LOCUS       NZ_CP151309             2690 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R22.1286 plasmid pR22.1286_2.6k, complete
            sequence.
ACCESSION   NZ_CP151309
VERSION     NZ_CP151309.1
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 2690)
  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  JOURNAL   Unpublished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 2690)
  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
            CP151309.1.
            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..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R22.1286"
                     /db_xref="taxon:624"
                     /plasmid="pR22.1286_2.6k"
                     /collected_by="Taiwan CDC"
     gene            complement(198..923)
                     /locus_tag="AADX63_RS25570"
                     /old_locus_tag="AADX63_25555"
     CDS             complement(198..923)
                     /locus_tag="AADX63_RS25570"
                     /old_locus_tag="AADX63_25555"
                     /inference="COORDINATES: protein motif:HMM:NF045398.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_005112197.1"
                     /translation="MKILNSNLITNISSTIRNHLLTSSKNIKTHPSPNMDVTSHRRLFQ
                     KDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFTRQKGDGWTVVPKNLRIDFYTKDNDF
                     TKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKVLANARNIPQSKLEEEMMSQAIYRKE
                     YATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKNIDIAFITDKNHKKHLSDIFKVINES
                     GVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(1200..1361)
                     /locus_tag="AADX63_RS25575"
                     /old_locus_tag="AADX63_25560"
     CDS             complement(1200..1361)
                     /locus_tag="AADX63_RS25575"
                     /old_locus_tag="AADX63_25560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(1859..2053)
                     /locus_tag="AADX63_RS25580"
                     /old_locus_tag="AADX63_25565"
     CDS             complement(1859..2053)
                     /locus_tag="AADX63_RS25580"
                     /old_locus_tag="AADX63_25565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2339..2662
                     /gene="mobA"
                     /locus_tag="AADX63_RS25585"
                     /old_locus_tag="AADX63_25570"
     CDS             2339..2662
                     /gene="mobA"
                     /locus_tag="AADX63_RS25585"
                     /old_locus_tag="AADX63_25570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          2092..2330
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(1290..1816)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          2340..2659
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 gacggtatga acacggtaag ctcccaaagt gatctccatt cgctttcatg catagctatg
       61 cagcgagctg aaaacgatcc tgacgcatcc ttcctgtttt tccggggtaa aacatctatt
      121 tttgtggtgt ctgcgtcaga atcgcgttca gcgcgtttca gtggtgcgta caattaaggg
      181 attatggtaa atgatgatta tttctcctct ctatttactc ggcaagcgcc aaagtgaatt
      241 acatcatatt ttactcctga ttcatttatt actttaaata tgtcagaaag gtgcttctta
      301 tgatttttat cagttataaa tgctatatca atatttttgt ttcctaagcc atcttgatgt
      361 ctttgtataa tattttgggc ttgttcatgg taatatagag catagttttt tatcttctca
      421 ttacttgttg cgtattcttt tctatatatg gcttgtgaca tcatttcttc ttctaatttt
      481 gattgaggta tattgcgcgc gttcgctaga acttttaggt catctttgct tatgtttagt
      541 gatggtgtta accctttttg agcttcagta tggcgtttgt ttacctctga aagaacgctt
      601 agtccctttg tgaagtcgtt gtcttttgta taaaaatcaa ttcttaggtt tttggggact
      661 acagtccatc catcgccttt ttgacgcgtg aatagtgttt gtggatggga gatctctttc
      721 catccaccat gcgacataat gacaagttgt gttgcttttc ctgtttggct caatcctatt
      781 ccgtctttct ggaataaacg acgatgactt gttacgtcca tgtttggtga tgggtgtgtt
      841 tttatatttt tggatgatgt tagaaggtga tttcttattg ttgatgatat gtttgttatg
      901 agattcgaat tgagtatttt catttgttaa caatccattt ttgcggtgtt ttttattgtt
      961 ttttttcttt tgtttaaggg tgtgtcggtg taagtgttta ttttatgggt taaagtagga
     1021 taccaagtgt gaaaaaaaat taaaggttct tcttgagatc ctttttttct gcgcgtaatc
     1081 tgctgcctgt aaacgaaaaa accgccctgc aaggcggttt ttcgaaggtt ctcagagcta
     1141 ccaactcttt gagccgaggt aactggcttg gaggagcgca gtcaccaaaa cttgttcttt
     1201 cagtttagcc ttaacaggcg catgacttca agtcttactc ctctaattcg gttatcagtg
     1261 gctgctgcca gtggcgataa ttcgtgtctt accgggttgg actcaagacg atagttaccg
     1321 gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga
     1381 acgacctaca ccgggccgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc
     1441 gaagggagaa aggcggacag gtatccggta aacggcaggg tcggaacagg agagcgcacg
     1501 agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc
     1561 tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
     1621 acctgcgcgg cctttgtccc tgccttcggc tttttgctca catgttcttt ccggcgttat
     1681 cccctgattc tgtggataac cgcattaccg cctttgagtg agctgacacc gctcgccgca
     1741 gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc cttatgtgac
     1801 attttctcct tacgcaccgg tataccgttc tgcatcctgt ctggagcagg atacactgtt
     1861 ataccccggt gccactttcc gcttcaaagc gtgtctgtat gctgttctgg agttcttccg
     1921 cgatttcgtg cagcttctca cacatggcgg cctgttcgtc ggcatcgagt gcgtccagct
     1981 tttcgagcag cgtcaggctc tggcttttta tgaatcccgc catgttgagt acggtttgct
     2041 gctgcttgtt catctttctg ttttctccgt tctgtctgtc atctgcgttg tgtgattata
     2101 tcgcgtacca cttttcgact gttttaccgc cggtattctg ccgtctgacg cattgacggg
     2161 tatttctgcc tgacaatact gtcactgcca aaaaaactgc cgtgcctttg tcggtaattc
     2221 gaacttgctg acaggacagg atgtgtaatt gttataccgc gcatacatgc acgctattac
     2281 aattaccctg gtcagggctt cgccccgaca ccccgtgtca gatacggagc catgttttat
     2341 gacaaaacga agtggaagta atacgcgcag gcgggctatc agtcgccctg ttcgtctgac
     2401 ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa tgcggcaaga ccgtttctgg
     2461 ttttttacgg gcggcagctc tcggtaagaa cgttaactca ctgactgatg atcgggtgct
     2521 gaaagaagtt atgagactgg gggcgttaca gaaaaaactc tttatcgacg gcaagcgtat
     2581 cggggacagg gagtatgcgg aggtgctgat cgctattacg gagtatcacc gtgccctgtt
     2641 atccaggctt atggcagatt agcttcccgg ggagaaaact gttgaaaaca
//
