LOCUS       NZ_CP151318             5114 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R21.0552 plasmid pR21.0552_5k, complete
            sequence.
ACCESSION   NZ_CP151318
VERSION     NZ_CP151318.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735802
            Assembly: GCF_038364745.1
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  JOURNAL   Unpublished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_038364745.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:43:35
            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)                     :: 5,428
            CDSs (total)                      :: 5,299
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            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)              :: 739
            CDSs (without protein)            :: 739
            Pseudo Genes (ambiguous residues) :: 0 of 739
            Pseudo Genes (frameshifted)       :: 212 of 739
            Pseudo Genes (incomplete)         :: 527 of 739
            Pseudo Genes (internal stop)      :: 127 of 739
            Pseudo Genes (multiple problems)  :: 121 of 739
            Pseudo Genes (short protein)      :: 3 of 739
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151318.1.
            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="R21.0552"
                     /db_xref="taxon:624"
                     /plasmid="pR21.0552_5k"
                     /collected_by="Taiwan CDC"
     gene            10..1110
                     /locus_tag="AADX62_RS27065"
                     /old_locus_tag="AADX62_27050"
     CDS             10..1110
                     /locus_tag="AADX62_RS27065"
                     /old_locus_tag="AADX62_27050"
                     /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"
     gene            complement(1306..2856)
                     /locus_tag="AADX62_RS27070"
                     /old_locus_tag="AADX62_27055"
     CDS             complement(1306..2856)
                     /locus_tag="AADX62_RS27070"
                     /old_locus_tag="AADX62_27055"
                     /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            3028..3474
                     /locus_tag="AADX62_RS27075"
                     /old_locus_tag="AADX62_27060"
     CDS             3028..3474
                     /locus_tag="AADX62_RS27075"
                     /old_locus_tag="AADX62_27060"
                     /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_341742849.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVGSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(3668..4603)
                     /locus_tag="AADX62_RS27080"
                     /old_locus_tag="AADX62_27065"
     CDS             complement(3668..4603)
                     /locus_tag="AADX62_RS27080"
                     /old_locus_tag="AADX62_27065"
                     /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"
     Typing          complement(3669..4603)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1310..2856)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgggaaaaa tgaatattaa ctttaaacat atccttcctt tattgtcgtc attttttatt
