LOCUS       NZ_CP117243             4439 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Staphylococcus aureus strain ATCC 14458 plasmid pATCC14458_2,
            complete sequence.
ACCESSION   NZ_CP117243
VERSION     NZ_CP117243.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32977647
            Assembly: GCF_028596165.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4439)
  AUTHORS   Johnson,J.D., Blankenship,H. and Soehnlen,M.
  TITLE     Long read genome assemblers struggle with small plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4439)
  AUTHORS   Johnson,J.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JAN-2023) Bureau of Laboratories, Michigan Department
            of Health and Human Services, 3350 N Martin Luther King Blvd.,
            Lansing, MI 48906, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2022
            Assembly Method                   :: Trycycler v. v0.5.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 108x
            Sequencing Technology             :: Oxford Nanopore, Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028596165.1-RS_2024_03_23
            Annotation Date                   :: 03/23/2024 03:22:04
            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)                     :: 2,977
            CDSs (total)                      :: 2,895
            Genes (coding)                    :: 2,826
            CDSs (with protein)               :: 2,826
            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)              :: 69
            CDSs (without protein)            :: 69
            Pseudo Genes (ambiguous residues) :: 0 of 69
            Pseudo Genes (frameshifted)       :: 33 of 69
            Pseudo Genes (incomplete)         :: 41 of 69
            Pseudo Genes (internal stop)      :: 11 of 69
            Pseudo Genes (multiple problems)  :: 16 of 69
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117243.1.
            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..4439
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="ATCC 14458"
                     /db_xref="taxon:1280"
                     /plasmid="pATCC14458_2"
                     /geo_loc_name="USA"
                     /collection_date="2022"
     gene            1..945
                     /locus_tag="PQQ25_RS14865"
                     /old_locus_tag="PQQ25_14860"
     CDS             1..945
                     /locus_tag="PQQ25_RS14865"
                     /old_locus_tag="PQQ25_14860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /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_000277654.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKQERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     VDLTDLMKSTLKANEKQLQKQIDFWQHEFKFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1107..2486
                     /gene="tet(K)"
                     /locus_tag="PQQ25_RS14870"
                     /old_locus_tag="PQQ25_14865"
     ARG             1108..2483
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2672..3913
                     /gene="mobV"
                     /locus_tag="PQQ25_RS14875"
                     /old_locus_tag="PQQ25_14870"
     CDS             2672..3913
                     /gene="mobV"
