LOCUS       NZ_CP146293             2101 bp    DNA     circular CON 19-MAY-2024
DEFINITION  Shigella sonnei strain R15.3427 plasmid unnamed5, complete sequence.
ACCESSION   NZ_CP146293
VERSION     NZ_CP146293.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123130
            Assembly: GCF_037042485.2
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2101)
  AUTHORS   Chiou,C.-S., Hong,Y.-P. and Chen,B.-H.
  TITLE     Shigella sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2101)
  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
  REMARK    Nucleotide sequence updated by submitter
REFERENCE   3  (bases 1 to 2101)
  AUTHORS   Chiou,C.-S., Hong,Y.-P. and Chen,B.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-FEB-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_037042485.2-RS_2024_05_19
            Annotation Date                   :: 05/19/2024 13:20:58
            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)                     :: 5,324
            CDSs (total)                      :: 5,192
            Genes (coding)                    :: 4,465
            CDSs (with protein)               :: 4,465
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 727
            CDSs (without protein)            :: 727
            Pseudo Genes (ambiguous residues) :: 0 of 727
            Pseudo Genes (frameshifted)       :: 209 of 727
            Pseudo Genes (incomplete)         :: 519 of 727
            Pseudo Genes (internal stop)      :: 128 of 727
            Pseudo Genes (multiple problems)  :: 119 of 727
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP146293.2.
            On May 19, 2024 this sequence version replaced NZ_CP146293.1.
            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..2101
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R15.3427"
                     /db_xref="taxon:624"
                     /plasmid="unnamed5"
                     /collected_by="Taiwan CDC"
     gene            complement(join(1638..2101,1..502))
                     /locus_tag="V8Z63_RS26595"
                     /old_locus_tag="V8Z63_26615"
     CDS             complement(join(1638..2101,1..502))
                     /locus_tag="V8Z63_RS26595"
                     /old_locus_tag="V8Z63_26615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            complement(1368..1634)
                     /locus_tag="V8Z63_RS26600"
                     /old_locus_tag="V8Z63_26610"
     CDS             complement(1368..1634)
                     /locus_tag="V8Z63_RS26600"
                     /old_locus_tag="V8Z63_26610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          complement(2..109)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.75e-49"
ORIGIN
        1 gcggatgtgc gctgccatcc ttacctcgcg tcacctccgt agccctgatc cacccctgaa
       61 caggtgatag ctcctttcgc ttttccattc gcttaaacgc cgcattcatt gctgtaagga
      121 ctgttccaag ttcacctatc tcgcagttcc tgacagttaa cgtcagaaac aaccatcggg
      181 aagacgggta atccacaacg attttcggta gagcctgata aaaacgggct tgccacatga
      241 gggttcttct ccactggcag acagggcaat gacggacacg gcaaaattgc gcactacgaa
      301 gccgtaggcg cgtttctccg gtttccatga tggtagacca accaaaacgt aacaaaccgc
      361 tacaggaggc catacggagt gcatagcgct cgaattcagc agcagtctgg tagatacccc
      421 cgacagaatc ggtaagcgtg cgctgggtat cccaaactgc atcacggggg ctgtagtccg
      481 aaaggaattt atcttctgac attaagcctg ctccgatctg ggcaggctgt gatttgatgt
      541 ggtatattca tcacgtacct gtgcattgcg agccagtaca tgtcaccaga gtttgccgct
      601 gaggtgacac attcgaaatg ttggggagtg ttgacgcact ccccaacgcc gattaaaaac
      661 gcctcaattc tgctccattt tctttgacct gtcaaaaccc actcaaagcc tcgtcattac
      721 tgggctaaac cactatttca tatccgccat ttatccctta agtataaata caaggatcac
      781 gcgcgagaat tgcgcaaaaa ataaccacaa ttttaacccc ccaaaacaag cacccccgaa
      841 cggcttaccc caaccttttc cacacacccg atcaccaaaa cagggaataa aaacaaaacc
      901 ctgtcttaca ggtggatggc ctcacttcgt gaaaccatcc accccgcata agttttttaa
      961 tcggtggtgt cgtcaatcac taaatcggaa ccccaaaggg gacccccacg atttagcatt
     1021 tgacgagatt aactctcgga gatggcatca tgcttttaac ggactttaaa aaacggtgaa
     1081 cggatgcgga ttttaatccg tgtctgtgag gcgttgagca acgagcaaag cgaggcggta
     1141 gaaagagagc cagcggcagg ctcaggacga taatccgggg aaaatatacc actcgcagag
     1201 tgttaacatt tgacatcgga ttgtctatcc tgcattggtg tcgagttggc aaggctgagg
     1261 ataatgctga ggataatgct gaggataatg caggatagac agagcactag agattgcatg
     1321 caatctcgta cctatcacct cagcctgccg ctggctcttt tccagaacta agaatgcgtt
     1381 cttaaaaatc caaacttgat accgtttaaa tctattttca caaaaagagt ttttaccctc
     1441 tcgtttgttt tctgaatata taaaattaat tcatcctcaa aaccttcgtg cggatgaaaa
     1501 ccaaatgtgc caaaacttaa tccatcaata agcaaaataa ggtttttaaa cctgtcagga
     1561 atcaccgctt cacttcttaa aaaaaataaa ccaatagtct tatttccatt caggtattca
     1621 atattaatat tcatacgtta atccgattta tccttctcag gggcgcgttt gtaacgccgt
     1681 ttacctgaat cccagacaaa cgccgtccgc ttcccgtcat cagtgccatc ccctacatcg
     1741 tcggcaatga caagatcctc attggtttct cgatccaact ggaggacgtt ttttagcgcc
     1801 ccaccggtcg agataaaacg gcgcttgtga agctgccgcg tcagctcaag aaaccactca
     1861 ggatcgtttg ccatatcttc cggtttaacg gagtatttca gcgtttcagc aaccgcgctt
     1921 tgcagttgct cggcaacgtt ggccacaacc tcacctgtct tagtttttac tgcccgaata
     1981 tcgatattcg gctcatagtt cacccgcaag caatcgcgcc agagttctac ccaacgttcg
     2041 tgcttaacgt agttcttccc tttaaaccaa gaaggttgca ccatcagcag acagtgaaaa
     2101 t
//
