LOCUS       NZ_OP038297             2699 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain 202108535 plasmid p202108535-13, complete
            sequence.
ACCESSION   NZ_OP038297
VERSION     NZ_OP038297.1
DBLINK      BioProject: PRJNA224116
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2699)
  AUTHORS   Lefevre,S., Njamkepo,E., Ruckly,C., Carle,I., Lejay-Collin,M.,
            Fabre,L., Maria Pardos de la Gandara,M. and Weill,F.-X.
  TITLE     Recent and rapid emergence of extensively drug-resistant Shigella
            sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2699)
  AUTHORS   Lefevre,S., Njamkepo,E., Ruckly,C., Carle,I., Lejay-Collin,M.,
            Fabre,L., Maria Pardos de la Gandara,M. and Weill,F.-X.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUL-2022) Enteric Bacterial Pathogens Unit, Institut
            Pasteur, 28 rue du Dr Roux, Paris 75724, France
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: unicycler v. 0.4.8
            Sequencing Technology             :: MinION
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/07/2024 04:07:24
            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)                     :: 3
            CDSs (total)                      :: 3
            Genes (coding)                    :: 2
            CDSs (with protein)               :: 2
            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
            OP038297.1.
            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..2699
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="202108535"
                     /isolation_source="human"
                     /db_xref="taxon:624"
                     /plasmid="p202108535-13"
     gene            complement(285..929)
                     /locus_tag="OVO70_RS00005"
                     /old_locus_tag="p202108535-13__00001"
     CDS             complement(285..929)
                     /locus_tag="OVO70_RS00005"
                     /old_locus_tag="p202108535-13__00001"
                     /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(1023..>1178)
                     /locus_tag="OVO70_RS00010"
                     /old_locus_tag="p202108535-13__00002"
                     /pseudo=""
     CDS             complement(1023..>1178)
                     /locus_tag="OVO70_RS00010"
                     /old_locus_tag="p202108535-13__00002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /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"
     gene            2246..2482
                     /locus_tag="OVO70_RS00015"
                     /old_locus_tag="p202108535-13__00003"
     CDS             2246..2482
                     /locus_tag="OVO70_RS00015"
                     /old_locus_tag="p202108535-13__00003"
                     /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"
     ARG             complement(289..929)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          1908..2081
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1438..1929)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ggtacaaaaa aaagccctta gggggctttt tttttgctat gagttagcca tattttcgtt
       61 aagacatggc ttcatgattc gggagtggtt attcgttgtt ctcgcgaaaa tgaattggtt
      121 agatattcat caaattcctg tccagaatgc agcattagat ggcatgtcgt tgatgcggta
      181 ggtcaggata ttcgtccact ggagaaaacg tttcacaatg cttgccagga gtcgtactgg
      241 ttaaaagtaa atcgtcaaac gcatctcccg gtgtaaacgc tgaactaacc aatcacagcg
      301 atgccaagcc gctccatgag caacgatgcc tggtagctgt ctaacttaac gccttgtaaa
      361 tcaacacccc gaatatctaa gtcacctaac tccgaattgg tcagatcgca atgtgtgaag
      421 tttgctgctc gccagtcgaa agtcgaaaac tcgccgccgg agagatctga accactgaac
      481 gtcgcaccca gtacctgagt ccccatccag cggttttccc acagctcaca cttttccaac
      541 acgactttcg aaaaattggc gtagcttaga ttagtattag tgatatatgc gctgcaaaac
      601 caggtgcgcg tggtgatcat attcataaag cttgcaccgc ggaaatctgc gccttgtgcg
      661 cggcagtggc gaatttcaat gcccaaggca ctgacgttgc ggaaatctgc cattgataaa
      721 tcacagcttt tgaaaatggc atctttcagc attgcgcgac taaaattgca ccctttctga
      781 ctttcgcgat catagaactg gcagccgata aattcagtgc cgctcaggtc ggcacctgaa
      841 aaatcgcagt taaaaaatgt actattttca actttctcac cggtgaagcg atttctgtca
      901 attttttcgc caactaatgc cagagtcata tctatgcctg tgtttttata cagtaatgac
      961 gccatggtaa accttatgac gttatgcgtc aaacccgcca gtatgacacc tgcaaatgcg
     1021 tattagatct ggtgtttctt cagcaaggca cgtagctgat gataagtcag acccagtaat
     1081 tcagcggctt ttttctggtt aaatttagcc tgctgtaagc tggtttgtag aaagtctttc
     1141 tcttgctgct gctggaattc acgcagatcc agcgttataa cgatgtgtat cctatgtgct
     1201 cggattggat agatttccat tacggtgaag gatcttcttg agatcctttc tgtggcgtcg
     1261 taatctcttg ctctgtaaac gaaaaaaccg ccctgcaagg cggtttttcg aaggttctca
     1321 gagcagcaac tctttgaacc gtggtaactg gcttacgagg agcgcagtaa ccaaatctgt
     1381 tctttcagtt tagccttaac aggcgcataa cttcaagact aactcctcta aatcagttac
     1441 cagtggctgc tgccagtggc gataagtcgt gtctttccgg gttggactca agatgatagt
     1501 taccggataa ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccatccagg
     1561 agcgaactgc cttcgcggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac
     1621 agcggaatga caccggtaaa ccgaaaggca ggaatgcggg ggagcacgag ggagccacca
     1681 gggggaaacg cctggtatct ttaagccgca tcgggtttcg ccaccactga tttgagcgtc
     1741 agatttcatg atgtttgtca ggggggcgga gcctatggaa aaacggcttc gccgcggcct
     1801 tatctcttcc ctgttaagct ccttcctggt atctcccagg aaatttccgc cccgcctgta
     1861 agccggcacc gctcgccgca gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc
     1921 ggaatatatc ctgtactaca tatcctgctg acgcgctggt gccgcctttt ttctcctgct
     1981 acatgaagca cttcactgat ttccacatcc gtgccaacat agtcagccag tatacactcc
     2041 gctagcgcta cgtgactggt tcagggctgc gccccgaaac cggctaaaag ctaatgacgc
     2101 gcctgcggct tgtccaacgc ctcacggcac cggattaaaa tccgctcccg ttcaccgttt
     2161 ctgactgcct ttcaccgtcg ctggcgcttc atcgtttcta ctgtgtctgg cagactgtgc
     2221 tgatttattc tgactggaga acgttatggc cagactgaca aacttgacgc ctgcagagaa
     2281 aaaatttctt gatgatgctg ttgccgcagc tgaaagagcg tcaggtaaaa agctaaatca
     2341 gcctaaccgg cacatcgtcc tgaacagagc gcgtgcgcaa attgagttgc agcgttacgc
     2401 cgaccgccag cgtgcattac gtgaggatga gcggcagcag tccgattttg cctggtcacg
     2461 tccgcgcgcg ccgcgccgct gattttggct tttggcggtt tagtggtgct gacgctgcga
     2521 aatcacctgc cattcacctg cgtgcatagc catgcagtcg cgcagaaatc atcaggggcg
     2581 tttttccggg atactggtga ggaaaggtgc tggaaacggc cctgatgcag caggattgcg
     2641 ctgagggcgc ctgcgggggt gcgggcaagg gatgttatgt ttaatcggtc tgaccgtca
//
