LOCUS       NZ_CP151354             4197 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R17.0261 plasmid pR17.0261_4k, complete
            sequence.
ACCESSION   NZ_CP151354
VERSION     NZ_CP151354.1
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 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  JOURNAL   Unpublished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_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
            CP151354.1.
            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="R17.0261"
                     /db_xref="taxon:624"
                     /plasmid="pR17.0261_4k"
                     /collected_by="Taiwan CDC"
     gene            799..993
                     /locus_tag="AADX58_RS25470"
                     /old_locus_tag="AADX58_25490"
     CDS             799..993
                     /locus_tag="AADX58_RS25470"
                     /old_locus_tag="AADX58_25490"
                     /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            1659..1820
                     /locus_tag="AADX58_RS25475"
                     /old_locus_tag="AADX58_25495"
     CDS             1659..1820
                     /locus_tag="AADX58_RS25475"
                     /old_locus_tag="AADX58_25495"
                     /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(2012..2968)
                     /locus_tag="AADX58_RS25480"
                     /old_locus_tag="AADX58_25500"
     CDS             complement(2012..2968)
                     /locus_tag="AADX58_RS25480"
                     /old_locus_tag="AADX58_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            3039..4178
                     /gene="dcm"
                     /locus_tag="AADX58_RS25485"
                     /old_locus_tag="AADX58_25505"
     CDS             3039..4178
                     /gene="dcm"
                     /locus_tag="AADX58_RS25485"
                     /old_locus_tag="AADX58_25505"
                     /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"
     Typing          complement(665..763)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1074..1159)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          1181..1731
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.213"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcggccca gaatccaatt accccccata tggatttacc ataacgtcgc attacgcgca
       61 ccgctaaaac gcgctgaacg cgattctgcc gcgaacaccg caaaaagaga tgttttttcc
      121 cggggtaaac cggaaaaacg cgtcaggatc gctttcagct cactgcatag ctatgcatga
      181 aagtgaatgg cgatcggttt gggcgcatat ggtgcccatg agacacattt tcggacattt
      241 tcagttcgtg aatccctgac tcattgctac atatctgaac agacacccct agcagcgctc
      301 ccaggggcgt tatgtaaaaa aaggcgacgc gcccctaggg gcgcacctac attaattaac
      361 tgttttttct acagatagtc agtactgacc ctaagtaggg tcgccatagc gtcgccatag
      421 ggtcgtcgac gacgtgcttt tgtataaatc tgaataagaa aatatatttt taaaaccata
      481 acaacatgat ttaaaaagca aatcagcaaa aagttggttt tgcgtggggt gtgggcattt
      541 cgggtatgag aacagactcg cgtttttccg gagtatcagc ggaattattg attaagaaac
      601 actcgatgca gagcgaaatt ttatgcaaca gcggctgcac tgcacaggga ttatttatca
      661 gttgatatgc tgtgccatga tacgtcctaa agaaacagga caggatgtgc aattgtaata
      721 ccgtcgcccg caacgtctta caattaccac ctgctcaggg tccccccgac acccggaact
      781 gacggagaac aacggaaggt gaataaacaa caacaaactg cgctgaatat ggcgcgattt
      841 atcaaaagcc agagcctgac actacttgaa aaactggatg ctctggatgc cgacgaacag
      901 gcgaccatgt gcgaacgact gcacgaactc gcagaaaaac tccagaacag catccagatt
      961 cgctttgagg ccgaaagtga aacaggaaca taacgaagct gacggaggcg gtcacggctt
     1021 tcccgtgagc gttttcggca gcagacaagc ccgtcagggc gcgtcagggg gttttagcgg
     1081 gtgtcggggc gcagccatga cccagtcacg tagcgatagc ggagtgtata ctggcttaac
     1141 tatgcggcat cagtgcagat tataagaaaa gagcaccata tgcggtgtga aataccgcac
