LOCUS       NZ_CP014418             3567 bp    DNA     circular CON 17-MAY-2024
DEFINITION  Staphylococcus aureus strain USA300-SUR15 plasmid pUSA07-1-SUR15,
            complete sequence.
ACCESSION   NZ_CP014418
VERSION     NZ_CP014418.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04497609
            Assembly: GCF_002000685.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3567)
  AUTHORS   Sabat,A.J., Hermelijn,S.M., Akkerboom,V., Juliana,A., Degener,J.E.,
            Grundmann,H. and Friedrich,A.W.
  TITLE     Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA
            USA300 (ST8-spa t008) in an academic hospital of Paramaribo,
            Republic of Suriname
  JOURNAL   Sci Rep 7, 41050 (2017)
   PUBMED   28106148
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3567)
  AUTHORS   Sabat,A.J., Hermelijn,S., Akkerboom,V., Degener,J.E., Grundmann,H.
            and Friedrich,A.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-FEB-2016) Medical Microbiology, University Medical
            Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SeqMan NGen v. 12.1.0
            Genome Coverage                   :: missing
            Sequencing Technology             :: Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002000685.1-RS_2024_05_17
            Annotation Date                   :: 05/17/2024 01:29:08
            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)                     :: 3,036
            CDSs (total)                      :: 2,955
            Genes (coding)                    :: 2,865
            CDSs (with protein)               :: 2,865
            Genes (RNA)                       :: 81
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 90
            CDSs (without protein)            :: 90
            Pseudo Genes (ambiguous residues) :: 0 of 90
            Pseudo Genes (frameshifted)       :: 49 of 90
            Pseudo Genes (incomplete)         :: 43 of 90
            Pseudo Genes (internal stop)      :: 18 of 90
            Pseudo Genes (multiple problems)  :: 19 of 90
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP014418.1.
            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..3567
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="USA300-SUR15"
                     /isolation_source="Nose"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pUSA07-1-SUR15"
                     /geo_loc_name="Suriname: Paramaribo"
                     /lat_lon="5.866667 N 55.166667 W"
                     /collection_date="2013-05-17"
                     /collected_by="Sandra Hermelijn"
     gene            29..967
                     /locus_tag="AYM28_RS15650"
                     /old_locus_tag="AYM28_15270"
     CDS             29..967
                     /locus_tag="AYM28_RS15650"
                     /old_locus_tag="AYM28_15270"
                     /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_029264623.1"
                     /translation="MIKKAEEIQAKQSLENENLNFSKTGYSNSRLSVQTLGQSQPKLSF
                     DAMTIVGNLNKNNAQKLSEFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHDEMLWLKKNVIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKTVK
                     KTVLYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVMSEHLWRVEVELKRDMV
                     DYWNDCFNDLHILKPAWTTLEKINEQAMVYTLLHEESMWGKLSRNTKYKFKNLIKEISP
                     VDLTELMKSTLKANEKQLQKQIDFWLSDFEF"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1209..2477
                     /gene="mobV"
                     /locus_tag="AYM28_RS15655"
                     /old_locus_tag="AYM28_15275"
     CDS             1209..2477
                     /gene="mobV"
                     /locus_tag="AYM28_RS15655"
                     /old_locus_tag="AYM28_15275"
                     /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_031766525.1"
                     /translation="MPYSIIRVAKVKSKTNTKGIQKHVQRQNKNYENMDIDLEKSYLNY
                     DLVNDSPIDYNQKIDEKIEQNYNGKRKIRKDAVKHIDGLITSGNEFFKNQTLEETKQFF
                     EHAKTFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITEDGRLSAKEVLGNKKALTEFQ
                     DRFNEHINSCGYDLSRGITRGVTPRRHEQISRYKNLTDYHKEEYEHESRKLDRIKQESE
                     EVMEQYQNALDVLKKPINVPYELETEKVGGLFNKETQETGNVVIDKNEFDLLQEQVKAS
                     QLITDDYEYIKSGKALKDFEEKNKRLEDRLLDEQIKNGKVIDEYNDLADSYNNLLEQNQ
                     EKEKELNRSYKLFNNVFKLIKGVMKEETYHSLINHIDNHLESSKMRETMIVDDNDEQFF
                     KKKYQRHEPEIIFEDERDDGYTL"
                     /name="mobV"
     gene            complement(2648..2971)
                     /gene="qacC"
                     /locus_tag="AYM28_RS15660"
                     /old_locus_tag="AYM28_15280"
     ARG             complement(2652..2971)
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="99.07"
                     /coverage="100.0"
     ARG             complement(2649..2971)