                     /locus_tag="PQQ25_RS14875"
                     /old_locus_tag="PQQ25_14870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000122374.1"
                     /translation="MSYSIVRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNANKQNFNNLIDEKIEQNYTGKRKIRTDAIKHIDGLITSDNDFFDNQTPEDTKQFF
                     EYAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKEVVGNKKALTAFQ
                     DRFNEHVKQRGYDLERGQSRQVTNAKHEQISQYKQKTEYHKQEYERESQKTDHIKQKND
                     KLMQEYQKSLNTLKKPINVPYEQETEKVGGLFSKEIQETGNVVISQKDFNEFQKQIKAA
                     QDISEDYEYIKSGRALDDKDKEIREKDDLLNKAVERIENADDNFNQLYENAKPLKENIE
                     IALKLLKILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQ
                     EQQKNQKRDRGMHL"
                     /name="mobV"
     Typing          2..945
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2673..3910
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtataaaa acaatcatgc aaatcattca aatcatttgg aaaatcacga tttagacaat
       61 ttttctaaaa ccggctactc taatagccgg ttggacgcac atactgtgtg catatctgat
      121 ccaaaattaa gttttgatgc aatgacgatc gttggaaatc tcaaccgaga caacgctcaa
      181 gccctttcta aatttatgag tgtagagccc caaataagac tttgggatat tcttcaaaca
      241 aagtttaaag ctaaagcact tcaagaaaaa gtttatattg aatatgacaa agtgaaagca
      301 gatagttggg atagacgtaa tatgcgtatt gaatttaatc caaacaaact tacacgagat
      361 gaaatgattt ggttaaaaca aaatataata agctacatgg aagatgacgg ttttacaaga
      421 ttagatttag cctttgattt tgaagatgat ttgagtgact actatgcaat gtctgataaa
      481 gcagttaaga aaactatttt ttatggtcgt aatggtaagc cagaaacaaa atattttggc
      541 gtgagagata gtaatagatt tattagaatt tataataaaa agcaagaacg taaagataat
      601 gcagatgctg aagttatgtc tgaacattta tggcgtgtag aaatcgaact taaaagagat
      661 atggtggatt actggaatga ttgctttagt gatttacata tcttgcaacc agattggaaa
      721 actatccaac gcactgcgga tagagcaata gtttttatgt tattgagtga tgaagaagaa
      781 tggggaaagc ttcacagaaa ttctagaaca aaatataaga atttgataaa agaaatttcg
      841 ccagtcgatt taacggactt aatgaaatcg actttaaaag cgaacgaaaa acaattgcaa
      901 aaacaaatcg atttttggca acatgaattt aaattttgga aatagtgtac atattaatat
      961 tactgaacaa aaatgatata tttaaactat tctaatttag gaggattttt ttatgaagtg
     1021 tctatttaaa aatttgggga atttatatga ggtgaaagaa taatttaccc ctataaactt
     1081 tagtcacctc aagtaaagag gtaaaattgt ttagtttata taaaaaattt aaaggtttgt
     1141 tttatagcgt tttattttgg ctttgtattc tttcattttt tagtgtatta aatgaaatgg
     1201 ttttaaatgt ttctttacct gatattgcaa atcattttaa tactactcct ggaattacaa
     1261 actgggtaaa cactgcatat atgttaactt tttcgatagg aacagcagta tatggaaaat
     1321 tatctgatta tataaatata aaaaaattgt taattattgg tattagtttg agctgtcttg
     1381 gttcattgat tgcttttatt ggtcacaatc acttttttat tttgattttt ggtaggttag
     1441 tacaaggagt aggatctgct gcattccctt cactgattat ggtggttgta gctagaaata
     1501 ttacaagaaa aaaacaaggc aaagcctttg gttttatagg atcaattgta gctttaggtg
     1561 aagggttagg tccttcaata gggggaataa tagcacatta tattcattgg tcttacctac
     1621 ttatacttcc tatgattaca atagtaacta taccttttct tattaaagta atggtacctg
     1681 gtaaatcaac aaaaaataca ttagatatcg taggtattgt tttaatgtct ataagtatta
     1741 tatgttttat gttatttacg acaaattata attggacttt tttaatactc ttcacaatct
     1801 tttttgtgat ttttattaaa catatttcaa gagtttctaa cccttttatt aatcctaaac
