LOCUS       NZ_CP151395             5250 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.0423 plasmid pR15.0423_5.2k, complete
            sequence.
ACCESSION   NZ_CP151395
VERSION     NZ_CP151395.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735790
            Assembly: GCF_038367755.1
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  JOURNAL   Unpublished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_038367755.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:40:44
            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)                     :: 5,363
            CDSs (total)                      :: 5,233
            Genes (coding)                    :: 4,513
            CDSs (with protein)               :: 4,513
            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)              :: 720
            CDSs (without protein)            :: 720
            Pseudo Genes (ambiguous residues) :: 0 of 720
            Pseudo Genes (frameshifted)       :: 202 of 720
            Pseudo Genes (incomplete)         :: 517 of 720
            Pseudo Genes (internal stop)      :: 124 of 720
            Pseudo Genes (multiple problems)  :: 116 of 720
            Pseudo Genes (short protein)      :: 3 of 720
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151395.1.
            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="R15.0423"
                     /db_xref="taxon:624"
                     /plasmid="pR15.0423_5.2k"
                     /collected_by="Taiwan CDC"
     gene            1..732
                     /locus_tag="AADX55_RS26665"
                     /old_locus_tag="AADX55_26690"
     CDS             1..732
                     /locus_tag="AADX55_RS26665"
                     /old_locus_tag="AADX55_26690"
                     /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"
     gene            812..1087
                     /locus_tag="AADX55_RS26670"
     CDS             812..1087
                     /locus_tag="AADX55_RS26670"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021579672.1"
                     /translation="MAGPSISEYQLKTRKEFYAYLDSKRKEGNSRFSLSLEKDPFSFSL
                     YLLFTSNEGIRNSDLIRRFRITSRGTRFIVSNFKFWLKEYNRGMFK"
                     /name="hypothetical protein"
     gene            1154..1912
                     /locus_tag="AADX55_RS26675"
                     /old_locus_tag="AADX55_26695"
     CDS             1154..1912
                     /locus_tag="AADX55_RS26675"
                     /old_locus_tag="AADX55_26695"
                     /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            1922..2191
                     /locus_tag="AADX55_RS26680"
                     /old_locus_tag="AADX55_26700"
     CDS             1922..2191
                     /locus_tag="AADX55_RS26680"
                     /old_locus_tag="AADX55_26700"
                     /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            2205..3281
                     /locus_tag="AADX55_RS26685"
                     /old_locus_tag="AADX55_26705"
     CDS             2205..3281
                     /locus_tag="AADX55_RS26685"
                     /old_locus_tag="AADX55_26705"
                     /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            3283..3486
                     /locus_tag="AADX55_RS26690"
                     /old_locus_tag="AADX55_26710"
     CDS             3283..3486
                     /locus_tag="AADX55_RS26690"
                     /old_locus_tag="AADX55_26710"
