LOCUS       NZ_CP151378             4197 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.1832 plasmid pR15.1832_4k, complete
            sequence.
ACCESSION   NZ_CP151378
VERSION     NZ_CP151378.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122663
            Assembly: GCF_038367355.1
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  JOURNAL   Unpublished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_038367355.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:29:12
            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)                     :: 5,193
            CDSs (total)                      :: 5,063
            Genes (coding)                    :: 4,437
            CDSs (with protein)               :: 4,437
            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)              :: 626
            CDSs (without protein)            :: 626
            Pseudo Genes (ambiguous residues) :: 0 of 626
            Pseudo Genes (frameshifted)       :: 168 of 626
            Pseudo Genes (incomplete)         :: 435 of 626
            Pseudo Genes (internal stop)      :: 108 of 626
            Pseudo Genes (multiple problems)  :: 82 of 626
            Pseudo Genes (short protein)      :: 3 of 626
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151378.1.
            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="R15.1832"
                     /db_xref="taxon:624"
                     /plasmid="pR15.1832_4k"
                     /collected_by="Taiwan CDC"
     gene            join(3797..4197,1..556)
                     /locus_tag="AADX60_RS25885"
                     /old_locus_tag="AADX60_25885"
     CDS             join(3797..4197,1..556)
                     /locus_tag="AADX60_RS25885"
                     /old_locus_tag="AADX60_25885"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /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(748..909)
                     /locus_tag="AADX60_RS25890"
                     /old_locus_tag="AADX60_25890"
     CDS             complement(748..909)
                     /locus_tag="AADX60_RS25890"
                     /old_locus_tag="AADX60_25890"
                     /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(1575..1769)
                     /locus_tag="AADX60_RS25895"
                     /old_locus_tag="AADX60_25895"
     CDS             complement(1575..1769)
                     /locus_tag="AADX60_RS25895"
                     /old_locus_tag="AADX60_25895"
                     /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            complement(2587..3726)
                     /gene="dcm"
                     /locus_tag="AADX60_RS25900"
                     /old_locus_tag="AADX60_25900"
     CDS             complement(2587..3726)
                     /gene="dcm"
                     /locus_tag="AADX60_RS25900"
                     /old_locus_tag="AADX60_25900"
                     /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          1410..1495
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          1806..1904
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(838..1388)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.213"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaagagttt gagtctattc ttgagctatt aatgatgggg gcaggaattc ctgttgatgt
       61 gcagggggct attgggaagt cattttttca aaaaaaccaa ataggtaaac ttgtagatct
      121 tgttatgcca ggtgtagtcc agtacacatc taacaaaaga aatacaatgt tgatttccgc
      181 taaaacaacg ctgagggagc gatggcaaga agtacctgaa gaggttaata gaacaggaat
      241 tagagaaatg tatctagcta cactagatga ttcttttagc gaggagacaa taaatatatt
      301 gtacgaggct aatgtggtcg ttgtaacgac gatagaaaat aaaaatttca aatataaaaa
      361 taataatagg gtgctaacct ttgaagatat gcttcagtca gcaatggaat tatcaagaaa
      421 gtggaataat gtaagttaca cagactctga aaaagaggaa attcaacggt caatattaaa
      481 acaaatagaa aaatatagtg atttccctta tgttgttaat tattatagaa ataggcttag
      541 tgctcttttt gactaaaaaa ctaaaaggat ctcttgagat cctttttttc tgcgcgtaat
      601 cttggatctg taaacgaaaa aaccaccctg gcaggtggtt ttttcgaagg ttagctaatc
      661 ctggcagatt atctaaccga ggtaatctgg cttcagcaga gcacagatac caaatactgt
      721 ccttccagtg tagccgtagt taggccatca cttcaagaac tctgtaagca tctggataaa
      781 tctcgctctg ctaatccggt taccagtggc tgctgccagt ggcgttaagg cgtgtcttac
