LOCUS       NZ_CP151379             3351 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.1832 plasmid pR15.1832_3k, complete
            sequence.
ACCESSION   NZ_CP151379
VERSION     NZ_CP151379.1
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 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  JOURNAL   Unpublished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_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
            CP151379.1.
            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="R15.1832"
                     /db_xref="taxon:624"
                     /plasmid="pR15.1832_3k"
                     /collected_by="Taiwan CDC"
     gene            1..318
                     /locus_tag="AADX60_RS25905"
                     /old_locus_tag="AADX60_25905"
     CDS             1..318
                     /locus_tag="AADX60_RS25905"
                     /old_locus_tag="AADX60_25905"
                     /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            323..1684
                     /locus_tag="AADX60_RS25910"
                     /old_locus_tag="AADX60_25910"
     CDS             323..1684
                     /locus_tag="AADX60_RS25910"
                     /old_locus_tag="AADX60_25910"
                     /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(1754..2035)
                     /locus_tag="AADX60_RS25915"
                     /old_locus_tag="AADX60_25915"
     CDS             complement(1754..2035)
                     /locus_tag="AADX60_RS25915"
                     /old_locus_tag="AADX60_25915"
                     /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"
     gene            complement(2032..2895)
                     /locus_tag="AADX60_RS25920"
                     /old_locus_tag="AADX60_25920"
     CDS             complement(2032..2895)
                     /locus_tag="AADX60_RS25920"
                     /old_locus_tag="AADX60_25920"
                     /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"
     Typing          309..1681
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.035"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaccgatg caaagcgcac caaatccatc aaaatccgcg tgaccgatga ggaactttcc
       61 gagcttaggg agcggtgtcc cgctggtgag cttgcgccgt ggttgcgtga acttgggctt
      121 ggtcagaagc gtccgcggcg agccgaacgt gtggaccccg cgctgctgag gcagttggcg
      181 ggggttggta atttactgaa tcagatcgcc cgtcgtatca attcaggtca gtggagttat
      241 ggcgatcgcg tagagattct cgcggcgctg tggcacatcg agaagcgatt acaggacatc
      301 aatatcaatg ctggttaagt tcatggcacg aggaaaaggc ggaggctccg gccctgttga
      361 ttatctcctc ggcaaggatc ggcagaggga gggagcaacc gtgttacgcg gtgaccctga
      421 acaggtgcgg gagctgataa acagcgccgg attcagtcgt aactacacca gcgcggtgtt
      481 gtccttcgaa gaatccagca taagccccga gttacgtcag cagtgcatgg atgagtttga
      541 gagggttctc ttacctggac tggatgctga tcagtacagt gccctttggg tggaacacac
      601 agacaagggg cgtgtggaac tgaatgttgt tatccctaac gttgaattac aaagcggcaa
      661 gcgcttacag ccatattacg accccgcaga ccgaccacgg gtggacgcat ggaaaacagc
      721 gataaacgcg gaacatggcc ttgcggatcc tgatgatccg actcggcaac gtgcgctatc
      781 cacatcccca gatttaccac gtgagcgtaa aacgctctca gaagctctta cacgcggttt
