LOCUS       NZ_CP119112             2271 bp    DNA     circular CON 05-MAY-2024
DEFINITION  Staphylococcus aureus strain GENOMIC22-001 plasmid pCFSAN126946_03,
            complete sequence.
ACCESSION   NZ_CP119112
VERSION     NZ_CP119112.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33425965
            Assembly: GCF_029094305.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2271)
  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  JOURNAL   Unpublished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 2271)
  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 Assembly v. SMRTLink v.11
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Pacbio Sequel IIe system
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029094305.1-RS_2024_05_05
            Annotation Date                   :: 05/05/2024 05:54:46
            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)                     :: 2,945
            CDSs (total)                      :: 2,864
            Genes (coding)                    :: 2,767
            CDSs (with protein)               :: 2,767
            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)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 50 of 97
            Pseudo Genes (incomplete)         :: 42 of 97
            Pseudo Genes (internal stop)      :: 28 of 97
            Pseudo Genes (multiple problems)  :: 20 of 97
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119112.1.
            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..2271
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="GENOMIC22-001"
                     /isolation_source="EQA test strain"
                     /db_xref="taxon:1280"
                     /plasmid="pCFSAN126946_03"
                     /geo_loc_name="Denmark"
                     /collection_date="2022"
                     /collected_by="DTU National Food Institute"
     gene            complement(join(2071..2271,1..804))
                     /locus_tag="PXV45_RS14685"
                     /old_locus_tag="PXV45_14685"
     CDS             complement(join(2071..2271,1..804))
                     /locus_tag="PXV45_RS14685"
                     /old_locus_tag="PXV45_14685"
                     /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_032489338.1"
                     /translation="MQYNTTRYVDENQDNETLKDMTKSGKQRPWREKKVDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVVKEKPKARWLFLTLSARNAIDGEHLEQSLKHMSKAFNKLKMYTKVKKNLIGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENSYFKNKVNYITQEEWVTLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            1080..1403
                     /gene="qacG"
                     /locus_tag="PXV45_RS14690"
                     /old_locus_tag="PXV45_14690"
     ARG             1081..1400
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacG"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2..804)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.881"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2072..2259)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.296"
                     /coverage="100.0"
                     /evalue="2.18e-82"
ORIGIN
        1 taaacctttt tctaaatcgt tcacgatttc ttgatttctt tcgtcatcat cagttaaaaa
       61 atcagatgac ttaaccgaat atttagaggt ttctttgata gctgcttgaa tatctttatc
      121 tcctttttga tttggtttga tcgctttaat atttgctact ggtcgataat ttacttgtaa
      181 tgctttttgc cataaagtaa cccattcttc ttgagttata taattaactt tattcttaaa
      241 atagctattt tcaacacaca ataaaacgtg catatgttga ttataactac cgtcattttt
      301 attaaccgtt acttcggttg aacgtaaaaa tccgattaaa ttctttttaa cttttgtata
      361 catttttaat ttattaaaag ccttagacat atgctttaaa ctttgttcta aatgttcacc
      421 gtctattgca tttcgtgctg atagcgtaag aaataaccaa cgtgcttttg gcttttcttt
      481 aaccacttct tcaatcactt tttgagcttg ataactattt ttcatagcac gcctccaatt
      541 acaaactggg cataattttg atttacaaaa ccatgtttta tgtaatttca aataaccttc
      601 atcagttggc ttgaactcta agacgttacc acattgtttt acgttaaaag ccttttttat
      661 ttttaaaatt tctagtatat ctgcataact tacattatca actttcttct ctctccatgg
      721 gcgttgtttc ccacttttcg tcatatcttt taatgtttca ttatcttgat tttcgtctac
      781 atatctagta gtattatatt gcatataaaa agcccccagt tttgattttg attcgacacc
      841 ttaatcatat aactggggtt ttttcatgtc aaattttctt tcaacaacaa aaacaaccaa
      901 aaatactgtt atatcaacat tcaaatgact ttttatatct ttgagttatt tctatatagt
      961 atcaagacaa gaagaaactc gttttcaact cgttttaaaa tacaaatctt aaaacttttt
     1021 ctttcactta atataaatta aaatataagc tatcaaatag aaattaaagg agaagcttaa
     1081 tgcattattt atatttattt atctcaattg caacagaaat aatcggaact agttttttaa
     1141 aaacatcaga aggtttcaca aagttatggc caacattagg tacactactt tcgtttggaa
     1201 tttgctttta ttttttaagt ttaacaataa aatttttgcc cttaaatata acttacgcaa
     1261 catgggcagg tctaggatta gtattaacaa caataatctc agttatcgtt tttaaagaaa
     1321 atgttaattt aattagtata atttctattg gcttaattgt tataggtgta gtgctcttaa
     1381 atgtatttgg agaaagccat tgattatttt attccaattg ctttattgac gttgagcctc
     1441 ggaaccctta acaatcccaa aacttgtcga atggtcggct taatagctca cgctatgccg
     1501 acattcgtct gcaagtttag ttaagggttc ttctcaacat caataaattt tctcggcata
     1561 aatgcgtgct ttaattatgt tataattaag caaattgagt aggaaaaata tagtactcaa
     1621 aaattaaatt aattagcttt tctattattt gtgttaatgc taagtacaac ttttttattg
     1681 ttgcacttag cattttttat ttttaaattt tcaaagatac caaattttaa atacctttat
     1741 tttgaattct aagggggcat tttaaagatt taagggtaaa tcatatagtt ttatacctaa
     1801 aaacctaaac aagcttttaa aacgcaaata tgagccaaat aaatatattc taattccaca
     1861 aacaaaaatt tgagcaaaac cagtgtcgaa ttttttaaac actgcccatt tacatgcaaa
     1921 ttaaaattta gcatgtaatg gcaaaaaaat ttagacactg cccagttacg cacaaaatta
     1981 tttttcgcga taaaaactgg gcaaccatgc cggttgaacg ctatagttcc cgcaggggca
     2041 aaaacacata aaaaaacgct agcttttaag ctaacgtttc aaatctttta agtaataatt
     2101 ttgtttttca aaattccaaa tcgcagtaat tgaatgcgcc ttttcttctt cgtctgttgt
     2161 tttatcttcg tcacttgtat taattaaatt gccatcttcg gcatcgtcta aatttaaaat
     2221 tttatgtttt tgtttaagca atccaccata actcaacata cgttttcggt a
//
