LOCUS       NZ_CP151397             4197 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.0423 plasmid pR15.0423_4.1k, complete
            sequence.
ACCESSION   NZ_CP151397
VERSION     NZ_CP151397.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735790
            Assembly: GCF_038367755.1
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  JOURNAL   Unpublished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_038367755.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:40:44
            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)                     :: 5,363
            CDSs (total)                      :: 5,233
            Genes (coding)                    :: 4,513
            CDSs (with protein)               :: 4,513
            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)              :: 720
            CDSs (without protein)            :: 720
            Pseudo Genes (ambiguous residues) :: 0 of 720
            Pseudo Genes (frameshifted)       :: 202 of 720
            Pseudo Genes (incomplete)         :: 517 of 720
            Pseudo Genes (internal stop)      :: 124 of 720
            Pseudo Genes (multiple problems)  :: 116 of 720
            Pseudo Genes (short protein)      :: 3 of 720
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151397.1.
            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="R15.0423"
                     /db_xref="taxon:624"
                     /plasmid="pR15.0423_4.1k"
                     /collected_by="Taiwan CDC"
     gene            1..1140
                     /gene="dcm"
                     /locus_tag="AADX55_RS26725"
                     /old_locus_tag="AADX55_26745"
     CDS             1..1140
                     /gene="dcm"
                     /locus_tag="AADX55_RS26725"
                     /old_locus_tag="AADX55_26745"
                     /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            1958..2152
                     /locus_tag="AADX55_RS26730"
                     /old_locus_tag="AADX55_26750"
     CDS             1958..2152
                     /locus_tag="AADX55_RS26730"
                     /old_locus_tag="AADX55_26750"
                     /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            2818..2979
                     /locus_tag="AADX55_RS26735"
                     /old_locus_tag="AADX55_26755"
     CDS             2818..2979
                     /locus_tag="AADX55_RS26735"
                     /old_locus_tag="AADX55_26755"
                     /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(3171..4127)
                     /locus_tag="AADX55_RS26740"
                     /old_locus_tag="AADX55_26760"
     CDS             complement(3171..4127)
                     /locus_tag="AADX55_RS26740"
                     /old_locus_tag="AADX55_26760"
                     /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(1824..1922)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2233..2318)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          2340..2890
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.213"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgactgata atatcgcagc aacaatcaaa gaaaaaagag aaagacttca tatgactcaa
       61 aaagagtttg cagacgccct tggtctttca aaatatggag acagaaccat aagaagatgg
      121 gagcgcgggg aaacaaaacc tactggggcg gaactaaaag cagttataga ctttccagac
      181 acaccacctt acccaaacaa cgagaatggc agatatcgca tgatcgattt atttgctgga
      241 atcggtggaa ccagacttgg atttcatcaa actaacgctg taaatgttgt tttttccagc
      301 gaatgggata agtttgctca aaagacatat catgcaaatt atggtgattt ccctgatggg
      361 gacataacaa aaatcgatga aaaagatatt cctgatcatg aaattcttgt cggtgggttt
      421 ccttgtgtag cattctctca agcaggcctc aaaaaaggat ttaatgatac aagaggaact
      481 ttgttttttg atatagcaag gataataaag gaaaaaaaac ctcatgcttt tttacttgaa
      541 aatgtaaaaa acttgctagg acatgataaa ggtagaactt tttcaataat aaaaaacaca
      601 cttgaagaat tgaattacac tgtgtattac aatatcttcg ctgcaaaaga ctttggtgtt
      661 ccacaaaata gagagcgcat atacattgta ggctttaata aagaaaaagt aagaaatcat
      721 gaacatttta cttttccaac cccattaaaa acaaaaacaa gagttggaga tattcttgaa
      781 aagagcgtag acaataaata tacgctatca gatgcgctct ggaatggaca ccaacgcagg
