LOCUS       NZ_CP151398             4091 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.0423 plasmid pR15.0423_4k, complete
            sequence.
ACCESSION   NZ_CP151398
VERSION     NZ_CP151398.1
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 4091)
  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  JOURNAL   Unpublished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 4091)
  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
            CP151398.1.
            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..4091
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R15.0423"
                     /db_xref="taxon:624"
                     /plasmid="pR15.0423_4k"
                     /collected_by="Taiwan CDC"
     gene            1..702
                     /locus_tag="AADX55_RS26745"
                     /old_locus_tag="AADX55_26765"
     CDS             1..702
                     /locus_tag="AADX55_RS26745"
                     /old_locus_tag="AADX55_26765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_011666799.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(951..3098)
                     /gene="mobQ"
                     /locus_tag="AADX55_RS26750"
                     /old_locus_tag="AADX55_26770"
     CDS             complement(951..3098)
                     /gene="mobQ"
                     /locus_tag="AADX55_RS26750"
                     /old_locus_tag="AADX55_26770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_024236174.1"
                     /translation="MAIYHLSMKILSRSKGYSAVASAAYRAGEKILDERTGVIHDYTRK
                     NGVASAVILTPANAPAWCANRAELWNAVEKAERRKNSQLAREFELAIPRELAQDAARET
                     VLNFVRENFVSRGMIADVAFHNLGGSNPHAHIMLSMRAITPDGFGEKVREWNDWTHAET
                     WRGSWADHANRALANAGYQEEIDHRSYERQGVEKTPGIHLGKSACAMEKWGIETERGEQ
                     NRLINRLNLEIQVSRDELRNSELTEPARRMADLLNIELPDNATSYILHDIIEALPTDSN
                     AAWKLTSKAMSMMADMQATRRRWEDLNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWV
                     APEYGREQEKIQSLSQRMEKLRQHHWKVEKQDIPASQKAFETQWQQWGASGLADLREQL
                     RKREEELRRKEQEETERRRAEQLRRNDNAVMDSGVLKAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRARIFESVDLMRDRSGYICERSEIGQRPPLQHVYSSATFEQ
                     LLTQVCQTWPQHTRDLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSMGGVVRLNGTLYPAFAVPTADNSQLVINALTDKGLRFA
                     GYGEAVNHDADSPARPAPELMQFHLKTWSEPLFAIVNTPEKQPDHLFRSLGFERTWDEW
                     QRDEYARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            3269..3559
                     /locus_tag="AADX55_RS26755"
                     /old_locus_tag="AADX55_26775"
     CDS             3269..3559
                     /locus_tag="AADX55_RS26755"
                     /old_locus_tag="AADX55_26775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001514113.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     GETQLRAWLLHLLKTEVTRQADVSRIQPLIDELNALPKPVPKEVSENDQQA"
                     /name="hypothetical protein"
     Typing          2744..3098
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3115..3265
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.157"
                     /coverage="85.0"
                     /evalue="1.64e-53"
     Typing          2..701
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.301"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(955..3140)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.726"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcggatc tgattgccta caaatccaat gcactggttg aggccagcta taaattgact
       61 cttcaggaac agcgattctt gttactttgc attggtcgat tgaagtcggg ttctgatgca
      121 gaatccactg aattgcaaaa gaccatgact gttaccgccg aagagtattt cgactcattc
      181 cctgatatgg ggcggaaaaa tgccgaggtt cagctacagg aagcaattga tcgtttgtgg
      241 gacaggtcga tcatccttaa ggacgatgag aagcgcgagg agttccgctg gatccagtat
      301 cgggcacagt acgctaaagg tgagggcaaa gcccaaatca ctttttcaga tgcggtcatg
      361 ccttatctga cacagttgaa ggggcaattt actagagttg taattaagaa catctccaat
      421 ttatcaagaa gttacagcat aagaatatac gaacttctcc agcaattccg cagcacaggg
      481 gaacgtatta tcgccctcga tgattttcgc tcaatgcttg atatagagca taaatatcaa
      541 acatataagt ctctgaacca gcaattatta agaccttgcg ttgacgaact gaatcaaaaa
      601 agcgacttgg ctgtaacgct tgagacgatc aagaaggggc gcacggttgt agccctgcat
