LOCUS       NZ_OP038286             2579 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain 202008118 plasmid p202008118-16, complete
            sequence.
ACCESSION   NZ_OP038286
VERSION     NZ_OP038286.1
DBLINK      BioProject: PRJNA224116
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2579)
  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  JOURNAL   Unpublished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 2579)
  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 04:10:55
            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
            OP038286.1.
            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..2579
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="202008118"
                     /isolation_source="human"
                     /db_xref="taxon:624"
                     /plasmid="p202008118-16"
     gene            complement(323..559)
                     /locus_tag="OVO80_RS00005"
                     /old_locus_tag="p202008118-16__00001"
     CDS             complement(323..559)
                     /locus_tag="OVO80_RS00005"
                     /old_locus_tag="p202008118-16__00001"
                     /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            <1627..1782
                     /locus_tag="OVO80_RS00010"
                     /old_locus_tag="p202008118-16__00002"
                     /pseudo=""
     CDS             <1627..1782
                     /locus_tag="OVO80_RS00010"
                     /old_locus_tag="p202008118-16__00002"
                     /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"
     gene            1876..2520
                     /locus_tag="OVO80_RS00015"
                     /old_locus_tag="p202008118-16__00003"
     CDS             1876..2520
                     /locus_tag="OVO80_RS00015"
                     /old_locus_tag="p202008118-16__00003"
                     /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"
     ARG             1877..2517
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(725..898)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          877..1368
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ttattgagtt tattatttat ctatgcgatt ccgatgaaaa attcgcacga aaatatggct
       61 aactcatagc aaaaaaaaag ccccctaagg gctttttttt gtacctgacg gtcagaccga
      121 ttaaacataa catcccttgc ccgcaccccc gcaggcgccc tcagcgcaat cctgctgcat
      181 cagggccgtt tccagcacct ttcctcacca gtatcccgga aaaacgcccc tgatgatttc
      241 tgcgcgactg catggctatg cacgcaggtg aatggcaggt gatttcgcag cgtcagcacc
      301 actaaaccgc caaaagccaa aatcagcggc gcggcgcgcg cggacgtgac caggcaaaat
      361 cggactgctg ccgctcatcc tcacgtaatg cacgctggcg gtcggcgtaa cgctgcaact
      421 caatttgcgc acgcgctctg ttcaggacga tgtgccggtt aggctgattt agctttttac
      481 ctgacgctct ttcagctgcg gcaacagcat catcaagaaa ttttttctct gcaggcgtca
      541 agtttgtcag tctggccata acgttctcca gtcagaataa atcagcacag tctgccagac
      601 acagtagaaa cgatgaagcg ccagcgacgg tgaaaggcag tcagaaacgg tgaacgggag
      661 cggattttaa tccggtgccg tgaggcgttg gacaagccgc aggcgcgtca ttagctttta
      721 gccggtttcg gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg tatactggct
      781 gactatgttg gcacggatgt ggaaatcagt gaagtgcttc atgtagcagg agaaaaaagg
      841 cggcaccagc gcgtcagcag gatatgtagt acaggatata ttccgcttcc tcgctcactg
      901 actcgctgcg ctcggtcgtt cggctgcggc gagcggtgcc ggcttacagg cggggcggaa
      961 atttcctggg agataccagg aaggagctta acagggaaga gataaggccg cggcgaagcc
     1021 gtttttccat aggctccgcc cccctgacaa acatcatgaa atctgacgct caaatcagtg
     1081 gtggcgaaac ccgatgcggc ttaaagatac caggcgtttc cccctggtgg ctccctcgtg
     1141 ctcccccgca ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgttta
     1201 tctcattcca cgcctgacac tcagttccgc gaaggcagtt cgctcctgga tggactgtat
     1261 gcacgaaccc cccgttcagt ccgactgctg cgccttatcc ggtaactatc atcttgagtc
     1321 caacccggaa agacacgact tatcgccact ggcagcagcc actggtaact gatttagagg
     1381 agttagtctt gaagttatgc gcctgttaag gctaaactga aagaacagat ttggttactg
     1441 cgctcctcgt aagccagtta ccacggttca aagagttgct gctctgagaa ccttcgaaaa
     1501 accgccttgc agggcggttt tttcgtttac agagcaagag attacgacgc cacagaaagg
     1561 atctcaagaa gatccttcac cgtaatggaa atctatccaa tccgagcaca taggatacac
     1621 atcgttataa cgctggatct gcgtgaattc cagcagcagc aagagaaaga ctttctacaa
     1681 accagcttac agcaggctaa atttaaccag aaaaaagccg ctgaattact gggtctgact
     1741 tatcatcagc tacgtgcctt gctgaagaaa caccagatct aatacgcatt tgcaggtgtc
     1801 atactggcgg gtttgacgca taacgtcata aggtttacca tggcgtcatt actgtataaa
     1861 aacacaggca tagatatgac tctggcatta gttggcgaaa aaattgacag aaatcgcttc
     1921 accggtgaga aagttgaaaa tagtacattt tttaactgcg atttttcagg tgccgacctg
     1981 agcggcactg aatttatcgg ctgccagttc tatgatcgcg aaagtcagaa agggtgcaat
     2041 tttagtcgcg caatgctgaa agatgccatt ttcaaaagct gtgatttatc aatggcagat
     2101 ttccgcaacg tcagtgcctt gggcattgaa attcgccact gccgcgcaca aggcgcagat
     2161 ttccgcggtg caagctttat gaatatgatc accacgcgca cctggttttg cagcgcatat
     2221 atcactaata ctaatctaag ctacgccaat ttttcgaaag tcgtgttgga aaagtgtgag
     2281 ctgtgggaaa accgctggat ggggactcag gtactgggtg cgacgttcag tggttcagat
     2341 ctctccggcg gcgagttttc gactttcgac tggcgagcag caaacttcac acattgcgat
     2401 ctgaccaatt cggagttagg tgacttagat attcggggtg ttgatttaca aggcgttaag
     2461 ttagacagct accaggcatc gttgctcatg gagcggcttg gcatcgctgt gattggttag
     2521 ttcagcgttt acaccgggag atgcgtttga cgatttactt ttacccgcga tcatcgcgt
//
