LOCUS       NZ_CP096537             2997 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Staphylococcus aureus strain RIVM_M047916 plasmid pM047916_2,
            complete sequence.
ACCESSION   NZ_CP096537
VERSION     NZ_CP096537.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27760539
            Assembly: GCF_026547095.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2997)
  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 2997)
  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_026547095.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 04:51:55
            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)                     :: 2,880
            CDSs (total)                      :: 2,798
            Genes (coding)                    :: 2,710
            CDSs (with protein)               :: 2,710
            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)              :: 88
            CDSs (without protein)            :: 88
            Pseudo Genes (ambiguous residues) :: 0 of 88
            Pseudo Genes (frameshifted)       :: 41 of 88
            Pseudo Genes (incomplete)         :: 43 of 88
            Pseudo Genes (internal stop)      :: 25 of 88
            Pseudo Genes (multiple problems)  :: 18 of 88
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096537.1.
            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..2997
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM_M047916"
                     /isolation_source="Nose"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pM047916_2"
                     /geo_loc_name="Netherlands"
                     /lat_lon="52.13 N 5.29 E"
                     /collection_date="2019-06-18"
                     /collected_by="RIVM"
                     /genotype="GG0398 (CC398)"
     gene            1..822
                     /locus_tag="M1F47_RS14365"
                     /old_locus_tag="M1F47_14350"
     CDS             1..822
                     /locus_tag="M1F47_RS14365"
                     /old_locus_tag="M1F47_14350"
                     /inference="COORDINATES: protein motif:HMM:NF025217.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative RNA methyltransferase"
                     /protein_id="WP_049948317.1"
                     /translation="MFFKCSICDEKLKRGYKTLACENNHTFDIAKEGYSNLISGHKKSK
                     YDKKLFIARRELNDSSNLYSILISKIIEIIKKYEIKTKNNVIDVGTGEGYILNEISKTF
                     LGENEFLGIDIAKEGVKKAAKSYKNINWLVADLADIPVMNGNVDFLINVLSPSNYDEFK
                     RVLDKEGKLIKIIPNSDYLKEIRNIVFSNHKNKDYDNSEVIDLFEANFNKIEMIDISYK
                     VKLNKEELNKLLDMTPLTWNLSDVEKEGIIKKNLSEITMSFKVLVGGFKTS"
                     /name="putative RNA methyltransferase"
     gene            1006..2010
                     /locus_tag="M1F47_RS14370"
                     /old_locus_tag="M1F47_14355"
     CDS             1006..2010
                     /locus_tag="M1F47_RS14370"
                     /old_locus_tag="M1F47_14355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_078099048.1"
                     /translation="MQDNHTKYIDENQDNKTLKDLTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQRVI
                     EEVVKEKPKARWLFLTLSTRNAIDGDTLEKSLKHLTESFRRLFKYKKVSKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVESKYFRGSENYISQNDWINLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     Typing          1007..2010
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.949"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtttttta agtgttctat atgtgatgaa aaattaaaga gaggttataa aactttagca
       61 tgtgagaata accatacttt tgatattgca aaagagggtt attcgaattt aatttcaggg