      841 aatggctcag gtaggggaag ggttgattag aacccgaaaa gacgttctgg aggccataca
      901 gagcgtagga ttggaaattt cgagggttac cagaaacagt atcagcgtga aggcaccgga
      961 cggtggaaaa aatatcagac tgaaagggac gatttatgag cgagattttg aatttagcca
     1021 ggagcttcga ggaaaaattg aagcagcagg catcggatac cgacgagaaa atcaaagccg
     1081 cgctgaagca gcacgaaagc gccttgctgg aatgcttgaa aacagagcag aagaaaatcg
     1141 aaagcgctat ccaagaacac agccggcgat tgagggccag cctgttaaag agttggcttg
     1201 gagcgcttat cgcgatgctg gcggtcctga tgctaggagg cgggattctg tactggatga
     1261 cgaccgaaat ccgcaaccgc tatgcggagc tggacaagtt gccgaacgcc aaagttacca
     1321 cttgtgggaa gctgggacgg ttatgcgtgg agatagatcc catagcaccg acttatggcc
     1381 cgaatggcga atatcgggta gtgaaagggg gctgaatgag ccagagccag atagagcaac
     1441 agcttgccca agccctgcgg gaagtggaaa cggagaggga agctttgcgc agattattgc
     1501 agactttgaa gagcgagtac gaacagacac gacgcgacaa caggaaactt cgcgaacaag
     1561 tcgagcaatt gagcgaggaa tttcaggaat tagcgcaagt attgagcacc tggaggcggt
     1621 ggtgatgcag atgcggcagg aatatgctca caggctcagc cgtggcatgt cgatgtctcg
     1681 ctaacgcctc cctacggtcg ttgtttgcta cggtcaaagg cacaaggcga gcttgaacct
     1741 ttgaccgtag cgcttattgt ctcggcatcg ctgcttttag atggcggcag tgctggtaat
     1801 acaggctacg cacagcgccg tagctgacgc ccattgcctc ggctatctcc tgccatttgg
     1861 caccagtaac gcgcatgtcg tagaccttct gacgccgttc cgcggcgcgt tctaggtatt
     1921 cgtcacgatc gagcgctaca aggcgctgga ttgtgcgcgg tgattttccg aatttttgcg
     1981 cggcctccct cgccgtcatg tttcgctctc tggcgatctt tttgattccg ctcattgcat
     2041 caaacccgct tgtatatcaa tcaattgcat ttgtcgtaag gtgtttgttt tgggtgctcc
     2101 tttcatacca cctaagcgcc cacggcgcgc ctgtttttct gaaaatctgg cattactggc
     2161 ggcaacgtcg aatcgctccc atgtccattt ggctacgctc ttggcggtgg ctttcagctc
     2221 gttgaactcc aaaggcgtag caaaggtgtt tagcgcttcg gcatgactca aacaggcgca
     2281 aaaccacgcc gtatggttgt cgtagttgcg gcggtggctg tacgcccaat gcctcagtga
     2341 ttcaaacagc gacacattgc gaccgacgcc gaccgcttcg gtttttttga tatgcctggg
     2401 caactccaga ttgtccggta ggtagtcgcg tagttcatcc aagccgtatg gctcaggacg
     2461 ccatacggtg gtgcgccaac gggcatggtt tggcgtcttg gtaatcagtc cgacatagcc
     2521 cctgtcggca ctcagggcgt ctgtcatggc gtgctgtatg cgtgccagta ggcgcagggg
     2581 tttgagccgc gccgcgtccg acttcgccac cggagcgctc agtgcgtaag caatgtgggc
     2641 gtgtccgttt tccgggtttt gtgccgtcca tgttggcggc ggcagtccgg ctgcgtccca
     2701 cgccatcgcc gccaggggat ggtcaacgtc gaacaggaga acccacacgc ggcgttgtgg
     2761 gttcgcttgg atgtagggac gccgtagcgc gtcctctagc gtttcgcgcc atatgccgtg
     2821 gctcagatcg tccgaacaca gcggacgact gggaaatggc atggttgcaa acaggtcttg
     2881 ttggtataat tccaatgcgg ggactccttt ttcagtcctt gccacgaccc cgaacggttg
     2941 ctcccgttgc ggggtttttc atgcctgaaa tttacgcgct tttgtgtatg tgttcaacta
     3001 cgtcaaacga gccataatca gatatacagg tttttggttg ctttttgcgc agtagttctt
     3061 ccgtcttgtt tctcctctcg atgtgtctcg ttgtgtttgt ttgtgtgtgt aggtagtgct
     3121 cgccgcagcc ccagcgaccg agcgtagcga gcgagtgggc gaggaagcac cagggagccg
     3181 gatgctgcat tgagcactta cgccacggtg ctccccctat gtcactcttc caatgtttat
     3241 ctccccatgc catcattaag tacagtaagc cagcacacac cgagacccct tcgggcctcc
     3301 gtggctggtt caggggctgc gcccccgaaa cccccaaaag aggagcaccg g
//
