LOCUS       NZ_CP151304             5250 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R22.1286 plasmid pR22.1286_5.2k, complete
            sequence.
ACCESSION   NZ_CP151304
VERSION     NZ_CP151304.1
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 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  JOURNAL   Unpublished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_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
            CP151304.1.
            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="R22.1286"
                     /db_xref="taxon:624"
                     /plasmid="pR22.1286_5.2k"
                     /collected_by="Taiwan CDC"
     gene            complement(729..1274)
                     /gene="ddp1"
                     /locus_tag="AADX63_RS25455"
                     /old_locus_tag="AADX63_25440"
     CDS             complement(729..1274)
                     /gene="ddp1"
                     /locus_tag="AADX63_RS25455"
                     /old_locus_tag="AADX63_25440"
                     /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(1386..1589)
                     /locus_tag="AADX63_RS25460"
                     /old_locus_tag="AADX63_25445"
     CDS             complement(1386..1589)
                     /locus_tag="AADX63_RS25460"
                     /old_locus_tag="AADX63_25445"
                     /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(1591..2667)
                     /locus_tag="AADX63_RS25465"
                     /old_locus_tag="AADX63_25450"
     CDS             complement(1591..2667)
                     /locus_tag="AADX63_RS25465"
                     /old_locus_tag="AADX63_25450"
                     /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(2681..2950)
                     /locus_tag="AADX63_RS25470"
                     /old_locus_tag="AADX63_25455"
     CDS             complement(2681..2950)
                     /locus_tag="AADX63_RS25470"
                     /old_locus_tag="AADX63_25455"
                     /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(2960..3718)
                     /locus_tag="AADX63_RS25475"
                     /old_locus_tag="AADX63_25460"
     CDS             complement(2960..3718)
                     /locus_tag="AADX63_RS25475"
                     /old_locus_tag="AADX63_25460"
                     /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(4140..4871)
                     /locus_tag="AADX63_RS25480"
                     /old_locus_tag="AADX63_25465"
     CDS             complement(4140..4871)
                     /locus_tag="AADX63_RS25480"
                     /old_locus_tag="AADX63_25465"
                     /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 atgcgtatgt gctcaactca cctacagact cacttccgct tcctcgctca ctcagtcgct
       61 acgctcctgc cgttcgactg cggcgagcgg taccacctct cgcatgttgt cggcgattcc
      121 gttgctgttc tgttcgaaaa tgcgttctgt gagccatcca gagcaccaga acgcgatttt
      181 ctggtggtgg taatggtttt cttcgtattg gcccttaaaa cgcgctcaga agctctcaga
      241 cgcacgaaac aggttttaaa tgcccgtcag ggcatggaag gcgcgaaaaa cgattacaga
