LOCUS       NZ_CP151376             5250 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.1832 plasmid pR15.1832_5.2k, complete
            sequence.
ACCESSION   NZ_CP151376
VERSION     NZ_CP151376.1
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 5250)
  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  JOURNAL   Unpublished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 5250)
  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
            CP151376.1.
            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..5250
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R15.1832"
                     /db_xref="taxon:624"
                     /plasmid="pR15.1832_5.2k"
                     /collected_by="Taiwan CDC"
     gene            complement(649..1194)
                     /gene="ddp1"
                     /locus_tag="AADX60_RS25830"
                     /old_locus_tag="AADX60_25830"
     CDS             complement(649..1194)
                     /gene="ddp1"
                     /locus_tag="AADX60_RS25830"
                     /old_locus_tag="AADX60_25830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000757693.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_052972377.1"
                     /translation="MKQIKFRLDDAKHHDLLICLKSLYPDEPGLTVSKGMKLLANALLK
                     SKKTNQIQNDYADENNFIKTTLYLTGKQRADIEKAANRHGWTLSRECRYRIQTTLNNRL
                     DFFDQELLMMNRCRNTIDKIGRNFHYIIVNDQTRVLDKDGFYQDAERLKTEIFSLKNQF
                     ENYIMLCKGRTVSNKVDV"
                     /name="ddp1"
     gene            complement(1306..1509)
                     /locus_tag="AADX60_RS25835"
                     /old_locus_tag="AADX60_25835"
     CDS             complement(1306..1509)
                     /locus_tag="AADX60_RS25835"
                     /old_locus_tag="AADX60_25835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677232.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047662947.1"
                     /translation="MSDINFGIFFIIAFGFITVGSFFIVLIRFLERAETILIGHLDLKS
                     KAIIHGLIILFIYWTLKFFAES"
                     /name="hypothetical protein"
     gene            complement(1511..2587)
                     /locus_tag="AADX60_RS25840"
                     /old_locus_tag="AADX60_25840"
     CDS             complement(1511..2587)
                     /locus_tag="AADX60_RS25840"
                     /old_locus_tag="AADX60_25840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000513453.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_052323655.1"
                     /translation="MATDNTYPVYDGNFFRATHDIILRAVEKSTSGMFDNYINIAYTLG
                     KYGVSLYILWYAFTVLARKQQTPVPDFIWNLCRFSIILMFVKNTGGWLDNANQAIDGLK
                     ETLAGGDPWLWMDQLWDKVITVGKKVWHLDTDTIPVVGVAAALLTYAGGILAMIVCAIV
                     FFSAEITLKILSITAPLFIMCLMFGFLRQMFNNWLQLIFSSLLIFMFAALALRAGMWQL
                     NGTLSSTLSSATAPNLFEAGATVLVSGIFMAWIIWQAKTYASQLAGVGVEGAMQGAAAM
                     GIGAGIFGASRMTRGALGMGRNAGIGAWKGLRRQEGGFGQSPGITGKAANLAGQGVNIG
