LOCUS       NZ_CP096525             3971 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Staphylococcus aureus strain RIVM_M085090 plasmid pM085090_3,
            complete sequence.
ACCESSION   NZ_CP096525
VERSION     NZ_CP096525.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27760544
            Assembly: GCF_026546985.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3971)
  AUTHORS   Schouls,L.M., Veldman,K., Brouwer,M.S.M., Dierikx,C., Witteveen,S.,
            van Santen-Verheuvel,M., Hendrickx,A.P.A., Landman,F., Hengeveld,P.,
            Wullings,B., Rapallini,M., Wit,B. and van Duijkeren,E.
  CONSRTM   Dutch MRSA surveillance study group
  TITLE     cfr and fexA genes in methicillin-resistant Staphylococcus aureus
            from humans and livestock in the Netherlands
  JOURNAL   Commun Med (Lond) 2, 135 (2022)
   PUBMED   36317053
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3971)
  AUTHORS   Schouls,L.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-APR-2022) Infectious Diseases Research, Diagnostics
            and laboratory Surveillance, National Institute for Public Health
            and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven,
            Utrecht 3720 BA, Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v.0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 30x
            Sequencing Technology :: Illumina MiSeq and HiSeq 2500, Nanopore
            GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_026546985.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 04:58:40
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,797
            CDSs (total)                      :: 2,716
            Genes (coding)                    :: 2,624
            CDSs (with protein)               :: 2,624
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 92
            CDSs (without protein)            :: 92
            Pseudo Genes (ambiguous residues) :: 0 of 92
            Pseudo Genes (frameshifted)       :: 44 of 92
            Pseudo Genes (incomplete)         :: 42 of 92
            Pseudo Genes (internal stop)      :: 27 of 92
            Pseudo Genes (multiple problems)  :: 18 of 92
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096525.1.
            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..3971
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM_M085090"
                     /isolation_source="pig farm dust"
                     /host="Environment"
                     /db_xref="taxon:1280"
                     /plasmid="pM085090_3"
                     /geo_loc_name="Netherlands"
                     /lat_lon="52.13 N 5.29 E"
                     /collection_date="2019-06-01"
                     /collected_by="WBVR"
                     /genotype="GG0398 (CC398)"
     gene            1..162
                     /locus_tag="M1F52_RS13960"
                     /old_locus_tag="M1F52_13940"
     CDS             1..162
                     /locus_tag="M1F52_RS13960"
                     /old_locus_tag="M1F52_13940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019835937.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_169409336.1"
                     /translation="MNDKKQRKRLNITLPPELIEELEKVNKKYKINKSSQIETLITKYL
                     RKEYGDLG"
                     /name="hypothetical protein"
     gene            245..820
                     /locus_tag="M1F52_RS13965"
                     /old_locus_tag="M1F52_13945"
     CDS             245..820
                     /locus_tag="M1F52_RS13965"
                     /old_locus_tag="M1F52_13945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002486348.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_031863896.1"
