NF013603.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001559000.1"
                     /translation="MLSYGGLLKEKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSIT
                     AIWNFEKQNYYLKNLRS"
                     /name="hypothetical protein"
     gene            4111..4257
                     /locus_tag="OS078_RS00110"
     CDS             4111..4257
                     /locus_tag="OS078_RS00110"
                     /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            4841..5029
                     /locus_tag="OS078_RS00115"
     CDS             4841..5029
                     /locus_tag="OS078_RS00115"
                     /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            5110..5232
                     /locus_tag="OS078_RS00120"
     CDS             5110..5232
                     /locus_tag="OS078_RS00120"
                     /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            5413..6029
                     /gene="cadD"
                     /locus_tag="OS078_RS00125"
                     /pseudo=""
     CDS             5413..6029
                     /gene="cadD"
                     /locus_tag="OS078_RS00125"
                     /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            6048..6395
                     /locus_tag="OS078_RS00130"
     CDS             6048..6395
                     /locus_tag="OS078_RS00130"
                     /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_000119692.1"
                     /translation="MSYENTCDVICVHEDKVNNALSFLEDDKSKKLLNILEKICDEKKL
                     KIILSLIKEDELCVCDISLILKMSVASTSHHLRLLYKNEVLDFYKDGKMAYYFIKDDGI
                     REFFSKNHEGF"
                     /name="metalloregulator ArsR/SmtB family transcription
                     factor"
     gene            complement(6761..>6869)
                     /locus_tag="OS078_RS00135"
                     /pseudo=""
     CDS             complement(6761..>6869)
                     /locus_tag="OS078_RS00135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001105942.1"
                     /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=2
                     /transl_table=11
                     /product="IS6 family transposase"
                     /name="IS6 family transposase"
     ARG             3..547
                     /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          2843..3788
                     /name="rep_cluster_1215"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.366"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3919..4096
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.179"
                     /coverage="95.0"
                     /evalue="3.73e-65"
ORIGIN
        1 agcggcgcga tttggaccga aaatagtgtt accttccgga attggaattg cagccattgg
       61 catgtttatt atgtatttct ttggtcatcc attatcatat tctataatgg ctttagcatt
      121 aattttagtt ggagctggta tggcttcact agcagttgca tctgctctaa taatgttaga
      181 aacacctaca tcaaaagcag gtaatgcagc tgctgttgaa gagtctatgt atgaccttgg
      241 aaatgttttt ggtgtagcag tacttggtag cctatcttct atgctttatc gtgtattttt
      301 agatatttca tctttttcat caaaaggtat agttggagat ttagctcatg tagctgaaga
      361 atctgtagtg ggcgctgtcg aagtagctaa agctacgggg ataaaacagc ttgcaaacga
      421 ggctgtaaca tcatttaatg atgcttttgt agcaactgct ttagtaggtg ggattatcat
      481 gattatcatt tcaatagttg tctatttgtt aattcccaaa tcacttgata taactaaaca
      541 aaaatagtac taaacatata tttttagata ttgtagatta gtttattttt aaaattagta
      601 atagttaaaa agtagaacca ttaattttaa atggttctac ttttttatta ttaagtaaaa
      661 ttataaaaga caatttctta aattaataat atgatatacc tatatctaat aatttattag
      721 tattaataaa ccttgaaagg atgattaact gatgaataga gcagatattt ttaaaatatt
      781 tgatgtagaa cttaatataa ctatattttt aggagcacta gtagcaactt tcatctattt