      841 aaacttgtaa atgcagcagc cggtaaaggc tttgggtatg gtttatttaa tgaaaatagc
      901 ccatatacta ataccataag tgcgaggtac tataaagatg gtagcgaaat attaatagag
      961 caaaaaggaa gtaacccaag aaaaataact ccgcgggaag cgtcaagact tcaagggttt
     1021 cctagtgatt ttattatccc tgtatcggat acacaggctt ataagcaatt tgggaattca
     1081 gtcgcagtcc ctgttatcaa tgcaatagca gaaaaaatca tatcgacctt agattcataa
     1141 actaagtcat gaggacacaa tgcggcccag aatccaatta ccccccatat ggatttacca
     1201 taacgtcgca ttacgcgcac cgctaaaacg cgctgaacgc gattctgccg cgaacaccgc
     1261 aaaaagagat gttttttccc ggggtaaacc ggaaaaacgc gtcaggatcg ctttcagctc
     1321 actgcatagc tatgcatgaa agtgaatggc gatcggtttg ggcgcatatg gtgcccatga
     1381 gacacatttt cggacatttt cagttcgtga atccctgact cattgctaca tatctgaaca
     1441 gacaccccta gcagcgctcc caggggcgtt atgtaaaaaa aggcgacgcg cccctagggg
     1501 cgcacctaca ttaattaact gttttttcta cagatagtca gtactgaccc taagtagggt
     1561 cgccatagcg tcgccatagg gtcgtcgacg acgtgctttt gtataaatct gaataagaaa
     1621 atatattttt aaaaccataa caacatgatt taaaaagcaa atcagcaaaa agttggtttt
     1681 gcgtggggtg tgggcatttc gggtatgaga acagactcgc gtttttccgg agtatcagcg
     1741 gaattattga ttaagaaaca ctcgatgcag agcgaaattt tatgcaacag cggctgcact
     1801 gcacagggat tatttatcag ttgatatgct gtgccatgat acgtcctaaa gaaacaggac
     1861 aggatgtgca attgtaatac cgtcgcccgc aacgtcttac aattaccacc tgctcagggt
     1921 ccccccgaca cccggaactg acggagaaca acggaaggtg aataaacaac aacaaactgc
     1981 gctgaatatg gcgcgattta tcaaaagcca gagcctgaca ctacttgaaa aactggatgc
     2041 tctggatgcc gacgaacagg cgaccatgtg cgaacgactg cacgaactcg cagaaaaact
     2101 ccagaacagc atccagattc gctttgaggc cgaaagtgaa acaggaacat aacgaagctg
     2161 acggaggcgg tcacggcttt cccgtgagcg ttttcggcag cagacaagcc cgtcagggcg
     2221 cgtcaggggg ttttagcggg tgtcggggcg cagccatgac ccagtcacgt agcgatagcg
     2281 gagtgtatac tggcttaact atgcggcatc agtgcagatt ataagaaaag agcaccatat
     2341 gcggtgtgaa ataccgcaca gatgcgtaag gagaaaatgc cgcatcaggc gctcttccgc
     2401 ttcctcgctc actgactcgc tacgctcggt cgttcggctg cggcgagcgg agtcggctca
     2461 cgcaaagacg gtaatgcggt tatccacaga atcaggggat aaggccggaa agaacatgtg
     2521 aacaaaaagg caaaaccaag gaaaaaggcc gcgccgctgg cgtttttcca taggctccgc
     2581 ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga
     2641 ctataaagat cccaggcgtt tccccctggt cgctccctcg tgcgctctcc tgttccgacc
     2701 ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     2761 agctcacgct gttggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
     2821 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     2881 aacccggtaa gacacgcctt aacgccactg gcagcagcca ctggtaaccg gattagcaga
     2941 gcgagattta tccagatgct tacagagttc ttgaagtgat ggcctaacta cggctacact
     3001 ggaaggacag tatttggtat ctgtgctctg ctgaagccag attacctcgg ttagataatc
     3061 tgccaggatt agctaacctt cgaaaaaacc acctgccagg gtggtttttt cgtttacaga
     3121 tccaagatta cgcgcagaaa aaaaggatct caagagatcc ttttagtttt ttagtcaaaa
     3181 agagcactaa gcctatttct ataataatta acaacataag ggaaatcact atatttttct
     3241 atttgtttta atattgaccg ttgaatttcc tctttttcag agtctgtgta acttacatta
     3301 ttccactttc ttgataattc cattgctgac tgaagcatat cttcaaaggt tagcacccta
     3361 ttattatttt tatatttgaa atttttattt tctatcgtcg ttacaacgac cacattagcc
     3421 tcgtacaata tatttattgt ctcctcgcta aaagaatcat ctagtgtagc tagatacatt
     3481 tctctaattc ctgttctatt aacctcttca ggtacttctt gccatcgctc cctcagcgtt
     3541 gttttagcgg aaatcaacat tgtatttctt ttgttagatg tgtactggac tacacctggc
     3601 ataacaagat ctacaagttt acctatttgg tttttttgaa aaaatgactt cccaatagcc
     3661 ccctgcacat caacaggaat tcctgccccc atcattaata gctcaagaat agactcaaac
     3721 tcttttcctg ccctgctacg tctggattga gtgttagaca gtgccaaatc atatatgtgt
     3781 gtagggtatt ccatcgtaaa atcacgaatg gcatcataag gactcatatc ttttattctt
     3841 tcttcatcaa taagatatga taacattctt gttgtgaatt ctttttcaaa tggttcaaat
     3901 tctttccaac agttttttct cattgcaatt atatattcac ttggattatt caaaaaataa
     3961 tcactatttt tttgatcata ccctaaatca caaaatgttt tataaaccaa agcaaatggc
     4021 gtaataaaat gcgattttct ctctttagaa attagagttt taaattcacc aggacttaat
     4081 ctttgcataa aaaataacct tttatatcta cttgaaagtt ttttcatgca cgttcataat
     4141 tggaatcaaa acaggacaaa ttgtcctaaa accaacactt aattctggta gacatgc
//
