LOCUS       NZ_CP151338             5250 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R19.2680 plasmid pR19.2680_5.2k, complete
            sequence.
ACCESSION   NZ_CP151338
VERSION     NZ_CP151338.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735797
            Assembly: GCF_038367145.1
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  JOURNAL   Unpublished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_038367145.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:32:41
            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)                     :: 5,099
            CDSs (total)                      :: 4,971
            Genes (coding)                    :: 4,342
            CDSs (with protein)               :: 4,342
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 629
            CDSs (without protein)            :: 629
            Pseudo Genes (ambiguous residues) :: 0 of 629
            Pseudo Genes (frameshifted)       :: 168 of 629
            Pseudo Genes (incomplete)         :: 437 of 629
            Pseudo Genes (internal stop)      :: 109 of 629
            Pseudo Genes (multiple problems)  :: 82 of 629
            Pseudo Genes (short protein)      :: 3 of 629
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151338.1.
            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="R19.2680"
                     /db_xref="taxon:624"
                     /plasmid="pR19.2680_5.2k"
                     /collected_by="Taiwan CDC"
     gene            complement(join(5019..5250,1..38))
                     /locus_tag="AADX56_RS25390"
                     /old_locus_tag="AADX56_25410"
     CDS             complement(join(5019..5250,1..38))
                     /locus_tag="AADX56_RS25390"
                     /old_locus_tag="AADX56_25410"
                     /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(48..806)
                     /locus_tag="AADX56_RS25395"
                     /old_locus_tag="AADX56_25415"
     CDS             complement(48..806)
                     /locus_tag="AADX56_RS25395"
                     /old_locus_tag="AADX56_25415"
                     /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(1228..1959)
                     /locus_tag="AADX56_RS25400"
                     /old_locus_tag="AADX56_25420"
     CDS             complement(1228..1959)
                     /locus_tag="AADX56_RS25400"
                     /old_locus_tag="AADX56_25420"
                     /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            complement(3067..3612)
                     /gene="ddp1"
                     /locus_tag="AADX56_RS25405"
                     /old_locus_tag="AADX56_25425"
     CDS             complement(3067..3612)
                     /gene="ddp1"
                     /locus_tag="AADX56_RS25405"
                     /old_locus_tag="AADX56_25425"
                     /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(3724..3927)
                     /locus_tag="AADX56_RS25410"
                     /old_locus_tag="AADX56_25430"
     CDS             complement(3724..3927)
                     /locus_tag="AADX56_RS25410"
                     /old_locus_tag="AADX56_25430"
                     /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(3929..5005)
                     /locus_tag="AADX56_RS25415"
                     /old_locus_tag="AADX56_25435"
