LOCUS       NZ_MH785256             4397 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Staphylococcus aureus strain tu2 plasmid pRIVM4390, complete
            sequence.
ACCESSION   NZ_MH785256
VERSION     NZ_MH785256.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN09846915
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4397)
  AUTHORS   Bukowski,M., Piwowarczyk,R., Madry,A., Zagorski-Przybylo,R.,
            Hydzik,M. and Wladyka,B.
  TITLE     Prevalence of Antibiotic and Heavy Metal Resistance Determinants and
            Virulence-Related Genetic Elements in Plasmids of Staphylococcus
            aureus
  JOURNAL   Front Microbiol 10, 805 (2019)
  REMARK    DOI: 10.3389/fmicb.2019.00805
REFERENCE   2  (bases 1 to 4397)
  AUTHORS   Bukowski,M., Hydzik,M., Sabat,A.J. and Wladyka,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-AUG-2018) Faculty of Biochemistry, Biophysics and
            Biotechnology, Department of Analytical Biochemistry, Jagiellonian
            University, Gronostajowa 7, Krakow, malopolskie 30-387, Poland
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/21/2023 01:09:03
            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)                     :: 6
            CDSs (total)                      :: 6
            Genes (coding)                    :: 5
            CDSs (with protein)               :: 5
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            MH785256.1.
            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="tu2"
                     /isolation_source="deep wounds and lesions"
                     /host="Farmed turkey"
                     /db_xref="taxon:1280"
                     /plasmid="pRIVM4390"
                     /geo_loc_name="Poland: Wroclaw"
                     /collection_date="2008"
     gene            61..1005
                     /locus_tag="D0Y82_RS00005"
                     /old_locus_tag="D0Y82_g00015"
     CDS             61..1005
                     /locus_tag="D0Y82_RS00005"
                     /old_locus_tag="D0Y82_g00015"
                     /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            1013..1861
                     /gene="str"
                     /locus_tag="D0Y82_RS00010"
                     /old_locus_tag="D0Y82_g00020"
     ARG             1014..1858
                     /name="str"
                     /gene="str"
                     /gene_name="streptomycin adenylyltransferase Str"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2131..2529
                     /gene="mobC"
                     /locus_tag="D0Y82_RS00015"
                     /old_locus_tag="D0Y82_g00000"
     CDS             2131..2529
                     /gene="mobC"
                     /locus_tag="D0Y82_RS00015"
                     /old_locus_tag="D0Y82_g00000"
                     /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            2511..>3155
                     /locus_tag="D0Y82_RS00020"
                     /old_locus_tag="D0Y82_g00005"
                     /pseudo=""
     CDS             2511..>3155
                     /locus_tag="D0Y82_RS00020"
                     /old_locus_tag="D0Y82_g00005"
                     /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            3268..3897
                     /locus_tag="D0Y82_RS00025"