                     /translation="MAKYTKSRTWGMVVYPESAPENWQELLSETFMQFAVSPLHDKDIN
                     PDGEIKKPHWHVILIWDGPVTQNAAMKIAEKVNAPQPVKLESVRGAYRYFTHMDNPEKY
                     QYDEKDIKLFNGFDISSYVSLTKEEKYEAIGKIMDIINENGITEYIDLLNILRVNDYNL
                     FKVACDNTILFTNVVRSLRHSEDKRKRF"
                     /name="replication protein"
     gene            1145..2779
                     /gene="mobV"
                     /locus_tag="M1F52_RS13970"
                     /old_locus_tag="M1F52_13950"
     CDS             1145..2779
                     /gene="mobV"
                     /locus_tag="M1F52_RS13970"
                     /old_locus_tag="M1F52_13950"
                     /inference="COORDINATES: protein motif:HMM:NF013258.4"
                     /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_119483344.1"
                     /translation="MSYSIIRVEKVKNSVNTTGIQKHVQRENNKYSNEDIQQELTQENY
                     DLVNEEPINFNDEIEKKIEERYTVNRAIRKDAVKHIDGIVTTDKNYFDDLTLEQTRDYF
                     NDSLDFIKDEYGEENILYATVHMDEATPHMHFGVVPITDDGRLSAKKMLGNKKAFTDFQ
                     NRYNEYMNQRGYNLERGKSKHITGAKHEEMNAYKQKTNYHKQEMERQQKEVESLKDEKQ
                     NIEKEMNEQITSSKAHIDDLQDKYKELGEMYEKDKERLEKPLNIQYEHEIKEEGGLFNK
                     QEVKTGNVVLKQEEFDELLEQSKSANRILDRYDDLNSGTEITELRNQIDEMNKDIDKLI
                     DSDKENKREKEQLRSKNKQLSNINQSLKTENKKQLEVINGVKDTFHNTMNAFEKVLGKD
                     RFKNCVLKVDKMLNNNQFFRNLVVGFDDKYKEIFTRNDKLNLAKENMYVSQKMDIKDMD
                     KQVIEAEFESMNGVFTKEVNVSDEKFMEYLNQPEKYMMVVPMSMDDEPLFMSIDDIDLD
                     KPLEFDKDLGIGDSQEIDIDLGLDLER"
                     /name="mobV"
     gene            3008..3277
                     /locus_tag="M1F52_RS13975"
                     /old_locus_tag="M1F52_13955"
     CDS             3008..3277
                     /locus_tag="M1F52_RS13975"
                     /old_locus_tag="M1F52_13955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002447832.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_031885230.1"
                     /translation="MVKIVPGYELDYFDWLVRQRLIKFPAMPIEGEWKQDSYGYDDIIF
                     ENEIEYQDLVIDTEKSYPEFDFYKMALESISLISLDDFHKKTKH"
                     /name="hypothetical protein"
     Typing          246..818
                     /name="rep_cluster_2340"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.456"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttgaacgata aaaaacagag aaaaagatta aatattacat tgccaccaga attaattgaa
       61 gagttagaaa aagttaataa aaaatataaa ataaacaagt ctagtcagat tgaaacgttg
      121 attactaaat acttaagaaa ggagtatggt gatttgggat aaaaaaaaga accttgcccc
      181 aacaagattc ttttgacgat gatgtcatga cctgacatgt tttgttaatc accaatataa
      241 tagcatggct aaatatacta aatcaagaac atggggaatg gttgtttacc ccgagtcagc
      301 gccagaaaat tggcaagaat tattatcaga gactttcatg caatttgcgg tttctccatt
      361 acatgataaa gatattaatc cagatggaga gataaaaaaa ccacattggc atgtgatttt
      421 aatatgggat ggtccagtta cgcaaaatgc agctatgaaa attgctgaaa aagttaatgc
      481 acctcaacct gtaaaattag aaagtgtaag gggtgcttat agatatttca cacatatgga
      541 taatccagaa aaatatcaat atgatgagaa agatataaaa ctttttaatg gtttcgatat
      601 atcatcgtat gtctcattga ccaaagagga aaaatatgag gctattggaa agattatgga
      661 tattattaat gaaaatggga ttactgaata tattgatttg ttaaatatac ttagagtgaa
      721 cgattataat ttgtttaagg ttgcttgtga taacacaatt ttattcacta atgttgttcg
      781 ttctttgaga cattcagaag ataagcgtaa gagattttga ttttatggaa gtgtcatttt
      841 gacacttcct tttttgcgta agcaaaaaca ggtttttgag tgaattaaat tttatacacg
      901 taagtgatca taaaatttat gaacggattt gcgcccactt ttttgggcgc atggttttga
      961 attttgggac tgatttattc agtccctttt tttgtgtttg cacaaaaaaa ctagccctct
