LOCUS       NZ_CP096524             4397 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Staphylococcus aureus strain RIVM_M085090 plasmid pM085090_2,
            complete sequence.
ACCESSION   NZ_CP096524
VERSION     NZ_CP096524.1
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 4397)
  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 4397)
  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
            CP096524.1.
            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..4397
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM_M085090"
                     /isolation_source="pig farm dust"
                     /host="Environment"
                     /db_xref="taxon:1280"
                     /plasmid="pM085090_2"
                     /geo_loc_name="Netherlands"
                     /lat_lon="52.13 N 5.29 E"
                     /collection_date="2019-06-01"
                     /collected_by="WBVR"
                     /genotype="GG0398 (CC398)"
     gene            join(4018..4397,1..19)
                     /gene="mobC"
                     /locus_tag="M1F52_RS13935"
                     /old_locus_tag="M1F52_13915"
     CDS             join(4018..4397,1..19)
                     /gene="mobC"
                     /locus_tag="M1F52_RS13935"
                     /old_locus_tag="M1F52_13915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002489523.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_001002114.1"
                     /translation="MNEHKDNLASDLSVGGNRKPNRKEPKQISFRVSEQEYSKLKQSAE
                     TLNMTVPNFVKKKAQGSRLVSPKLDKETRQSIAKDLSHLGSNVNQIAKWFNQNKDKATH
                     LPEEKYHDLEKQFDDVKKELHKIWQQLN"
                     /name="mobC"
     gene            1..963
                     /locus_tag="M1F52_RS13940"
                     /old_locus_tag="M1F52_13920"
     CDS             1..963
                     /locus_tag="M1F52_RS13940"
                     /old_locus_tag="M1F52_13920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011167204.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_346733042.1"
                     /translation="MATTKLGNTKSASRAINYAEERAEEKSGLNCDVDYAKSYFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTAKECNEIGLELAKKIAPDYQVAVYTHTDKDHYHNHI
                     IINSVNLETGNKYQSNKEQRDFIKKANDQLCEERGLSVPEKSSEIRYTLAEQNMIDKDK
                     RSWKNDIRMAVEETKDNAVDFEEFNTLLKEKGVEITRVTKNNITYRHIEEDKKVRGNKL
                     GDSYDKGVIENGFAIEKFRREREEEREYDEYADTFEVDWDAVAENSEDLRKRRIARTEE
                     TKQASNKIYIRDERTTGLERKGIAGNQVEFEKDDGGLSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            932..1387
                     /locus_tag="M1F52_RS13945"
                     /old_locus_tag="M1F52_13925"
     CDS             932..1387
                     /locus_tag="M1F52_RS13945"
                     /old_locus_tag="M1F52_13925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002485179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF334 domain-containing protein"
                     /protein_id="WP_000753824.1"
                     /translation="MKKTTEDFQGRGKKVHNDFVRLLQKNLNRVNAEDIEIEVRKDVYG
                     VREEIHSMLREVKQSHEHYQKRQKQLFTGIGAMLLVFMLFALIMTIGRDFMGFLHVDVL
                     QNAIASKIKASEGFISVLWYIAYGLPYILAIGLFIWLYEWIRARFHD"
                     /name="DUF334 domain-containing protein"
     gene            1948..2892
                     /locus_tag="M1F52_RS13950"
                     /old_locus_tag="M1F52_13930"