                     AKKLRQAAIERAKKMYGG"
                     /name="type IV secretion system protein"
     gene            complement(2601..2870)
                     /locus_tag="AADX60_RS25845"
                     /old_locus_tag="AADX60_25845"
     CDS             complement(2601..2870)
                     /locus_tag="AADX60_RS25845"
                     /old_locus_tag="AADX60_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_047662946.1"
                     /translation="MKYIVLVFLASLSFILTGCNEDTKSVDWWTNHPKEAVDKYKECKK
                     TGSDSDNCKNVRRAGLIIADTYPPMSEIYKQEARELDKKLGVSK"
                     /name="EexN family lipoprotein"
     gene            complement(2880..3638)
                     /locus_tag="AADX60_RS25850"
                     /old_locus_tag="AADX60_25850"
     CDS             complement(2880..3638)
                     /locus_tag="AADX60_RS25850"
                     /old_locus_tag="AADX60_25850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677228.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_047662945.1"
                     /translation="MKKRIISAVLASLSVISVAQAGIPVAIDANPEWAVEAGRWTERLK
                     QWAETVKHYENQINAYKQELLSKTGIRDVQGLVQSAQSVSQELMQIYDQGNAFIDDYIK
                     NPESALSEQAKSLLSDYRVTDTCQNLGYSGDQVRGCEATFLSQLASVEYGNKLESKLRQ
                     DNQTMKDLIEQVKNAKDTKATQDATNAVALEQLKFEKLKFQYQMYIDKQKQLSEYKKEM
                     AKASFRHEQINAKPIDYREAFSTQDFDLIK"
                     /name="type IV secretion system protein"
     gene            complement(4060..4791)
                     /locus_tag="AADX60_RS25855"
                     /old_locus_tag="AADX60_25855"
     CDS             complement(4060..4791)
                     /locus_tag="AADX60_RS25855"
                     /old_locus_tag="AADX60_25855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677229.1"
                     /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_021579673.1"
                     /translation="MTKKNVDQPMTMTVSLRGKNVVMSNAISRAAQSLSLAEKRIIFAA
                     IAQMGGKYAPVRITAQEYANTFGMPLKQAYSQLKEASENFFNRYIRFKLNEVSEIDVDV
                     WKIRWLGAYKYNDGEANVLLHFTPQVMPYLCELEDNFTKYQLSQACALRSVHSWRLLEL
                     FEQMNTNKENNGWLSISLEDFHHAMESPDSYKTTFGLLRKYMIEPAVKELTEKDHWMID
                     WKPIKKGRKVVRLEFWFRKEN"
                     /name="replication initiation protein"
ORIGIN
        1 cggcgagcgg taccacctct cgcatgttgt cggcgattcc gttgctgttc tgttcgaaaa
       61 tgcgttctgt gagccatcca gagcaccaga acgcgatttt ctggtggtgg taatggtttt
      121 cttcgtattg gcccttaaaa cgcgctcaga agctctcaga cgcacgaaac aggttttaaa
      181 tgcccgtcag ggcatggaag gcgcgaaaaa cgattacaga gcgtttcagg aggtcaggcg
      241 cgccgatacc cctaaccagg ggctttcagg aagcaggaga ccgcgccagc tccctgcaaa
      301 ggccgtttgc acaggaataa caacgatgat ctcattactg gaactgacta acgtttagac
      361 gtgacaaaac acaagctaac cgtagttgct cgtaataaat cacatctcta tggagagaga
      421 ttttttatta ttgcgcaaag tttatactat aaacagttta cagctatatc aagactgaaa