      661 tttcgcttca aggaagacaa acagatcaag atgacgatct agaatcgatt ttaaggcctc
      721 taaaacgctc tctgacgcgt tttttttgtg tttggcatgc gaaggtactg gtgaagtaaa
      781 aaattgcgtc ataaacgctc tggcacagtg aaaaaagaac ccccaatttt tcgggggcgg
      841 gaaaactata aagttgattt gtgttatgtg tgtgcttctt gcattcatcc ctgtcgatga
      901 acatcgacga acataacacg atgttaaaca aaacaaaata ttggtcacat tcactgtgac
      961 caaccgcgat catgtctcct ctcggtggcg tgtgttcggg catattcatc acgttgccat
     1021 tcatcccagg tgcgctcaaa gcccagcgag cggaacagat gatccggctg tttttctggc
     1081 gtgttgacga tagcaaaaag cggttcgctc caggttttca gatgaaactg cataagttcc
     1141 ggcgcaggac gtgccggact gtcagcatcg tggtttaccg cttcaccata gcctgcaaag
     1201 cgtaaacctt tgtcggtcag tgcattgatt accagctggc tgttgtcggc tgtggggacg
     1261 gcaaacgcgg gatacagcgt accattaagc cggacaacac cgcccataga gtcatccaca
     1321 cccatgacca gcaaaagctg aagctggcgg gtttcacggt cgacagaact cattaccggc
     1381 atcagagtcg gtggcagacg tccctgcgta aaatccacct tccttgccgc cagtgatggc
     1441 atggctggct ggcggtcttc tccaagacag aaagactccg gccatgtctt cggctggcgg
     1501 agatcgcggg tatgttgcgg ccatgtctgg caaacctgcg tcagcagttg ctcaaaggtc
     1561 gcagaggaat aaacatgttg cagtggtgga cgttgaccga tttcgcttcg ctcacagata
     1621 taaccactcc tgtcacgcat taaatcaaca ctctcaaaaa ttctggcgcg gtatttctcc
     1681 agttcgttcc cccagagcgt atattctccg ttccggttgt gaagcagaag gtaacaggtc
     1741 atttccccgt tacctggcat gggggcctcg ccataccccg taacgactgc tttcagtacc
     1801 cctgaatcca taacggcatt gtcatttctc ctgagctgct ccgcccgacg acgttctgtt
     1861 tcctcctgct ccttccggcg caattcctct tcacgtttac gcaactgttc tcggagatct
     1921 gcaaggccag atgcacccca ctgctgccac tgtgtttcaa atgctttttg actcgcggga
     1981 atgtcctgtt tctcaacctt ccagtgatgc tgccgcaatt tttccatgcg ctggctcaac
     2041 gactggattt tttcctgttc gcggccgtat tccggtgcaa cccattgcat caggggaata
     2101 cgggaaaaac cggacgaaaa cggcgatgat tttttcaggc tggcagcatg gctcatcgct
     2161 tcctttcgtt cggtgttcag atcttcccag cgtctgcgcg tcgcctgcat atctgccatc
     2221 atcgacatgg ctttactggt gagtttccat gctgcgttac tgtccgtcgg caacgcttcg
     2281 atgatgtcat gcagtatgta cgaagttgcg ttgtcaggaa gctcaatatt cagaaggtca
     2341 gccatacggc gtgcgggctc tgtcagctca ctgttcctga gttcgtcgcg ggaaacctgt
     2401 atttccaggt taagcctgtt aatcaggcga ttctgttcgc cgcgttctgt ttcgatgccc
     2461 cacttttcca tcgcacaggc cgactttccg aggtgaatgc caggcgtttt ctcaaccccc
     2521 tgtcgctcgt atgaacgatg gtctatctct tcctgataac cggcgttcgc cagcgccctg
     2581 ttcgcatggt ctgcccatga tccccgccat gtttcggcgt gagtccagtc attccactca
     2641 cggactttct ccccgaagcc gtcaggcgtg attgccctca tggatagcat gatgtgcgcg
     2701 tgtgggtttg acccgcccag attgtgaaag gccacgtcgg cgatcatgcc gcgactgaca
     2761 aagttttccc ttacgaagtt gagaactgtt tcccgtgcgg catcctgcgc cagttcacgg
     2821 gggatggcga gttcgaactc ccgcgcaagt tgtgagtttt tccgccgctc ggctttttca
     2881 acagcattcc agagttcggc gcggttcgca caccatgctg gggcgtttgc tggcgtcaga
     2941 atcactgcgc tggctacacc gtttttgcgg gtgtagtcgt gaatcactcc ggtgcgctca
     3001 tccagtattt tttctccggc acgataggca gcagaagcaa cggcgctgta gcccttgctt
     3061 ctggaaagaa tcttcatgct gagatgataa attgccatcg tgtcgttgtt gccgttttct
     3121 tttagccccg cagggcgcac acaaactcga cgaaggagag tttgtataag tgcgcacttc
     3181 gtgatttgct gtgcattatg ccagttcagt ttttaaacta ccagtgacgc gctaaaatac
     3241 gatttttcac cgcgcacgga gttacggaat gagtagaaca ctcgaacaga agattgccga
     3301 tgctgaggcc agattgcagc gtctgaaggc gaagagcagg agcctggaca cagcgcagaa
     3361 ggtcattgtg ggagcggcat tgctggcaaa ggtcaggaag cctggggaaa cacaactacg
     3421 agcctggttg cttcatctcc tgaagacaga ggtaacacgg caggctgatg tgagcaggat
     3481 acagccgttg attgacgaac tgaacgcgtt accaaaacca gtccccaaag aagtgtcaga
     3541 aaacgaccaa caggcgtgaa tgcaccgtcc gctcgccgca gccccagcga ccgagcgtta
     3601 gcgagcgagt gggcgaggaa gcggaagtga atccgtcgcc agattgagca catacgcacg
     3661 gtttttcgac aggtgatatg cgctgaaccc gcatgaatac tggatttcca cagggttgag
     3721 cggggttttg ctaaagcttg cgaacctgct tttttgtaac ctgttgtttt tcatgatttt
     3781 ttgttttgaa caccccaagt tttccacagg ctcgccgtta agtttttaga tcttgttttt
     3841 aagatcttgt ttttaatact tgttttaggg tcgaattttc ttatgaaatt caagagttta
     3901 gaagactata ggtaatataa tttaaggtaa aggcaatatg atttaaggtg gataggcaat
     3961 atgatttaag gtaaaggcaa tatgatttaa ggtaatattc acaggaaaag ggatattaaa
     4021 attaaatcat attgccttta cctaaaggaa tgtttatatt ttactcatta ccttaggttg
     4081 agggatttac a
//