      841 tataagttac atgaacaatg taaatgaatt aattacatta tgcttaacat tagcttttcc
      901 tgcatattta ttaaaaatta gcagatcgtt cgaggttatt ttattagagg aaaaaataaa
      961 aaatagtaaa atcaaaatct gtgacaaaga tagaattgaa cgagagatac tggtgaaaaa
     1021 gaacctaata gatgaactat tgtttcctaa tagagttatt aaaaaatata cactgacaat
     1081 tttaatttac agtataggta ttattattct tttactactt tgtaatatgt taagttatgg
     1141 aattggtgaa aatgtcaatt ttatctggag attactagct tgttatgtaa cgagtgtcac
     1201 agtgattata gttgccttga ttataatgat aatgatattt gatcttataa ttggattact
     1261 attaaatttt caaatatttt taaaaaataa aaagtatgat gactttttat aattattcga
     1321 tttatataat gaaaaattaa atgattaaac atagaaacct caaaacaaac catatttaat
     1381 agagtttatg gcgccttata caaataaagg ctatgctgtt aaagaattat gtagctatct
     1441 tcagattaat atggatgatg tttatactat tggcgataga aaattgattt acctatgttt
     1501 aataccctag ataattcttc tgataattta gtttttgtta gagtttaaca taactgatga
     1561 ttaccagaag ttctcactat ataaaaggca ctaaaagtta taaactttta gtgcctaatt
     1621 aattatttta gctaccaaac aaacgactcc aaaacccctt tttaggtgtt tctacttccc
     1681 tgtcctcagg tccactctct atttcttcag atagtttatc atctctcttt aatacgtctt
     1741 cgtttgaact gtcatccttt ttcgctttag ttatgccctt atgatttaat tctgcttcta
     1801 ttggttgtat tttcttttgt tgttggttgc tattttgata ttcttcagta aaagttgctt
     1861 cttgcggatt aatgctttgt ctatcattag tcgctgtatc aaaagagtaa ttaagctgtc
     1921 tttcttcttc taattggttt tctagttttt gaatcttttt attactttct aaagctaata
     1981 tttgttgatt ctccaacagt ttatttaatg tattaacatt gctattttgt tgatctagtt
     2041 gtttagttaa attctcaata tatttttcgt catttttagc tctagtttca aagatttcta
     2101 tttgcttttc taattcattt acttttgttt ttaatgactc aaaaccattt gaattattgt
     2161 atatatgctt ttcaaactct gcagtatttt cattaaatct ttcttttttt attgattctt
     2221 tattttgcat tgtcctttct ttcttagtga tcttttctat aatttttaaa caatcattat
     2281 cattaatata attaattcca ttttcttttt taaaagatat atttaagttt ttagcattat
     2341 taacaatagt ttgtttagtt acattcaatt catcagcaac cattttaata gttttcataa
     2401 cattcatcct taggtacata aattggtacc taaattttac cacctaacaa atattttttc
     2461 atctttcgac atctaaattt actacctatt tcactacttt agtacctaat tagccgttaa
     2521 aaccttctat aggtgactaa ttaggtacta aagtggtgaa tttttatcat tttaaagtta
     2581 caatgttctt tcaactaaac ttaaaaagct ttatatacaa tcttaaaagt gttaatatta
     2641 ctttgtgaat attaaaagag tcgatactat tggcgtagca tcgactctcg gtaataaaac
     2701 gattcgcatt cgtctgttta tataattttt tgatacttgt attatatata tctaatcata
     2761 taagtgcaag tacaaaacat ataacctacg taaaaattgt tttattacct ctatccaaaa
     2821 agtggaaatg aggtttttat tatgcccaat tttgagaaat acaatttatc acaagtaaaa
     2881 actgaaagat tttaccaact tcctaaatat ttgttcgaag atgcatattt taagaaaatg
     2941 tcagcagaag ccaaaattat gtatgcatta ttaaaagatc gtttcgaatt atccatccaa
     3001 aatgaatggg tagatagaaa taataacatt tactttattt tcagtaataa acatttgtgc
     3061 gagtacttag gttatggaga acaaaaaatc ataaaattga aaaaaagagt tagtaaattt
     3121 taatttatta actcaagagc gtgttggcct taataaacca aatagattat atttattaaa
     3181 accaaattat gatattgaag caagtcttac caaggaactt ccaaattcac agttccagaa
     3241 caatgaattt ggaagttcta gaactgtgaa tttaagtggt caagaacttc caaattcaca
     3301 gtctaatgat actgagttaa ataatactaa ttatatagaa aatgaggata atgatacgta
     3361 tgatatgaat gatattatat ctaatacttt aataaataat aatcatcatt cgaatcatac
     3421 aaatcatcaa aaaactgaat ttaataatga cgcccttaag ttccaagtac tcgaagaatt
     3481 gccacaacaa cttcaagact atttaagtaa atttgaaatt agagaaattc ggattattaa
     3541 aagcgtatta ctcaaaggga aaaaagtcat ttaatacttc acatgatact tattatcgtt
     3601 tagaagatgt tgagtttgaa attgtaagtg tattgaaacg ttttaaagcg atgttgctac
     3661 aaaagaatga aaccgttgaa gctatgcaag gttatttaat gcaatccatt aaagctgaac
     3721 ttgaagaaac acatgccctt tatatgcgcc gtaaaaacat gaaacaatat aatatcttta
     3781 atcaataatt caaatgattt tataacaatc aaagagacat caaaatattc cgttaaatca
