LOCUS       NZ_CP151311             1778 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R22.1286 plasmid pR22.1286_1.7k, complete
            sequence.
ACCESSION   NZ_CP151311
VERSION     NZ_CP151311.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122667
            Assembly: GCF_038363105.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1778)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W., Teng,R.-H. and Chen,B.-H.
  TITLE     WGS of Shigella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1778)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W., Teng,R.-H. and Chen,B.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-2024) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: flye v. v2.9.2
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038363105.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:39:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,120
            CDSs (total)                      :: 4,990
            Genes (coding)                    :: 4,358
            CDSs (with protein)               :: 4,358
            Genes (RNA)                       :: 130
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 632
            CDSs (without protein)            :: 632
            Pseudo Genes (ambiguous residues) :: 0 of 632
            Pseudo Genes (frameshifted)       :: 173 of 632
            Pseudo Genes (incomplete)         :: 436 of 632
            Pseudo Genes (internal stop)      :: 109 of 632
            Pseudo Genes (multiple problems)  :: 83 of 632
            Pseudo Genes (short protein)      :: 3 of 632
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151311.1.
            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..1778
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R22.1286"
                     /db_xref="taxon:624"
                     /plasmid="pR22.1286_1.7k"
                     /collected_by="Taiwan CDC"
     gene            complement(join(1558..1778,1..319))
                     /locus_tag="AADX63_RS25600"
                     /old_locus_tag="AADX63_25585"
     CDS             complement(join(1558..1778,1..319))
                     /locus_tag="AADX63_RS25600"
                     /old_locus_tag="AADX63_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000893324.1"
                     /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_000893325.1"
                     /translation="MLEQQFEDFEQQKRRDHQVQDQSKNAKQKRDRLNPPDWSQVTKAG
                     WNMLDAISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNNTKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFESSLKYSNHDSEQG"
                     /name="replication/maintenance protein RepL"
     Typing          complement(696..777)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.59"
                     /coverage="100.0"
                     /evalue="2.9e-32"
     Typing          892..1150
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.308"
                     /coverage="99.0"
                     /evalue="1.08e-121"
ORIGIN
        1 cgccaatact ttctaaatct ccaatccaat attggatcgt tcttaaacta acaccgaaat
       61 aatcagctaa gaatttttga tcacatacaa cagccccaca tgatttatct atattctggg
      121 caaaaaaaga atataaccga aatgctctag gaactttttc tgatatagcg tccaacatat
      181 tccaaccagc cttagtaacc tgcgaccagt ctggaggatt caaccgatct cgtttttgct
      241 tagcgttctt ggattgatct tgtacctgat gatctcgccg tttttgctgt tcaaagtctt
      301 caaattgctg ttccaacata cttgcatcct tacctgcaat gatatttcgc accttacgaa
      361 atttatatcg tacagtacga aacaacacat gcaaacatgt ttgcgtatac acatgcaaat
      421 aacgtttcgt atgaaggtgt cttaagtcaa tgatttttaa agaaatgtca atttttgctc
      481 taaagatcta tcaaagcgtt tttttactgc tcatgattta acactaccta actgcttttg
      541 gggtgtcggg gcgcagccct gacccagtca cgtagcgata gcggagtgta tactggctta
      601 ctcctctgca agccttacca gccgtgattt ttgccagatt tcatgctctc aacgttcaac
      661 aactccatca tggttttgcc gtccgttcac cgctaaaaag cctcagaaat cgggacagga
      721 tgtgggaatg tcggaccgcg cacgcgcact cagacattca ccacctggtc agggcttcac
      781 cccgacaccc cgcatcagtg cgtaagtgct caatgtggct tccggttctc ttccgcttcc
      841 tcgtcgattc gctcgctacg ctcggtcatc gacttgcggc gagcggtgtc acctctcgca
      901 tgttgtcggt gatcccgttg ttgttctttc agggatgagt cgtcagatag cccttcaaac
      961 gcgctcagaa gctctcagac gcacgaaacg ggttttaaat gcccgtcagg gcatggaagg
     1021 cgcgaaaaac gcttacagag gctctcagga ggtcaggcgc gccgataccc ctaaccaggg
     1081 gctttcaggt cgccaggaac agcgtcagcc ccctgcaaag cctatttgca cggcataggc
     1141 agctattcgg ctggtaggtg gtcgtagacc gtcggtatta cagcgatggg ggtctggggt
     1201 tctccccaga cggtttccgg ttgcgctcaa ggcgctatcg gaaccgtggc ggctcggtcg
     1261 ttctggagag cgtggaacaa aaacacgcaa gggattcgag gcggcaaaag agcaatgcag
     1321 gatagacaat caaggtcaga acgttaacac gtagcccctg attgtccgcc tgccgctggc
     1381 tcaatggtca tttttttcga tatttatcta gctcaattac aggtgctgga gtttttttct
     1441 ttgctatttt ttttggcttt tgtatttttt catcgttgct aacgacaaac attattttat
     1501 ttccatcttt agttcttcta atctccaacg tgattcatat ttaattctca tagtgcatca
     1561 cccctgctct gagtcatgat tagagtactt taaggaactt tcaaactctt cacgcctaga
     1621 aagcataagc cgcaatttac gatctataac cccatctttt tgagttaatg tttttgcgtt
     1681 aaatgctgca tattttttag tattgttata tccacgccat acctgataag gatctaatgc
     1741 ataggcataa tatatgccta ctggtatttt aactattg
//
