LOCUS       NZ_CP013617             2362 bp    DNA     circular CON 03-MAR-2024
DEFINITION  Staphylococcus aureus strain RIVM1295 plasmid pRIVM1295-1, complete
            sequence.
ACCESSION   NZ_CP013617
VERSION     NZ_CP013617.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04325935
            Assembly: GCF_001465635.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2362)
  AUTHORS   Bosch,T., Witteveen,S., Haenen,A., Landman,F. and Schouls,L.M.
  TITLE     Next-Generation Sequencing Confirms Presumed Nosocomial Transmission
            of Livestock-Associated Methicillin-Resistant Staphylococcus aureus
            in the Netherlands
  JOURNAL   Appl Environ Microbiol 82 (14), 4081-4089 (2016)
   PUBMED   27129960
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2362)
  AUTHORS   Witteveen,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-DEC-2015) Laboratory for Infectious Diseases &
            Screening, National Institute for Public Health & the Environment
            (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The
            Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: CLC Genomics Workbench v. version 8.5.1
            Sequencing Technology             :: 454; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/03/2024 08:02:28
            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)                     :: 2,742
            CDSs (total)                      :: 2,660
            Genes (coding)                    :: 2,566
            CDSs (with protein)               :: 2,566
            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)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 49 of 94
            Pseudo Genes (incomplete)         :: 38 of 94
            Pseudo Genes (internal stop)      :: 28 of 94
            Pseudo Genes (multiple problems)  :: 17 of 94
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP013617.1.
            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..2362
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM1295"
                     /isolation_source="unavailable"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pRIVM1295-1"
                     /geo_loc_name="Netherlands: Bilthoven"
                     /lat_lon="52.13 N 5.210 E"
                     /collection_date="2009-03-26"
                     /collected_by="Dutch National Institute for Public Health
                     and the Environment (RIVM)"
     gene            complement(434..910)
                     /locus_tag="AUC48_RS13885"
                     /old_locus_tag="AUC48_13875"
     CDS             complement(434..910)
                     /locus_tag="AUC48_RS13885"
                     /old_locus_tag="AUC48_13875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000664727.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     gene            complement(1358..2092)
                     /gene="erm(C)"
                     /locus_tag="AUC48_RS13890"
                     /old_locus_tag="AUC48_13880"
     ARG             complement(1362..2092)
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1359..2092)
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          complement(425..910)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 attagtgcat ttaagcgtca gagcatggct ttatgccgag aaaactattg gttggaatgg
       61 cgtgtgtgtt agccaaagct ttggcgagtt ggttgggggt ttcatgggat taatcccatg
      121 aaagtaccaa ctcaacaaca cactaacgcc tgttggttcc aaccaatagg aaattggaat
      181 aagcaattag tataatgaga gtataatgtt ggtataacgt tagtataatg atgctttttt
      241 tcattatatt ttttatgtac tttaaacctg cacgcttatg tgaattagaa aaagcttaat
      301 cgcatttcat agattgacct cccaataact acgtggtgtt attgggaggt caatctattt
      361 catttgcgtt aagcttttga tctacattaa gcgtgcaggt tttttgtcta tttgtagacg
      421 attttatgtt atactagtcc ttgaaagaat aataatcaga taatgcattt tcttgttttt
      481 catttgcctc ttgctcaaag ttcccaaatt cgagtaagag gtatttttgt ttttggtcgt
      541 cgcctctcat tagtagttca gggtttaaca ttaatactcc agtttttctt tttataatat
      601 ttccttcttc taagatttta agtgttgtta ttactgtttg tagacttgtt cctgtagctt
      661 ttgctatttc tcttgttgta gctatcattg tattgttact taagtggaca ttatctagga
      721 tatagttaac gattttaagt ttttttccgc caatcatatc taacatactt attaattgca
      781 ctatatatgc ctttacgaag ttaccagacg tttgtttacg gtataacttg tctacctcta
      841 tgacttctcc actttcttcg tctatgagcc tctgagagcc tttatagact gttccatatc
      901 tttctttcat ctttttctca ctccttattt taaactattc taactatatc ataactgttc
      961 taaaaaaaaa agaacatttg ttaaaagaaa ttagaacaaa atgagtgaaa aattagaaca
     1021 aacaaattcc ttataaacct tatcatctca acctatatta agattttacc tagttgaatc
     1081 ttcttttcta tataaagcgt cggagcatat cagggggtta tctaacgtaa atgctaccct
     1141 tcggctcgct ttcgctcggc attgacgtca gatactgcac cccctgaacc cccatgctcc
     1201 aacagcaaaa aggaaacttt ttgctgcttt tccgacgctt attcgcttcg ctcatattta
     1261 tatagaaaag aagtgaatgc gcaaaagaca taatcgattc acaaaaaata ggtacacgaa
     1321 aaacaagtta agggatgcat aaactgcatc ccttaactta cttattaaat aatttatagc
     1381 tattgaaaag agataagaat tgttcaaagc taatattgtt taaatcgtca attcctgcat
     1441 gttttaagga attgttaaat tgattttttg taaatatttt cttgtattct ttgttaaccc
     1501 atttcataac gaaataatta tacttctgtt tatctttgtg tgatattctt gatttttttc
     1561 tatttaatct gataagtgag ctattcactt taggtttagg atgaaaatat tctcttggaa
     1621 ccatacttaa tatagaaata tcaacttctg ccattaaaaa taatgccaat gagcgttttg
     1681 tatttaataa tcttttagca aacccgtatt ccacgattaa ataaatctca tcagctatac
     1741 tatcaaaaac aattttgcgt attatatccg tacttatgtt ataaggtata ttaccaaata
     1801 ttttatagga ttggttttta ggaaatttaa actgcaatat atccttgttt aaaacttgga
     1861 aattatcgtg atcaacaagt ttattttctg tagttttgca taatttatgg tctatttcaa
     1921 tggcagttac gaaattacac ctctgtacta attcaagggt aaaatgccct tttcctgagc
     1981 cgatttcaaa gatattatca tgttcattta atcttatatt tgtcattatt ttatctatat
     2041 tatgttttga agtaataaag ttttgactgt gttttatatt tttctcgttc attataaccc
     2101 tcttttttcc tccttataaa attagtataa ttatagcacg agctctgata aatatgaaca
     2161 tgatgagtga tcgttaaatt tatactgcaa tctgatgcga ttattgaata aaagatatga
     2221 gagatttatc tagtttcttt ttttacaaga aaaaagaaag ttcttaaagg ttttatactt
     2281 ttggtcgtag agcacacggt ttaacgactt aattacgaag taaataagtc tagtgtgtta
     2341 gactttaatg tttttttaag gc
//