      301 gcgtttcagg aggtcaggcg cgccgatacc cctaaccagg ggctttcagg aagcaggaga
      361 ccgcgccagc tccctgcaaa ggccgtttgc acaggaataa caacgatgat ctcattactg
      421 gaactgacta acgtttagac gtgacaaaac acaagctaac cgtagttgct cgtaataaat
      481 cacatctcta tggagagaga ttttttatta ttgcgcaaag tttatactat aaacagttta
      541 cagctatatc aagactgaaa tagtaacaaa tttgccagta gttccgtttc tactagacgc
      601 tccttcgact cggatgaccc cgaagcaaag aaaaaaacaa aaggataaat tcacatctcg
      661 caaagactct atcagcaaca tgtagtttat tcaacaatac aaactagatt tagttatcaa
      721 tgtggacttc atacatctac cttgtttgaa actgttctcc ccttacataa cataatgtaa
      781 ttctcaaact gatttttaag actaaaaatt tctgtcttaa gacgttccgc atcctgatag
      841 aaaccatctt tatcaagaac cctggtctga tcattaacaa tgatataatg aaagttacga
      901 ccaattttat ctatagtatt tcggcagcga ttcatcatca gcagttcctg gtcgaagaaa
      961 tcaagcctat tattcagtgt ggtttgaatc ctatatcgac attcccgtga taatgtccac
     1021 ccatgacggt tagctgcttt ttcaatatca gccctttgtt tacctgttaa gtaaagcgtg
     1081 gttttgatga aattgttttc atcagcataa tcattttgta tctggttagt ttttttgctt
     1141 ttcagcaatg cattggcaag cagtttcata ccttttgata cagtcaagcc tggttcatca
     1201 ggataaagag actttaggca gatcagcagg tcatgatgct tggcatcatc aagcctgaat
     1261 ttgatttgtt tcatatttgc acttcctaca gcacatgaat atttactccg atgcaggata
     1321 gggcaaacgc cgcaaaatgg ttccattttg gccgtttgcc cggtgaccta cagtcggttc
     1381 tttgattaag attctgcaaa aaatttaagc gtccagtata taaataatat aattaaccca
     1441 tgaataatgg ctttagattt taaatctaaa tgaccaatca atatggtttc tgcacgttca
     1501 agaaaacgga taagcacaat aaaaaatgaa ccaacagtaa tgaagccaaa tgcgattata
     1561 aaaaagatac caaagttaat atcactcata ttaaccaccg tacatttttt ttgctctctc
     1621 aatagcggcc tgacgaagtt ttttggcacc aatattaacg ccctgtccgg ccaggttagc
     1681 ggctttgccc gttattcccg gagactgtcc gaacccgcct tcctgacgac gcagaccttt
     1741 ccatgcacca ataccggcat ttctgcccat accaagtgca ccacgcgtca tacgggatgc
     1801 accgaaaatg ccagcaccaa tccccatagc ggctgcgccc tgcatggcac cttcaacacc
     1861 cacgccagca agctgtgaag cataggtttt tgcctgccag ataatccatg ccataaagat
     1921 acctgagaca agaactgtcg cacctgcttc aaataaatta ggagctgttg ctgaagataa
     1981 agtgctgctt aatgttccat tcaattgcca catacctgca cgtaacgcca gtgctgcaaa
     2041 cataaaaata agtaatgaac tgaaaataag ctgtaaccag ttattaaaca tctgacgaag
     2101 aaaaccgaac atcagacaca taataaataa cggtgctgta atagaaagga tttttaacgt
     2161 aatttctgct gaaaaaaata ctattgcaca cacgatcatt gctaaaatgc ctccggcata
     2221 agtaagcaag gccgctgcaa cacctacaac ggggattgta tctgtatcaa gatgccaaac
     2281 ctttttacca acagtaatta ctttatccca aagttgatcc atccataacc aaggatcacc
     2341 accggcgaga gtctctttta agccatctat agcttgattg gcgttatcaa gccatccccc
     2401 tgtattttta acgaacatta aaattatcga aaacctgcac aaattccaga taaaatctgg
     2461 aacaggagtt tgttgttttc ttgctaagac agtgaatgca taccataaga tatataaaga
     2521 aacaccatat ttacccagtg tataagcaat attgatataa ttatcgaaca ttcctgatgt
     2581 tgatttctca actgctctta atattatatc atgagttgct ctaaagaaat ttccatcata
     2641 tacgggataa gtattatctg tagccatata accccctcag ttattttgaa acgcctaatt
     2701 tcttatcaag ttctctggct tcttgcttgt atatttcact catcggagga taagtgtcag
