LOCUS       NZ_CP076841             4397 bp    DNA     circular CON 19-JUL-2023
DEFINITION  Staphylococcus aureus strain 55-100-016 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP076841
VERSION     NZ_CP076841.1
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 4397)
  AUTHORS   Larsen,J.
  TITLE     Pleuromutilin-resistance in MRSA CC398
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4397)
  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
            CP076841.1.
            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..4397
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="55-100-016"
                     /host="Sus scrofa"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed2"
                     /geo_loc_name="Denmark"
                     /collection_date="2014"
     gene            complement(503..901)
                     /gene="mobC"
                     /locus_tag="KRH48_RS13820"
                     /old_locus_tag="KRH48_13820"
     CDS             complement(503..901)
                     /gene="mobC"
                     /locus_tag="KRH48_RS13820"
                     /old_locus_tag="KRH48_13820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002489523.1"
                     /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_001002114.1"
                     /translation="MNEHKDNLASDLSVGGNRKPNRKEPKQISFRVSEQEYSKLKQSAE
                     TLNMTVPNFVKKKAQGSRLVSPKLDKETRQSIAKDLSHLGSNVNQIAKWFNQNKDKATH
                     LPEEKYHDLEKQFDDVKKELHKIWQQLN"
                     /name="mobC"
     gene            complement(1171..2019)
                     /gene="str"
                     /locus_tag="KRH48_RS13825"
                     /old_locus_tag="KRH48_13825"
     ARG             complement(1175..2019)
                     /name="str"
                     /gene="str"
                     /gene_name="streptomycin adenylyltransferase Str"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(2027..2971)
                     /locus_tag="KRH48_RS13830"
                     /old_locus_tag="KRH48_13830"
     CDS             complement(2027..2971)
                     /locus_tag="KRH48_RS13830"
                     /old_locus_tag="KRH48_13830"
                     /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            complement(3532..4161)
                     /locus_tag="KRH48_RS13835"
                     /old_locus_tag="KRH48_13835"
     CDS             complement(3532..4161)
                     /locus_tag="KRH48_RS13835"
                     /old_locus_tag="KRH48_13835"
                     /inference="COORDINATES: protein motif:HMM:NF015839.2"
                     /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_223876725.1"
                     /translation="MQTRSKLTGTQSQKIQKTLENEELQELKKQNKLVIKYISEMKEQQ
                     DLREKELQAIKSSLKKTTEDFQGRGKKVHNDFVRLLQKNLNRVNAEDIEIEVRKDVYGV
                     REEIHSMLREVKQSHEHYQKRQKQLFTGIGAMLLVFMLFALIMTIGRDFMGFLHVDVLQ
                     NAIASKIKASEGFISVLWYIAYGLPYILAIGLFIWLYEWIRARFHD"
                     /name="DUF334 domain-containing protein"
     Typing          873..1107
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="100.0"
                     /evalue="1.4099999999999999e-40"
     Typing          complement(2028..2971)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..521)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="5.93e-113"
     Typing          complement(3960..4396)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="6.07e-80"
ORIGIN
        1 actgccattc ttatatcatt tttccatgac cttttatctt tatctatcat gttctgttct
       61 gccaacgtat atctgatttc tgatgacttt tctggcacag ataaaccacg ttcttcacat
      121 aactgatcat tcgccttttt tataaaatca cgttgttctt tgtttgactg atacttgttg
      181 cctgtttcta aatttactga attaataata atgtgattgt gataatggtc tttgtctgta
      241 tgtgtataaa ctgcaacttg ataatctggt gcaatttttt tagctaattc taaacctatc
      301 tcattacact ctttagctgt tacttcgcca ggcttaaaag attgaatgac tgtatgtgct
      361 tgaacaccat tctctttgcc atataacgcc ctagtttgct taaaatatga tttagcataa
      421 tcaacatcac aatttaagcc gcttttttct tctgcacgtt cttctgcgta attaatggca
      481 cgacttgccg acttcgtatt gcctaattta gttgttgcca tatcttatgc aactcctttt
      541 tcacatcatc aaattgcttt tctaaatcat gatatttctc ttctggtaaa tgtgtagcct
      601 tatctttatt ttgattaaac cacttagcaa tctgattcac attactaccc aaatgactta
      661 aatctttggc aatcgattgt cgcgtttctt tgtctaattt tggcgacact aatcgactgc
      721 cttgtgcctt tttcttaacg aaattaggca ctgtcatatt caaagtttct gccgactgtt
