LOCUS       NZ_CP119111             4301 bp    DNA     circular CON 05-MAY-2024
DEFINITION  Staphylococcus aureus strain GENOMIC22-001 plasmid pCFSAN126946_02,
            complete sequence.
ACCESSION   NZ_CP119111
VERSION     NZ_CP119111.1
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 4301)
  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  JOURNAL   Unpublished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 4301)
  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
            CP119111.1.
            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..4301
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="GENOMIC22-001"
                     /isolation_source="EQA test strain"
                     /db_xref="taxon:1280"
                     /plasmid="pCFSAN126946_02"
                     /geo_loc_name="Denmark"
                     /collection_date="2022"
                     /collected_by="DTU National Food Institute"
     gene            join(4247..4301,1..377)
                     /gene="mobC"
                     /locus_tag="PXV45_RS14660"
                     /old_locus_tag="PXV45_14660"
     CDS             join(4247..4301,1..377)
                     /gene="mobC"
                     /locus_tag="PXV45_RS14660"
                     /old_locus_tag="PXV45_14660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002449121.1"
                     /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_275276609.1"
                     /translation="MFRTKWLEYTTLAKPLYYLASDLSVGGNRKPNRKEPKQISFRVSE
                     QEYSKLKQSAETLNMTVPNFVKKKAQGSRLVSPKLDKETRQSIAKDLSHLGSNVNQIAK
                     WFNQNKDKATHLPEEKYHDLEKQFDDVKKELHKIWQQLN"
                     /name="mobC"
     gene            359..1321
                     /locus_tag="PXV45_RS14665"
                     /old_locus_tag="PXV45_14665"
     CDS             359..1321
                     /locus_tag="PXV45_RS14665"
                     /old_locus_tag="PXV45_14665"
                     /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_000246202.1"
                     /translation="MATTKLGNTKSASRAINYAEERAEEKSGLNCDVDYAKSYFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTAKECNEIGLELAKKIAPDYQVAVYTHTDKDHYHNHI
                     IINSVNLETGNKYQSNKEQRDFIKKANDQLCEERGLSVPEKSSEIRYTLAEQNMIDKDK
                     RSWKNDIRMAVEETKDNAVDFEEFNTLLKEKGVEITRVTKNNVTYRHIEEDKKVRGNKL
                     GDSYDKGVIENGFAIEKFRREREEEREYDEYADTFEVDWDAVAENSEDLRKRRIARTEE
                     TKQASNKIYIRDERTTGLERKGIAGNQVEFEKDDGGLSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1290..1745
                     /locus_tag="PXV45_RS14670"
                     /old_locus_tag="PXV45_14670"
     CDS             1290..1745
                     /locus_tag="PXV45_RS14670"
                     /old_locus_tag="PXV45_14670"
                     /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            2306..3250
                     /locus_tag="PXV45_RS14675"
                     /old_locus_tag="PXV45_14675"
     CDS             2306..3250
                     /locus_tag="PXV45_RS14675"
                     /old_locus_tag="PXV45_14675"
                     /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            3258..4106
                     /gene="str"
                     /locus_tag="PXV45_RS14680"
                     /old_locus_tag="PXV45_14680"
     ARG             3259..4103
                     /name="str"
                     /gene="str"
                     /gene_name="streptomycin adenylyltransferase Str"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2307..3250
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          360..1318
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggctagcga tttgtctgtt gggggaaacc gtaaacccaa ccgcaaagag ccaaaacaaa
       61 ttagtttcag agtgagtgaa caggaatatt caaagttgaa acagtcggca gaaactttga
      121 atatgacagt gcctaatttc gttaagaaaa aggcacaagg cagtcgatta gtgtcgccaa
      181 aattagacaa agaaacgcga caatcgattg ccaaagattt aagtcatttg ggtagtaatg
      241 tgaatcagat tgctaagtgg tttaatcaaa ataaagataa ggctacacat ttaccagaag
      301 agaaatatca tgatttagaa aagcaatttg atgatgtgaa aaaggagttg cataagatat
      361 ggcaacaact aaattaggca atacgaagtc ggcaagtcgt gccattaatt acgcagaaga
      421 acgtgcagaa gaaaaaagcg gcttaaattg tgatgttgat tatgctaaat catattttaa
      481 gcaaactagg gcgttatatg gcaaagagaa tggtgttcaa gcacatacag tcattcaatc
      541 ttttaagcct ggcgaagtaa cagctaaaga gtgtaatgag ataggtttag aattagctaa
      601 aaaaattgca ccagattatc aagttgcagt ttatacacat acagacaaag accattatca
