LOCUS       NZ_CP076842             3113 bp    DNA     circular CON 19-JUL-2023
DEFINITION  Staphylococcus aureus strain 55-100-016 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP076842
VERSION     NZ_CP076842.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19718690
            Assembly: GCF_018987325.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3113)
  AUTHORS   Larsen,J.
  TITLE     Pleuromutilin-resistance in MRSA CC398
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3113)
  AUTHORS   Larsen,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-JUN-2021) Depaertment of Bacteria, Parasites and
            Fungi, Statens Serum Institut, Artillerivej 5, Copenhagen S 2300,
            Denmark
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8-beta
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 300.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/19/2023 03:18:14
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,792
            CDSs (total)                      :: 2,710
            Genes (coding)                    :: 2,618
            CDSs (with protein)               :: 2,618
            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)              :: 92
            CDSs (without protein)            :: 92
            Pseudo Genes (ambiguous residues) :: 0 of 92
            Pseudo Genes (frameshifted)       :: 45 of 92
            Pseudo Genes (incomplete)         :: 41 of 92
            Pseudo Genes (internal stop)      :: 27 of 92
            Pseudo Genes (multiple problems)  :: 19 of 92
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP076842.1.
            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..3113
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="55-100-016"
                     /host="Sus scrofa"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed3"
                     /geo_loc_name="Denmark"
                     /collection_date="2014"
     gene            complement(757..1761)
                     /locus_tag="KRH48_RS13840"
                     /old_locus_tag="KRH48_13840"
     CDS             complement(757..1761)
                     /locus_tag="KRH48_RS13840"
                     /old_locus_tag="KRH48_13840"
                     /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_078099048.1"
                     /translation="MQDNHTKYIDENQDNKTLKDLTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQRVI
                     EEVVKEKPKARWLFLTLSTRNAIDGDTLEKSLKHLTESFRRLFKYKKVSKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVESKYFRGSENYISQNDWINLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            complement(1978..2838)
                     /locus_tag="KRH48_RS13845"
                     /old_locus_tag="KRH48_13845"
     CDS             complement(1978..2838)
                     /locus_tag="KRH48_RS13845"
                     /old_locus_tag="KRH48_13845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017001149.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AraC family transcriptional regulator"
                     /protein_id="WP_078099425.1"
                     /translation="MILKNLNDSIDYIDQNLTKDLNLYDIANFVGLPEQHYRNLFIFLT
                     GIGLSEYIKKRKLYFANKDLLNKESVTSVAIKYGYSIDGFTKSFKDWSGYLPSQIYEEQ
                     VLISYPKLSFAINVKGGIDMKTRIVDLPKINIVGVKKRVRMQYEGVNNEIEELANSITN
                     IQKEEMNNLQNIEPKEIVNVSYDADENFIKEEGYLTHMIGVITTENNISDQLDVINIDE
                     SKWIVFENEGKFPKVLQDTYAKIYSEWLPETEYKLANVPMFSFTKFNDSDSDNAYSEIW
                     VAVNN"
                     /name="AraC family transcriptional regulator"
     Typing          complement(758..1761)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.949"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caaagtagac ccaactgtta ttgctttaca ggtctatttt tcgtcgttat aatctagtta