      781 tcaactttga atattcctgt tcactcactc tgaaactaat ttgttttggc tctttgcggt
      841 tgggtttacg gtttccccca acagacaaat cgctagccaa attatcttta tgttcgttca
      901 caagtcccac cacctttctg acgaaaaata ttccttttca taaatatagc ttataatata
      961 atctatattt tctcaagtaa tatagtggtt tggcaagcgt cgtatattct agccacttcg
     1021 ttctgaatat accggcttgc tgggattaat cccagaccct ttatgttttt gctaacgcaa
     1081 aaaatgagtg gcaaaatgct agccactcat agttcaaaac caaattcaaa atcaaaacaa
     1141 aagcaaccaa aaatgtggtt gctaataaaa ttaattctca taattattac gaataaaatt
     1201 ctcaatattt ttttcgtaat ttggatagtt ataatttcct aaacaactta ctttatttga
     1261 ataatattta aataattcac aacaaagctt aaaagattgg tatgtctttc tatatccatt
     1321 catctcaaaa gtagctaaaa gcatattgaa ttctttatca gttaaatatt tgtttataaa
     1381 cttataattc tttcctaaac taaaatcaaa acccctatta aagccaatat accaagaaat
     1441 cattcttaat aattcaggac gtaaaatatt attgaaatga tctaaagcaa ataatatttc
     1501 tcttctaaaa acaccctttg ctacatacgt tgagacactc caaaactcat tacagcaatc
     1561 ataaaattct cgttctgttg gtttttttaa ccaataattt gagtcatctg gaacaatttc
     1621 ttgagttact aaattatctt tatcaactaa aatttttaca agaccatcag aatcactaaa
     1681 ataacgattt aaatctttta aattaattaa tgtaatatcc atttttatgc catctttaaa
     1741 atacattata taactgtaac cataatctaa atcaggtggg aataattcca tatcttctgg
     1801 tttctgtata aacaataatt ctccaaataa acttaaccaa ctttcttcat gtgtgaaata
     1861 ctcaatatct gatacgaaaa aagcaaaatc ataatcttga aacttatctt tttttatatt
     1921 ttcattagtt cttgaaccct cgagagcaat aatttttaca ttgcttcgtt gataagcaaa
     1981 ttcagaaact aaatttaaaa tttctttttc agtcctcatt gttttttcac tcccaaaatc
     2041 taaattcacg ctgccaaaat tcaatctgct tttgcaattg tttttcattc tcttttaaag
     2101 tcaatttcat taagtccgtt aaatcaattt ctgaaatact ttttaacatt tctctgtatt
     2161 tattttttgt acgtctttct aatttacccc atgtactttc ttcatgaatt agcatataaa
     2221 tcattgcttg gtcttttact ttttctaaac tagaccaatc tggtttcaaa atatgtaaat
     2281 cattaaaaca atcgttccaa taatcaacca tatctctttt taattcaatt tctacacgcc
     2341 ataagtgttc agacataact tcaatgtctg cattatcctt acgttcttgt tttttattat
     2401 aaattctaat aaatctatca ctgtcacgaa caccaaaata ttttgtttct ggtttaccgt
     2461 tacgaccata aaaaatagtt ttcttaactg atttatcagt catcgcataa taatcgctca
     2521 aatcgtcttc aaaatcaaaa gccaaatcta atcttgtaaa accatcatct tccatgtagt
     2581 caatgatgtt ttgttttaac caaagcattt cttcatgcgt aagtttatta ggattaaatt
     2641 caacacgcat attacgtcta tcccacgcat ctgcttttac tttatcatat tcgatgtaaa
     2701 ctttttcttg tagagcctta gctttaaatt tggtttgtaa tatatcccaa agtctaattt
     2761 gtggcgcaat actcataaat tcagacagtt tgtgagcatt gttcttatta agattcccaa
     2821 caattgtcat agcatcaaag tgtaattttg gttcgggggt gtacataata tgtcggttta
     2881 accggctatt agagtatccg gttttagaaa aatttgagtt ttccttttcc aaactttgtt
     2941 ttgcctgaat ttcttctgct tttttactca taaaaaatcg actccttatt ttgtttaaga
     3001 agtcgctcac ccgaatatat atcttgaaga ataaaccaat atcgtttaat atctagatat
     3061 acaaaaatta agaaaaaaac accaactgtt tttctttaag gtaagtcgca ttcacaaact
     3121 ttggtcaggg agtgagcgac ttcttttttt gtttttttat ttgcatatta atataacact
     3181 aacaaaaggc ttggtctatt cagactaagt ctttttttat taggctgaat attttttaga
     3241 atatttatat tgctgataag tgttataaag tattaacgcc tgcactacta cttgagcaat
     3301 tgatattgct aaattaatct ttttcttctt actcattttc ttcaaccccc tttgttgctt
     3361 tattccaatt gctttattta cattgagcct ctgtaccctt aacaaaccca aaacttgtcg
     3421 aatggtcggg ctaatagctc acgctatgcc gacattcgtc tgcaagttta gttaagggta
     3481 cttctcaata taaataaatt ttctcggcat aaaagcctga tcatactttg tttaatcatg
     3541 gaatcttgct cttatccact catacaacca aataaatagc cctatagcga gtatataagg
     3601 taaaccataa gcaatgtacc ataaaactga aataaagccc tcagaagcct ttattttgct
     3661 tgctatggca ttctgtaata catctacatg taaaaagccc ataaaatctc tgccaatcgt
     3721 cataatcaaa gcaaaaagca taaacactaa taacattgca ccaataccag taaataattg
     3781 cttttgtctt ttttgataat gttcatgtga ttgtttaact tcacgcaaca ttgaatgaat
     3841 ttcttctcga actccataaa catcttttcg aacctctatc tcaatatctt ctgcattcac
     3901 tcgatttaaa ttcttttgta acaaacgaac aaaatcatta tggacttttt tacctctacc
     3961 ttgaaagtcc tccgtcgtct ttttcaaact cgacttgatt gcctgcaatt ccttttctct
     4021 caagtcctgt tgttctttca tctctgatat atattttatt actagcttgt tttgtttctt
     4081 cagttcttgc aattcttcgt tttctaaggt cttctgaatt ttctgcgact gcgtcccagt
     4141 caacttcgaa cgtgtctgca tattcatcgt attctcgttc ttcttctcgt tctcgtctga
     4201 atttctcgat tgcaaagcca ttttcaatca ctcctttgtc ataagaatcg cccaacttat
     4261 tcccacgtac ttttttatct tcttcaatgt gtctatacgt tacgttgttt ttcgttactc
     4321 tcgtgatttc aacacctttt tcttttagca aagtattaaa ttcttcaaag tctactgcgt
     4381 tatcctttgt ttcttca
//
