LOCUS       NZ_CP151306             4197 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R22.1286 plasmid pR22.1286_4k, complete
            sequence.
ACCESSION   NZ_CP151306
VERSION     NZ_CP151306.1
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 4197)
  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  JOURNAL   Unpublished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 4197)
  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
            CP151306.1.
            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..4197
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R22.1286"
                     /db_xref="taxon:624"
                     /plasmid="pR22.1286_4k"
                     /collected_by="Taiwan CDC"
     gene            complement(112..1251)
                     /gene="dcm"
                     /locus_tag="AADX63_RS25510"
                     /old_locus_tag="AADX63_25495"
     CDS             complement(112..1251)
                     /gene="dcm"
                     /locus_tag="AADX63_RS25510"
                     /old_locus_tag="AADX63_25495"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="WP_000131511.1"
                     /translation="MTDNIAATIKEKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVIDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            1322..2278
                     /locus_tag="AADX63_RS25515"
                     /old_locus_tag="AADX63_25500"
     CDS             1322..2278
                     /locus_tag="AADX63_RS25515"
                     /old_locus_tag="AADX63_25500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001189381.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_014640333.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVYKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQRSILKQIEKYSDFPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            complement(2470..2631)
                     /locus_tag="AADX63_RS25520"
                     /old_locus_tag="AADX63_25505"
     CDS             complement(2470..2631)
                     /locus_tag="AADX63_RS25520"
                     /old_locus_tag="AADX63_25505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071596883.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRARFI
                     QMLTEFLK"
                     /name="replication initiation protein"
     gene            complement(3297..3491)
                     /locus_tag="AADX63_RS25525"
                     /old_locus_tag="AADX63_25510"
     CDS             complement(3297..3491)
                     /locus_tag="AADX63_RS25525"
                     /old_locus_tag="AADX63_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041635.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQATMCERLHELA
                     EKLQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3132..3217
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          3528..3626
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2560..3110)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.213"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcggcagaat cgcgttcagc gcgttttagc ggtgcgcgta atgcgacgtt atggtaaatc
       61 catatggggg gtaattggat tctgggccgc attgtgtcct catgacttag tttatgaatc
      121 taaggtcgat atgatttttt ctgctattgc attgataaca gggactgcga ctgaattccc
      181 aaattgctta taagcctgtg tatccgatac agggataata aaatcactag gaaacccttg
      241 aagtcttgac gcttcccgcg gagttatttt tcttgggtta cttccttttt gctctattaa
      301 tatttcgcta ccatctttat agtacctcgc acttatggta ttagtatatg ggctattttc
      361 attaaataaa ccatacccaa agcctttacc ggctgctgca tttacaagtt tcctgcgttg
      421 gtgtccattc cagagcgcat ctgatagcgt atatttattg tctacgctct tttcaagaat
      481 atctccaact cttgtttttg tttttaatgg ggttggaaaa gtaaaatgtt catgatttct
      541 tactttttct ttattaaagc ctacaatgta tatgcgctct ctattttgtg gaacaccaaa
      601 gtcttttgca gcgaagatat tgtaatacac agtgtaattc aattcttcaa gtgtgttttt
      661 tattattgaa aaagttctac ctttatcatg tcctagcaag ttttttacat tttcaagtaa
      721 aaaagcatga ggtttttttt cctttattat ccttgctata tcaaaaaaca aagttcctct
      781 tgtatcatta aatccttttt tgaggcctgc ttgagagaat gctacacaag gaaacccacc