     1021 gcaagagcat acggtttaat gactttatgg aacgaagtgg aataaagtct agtatgttat
     1081 actttatata ttaaagatac cccaaaatcc tagatagagg aataaatttt gcgaggtggt
     1141 taagatgagt tattccatta ttcgagttga aaaagttaaa aatagcgtga atacaactgg
     1201 aattcaaaaa catgttcaac gagagaataa taaatatagt aacgaagata tacagcaaga
     1261 attaacacaa gaaaattatg atttggtaaa tgaggaacca attaatttta atgacgaaat
     1321 agaaaagaaa attgaagaac gttatacggt taatcgagca atcagaaaag atgcagtaaa
     1381 acatatagac ggtattgtaa ctacagataa aaactatttt gatgatttaa cattagaaca
     1441 gacgagagac tattttaatg attctctaga ctttattaaa gatgaatatg gagaagagaa
     1501 tattttatat gcaacagttc acatggacga ggctacacca catatgcact ttggtgttgt
     1561 accgattact gacgacggta gattgtcagc aaagaagatg ttaggtaata aaaaagcttt
     1621 tacagatttc caaaatcgtt ataacgaata tatgaaccaa agaggttaca atttggaacg
     1681 tggaaaatct aagcatatta caggtgcaaa acatgaagaa atgaatgctt ataagcaaaa
     1741 aacaaattat cataaacaag aaatggaaag acaacaaaaa gaagttgaat cacttaaaga
     1801 tgaaaaacaa aatatagaaa aagaaatgaa tgaacaaatc acatcttcta aggctcatat
     1861 agacgatttg caggataaat ataaagagtt aggggaaatg tatgaaaaag ataaagaacg
     1921 cctagaaaag cctttaaata tccaatatga gcatgaaatt aaagaagaag gtggattgtt
     1981 taataagcaa gaagtaaaaa caggtaatgt tgtcttaaag caagaagaat ttgatgaatt
     2041 gctagaacaa tctaaatcag ctaatcgtat tttagatcgt tatgatgatt taaatagtgg
     2101 gactgagata actgaattaa gaaatcaaat tgatgaaatg aataaggata tagataaatt
     2161 aattgattct gataaagaaa ataaacgaga gaaagaacaa ttacgctcaa aaaataaaca
     2221 attaagcaat attaaccaat cattaaaaac tgagaataaa aaacaattgg aagtaattaa
     2281 tggggtcaaa gatacatttc ataacaccat gaatgctttt gaaaaggttt tgggtaaaga
     2341 tagatttaaa aattgtgtgt taaaagtgga taaaatgctt aataataatc aattctttag
     2401 aaatttagtt gtcggctttg atgataaata taaagaaata ttcacgcgta atgataagtt
     2461 gaatttggct aaagaaaata tgtatgtatc ccaaaaaatg gatattaaag atatggataa
     2521 acaagttata gaggcagaat ttgaatctat gaacggtgtg tttacaaaag aagttaatgt
     2581 aagtgatgaa aaatttatgg agtatttaaa tcaaccagag aaatatatga tggttgtacc
     2641 gatgagtatg gatgatgaac cgctttttat gtctattgat gatatagatt tggataaacc
     2701 attagaattt gataaagatt taggtatagg agattcacaa gaaatagaca tagatttagg
     2761 tttagactta gaacggtaaa atgcggaagt ttcatttttt aacttccttg tggcacaagg
     2821 gatagagcac gttttatgcc gagaaaactt attggttgga atgggctatg tgttagctaa
     2881 cttgattagc gtgttgggtg gggttgattt gggattaatc ccaatgaaac accaacacaa
     2941 caacacataa agccctgtag gttccaacca ataaggaaat tggaataaat attttaggag
     3001 gaatagaatg gtaaaaatag ttcctggata tgagttagat tattttgatt ggttagttag
     3061 acaaagactg ataaagtttc ctgcaatgcc tattgaaggg gaatggaaac aagattcgta
     3121 tggatatgat gatattattt tcgaaaacga gattgagtat caagatttag taattgatac
     3181 tgagaagagt tatcctgagt ttgattttta taaaatggca ttagaaagta tatctcttat
     3241 tagtttggac gattttcata aaaaaacaaa gcactgatcg aattaggatc agtgctttgt
     3301 taatagcata ttgcctcaac taacagagga atatagtgca tttaattgtt acgtttgcgc
     3361 actaacgcca aacgacagac aggcttatta ctagttagtt gaaacgccaa ccttccgtaa
     3421 acgtttctag tgctattcgt ttttaatttt tatatctgcc atgaatagct tagccgatta
     3481 ctacaatatg ctattagaat gttataacat aaaaaatcag tttaacaaag aagttttctt
     3541 atattatact gtgaaagcac ttcctgtgcg tgaaaggagg tgtcacatac agtgattatt
     3601 tgtttgtttg tactaaaaaa tatcgtttgt ccaattattg ttggatatgt tctttactta
     3661 ataactaaag aacacaaacg ataaaaaaag aaaccccagc atatgctttg gtcggcatgc
     3721 tggggttttc acatacaatg atgtatctgt ttgtttgtta aattcagtat attatttttg
     3781 atatcttttg taaaattttg gatttttata tctgattttt aggtacttat tttggatatt
     3841 tcctaggggg gtactacgac cccccctagg agtgcattgt gcattgtgca aaaaaatgag
     3901 tatgaatttg actttgtgcg cataaatatg tatattcgac acataaggaa atttggaggt
     3961 gttttaaggt a
//
