LOCUS       NZ_CP140631             2579 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm013, complete sequence.
ACCESSION   NZ_CP140631
VERSION     NZ_CP140631.1
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 2579)
  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  JOURNAL   Unpublished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 2579)
  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
            CP140631.1.
            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..2579
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm013"
                     /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            join(2545..2579,1..610)
                     /locus_tag="O5Y90_RS26800"
                     /old_locus_tag="O5Y90_26795"
     CDS             join(2545..2579,1..610)
                     /locus_tag="O5Y90_RS26800"
                     /old_locus_tag="O5Y90_26795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(992..1228)
                     /locus_tag="O5Y90_RS26805"
                     /old_locus_tag="O5Y90_26800"
     CDS             complement(992..1228)
                     /locus_tag="O5Y90_RS26805"
                     /old_locus_tag="O5Y90_26800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012772745.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            <2296..2451
                     /locus_tag="O5Y90_RS26810"
                     /old_locus_tag="O5Y90_26805"
                     /pseudo=""
     CDS             <2296..2451
                     /locus_tag="O5Y90_RS26810"
                     /old_locus_tag="O5Y90_26805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707212.3"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     ARG             3..607
                     /name="qnrB"
                     /gene="qnrB"
                     /gene_name="QnrB family quinolone resistance pentapeptide
                     repeat protein"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="94.39"
     ARG             2510..2577
                     /name="QnrB59"
                     /gene="QnrB59"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="95.65"
                     /coverage="10.18"
     ARG             3..610
                     /name="QnrB5"
                     /gene="QnrB5"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.5"
                     /coverage="89.38"
     Typing          complement(1394..1567)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1546..2037
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 aaatcgcttc accggtgaga aagttgaaaa tagtacattt tttaactgcg atttttcagg
       61 tgccgacctg agcggcactg aatttatcgg ctgccagttc tatgatcgcg aaagtcagaa
      121 agggtgcaat tttagtcgcg caatgctgaa agatgccatt ttcaaaagct gtgatttatc
      181 aatggcagat ttccgcaacg tcagtgcctt gggcattgaa attcgccact gccgcgcaca
      241 aggcgcagat ttccgcggtg caagctttat gaatatgatc accacgcgca cctggttttg
      301 cagcgcatat atcactaata ctaatctaag ctacgccaat ttttcgaaag tcgtgttgga
      361 aaagtgtgag ctgtgggaaa accgctggat ggggactcag gtactgggtg cgacgttcag
      421 tggttcagat ctctccggcg gcgagttttc gactttcgac tggcgagcag caaacttcac
      481 acattgcgat ctgaccaatt cggagttagg tgacttagat attcggggtg ttgatttaca
      541 aggcgttaag ttagacagct accaggcatc gttgctcatg gagcggcttg gcatcgctgt
      601 gattggttag ttcagcgttt acaccgggag atgcgtttga cgatttactt ttacccgcga
      661 tcatcgcgtt tattgagttt attatttatc tatgcgattc cgatgaaaaa ttcgcacgaa
      721 aatatggcta actcatagca aaaaaaaagc cccctaaggg cttttttttg tacctgacgg
      781 tcagaccgat taaacataac atcccttgcc cgcacccccg caggcgccct cagcgcaatc
      841 ctgctgcatc agggccgttt ccagcacctt tcctcaccag tatcccggaa aaacgcccct
      901 gatgatttct gcgcgactgc atggctatgc acgcaggtga atggcaggtg atttcgcagc
      961 gtcagcacca ctaaaccgcc aaaagccaaa atcagcggcg cggcgcgcgc ggacgtgacc
     1021 aggcaaaatc ggactgctgc cgctcatcct cacgtaatgc acgctggcgg tcggcgtaac
     1081 gctgcaactc aatttgcgca cgcgctctgt tcaggacgat gtgccggtta ggctgattta
     1141 gctttttacc tgacgctctt tcagctgcgg caacagcatc atcaagaaat tttttctctg
     1201 caggcgtcaa gtttgtcagt ctggccataa cgttctccag tcagaataaa tcagcacagt
     1261 ctgccagaca cagtagaaac gatgaagcgc cagcgacggt gaaaggcagt cagaaacggt
     1321 gaacgggagc ggattttaat ccggtgccgt gaggcgttgg acaagccgca ggcgcgtcat
     1381 tagcttttag ccggtttcgg ggcgcagccc tgaaccagtc acgtagcgct agcggagtgt
     1441 atactggctg actatgttgg cacggatgtg gaaatcagtg aagtgcttca tgtagcagga
     1501 gaaaaaaggc ggcaccagcg cgtcagcagg atatgtagta caggatatat tccgcttcct
     1561 cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg agcggtgccg gcttacaggc
     1621 ggggcggaaa tttcctggga gataccagga aggagcttaa cagggaagag ataaggccgc
     1681 ggcgaagccg tttttccata ggctccgccc ccctgacaaa catcatgaaa tctgacgctc
     1741 aaatcagtgg tggcgaaacc cgatgcggct taaagatacc aggcgtttcc ccctggtggc
     1801 tccctcgtgc tcccccgcat tcctgccttt cggtttaccg gtgtcattcc gctgttatgg
     1861 ccgcgtttat ctcattccac gcctgacact cagttccgcg aaggcagttc gctcctggat
     1921 ggactgtatg cacgaacccc ccgttcagtc cgactgctgc gccttatccg gtaactatca
     1981 tcttgagtcc aacccggaaa gacacgactt atcgccactg gcagcagcca ctggtaactg
     2041 atttagagga gttagtcttg aagttatgcg cctgttaagg ctaaactgaa agaacagatt
     2101 tggttactgc gctcctcgta agccagttac cacggttcaa agagttgctg ctctgagaac
     2161 cttcgaaaaa ccgccttgca gggcggtttt ttcgtttaca gagcaagaga ttacgacgcc
     2221 acagaaagga tctcaagaag atccttcacc gtaatggaaa tctatccaat ccgagcacat
     2281 aggatacaca tcgttataac gctggatctg cgtgaattcc agcagcagca agagaaagac
     2341 tttctacaaa ccagcttaca gcaggctaaa tttaaccaga aaaaagccgc tgaattactg
     2401 ggtctgactt atcatcagct acgtgccttg ctgaagaaac accagatcta atacgcattt
     2461 gcaggtgtca tactggcggg tttgacgcat aacgtcataa ggtttaccat ggcgtcatta
     2521 ctgtataaaa acacaggcat agatatgact ctggcattag ttggcgaaaa aattgacag
//