       61 tcaggatgcg actctgatgg aataagcaag gtaaagtctt tcgtatatta cgacattgac
      121 gactcaatga ctgttggtaa agccttcgat acaaggagtg attgcatcaa tggcacatgg
      181 agtgaaaaag aggatgatcg aggaagaacc atcgtcacat atacctgtga tattagtgaa
      241 agtggcctaa aaataataaa ttcagccatt atgcaagaac ctgaagataa ggctgaatat
      301 tctatagcac aaaataacaa cagcataaaa tcaaccaatg aatcactaga ggaatacaaa
      361 cagaaaacgc ctctggtgga aaaaacaaaa gaggtcataa tagatcatat aagaaagcta
      421 aacagtgctt ttaatgaaga tccaatgata tatagcaaac tcacaattag cccttattta
      481 gacagaatgc tatatctaaa ggaccataat gacaatgcgc taaatgaaat ttgtggtggg
      541 tacgaataca ttcaatctgc cgatagttac agttggcgtg atgtaagtga agagtatgca
      601 aaagaatcat gcgaaaagca tatatataaa gtatatcaat cgtttaagaa aaatgcatca
      661 ccattaataa ctaaaaactt ccccggtttc tacgaacgtg tccccccctg tgagaacgca
      721 gatgaatgca taaaaaaaac aaatatatac tttgatgata actttctaaa tatctacaaa
      781 agaagccaag atagagcacc tcaaataatt tctgatttaa aaaaacacaa tatagaaata
      841 ggtgaaaagt taaatgattg taggaaaaaa ctaaatatct cagatgtcaa attaacctat
      901 tactggtttg taacagatac cggaggagtt gattatttag atggggtgtt gacatataat
      961 tttcagggaa agaatagagc tgaaaacttt cataaacaac tattgcaata tgcatacatt
     1021 aactacagca aaaatcaaat acctcgggac tttgtaacat caataaaaaa tagtatttat
     1081 tataaaatag aagattgcac taagttttag tccttccctt acaggtggtt acacatataa
     1141 ccacctgcaa atatttaaca cctgttaact tcattaatct gaactgtgag taaatcaaaa
     1201 cgacaatttt tctcattcag aaaacgtttc acgggacgcg gaattttttc gcgttccgtg
     1261 aaacgttggc ggggttcggg gcgcagtccc gatattgcta cattttcaac gctccatatc
     1321 ttgatcacgt tcgttactac gtgatacccc cctggcccag gatcgctgta tacacagtgc
     1381 tttttcctcc tgttgctgcc gttcctgcgc catttctgcc agtaactcat gtcgcatttg
     1441 agctttttca tctccagata tactgagttc aggctccaga gataacatct ggctacgggc
     1501 aacggatacc tcttcagcaa ccttttgcct ggtgttctct aaagatgccg ccgccagaat
     1561 ctcgcgttct ctgtacctgt ccagctcccc aacgtactta tatccctcgg tacgcttaaa
     1621 agcagcgttt tctttgtccc actcggattc ggcttgctgt agcttgttcc tgaattcatt
     1681 cctttcatgt tcagcggttt ccagcacact tttttgctcc agaatacgcg catcaatctc
     1741 ccttttgtca gccccccgaa acaggccacg aatcccattc aaagcattgc gttgttcctg
     1801 tagctcccgc agctcccttt gtgcggaaac aacattacgc cccagtttgt ctaaataccg
     1861 tgccccttca tatattcgtc tactccattc ggaaagagag tcttttttag ctttcgcatt
     1921 ctgaagcagc ttatgttctt tgagcgcatt gggattggca tcccctaaac gagcaagcct
     1981 tgcctctccc tgaatgaccg ttttcataac cttgcggtac tgaagcaata actccggtga
     2041 acgggctgaa cgaacaggct caactgcctt gattttttgc ttttgctcct gttcctgctg
     2101 aatggcattt gcggcatctc tggcggtctt gagttcccgc tcggcattcc tccgttcctg
     2161 gattgcaaca atctgctccc cattcagact ggcggcctga acggggccaa gatgaacttc
     2221 cggcgtgcga ttgataccct gttctttcag agaacgatga tctacgcgcg actcgtgacc
     2281 gtgtcgcgca aggtgctcat tctgcacatc tgcccagcgg gaacgcagcg caacaagggc
     2341 ggcttttcgc tctccggctg tctggggaat actcgctttt tttgcgcctc cccgctctgg
     2401 tgatttgctg ttggcacgtt taaaaaattg ctgtggatcg cgttcaatac catcattaat
     2461 ccgctcgcaa aacatgatat gcgcgtgtgg ctgttccttt ccgtcgattg cacctggcgg
     2521 attgtggatc gcgtactggt aggcatggcg atcgccaagt tccttttgca cgaaatcttc