     1861 tagggaaaaa cattccgttt atgcttggtt tgttttctgg tgggctaata ttttctatag
     1921 tagctggttt tatatcaatg gtgccttata tgatgaaaac tatttatcat gtaaatgtag
     1981 cgacaatagg taatagtgtt atttttcctg gaaccatgag tgttattgtt tttggttatt
     2041 ttggtggttt tttagtggat agaaaaggat cattatttgt ttttatttta ggatcattgt
     2101 ctatctctat aagtttttta actattgcat tttttgttga gtttagtatg tggttgacta
     2161 cttttatgtt tatatttgtt atgggcggat tatcttttac taaaacagtt atatcaaaaa
     2221 tagtatcaag tagtctttct gaagaagaag ttgcttctgg aatgagtttg ctaaatttca
     2281 caagtttttt atcagaggga acaggtatag caattgtagg aggtttattg tcactacaat
     2341 tgattaatcg taaactagtt ctggaattta taaattattc ttctggagtg tatagtaata
     2401 ttcttgtagc catggctatc cttattattt tatgttgtct tttgacgatt attgtattta
     2461 aacgttctga aaagcagttt gaatagttat attatatttt ggtttagaac tatgagtggc
     2521 tagcattttg ccactcattt tttgcgttag caaaaacagg tttaagcctc gcagagcaca
     2581 cgtattaacg acttattaaa aataagtcta gtgtgttaga cttaaactat taaatacaca
     2641 tgaaaccttt gtgcttagga gtgattttta tatgtcttat tccattgtta gagtttcaaa
     2701 agttaaatct ggaacaaata caacgggcat acaaaaacat gttcaaagag aaaataataa
     2761 ttatgaaaat gaagatatag accatagtaa aacttactta aattatgatt tggtaaatgc
     2821 taataaacag aattttaata acttgattga tgaaaaaatc gaacagaatt atacaggcaa
     2881 aagaaaaatt agaacagacg cgattaaaca cattgatggt ttaattacat cagacaatga
     2941 tttctttgat aatcaaacgc cagaagatac aaagcagttt tttgaatatg ctaaagagtt
     3001 tttagaacaa gaatacggta aagataattt attatatgca acagttcaca tggacgaaaa
     3061 aacaccacat atgcattatg gcgttgttcc aataactgat gatggtcgtt taagtgctaa
     3121 agaagttgta ggtaataaaa aagctttaac agcgtttcaa gatagattta atgagcatgt
     3181 taaacaacga ggatatgatt tagaacgtgg gcaatcaaga caagtaacaa atgctaaaca
     3241 tgagcaaata agtcagtata aacaaaaaac agaatatcat aagcaagaat atgaacgtga
     3301 gagccaaaaa acagaccata taaagcaaaa gaacgataaa ttaatgcaag agtaccaaaa
     3361 atcgttaaat acgcttaaaa agcctataaa tgttccgtat gagcaagaaa ctgaaaaagt
     3421 aggtggttta tttagcaaag aaatacaaga aactggaaat gttgtaataa gccaaaaaga
     3481 tttcaatgaa tttcagaaac agataaaagc tgctcaagat atttcggaag attacgagta
     3541 tataaagtct ggtagagcct tagatgataa agataaggaa atacgagaga aagatgattt
     3601 attaaataaa gcagttgagc gtattgaaaa cgcagacgat aattttaacc aactttacga
     3661 aaatgcaaag ccacttaaag agaatataga aatagcgtta aagcttttaa aaatcttact
     3721 aaaagagtta gaacgagttt taggaagaaa tacctttgcg gaaagagtta ataagttaac
     3781 agaagatgaa ccaaaactaa atggtttagc aggaaactta gataaaaaaa tgaatccaga
     3841 attatattca gaacaggaac agcaacaaga acaacaaaag aatcaaaaac gagatagagg
     3901 tatgcactta tagaacatgc atttatgccg agaaaactta ttggttggaa tgggctatgt
     3961 gttagctaac ttgttagcga gttggttgga cttgaattgg gattaatccc aagaaagtac
     4021 caactcaaca acacataaag ccctgtaggt tccgaccaat aaggaaattg gaataaagca
     4081 ataaaaggag ttgaagaaat gaaattcaga gaagcctttg agaattttat aacaagtaag
     4141 tatgtacttg gtgttttagt agttttaact gtttaccaga taatacaaat gcttaaataa
     4201 aaaaagactt gatctgatta gaccaagtct tttgatagtg ttatattaat aacaaaataa
     4261 aaaggagtcg ctcacgccct gatcaaagtt tgtgaacgac atcattcaaa gaaaaaaaca
     4321 ctgagttgtt tttataatct tgtatattta gatattaaac gatatttaaa tatacatcaa
     4381 gatatatatt tgggtgagcg attccttaaa cgaaattgag attaaggagt cgatttttt
//
