LOCUS       NZ_CP117241             4326 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Staphylococcus aureus strain ATCC 14458 plasmid pATCC14458_1,
            complete sequence.
ACCESSION   NZ_CP117241
VERSION     NZ_CP117241.1
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 4326)
  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  JOURNAL   Unpublished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 4326)
  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
            CP117241.1.
            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..4326
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="ATCC 14458"
                     /db_xref="taxon:1280"
                     /plasmid="pATCC14458_1"
                     /geo_loc_name="USA"
                     /collection_date="2022"
     gene            complement(437..1987)
                     /gene="mobV"
                     /locus_tag="PQQ25_RS00280"
                     /old_locus_tag="PQQ25_00280"
     CDS             complement(437..1987)
                     /gene="mobV"
                     /locus_tag="PQQ25_RS00280"
                     /old_locus_tag="PQQ25_00280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000331753.1"
                     /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_083553339.1"
                     /translation="MSYSIIRVAKVKGKTNTTGIQKHVQRENKNYENLDIDLEKSHLNY
                     DLVNDEPIEFNSMIDEKIEENYTGNRKIRSDAVKHVDGIITSDNEFFDFKSQQQIQAFF
                     EDSKQFLEDEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKDVVGNKKALTEFQ
                     DRFNQYLNDKGHNLERGESKHKTERKHKQVERYKSETQYHGKEKNKAERLAKITEIQVR
                     DKEQLLKRYDKELQPMKKQYDEMKNEVDDWEKVKIPKLKQKAKELNNQNAQESRKIDDL
                     KQKQDDLISTFRRIDSDIEKYKEQREHEKALRDQIRADKEKEEEQYQNLVKVLNEPIND
                     EYEHEYKKPSIFSKEKEPTGKVIISENDYKILKQRSALAARLEPTFTELNSGKERKQDK
                     EHIGRLQDENSKLKKQNKKVANERDEVIREHKSDISLVKSGCKIIKKAVGEDVYHKGIN
                     MIDNKVKSNFKDKYREMVTVDDNDKRMFQLKDNEVKRMQFENSKMRSKGKDKGFDLDR"
                     /name="mobV"
     gene            complement(2239..2886)
                     /locus_tag="PQQ25_RS00285"
                     /old_locus_tag="PQQ25_00285"
     CDS             complement(2239..2886)
                     /locus_tag="PQQ25_RS00285"
                     /old_locus_tag="PQQ25_00285"
                     /EC_number="2.3.1.28"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000143686.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type A-8 chloramphenicol O-acetyltransferase"
                     /protein_id="WP_002352254.1"
                     /translation="MTFNIINLETWDRKEYFNHYFNQQTTYSVTKEFDITLLKSMIKNK
                     GYELYPALIYTIVNIINQNKVFRTGINSEGNLGYWDKLNPLYTVFNKETEKFSNIWTES
                     NVSFNSFYNSYKSDLLEYKDKNEMFPKKPIPENTVPISMIPWIDFSSFNLNIGNNSRFL
                     LPIITIGKFYSKNNKIYLPVSLQVHHAVCDGYHVSLFMSEFQNIVDSVNEWI"
                     /name="type A-8 chloramphenicol O-acetyltransferase"
     gene            complement(3021..3965)
                     /locus_tag="PQQ25_RS00290"
                     /old_locus_tag="PQQ25_00290"
     CDS             complement(3021..3965)
                     /locus_tag="PQQ25_RS00290"
                     /old_locus_tag="PQQ25_00290"
                     /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_017431565.1"
