LOCUS       NZ_CP151307             3351 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R22.1286 plasmid pR22.1286_3.3k, complete
            sequence.
ACCESSION   NZ_CP151307
VERSION     NZ_CP151307.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122667
            Assembly: GCF_038363105.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3351)
  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  JOURNAL   Unpublished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 3351)
  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_038363105.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:39:45
            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)                     :: 5,120
            CDSs (total)                      :: 4,990
            Genes (coding)                    :: 4,358
            CDSs (with protein)               :: 4,358
            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)              :: 632
            CDSs (without protein)            :: 632
            Pseudo Genes (ambiguous residues) :: 0 of 632
            Pseudo Genes (frameshifted)       :: 173 of 632
            Pseudo Genes (incomplete)         :: 436 of 632
            Pseudo Genes (internal stop)      :: 109 of 632
            Pseudo Genes (multiple problems)  :: 83 of 632
            Pseudo Genes (short protein)      :: 3 of 632
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151307.1.
            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..3351
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R22.1286"
                     /db_xref="taxon:624"
                     /plasmid="pR22.1286_3.3k"
                     /collected_by="Taiwan CDC"
     gene            complement(32..1393)
                     /locus_tag="AADX63_RS25530"
                     /old_locus_tag="AADX63_25515"
     CDS             complement(32..1393)
                     /locus_tag="AADX63_RS25530"
                     /old_locus_tag="AADX63_25515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003030985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_341742773.1"
                     /translation="MARGKGGGSGPVDYLLGKDRQREGATVLRGDPEQVRELINSAGFS
                     RNYTSAVLSFEESSISPELRQQCMDEFERVLLPGLDADQYSALWVEHTDKGRVELNVVI
                     PNVELQSGKRLQPYYDPADRPRVDAWKTAINAEHGLADPDDPTRQRALSTSPDLPRERK
                     TLSEALTRGLMAQVGEGLIRTRKDVLEAIQSVGLEISRVTRNSISVKAPDGGKNIRLKG
                     TIYERDFEFSQELRGKIEAAGIGYRRENQSRAEAARKRLAGMLENRAEENRKRYPRTQP
                     AIEGQPVKELAWSAYRDAGGPDARRRDSVLDDDRNPQPLCGAGQVAERQSYHLWEAGTV
                     MRGDRSHSTDLWPEWRISGSERGLNEPEPDRATACPSPAGSGNGEGSFAQIIADFEERV
                     RTDTTRQQETSRTSRAIERGISGISASIEHLEAVVMQMRQEYAHRLSRGMSMSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1398..1715)
                     /locus_tag="AADX63_RS25535"
                     /old_locus_tag="AADX63_25520"
     CDS             complement(1398..1715)
                     /locus_tag="AADX63_RS25535"
                     /old_locus_tag="AADX63_25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011178376.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_013246618.1"
                     /translation="MTDAKRTKSIKIRVTDEELSELRERCPAGELAPWLRELGLGQKRP
