LOCUS       NZ_CP076844             4397 bp    DNA     circular CON 19-JUL-2023
DEFINITION  Staphylococcus aureus strain 55-100-003 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP076844
VERSION     NZ_CP076844.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19718724
            Assembly: GCF_018987345.1
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  JOURNAL   Unpublished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 NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/19/2023 03:16:06
            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)                     :: 2,754
            CDSs (total)                      :: 2,673
            Genes (coding)                    :: 2,555
            CDSs (with protein)               :: 2,555
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 76 of 118
            Pseudo Genes (incomplete)         :: 36 of 118
            Pseudo Genes (internal stop)      :: 25 of 118
            Pseudo Genes (multiple problems)  :: 17 of 118
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP076844.1.
            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="55-100-003"
                     /host="Sus scrofa"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="Denmark"
                     /collection_date="2014"
     gene            join(3757..4397,1..208)
                     /gene="str"
                     /locus_tag="KRH49_RS13630"
                     /old_locus_tag="KRH49_13630"
     CDS             join(3757..4397,1..208)
                     /gene="str"
                     /locus_tag="KRH49_RS13630"
                     /old_locus_tag="KRH49_13630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258486.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="streptomycin adenylyltransferase Str"
                     /protein_id="WP_001258486.1"
                     /translation="MRTEKEILNLVSEFAYQRSNVKIIALEGSRTNENIKKDKFQDYDF
                     AFFVSDIEYFTHEESWLSLFGELLFIQKPEDMELFPPDLDYGYSYIMYFKDGIKMDITL
                     INLKDLNRYFSDSDGLVKILVDKDNLVTQEIVPDDSNYWLKKPTEREFYDCCNEFWSVS
                     TYVAKGVFRREILFALDHFNNILRPELLRMISWYIGFNRGFDFSLGKNYKFINKYLTDK
                     EFNMLLATFEMNGYRKTYQSFKLCCELFKYYSNKVSCLGNYNYPNYEKNIENFIRNNYE
                     N"
                     /name="str"
     gene            478..876
                     /gene="mobC"
                     /locus_tag="KRH49_RS13635"
                     /old_locus_tag="KRH49_13635"
     CDS             478..876
                     /gene="mobC"
                     /locus_tag="KRH49_RS13635"
                     /old_locus_tag="KRH49_13635"
                     /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            858..>1502
                     /locus_tag="KRH49_RS13640"
                     /old_locus_tag="KRH49_13640"
                     /pseudo=""
     CDS             858..>1502
                     /locus_tag="KRH49_RS13640"
                     /old_locus_tag="KRH49_13640"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1615..2244
                     /locus_tag="KRH49_RS13645"
                     /old_locus_tag="KRH49_13645"
     CDS             1615..2244
                     /locus_tag="KRH49_RS13645"
                     /old_locus_tag="KRH49_13645"
                     /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"
     gene            2805..3749
                     /locus_tag="KRH49_RS13650"
                     /old_locus_tag="KRH49_13650"
     CDS             2805..3749
                     /locus_tag="KRH49_RS13650"
                     /old_locus_tag="KRH49_13650"
                     /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"
     Typing          complement(273..507)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="100.0"
                     /evalue="1.4099999999999999e-40"
     Typing          2806..3749
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          859..1817
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tataaacaaa tatttaactg ataaagaatt caatatgctt ttagctactt ttgagatgaa
       61 tggatataga aagacatacc aatcttttaa gctttgttgt gaattattta aatattattc
      121 aaataaagta agttgtttag gaaattataa ctatccaaat tacgaaaaaa atattgagaa
      181 ttttattcgt aataattatg agaattaatt ttattagcaa ccacattttt ggttgctttt
      241 gttttgattt tgaatttggt tttgaactat gagtggctag cattttgcca ctcatttttt
      301 gcgttagcaa aaacataaag ggtctgggat taatcccagc aagccggtat attcagaacg
      361 aagtggctag aatatacgac gcttgccaaa ccactatatt acttgagaaa atatagatta
      421 tattataagc tatatttatg aaaaggaata tttttcgtca gaaaggtggt gggacttgtg
      481 aacgaacata aagataattt ggctagcgat ttgtctgttg ggggaaaccg taaacccaac
      541 cgcaaagagc caaaacaaat tagtttcaga gtgagtgaac aggaatattc aaagttgaaa
