LOCUS       NZ_CP136531             3125 bp    DNA     circular CON 20-OCT-2023
DEFINITION  Staphylococcus aureus strain BAA-1556_Catania plasmid pUSA01,
            complete sequence.
ACCESSION   NZ_CP136531
VERSION     NZ_CP136531.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37705136
            Assembly: GCF_032809245.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3125)
  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  JOURNAL   Unpublished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 3125)
  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
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 85x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/20/2023 13:22:02
            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)                     :: 2,940
            CDSs (total)                      :: 2,858
            Genes (coding)                    :: 2,780
            CDSs (with protein)               :: 2,780
            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)              :: 78
            CDSs (without protein)            :: 78
            Pseudo Genes (ambiguous residues) :: 0 of 78
            Pseudo Genes (frameshifted)       :: 43 of 78
            Pseudo Genes (incomplete)         :: 38 of 78
            Pseudo Genes (internal stop)      :: 14 of 78
            Pseudo Genes (multiple problems)  :: 16 of 78
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP136531.1.
            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..3125
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="BAA-1556_Catania"
                     /isolation_source="University of Catania"
                     /host="Homo sapiens"
                     /culture_collection="ATCC:BAA-1556"
                     /db_xref="taxon:1280"
                     /plasmid="pUSA01"
                     /geo_loc_name="Italy:Catania"
                     /lat_lon="37.52 N 15.06 E"
                     /collection_date="2021"
                     /collected_by="University of Catania"
     gene            1..996
                     /locus_tag="RZS17_RS14690"
                     /old_locus_tag="RZS17_14690"
     CDS             1..996
                     /locus_tag="RZS17_RS14690"
                     /old_locus_tag="RZS17_14690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199892.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EKVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANVKAI
                     KPNRKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDVEDGNLINASDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     gene            1579..1767
                     /locus_tag="RZS17_RS14695"
                     /old_locus_tag="RZS17_14695"
     CDS             1579..1767
                     /locus_tag="RZS17_RS14695"
                     /old_locus_tag="RZS17_14695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001039248.1"
                     /translation="MNKNTVLDEGYVIATILNVFFLLGLIFISHLENLYILIPYVILMG
                     INAIYLVVKVMNFKKNN"
                     /name="hypothetical protein"
     gene            complement(2093..2674)
                     /locus_tag="RZS17_RS14700"
                     /old_locus_tag="RZS17_14700"
     CDS             complement(2093..2674)
                     /locus_tag="RZS17_RS14700"
                     /old_locus_tag="RZS17_14700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000991705.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     Typing          1067..1231
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          2..996
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcaatata atactactag aagtataacc gaaaatcaag ataataaaac gttaaaagat
       61 atgacgaaaa gtgggaaaca acgcccatgg agagaaaaga aaatagataa tgtaagctat