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="71.03"
                     /coverage="100.0"
     Typing          78..947
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.317"
                     /coverage="93.0"
                     /evalue="0.0"
     Typing          1150..2474
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.774"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttaaattaaa ttaaggagtt gtttttttat gattaaaaaa gcagaagaaa ttcaggcaaa
       61 acaaagctta gaaaacgaaa acttaaattt ttctaaaacc ggatactcta atagccggtt
      121 aagtgttcaa actttgggac aatctcaacc aaaattaagt tttgatgcta tgactattgt
      181 tggaaatctt aataaaaata atgctcaaaa actatctgaa tttatgagtg ttgagccaca
      241 aattagactt tgggatatat tacaaacaaa atttaaagct aaagcacttc aagaaaaagt
      301 ttatattgaa tatgacaaag taaaagcaga tacatgggat agacgtaata tgcgggttga
      361 atttaatccg aataaattaa cacacgatga aatgctatgg ttaaagaaaa atgttatcga
      421 ctacatggaa gatgacggtt ttacaagatt agatttggct tttgattttg aagatgattt
      481 aagcgattac tatgcaatga ctgataaaac agttaaaaaa actgttttat atggtcgtaa
      541 tggcaagcca gaaacaaaat attttggagt tcgtgatagt gatagattta ttagaattta
      601 taataaaaaa caagaacgta aagataacgc agatgttgaa gttatgtctg aacatctgtg
      661 gcgtgtagaa gttgaattga aaagagatat ggttgattac tggaatgatt gttttaatga
      721 cttacacatt ttgaaacctg cgtggactac tttagaaaaa attaatgagc aagctatggt
      781 ttatactttg ctgcatgaag aaagtatgtg gggaaaatta agtaggaata ctaagtataa
      841 atttaaaaat ttaattaaag aaatatctcc agttgattta acggaattaa tgaaatcgac
      901 tttaaaagca aacgaaaaac aattgcaaaa gcagattgat ttttggctat cagattttga
      961 attttgagtg cattaaattt tatacacgaa gtgatcataa aatttaaaaa cgaatttgcg
     1021 accaccattt ttggtcgcag gttttgaact tatggactga cttgttcagt ccattttttg
     1081 tgcttgcaca aaaactagcc tcgcagagca cacggtttaa cgacttaatt acgaagtaaa
     1141 taagtctagt gtgttatact ttaataaata aagctacgca aaaacatgtg cagtggaggg
     1201 attttaatat gccgtattct attatcagag ttgctaaagt aaaatcaaaa acgaatacaa
     1261 aaggtattca aaaacatgta caaagacaaa ataaaaatta tgaaaatatg gatattgatt
     1321 tagaaaaatc atacttaaat tatgatttag tcaatgatag tccgattgat tataatcaaa
     1381 aaatcgatga gaaaattgaa caaaattata atgggaaacg caaaattaga aaagacgcag
     1441 taaaacatat tgatggttta attacatctg gtaatgaatt ttttaaaaat caaacacttg
     1501 aagaaacaaa gcagtttttt gaacatgcta aaacgttttt agaacaagag tatggaaaag
     1561 ataatttatt atatgcaaca gtgcatatgg acgaaaaaac acctcatatg cattatgggg
     1621 tagttccgat tacagaagat ggtcgattga gtgcgaaaga ggttttaggt aataaaaagg
     1681 cactaactga atttcaagat agatttaacg aacatatcaa tagttgtggt tatgacttga
     1741 gtagaggtat aacaaggggc gttacaccga gacgacatga gcagataagt cgttataaaa
     1801 atttaacaga ttatcacaaa gaagaatatg agcatgagag ccgaaaatta gaccgtataa
     1861 agcaagaaag cgaagaagta atggaacagt atcaaaatgc tttagatgtt ctaaaaaagc
     1921 ctataaatgt cccatatgag cttgaaactg aaaaagttgg tggactgttc aacaaagaaa
     1981 cacaggaaac aggtaacgtc gttattgata aaaatgaatt tgatttattg caggaacaag
     2041 taaaagcttc tcaactcatt actgatgatt atgaatatat taaaagcgga aaggctttaa
     2101 aagattttga ggaaaaaaac aaaagattag aagatagatt attagacgaa cagattaaaa
     2161 atggaaaagt aatagatgaa tacaatgatt tagcggatag ttataataat ttattggaac
     2221 aaaatcaaga aaaagaaaaa gagttaaacc gttcgtataa actatttaac aatgtgttta
     2281 agttgattaa aggtgtgatg aaagaagaaa catatcattc gttgattaac catattgata
     2341 atcacttaga aagctcaaaa atgcgagaaa caatgattgt agatgataac gatgaacaat
     2401 tctttaagaa aaaatatcaa aggcatgaac cagaaattat ttttgaagat gaacgagatg
     2461 atggctacac tttataaaga cgacgcattt atgccgagaa aatttattgt gcgttgagaa
     2521 gaacccttaa ctaaacttgc agacgaaagt cggcatagcg tgagctatta agccgaccat
     2581 tcgacaagtt ttgggtttgt taagggttcg gaggctcaac gtcaataaag caattggaat
     2641 aaagcaatta atgcgatgtt ccgaaaatgt ttaacgaaac tacgccgact atgattaaaa
     2701 ctatagatac tatagttatt agatttattt gttctttgaa aataattatt gagactacgg
     2761 ttgttaagac taaacctagt cccgcccaag ttgcataagt tatatttagt ggtaggtgtt
     2821 gcattgtttt acttaaaaaa tagaaacaaa ttccaaatga aattattgtt cctaaggatg
     2881 gtataaattt tgaaaagcct tctgaagatt taagaaatgc acttccaata acttcagtac
     2941 ttatggatat tattaaataa atataaggca tttttaactc cttttaattt tcgtatttta
     3001 tttaatttta ttctaagtat ttttcatttg caacgatcct tttatttttt atttgtatca
     3061 gtatcaattt tacagtaaac atgcatttat gccgagaaaa tttattgatg ttgagaagaa
     3121 cccttaacta aacttggaga cgaatgtcgg catagcgtga gctattaagc cgaccattcg
     3181 acaagttttg ggattgttaa gggttccgag gctcaacgtc aataaagcaa ttggaataaa
     3241 gcaataaaag gagttgaaga aatgaaattt agagaagctt ttgagaattt tatagcaagt
     3301 aagtatgtac ttggtgtttt agtagtttta actgtttacc agataataca aatgcttaaa
     3361 taaaaaaaga cctgatctga ttagaccaag tcttttgata gtgttatatt aataacaaaa
     3421 taaaaagaag tcgctcactc cctcgccaaa gtttgtgata gcgacttacc tagaaaaaac
     3481 actaagttgt ttttttatat cttgtatatc tagatattaa acgatataag tttattcttc
     3541 aagatatata ttcgggtgag cgacttc
//