     2581 aacaagttct atccgttgtt cgcgtgtcag ttcacgcggt aacgcgatct caatttcacg
     2641 gtatgcagtc ccgttttttc gttcaaattc atctgcggct ttccatagct ctgcgggatt
     2701 tttcttcgcc catgatggca tgttaccgga tgacgaaaat tccagatcct cccgcgattt
     2761 gtaactctta tattcgccgg atctggaaat gtaatcagca tgttttaagg cactgccttt
     2821 tgctccagct ttgacagtgc aatggtagct tgccatctgc cttttagccc tccgcaggag
     2881 cgcacagttt ctcgacgaag gagagaaact actaagtgcg catccctgaa ttaatcatgg
     2941 atgattttac ggtctcacac gcaggcaaac aaggtgatat tatgcataat aacaactcac
     3001 attaacggca aaagtgcaga ggtaagaatg acaaatcgtg aagagtggtt aagtgcaaaa
     3061 attgcctaca tcaacggact gaaatcacca tcagagcagc agagattact tgtgttactg
     3121 gcagagaaaa aaaaccgaac aacgacggat gaaaaaacgt tgtccgcact gatacgggca
     3181 gaaaaaaccg cagagaaagc agccgcagca aaagccagag taacggcaat catagcggca
     3241 gaacggaagg cagccgcaag ggcggaacga aaggcgcggg atcatgaact ctacaaggcc
     3301 gcaggcctca tgattgtggc aggactggtg ggcagcaaaa ccggaaagcc aaagtttagt
     3361 gctgccgaac tggtaggcgc actcgcagga atcgcagagc taccgcacaa ccatccaaaa
     3421 tggcaggaat gggaaaaacg cgggaaagag ctactcacca aagacagtgc gtaagagcct
     3481 ccgttcacgt tccagttccc tggtgcttcc tcgctcattc gctcgctacg ctcggtcatg
     3541 agactgcggc gagcacgacc acctcaatca tacggtaagc cgcaccattg ctgggctgaa
     3601 aggagaaaac cgccggaaag cccgctgctc aaaaagacgc cgaaaaggcg ctgttatctg
     3661 atataggcta tttgtgcatt gcccaattac ggatcgtatt acgatgtaca ttcagcatcg
     3721 ccgcaatagc tttctgagaa tatccattct ccagcataca tagcgccatg aaacgcttgt
     3781 catcgtaggc ttcgccttta gcgatgccac ctttccggcc tctcttggcc tgtatttctg
     3841 gtgtgtgcgt atcagccaca tactgtgcga aactttccgg cgtgaagttc ctgtgcgtgt
     3901 atttcgcaat gctcttgcca atagcccgac attcaggcgg agaaagcgga acgggaagcg
     3961 atgcgttgta catttcgaca cgctgaatca cagcatcaag ccactgtgag aatgctggcc
     4021 agccctgccg aatcgccctg taagcccatt tgcgcgtcat ttcgaacaga tggcagtttc
     4081 gccccagccc gtaatgttta tcgacgctac gacgctctga ggctctcaaa tcgagataat
     4141 cagccagttc atcgagggcg taggcttcct cgcgccactc catcacctgc cattccaggt
     4201 ggaacggatt tttgcaaatc agtccgctgt agttcacatc tgcgtcaagt ttctcacaca
     4261 gcgcacgttc aattgcagcg gcgtatttca gcgccttaac cgacgcatca ggcgcggttc
     4321 tcacggcaag attgagcgcg tagagcaggt gagcgtgccc gttctcggga ttttttacgg
     4381 tgatgttcgg cgcgggggcg ttccggtcgc tccagtcaat cgcagctcct acgcggtcaa
     4441 cgtcaaaaac cagccagaac tgcgcatgag gctgattttg ctggatgtag cgagcaagca
     4501 gcgcacgccc tttgccggag atacgaagac cgaaagcgag ctcatccgtg tgatagggac
     4561 ggtgaggtaa attttcttcg aagtattgaa gcgcggcgct catgtgttac gattccttcc
     4621 aggttatcga ccgacatcgc ccctgtatct tcgtgaaagt cttgccggat agacacgaat
     4681 ttcaggggcg tttgtttttc agtcgcttac actaccccca acgacaaaac ctgtcgagtc
     4741 ttcccgcaaa cccgatccat ttaccataac tcccgttgtg cgcccccctt aaaacgccct
     4801 cagtcgcttt ctgtcgcaaa aaacgcaaaa agacagggaa acaacaggcc agaccaaaaa
     4861 aacgcgccag aattgttttc agggggctgc ataactatgc acgaaagcga ttcatgtccg
     4921 gtttcactcg ttttgaacag cgaacaggtc aaaacagcaa actttctcat ccagaaaaag
     4981 gtgaactggt gcgaaatctt ttcgaactgc gtaagacgtt gagcacaaac atagtaagtc
     5041 ggtttatcgg tatgtatgga ttccattaac atatcgcctg tattaatatt tcctcgttat
     5101 tgttagaaat aaaa
//
