LOCUS       NZ_CP140634             1822 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm016, complete sequence.
ACCESSION   NZ_CP140634
VERSION     NZ_CP140634.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32329321
            Assembly: GCF_034554795.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1822)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Complete genome assembly and description of a Shigella sonnei
            clinical strain resistant to third- and fourth-generation
            cephalosporins isolated in Northern Italy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1822)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2022) Microbiology, Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, Bologna, BO 40138, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 13-APR-2022
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: SO87
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 261.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/06/2024 22:59:22
            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)                     :: 5,368
            CDSs (total)                      :: 5,245
            Genes (coding)                    :: 4,512
            CDSs (with protein)               :: 4,512
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 733
            CDSs (without protein)            :: 733
            Pseudo Genes (ambiguous residues) :: 0 of 733
            Pseudo Genes (frameshifted)       :: 204 of 733
            Pseudo Genes (incomplete)         :: 529 of 733
            Pseudo Genes (internal stop)      :: 125 of 733
            Pseudo Genes (multiple problems)  :: 119 of 733
            Pseudo Genes (short protein)      :: 3 of 733
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP140634.1.
            Bacteria and source DNA available from Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, 40138, Bologna (Italy).
            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..1822
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm016"
                     /geo_loc_name="Italy: Bologna"
                     /lat_lon="44.4912 N 11.3615 E"
                     /collection_date="2021-11-30"
                     /collected_by="IRCCS Policlinico S. Orsola - Malpighi"
     gene            265..798
                     /locus_tag="O5Y90_RS26835"
                     /old_locus_tag="O5Y90_26830"
     CDS             265..798
                     /locus_tag="O5Y90_RS26835"
                     /old_locus_tag="O5Y90_26830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005707163.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000893324.1"
                     /translation="MLEQQFEDFEQQKRRDHQAQDQSKSAKQKRDRLNPPDWSQVTKAG
                     WNMLDSISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFEGSLKTSNHDLD"
                     /name="replication/maintenance protein RepL"
     gene            811..1098
                     /locus_tag="O5Y90_RS26840"
                     /old_locus_tag="O5Y90_26835"
     CDS             811..1098
                     /locus_tag="O5Y90_RS26840"
                     /old_locus_tag="O5Y90_26835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001220925.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_171803770.1"
                     /translation="MRIKYESRWKLEELKLEICRSIDSLIDEYHIEYAMGINLYMNCED
                     KEFNPVDIVNEDGKNIMFVVSNNEKIQKTKKSAKKKNPAPVIELDKYRKK"
                     /name="hypothetical protein"
     Typing          complement(1341..1601)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 cgctatcgct acgtgactgg gtcagggctt cgccccgaca ccccaaatgt tcgatgaact
       61 aattaaatct tgtgtagcaa aaaagtgctt tgatagatct ttagagcaaa aatcgacatt
      121 ctcttaaaaa tcaaagcatt atggcaccaa catacgaaac gttatttgca tgtgtatacg
      181 caaacatgtt tgcgtgtgtt gtttcgtaat gtacgatata aatttcgtaa ggtacgaaac
      241 aacgttgcag gtaaggatgc aagtatgctg gaacagcaat ttgaagattt cgaacagcaa
      301 aaacggcgag atcatcaggc acaagatcaa tccaaaagtg ctaagcaaaa acgagatcgg
      361 ttgaatccac ctgactggtc gcaggttact aaggcgggct ggaatatgtt ggactctata
      421 tctgagaagg ttcccagagc atttaggcta tattcttttt ttgctcaaaa tatagataaa
      481 tcgtgtgggg ctgttgtatg tgaccaaaaa ttcttagctg attatttcgg tgttagttta
      541 aggacgatcc aatattggat tggagattta gaaagtattg gtgccatcgt gaaaatacca
      601 gtaggtatct attatgctta tgcgttagat ccgtatcagg tatggcgcgg atataataaa
      661 tctaaaaaat atgcagcgtt taacgcaaaa acattaactc aaaaagatgg cgttattgat
      721 cgcaagttgc ggctcatgct ctctaggaga gaagagtttg aaggctcgct taagacatct
      781 aatcatgact tggactaggt atgatgcgct atgagaatta aatatgaatc acgttggaaa
      841 ttagaagaac taaaattaga aatatgtaga tcaatagatt cgttaattga tgaatatcat
      901 atcgaatatg caatgggaat aaatctatat atgaattgtg aagataagga gtttaatccc
      961 gttgatattg tcaatgaaga tggaaagaat attatgtttg ttgttagcaa caatgaaaaa
     1021 atacaaaaaa caaaaaaaag tgcgaagaaa aaaaatcctg cacctgtaat tgagttagat
     1081 aaatatcgga aaaagtgatg gccatacaga gccagcggca ggcggacaat ccacagaaca
     1141 ttgcatgcaa tttctagttg attgtctatc ctgcattgct cttttgccgc ctcaaaatcc
     1201 cttgcgtctt tttgctcccc gttttccaga acgaccgagc cgccacggtt ccggcagcgc
     1261 cttgagcgca accggaaacc gtctggggag aaccccagac ccccatcgct gtaacatcga
     1321 cggtctacga ccacctacca accgcgtggc tgcctattcc gtgcaaatgg gctttgcagg
     1381 gggctgacgc ggttcctggc gacctgaaat cccctggtta ggggtatcgg cgcgcctgac
     1441 ctcctaaaac cctctgtaag cgtttttcgc gccttccatg ccctgatggg catttaaaac
     1501 ccgtttcgtg cgtctgagag cttctgagag cgtttgaaga gctatctggc gactcatccc
     1561 cgaaagaaca acagcggaat caccgataac atgcgagagg tggcaccgct cgccgcagcc
     1621 ccagcgaccg aacgttagtg agcgagtggg cgaggaagcg gaagagaacc ggaaaccaca
     1681 ttgagcacgt acgcactgat gcggggcgtt ttagcggtga acggactgca aaaacatgat
     1741 cgagctgttg aacgtggaga gcgcgaaatc gggcaaaatc acggctgacg aggcttgcag
     1801 aagagtaagc cagtatacac tc
//
