LOCUS       NZ_CP151369             5114 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R16.0937 plasmid pR16.0937_5.1k, complete
            sequence.
ACCESSION   NZ_CP151369
VERSION     NZ_CP151369.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122664
            Assembly: GCF_038367185.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5114)
  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  JOURNAL   Unpublished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 5114)
  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_038367185.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:38:13
            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)                     :: 5,030
            CDSs (total)                      :: 4,901
            Genes (coding)                    :: 4,266
            CDSs (with protein)               :: 4,266
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 635
            CDSs (without protein)            :: 635
            Pseudo Genes (ambiguous residues) :: 0 of 635
            Pseudo Genes (frameshifted)       :: 172 of 635
            Pseudo Genes (incomplete)         :: 435 of 635
            Pseudo Genes (internal stop)      :: 111 of 635
            Pseudo Genes (multiple problems)  :: 81 of 635
            Pseudo Genes (short protein)      :: 3 of 635
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151369.1.
            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..5114
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R16.0937"
                     /db_xref="taxon:624"
                     /plasmid="pR16.0937_5.1k"
                     /collected_by="Taiwan CDC"
     gene            464..1399
                     /locus_tag="AADX59_RS25105"
                     /old_locus_tag="AADX59_25115"
     CDS             464..1399
                     /locus_tag="AADX59_RS25105"
                     /old_locus_tag="AADX59_25115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_024235833.1"
                     /translation="MSAALQYFEENLPHRPYHTDELAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDRVGAAIDWSDRNAPAPNITVKNPENGHAHLLYALNLAVRTAPDASVKA
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYALDELADYLDLRASE
                     RRSVDKHYGLGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPESFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLNVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(1593..2039)
                     /locus_tag="AADX59_RS25110"
                     /old_locus_tag="AADX59_25120"
     CDS             complement(1593..2039)
                     /locus_tag="AADX59_RS25110"
                     /old_locus_tag="AADX59_25120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_024235834.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            2211..3761
                     /locus_tag="AADX59_RS25115"
                     /old_locus_tag="AADX59_25125"
     CDS             2211..3761
                     /locus_tag="AADX59_RS25115"
                     /old_locus_tag="AADX59_25125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_039063720.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGELDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALCIQRSWARGVSRSNERDQDMER"
                     /name="MobA/MobL family protein"
     gene            complement(3957..5057)
                     /locus_tag="AADX59_RS25120"
                     /old_locus_tag="AADX59_25130"
     CDS             complement(3957..5057)
                     /locus_tag="AADX59_RS25120"
                     /old_locus_tag="AADX59_25130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001569522.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024235836.1"