      841 gacaagaatt tcatgatcag gaatatcttt ttcatcgatt tttgttatgt ccccatcagg
      901 gaaatcacca taatttgcat gatatgtctt ttgagcaaac ttatcccatt cgctggaaaa
      961 aacaacattt acagcgttag tttgatgaaa tccaagtctg gttccaccga ttccagcaaa
     1021 taaatcgatc atgcgatatc tgccattctc gttgtttggg taaggtggtg tgtctggaaa
     1081 gtctataact gcttttagtt ccgccccagt aggttttgtt tccccgcgct cccatcttct
     1141 tatggttctg tctccatatt ttgaaagacc aagggcgtct gcaaactctt tttgagtcat
     1201 atgaagtctt tctctttttt ctttgattgt tgctgcgata ttatcagtca tgcatgtcta
     1261 ccagaattaa gtgttggttt taggacaatt tgtcctgttt tgattccaat tatgaacgtg
     1321 catgaaaaaa ctttcaagta gatataaaag gttatttttt atgcaaagat taagtcctgg
     1381 tgaatttaaa actctaattt ctaaagagag aaaatcgcat tttattacgc catttgcttt
     1441 ggtttataaa acattttgtg atttagggta tgatcaaaaa aatagtgatt attttttgaa
     1501 taatccaagt gaatatataa ttgcaatgag aaaaaactgt tggaaagaat ttgaaccatt
     1561 tgaaaaagaa ttcacaacaa gaatgttatc atatcttatt gatgaagaaa gaataaaaga
     1621 tatgagtcct tatgatgcca ttcgtgattt tacgatggaa taccctacac acatatatga
     1681 tttggcactg tctaacactc aatccagacg tagcagggca ggaaaagagt ttgagtctat
     1741 tcttgagcta ttaatgatgg gggcaggaat tcctgttgat gtgcaggggg ctattgggaa
     1801 gtcatttttt caaaaaaacc aaataggtaa acttgtagat cttgttatgc caggtgtagt
     1861 ccagtacaca tctaacaaaa gaaatacaat gttgatttcc gctaaaacaa cgctgaggga
     1921 gcgatggcaa gaagtacctg aagaggttaa tagaacagga attagagaaa tgtatctagc
     1981 tacactagat gattctttta gcgaggagac aataaatata ttgtacgagg ctaatgtggt
     2041 cgttgtaacg acgatagaaa ataaaaattt caaatataaa aataataata gggtgctaac
     2101 ctttgaagat atgcttcagt cagcaatgga attatcaaga aagtggaata atgtaagtta
     2161 cacagactct gaaaaagagg aaattcaacg gtcaatatta aaacaaatag aaaaatatag
     2221 tgatttccct tatgttgtta attattatag aaataggctt agtgctcttt ttgactaaaa
     2281 aactaaaagg atctcttgag atcctttttt tctgcgcgta atcttggatc tgtaaacgaa
     2341 aaaaccaccc tggcaggtgg ttttttcgaa ggttagctaa tcctggcaga ttatctaacc
     2401 gaggtaatct ggcttcagca gagcacagat accaaatact gtccttccag tgtagccgta
     2461 gttaggccat cacttcaaga actctgtaag catctggata aatctcgctc tgctaatccg
     2521 gttaccagtg gctgctgcca gtggcgttaa ggcgtgtctt accgggttgg actcaagacg
     2581 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag
     2641 cttggagcga acgacctaca ccgaactgag ataccaacag cgtgagctat gagaaagcgc
     2701 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg
     2761 agagcgcacg agggagcgac cagggggaaa cgcctgggat ctttatagtc ctgtcgggtt
     2821 tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg
     2881 gaaaaacgcc agcggcgcgg cctttttcct tggttttgcc tttttgttca catgttcttt
     2941 ccggccttat cccctgattc tgtggataac cgcattaccg tctttgcgtg agccgactcc
     3001 gctcgccgca gccgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc
     3061 ctgatgcggc attttctcct tacgcatctg tgcggtattt cacaccgcat atggtgctct
     3121 tttcttataa tctgcactga tgccgcatag ttaagccagt atacactccg ctatcgctac
     3181 gtgactgggt catggctgcg ccccgacacc cgctaaaacc ccctgacgcg ccctgacggg
     3241 cttgtctgct gccgaaaacg ctcacgggaa agccgtgacc gcctccgtca gcttcgttat
     3301 gttcctgttt cactttcggc ctcaaagcga atctggatgc tgttctggag tttttctgcg
     3361 agttcgtgca gtcgttcgca catggtcgcc tgttcgtcgg catccagagc atccagtttt
     3421 tcaagtagtg tcaggctctg gcttttgata aatcgcgcca tattcagcgc agtttgttgt
     3481 tgtttattca ccttccgttg ttctccgtca gttccgggtg tcggggggac cctgagcagg
     3541 tggtaattgt aagacgttgc gggcgacggt attacaattg cacatcctgt cctgtttctt
     3601 taggacgtat catggcacag catatcaact gataaataat ccctgtgcag tgcagccgct
     3661 gttgcataaa atttcgctct gcatcgagtg tttcttaatc aataattccg ctgatactcc
     3721 ggaaaaacgc gagtctgttc tcatacccga aatgcccaca ccccacgcaa aaccaacttt
     3781 ttgctgattt gctttttaaa tcatgttgtt atggttttaa aaatatattt tcttattcag
     3841 atttatacaa aagcacgtcg tcgacgaccc tatggcgacg ctatggcgac cctacttagg
     3901 gtcagtactg actatctgta gaaaaaacag ttaattaatg taggtgcgcc cctaggggcg
     3961 cgtcgccttt ttttacataa cgcccctggg agcgctgcta ggggtgtctg ttcagatatg
     4021 tagcaatgag tcagggattc acgaactgaa aatgtccgaa aatgtgtctc atgggcacca
     4081 tatgcgccca aaccgatcgc cattcacttt catgcatagc tatgcagtga gctgaaagcg
     4141 atcctgacgc gtttttccgg tttaccccgg gaaaaaacat ctctttttgc ggtgttc
//
