LOCUS       NZ_CP136526             4439 bp    DNA     circular CON 20-OCT-2023
DEFINITION  Staphylococcus aureus strain BAA-1556_Catania_SCV plasmid pUSA02,
            complete sequence.
ACCESSION   NZ_CP136526
VERSION     NZ_CP136526.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37705137
            Assembly: GCF_032808505.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4439)
  AUTHORS   Bivona,D.A., Bonomo,C., Colombini,L., Bonacci,P.G., Privitera,G.F.,
            Caruso,G., Caraci,F., Santoro,F., Musso,N., Bongiorno,D.,
            Iannelli,F. and Stefani,S.
  TITLE     Phagosomal escape, intracellular survival, and small colony variants
            formation of USA300 Staphylococcus aureus in RAW 264.7 murine
            macrophages
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4439)
  AUTHORS   Bivona,D.A., Bonomo,C., Colombini,L., Bonacci,P.G., Privitera,G.F.,
            Caruso,G., Caraci,F., Santoro,F., Musso,N., Bongiorno,D.,
            Iannelli,F. and Stefani,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-OCT-2023) Department of Medical Biotechnologies,
            University of Siena, viale Bracci, 16, Siena 53100, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-OCT-2023
            Assembly Method :: Flye v. 2.7.1; Medaka v. 0.7.1; Pilon v. 1.22
            Assembly Name                     :: USA300_BAA-1556_Catania_SCV
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 181x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/20/2023 13:22:38
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,939
            CDSs (total)                      :: 2,857
            Genes (coding)                    :: 2,778
            CDSs (with protein)               :: 2,778
            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)              :: 79
            CDSs (without protein)            :: 79
            Pseudo Genes (ambiguous residues) :: 0 of 79
            Pseudo Genes (frameshifted)       :: 43 of 79
            Pseudo Genes (incomplete)         :: 38 of 79
            Pseudo Genes (internal stop)      :: 15 of 79
            Pseudo Genes (multiple problems)  :: 16 of 79
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP136526.1.
            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..4439
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="BAA-1556_Catania_SCV"
                     /isolation_source="University of Catania"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pUSA02"
                     /geo_loc_name="Italy:Catania"
                     /lat_lon="37.52 N 15.06 E"
                     /collection_date="2021"
                     /collected_by="University of Catania"
     gene            36..1415
                     /gene="tet(K)"
                     /locus_tag="RZS16_RS14670"
                     /old_locus_tag="RZS16_14665"
     ARG             37..1412
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1601..2842
                     /gene="mobV"
                     /locus_tag="RZS16_RS14675"
                     /old_locus_tag="RZS16_14670"
     CDS             1601..2842
                     /gene="mobV"
                     /locus_tag="RZS16_RS14675"
                     /old_locus_tag="RZS16_14670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /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_000122374.1"
