LOCUS       NZ_CP151355             2690 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R17.0261 plasmid pR17.0261_2.6k, complete
            sequence.
ACCESSION   NZ_CP151355
VERSION     NZ_CP151355.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122666
            Assembly: GCF_038367155.1
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  JOURNAL   Unpublished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_038367155.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:46:18
            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)                     :: 5,103
            CDSs (total)                      :: 4,973
            Genes (coding)                    :: 4,344
            CDSs (with protein)               :: 4,344
            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)              :: 629
            CDSs (without protein)            :: 629
            Pseudo Genes (ambiguous residues) :: 0 of 629
            Pseudo Genes (frameshifted)       :: 169 of 629
            Pseudo Genes (incomplete)         :: 437 of 629
            Pseudo Genes (internal stop)      :: 110 of 629
            Pseudo Genes (multiple problems)  :: 84 of 629
            Pseudo Genes (short protein)      :: 3 of 629
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151355.1.
            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="R17.0261"
                     /db_xref="taxon:624"
                     /plasmid="pR17.0261_2.6k"
                     /collected_by="Taiwan CDC"
     gene            1..195
                     /locus_tag="AADX58_RS25490"
                     /old_locus_tag="AADX58_25510"
     CDS             1..195
                     /locus_tag="AADX58_RS25490"
                     /old_locus_tag="AADX58_25510"
                     /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            693..854
                     /locus_tag="AADX58_RS25495"
                     /old_locus_tag="AADX58_25515"
     CDS             693..854
                     /locus_tag="AADX58_RS25495"
                     /old_locus_tag="AADX58_25515"
                     /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            1131..1856
                     /locus_tag="AADX58_RS25500"
                     /old_locus_tag="AADX58_25520"
     CDS             1131..1856
                     /locus_tag="AADX58_RS25500"
                     /old_locus_tag="AADX58_25520"
                     /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(2082..2405)
                     /gene="mobA"
                     /locus_tag="AADX58_RS25505"
                     /old_locus_tag="AADX58_25525"
     CDS             complement(2082..2405)
                     /gene="mobA"
                     /locus_tag="AADX58_RS25505"
                     /old_locus_tag="AADX58_25525"
                     /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          complement(2415..2653)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          239..765
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(2086..2405)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 atgaacaagc agcagcaaac cgtactcaac atggcgggat tcataaaaag ccagagcctg
       61 acgctgctcg aaaagctgga cgcactcgat gccgacgaac aggccgccat gtgtgagaag
      121 ctgcacgaaa tcgcggaaga actccagaac agcatacaga cacgctttga agcggaaagt
      181 ggcaccgggg tataacagtg tatcctgctc cagacaggat gcagaacggt ataccggtgc
      241 gtaaggagaa aatgtcacat aaggcgctct tccgcttcct cgctcactga ctcgctacgc
      301 tcggtcgttc gactgcggcg agcggtgtca gctcactcaa aggcggtaat gcggttatcc
      361 acagaatcag gggataacgc cggaaagaac atgtgagcaa aaagccgaag gcagggacaa
      421 aggccgcgca ggtggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc
      481 gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc
      541 ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gtttaccgga tacctgtccg
      601 cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg tatctcggcc
      661 cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc
      721 gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gaattatcgc
      781 cactggcagc agccactgat aaccgaatta gaggagtaag acttgaagtc atgcgcctgt
      841 taaggctaaa ctgaaagaac aagttttggt gactgcgctc ctccaagcca gttacctcgg
      901 ctcaaagagt tggtagctct gagaaccttc gaaaaaccgc cttgcagggc ggttttttcg
      961 tttacaggca gcagattacg cgcagaaaaa aaggatctca agaagaacct ttaatttttt
     1021 ttcacacttg gtatcctact ttaacccata aaataaacac ttacaccgac acacccttaa
     1081 acaaaagaaa aaaaacaata aaaaacaccg caaaaatgga ttgttaacaa atgaaaatac
     1141 tcaattcgaa tctcataaca aacatatcat caacaataag aaatcacctt ctaacatcat
     1201 ccaaaaatat aaaaacacac ccatcaccaa acatggacgt aacaagtcat cgtcgtttat
     1261 tccagaaaga cggaatagga ttgagccaaa caggaaaagc aacacaactt gtcattatgt
     1321 cgcatggtgg atggaaagag atctcccatc cacaaacact attcacgcgt caaaaaggcg
     1381 atggatggac tgtagtcccc aaaaacctaa gaattgattt ttatacaaaa gacaacgact
     1441 tcacaaaggg actaagcgtt ctttcagagg taaacaaacg ccatactgaa gctcaaaaag
     1501 ggttaacacc atcactaaac ataagcaaag atgacctaaa agttctagcg aacgcgcgca
     1561 atatacctca atcaaaatta gaagaagaaa tgatgtcaca agccatatat agaaaagaat
     1621 acgcaacaag taatgagaag ataaaaaact atgctctata ttaccatgaa caagcccaaa
     1681 atattataca aagacatcaa gatggcttag gaaacaaaaa tattgatata gcatttataa
     1741 ctgataaaaa tcataagaag cacctttctg acatatttaa agtaataaat gaatcaggag
     1801 taaaatatga tgtaattcac tttggcgctt gccgagtaaa tagagaggag aaataatcat
     1861 catttaccat aatcccttaa ttgtacgcac cactgaaacg cgctgaacgc gattctgacg
     1921 cagacaccac aaaaatagat gttttacccc ggaaaaacag gaaggatgcg tcaggatcgt
     1981 tttcagctcg ctgcatagct atgcatgaaa gcgaatggag atcactttgg gagcttaccg
     2041 tgttcatacc gtctgttttc aacagttttc tccccgggaa gctaatctgc cataagcctg
     2101 gataacaggg cacggtgata ctccgtaata gcgatcagca cctccgcata ctccctgtcc
     2161 ccgatacgct tgccgtcgat aaagagtttt ttctgtaacg cccccagtct cataacttct
     2221 ttcagcaccc gatcatcagt cagtgagtta acgttcttac cgagagctgc cgcccgtaaa
     2281 aaaccagaaa cggtcttgcc gcattcagca gccctttttc tgatttcctg gtcttcttct
     2341 gccgtcagac gaacagggcg actgatagcc cgcctgcgcg tattacttcc acttcgtttt
     2401 gtcataaaac atggctccgt atctgacacg gggtgtcggg gcgaagccct gaccagggta
     2461 attgtaatag cgtgcatgta tgcgcggtat aacaattaca catcctgtcc tgtcagcaag
     2521 ttcgaattac cgacaaaggc acggcagttt ttttggcagt gacagtattg tcaggcagaa
     2581 atacccgtca atgcgtcaga cggcagaata ccggcggtaa aacagtcgaa aagtggtacg
     2641 cgatataatc acacaacgca gatgacagac agaacggaga aaacagaaag
//