                     RRAERVDPALLRQLAGVGNLLNQIARRINSGQWSYGDRVEILAALWHIEKRLQDININA
                     G"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2172..3035
                     /locus_tag="AADX63_RS25540"
                     /old_locus_tag="AADX63_25525"
     CDS             2172..3035
                     /locus_tag="AADX63_RS25540"
                     /old_locus_tag="AADX63_25525"
                     /inference="COORDINATES: protein motif:HMM:NF015076.4"
                     /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_077248426.1"
                     /translation="MELYQQDLFATMPFPSRPLCSDDLSHGIWRETLEDALRRPYIQAN
                     PQRRVWVLLFDVDHPLAAMAWDAAGLPPPTWTAQNPENGHAHIAYALSAPVAKSDAARL
                     KPLRLLARIQHAMTDALSADRGYVGLITKTPNHARWRTTVWRPEPYGLDELRDYLPDNL
                     ELPRHIKKTEAVGVGRNVSLFESLRHWAYSHRRNYDNHTAWFCACLSHAEALNTFATPL
                     EFNELKATAKSVAKWTWERFDVAASNARFSEKQARRGRLGGMKGAPKTNTLRQMQLIDI
                     QAGLMQ"
                     /name="replication initiation protein"
     gene            3032..3313
                     /locus_tag="AADX63_RS25545"
                     /old_locus_tag="AADX63_25530"
     CDS             3032..3313
                     /locus_tag="AADX63_RS25545"
                     /old_locus_tag="AADX63_25530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010840487.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]; GO:0016987 - sigma factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006352 - DNA-templated transcription
                     initiation [Evidence IEA]; GO:0006355 - regulation of
                     DNA-templated transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sigma factor-like helix-turn-helix DNA-binding
                     protein"
                     /protein_id="WP_050952183.1"
                     /translation="MSGIKKIARERNMTAREAAQKFGKSPRTIQRLVALDRDEYLERAA
                     ERRQKVYDMRVTGAKWQEIAEAMGVSYGAVRSLYYQHCRHLKAAMPRQ"
                     /name="sigma factor-like helix-turn-helix DNA-binding
                     protein"
     Typing          complement(36..1408)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.035"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaccgtagca aacaacgacc gtagggaggc gttagcgaga catcgacatg ccacggctga
       61 gcctgtgagc atattcctgc cgcatctgca tcaccaccgc ctccaggtgc tcaatacttg
      121 cgctaattcc tgaaattcct cgctcaattg ctcgacttgt tcgcgaagtt tcctgttgtc
      181 gcgtcgtgtc tgttcgtact cgctcttcaa agtctgcaat aatctgcgca aagcttccct
      241 ctccgtttcc acttcccgca gggcttgggc aagctgttgc tctatctggc tctggctcat
      301 tcagccccct ttcactaccc gatattcgcc attcgggcca taagtcggtg ctatgggatc
      361 tatctccacg cataaccgtc ccagcttccc acaagtggta actttggcgt tcggcaactt
      421 gtccagctcc gcatagcggt tgcggatttc ggtcgtcatc cagtacagaa tcccgcctcc
      481 tagcatcagg accgccagca tcgcgataag cgctccaagc caactcttta acaggctggc
      541 cctcaatcgc cggctgtgtt cttggatagc gctttcgatt ttcttctgct ctgttttcaa
      601 gcattccagc aaggcgcttt cgtgctgctt cagcgcggct ttgattttct cgtcggtatc
      661 cgatgcctgc tgcttcaatt tttcctcgaa gctcctggct aaattcaaaa tctcgctcat
      721 aaatcgtccc tttcagtctg atattttttc caccgtccgg tgccttcacg ctgatactgt