                     /translation="MSYSIVRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNANKQNFNNLIDEKIEQNYTGKRKIRTDAIKHIDGLITSDNDFFDNQTPEDTKQFF
                     EYAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKEVVGNKKALTAFQ
                     DRFNEHVKQRGYDLERGQSRQVTNAKHEQISQYKQKTEYHKQEYERESQKTDHIKQKND
                     KLMQEYQKSLNTLKKPINVPYEQETEKVGGLFSKEIQETGNVVISQKDFNEFQKQIKAA
                     QDISEDYEYIKSGRALDDKDKEIREKDDLLNKAVERIENADDNFNQLYENAKPLKENIE
                     IALKLLKILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQ
                     EQQKNQKRDRGMHL"
                     /name="mobV"
     gene            3369..4313
                     /locus_tag="RZS16_RS14680"
                     /old_locus_tag="RZS16_14675"
     CDS             3369..4313
                     /locus_tag="RZS16_RS14680"
                     /old_locus_tag="RZS16_14675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /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_000277652.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKKERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     VDLTDLMKSTLKANEKQLQKQIDFWQHEFKFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          3370..4313
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1602..2839
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tataaacttt agtcacctca agtaaagagg taaaattgtt tagtttatat aaaaaattta
       61 aaggtttgtt ttatagcgtt ttattttggc tttgtattct ttcatttttt agtgtattaa
      121 atgaaatggt tttaaatgtt tctttacctg atattgcaaa tcattttaat actactcctg
      181 gaattacaaa ctgggtaaac actgcatata tgttaacttt ttcgatagga acagcagtat
      241 atggaaaatt atctgattat ataaatataa aaaaattgtt aattattggt attagtttga
      301 gctgtcttgg ttcattgatt gcttttattg gtcacaatca cttttttatt ttgatttttg
      361 gtaggttagt acaaggagta ggatctgctg cattcccttc actgattatg gtggttgtag
      421 ctagaaatat tacaagaaaa aaacaaggca aagcctttgg ttttatagga tcaattgtag
      481 ctttaggtga agggttaggt ccttcaatag ggggaataat agcacattat attcattggt
      541 cttacctact tatacttcct atgattacaa tagtaactat accttttctt attaaagtaa
      601 tggtacctgg taaatcaaca aaaaatacat tagatatcgt aggtattgtt ttaatgtcta
      661 taagtattat atgttttatg ttatttacga caaattataa ttggactttt ttaatactct
      721 tcacaatctt ttttgtgatt tttattaaac atatttcaag agtttctaac ccttttatta
      781 atcctaaact agggaaaaac attccgttta tgcttggttt gttttctggt gggctaatat
      841 tttctatagt agctggtttt atatcaatgg tgccttatat gatgaaaact atttatcatg
      901 taaatgtagc gacaataggt aatagtgtta tttttcctgg aaccatgagt gttattgttt
      961 ttggttattt tggtggtttt ttagtggata gaaaaggatc attatttgtt tttattttag
     1021 gatcattgtc tatctctata agttttttaa ctattgcatt ttttgttgag tttagtatgt
     1081 ggttgactac ttttatgttt atatttgtta tgggcggatt atcttttact aaaacagtta
     1141 tatcaaaaat agtatcaagt agtctttctg aagaagaagt tgcttctgga atgagtttgc
     1201 taaatttcac aagtttttta tcagagggaa caggtatagc aattgtagga ggtttattgt
     1261 cactacaatt gattaatcgt aaactagttc tggaatttat aaattattct tctggagtgt
     1321 atagtaatat tcttgtagcc atggctatcc ttattatttt atgttgtctt ttgacgatta
     1381 ttgtatttaa acgttctaaa aagcagtttg aatagttata ttatattttg gtttagaact
     1441 atgagtggct agcattttgc cactcatttt ttgcgttagc aaaaacaggt ttaagcctcg
     1501 cagagcacac gtattaacga cttattaaaa ataagtctag tgtgttagac ttaaactatt
     1561 aaatacacat gaaacctttg tgcttaggag tgatttttat atgtcttatt ccattgttag
     1621 agtttcaaaa gttaaatctg gaacaaatac aacgggcata caaaaacatg ttcaaagaga
     1681 aaataataat tatgaaaatg aagatataga ccatagtaaa acttacttaa attatgattt