                     /translation="MSKNNHANHSNHLENHDLDNFSKTGYSNSRLNRHTMYTPEPKLSF
                     DAMTIVGNLNKNNAHKLSEFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEYDLSDYYAMTDKSVK
                     KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADIKIMSEHLWRVEIELKRDMV
                     DYWNDCFNDLHILQPDWKTIERTSDRAMVFMLLNDEEEWGKLERRTKNKYKKLIKEISL
                     IDLTDLMKSTLKANEKQLQKQIDFWQREFRFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     ARG             complement(2243..2886)
                     /name="catA"
                     /gene="catA"
                     /gene_name="type A-8 chloramphenicol O-acetyltransferase"
                     /tool="amrfinderplus"
                     /drug_class="PHENICOL"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(2240..2886)
                     /name="catA8"
                     /gene="catA8"
                     /gene_name="chloramphenicol acetyltransferase (CAT)"
                     /tool="rgi"
                     /drug_class="phenicol antibiotic"
                     /identity="99.53"
                     /coverage="100.0"
     Typing          complement(3022..3908)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.887"
                     /coverage="94.0"
                     /evalue="0.0"
ORIGIN
        1 tttattccaa ttgctttatt gacgttgagc ctcggaaccc ttaacaatcc caaaacttgt
       61 cgaatggtcg gcttaatagc tcacgctatg ccgacattcg tctgcaagtt tagttaaggg
      121 ttcttctcaa catcaataaa ttttctcggc ataaatgcgt gctctacttt ttattttcac
      181 tcactttgat aacaagaaat gccattccaa tacaaaacca catacctata atcgatatcc
      241 aaatagcagt cataaaatcg ctccttttta gcaaacttta tcacaaaaaa tattaaaatt
      301 ttaaatacct gttataatat taatatagca atgagaagtg acggcttctc cttcagaaat
      361 catcaatcaa tgatttcttt tataagtgtt aataaggctt ttaacagatt aattatttct
      421 gttaaaagcc ttatttttat ctatccaaat caaaaccttt atctttgcct ttactacgca
      481 tcttactatt ctcaaattgc atacgtttca cttcgttatc ttttagttgg aacatacgtt
      541 tatcattgtc atcaacagta accatttctc tgtatttatc tttaaaatta cttttaactt
      601 tattatcaat catattaatc cctttatgat aaacatcttc cccaactgct tttttgatta
      661 ttttacatcc acttttcaca agacttatat ctgatttatg ctctcttatc acttcatcac
      721 gttcatttgc tactttttta ttttgtttct taagttttga attttcatcc tgtaaacgtc
      781 caatatgctc tttatcttgc ttacgttctt ttcctgagtt taattctgtg aatgttggtt
      841 ctaaacgagc agctaacgct gatcgttgtt taagtatttt ataatcattt tcagaaataa
      901 ttaccttccc tgttggctct ttctcttttg aaaatatact cggcttttta tattcatgct
      961 catattcgtc atttataggc tcatttagga ctttcactaa attttggtat tgttcttctt
     1021 ccttttcttt atcggctctt atttggtctc tcagtgcctt ctcatgctct ctttgctctt
     1081 tatatttctc gatatcgcta tctattctcc taaatgtgct tataaggtca tcttgtttct
     1141 gttttaaatc atctattttt cgagattctt gcgcattttg attatttaat tctttcgctt
     1201 tctgtttcaa tttcggtatt ttaactttct cccaatcatc aacttcattt ttcatctcgt
     1261 catattgttt tttcatcggt tgcaattctt tgtcataacg cttgagtaat tgttctttat
     1321 cacgtacttg tatttcagtg atcttagcta atctttcggc tttatttttc tcttttccat
     1381 gatactgtgt ttcactctta tatctttcaa cctgcttatg cttacgctct gttttatgtt
     1441 tggattctcc acgctctaaa ttatgccctt tatcattcaa atattgatta aatctatctt
     1501 gaaattccgt taaagctttt ttattaccca caacatcttt agcacttaaa cgaccatcat
     1561 ctgtaattgg cacaacacca taatgcatat gtggtgtttt ctcgtccata tggacggttg