      121 cataaaaaaa gtaaatacga taaaaaattg tttattgcta gaagagaatt gaatgatagt
      181 agcaatttgt attcgatatt aatttcaaaa atcatagaaa ttattaaaaa atatgagatt
      241 aaaactaaaa ataatgtgat agatgttggt actggtgagg gttatatttt aaatgaaatt
      301 agtaaaacat ttcttggtga aaatgaattc ttaggtatag acattgcaaa agaaggtgta
      361 aaaaaagcag caaaatcata taaaaatata aattggttgg ttgctgatct agctgatata
      421 ccagttatga atgggaatgt agacttttta attaatgtgc ttagcccttc taattatgat
      481 gagtttaaaa gagttctaga taaagagggg aaattgataa aaataattcc taatagtgat
      541 tatttaaaag aaataaggaa tatagtcttt agtaatcata aaaataagga ttatgataat
      601 tctgaggtta tagatttatt tgaagctaat tttaataaaa ttgaaatgat agacattagt
      661 tataaggtta aattaaataa agaagaattg aataaattac ttgatatgac gcctttaacg
      721 tggaatttaa gtgacgtaga aaaagaagga ataattaaga aaaacttaag tgaaattacg
      781 atgagtttta aggttttggt tggtggtttt aaaacgagtt gaaaacgagt ttcttcttgt
      841 cttgatacta tatagaaata acgttctttt ttaaaatgtt gtttcaagct tgatgtaaca
      901 gtgttttgaa agatttttag tgtataaaat aaaatttgac ataaaaaaac tccagtaata
      961 agattaaagt gtcgagctaa aatcaaatac tggaggtctt tttatatgca agacaatcat
     1021 acaaaatata tagatgaaaa tcaagataat aaaacactaa aagacttaac gaaaagtggg
     1081 aaacaacgcc cgtggagaga aaagaaaatc gataatgtaa gttatgcaga tatactagaa
     1141 atcttaaaaa ttaaaaaggc ttttaacgta aaacaatgtg gtaacgtctt agagttcaag
     1201 cctactgatg aaggttattt gaagttacat aagacatggt tttgtaaatc aaaattgtgt
     1261 ccagtttgta attggaggcg tgctatgaaa aatagttatc aagctcaaag agtgattgaa
     1321 gaagtggtta aagaaaagcc gaaagcacgt tggttgtttc ttacactatc aacacgaaat
     1381 gcgatagatg gagatacttt agaaaaaagt cttaaacatt taactgaatc atttagaaga
     1441 ttatttaaat ataaaaaagt tagtaaaaat ttaattggtt ttatgcgttc gacagaggtt
     1501 acagttaata aaaatgacgg tagttataat caacatatgc atgttttatt gtgtgttgaa
     1561 agtaaatatt ttagaggttc tgagaattac atttctcaaa atgattggat taatttatgg
     1621 caaaaagcat tacaagttaa ttatcggcca gtagcaaata ttaaagcgat caaaccaaat
     1681 caaaaaggcg ataaagatat tcaagcagca atcaaagaaa cctcgaaata ttcggttaaa
     1741 tcatctgatt ttttaactga tgatgacgaa agaaatcagg aaatcgtgaa tgatttagaa
     1801 aaaggtttat accgaaaacg tatgttgagt tatggtggat tgcttaaaca aaaacataaa
     1861 attttaaatt tagacgatgc cgaagatggc aatttaatta atacaagtga cgaagataaa
     1921 acaacagacg aagaagaaaa agcacattca attactgcaa tttggaattt tgaaaaacaa
     1981 aattattact taaaagattt gaaacgttag cttaaaagct agcgtttttt ttatgtattt
     2041 ttgcccctgc aggaactata gcgttcaacc ggcatggttg accagtttta ccatgaaaat
     2101 tttaatttgc atgtaaatgg gcagtgcagt gtctgaaaaa ttcgccactg gttatgtaca
     2161 aaaaatgaga taaacaattt aactttttaa gttatataaa ttttagggag ttccaatcaa
     2221 attagaaaaa tatatataaa agttatatcg tttttctggc ttatgtttaa aaagtacaag
     2281 tgattgtatt taaaatgact ttagcaactt aagtaatatg tcttttgaat acaagttaaa
     2341 tgtcagaaag atgtaccctt attttgctca tatttgcgtt ttaagaaaca tatataaata
     2401 tacaggtata aaaatatata aatatagagt ttgctctaaa taccccctta aaattcaaaa
     2461 taaaggcatt taaaaattaa gaaaataaaa aagctactag caaaaaacta gtagcttaaa
     2521 tcttagttaa atttctatgt agtattaatt tttatatcta cgctacaacg tcgattctag
     2581 ttcgtgcagt attaattttt atatctgcgc tacaacgccg attccttaaa actaagataa
     2641 aaattgacga aggtcgatta tggtttttta cgcgttcttt ttagaacgca taagtgcgcc
     2701 cttacgggat ttaactagat tataacgacg aaaaatagac ctgtaaagca ataacagttg
     2761 ggtctacttt gtctactggg cagacaagaa aagaacacgc atttatgccg agaaaattta
     2821 ttgatgttga gaagaaccct taactaaact tgcagacgaa tgtcggcata gcgtgagcta
     2881 ttaagccgac cattcgacaa gttttgggat tgttaagggt tccgaggctc aacgtcaata
     2941 aagcaattgg aataaagcaa ctttgttatt tataattatt tgattggagg tgtgaat
//