                     /translation="MNINFKHILPLLSSFFISGCDSDGISKVKSFVYYDIDDSMTVGKA
                     FDTRSDCINGTWSEKEDDRGRTIVTYTCDISESGLKIINSAIMQEPEDKAEYSIAQNNN
                     SIKSTNESLEEYKQKTPLVEKTKEVIIDHIRKLNSAFNEDPMIYSKLTISPYLDRMLYL
                     KDHNDNALNEICGGYEYIQSADSYSWRDVSEEYAKESCEKHIYKVYQSFKKNASPLITK
                     NFPGFYERVPPCENADECIKKTNIYFDDNFLNIYKRSQDRAPQIISDLKKHNIEIGEKL
                     NDCRKKLNISDVKLTYYWFVTDTGGVDYLDGVLTYNFQGKNRAENFHKQLLQYAYINYS
                     KNQIPRDFVTSIKNSIYYKIEDCTKF"
                     /name="hypothetical protein"
     Typing          465..1399
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2212..3758
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggaatcca tacataccga taaaccgact tactatgttt gtgctcaacg tcttacgcag
       61 ttcgaaaaga tttcgcacca gttcaccttt ttctggatga gaaagtttgc tgttttgacc
      121 tgttcgctgt tcaaaacgag tgaaaccgga catgaatcgc tttcgtgcat agttatgcag
      181 ccccctgaaa acaattctgg cgcgtttttt tggtctggcc tgttgtttcc ctgtcttttt
      241 gcgttttttg cgacagaaag cgactgaggg cgttttaagg ggggcgcaca acgggagtta
      301 tggtaaatgg atcgggtttg cgggaagact cgacaggttt tgtcgttggg ggtagtgtaa
      361 gcgactgaaa aacaaacgcc cctgaaattc gtgtctatcc ggcaagactt tcacgaagat
      421 acaggggcga tgtcggtcga taacctggaa ggaatcgtaa cacatgagcg ccgcgcttca
      481 atacttcgaa gaaaatttac ctcaccgtcc ctatcacacg gatgagctcg ctttcggtct
      541 tcgtatctcc ggcaaagggc gtgcgctgct tgctcgctac atccagcaaa atcagcctca
      601 tgcgcagttc tggctggttt ttgacgttga ccgcgtagga gctgcgattg actggagcga
      661 ccggaacgcc cccgcgccga acatcaccgt aaaaaatccc gagaacgggc acgctcacct
      721 gctctacgcg ctcaatcttg ccgtgagaac cgcgcctgat gcgtcggtta aggcgctgaa
      781 atacgccgct gcaattgaac gtgcgctgtg tgagaaactt gacgcagatg tgaactacag
      841 cggactgatt tgcaaaaatc cgttccacct ggaatggcag gtgatggagt ggcgcgagga
      901 agcctacgcc ctcgatgaac tggctgatta tctcgatttg agagcctcag agcgtcgtag
      961 cgtcgataaa cattacgggc tggggcgaaa ctgccatctg ttcgaaatga cgcgcaaatg
     1021 ggcttacagg gcgattcggc agggctggcc agcattctca cagtggcttg atgctgtgat
     1081 tcagcgtgtc gaaatgtaca acgcatcgct tcccgttccg ctttctccgc ctgaatgtcg
     1141 ggctattggc aagagcattg cgaaatacac gcacaggaac ttcacgccgg aaagtttcgc
     1201 acagtatgtg gctgatacgc acacaccaga aatacaggcc aagagaggcc ggaaaggtgg
     1261 catcgctaaa ggcgaagcct acgatgacaa gcgtttcatg gcgctatgta tgctggagaa
     1321 tggatattct cagaaagcta ttgcggcgat gctgaatgta catcgtaata cgatccgtaa
     1381 ttgggcaatg cacaaatagc ctatatcaga taacagcgcc ttttcggcgt ctttttgagc
     1441 agcgggcttt ccggcggttt tctcctttca gcccagcaat ggtgcggctt accgtatgat
     1501 tgaggtggtc gtgctcgccg cagtctcatg accgagcgta gcgagcgaat gagcgaggaa
     1561 gcaccaggga actggaacgt gaacggaggc tcttacgcac tgtctttggt gagtagctct
     1621 ttcccgcgtt tttcccattc ctgccatttt ggatggttgt gcggtagctc tgcgattcct
     1681 gcgagtgcgc ctaccagttc ggcagcacta aactttggct ttccggtttt gctgtccacc
     1741 agtcctgcca caatcatgag gcctgcggcc ttgtagagtt catgatcccg cgcctttcgt
     1801 tccgcccttg cggctgcctt ccgttctgcc gctatgattg ccgttactct ggcttttgct
     1861 gcggctgctt tctctgcggt tttttctgcc cgtatcagtg cggacaacgt tttttcatcc
     1921 gtcgttgttc ggtttttttt ctctgccagt aacacaagta atctctgctg ctctgatggt
     1981 gatttcagtc cgttgatgta ggcaattttt gcacttaacc actcttcacg atttgtcatt
     2041 cttacctctg cacttttgcc gttaatgtga gttgttatta tgcataatat caccttgttt
     2101 gcctgcgtgt gagaccgtaa aatcatccat gattaattca gggatgcgca cttagtagtt
     2161 tctctccttc gtcgagaaac tgtgcgctcc tgcggagggc taaaaggcag atggcaagct