     1621 cataaagtaa attatctttt ccgtactcat cttctagaaa ttgctttgaa tcttcaaaaa
     1681 aggcctgtat ttgttgttgt gacttaaaat caaaaaattc attatctgac gtaataatgc
     1741 catcaacatg tttaactgca tcacttcgta tttttctatt acctgtataa ttctcttcaa
     1801 ttttttcatc aatcatcgaa ttaaattcaa tcggctcatc atttactaaa tcataattca
     1861 aatgtgattt ttctaaatct atatccaaat tttcatagtt tttattttct ctttgtacat
     1921 gtttttgaat acctgttgta tttgtttttc ctttgacttt agcaactcga attatggaat
     1981 aagacatatt aaattccctc cactcattat gttttcaagg actttatttc tattaagtat
     2041 aacacactag acttatttac tacgtttcat aagtcattag tgcgtgtgct ctgcgaggct
     2101 tgtttttgtg caagcacaaa aaatggactg aacaagtcag tccataagtt caaaacctaa
     2161 acctaagcaa ccaaaattgt ggttgctata aacttataaa tatcataatt acttaagttt
     2221 atgaaagtta ttttagattt aaatccattc atttacacta tcaactatat tttgaaattc
     2281 actcataaat aatgaaacat ggtaaccatc acataccgca tgatgaactt gcaatgagac
     2341 tggtaaatag atcttattat tcttactata aaatttacct attgtaataa ttggcaatag
     2401 gaatctacta ttattaccaa tatttaaatt aaatgaacta aaatcaatcc aaggaatcat
     2461 cgaaatagga actgtgtttt caggtattgg ttttttagga aacatttcat ttttatcttt
     2521 atattcaagt aagtcactct tataactatt ataaaaagaa ttaaaactaa catttgattc
     2581 tgtccaaatg ttagaaaatt tttcagtttc tttattaaag actgtatata aagggtttaa
     2641 tttatcccaa taacccaaat ttccctcact attaattcct gttctaaata ctttattttg
     2701 atttataata tttacaattg tataaatcaa agcaggatac agttcatatc ctttattttt
     2761 tatcatactt ttaagtaaag tgatatcaaa ttctttagta acactgtaag ttgtttgttg
     2821 attgaaataa tgattaaaat attcttttct atcccaagtt tccaaattaa taatattaaa
     2881 agtcatatat aattttcctc ctaaatttca tcttatctct ttgtatttag gaggaataat
     2941 cctctgattt tttcatatat tgtgtcacct cttaaacgtt aattatacta aagtaacatt
     3001 ttgtataaaa caaagttact ttacttccaa aatctaaatt cacgttgcca aaaatcaatc
     3061 tgcttttgca attgtttttc gttcgctttt aaagtcgatt tcattaaatc agttaaatca
     3121 attagagata tttctttaat taatttttta tatttattct tagtacgtct ttctaatttt
     3181 ccccattctt cttcatcatt caacaacata aaaaccattg ctctatcaga agtacgttcg
     3241 atagttttcc aatctggttg taatatatgt aaatcattaa aacaatcgtt ccaataatca
     3301 accatatctc tttttaattc aatttctaca cgccataagt gttcagacat aattttaata
     3361 tctgcattat ctttgcgttc ctgtttttta ttataaattc taataaatct atcactgtca
     3421 cgaacaccaa aatatttcgt ttctggttta ccgttacgac cataaaaaat agttttctta
     3481 actgatttat cagtcattgc ataataatca cttaaatcat attcaaaatc aaaagctaaa
     3541 tctaatcttg taaaaccatc gtcttccatg tagtcgataa tgttttgttt taaccaaagc
     3601 atttcttcat gcgtaagttt atttggatta aattcaacac gcatattacg tctatcccac
     3661 gtatctgctt ttactttgtc atattcgata taaacttttt cttgtagagc tttagcttta
     3721 aatttagttt gtagtatatc ccaaagtcga atttgtggct cgacactcat aaattcagat
     3781 agtttgtgag cattattttt attaagattt ccaacaatag tcatagcgtc aaaacttaat
     3841 tttggttccg gggtgtacat agtatgtcgg tttaaccggc tattagagta gccggtttta
     3901 gaaaaattgt ctaaatcgtg attttctaaa tgatttgaat gatttgcgtg attattttta
     3961 ctcataaaaa atcgactcct taatttactt taagaagtcg ctcacccaaa tatatatctt
     4021 gaagaataaa cttatatcgt ttaatatcta gatatacaaa aattaataaa acataactct
     4081 ttatatttta tttaggtaag tcgcattcac aaactttggt aggggcgtga gcgacttctt
     4141 tttatttgtt tattaatata acactatcaa aagacttggt ctaattagat caggtctttt
     4201 ttagtaccaa aacttattac ataatcaaaa ttaaaattat ctataaaata agtcatatca
     4261 aggaacttaa attttctcgg caacggaact taaaatctgt cggtacggga acttaaattt
     4321 tgttgc
//