      481 tagtaacaaa tttgccagta gttccgtttc tactagacgc tccttcgact cggatgaccc
      541 cgaagcaaag aaaaaaacaa aaggataaat tcacatctcg caaagactct atcagcaaca
      601 tgtagtttat tcaacaatac aaactagatt tagttatcaa tgtggacttc atacatctac
      661 cttgtttgaa actgttctcc ccttacataa cataatgtaa ttctcaaact gatttttaag
      721 actaaaaatt tctgtcttaa gacgttccgc atcctgatag aaaccatctt tatcaagaac
      781 cctggtctga tcattaacaa tgatataatg aaagttacga ccaattttat ctatagtatt
      841 tcggcagcga ttcatcatca gcagttcctg gtcgaagaaa tcaagcctat tattcagtgt
      901 ggtttgaatc ctatatcgac attcccgtga taatgtccac ccatgacggt tagctgcttt
      961 ttcaatatca gccctttgtt tacctgttaa gtaaagcgtg gttttgatga aattgttttc
     1021 atcagcataa tcattttgta tctggttagt ttttttgctt ttcagcaatg cattggcaag
     1081 cagtttcata ccttttgata cagtcaagcc tggttcatca ggataaagag actttaggca
     1141 gatcagcagg tcatgatgct tggcatcatc aagcctgaat ttgatttgtt tcatatttgc
     1201 acttcctaca gcacatgaat atttactccg atgcaggata gggcaaacgc cgcaaaatgg
     1261 ttccattttg gccgtttgcc cggtgaccta cagtcggttc tttgattaag attctgcaaa
     1321 aaatttaagc gtccagtata taaataatat aattaaccca tgaataatgg ctttagattt
     1381 taaatctaaa tgaccaatca atatggtttc tgcacgttca agaaaacgga taagcacaat
     1441 aaaaaatgaa ccaacagtaa tgaagccaaa tgcgattata aaaaagatac caaagttaat
     1501 atcactcata ttaaccaccg tacatttttt ttgctctctc aatagcggcc tgacgaagtt
     1561 ttttggcacc aatattaacg ccctgtccgg ccaggttagc ggctttgccc gttattcccg
     1621 gagactgtcc gaacccgcct tcctgacgac gcagaccttt ccatgcacca ataccggcat
     1681 ttctgcccat accaagtgca ccacgcgtca tacgggatgc accgaaaatg ccagcaccaa
     1741 tccccatagc ggctgcgccc tgcatggcac cttcaacacc cacgccagca agctgtgaag
     1801 cataggtttt tgcctgccag ataatccatg ccataaagat acctgagaca agaactgtcg
     1861 cacctgcttc aaataaatta ggagctgttg ctgaagataa agtgctgctt aatgttccat
     1921 tcaattgcca catacctgca cgtaacgcca gtgctgcaaa cataaaaata agtaatgaac
     1981 tgaaaataag ctgtaaccag ttattaaaca tctgacgaag aaaaccgaac atcagacaca
     2041 taataaataa cggtgctgta atagaaagga tttttaacgt aatttctgct gaaaaaaata
     2101 ctattgcaca cacgatcatt gctaaaatgc ctccggcata agtaagcaag gccgctgcaa
     2161 cacctacaac ggggattgta tctgtatcaa gatgccaaac ctttttacca acagtaatta
     2221 ctttatccca aagttgatcc atccataacc aaggatcacc accggcgaga gtctctttta
     2281 agccatctat agcttgattg gcgttatcaa gccatccccc tgtattttta acgaacatta
     2341 aaattatcga aaacctgcac aaattccaga taaaatctgg aacaggagtt tgttgttttc
     2401 ttgctaagac agtgaatgca taccataaga tatataaaga aacaccatat ttacccagtg
     2461 tataagcaat attgatataa ttatcgaaca ttcctgatgt tgatttctca actgctctta
     2521 atattatatc atgagttgct ctaaagaaat ttccatcata tacgggataa gtattatctg
     2581 tagccatata accccctcag ttattttgaa acgcctaatt tcttatcaag ttctctggct
     2641 tcttgcttgt atatttcact catcggagga taagtgtcag cgattataag tcccgcacgt
     2701 cttacgtttt tacaattatc tgagtcactt cctgttttct tgcattcttt atatttatcg
     2761 acagcttctt tcgggtgatt agtccaccaa tcgacagatt ttgtatcttc attacatccg
     2821 gtaagaataa atgataaaga tgctaaaaat accaagacga tatatttcat aaaaacccct