     CDS             complement(3929..5005)
                     /locus_tag="AADX56_RS25415"
                     /old_locus_tag="AADX56_25435"
                     /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"
ORIGIN
        1 gataaagatg ctaaaaatac caagacgata tatttcataa aaacccctta tttgatcaaa
       61 tcaaagtctt gtgttgaaaa tgcttctctg taatcaattg gttttgcatt aatttgttca
      121 tgacgaaaag aagctttcgc catttccttt ttatattcag acagttgttt ttgtttatcg
      181 atgtacattt gatactgaaa tttgagcttc tcaaacttca gttgttcaag tgcaacggcg
      241 tttgttgcat cctgcgtggc tttcgtatcc ttcgcatttt taacctgctc gataaggtct
      301 ttcattgtct gattgtcctg acgaagcttg ctctccagct tgttaccgta ttccacgctt
      361 gccagttgag aaaggaacgt cgcttcacat ccccgtacct ggtcaccaga atatcccagg
      421 ttctggcagg tatccgttac cctgtaatct gacaataacg atttggcctg ttccgataac
      481 gcactttcag gatttttaat gtaatcgtca ataaaagcat tcccctgatc ataaatctgc
      541 atcagttcct gactcactga ctgtgcggac tgcaccagtc cctgcacatc acggataccc
      601 gtttttgaca gcagctcctg tttgtacgca tttatctgat tttcgtaatg tttcaccgtt
      661 tctgcccatt gcttcagacg ttctgtccat cgtccggctt caaccgccca ttccggattg
      721 gcatcaatgg caacaggtat ccccgcctga gcgacggaaa taaccgagag cgaagcgagc
      781 accgccgata taatgcgttt cttcattatt gatctccact aaatataatc ctgataatta
      841 gccctctcct ttaattaaag agagggctaa catcacttaa acataccgcg attgtattcc
      901 ttaagccaga atttaaagtt acttacaata aacctcgtgc ccctgctagt aattcggaag
      961 cgacggatta aatcactatt acgaatacct tcattacttg tgaacaaaag atataaagaa
     1021 aaagagaaag ggtctttctc aagggataaa ctaaatctcg agtttccttc tttcctctta
     1081 ctatcaagat aagcgtaaaa ttctttgcgg gtttttaact gatattcaga tatacttggg
     1141 ccagccatac agcctccgaa caggttgttg tggttagctg gtagtgaggg tggcagccct
     1201 cattaccagc gttaatcatt gatatgatta gttttctttc ctaaaccaga actcaagacg
     1261 aacgactttt ctccccttct taataggttt ccagtcgatc atccagtgat ctttctctgt
     1321 taactccttt accgccggtt caatcatata cttacgaagt aatccaaacg ttgttttata
     1381 actatcgggt gattccatag catgatgaaa atcttctaac gatatggata accatccatt
     1441 attttccttg ttcgtattca tttgttcaaa gagttctaac aaacgccatg aatgtactga
     1501 acgcaatgcg caagcttgag atagctgata cttcgtaaaa ttatcttcca gttcgcataa
     1561 atatggcatt acttgaggcg taaaatgtaa aagaacatta gcttcaccat cattatattt
     1621 atacgcccct aaccatctaa tcttccatac atcaacatca atctcactaa cttcatttaa
     1681 tttaaagcga atatatctat taaagaaatt ttccgaagcc tcttttaatt gtgaatatgc
     1741 ttgctttaaa ggcattccaa aggtgttagc atattcctgt gctgtaatcc ttactggcgc
     1801 atatttccca cccatctgag caatagctgc aaaaatgatg cgcttttcag ccaaagaaag
     1861 gctttgcgcg gcacgagata tagcattact catgacaaca tttttgccac gtaaactgac
     1921 agtcatcgtc attggttggt caacattctt cttggtcatt attcactcaa aagtaagatg
     1981 tacagggcaa gagtaagtac gtaaatcata cttacaaaaa atgaaaagta aaatcatttt
     2041 ttactcttac agttagctgt ggataatgcc cgaaaaaact tacttttaac ccgaaaaaac
     2101 ttacttttaa cccgaaaaaa cttactttta acccgaaaaa acttactttt aactctataa
     2161 catcatgatt tcaaaagagt tttggcgtct aaaaaggttt taaaaagaaa agataaaaag
     2221 ggtttaaaaa ggaatttgcc cccaaaatct gtggataacc atgctcaaac caagaggaca
     2281 gatcacgtta agctagagct acaataccta aaaacaatcc gctcgttttt taaccgctat
     2341 gcgtatgtgc tcaactcacc tacagactca cttccgcttc ctcgctcact cagtcgctac
     2401 gctcctgccg ttcgactgcg gcgagcggta ccacctctcg catgttgtcg gcgattccgt
     2461 tgctgttctg ttcgaaaatg cgttctgtga gccatccaga gcaccagaac gcgattttct