       61 aatcccgtaa gggcgcactt atgcgttcta aaaagaacgc gtaaaaaacc ataatcgacc
      121 ttcgtcaatt tttatcttag ttttaaggaa tcggcgttgt agcgcagata taaaaattaa
      181 tactgcacga actagaatcg acgttgtagc gtagatataa aaattaatac tacatagaaa
      241 tttaactaag atttaagcta ctagtttttt gctagtagct tttttatttt cttaattttt
      301 aaatgccttt attttgaatt ttaagggggt atttagagca aactctatat ttatatattt
      361 ttatacctgt atatttatat atgtttctta aaacgcaaat atgagcaaaa taagggtaca
      421 tctttctgac atttaacttg tattcaaaag acatattact taagttgcta aagtcatttt
      481 aaatacaatc acttgtactt tttaaacata agccagaaaa acgatataac ttttatatat
      541 atttttctaa tttgattgga actccctaaa atttatataa cttaaaaagt taaattgttt
      601 atctcatttt ttgtacataa ccagtggcga atttttcaga cactgcccat ttacatgcaa
      661 attaaaattt tcatggtaaa actggtcaac catgccggtt gaacgctata gttcctgcag
      721 gggcaaaaat acataaaaaa aacgctagct tttaagctaa cgtttcaaat cttttaagta
      781 ataattttgt ttttcaaaat tccaaattgc agtaattgaa tgtgcttttt cttcttcgtc
      841 tgttgtttta tcttcgtcac ttgtattaat taaattgcca tcttcggcat cgtctaaatt
      901 taaaatttta tgtttttgtt taagcaatcc accataactc aacatacgtt ttcggtataa
      961 acctttttct aaatcattca cgatttcctg atttctttcg tcatcatcag ttaaaaaatc
     1021 agatgattta accgaatatt tcgaggtttc tttgattgct gcttgaatat ctttatcgcc
     1081 tttttgattt ggtttgatcg ctttaatatt tgctactggc cgataattaa cttgtaatgc
     1141 tttttgccat aaattaatcc aatcattttg agaaatgtaa ttctcagaac ctctaaaata
     1201 tttactttca acacacaata aaacatgcat atgttgatta taactaccgt catttttatt
     1261 aactgtaacc tctgtcgaac gcataaaacc aattaaattt ttactaactt ttttatattt
     1321 aaataatctt ctaaatgatt cagttaaatg tttaagactt ttttctaaag tatctccatc
     1381 tatcgcattt cgtgttgata gtgtaagaaa caaccaacgt gctttcggct tttctttaac
     1441 cacttcttca atcactcttt gagcttgata actatttttc atagcacgcc tccaattaca
     1501 aactggacac aattttgatt tacaaaacca tgtcttatgt aacttcaaat aaccttcatc
     1561 agtaggcttg aactctaaga cgttaccaca ttgttttacg ttaaaagcct ttttaatttt
     1621 taagatttct agtatatctg cataacttac attatcgatt ttcttttctc tccacgggcg
     1681 ttgtttccca cttttcgtta agtcttttag tgttttatta tcttgatttt catctatata
     1741 ttttgtatga ttgtcttgca tataaaaaga cctccagtat ttgattttag ctcgacactt
     1801 taatcttatt actggagttt ttttatgtca aattttattt tatacactaa aaatctttca
     1861 aaacactgtt acatcaagct tgaaacaaca ttttaaaaaa gaacgttatt tctatatagt
     1921 atcaagacaa gaagaaactc gttttcaact cgtttctaaa accttaaata tctaaaatca
     1981 attattaact gcaacccaaa tttcactata agcattatca ctatctgaat cattaaattt
     2041 agtaaaagaa aacattggta cattagctaa tttatattct gtttctggca accattcaga
     2101 ataaatttta gcgtatgtgt cttgcaaaac ttttggaaat ttaccttcat tttcaaagac
     2161 tatccattta ctttcatcaa tatttataac atcaagttga tcgcttatat tattttctgt
     2221 tgttataaca ccaatcatat gagttaaata accctcttct ttaataaaat tctcatcagc
     2281 atcatatgaa acatttacaa tttctttagg ttcaatgttt tgtaaattgt tcatttcttc
     2341 tttttgtata ttagtaatac tatttgctag ttcttcaatt tcattgttaa caccctcgta
     2401 ttgcatacga acgcgttttt ttacgcctac tatattaatt tttggcaaat ctacaattct
     2461 agttttcatg tctattcctc ctttaacatt aatagcaaat gaaagtttcg gatacgaaat
     2521 taaaacttgt tcttcatata tttgagatgg taaataccca ctccaatctt taaaagactt
     2581 tgtaaaacca tcaattgaat atccatattt tatagctaca ctcgttactg attctttatt
     2641 taataaatct ttgttagcaa aatacaattt tctttttttt atatactcag ataaaccaat
     2701 accagtaaga aatataaata aatttctata atgttgctcg ggtaaaccaa caaaattcgc
     2761 tatatcatat aaatttaaat cttttgttaa attctgatct atataatcta tagaatcatt
     2821 taaatttttt aatatcatat ccatcacctt tcaatcctat agtaatcaat aatcaaagaa
     2881 atgactcgat aatttatata taacaattat cgaataaaaa ataattgctt tattccaatt
     2941 gctttattga cgttgagcct cggaaccctt aacaatccca aaacttgtcg aatggtcggc
     3001 ttaatagctc acgctatgcc gacattcgtc tgcaagttta gttaagggtt cttctcaaca
     3061 tcaataaatt ttctcggcat aaatgcgtgt tcttttcttg tctgcccagt aga
//