                     /old_locus_tag="D0Y82_g00025"
     CDS             3268..3897
                     /locus_tag="D0Y82_RS00025"
                     /old_locus_tag="D0Y82_g00025"
                     /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            4018..4209
                     /locus_tag="D0Y82_RS00030"
                     /old_locus_tag="D0Y82_g00010"
     CDS             4018..4209
                     /locus_tag="D0Y82_RS00030"
                     /old_locus_tag="D0Y82_g00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002440613.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_014532527.1"
                     /translation="MGLLRVQRLNVNKAIGIKQQRGLKKMSKKKKINLAISIAQVVVQA
                     LILYNTYQQYKYSKKYSA"
                     /name="hypothetical protein"
     Typing          complement(1926..2160)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="100.0"
                     /evalue="1.4099999999999999e-40"
     Typing          62..1005
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2512..3470
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcttcaaga tatatattcg ggtgagcgac ttcttaaaca aaataaggag tcgatttttt
       61 atgagtaaaa aagcagaaga aattcaggca aaacaaagtt tggaaaagga aaactcaaat
      121 ttttctaaaa ccggatactc taatagccgg ttaaaccgac atattatgta cacccccgaa
      181 ccaaaattac actttgatgc tatgacaatt gttgggaatc ttaataagaa caatgctcac
      241 aaactgtctg aatttatgag tattgcgcca caaattagac tttgggatat attacaaacc
      301 aaatttaaag ctaaggctct acaagaaaaa gtttacatcg aatatgataa agtaaaagca
      361 gatgcgtggg atagacgtaa tatgcgtgtt gaatttaatc ctaataaact tacgcatgaa
      421 gaaatgcttt ggttaaaaca aaacatcatt gactacatgg aagatgatgg ttttacaaga
      481 ttagatttgg cttttgattt tgaagacgat ttgagcgatt attatgcgat gactgataaa
      541 tcagttaaga aaactatttt ttatggtcgt aacggtaaac cagaaacaaa atattttggt
      601 gttcgtgaca gtgatagatt tattagaatt tataataaaa aacaagaacg taaggataat
      661 gcagacattg aagttatgtc tgaacactta tggcgtgtag aaattgaatt aaaaagagat
      721 atggttgatt attggaacga ttgttttaat gatttacata ttttgaaacc agattggtct
      781 agtttagaaa aagtaaaaga ccaagcaatg atttatatgc taattcatga agaaagtaca
      841 tggggtaaat tagaaagacg tacaaaaaat aaatacagag aaatgttaaa aagtatttca
      901 gaaattgatt taacggactt aatgaaattg actttaaaag agaatgaaaa acaattgcaa
      961 aagcagattg aattttggca gcgtgaattt agattttggg agtgaaaaaa caatgaggac
     1021 tgaaaaagaa attttaaatt tagtttctga atttgcttat caacgaagca atgtaaaaat
     1081 tattgctctc gagggttcaa gaactaatga aaatataaaa aaagataagt ttcaagatta
     1141 tgattttgct tttttcgtat cagatattga gtatttcaca catgaagaaa gttggttaag
     1201 tttatttgga gaattattgt ttatacagaa accagaagat atggaattat tcccacctga
     1261 tttagattat ggttacagtt atataatgta ttttaaagat ggcataaaaa tggatattac
     1321 attaattaat ttaaaagatt taaatcgtta ttttagtgat tctgatggtc ttgtaaaaat
     1381 tttagttgat aaagataatt tagtaactca agaaattgtt ccagatgact caaattattg
     1441 gttaaaaaaa ccaacagaac gagaatttta tgattgctgt aatgagtttt ggagtgtctc
     1501 aacgtatgta gcaaagggtg tttttagaag agaaatatta tttgctttag atcatttcaa
     1561 taatatttta cgtcctgaat tattaagaat gatttcttgg tatattggct ttaatagggg
     1621 ttttgatttt agtttaggaa agaattataa gtttataaac aaatatttaa ctgataaaga
     1681 attcaatatg cttttagcta cttttgagat gaatggatat agaaagacat accaatcttt