      121 gcagatatac tagaaatttt aaaaatcaaa aaggctttta atgtaaaaca atgtggtaat
      181 attttagaat ttaagccaac tgatgaaggc tatttgaagt tacataagac atggttttgt
      241 aaatcaaaat tatgtccggt ttgtaattgg agacgtgcta tgaaaaatag ttatcaagct
      301 caaaaagtga ttgaaaaagt aattaaggaa aagccaaaag cacgttggtt gtttttaaca
      361 ctttcaacaa aaaatgcgat agatggagat actttagaac aaagtttgaa gcatctaact
      421 aaagcatttg ataggttgag tagatataaa aaggttaaac aaaatcttgt tggatttatg
      481 cgttcaacag aagttaccgt taataaaaat gacggtagtt ataatcagca catgcatgtt
      541 ttgttatgtg ttgaaaatgc atattttaga aaaaaagaga attatataac tcaagaagaa
      601 tgggttaatt tatggcaaag agcattacaa gttgactatc gacctgttgc taatgttaaa
      661 gcgatcaaac cgaatagaaa aggcgataaa gacattgaat cggcaatcaa agagacctca
      721 aaatattcgg ttaaatcatc tgatttttta actgatgatg atgaaaaaaa tcaagaaatt
      781 gtaagtgatt tagaaaaagg tttgtatcga aaacgtatgt taagttatgg tggattgctt
      841 aaacaaaaac ataaaatttt aaacttagac gatgtcgaag atggtaattt gattaatgca
      901 agtgatgaag ataaaacaac agacgaagaa gaaaaagcac attcaattac cgcaatttgg
      961 aatttcgaaa agcaaaatta ttatttaaga cattagtgtt gactaatgtc ttttttgttg
     1021 attttttata aaaaagtact gtcttatttt tgtgacaaat gctgtatgta gtgtcacaaa
     1081 aataagacaa acgcaatata ttgtgtcaca aaaataagac agtacagctt tgtatgatat
     1141 cactttaaaa taccttaaaa cccctggaat ttctggcttt gccagaccta tcatttttga
     1201 atgatagcaa attctcctta tgctcttacg gagtttttag agaaaaatta aaaattctcg
     1261 atttttgata aaaaacgccc tgcaggaatt tagaaaaaca tgtggaagtt ttaaaggatt
     1321 ttatgctaat ttttaatttg catgtaaatg ggcagtgtta aaaaattagt cactggtttt
     1381 gctgaaattt ttgtttgtga aattaccata tatttatttg gctcatattt gcgttttaag
     1441 agcttgtata tatttttaag ttaaaaacct atatgatacc ccctaaacct ttaaaatacc
     1501 cccttaaaac tcaaaataaa ggtatttata atttgagtaa gtcttgtgat aaagtttttt
     1561 aaaaaaggag tgtttatttt gaataaaaac acagtgttag atgaaggtta cgttatagca
     1621 actattttaa atgttttctt tttacttgga ttaattttta tatctcattt ggaaaattta
     1681 tatatattaa ttccgtatgt tattttgatg ggaataaatg ctatttattt ggttgttaag
     1741 gttatgaatt tcaaaaagaa taattagaat atttgagggg attttgaaac gagtttcttc
     1801 ttgttttcac actgtttttt tattcctatt ggtgttgttg cttacttttt gtttttctat
     1861 aaagatgatg cttttgacga gatggaagaa aaatatgatt atcatgaaga taataaaaaa
     1921 tagacgacgc atttatgccg agaaaattta ttgatgttga gaagaaccct taactaaact
     1981 tgcagacgaa tgtcggcata gcgtgagcta ttaagccgac cattcgacaa gttttgggat
     2041 tgttaagggt tccgaggctc aacgtcaata aagcaattgg aataaatagt atctaaagta
     2101 acccgtattt aagattacat tgtacatcct tcgaaaccat agtagctgcg attccagcta
     2161 ggtttccttt tatcccaatt ttagctaatt tttttgctac gccctttaag tttttggctt
     2221 taacatcttc aaaaactgct gtgattatgt ttccagttaa aagttctcca tatgagttta
     2281 aaacttcaga atagaaacag tcaccgctat ttttgtagtt cccaccaact gctctaggtg
     2341 atattgaact agttttcttt ttattctcta tgtcgttttt tagtttttgg aatccttcag
     2401 gaacatatcc atatcgagat ttggcatttt ctagattaac atctttagct gttccgtctt
     2461 tatctaaaat aataattttg ccatatatgt attttagttc tttttcaatt tctttttcgt
     2521 ttaaagtttc aacgttttta tctgcaatgt tatttttgtt ttgggcttga gcttctttga
     2581 aattaaaatc caagaccatt gaaagtatgg ttaaaatact taaagatact actaaaatct
     2641 ttcttagtga tatactgttt tgaattgcat tcattgtaaa tgcccccttg ttttgttatt
     2701 taaatgaatt caatataata ttaacatata aaaacaaagg agtttaatat gaataagttt
     2761 ttttactttt tgattatttt attatctgta tttttaattt ttaattttgt taattcgatt
     2821 ttatttgata atccttttga ctttttagaa agttttattt attcattggt tttcacatta
     2881 atttatttag gtttagaggg tcataaaaag aagaaggaat aggttgtttt ttgaaacgag
     2941 tgtgaacgag tttcttcttg tcttgatact atatagaaat aactcgattt tatatatata
     3001 gctgtaactg ttgatattac agtgtttaaa cgtgtttttg tgcgtgaaag gaaaatttga
     3061 caataaaaaa ccccagttat attattaagg tgtcgaatct taaataatac tgggggtctt
     3121 tttat
//