      781 ttctggtaac cctcgaaatt tccaatccta cgctctgtat ggcctccaga acgtcttttc
      841 gggttctaat caacccttcc cctacctgag ccattaaacc gcgtgtaaga gcttctgaga
      901 gcgttttacg ctcacgtggt aaatctgggg atgtggatag cgcacgttgc cgagtcggat
      961 catcaggatc cgcaaggcca tgttccgcgt ttatcgctgt tttccatgcg tccacccgtg
     1021 gtcggtctgc ggggtcgtaa tatggctgta agcgcttgcc gctttgtaat tcaacgttag
     1081 ggataacaac attcagttcc acacgcccct tgtctgtgtg ttccacccaa agggcactgt
     1141 actgatcagc atccagtcca ggtaagagaa ccctctcaaa ctcatccatg cactgctgac
     1201 gtaactcggg gcttatgctg gattcttcga aggacaacac cgcgctggtg tagttacgac
     1261 tgaatccggc gctgtttatc agctcccgca cctgttcagg gtcaccgcgt aacacggttg
     1321 ctccctccct ctgccgatcc ttgccgagga gataatcaac agggccggag cctccgcctt
     1381 ttcctcgtgc catgaactta accagcattg atattgatgt cctgtaatcg cttctcgatg
     1441 tgccacagcg ccgcgagaat ctctacgcga tcgccataac tccactgacc tgaattgata
     1501 cgacgggcga tctgattcag taaattacca acccccgcca actgcctcag cagcgcgggg
     1561 tccacacgtt cggctcgccg cggacgcttc tgaccaagcc caagttcacg caaccacggc
     1621 gcaagctcac cagcgggaca ccgctcccta agctcggaaa gttcctcatc ggtcacgcgg
     1681 attttgatgg atttggtgcg ctttgcatcg gtcatccggt gctcctcttt tgggggtttc
     1741 gggggcgcag cccctgaacc agccacggag gcccgaaggg gtctctgtgt gtgctggctt
     1801 actgtactta atgatggcat ggggagataa acattggaag agtgacatag ggggagcacc
     1861 gtggcgtaag tgctcaatgc agcatccggc tccctggtgc ttcctcgccc actcgctcgc
     1921 tacgctcggt cgctggggct gcggcgagca ctacctacac acacaaacaa acacaacgag
     1981 acacatcgag aggagaaaca agacggaaga actactgcgc aaaaagcaac caaaaacctg
     2041 tatatctgat tatggctcgt ttgacgtagt tgaacacata cacaaaagcg cgtaaatttc
     2101 aggcatgaaa aaccccgcaa cgggagcaac cgttcggggt cgtggcaagg actgaaaaag
     2161 gagtccccgc attggaatta taccaacaag acctgtttgc aaccatgcca tttcccagtc
     2221 gtccgctgtg ttcggacgat ctgagccacg gcatatggcg cgaaacgcta gaggacgcgc
     2281 tacggcgtcc ctacatccaa gcgaacccac aacgccgcgt gtgggttctc ctgttcgacg
     2341 ttgaccatcc cctggcggcg atggcgtggg acgcagccgg actgccgccg ccaacatgga
     2401 cggcacaaaa cccggaaaac ggacacgccc acattgctta cgcactgagc gctccggtgg
     2461 cgaagtcgga cgcggcgcgg ctcaaacccc tgcgcctact ggcacgcata cagcacgcca
     2521 tgacagacgc cctgagtgcc gacaggggct atgtcggact gattaccaag acgccaaacc
     2581 atgcccgttg gcgcaccacc gtatggcgtc ctgagccata cggcttggat gaactacgcg
     2641 actacctacc ggacaatctg gagttgccca ggcatatcaa aaaaaccgaa gcggtcggcg
     2701 tcggtcgcaa tgtgtcgctg tttgaatcac tgaggcattg ggcgtacagc caccgccgca
     2761 actacgacaa ccatacggcg tggttttgcg cctgtttgag tcatgccgaa gcgctaaaca
     2821 cctttgctac gcctttggag ttcaacgagc tgaaagccac cgccaagagc gtagccaaat
     2881 ggacatggga gcgattcgac gttgccgcca gtaatgccag attttcagaa aaacaggcgc
     2941 gccgtgggcg cttaggtggt atgaaaggag cacccaaaac aaacacctta cgacaaatgc
     3001 aattgattga tatacaagcg ggtttgatgc aatgagcgga atcaaaaaga tcgccagaga
     3061 gcgaaacatg acggcgaggg aggccgcgca aaaattcgga aaatcaccgc gcacaatcca
     3121 gcgccttgta gcgctcgatc gtgacgaata cctagaacgc gccgcggaac ggcgtcagaa
     3181 ggtctacgac atgcgcgtta ctggtgccaa atggcaggag atagccgagg caatgggcgt
     3241 cagctacggc gctgtgcgta gcctgtatta ccagcactgc cgccatctaa aagcagcgat
     3301 gccgagacaa taagcgctac ggtcaaaggt tcaagctcgc cttgtgcctt t
//
