LOCUS       NZ_CP151340             4197 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R19.2680 plasmid pR19.2680_4k, complete
            sequence.
ACCESSION   NZ_CP151340
VERSION     NZ_CP151340.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735797
            Assembly: GCF_038367145.1
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  JOURNAL   Unpublished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_038367145.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:32:41
            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)                     :: 5,099
            CDSs (total)                      :: 4,971
            Genes (coding)                    :: 4,342
            CDSs (with protein)               :: 4,342
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 629
            CDSs (without protein)            :: 629
            Pseudo Genes (ambiguous residues) :: 0 of 629
            Pseudo Genes (frameshifted)       :: 168 of 629
            Pseudo Genes (incomplete)         :: 437 of 629
            Pseudo Genes (internal stop)      :: 109 of 629
            Pseudo Genes (multiple problems)  :: 82 of 629
            Pseudo Genes (short protein)      :: 3 of 629
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151340.1.
            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="R19.2680"
                     /db_xref="taxon:624"
                     /plasmid="pR19.2680_4k"
                     /collected_by="Taiwan CDC"
     gene            join(4147..4197,1..1089)
                     /gene="dcm"
                     /locus_tag="AADX56_RS25445"
                     /old_locus_tag="AADX56_25465"
     CDS             join(4147..4197,1..1089)
                     /gene="dcm"
                     /locus_tag="AADX56_RS25445"
                     /old_locus_tag="AADX56_25465"
                     /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            1907..2101
                     /locus_tag="AADX56_RS25450"
                     /old_locus_tag="AADX56_25470"
     CDS             1907..2101
                     /locus_tag="AADX56_RS25450"
                     /old_locus_tag="AADX56_25470"
                     /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"
     gene            2767..2928
                     /locus_tag="AADX56_RS25455"
                     /old_locus_tag="AADX56_25475"
     CDS             2767..2928
                     /locus_tag="AADX56_RS25455"
                     /old_locus_tag="AADX56_25475"
                     /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(3120..4076)
                     /locus_tag="AADX56_RS25460"
                     /old_locus_tag="AADX56_25480"
     CDS             complement(3120..4076)
                     /locus_tag="AADX56_RS25460"
                     /old_locus_tag="AADX56_25480"
                     /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"
     Typing          complement(1773..1871)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2182..2267)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          2289..2839
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.213"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgactcaaa aagagtttgc agacgccctt ggtctttcaa aatatggaga cagaaccata
       61 agaagatggg agcgcgggga aacaaaacct actggggcgg aactaaaagc agttatagac
      121 tttccagaca caccacctta cccaaacaac gagaatggca gatatcgcat gatcgattta
      181 tttgctggaa tcggtggaac cagacttgga tttcatcaaa ctaacgctgt aaatgttgtt
      241 ttttccagcg aatgggataa gtttgctcaa aagacatatc atgcaaatta tggtgatttc
      301 cctgatgggg acataacaaa aatcgatgaa aaagatattc ctgatcatga aattcttgtc
      361 ggtgggtttc cttgtgtagc attctctcaa gcaggcctca aaaaaggatt taatgataca
      421 agaggaactt tgttttttga tatagcaagg ataataaagg aaaaaaaacc tcatgctttt
      481 ttacttgaaa atgtaaaaaa cttgctagga catgataaag gtagaacttt ttcaataata
      541 aaaaacacac ttgaagaatt gaattacact gtgtattaca atatcttcgc tgcaaaagac
      601 tttggtgttc cacaaaatag agagcgcata tacattgtag gctttaataa agaaaaagta
      661 agaaatcatg aacattttac ttttccaacc ccattaaaaa caaaaacaag agttggagat
      721 attcttgaaa agagcgtaga caataaatat acgctatcag atgcgctctg gaatggacac
      781 caacgcagga aacttgtaaa tgcagcagcc ggtaaaggct ttgggtatgg tttatttaat