     2881 tatttgatca aatcaaagtc ttgtgttgaa aatgcttctc tgtaatcaat tggttttgca
     2941 ttaatttgtt catgacgaaa agaagctttc gccatttcct ttttatattc agacagttgt
     3001 ttttgtttat cgatgtacat ttgatactga aatttgagct tctcaaactt cagttgttca
     3061 agtgcaacgg cgtttgttgc atcctgcgtg gctttcgtat ccttcgcatt tttaacctgc
     3121 tcgataaggt ctttcattgt ctgattgtcc tgacgaagct tgctctccag cttgttaccg
     3181 tattccacgc ttgccagttg agaaaggaac gtcgcttcac atccccgtac ctggtcacca
     3241 gaatatccca ggttctggca ggtatccgtt accctgtaat ctgacaataa cgatttggcc
     3301 tgttccgata acgcactttc aggattttta atgtaatcgt caataaaagc attcccctga
     3361 tcataaatct gcatcagttc ctgactcact gactgtgcgg actgcaccag tccctgcaca
     3421 tcacggatac ccgtttttga cagcagctcc tgtttgtacg catttatctg attttcgtaa
     3481 tgtttcaccg tttctgccca ttgcttcaga cgttctgtcc atcgtccggc ttcaaccgcc
     3541 cattccggat tggcatcaat ggcaacaggt atccccgcct gagcgacgga aataaccgag
     3601 agcgaagcga gcaccgccga tataatgcgt ttcttcatta ttgatctcca ctaaatataa
     3661 tcctgataat tagccctctc ctttaattaa agagagggct aacatcactt aaacataccg
     3721 cgattgtatt ccttaagcca gaatttaaag ttacttacaa taaacctcgt gcccctgcta
     3781 gtaattcgga agcgacggat taaatcacta ttacgaatac cttcattact tgtgaacaaa
     3841 agatataaag aaaaagagaa agggtctttc tcaagggata aactaaatct cgagtttcct
     3901 tctttcctct tactatcaag ataagcgtaa aattctttgc gggtttttaa ctgatattca
     3961 gatatacttg ggccagccat acagcctccg aacaggttgt tgtggttagc tggtagtgag
     4021 ggtggcagcc ctcattacca gcgttaatca ttgatatgat tagttttctt tcctaaacca
     4081 gaactcaaga cgaacgactt ttctcccctt cttaataggt ttccagtcga tcatccagtg
     4141 atctttctct gttaactcct ttaccgccgg ttcaatcata tacttacgaa gtaatccaaa
     4201 cgttgtttta taactatcgg gtgattccat agcatgatga aaatcttcta acgatatgga
     4261 taaccatcca ttattttcct tgttcgtatt catttgttca aagagttcta acaaacgcca
     4321 tgaatgtact gaacgcaatg cgcaagcttg agatagctga tacttcgtaa aattatcttc
     4381 cagttcgcat aaatatggca ttacttgagg cgtaaaatgt aaaagaacat tagcttcacc
     4441 atcattatat ttatacgccc ctaaccatct aatcttccat acatcaacat caatctcact
     4501 aacttcattt aatttaaagc gaatatatct attaaagaaa ttttccgaag cctcttttaa
     4561 ttgtgaatat gcttgcttta aaggcattcc aaaggtgtta gcatattcct gtgctgtaat
     4621 ccttactggc gcatatttcc cacccatctg agcaatagct gcaaaaatga tgcgcttttc
     4681 agccaaagaa aggctttgcg cggcacgaga tatagcatta ctcatgacaa catttttgcc
     4741 acgtaaactg acagtcatcg tcattggttg gtcaacattc ttcttggtca ttattcactc
     4801 aaaagtaaga tgtacagggc aagagtaagt acgtaaatca tacttacaaa aaatgaaaag
     4861 taaaatcatt ttttactctt acagttagct gtggataatg cccgaaaaaa cttactttta
     4921 acccgaaaaa acttactttt aacccgaaaa aacttacttt taacccgaaa aaacttactt
     4981 ttaactctat aacatcatga tttcaaaaga gttttggcgt ctaaaaaggt tttaaaaaga
     5041 aaagataaaa agggtttaaa aaggaatttg cccccaaaat ctgtggataa ccatgctcaa
     5101 accaagagga cagatcacgt taagctagag ctacaatacc taaaaacaat ccgctcgttt
     5161 tttaaccgct atgcgtatgt gctcaactca cctacagact cacttccgct tcctcgctca
     5221 ctcagtcgct acgctcctgc cgttcgactg
//