      841 cgggttggac tcaagacgat agttaccgga taaggcgcag cggtcgggct gaacgggggg
      901 ttcgtgcaca cagcccagct tggagcgaac gacctacacc gaactgagat accaacagcg
      961 tgagctatga gaaagcgcca cgcttcccga agggagaaag gcggacaggt atccggtaag
     1021 cggcagggtc ggaacaggag agcgcacgag ggagcgacca gggggaaacg cctgggatct
     1081 ttatagtcct gtcgggtttc gccacctctg acttgagcgt cgatttttgt gatgctcgtc
     1141 aggggggcgg agcctatgga aaaacgccag cggcgcggcc tttttccttg gttttgcctt
     1201 tttgttcaca tgttctttcc ggccttatcc cctgattctg tggataaccg cattaccgtc
     1261 tttgcgtgag ccgactccgc tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc
     1321 gaggaagcgg aagagcgcct gatgcggcat tttctcctta cgcatctgtg cggtatttca
     1381 caccgcatat ggtgctcttt tcttataatc tgcactgatg ccgcatagtt aagccagtat
     1441 acactccgct atcgctacgt gactgggtca tggctgcgcc ccgacacccg ctaaaacccc
     1501 ctgacgcgcc ctgacgggct tgtctgctgc cgaaaacgct cacgggaaag ccgtgaccgc
     1561 ctccgtcagc ttcgttatgt tcctgtttca ctttcggcct caaagcgaat ctggatgctg
     1621 ttctggagtt tttctgcgag ttcgtgcagt cgttcgcaca tggtcgcctg ttcgtcggca
     1681 tccagagcat ccagtttttc aagtagtgtc aggctctggc ttttgataaa tcgcgccata
     1741 ttcagcgcag tttgttgttg tttattcacc ttccgttgtt ctccgtcagt tccgggtgtc
     1801 ggggggaccc tgagcaggtg gtaattgtaa gacgttgcgg gcgacggtat tacaattgca
     1861 catcctgtcc tgtttcttta ggacgtatca tggcacagca tatcaactga taaataatcc
     1921 ctgtgcagtg cagccgctgt tgcataaaat ttcgctctgc atcgagtgtt tcttaatcaa
     1981 taattccgct gatactccgg aaaaacgcga gtctgttctc atacccgaaa tgcccacacc
     2041 ccacgcaaaa ccaacttttt gctgatttgc tttttaaatc atgttgttat ggttttaaaa
     2101 atatattttc ttattcagat ttatacaaaa gcacgtcgtc gacgacccta tggcgacgct
     2161 atggcgaccc tacttagggt cagtactgac tatctgtaga aaaaacagtt aattaatgta
     2221 ggtgcgcccc taggggcgcg tcgccttttt ttacataacg cccctgggag cgctgctagg
     2281 ggtgtctgtt cagatatgta gcaatgagtc agggattcac gaactgaaaa tgtccgaaaa
     2341 tgtgtctcat gggcaccata tgcgcccaaa ccgatcgcca ttcactttca tgcatagcta
     2401 tgcagtgagc tgaaagcgat cctgacgcgt ttttccggtt taccccggga aaaaacatct
     2461 ctttttgcgg tgttcgcggc agaatcgcgt tcagcgcgtt ttagcggtgc gcgtaatgcg
     2521 acgttatggt aaatccatat ggggggtaat tggattctgg gccgcattgt gtcctcatga
     2581 cttagtttat gaatctaagg tcgatatgat tttttctgct attgcattga taacagggac
     2641 tgcgactgaa ttcccaaatt gcttataagc ctgtgtatcc gatacaggga taataaaatc
     2701 actaggaaac ccttgaagtc ttgacgcttc ccgcggagtt atttttcttg ggttacttcc
     2761 tttttgctct attaatattt cgctaccatc tttatagtac ctcgcactta tggtattagt
     2821 atatgggcta ttttcattaa ataaaccata cccaaagcct ttaccggctg ctgcatttac
     2881 aagtttcctg cgttggtgtc cattccagag cgcatctgat agcgtatatt tattgtctac
     2941 gctcttttca agaatatctc caactcttgt ttttgttttt aatggggttg gaaaagtaaa
     3001 atgttcatga tttcttactt tttctttatt aaagcctaca atgtatatgc gctctctatt
     3061 ttgtggaaca ccaaagtctt ttgcagcgaa gatattgtaa tacacagtgt aattcaattc
     3121 ttcaagtgtg ttttttatta ttgaaaaagt tctaccttta tcatgtccta gcaagttttt
     3181 tacattttca agtaaaaaag catgaggttt tttttccttt attatccttg ctatatcaaa
     3241 aaacaaagtt cctcttgtat cattaaatcc ttttttgagg cctgcttgag agaatgctac
     3301 acaaggaaac ccaccgacaa gaatttcatg atcaggaata tctttttcat cgatttttgt
     3361 tatgtcccca tcagggaaat caccataatt tgcatgatat gtcttttgag caaacttatc
     3421 ccattcgctg gaaaaaacaa catttacagc gttagtttga tgaaatccaa gtctggttcc
     3481 accgattcca gcaaataaat cgatcatgcg atatctgcca ttctcgttgt ttgggtaagg
     3541 tggtgtgtct ggaaagtcta taactgcttt tagttccgcc ccagtaggtt ttgtttcccc
     3601 gcgctcccat cttcttatgg ttctgtctcc atattttgaa agaccaaggg cgtctgcaaa
     3661 ctctttttga gtcatatgaa gtctttctct tttttctttg attgttgctg cgatattatc
     3721 agtcatgcat gtctaccaga attaagtgtt ggttttagga caatttgtcc tgttttgatt
     3781 ccaattatga acgtgcatga aaaaactttc aagtagatat aaaaggttat tttttatgca
     3841 aagattaagt cctggtgaat ttaaaactct aatttctaaa gagagaaaat cgcattttat
     3901 tacgccattt gctttggttt ataaaacatt ttgtgattta gggtatgatc aaaaaaatag
     3961 tgattatttt ttgaataatc caagtgaata tataattgca atgagaaaaa actgttggaa
     4021 agaatttgaa ccatttgaaa aagaattcac aacaagaatg ttatcatatc ttattgatga
     4081 agaaagaata aaagatatga gtccttatga tgccattcgt gattttacga tggaataccc
     4141 tacacacata tatgatttgg cactgtctaa cactcaatcc agacgtagca gggcagg
//