     1741 ggtaaatgct aataaacaga attttaataa cttgattgat gaaaaaatcg aacagaatta
     1801 tacaggcaaa agaaaaatta gaacagacgc gattaaacac attgatggtt taattacatc
     1861 agacaatgat ttctttgata atcaaacgcc agaagataca aagcagtttt ttgaatatgc
     1921 taaagagttt ttagaacaag aatacggtaa agataattta ttatatgcaa cagttcacat
     1981 ggacgaaaaa acaccacata tgcattatgg cgttgttcca ataactgatg atggtcgttt
     2041 aagtgctaaa gaagttgtag gtaataaaaa agctttaaca gcgtttcaag atagatttaa
     2101 tgagcatgtt aaacaacgag gatatgattt agaacgtggg caatcaagac aagtaacaaa
     2161 tgctaaacat gagcaaataa gtcagtataa acaaaaaaca gaatatcata agcaagaata
     2221 tgaacgtgag agccaaaaaa cagaccatat aaagcaaaag aacgataaat taatgcaaga
     2281 gtaccaaaaa tcgttaaata cgcttaaaaa gcctataaat gttccgtatg agcaagaaac
     2341 tgaaaaagta ggtggtttat ttagcaaaga aatacaagaa actggaaatg ttgtaataag
     2401 ccaaaaagat ttcaatgaat ttcagaaaca gataaaagct gctcaagata tttcggaaga
     2461 ttacgagtat ataaagtctg gtagagcctt agatgataaa gataaggaaa tacgagagaa
     2521 agatgattta ttaaataaag cagttgagcg tattgaaaac gcagacgata attttaacca
     2581 actttacgaa aatgcaaagc cacttaaaga gaatatagaa atagcgttaa agcttttaaa
     2641 aatcttacta aaagagttag aacgagtttt aggaagaaat acctttgcgg aaagagttaa
     2701 taagttaaca gaagatgaac caaaactaaa tggtttagca ggaaacttag ataaaaaaat
     2761 gaatccagaa ttatattcag aacaggaaca gcaacaagaa caacaaaaga atcaaaaacg
     2821 agatagaggt atgcacttat agaacatgca tttatgccga gaaaacttat tggttggaat
     2881 gggctatgtg ttagctaact tgttagcgag ttggttggac ttgaattggg attaatccca
     2941 agaaagtacc aactcaacaa cacataaagc cctgtaggtt ccgaccaata aggaaattgg
     3001 aataaagcaa taaaaggagt tgaagaaatg aaattcagag aagcctttga gaattttata
     3061 acaagtaagt atgtacttgg tgttttagta gttttaactg tttaccagat aatacaaatg
     3121 cttaaataaa aaaagacttg atctgattag accaagtctt ttgatagtgt tatattaata
     3181 acaaaataaa aaggagtcgc tcacgccctg accaaagttt gtgaacgaca tcattcaaag
     3241 aaaaaaacac tgagttattt ttataatctt gtatatttag atattaaacg atatttaaat
     3301 atacatcaag atatatattt gggtgagcga ttccttaaac gaaattgaga ttaaggagtc
     3361 gattttttat gtataaaaac aatcatgcaa atcattcaaa tcatttggaa aatcacgatt
     3421 tagacaattt ttctaaaacc ggctactcta atagccggtt ggacgcacat actgtgtgca
     3481 tatctgatcc aaaattaagt tttgatgcaa tgacgatcgt tggaaatctc aaccgagaca
     3541 acgctcaagc cctttctaaa tttatgagtg tagagcccca aataagactt tgggatattc
     3601 ttcaaacaaa gtttaaagct aaagcacttc aagaaaaagt ttatattgaa tatgacaaag
     3661 tgaaagcaga tagttgggat agacgtaata tgcgtattga atttaatcca aacaaactta
     3721 cacgagatga aatgatttgg ttaaaacaaa atataataag ctacatggaa gatgacggtt
     3781 ttacaagatt agatttagcc tttgattttg aagatgattt gagtgactac tatgcaatgt
     3841 ctgataaagc agttaagaaa actatttttt atggtcgtaa tggtaagcca gaaacaaaat
     3901 attttggcgt gagagatagt aatagattta ttagaattta taataaaaag aaagaacgta
     3961 aagataatgc agatgctgaa gttatgtctg aacatttatg gcgtgtagaa atcgaactta
     4021 aaagagatat ggtggattac tggaatgatt gctttagtga tttacatatc ttgcaaccag
     4081 attggaaaac tatccaacgc actgcggata gagcaatagt ttttatgtta ttgagtgatg
     4141 aagaagaatg gggaaagctt cacagaaatt ctagaacaaa atataagaat ttgataaaag
     4201 aaatttcgcc agtcgattta acggacttaa tgaaatcgac tttaaaagcg aacgaaaaac
     4261 aattgcaaaa acaaatcgat ttttggcaac atgaatttaa attttggaaa tagtgtacat
     4321 attaatatta ctgaacaaaa atgatatatt taaactattc taatttagga ggattttttt
     4381 atgaagtgtc tatttaaaaa tttggggaat ttatatgagg tgaaagaata atttacccc
//
