LOCUS       NZ_CP119114             2391 bp    DNA     circular CON 05-MAY-2024
DEFINITION  Staphylococcus aureus strain GENOMIC22-002 plasmid pCFSAN126947_01,
            complete sequence.
ACCESSION   NZ_CP119114
VERSION     NZ_CP119114.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33425966
            Assembly: GCF_029094145.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2391)
  AUTHORS   Hoffmann,M., Luo,Y., Sorensen,L.H., Pedersen,S.K. and
            Hendriksen,R.S.
  TITLE     Results of the 2020 Genomic Proficiency Test for the network of
            European Union Reference Laboratory for Antimicrobial Resistance
            assessing whole genome sequencing capacities
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2391)
  AUTHORS   Hoffmann,M., Luo,Y., Sorensen,L.H., Pedersen,S.K. and
            Hendriksen,R.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-FEB-2023) CFSAN, US FDA, 5001 Campus Drive, College
            Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Microbial Genome Analysis v. SMRT Link
            11.0.0.146107
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 700.0x
            Sequencing Technology             :: Pacbio Sequel IIe system
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029094145.1-RS_2024_05_05
            Annotation Date                   :: 05/05/2024 05:46:48
            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)                     :: 2,911
            CDSs (total)                      :: 2,829
            Genes (coding)                    :: 2,729
            CDSs (with protein)               :: 2,729
            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)              :: 100
            CDSs (without protein)            :: 100
            Pseudo Genes (ambiguous residues) :: 0 of 100
            Pseudo Genes (frameshifted)       :: 50 of 100
            Pseudo Genes (incomplete)         :: 45 of 100
            Pseudo Genes (internal stop)      :: 26 of 100
            Pseudo Genes (multiple problems)  :: 18 of 100
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119114.1.
            Bacteria and source DNA available from Sorensen, Lauge Holm,
            lahoso@food.dtu.dk.
            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..2391
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="GENOMIC22-002"
                     /isolation_source="EQA test strain"
                     /db_xref="taxon:1280"
                     /plasmid="pCFSAN126947_01"
                     /geo_loc_name="Denmark"
                     /collection_date="2022"
                     /collected_by="DTU National Food Institute"
     gene            297..1031
                     /gene="erm(C)"
                     /locus_tag="PXV46_RS14535"
                     /old_locus_tag="PXV46_14535"
     ARG             298..1028
                     /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"
     gene            1479..1980
                     /locus_tag="PXV46_RS14540"
                     /old_locus_tag="PXV46_14540"
                     /pseudo=""
     CDS             1479..1980
                     /locus_tag="PXV46_RS14540"
                     /old_locus_tag="PXV46_14540"
                     /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="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /name="replication/maintenance protein RepL"
     ARG             298..1031
                     /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          1480..1990
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.747"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctgacgctt aaatgcacta atgccttaaa aaaacattaa agtctaacac actagactta
       61 tttacttcgt aattaagtcg ttaaaccgtg tgctctacga ccaaaagtat aaaaccttta
      121 agaactttct tttttcttgt aaaaaaagaa actagataaa tctctcatat cttttattca
      181 ataatcgcat cagattgcag tataaattta acgatcactc atcatgttca tatttatcag
      241 agctcgtgct ataattatac taattttata aggaggaaaa aataaagagg gttataatga
      301 acgagaaaaa tataaaacac agtcaaaact ttattacttc aaaacataat atagataaaa
      361 taatgacaaa tataagatta aatgaacatg ataatatctt tgaaatcggc tcaggaaaag
      421 ggcattttac ccttgaatta gtacagaggt gtaatttcgt aactgccatt gaaatagacc
      481 ataaattatg caaaactaca gaaaataaac ttgttgatca cgataatttc caagttttaa
      541 acaaggatat attgcagttt aaatttccta aaaaccaatc ctataaaata tttggtaata
      601 taccttataa cataagtacg gatataatac gcaaaattgt ttttgatagt atagctgatg
      661 agatttattt aatcgtggaa tacgggtttg ctaaaagatt attaaataca aaacgctcat
      721 tggcattatt tttaatggca gaagttgata tttctatatt aagtatggtt ccaagagaat
      781 attttcatcc taaacctaaa gtgaatagct cacttatcag attaaataga aaaaaatcaa
      841 gaatatcaca caaagataaa cagaagtata attatttcgt tatgaaatgg gttaacaaag
      901 aatacaagaa aatatttaca aaaaatcaat ttaacaattc cttaaaacat gcaggaattg
      961 acgatttaaa caatattagc tttgaacaat tcttatctct tttcaatagc tataaattat
     1021 ttaataagta agttaaggga tgcataaact gcatccctta acttgttttt cgtgtaccta
     1081 ttttttgtga atcgattatg tcttttgcgc attcacttct tttctatata aatatgagcg
     1141 aagcgaataa gcgtcggaaa agcagcaaaa agtttccttt ttgctgttgg agcatggggg
     1201 ttcagggggt gcagtatctg acgtcaatgc cgagcgaaag cgagccgaag ggtagcattt
     1261 acgttagata accccctgat atgctccgac gctttatata gaaaagaaga ttcaactagg
     1321 taaaatctta atataggttg agatgataag gtttataagg aatttgtttg ttctaatttt
     1381 tcactcattt tgttctaatt tcttttaaca aatgttcttt tttttttaga acagttatga
     1441 tatagttaga atagtttaaa ataaggagtg agaaaaagat gaaagaaaga tatggaacag
     1501 tctataaagg ctctcagagg ctcatagacg aagaaagtgg agaagtcata gaggtagaca
     1561 agttataccg taaacaaacg tctggtaact tcgtaaaggc atatatagtg caattaataa
     1621 gtatgttaga tatgattggc ggaaaaaaac ttaaaatcgt taactatatc ctagataatg
     1681 tccacttaag taacaataca atgatagcta caacaagaga aatagcaaaa gctacaggaa
     1741 caagtctaca aacagtaata acaacactta aaatcttaga agaaggaaat agaactacta
     1801 atgagaggcg acgctattat aaaaagaaaa actggagtat taatgttaaa ccctgaacta
     1861 ctaatgagag gcgacgacca aaaacaaaaa tacctcttac tcgaatttgg gaactttgag
     1921 caagaggcaa atgaaaaaca agaaaatgca ttatctgatt attattcttt caaggactag
     1981 tataacataa aatcgtctac aaatagacaa aaaacctgca cgcttaatgt agatcaaaag
     2041 cttaacgcaa atgaaataga ttgacctccc aataacacca cgtagttatt gggaggtcaa
     2101 tctatgaaat gcgattaagc tttttctaat tcacataagc gtgcaggttt aaagtacata
     2161 aaaaatataa tgaaaaaaag catcattata ctaacgttat accaacatta tactctcatt
     2221 atactaattg cttattccaa tttcctattg gttggaacca acaggcgtta gtgtgttgtt
     2281 gagttggtac tttcatggga ttaatcccat gaaaccccca accaactcgc caaagctttg
     2341 gctaacacac acgccattcc aaccaatagt tttctcggca taaagccatg c
//