     2761 cgattataag tcccgcacgt cttacgtttt tacaattatc tgagtcactt cctgttttct
     2821 tgcattcttt atatttatcg acagcttctt tcgggtgatt agtccaccaa tcgacagatt
     2881 ttgtatcttc attacatccg gtaagaataa atgataaaga tgctaaaaat accaagacga
     2941 tatatttcat aaaaacccct tatttgatca aatcaaagtc ttgtgttgaa aatgcttctc
     3001 tgtaatcaat tggttttgca ttaatttgtt catgacgaaa agaagctttc gccatttcct
     3061 ttttatattc agacagttgt ttttgtttat cgatgtacat ttgatactga aatttgagct
     3121 tctcaaactt cagttgttca agtgcaacgg cgtttgttgc atcctgcgtg gctttcgtat
     3181 ccttcgcatt tttaacctgc tcgataaggt ctttcattgt ctgattgtcc tgacgaagct
     3241 tgctctccag cttgttaccg tattccacgc ttgccagttg agaaaggaac gtcgcttcac
     3301 atccccgtac ctggtcacca gaatatccca ggttctggca ggtatccgtt accctgtaat
     3361 ctgacaataa cgatttggcc tgttccgata acgcactttc aggattttta atgtaatcgt
     3421 caataaaagc attcccctga tcataaatct gcatcagttc ctgactcact gactgtgcgg
     3481 actgcaccag tccctgcaca tcacggatac ccgtttttga cagcagctcc tgtttgtacg
     3541 catttatctg attttcgtaa tgtttcaccg tttctgccca ttgcttcaga cgttctgtcc
     3601 atcgtccggc ttcaaccgcc cattccggat tggcatcaat ggcaacaggt atccccgcct
     3661 gagcgacgga aataaccgag agcgaagcga gcaccgccga tataatgcgt ttcttcatta
     3721 ttgatctcca ctaaatataa tcctgataat tagccctctc ctttaattaa agagagggct
     3781 aacatcactt aaacataccg cgattgtatt ccttaagcca gaatttaaag ttacttacaa
     3841 taaacctcgt gcccctgcta gtaattcgga agcgacggat taaatcacta ttacgaatac
     3901 cttcattact tgtgaacaaa agatataaag aaaaagagaa agggtctttc tcaagggata
     3961 aactaaatct cgagtttcct tctttcctct tactatcaag ataagcgtaa aattctttgc
     4021 gggtttttaa ctgatattca gatatacttg ggccagccat acagcctccg aacaggttgt
     4081 tgtggttagc tggtagtgag ggtggcagcc ctcattacca gcgttaatca ttgatatgat
     4141 tagttttctt tcctaaacca gaactcaaga cgaacgactt ttctcccctt cttaataggt
     4201 ttccagtcga tcatccagtg atctttctct gttaactcct ttaccgccgg ttcaatcata
     4261 tacttacgaa gtaatccaaa cgttgtttta taactatcgg gtgattccat agcatgatga
     4321 aaatcttcta acgatatgga taaccatcca ttattttcct tgttcgtatt catttgttca
     4381 aagagttcta acaaacgcca tgaatgtact gaacgcaatg cgcaagcttg agatagctga
     4441 tacttcgtaa aattatcttc cagttcgcat aaatatggca ttacttgagg cgtaaaatgt
     4501 aaaagaacat tagcttcacc atcattatat ttatacgccc ctaaccatct aatcttccat
     4561 acatcaacat caatctcact aacttcattt aatttaaagc gaatatatct attaaagaaa
     4621 ttttccgaag cctcttttaa ttgtgaatat gcttgcttta aaggcattcc aaaggtgtta
     4681 gcatattcct gtgctgtaat ccttactggc gcatatttcc cacccatctg agcaatagct
     4741 gcaaaaatga tgcgcttttc agccaaagaa aggctttgcg cggcacgaga tatagcatta
     4801 ctcatgacaa catttttgcc acgtaaactg acagtcatcg tcattggttg gtcaacattc
     4861 ttcttggtca ttattcactc aaaagtaaga tgtacagggc aagagtaagt acgtaaatca
     4921 tacttacaaa aaatgaaaag taaaatcatt ttttactctt acagttagct gtggataatg
     4981 cccgaaaaaa cttactttta acccgaaaaa acttactttt aacccgaaaa aacttacttt
     5041 taacccgaaa aaacttactt ttaactctat aacatcatga tttcaaaaga gttttggcgt
     5101 ctaaaaaggt tttaaaaaga aaagataaaa agggtttaaa aaggaatttg cccccaaaat
     5161 ctgtggataa ccatgctcaa accaagagga cagatcacgt taagctagag ctacaatacc
     5221 taaaaacaat ccgctcgttt tttaaccgct
//