                     /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            3598..4143
                     /gene="ddp1"
                     /locus_tag="AADX55_RS26695"
                     /old_locus_tag="AADX55_26715"
     CDS             3598..4143
                     /gene="ddp1"
                     /locus_tag="AADX55_RS26695"
                     /old_locus_tag="AADX55_26715"
                     /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"
ORIGIN
        1 atgaccaaga agaatgttga ccaaccaatg acgatgactg tcagtttacg tggcaaaaat
       61 gttgtcatga gtaatgctat atctcgtgcc gcgcaaagcc tttctttggc tgaaaagcgc
      121 atcatttttg cagctattgc tcagatgggt gggaaatatg cgccagtaag gattacagca
      181 caggaatatg ctaacacctt tggaatgcct ttaaagcaag catattcaca attaaaagag
      241 gcttcggaaa atttctttaa tagatatatt cgctttaaat taaatgaagt tagtgagatt
      301 gatgttgatg tatggaagat tagatggtta ggggcgtata aatataatga tggtgaagct
      361 aatgttcttt tacattttac gcctcaagta atgccatatt tatgcgaact ggaagataat
      421 tttacgaagt atcagctatc tcaagcttgc gcattgcgtt cagtacattc atggcgtttg
      481 ttagaactct ttgaacaaat gaatacgaac aaggaaaata atggatggtt atccatatcg
      541 ttagaagatt ttcatcatgc tatggaatca cccgatagtt ataaaacaac gtttggatta
      601 cttcgtaagt atatgattga accggcggta aaggagttaa cagagaaaga tcactggatg
      661 atcgactgga aacctattaa gaaggggaga aaagtcgttc gtcttgagtt ctggtttagg
      721 aaagaaaact aatcatatca atgattaacg ctggtaatga gggctgccac cctcactacc
      781 agctaaccac aacaacctgt tcggaggctg tatggctggc ccaagtatat ctgaatatca
      841 gttaaaaacc cgcaaagaat tttacgctta tcttgatagt aagaggaaag aaggaaactc
      901 gagatttagt ttatcccttg agaaagaccc tttctctttt tctttatatc ttttgttcac
      961 aagtaatgaa ggtattcgta atagtgattt aatccgtcgc ttccgaatta ctagcagggg
     1021 cacgaggttt attgtaagta actttaaatt ctggcttaag gaatacaatc gcggtatgtt
     1081 taagtgatgt tagccctctc tttaattaaa ggagagggct aattatcagg attatattta
     1141 gtggagatca ataatgaaga aacgcattat atcggcggtg ctcgcttcgc tctcggttat
     1201 ttccgtcgct caggcgggga tacctgttgc cattgatgcc aatccggaat gggcggttga
     1261 agccggacga tggacagaac gtctgaagca atgggcagaa acggtgaaac attacgaaaa
     1321 tcagataaat gcgtacaaac aggagctgct gtcaaaaacg ggtatccgtg atgtgcaggg
     1381 actggtgcag tccgcacagt cagtgagtca ggaactgatg cagatttatg atcaggggaa
     1441 tgcttttatt gacgattaca ttaaaaatcc tgaaagtgcg ttatcggaac aggccaaatc
     1501 gttattgtca gattacaggg taacggatac ctgccagaac ctgggatatt ctggtgacca
     1561 ggtacgggga tgtgaagcga cgttcctttc tcaactggca agcgtggaat acggtaacaa
     1621 gctggagagc aagcttcgtc aggacaatca gacaatgaaa gaccttatcg agcaggttaa
     1681 aaatgcgaag gatacgaaag ccacgcagga tgcaacaaac gccgttgcac ttgaacaact
     1741 gaagtttgag aagctcaaat ttcagtatca aatgtacatc gataaacaaa aacaactgtc
     1801 tgaatataaa aaggaaatgg cgaaagcttc ttttcgtcat gaacaaatta atgcaaaacc
     1861 aattgattac agagaagcat tttcaacaca agactttgat ttgatcaaat aaggggtttt
     1921 tatgaaatat atcgtcttgg tatttttagc atctttatca tttattctta ccggatgtaa
     1981 tgaagataca aaatctgtcg attggtggac taatcacccg aaagaagctg tcgataaata
     2041 taaagaatgc aagaaaacag gaagtgactc agataattgt aaaaacgtaa gacgtgcggg
     2101 acttataatc gctgacactt atcctccgat gagtgaaata tacaagcaag aagccagaga
     2161 acttgataag aaattaggcg tttcaaaata actgaggggg ttatatggct acagataata
     2221 cttatcccgt atatgatgga aatttcttta gagcaactca tgatataata ttaagagcag
     2281 ttgagaaatc aacatcagga atgttcgata attatatcaa tattgcttat acactgggta
     2341 aatatggtgt ttctttatat atcttatggt atgcattcac tgtcttagca agaaaacaac
     2401 aaactcctgt tccagatttt atctggaatt tgtgcaggtt ttcgataatt ttaatgttcg