     1741 taagctttgt tgtgaattat ttaaatatta ttcaaataaa gtaagttgtt taggaaatta
     1801 taactatcca aattacgaaa aaaatattga gaattttatt cgtaataatt atgagaatta
     1861 attttattag caaccacatt tttggttgct tttgttttga ttttgaattt ggttttgaac
     1921 tatgagtggc tagcattttg ccactcattt tttgcgttag caaaaacata aagggtctgg
     1981 gattaatccc agcaagccgg tatattcaga acgaagtggc tagaatatac gacgcttgcc
     2041 aaaccactat attacttgag aaaatataga ttatattata agctatattt atgaaaagga
     2101 atatttttcg tcagaaaggt ggtgggactt gtgaacgaac ataaagataa tttggctagc
     2161 gatttgtctg ttgggggaaa ccgtaaaccc aaccgcaaag agccaaaaca aattagtttc
     2221 agagtgagtg aacaggaata ttcaaagttg aaacagtcgg cagaaacttt gaatatgaca
     2281 gtgcctaatt tcgttaagaa aaaggcacaa ggcagtcgat tagtgtcgcc aaaattagac
     2341 aaagaaacgc gacaatcgat tgccaaagat ttaagtcatt tgggtagtaa tgtgaatcag
     2401 attgctaagt ggtttaatca aaataaagat aaggctacac atttaccaga agagaaatat
     2461 catgatttag aaaagcaatt tgatgatgtg aaaaaggagt tgcataagat atggcaacaa
     2521 ctaaattagg caatacgaag tcggcaagtc gtgccattaa ttacgcagaa gaacgtgcag
     2581 aagaaaaaag cggcttaaat tgtgatgttg attatgctaa atcatatttt aagcaaacta
     2641 gggcgttata tggcaaagag aatggtgttc aagcacatac agtcattcaa tcttttaagc
     2701 ctggcgaagt aacagctaaa gagtgtaatg agataggttt agaattagct aaaaaaattg
     2761 caccagatta tcaagttgca gtttatacac atacagacaa agaccattat cacaatcaca
     2821 ttattattaa ttcagtaaat ttagaaacag gcaacaagta tcagtcaaac aaagaacaac
     2881 gtgattttat aaaaaaggcg aatgatcagt tatgtgaaga acgtggttta tctgtgccag
     2941 aaaagtcatc agaaatcaga tatacgttgg cagaacagaa catgatagat aaagataaaa
     3001 ggtcatggaa aaatgatata agaatggcag ttgaagaaac aaaggataac gcagtagact
     3061 ttgaagaatt taatactttg ctaaaagaaa aaggtgttga aatcacgaga gtaacgaaaa
     3121 acaacgtaac gtatagacac attgaagaag ataaaaaagt acgtgggaat aagttgggcg
     3181 attcttatga caaaggagtg attgaaaatg gctttgcaat cgagaaattc agacgagaac
     3241 gagaagaaga acgagaatac gatgaatatg cagacacgtt cgaagttgac tgggacgcag
     3301 tcgcagaaaa ttcagaagac cttagaaaac gaagaattgc aagaactgaa gaaacaaaac
     3361 aagctagtaa taaaatatat atcagagatg aaagaacaac aggacttgag agaaaaggaa
     3421 ttgcaggcaa tcaagtcgag tttgaaaaag acgacggagg actttcaagg tagaggtaaa
     3481 aaagtccata atgattttgt tcgtttgtta caaaagaatt taaatcgagt gaatgcagaa
     3541 gatattgaga tagaggttcg aaaagatgtt tatggagttc gagaagaaat tcattcgatg
     3601 ttgcgtgaag ttaaacaatc acatgaacat tatcaaaaaa gacaaaagca attatttact
     3661 ggtattggtg caatgttatt agtgtttatg ctttttgctt tgattatgac gattggcaga
     3721 gattttatgg gctttttaca tgtagatgta ttacagaatg ccatagcaag caaaataaag
     3781 gcttctgagg gctttatttc agttttatgg tacattgctt atggtttacc ttatatactc
     3841 gctatagggc tatttatttg gttgtatgag tggataagag caagattcca tgattaaaca
     3901 aagtatgatc aggcttttat gccgagaaaa tttatttata ttgagaagta cccttaacta
     3961 aacttgcaga cgaatgtcgg catagcgtga gctattagcc cgaccattcg acaagttttg
     4021 ggtttgttaa gggtacagag gctcaatgta aataaagcaa ttggaataaa gcaacaaagg
     4081 gggttgaaga aaatgagtaa gaagaaaaag attaatttag caatatcaat tgctcaagta
     4141 gtagtgcagg cgttaatact ttataacact tatcagcaat ataaatattc taaaaaatat
     4201 tcagcctaat aaaaaaagac ttagtctgaa tagaccaagc cttttgttag tgttatatta
     4261 atatgcaaat aaaaaaacaa aaaaagaagt cgctcactcc ctgaccaaag tttgtgaatg
     4321 cgacttacct taaagaaaaa cagttggtgt ttttttctta atttttgtat atctagatat
     4381 taaacgatat tggttta
//