     2221 accattgcac tgtcaaagct ggagcaaaag gcagtgcctt aaaacatgct gattacattt
     2281 ccagatccgg cgaatataag agttacaaat cgcgggagga tctggaattt tcgtcatccg
     2341 gtaacatgcc atcatgggcg aagaaaaatc ccgcagagct atggaaagcc gcagatgaat
     2401 ttgaacgaaa aaacgggact gcataccgtg aaattgagat cgcgttaccg cgtgaactga
     2461 cacgcgaaca acggatagaa cttgttgaag atttcgtgca aaaggaactt ggcgatcgcc
     2521 atgcctacca gtacgcgatc cacaatccgc caggtgcaat cgacggaaag gaacagccac
     2581 acgcgcatat catgttttgc gagcggatta atgatggtat tgaacgcgat ccacagcaat
     2641 tttttaaacg tgccaacagc aaatcaccag agcggggagg cgcaaaaaaa gcgagtattc
     2701 cccagacagc cggagagcga aaagccgccc ttgttgcgct gcgttcccgc tgggcagatg
     2761 tgcagaatga gcaccttgcg cgacacggtc acgagtcgcg cgtagatcat cgttctctga
     2821 aagaacaggg tatcaatcgc acgccggaag ttcatcttgg ccccgttcag gccgccagtc
     2881 tgaatgggga gcagattgtt gcaatccagg aacggaggaa tgccgagcgg gaactcaaga
     2941 ccgccagaga tgccgcaaat gccattcagc aggaacagga gcaaaagcaa aaaatcaagg
     3001 cagttgagcc tgttcgttca gcccgttcac cggagttatt gcttcagtac cgcaaggtta
     3061 tgaaaacggt cattcaggga gaggcaaggc ttgctcgttt aggggatgcc aatcccaatg
     3121 cgctcaaaga acataagctg cttcagaatg cgaaagctaa aaaagactct ctttccgaat
     3181 ggagtagacg aatatatgaa ggggcacggt atttagacaa actggggcgt aatgttgttt
     3241 ccgcacaaag ggagctgcgg gagctacagg aacaacgcaa tgctttgaat gggattcgtg
     3301 gcctgtttcg gggggctgac aaaagggaga ttgatgcgcg tattctggag caaaaaagtg
     3361 tgctggaaac cgctgaacat gaaaggaatg aattcaggaa caagctacag caagccgaat
     3421 ccgagtggga caaagaaaac gctgctttta agcgtaccga gggatataag tacgttgggg
     3481 agctggacag gtacagagaa cgcgagattc tggcggcggc atctttagag aacaccaggc
     3541 aaaaggttgc tgaagaggta tccgttgccc gtagccagat gttatctctg gagcctgaac
     3601 tcagtatatc tggagatgaa aaagctcaaa tgcgacatga gttactggca gaaatggcgc
     3661 aggaacggca gcaacaggag gaaaaagcac tgtgtataca gcgatcctgg gccagggggg
     3721 tatcacgtag taacgaacgt gatcaagata tggagcgttg aaaatgtagc aatatcggga
     3781 ctgcgccccg aaccccgcca acgtttcacg gaacgcgaaa aaattccgcg tcccgtgaaa
     3841 cgttttctga atgagaaaaa ttgtcgtttt gatttactca cagttcagat taatgaagtt
     3901 aacaggtgtt aaatatttgc aggtggttat atgtgtaacc acctgtaagg gaaggactaa
     3961 aacttagtgc aatcttctat tttataataa atactatttt ttattgatgt tacaaagtcc
     4021 cgaggtattt gatttttgct gtagttaatg tatgcatatt gcaatagttg tttatgaaag
     4081 ttttcagctc tattctttcc ctgaaaatta tatgtcaaca ccccatctaa ataatcaact
     4141 cctccggtat ctgttacaaa ccagtaatag gttaatttga catctgagat atttagtttt
     4201 ttcctacaat catttaactt ttcacctatt tctatattgt gtttttttaa atcagaaatt
     4261 atttgaggtg ctctatcttg gcttcttttg tagatattta gaaagttatc atcaaagtat
     4321 atatttgttt tttttatgca ttcatctgcg ttctcacagg gggggacacg ttcgtagaaa
     4381 ccggggaagt ttttagttat taatggtgat gcatttttct taaacgattg atatacttta
     4441 tatatatgct tttcgcatga ttcttttgca tactcttcac ttacatcacg ccaactgtaa
     4501 ctatcggcag attgaatgta ttcgtaccca ccacaaattt catttagcgc attgtcatta
     4561 tggtccttta gatatagcat tctgtctaaa taagggctaa ttgtgagttt gctatatatc
     4621 attggatctt cattaaaagc actgtttagc tttcttatat gatctattat gacctctttt
     4681 gttttttcca ccagaggcgt tttctgtttg tattcctcta gtgattcatt ggttgatttt
     4741 atgctgttgt tattttgtgc tatagaatat tcagccttat cttcaggttc ttgcataatg
     4801 gctgaattta ttatttttag gccactttca ctaatatcac aggtatatgt gacgatggtt
     4861 cttcctcgat catcctcttt ttcactccat gtgccattga tgcaatcact ccttgtatcg
     4921 aaggctttac caacagtcat tgagtcgtca atgtcgtaat atacgaaaga ctttaccttg
     4981 cttattccat cagagtcgca tcctgaaata aaaaatgacg acaataaagg aaggatatgt
     5041 ttaaagttaa tattcatttt tcccattttt atttctaaca ataacgagga aatattaata
     5101 caggcgatat gtta
//