      841 gaaaatagcc catatactaa taccataagt gcgaggtact ataaagatgg tagcgaaata
      901 ttaatagagc aaaaaggaag taacccaaga aaaataactc cgcgggaagc gtcaagactt
      961 caagggtttc ctagtgattt tattatccct gtatcggata cacaggctta taagcaattt
     1021 gggaattcag tcgcagtccc tgttatcaat gcaatagcag aaaaaatcat atcgacctta
     1081 gattcataaa ctaagtcatg aggacacaat gcggcccaga atccaattac cccccatatg
     1141 gatttaccat aacgtcgcat tacgcgcacc gctaaaacgc gctgaacgcg attctgccgc
     1201 gaacaccgca aaaagagatg ttttttcccg gggtaaaccg gaaaaacgcg tcaggatcgc
     1261 tttcagctca ctgcatagct atgcatgaaa gtgaatggcg atcggtttgg gcgcatatgg
     1321 tgcccatgag acacattttc ggacattttc agttcgtgaa tccctgactc attgctacat
     1381 atctgaacag acacccctag cagcgctccc aggggcgtta tgtaaaaaaa ggcgacgcgc
     1441 ccctaggggc gcacctacat taattaactg ttttttctac agatagtcag tactgaccct
     1501 aagtagggtc gccatagcgt cgccataggg tcgtcgacga cgtgcttttg tataaatctg
     1561 aataagaaaa tatattttta aaaccataac aacatgattt aaaaagcaaa tcagcaaaaa
     1621 gttggttttg cgtggggtgt gggcatttcg ggtatgagaa cagactcgcg tttttccgga
     1681 gtatcagcgg aattattgat taagaaacac tcgatgcaga gcgaaatttt atgcaacagc
     1741 ggctgcactg cacagggatt atttatcagt tgatatgctg tgccatgata cgtcctaaag
     1801 aaacaggaca ggatgtgcaa ttgtaatacc gtcgcccgca acgtcttaca attaccacct
     1861 gctcagggtc cccccgacac ccggaactga cggagaacaa cggaaggtga ataaacaaca
     1921 acaaactgcg ctgaatatgg cgcgatttat caaaagccag agcctgacac tacttgaaaa
     1981 actggatgct ctggatgccg acgaacaggc gaccatgtgc gaacgactgc acgaactcgc
     2041 agaaaaactc cagaacagca tccagattcg ctttgaggcc gaaagtgaaa caggaacata
     2101 acgaagctga cggaggcggt cacggctttc ccgtgagcgt tttcggcagc agacaagccc
     2161 gtcagggcgc gtcagggggt tttagcgggt gtcggggcgc agccatgacc cagtcacgta
     2221 gcgatagcgg agtgtatact ggcttaacta tgcggcatca gtgcagatta taagaaaaga
     2281 gcaccatatg cggtgtgaaa taccgcacag atgcgtaagg agaaaatgcc gcatcaggcg
     2341 ctcttccgct tcctcgctca ctgactcgct acgctcggtc gttcggctgc ggcgagcgga
     2401 gtcggctcac gcaaagacgg taatgcggtt atccacagaa tcaggggata aggccggaaa
     2461 gaacatgtga acaaaaaggc aaaaccaagg aaaaaggccg cgccgctggc gtttttccat
     2521 aggctccgcc cccctgacga gcatcacaaa aatcgacgct caagtcagag gtggcgaaac
     2581 ccgacaggac tataaagatc ccaggcgttt ccccctggtc gctccctcgt gcgctctcct
     2641 gttccgaccc tgccgcttac cggatacctg tccgcctttc tcccttcggg aagcgtggcg
     2701 ctttctcata gctcacgctg ttggtatctc agttcggtgt aggtcgttcg ctccaagctg
     2761 ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg ccttatccgg taactatcgt
     2821 cttgagtcca acccggtaag acacgcctta acgccactgg cagcagccac tggtaaccgg
     2881 attagcagag cgagatttat ccagatgctt acagagttct tgaagtgatg gcctaactac
     2941 ggctacactg gaaggacagt atttggtatc tgtgctctgc tgaagccaga ttacctcggt
     3001 tagataatct gccaggatta gctaaccttc gaaaaaacca cctgccaggg tggttttttc
     3061 gtttacagat ccaagattac gcgcagaaaa aaaggatctc aagagatcct tttagttttt
     3121 tagtcaaaaa gagcactaag cctatttcta taataattaa caacataagg gaaatcacta
     3181 tatttttcta tttgttttaa tattgaccgt tgaatttcct ctttttcaga gtctgtgtaa
     3241 cttacattat tccactttct tgataattcc attgctgact gaagcatatc ttcaaaggtt
     3301 agcaccctat tattattttt atatttgaaa tttttatttt ctatcgtcgt tacaacgacc
     3361 acattagcct cgtacaatat atttattgtc tcctcgctaa aagaatcatc tagtgtagct
     3421 agatacattt ctctaattcc tgttctatta acctcttcag gtacttcttg ccatcgctcc
     3481 ctcagcgttg ttttagcgga aatcaacatt gtatttcttt tgttagatgt gtactggact
     3541 acacctggca taacaagatc tacaagttta cctatttggt ttttttgaaa aaatgacttc
     3601 ccaatagccc cctgcacatc aacaggaatt cctgccccca tcattaatag ctcaagaata
     3661 gactcaaact cttttcctgc cctgctacgt ctggattgag tgttagacag tgccaaatca
     3721 tatatgtgtg tagggtattc catcgtaaaa tcacgaatgg catcataagg actcatatct
     3781 tttattcttt cttcatcaat aagatatgat aacattcttg ttgtgaattc tttttcaaat
     3841 ggttcaaatt ctttccaaca gttttttctc attgcaatta tatattcact tggattattc
     3901 aaaaaataat cactattttt ttgatcatac cctaaatcac aaaatgtttt ataaaccaaa
     3961 gcaaatggcg taataaaatg cgattttctc tctttagaaa ttagagtttt aaattcacca
     4021 ggacttaatc tttgcataaa aaataacctt ttatatctac ttgaaagttt tttcatgcac
     4081 gttcataatt ggaatcaaaa caggacaaat tgtcctaaaa ccaacactta attctggtag
     4141 acatgcatga ctgataatat cgcagcaaca atcaaagaaa aaagagaaag acttcat
//