     2521 ggtggtggta atggttttct tcgtattggc ccttaaaacg cgctcagaag ctctcagacg
     2581 cacgaaacag gttttaaatg cccgtcaggg catggaaggc gcgaaaaacg attacagagc
     2641 gtttcaggag gtcaggcgcg ccgatacccc taaccagggg ctttcaggaa gcaggagacc
     2701 gcgccagctc cctgcaaagg ccgtttgcac aggaataaca acgatgatct cattactgga
     2761 actgactaac gtttagacgt gacaaaacac aagctaaccg tagttgctcg taataaatca
     2821 catctctatg gagagagatt ttttattatt gcgcaaagtt tatactataa acagtttaca
     2881 gctatatcaa gactgaaata gtaacaaatt tgccagtagt tccgtttcta ctagacgctc
     2941 cttcgactcg gatgaccccg aagcaaagaa aaaaacaaaa ggataaattc acatctcgca
     3001 aagactctat cagcaacatg tagtttattc aacaatacaa actagattta gttatcaatg
     3061 tggacttcat acatctacct tgtttgaaac tgttctcccc ttacataaca taatgtaatt
     3121 ctcaaactga tttttaagac taaaaatttc tgtcttaaga cgttccgcat cctgatagaa
     3181 accatcttta tcaagaaccc tggtctgatc attaacaatg atataatgaa agttacgacc
     3241 aattttatct atagtatttc ggcagcgatt catcatcagc agttcctggt cgaagaaatc
     3301 aagcctatta ttcagtgtgg tttgaatcct atatcgacat tcccgtgata atgtccaccc
     3361 atgacggtta gctgcttttt caatatcagc cctttgttta cctgttaagt aaagcgtggt
     3421 tttgatgaaa ttgttttcat cagcataatc attttgtatc tggttagttt ttttgctttt
     3481 cagcaatgca ttggcaagca gtttcatacc ttttgataca gtcaagcctg gttcatcagg
     3541 ataaagagac tttaggcaga tcagcaggtc atgatgcttg gcatcatcaa gcctgaattt
     3601 gatttgtttc atatttgcac ttcctacagc acatgaatat ttactccgat gcaggatagg
     3661 gcaaacgccg caaaatggtt ccattttggc cgtttgcccg gtgacctaca gtcggttctt
     3721 tgattaagat tctgcaaaaa atttaagcgt ccagtatata aataatataa ttaacccatg
     3781 aataatggct ttagatttta aatctaaatg accaatcaat atggtttctg cacgttcaag
     3841 aaaacggata agcacaataa aaaatgaacc aacagtaatg aagccaaatg cgattataaa
     3901 aaagatacca aagttaatat cactcatatt aaccaccgta catttttttt gctctctcaa
     3961 tagcggcctg acgaagtttt ttggcaccaa tattaacgcc ctgtccggcc aggttagcgg
     4021 ctttgcccgt tattcccgga gactgtccga acccgccttc ctgacgacgc agacctttcc
     4081 atgcaccaat accggcattt ctgcccatac caagtgcacc acgcgtcata cgggatgcac
     4141 cgaaaatgcc agcaccaatc cccatagcgg ctgcgccctg catggcacct tcaacaccca
     4201 cgccagcaag ctgtgaagca taggtttttg cctgccagat aatccatgcc ataaagatac
     4261 ctgagacaag aactgtcgca cctgcttcaa ataaattagg agctgttgct gaagataaag
     4321 tgctgcttaa tgttccattc aattgccaca tacctgcacg taacgccagt gctgcaaaca
     4381 taaaaataag taatgaactg aaaataagct gtaaccagtt attaaacatc tgacgaagaa
     4441 aaccgaacat cagacacata ataaataacg gtgctgtaat agaaaggatt tttaacgtaa
     4501 tttctgctga aaaaaatact attgcacaca cgatcattgc taaaatgcct ccggcataag
     4561 taagcaaggc cgctgcaaca cctacaacgg ggattgtatc tgtatcaaga tgccaaacct
     4621 ttttaccaac agtaattact ttatcccaaa gttgatccat ccataaccaa ggatcaccac
     4681 cggcgagagt ctcttttaag ccatctatag cttgattggc gttatcaagc catccccctg
     4741 tatttttaac gaacattaaa attatcgaaa acctgcacaa attccagata aaatctggaa
     4801 caggagtttg ttgttttctt gctaagacag tgaatgcata ccataagata tataaagaaa
     4861 caccatattt acccagtgta taagcaatat tgatataatt atcgaacatt cctgatgttg
     4921 atttctcaac tgctcttaat attatatcat gagttgctct aaagaaattt ccatcatata
     4981 cgggataagt attatctgta gccatataac cccctcagtt attttgaaac gcctaatttc
     5041 ttatcaagtt ctctggcttc ttgcttgtat atttcactca tcggaggata agtgtcagcg
     5101 attataagtc ccgcacgtct tacgttttta caattatctg agtcacttcc tgttttcttg
     5161 cattctttat atttatcgac agcttctttc gggtgattag tccaccaatc gacagatttt
     5221 gtatcttcat tacatccggt aagaataaat
//