     2461 ttaaaaatac agggggatgg cttgataacg ccaatcaagc tatagatggc ttaaaagaga
     2521 ctctcgccgg tggtgatcct tggttatgga tggatcaact ttgggataaa gtaattactg
     2581 ttggtaaaaa ggtttggcat cttgatacag atacaatccc cgttgtaggt gttgcagcgg
     2641 ccttgcttac ttatgccgga ggcattttag caatgatcgt gtgtgcaata gtattttttt
     2701 cagcagaaat tacgttaaaa atcctttcta ttacagcacc gttatttatt atgtgtctga
     2761 tgttcggttt tcttcgtcag atgtttaata actggttaca gcttattttc agttcattac
     2821 ttatttttat gtttgcagca ctggcgttac gtgcaggtat gtggcaattg aatggaacat
     2881 taagcagcac tttatcttca gcaacagctc ctaatttatt tgaagcaggt gcgacagttc
     2941 ttgtctcagg tatctttatg gcatggatta tctggcaggc aaaaacctat gcttcacagc
     3001 ttgctggcgt gggtgttgaa ggtgccatgc agggcgcagc cgctatgggg attggtgctg
     3061 gcattttcgg tgcatcccgt atgacgcgtg gtgcacttgg tatgggcaga aatgccggta
     3121 ttggtgcatg gaaaggtctg cgtcgtcagg aaggcgggtt cggacagtct ccgggaataa
     3181 cgggcaaagc cgctaacctg gccggacagg gcgttaatat tggtgccaaa aaacttcgtc
     3241 aggccgctat tgagagagca aaaaaaatgt acggtggtta atatgagtga tattaacttt
     3301 ggtatctttt ttataatcgc atttggcttc attactgttg gttcattttt tattgtgctt
     3361 atccgttttc ttgaacgtgc agaaaccata ttgattggtc atttagattt aaaatctaaa
     3421 gccattattc atgggttaat tatattattt atatactgga cgcttaaatt ttttgcagaa
     3481 tcttaatcaa agaaccgact gtaggtcacc gggcaaacgg ccaaaatgga accattttgc
     3541 ggcgtttgcc ctatcctgca tcggagtaaa tattcatgtg ctgtaggaag tgcaaatatg
     3601 aaacaaatca aattcaggct tgatgatgcc aagcatcatg acctgctgat ctgcctaaag
     3661 tctctttatc ctgatgaacc aggcttgact gtatcaaaag gtatgaaact gcttgccaat
     3721 gcattgctga aaagcaaaaa aactaaccag atacaaaatg attatgctga tgaaaacaat
     3781 ttcatcaaaa ccacgcttta cttaacaggt aaacaaaggg ctgatattga aaaagcagct
     3841 aaccgtcatg ggtggacatt atcacgggaa tgtcgatata ggattcaaac cacactgaat
     3901 aataggcttg atttcttcga ccaggaactg ctgatgatga atcgctgccg aaatactata
     3961 gataaaattg gtcgtaactt tcattatatc attgttaatg atcagaccag ggttcttgat
     4021 aaagatggtt tctatcagga tgcggaacgt cttaagacag aaatttttag tcttaaaaat
     4081 cagtttgaga attacattat gttatgtaag gggagaacag tttcaaacaa ggtagatgta
     4141 tgaagtccac attgataact aaatctagtt tgtattgttg aataaactac atgttgctga
     4201 tagagtcttt gcgagatgtg aatttatcct tttgtttttt tctttgcttc ggggtcatcc
     4261 gagtcgaagg agcgtctagt agaaacggaa ctactggcaa atttgttact atttcagtct
     4321 tgatatagct gtaaactgtt tatagtataa actttgcgca ataataaaaa atctctctcc
     4381 atagagatgt gatttattac gagcaactac ggttagcttg tgttttgtca cgtctaaacg
     4441 ttagtcagtt ccagtaatga gatcatcgtt gttattcctg tgcaaacggc ctttgcaggg
     4501 agctggcgcg gtctcctgct tcctgaaagc ccctggttag gggtatcggc gcgcctgacc
     4561 tcctgaaacg ctctgtaatc gtttttcgcg ccttccatgc cctgacgggc atttaaaacc
     4621 tgtttcgtgc gtctgagagc ttctgagcgc gttttaaggg ccaatacgaa gaaaaccatt
     4681 accaccacca gaaaatcgcg ttctggtgct ctggatggct cacagaacgc attttcgaac
     4741 agaacagcaa cggaatcgcc gacaacatgc gagaggtggt accgctcgcc gcagtcgaac
     4801 ggcaggagcg tagcgactga gtgagcgagg aagcggaagt gagtctgtag gtgagttgag
     4861 cacatacgca tagcggttaa aaaacgagcg gattgttttt aggtattgta gctctagctt
     4921 aacgtgatct gtcctcttgg tttgagcatg gttatccaca gattttgggg gcaaattcct
     4981 ttttaaaccc tttttatctt ttctttttaa aaccttttta gacgccaaaa ctcttttgaa
     5041 atcatgatgt tatagagtta aaagtaagtt ttttcgggtt aaaagtaagt tttttcgggt
     5101 taaaagtaag ttttttcggg ttaaaagtaa gttttttcgg gcattatcca cagctaactg
     5161 taagagtaaa aaatgatttt acttttcatt ttttgtaagt atgatttacg tacttactct
     5221 tgccctgtac atcttacttt tgagtgaata
//
