LOCUS       NZ_OP038289             2579 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain 202008564 plasmid p202008564-21, complete
            sequence.
ACCESSION   NZ_OP038289
VERSION     NZ_OP038289.1
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  JOURNAL   Unpublished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 04:03:43
            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
            OP038289.1.
            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="202008564"
                     /isolation_source="human"
                     /db_xref="taxon:624"
                     /plasmid="p202008564-21"
     gene            207..443
                     /locus_tag="OVO63_RS00005"
                     /old_locus_tag="p202008564-21__00001"
     CDS             207..443
                     /locus_tag="OVO63_RS00005"
                     /old_locus_tag="p202008564-21__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            complement(825..1469)
                     /locus_tag="OVO63_RS00010"
                     /old_locus_tag="p202008564-21__00002"
     CDS             complement(825..1469)
                     /locus_tag="OVO63_RS00010"
                     /old_locus_tag="p202008564-21__00002"
                     /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(1563..>1718)
                     /locus_tag="OVO63_RS00015"
                     /old_locus_tag="p202008564-21__00003"
                     /pseudo=""
     CDS             complement(1563..>1718)
                     /locus_tag="OVO63_RS00015"
                     /old_locus_tag="p202008564-21__00003"
                     /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"
     ARG             complement(829..1469)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2448..2579
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.699999999999999e-63"
     Typing          complement(1978..2469)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 cgctagcgct acgtgactgg ttcagggctg cgccccgaaa ccggctaaaa gctaatgacg
       61 cgcctgcggc ttgtccaacg cctcacggca ccggattaaa atccgctccc gttcaccgtt
      121 tctgactgcc tttcaccgtc gctggcgctt catcgtttct actgtgtctg gcagactgtg
      181 ctgatttatt ctgactggag aacgttatgg ccagactgac aaacttgacg cctgcagaga
      241 aaaaatttct tgatgatgct gttgccgcag ctgaaagagc gtcaggtaaa aagctaaatc
      301 agcctaaccg gcacatcgtc ctgaacagag cgcgtgcgca aattgagttg cagcgttacg
      361 ccgaccgcca gcgtgcatta cgtgaggatg agcggcagca gtccgatttt gcctggtcac
      421 gtccgcgcgc gccgcgccgc tgattttggc ttttggcggt ttagtggtgc tgacgctgcg
      481 aaatcacctg ccattcacct gcgtgcatag ccatgcagtc gcgcagaaat catcaggggc
      541 gtttttccgg gatactggtg aggaaaggtg ctggaaacgg ccctgatgca gcaggattgc
      601 gctgagggcg cctgcggggg tgcgggcaag ggatgttatg tttaatcggt ctgaccgtca
      661 ggtacaaaaa aaagccctta gggggctttt tttttgctat gagttagcca tattttcgtg
      721 cgaatttttc atcggaatcg catagataaa taataaactc aataaacgcg atgatcgcgg
      781 gtaaaagtaa atcgtcaaac gcatctcccg gtgtaaacgc tgaactaacc aatcacagcg
      841 atgccaagcc gctccatgag caacgatgcc tggtagctgt ctaacttaac gccttgtaaa
      901 tcaacacccc gaatatctaa gtcacctaac tccgaattgg tcagatcgca atgtgtgaag
      961 tttgctgctc gccagtcgaa agtcgaaaac tcgccgccgg agagatctga accactgaac
     1021 gtcgcaccca gtacctgagt ccccatccag cggttttccc acagctcaca cttttccaac
     1081 acgactttcg aaaaattggc gtagcttaga ttagtattag tgatatatgc gctgcaaaac
     1141 caggtgcgcg tggtgatcat attcataaag cttgcaccgc ggaaatctgc gccttgtgcg
     1201 cggcagtggc gaatttcaat gcccaaggca ctgacgttgc ggaaatctgc cattgataaa
     1261 tcacagcttt tgaaaatggc atctttcagc attgcgcgac taaaattgca ccctttctga
     1321 ctttcgcgat catagaactg gcagccgata aattcagtgc cgctcaggtc ggcacctgaa
     1381 aaatcgcagt taaaaaatgt actattttca actttctcac cggtgaagcg atttctgtca
     1441 attttttcgc caactaatgc cagagtcata tctatgcctg tgtttttata cagtaatgac
     1501 gccatggtaa accttatgac gttatgcgtc aaacccgcca gtatgacacc tgcaaatgcg
     1561 tattagatct ggtgtttctt cagcaaggca cgtagctgat gataagtcag acccagtaat
     1621 tcagcggctt ttttctggtt aaatttagcc tgctgtaagc tggtttgtag aaagtctttc
     1681 tcttgctgct gctggaattc acgcagatcc agcgttataa cgatgtgtat cctatgtgct
     1741 cggattggat agatttccat tacggtgaag gatcttcttg agatcctttc tgtggcgtcg
     1801 taatctcttg ctctgtaaac gaaaaaaccg ccctgcaagg cggtttttcg aaggttctca
     1861 gagcagcaac tctttgaacc gtggtaactg gcttacgagg agcgcagtaa ccaaatctgt
     1921 tctttcagtt tagccttaac aggcgcataa cttcaagact aactcctcta aatcagttac
     1981 cagtggctgc tgccagtggc gataagtcgt gtctttccgg gttggactca agatgatagt
     2041 taccggataa ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccatccagg
     2101 agcgaactgc cttcgcggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac
     2161 agcggaatga caccggtaaa ccgaaaggca ggaatgcggg ggagcacgag ggagccacca
     2221 gggggaaacg cctggtatct ttaagccgca tcgggtttcg ccaccactga tttgagcgtc
     2281 agatttcatg atgtttgtca ggggggcgga gcctatggaa aaacggcttc gccgcggcct
     2341 tatctcttcc ctgttaagct ccttcctggt atctcccagg aaatttccgc cccgcctgta
     2401 agccggcacc gctcgccgca gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc
     2461 ggaatatatc ctgtactaca tatcctgctg acgcgctggt gccgcctttt ttctcctgct
     2521 acatgaagca cttcactgat ttccacatcc gtgccaacat agtcagccag tatacactc
//