      661 caatcacatt attattaatt cagtaaattt agaaacaggc aacaagtatc agtcaaacaa
      721 agaacaacgt gattttataa aaaaggcgaa tgatcagtta tgtgaagaac gtggtttatc
      781 tgtgccagaa aagtcatcag aaatcagata tacgttggca gaacagaaca tgatagataa
      841 agataaaagg tcatggaaaa atgatataag aatggcagtt gaagaaacaa aggataacgc
      901 agtagacttt gaagaattta atactttgct aaaagaaaaa ggtgttgaaa tcacgagagt
      961 aacgaaaaac aacgtaacgt atagacacat tgaagaagat aaaaaagtac gtgggaataa
     1021 gttgggcgat tcttatgaca aaggagtgat tgaaaatggc tttgcaatcg agaaattcag
     1081 acgagaacga gaagaagaac gagaatacga tgaatatgca gacacgttcg aagttgactg
     1141 ggacgcagtc gcagaaaatt cagaagacct tagaaaacga agaattgcaa gaactgaaga
     1201 aacaaaacaa gctagtaata aaatatatat cagagatgaa agaacaacag gacttgagag
     1261 aaaaggaatt gcaggcaatc aagtcgagtt tgaaaaagac gacggaggac tttcaaggta
     1321 gaggtaaaaa agtccataat gattttgttc gtttgttaca aaagaattta aatcgagtga
     1381 atgcagaaga tattgagata gaggttcgaa aagatgttta tggagttcga gaagaaattc
     1441 attcgatgtt gcgtgaagtt aaacaatcac atgaacatta tcaaaaaaga caaaagcaat
     1501 tatttactgg tattggtgca atgttattag tgtttatgct ttttgctttg attatgacga
     1561 ttggcagaga ttttatgggc tttttacatg tagatgtatt acagaatgcc atagcaagca
     1621 aaataaaggc ttctgagggc tttatttcag ttttatggta cattgcttat ggtttacctt
     1681 atatactcgc tatagggcta tttatttggt tgtatgagtg gataagagca agattccatg
     1741 attaaacaaa gtatgatcag gcttttatgc cgagaaaatt tatttatatt gagaagtacc
     1801 cttaactaaa cttgcagacg aatgtcggca tagcgtgagc tattagcccg accattcgac
     1861 aagttttggg tttgttaagg gtacagaggc tcaatgtaaa taaagcaatt ggaataaagc
     1921 aacaaagggg gttgaagaaa atgagtaaga agaaaaagat taatttagca atatcaattg
     1981 ctcaagtagt agtgcaggcg ttaatacttt ataacactta tcagcaatat aaatattcta
     2041 aaaaatattc agcctaataa aaaaagactt agtctgaata gaccaagcct tttgttagtg
     2101 ttatattaat atgcaaataa aaaaacaaaa aaagaagtcg ctcactccct gaccaaagtt
     2161 tgtgaatgcg acttacctta aagaaaaaca gttggtgttt ttttcttaat ttttgtatat
     2221 ctagatatta aacgatattg gtttattctt caagatatat attcgggtga gcgacttctt
     2281 aaacaaaata aggagtcgat tttttatgag taaaaaagca gaagaaattc aggcaaaaca
     2341 aagtttggaa aaggaaaact caaatttttc taaaaccgga tactctaata gccggttaaa
     2401 ccgacatatt atgtacaccc ccgaaccaaa attacacttt gatgctatga caattgttgg
     2461 gaatcttaat aagaacaatg ctcacaaact gtctgaattt atgagtattg cgccacaaat
     2521 tagactttgg gatatattac aaaccaaatt taaagctaag gctctacaag aaaaagttta
     2581 catcgaatat gataaagtaa aagcagatgc gtgggataga cgtaatatgc gtgttgaatt
     2641 taatcctaat aaacttacgc atgaagaaat gctttggtta aaacaaaaca tcattgacta
     2701 catggaagat gatggtttta caagattaga tttggctttt gattttgaag acgatttgag
     2761 cgattattat gcgatgactg ataaatcagt taagaaaact attttttatg gtcgtaacgg
     2821 taaaccagaa acaaaatatt ttggtgttcg tgacagtgat agatttatta gaatttataa
     2881 taaaaaacaa gaacgtaagg ataatgcaga cattgaagtt atgtctgaac acttatggcg
     2941 tgtagaaatt gaattaaaaa gagatatggt tgattattgg aacgattgtt ttaatgattt
     3001 acatattttg aaaccagatt ggtctagttt agaaaaagta aaagaccaag caatgattta
     3061 tatgctaatt catgaagaaa gtacatgggg taaattagaa agacgtacaa aaaataaata
     3121 cagagaaatg ttaaaaagta tttcagaaat tgatttaacg gacttaatga aattgacttt
     3181 aaaagagaat gaaaaacaat tgcaaaagca gattgaattt tggcagcgtg aatttagatt
     3241 ttgggagtga aaaaacaatg aggactgaaa aagaaatttt aaatttagtt tctgaatttg
     3301 cttatcaacg aagcaatgta aaaattattg ctctcgaggg ttcaagaact aatgaaaata
     3361 taaaaaaaga taagtttcaa gattatgatt ttgctttttt cgtatcagat attgagtatt
     3421 tcacacatga agaaagttgg ttaagtttat ttggagaatt attgtttata cagaaaccag
     3481 aagatatgga attattccca cctgatttag attatggtta cagttatata atgtatttta
     3541 aagatggcat aaaaatggat attacattaa ttaatttaaa agatttaaat cgttatttta
     3601 gtgattctga tggtcttgta aaaattttag ttgataaaga taatttagta actcaagaaa
     3661 ttgttccaga tgactcaaat tattggttaa aaaaaccaac agaacgagaa ttttatgatt
     3721 gctgtaatga gttttggagt gtctcaacgt atgtagcaaa gggtgttttt agaagagaaa
     3781 tattatttgc tttagatcat ttcaataata ttttacgtcc tgaattatta agaatgattt
     3841 cttggtatat tggctttaat aggggttttg attttagttt aggaaagaat tataagttta
     3901 taaacaaata tttaactgat aaagaattca atatgctttt agctactttt gagatgaatg
     3961 gatatagaaa gacataccaa tcttttaagc tttgttgtga attatttaaa tattattcaa
     4021 ataaagtaag ttgtttagga aattataact atccaaatta cgaaaaaaat attgagaatt
     4081 ttattcgtaa taattatgag aattaatttt attagcaacc acatttttgg ttgcttttgt
     4141 tttgattttg aatttggttt tgaactatga gtggctagca ttttgccact cattttttgc
     4201 gttagcaaaa acataaaggg tctgggatta atcccagcaa gccggtatat tcagaacgaa
     4261 gtggctagaa tatacgacgc ttgccaaacc actatattac t
//