     CDS             1948..2892
                     /locus_tag="M1F52_RS13950"
                     /old_locus_tag="M1F52_13930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011167206.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_011167206.1"
                     /translation="MSKKAEEIQAKQSLEKENSNFSKTGYSNSRLNRHIMYTPEPKLHF
                     DAMTIVGNLNKNNAHKLSEFMSIAPQIRLWDILQTKFKAKALQEKVYIEYDKVKADAWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVK
                     KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADIEVMSEHLWRVEIELKRDMV
                     DYWNDCFNDLHILKPDWSSLEKVKDQAMIYMLIHEESTWGKLERRTKNKYREMLKSISE
                     IDLTDLMKLTLKENEKQLQKQIEFWQREFRFWE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2900..3748
                     /gene="str"
                     /locus_tag="M1F52_RS13955"
                     /old_locus_tag="M1F52_13935"
     ARG             2901..3745
                     /name="str"
                     /gene="str"
                     /gene_name="streptomycin adenylyltransferase Str"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(3813..4047)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="100.0"
                     /evalue="1.4099999999999999e-40"
     Typing          1949..2892
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..960
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.688"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcaacaa ctaaattagg caatacgaag tcggcaagtc gtgccattaa ttacgcagaa
       61 gaacgtgcag aagaaaaaag cggcttaaat tgtgatgttg attatgctaa atcatatttt
      121 aagcaaacta gggcgttata tggcaaagag aatggtgttc aagcacatac agtcattcaa
      181 tcttttaagc ctggcgaagt aacagctaaa gagtgtaatg agataggttt agaattagct
      241 aaaaaaattg caccagatta tcaagttgca gtttatacac atacagacaa agaccattat
      301 cacaatcaca ttattattaa ttcagtaaat ttagaaacag gcaacaagta tcagtcaaac
      361 aaagaacaac gtgattttat aaaaaaggcg aatgatcagt tatgtgaaga acgtggttta
      421 tctgtgccag aaaagtcatc agaaatcaga tatacgttgg cagaacagaa catgatagat
      481 aaagataaaa ggtcatggaa aaatgatata agaatggcag ttgaagaaac aaaggataac
      541 gcagtagact ttgaagaatt taatactttg ctaaaagaaa aaggtgttga aatcacgaga
      601 gtaacgaaaa acaacataac gtatagacac attgaagaag ataaaaaagt acgtgggaat
      661 aagttgggcg attcttatga caaaggagtg attgaaaatg gctttgcaat cgagaaattc
      721 agacgagaac gagaagaaga acgagaatac gatgaatatg cagacacgtt cgaagttgac
      781 tgggacgcag tcgcagaaaa ttcagaagac cttagaaaac gaagaattgc aagaactgaa
      841 gaaacaaaac aagctagtaa taaaatatat atcagagatg aaagaacaac aggacttgag
      901 agaaaaggaa ttgcaggcaa tcaagtcgag tttgaaaaag acgacggagg actttcaagg
      961 tagaggtaaa aaagtccata atgattttgt tcgtttgtta caaaagaatt taaatcgagt
     1021 gaatgcagaa gatattgaga tagaggttcg aaaagatgtt tatggagttc gagaagaaat
     1081 tcattcaatg ttgcgtgaag ttaaacaatc acatgaacat tatcaaaaaa gacaaaagca
     1141 attatttact ggtattggtg caatgttatt agtgtttatg ctttttgctt tgattatgac
     1201 gattggcaga gattttatgg gctttttaca tgtagatgta ttacagaatg ccatagcaag
     1261 caaaataaag gcttctgagg gctttatttc agttttatgg tacattgctt atggtttacc
     1321 ttatatactc gctatagggc tatttatttg gttgtatgag tggataagag caagattcca
     1381 tgattaaaca aagtatgatc aggcttttat gccgagaaaa tttatttata ttgagaagta
     1441 cccttaacta aacttgcaga cgaatgtcgg catagcgtga gctattagcc cgaccattcg
     1501 acaagttttg ggtttgttaa gggtacagag gctcaatgta aataaagcaa ttggaataaa
     1561 gcaacaaagg gggttgaaga aaatgagtaa gaagaaaaag attaatttag caatatcaat