     3841 tctgactttt taactgatga cgacgaaaaa aatcaagaaa ttttaagtga tctagaaaag
     3901 gtttgtatcg aaaacgtatg ttaagttatg gtggattact taaagaaaag cataaaattt
     3961 taaacttaga cgatgccgaa gatggtaatt tgattaatac aagtgatgaa gataaaacga
     4021 cagacgaaga agaaaaagca cattcgatta cagcaatttg gaatttcgaa aagcaaaatt
     4081 attatttaaa aaatttaagg agttaaaaat atgaacacta aaattttaac tggaatgact
     4141 ggaagttctt tagaacgaaa aatcaataat tttattaatg ataaccaaat cgaagtcatt
     4201 gatattaagt tttcaagttc tgtattttat tttggggtaa tgattattta taaataatta
     4261 aagagtttaa gacattagtg atgactgatg tcttttttta ctgttttttt ataaaaaagt
     4321 actggcttat ttttgtgaca aatgcaatat attgtgtcac aaaagtgtga cacttaagct
     4381 ttttatgacc ccacataaaa atattgttga agctttgaat tgtctggctt tgccagatac
     4441 cccatgtata catggggtca aatttccctt atgctcttac ggagttacgg agttcttaga
     4501 gaaaaaataa aaattctcga ttttgataaa aaatgtcttg caggaattta gaaaaacatg
     4561 gggggaagtt ttaaaggatt ttatgctaac ttttaatttg catgtaaatg ggcagtgttt
     4621 aaaaaaaata gtcattggtt ttatttaaaa ttttgttttt gaaaatagca tatatgtatt
     4681 tggttcatat ttgcgtttta agagattatg taggttttag ataggaaaac tatatgattt
     4741 acccctaaat ctttaaaata ccccccttaa aattcaaaat aaaggtattt ataatttgag
     4801 taagtcttgt gataaagttt tttaaaaagg agtttttatt ttgaataaag acacaatgtt
     4861 agataaaggt tacgttatag caactatttt aaatgttttc tttttacttg gattaatttt
     4921 tatatctcat ttggaaaatt tatatatatt aattccgtat gttattttga tgggaataaa
     4981 tgctatttat ttggttgtta aagttatgaa tttcaaaaag aataattaga atatttgagg
     5041 ggattttgaa acgagtttct tcttgttttc acactatttt ttattcctat tggtgttgtt
     5101 gcttactttt tgtttttcta tgaagatgat gattttgacg agatggaaga aaaatatgat
     5161 tatcatgaag ataaaaaaat agacgacgca tttatgccga gaaaatttat tgatgttgag
     5221 aagaaccctt aactaaactt gaagacgaat gtcggcatag cgtgagctat taagccgacc
     5281 attcgacaag ttttgggatt gttaggggtt ccgaggctca acgtcaataa agcaattgga
     5341 ataaagcacc tatgattatt taaaaatatt agttataata cattcaaaaa tatttttgaa
     5401 tgaggtgtat gtatgattca aacggttgtc actgctgcta ttctttatat tgctacagca
     5461 tttgatttat tagtaatttt attaatattt tttgctagag caaagactaa aaaagaatat
     5521 agagatattt atattggtca atatttaggg tctattattt taatattagt tagtttgttt
     5581 ttagcttttg tattaaatta tgtttcagag aagtggatat taggtttatt gggtttaata
     5641 ccaatttatc ttggaattaa agtggctatt tatgtgattg tgaaggagaa aagagagcta
     5701 aaaaagaact gaatgaaaaa ggattgtcta aattagttgg tacggttgca attgttacga
     5761 tagcaagttg tggcgccgat aatattggtt tatttgttcc gtattttgtg acattaagtg
     5821 ttactaattt attacttact ctgtttgtct ttttaatttt aattttcttc ttggtgttta
     5881 ctgcacaaaa attagctaat atcccaggaa ttggagaaat tgttgagaaa tttagtcgtt
     5941 ggattatggc tattatttat atagctttag gtttatttat tattattgaa aatgacacta
     6001 ttcaaacaat tttaggattt atattttaat ttagggtgtg attttatatg agttatgaaa
     6061 atacttgtga tgtgatctgt gtacatgagg ataaagttaa caatgcttta agttttttag
     6121 aagatgataa atctaagaaa ttacttaaca ttttagaaaa aatttgtgat gagaagaaat
     6181 tgaaaatcat attatctttg attaaagaag atgagttgtg tgtttgtgat atttctttga
     6241 tattgaaaat gagtgttgct tcaacttcac atcatttaag gcttttatat aaaaatgagg
     6301 tacttgattt ttataaagat ggaaagatgg catattattt tattaaagac gatggaataa
     6361 gagagttttt ctctaaaaat catgagggtt tttgaaacga gtgaaacgag tttcttcttg
     6421 tcttgatact atatagaaat aacgttcttt tctaaaatcc ttttgaagcg ttgatatgac
     6481 ggcgtttcat actgttttgc ttggggaaaa taaaatttga cataaaaaaa ctccagtaat
     6541 atgattaagg tgtctaatct aaatcaatac tggagttctt tttatatgca atataatact
     6601 actagaagta taaccgaaaa tcaagataat aaaacgttaa aagatatgac gaaaagtgga
     6661 aaacaacgcc catggagaga aaagaaaata gataatgtaa ggttctgttg caaagttaaa
     6721 aaataagtgt ctaaccttat gtttaaagta atactttgta ttaactagct agcatgatgc
     6781 taattacacg gcatggcgaa aacccgtaga tctgaagaga tctgcggttc tttttatata
     6841 gtccataaat acattcaatg cctgtgtat
//
