LOCUS       NZ_CP014374             2473 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Staphylococcus aureus strain USA300-SUR4 plasmid pUSA05-1-SUR4,
            complete sequence.
ACCESSION   NZ_CP014374
VERSION     NZ_CP014374.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04497598
            Assembly: GCF_003595425.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2473)
  AUTHORS   Sabat,A.J., Hermelijn,S.M., Akkerboom,V., Juliana,A., Degener,J.E.,
            Grundmann,H. and Friedrich,A.W.
  TITLE     Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA
            USA300 (ST8-spa t008) in an academic hospital of Paramaribo,
            Republic of Suriname
  JOURNAL   Sci Rep 7, 41050 (2017)
   PUBMED   28106148
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2473)
  AUTHORS   Sabat,A.J., Hermelijn,S., Akkerboom,V., Degener,J.E., Grundmann,H.
            and Friedrich,A.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-FEB-2016) Medical Microbiology, University Medical
            Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SeqMan NGen v. 12.1.0
            Genome Coverage                   :: missing
            Sequencing Technology             :: Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003595425.1-RS_2024_05_07
            Annotation Date                   :: 05/07/2024 04:16:44
            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)                     :: 3,001
            CDSs (total)                      :: 2,920
            Genes (coding)                    :: 2,830
            CDSs (with protein)               :: 2,830
            Genes (RNA)                       :: 81
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 90
            CDSs (without protein)            :: 90
            Pseudo Genes (ambiguous residues) :: 0 of 90
            Pseudo Genes (frameshifted)       :: 51 of 90
            Pseudo Genes (incomplete)         :: 42 of 90
            Pseudo Genes (internal stop)      :: 18 of 90
            Pseudo Genes (multiple problems)  :: 20 of 90
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP014374.1.
            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..2473
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="USA300-SUR4"
                     /isolation_source="Urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pUSA05-1-SUR4"
                     /geo_loc_name="Suriname: Paramaribo"
                     /lat_lon="5.866667 N 55.166667 W"
                     /collection_date="2013-04-25"
                     /collected_by="Sandra Hermelijn"
     gene            1..477
                     /locus_tag="AYM16_RS15620"
                     /old_locus_tag="AYM16_15235"
     CDS             1..477
                     /locus_tag="AYM16_RS15620"
                     /old_locus_tag="AYM16_15235"
                     /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            1172..1231
                     /gene="ermCL"
                     /locus_tag="AYM16_RS15625"
     CDS             1172..1231
                     /gene="ermCL"
                     /locus_tag="AYM16_RS15625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methylase leader peptide ErmCL"
                     /protein_id="WP_002497446.1"
                     /translation="MGIFSIFVISTVHYQPNKK"
                     /name="ermCL"
     gene            1292..2026
                     /gene="erm(C)"
                     /locus_tag="AYM16_RS15630"
                     /old_locus_tag="AYM16_15240"
     ARG             1293..2023
                     /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             1293..2026
                     /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          2..487
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaaagaaa gatatggaac agtctataaa ggctctcaga ggctcataga cgaagaaagt
       61 ggagaagtca tagaggtaga caagttatac cgtaaacaaa cgtctggtaa cttcgtaaag
      121 gcatatatag tgcaattaat aagtatgtta gatatgattg gcggaaaaaa acttaaaatc
      181 gttaactata tcctagataa tgtccactta agtaacaata caatgatagc tacaacaaga
      241 gaaatagcaa aagctacagg aacaagtcta caaacagtaa taacaacact taaaatctta
      301 gaagaaggaa atattataaa aagaaaaact ggagtattaa tgttaaaccc tgaactacta
      361 atgagaggcg acgaccaaaa acaaaaatac ctcttactcg aatttgggaa ctttgagcaa
      421 gaggcaaatg aaaaacaaga aaatgcatta tctgattatt attctttcaa ggactagtat
      481 aacataaaat cgtctacaaa tagacaaaaa acctgcacgc ttaatgtaga tcaaaagctt
      541 aacgcaaatg aaatagattg acctcccaat aacaccacgt agttattggg aggtcaatct
      601 atgaaatgcg attaagcttt ttctaattca cataagcgtg caggtttaaa gtacataaaa
      661 aatataatga aaaaaagcat cattatacta acgttatacc aacattatac tctcattata
      721 ctaattgctt attccaattt cctattggtt ggaaccaaca ggcgttagtg tgttgttgag
      781 ttggtacttt catgggatta atcccatgaa acccccaacc aactcgccaa agctttggct
      841 aacacacacg ccattccaac caatagtttt ctcggcataa agccatgctc tgacgcttaa
      901 atgcactaat gccttaaaaa aacattaaag tctaacacac tagacttatt tacttcgtaa
      961 ttaagtcgtt aaaccgtgtg ctctacgacc aaaagtataa aacctttaag aactttcttt
     1021 tttcttgtaa aaaaagaaac tagataaatc tctcatatct tttattcaat aatcgcatca
     1081 gattgcagta taaatttaac gatcactcat catgttcata tttatcagag ctcgtgctat
     1141 aattatacta attttataag gaggaaaaaa tatgggcatt tttagtattt ttgtaatcag
     1201 cacagttcat tatcaaccaa acaaaaaata agtggttata atgaatcgtt aataagcaaa
     1261 attcattata accaaattaa agagggttat aatgaacgag aaaaatataa aacacagtca
     1321 aaactttatt acttcaaaac ataatataga taaaataatg acaaatataa gattaaatga
     1381 acatgataat atctttgaaa tcggctcagg aaaagggcat tttacccttg aattagtaca
     1441 gaggtgtaat ttcgtaactg ccattgaaat agaccataaa ttatgcaaaa ctacagaaaa
     1501 taaacttgtt gatcacgata atttccaagt tttaaacaag gatatattgc agtttaaatt
     1561 tcctaaaaac caatcctata aaatatttgg taatatacct tataacataa gtacggatat
     1621 aatacgcaaa attgtttttg atagtatagc tgatgagatt tatttaatcg tggaatacgg
     1681 gtttgctaaa agattattaa atacaaaacg ctcattggca ttatttttaa tggcagaagt
     1741 tgatatttct atattaagta tggttccaag agaatatttt catcctaaac ctaaagtgaa
     1801 tagctcactt atcagattaa atagaaaaaa atcaagaata tcacacaaag ataaacagaa
     1861 gtataattat ttcgttatga aatgggttaa caaagaatac aagaaaatat ttacaaaaaa
     1921 tcaatttaac aattccttaa aacatgcagg aattgacgat ttaaacaata ttagctttga
     1981 acaattctta tctcttttca atagctataa attatttaat aagtaagtta agggatgcag
     2041 tttatgcatc ccttaacttg tttttcgtgt acctattttt tgtgaatcga ttatgtcttt
     2101 tgcgcattca cttcttttct atataaatat gagcgaagcg aataagcgtc ggaaaagcag
     2161 caaaaagttt cctttttgct gttggagcat gggggttcag ggggtgcagt atctgacgtc
     2221 aatgccgagc gaaagcgagc cgaagggtag catttacgtt agataacccc ctgatatgct
     2281 ccgacgcttt atatagaaaa gaagattcaa ctaggtaaaa tcttaatata ggttgagatg
     2341 ataaggttta taaggaattt gtttgttcta atttttcact cattttgttc taatttcttt
     2401 taacaaatgt tctttttttt ttagaacagt tatgatatag ttagaatagt ttaaaataag
     2461 gagtgagaaa aag
//