     1621 tgctcaagta gtagtgcagg cgttaatact ttataacact tatcagcaat ataaatattc
     1681 taaaaaatat tcagcctaat aaaaaaagac ttagtctgaa tagaccaagc cttttgttag
     1741 tgttatatta atatgcaaat aaaaaaacaa aaaaagaagt cgctcactcc ctgaccaaag
     1801 tttgtgaatg cgacttacct taaagaaaaa cagttggtgt ttttttctta atttttgtat
     1861 atctagatat taaacgatat tggtttattc ttcaagatat atattcgggt gagcgacttc
     1921 ttaaacaaaa taaggagtcg attttttatg agtaaaaaag cagaagaaat tcaggcaaaa
     1981 caaagtttgg aaaaggaaaa ctcaaatttt tctaaaaccg gatactctaa tagccggtta
     2041 aaccgacata ttatgtacac ccccgaacca aaattacact ttgatgctat gacaattgtt
     2101 gggaatctta ataagaacaa tgctcacaaa ctgtctgaat ttatgagtat tgcgccacaa
     2161 attagacttt gggatatatt acaaaccaaa tttaaagcta aggctctaca agaaaaagtt
     2221 tacatcgaat atgataaagt aaaagcagat gcgtgggata gacgtaatat gcgtgttgaa
     2281 tttaatccta ataaacttac gcatgaagaa atgctttggt taaaacaaaa catcattgac
     2341 tacatggaag atgatggttt tacaagatta gatttggctt ttgattttga agacgatttg
     2401 agcgattatt atgcgatgac tgataaatca gttaagaaaa ctatttttta tggtcgtaac
     2461 ggtaaaccag aaacaaaata ttttggtgtt cgtgacagtg atagatttat tagaatttat
     2521 aataaaaaac aagaacgtaa ggataatgca gacattgaag ttatgtctga acacttatgg
     2581 cgtgtagaaa ttgaattaaa aagagatatg gttgattatt ggaacgattg ttttaatgat
     2641 ttacatattt tgaaaccaga ttggtctagt ttagaaaaag taaaagacca agcaatgatt
     2701 tatatgctaa ttcatgaaga aagtacatgg ggtaaattag aaagacgtac aaaaaataaa
     2761 tacagagaaa tgttaaaaag tatttcagaa attgatttaa cggacttaat gaaattgact
     2821 ttaaaagaga atgaaaaaca attgcaaaag cagattgaat tttggcagcg tgaatttaga
     2881 ttttgggagt gaaaaaacaa tgaggactga aaaagaaatt ttaaatttag tttctgaatt
     2941 tgcttatcaa cgaagcaatg taaaaattat tgctctcgag ggttcaagaa ctaatgaaaa
     3001 tataaaaaaa gataagtttc aagattatga ttttgctttt ttcgtatcag atattgagta
     3061 tttcacacat gaagaaagtt ggttaagttt atttggagaa ttattgttta tacagaaacc
     3121 agaagatatg gaattattcc cacctgattt agattatggt tacagttata taatgtattt
     3181 taaagatggc ataaaaatgg atattacatt aattaattta aaagatttaa atcgttattt
     3241 tagtgattct gatggtcttg taaaaatttt agttgataaa gataatttag taactcaaga
     3301 aattgttcca gatgactcaa attattggtt aaaaaaacca acagaacgag aattttatga
     3361 ttgctgtaat gagttttgga gtgtctcaac gtatgtagca aagggtgttt ttagaagaga
     3421 aatattattt gctttagatc atttcaataa tattttacgt cctgaattat taagaatgat
     3481 ttcttggtat attggcttta ataggggttt tgattttagt ttaggaaaga attataagtt
     3541 tataaacaaa tatttaactg ataaagaatt caatatgctt ttagctactt ttgagatgaa
     3601 tggatataga aagacatacc aatcttttaa gctttgttgt gaattattta aatattattc
     3661 aaataaagta agttgtttag gaaattataa ctatccaaat tacgaaaaaa atattgagaa
     3721 ttttattcgt aataattatg agaattaatt ttattagcaa ccacattttt ggttgctttt
     3781 gttttgattt tgaatttggt tttgaactat gagtggctag cattttgcca ctcatttttt
     3841 gcgttagcaa aaacataaag ggtctgggat taatcccagc aagccggtat attcagaacg
     3901 aagtggctag aatatacgac gcttgccaaa ccactatatt acttgagaaa atatagatta
     3961 tattataagc tatatttatg aaaaggaata tttttcgtca gaaaggtggt gggacttgtg
     4021 aacgaacata aagataattt ggctagcgat ttgtctgttg ggggaaaccg taaacccaac
     4081 cgcaaagagc caaaacaaat tagtttcaga gtgagtgaac aggaatattc aaagttgaaa
     4141 cagtcggcag aaactttgaa tatgacagtg cctaatttcg ttaagaaaaa ggcacaaggc
     4201 agtcgattag tgtcgccaaa attagacaaa gaaacgcgac aatcgattgc caaagattta
     4261 agtcatttgg gtagtaatgt gaatcagatt gctaagtggt ttaatcaaaa taaagataag
     4321 gctacacatt taccagaaga gaaatatcat gatttagaaa agcaatttga tgatgtgaaa
     4381 aaggagttgc ataagat
//