     1201 agatgcgtaa ggagaaaatg ccgcatcagg cgctcttccg cttcctcgct cactgactcg
     1261 ctacgctcgg tcgttcggct gcggcgagcg gagtcggctc acgcaaagac ggtaatgcgg
     1321 ttatccacag aatcagggga taaggccgga aagaacatgt gaacaaaaag gcaaaaccaa
     1381 ggaaaaaggc cgcgccgctg gcgtttttcc ataggctccg cccccctgac gagcatcaca
     1441 aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga tcccaggcgt
     1501 ttccccctgg tcgctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc
     1561 tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgttggtatc
     1621 tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc
     1681 ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgcct
     1741 taacgccact ggcagcagcc actggtaacc ggattagcag agcgagattt atccagatgc
     1801 ttacagagtt cttgaagtga tggcctaact acggctacac tggaaggaca gtatttggta
     1861 tctgtgctct gctgaagcca gattacctcg gttagataat ctgccaggat tagctaacct
     1921 tcgaaaaaac cacctgccag ggtggttttt tcgtttacag atccaagatt acgcgcagaa
     1981 aaaaaggatc tcaagagatc cttttagttt tttagtcaaa aagagcacta agcctatttc
     2041 tataataatt aacaacataa gggaaatcac tatatttttc tatttgtttt aatattgacc
     2101 gttgaatttc ctctttttca gagtctgtgt aacttacatt attccacttt cttgataatt
     2161 ccattgctga ctgaagcata tcttcaaagg ttagcaccct attattattt ttatatttga
     2221 aatttttatt ttctatcgtc gttacaacga ccacattagc ctcgtacaat atatttattg
     2281 tctcctcgct aaaagaatca tctagtgtag ctagatacat ttctctaatt cctgttctat
     2341 taacctcttc aggtacttct tgccatcgct ccctcagcgt tgttttagcg gaaatcaaca
     2401 ttgtatttct tttgttagat gtgtactgga ctacacctgg cataacaaga tctacaagtt
     2461 tacctatttg gtttttttga aaaaatgact tcccaatagc cccctgcaca tcaacaggaa
     2521 ttcctgcccc catcattaat agctcaagaa tagactcaaa ctcttttcct gccctgctac
     2581 gtctggattg agtgttagac agtgccaaat catatatgtg tgtagggtat tccatcgtaa
     2641 aatcacgaat ggcatcataa ggactcatat cttttattct ttcttcatca ataagatatg
     2701 ataacattct tgttgtgaat tctttttcaa atggttcaaa ttctttccaa cagttttttc
     2761 tcattgcaat tatatattca cttggattat tcaaaaaata atcactattt ttttgatcat
     2821 accctaaatc acaaaatgtt ttataaacca aagcaaatgg cgtaataaaa tgcgattttc
     2881 tctctttaga aattagagtt ttaaattcac caggacttaa tctttgcata aaaaataacc
     2941 ttttatatct acttgaaagt tttttcatgc acgttcataa ttggaatcaa aacaggacaa
     3001 attgtcctaa aaccaacact taattctggt agacatgcat gactgataat atcgcagcaa
     3061 caatcaaaga aaaaagagaa agacttcata tgactcaaaa agagtttgca gacgcccttg
     3121 gtctttcaaa atatggagac agaaccataa gaagatggga gcgcggggaa acaaaaccta
     3181 ctggggcgga actaaaagca gttatagact ttccagacac accaccttac ccaaacaacg
     3241 agaatggcag atatcgcatg atcgatttat ttgctggaat cggtggaacc agacttggat
     3301 ttcatcaaac taacgctgta aatgttgttt tttccagcga atgggataag tttgctcaaa
     3361 agacatatca tgcaaattat ggtgatttcc ctgatgggga cataacaaaa atcgatgaaa
     3421 aagatattcc tgatcatgaa attcttgtcg gtgggtttcc ttgtgtagca ttctctcaag
     3481 caggcctcaa aaaaggattt aatgatacaa gaggaacttt gttttttgat atagcaagga
     3541 taataaagga aaaaaaacct catgcttttt tacttgaaaa tgtaaaaaac ttgctaggac
     3601 atgataaagg tagaactttt tcaataataa aaaacacact tgaagaattg aattacactg
     3661 tgtattacaa tatcttcgct gcaaaagact ttggtgttcc acaaaataga gagcgcatat
     3721 acattgtagg ctttaataaa gaaaaagtaa gaaatcatga acattttact tttccaaccc
     3781 cattaaaaac aaaaacaaga gttggagata ttcttgaaaa gagcgtagac aataaatata
     3841 cgctatcaga tgcgctctgg aatggacacc aacgcaggaa acttgtaaat gcagcagccg
     3901 gtaaaggctt tgggtatggt ttatttaatg aaaatagccc atatactaat accataagtg
     3961 cgaggtacta taaagatggt agcgaaatat taatagagca aaaaggaagt aacccaagaa
     4021 aaataactcc gcgggaagcg tcaagacttc aagggtttcc tagtgatttt attatccctg
     4081 tatcggatac acaggcttat aagcaatttg ggaattcagt cgcagtccct gttatcaatg
     4141 caatagcaga aaaaatcata tcgaccttag attcataaac taagtcatga ggacaca
//