      601 cagtcggcag aaactttgaa tatgacagtg cctaatttcg ttaagaaaaa ggcacaaggc
      661 agtcgattag tgtcgccaaa attagacaaa gaaacgcgac aatcgattgc caaagattta
      721 agtcatttgg gtagtaatgt gaatcagatt gctaagtggt ttaatcaaaa taaagataag
      781 gctacacatt taccagaaga gaaatatcat gatttagaaa agcaatttga tgatgtgaaa
      841 aaggagttgc ataagatatg gcaacaacta aattaggcaa tacgaagtcg gcaagtcgtg
      901 ccattaatta cgcagaagaa cgtgcagaag aaaaaagcgg cttaaattgt gatgttgatt
      961 atgctaaatc atattttaag caaactaggg cgttatatgg caaagagaat ggtgttcaag
     1021 cacatacagt cattcaatct tttaagcctg gcgaagtaac agctaaagag tgtaatgaga
     1081 taggtttaga attagctaaa aaaattgcac cagattatca agttgcagtt tatacacata
     1141 cagacaaaga ccattatcac aatcacatta ttattaattc agtaaattta gaaacaggca
     1201 acaagtatca gtcaaacaaa gaacaacgtg attttataaa aaaggcgaat gatcagttat
     1261 gtgaagaacg tggtttatct gtgccagaaa agtcatcaga aatcagatat acgttggcag
     1321 aacagaacat gatagataaa gataaaaggt catggaaaaa tgatataaga atggcagttg
     1381 aagaaacaaa ggataacgca gtagactttg aagaatttaa tactttgcta aaagaaaaag
     1441 gtgttgaaat cacgagagta acgaaaaaca acgtaacgta tagacacatt gaagaagata
     1501 aaaaagtacg tgggaataag ttgggcgatt cttatgacaa aggagtgatt gaaaatggct
     1561 ttgcaatcga gaaattcaga cgagaacgag aagaagaacg agaatacgat gaatatgcag
     1621 acacgttcga agttgactgg gacgcagtcg cagaaaattc agaagacctt agaaaacgaa
     1681 gaattgcaag aactgaagaa acaaaacaag ctagtaataa aatatatatc agagatgaaa
     1741 gaacaacagg acttgagaga aaaggaattg caggcaatca agtcgagttt gaaaaagacg
     1801 acggaggact ttcaaggtag aggtaaaaaa gtccataatg attttgttcg tttgttacaa
     1861 aagaatttaa atcgagtgaa tgcagaagat attgagatag aggttcgaaa agatgtttat
     1921 ggagttcgag aagaaattca ttcgatgttg cgtgaagtta aacaatcaca tgaacattat
     1981 caaaaaagac aaaagcaatt atttactggt attggtgcaa tgttattagt gtttatgctt
     2041 tttgctttga ttatgacgat tggcagagat tttatgggct ttttacatgt agatgtatta
     2101 cagaatgcca tagcaagcaa aataaaggct tctgagggct ttatttcagt tttatggtac
     2161 attgcttatg gtttacctta tatactcgct atagggctat ttatttggtt gtatgagtgg
     2221 ataagagcaa gattccatga ttaaacaaag tatgatcagg cttttatgcc gagaaaattt
     2281 atttatattg agaagtaccc ttaactaaac ttgcagacga atgtcggcat agcgtgagct
     2341 attagcccga ccattcgaca agttttgggt ttgttaaggg tacagaggct caatgtaaat
     2401 aaagcaattg gaataaagca acaaaggggg ttgaagaaaa tgagtaagaa gaaaaagatt
     2461 aatttagcaa tatcaattgc tcaagtagta gtgcaggcgt taatacttta taacacttat
     2521 cagcaatata aatattctaa aaaatattca gcctaataaa aaaagactta gtctgaatag
     2581 accaagcctt ttgttagtgt tatattaata tgcaaataaa aaaacaaaaa aagaagtcgc
     2641 tcactccctg accaaagttt gtgaatgcga cttaccttaa agaaaaacag ttggtgtttt
     2701 tttcttaatt tttgtatatc tagatattaa acgatattgg tttattcttc aagatatata
     2761 ttcgggtgag cgacttctta aacaaaataa ggagtcgatt ttttatgagt aaaaaagcag
     2821 aagaaattca ggcaaaacaa agtttggaaa aggaaaactc aaatttttct aaaaccggat
     2881 actctaatag ccggttaaac cgacatatta tgtacacccc cgaaccaaaa ttacactttg
     2941 atgctatgac aattgttggg aatcttaata agaacaatgc tcacaaactg tctgaattta
     3001 tgagtattgc gccacaaatt agactttggg atatattaca aaccaaattt aaagctaagg
     3061 ctctacaaga aaaagtttac atcgaatatg ataaagtaaa agcagatgcg tgggatagac
     3121 gtaatatgcg tgttgaattt aatcctaata aacttacgca tgaagaaatg ctttggttaa
     3181 aacaaaacat cattgactac atggaagatg atggttttac aagattagat ttggcttttg
     3241 attttgaaga cgatttgagc gattattatg cgatgactga taaatcagtt aagaaaacta
     3301 ttttttatgg tcgtaacggt aaaccagaaa caaaatattt tggtgttcgt gacagtgata
     3361 gatttattag aatttataat aaaaaacaag aacgtaagga taatgcagac attgaagtta
     3421 tgtctgaaca cttatggcgt gtagaaattg aattaaaaag agatatggtt gattattgga
     3481 acgattgttt taatgattta catattttga aaccagattg gtctagttta gaaaaagtaa
     3541 aagaccaagc aatgatttat atgctaattc atgaagaaag tacatggggt aaattagaaa
     3601 gacgtacaaa aaataaatac agagaaatgt taaaaagtat ttcagaaatt gatttaacgg
     3661 acttaatgaa attgacttta aaagagaatg aaaaacaatt gcaaaagcag attgaatttt
     3721 ggcagcgtga atttagattt tgggagtgaa aaaacaatga ggactgaaaa agaaatttta
     3781 aatttagttt ctgaatttgc ttatcaacga agcaatgtaa aaattattgc tctcgagggt
     3841 tcaagaacta atgaaaatat aaaaaaagat aagtttcaag attatgattt tgcttttttc
     3901 gtatcagata ttgagtattt cacacatgaa gaaagttggt taagtttatt tggagaatta
     3961 ttgtttatac agaaaccaga agatatggaa ttattcccac ctgatttaga ttatggttac
     4021 agttatataa tgtattttaa agatggcata aaaatggata ttacattaat taatttaaaa
     4081 gatttaaatc gttattttag tgattctgat ggtcttgtaa aaattttagt tgataaagat
     4141 aatttagtaa ctcaagaaat tgttccagat gactcaaatt attggttaaa aaaaccaaca
     4201 gaacgagaat tttatgattg ctgtaatgag ttttggagtg tctcaacgta tgtagcaaag
     4261 ggtgttttta gaagagaaat attatttgct ttagatcatt tcaataatat tttacgtcct
     4321 gaattattaa gaatgatttc ttggtatatt ggctttaata ggggttttga ttttagttta
     4381 ggaaagaatt ataagtt
//
