LOCUS       NZ_CP152301             5538 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Shigella sonnei strain R16.0823 plasmid pR16.0823_5.5k, complete
            sequence.
ACCESSION   NZ_CP152301
VERSION     NZ_CP152301.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123227
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5538)
  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  JOURNAL   Unpublished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 5538)
  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_039684335.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 12:02:37
            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)                     :: 8
            CDSs (total)                      :: 8
            Genes (coding)                    :: 7
            CDSs (with protein)               :: 7
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP152301.1.
            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..5538
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R16.0823"
                     /db_xref="taxon:624"
                     /plasmid="pR16.0823_5.5k"
                     /collected_by="Taiwan CDC"
     gene            complement(455..751)
                     /locus_tag="V8Z64_RS00005"
     CDS             complement(455..751)
                     /locus_tag="V8Z64_RS00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001555328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_013188527.1"
                     /translation="MQQIDSCIETTINRLSSEAGTMVSNFYLDLRSPGRQRITEKLVEQ
                     SIDLCRSRGIYAEREGNGLLVRVDLRTCYLNPGQAEMFNIAIGYTRSVHGNHL"
                     /name="hypothetical protein"
     gene            978..1514
                     /locus_tag="V8Z64_RS00010"
                     /old_locus_tag="V8Z64_25165"
     CDS             978..1514
                     /locus_tag="V8Z64_RS00010"
                     /old_locus_tag="V8Z64_25165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001555327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654319.1"
                     /translation="MKDNKAVVVFTGKDLNIMRAEGGSGYWLAKAERLNDAKYLIAVRN
                     RRETWAVKDLEHGTGFLIAKITGCFKNPDYDDRNVITFEEYAEISVKKAWKMLTGGQRY
                     PVAYLTAEEAFSRIGITLEQLEWKKLQTSTLSQPIPSAEAPKKLSLNEAVERAKQDISN
                     ATDIDVSSITITINI"
                     /name="hypothetical protein"
     gene            1570..2394
                     /locus_tag="V8Z64_RS00015"
                     /old_locus_tag="V8Z64_25170"
     CDS             1570..2394
                     /locus_tag="V8Z64_RS00015"
                     /old_locus_tag="V8Z64_25170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000213997.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000213997.1"
                     /translation="MTTTIYREFEFAACDSKWSVDGHLRRDVIEKKAIHIDFKGKEAIS
                     LMCGDHPMIVLMQAMQLKVITPEQYASLMSLYMDVEDFTFGMVVLDKHSGAILVGMYTP
                     PMIAIKSKQIVYDLGSTGGEFAAHCLYYAEKRLRKKKRHRGYSTSSVGCKITSAVKYAY
                     RRDRYSGGKVYKIIWKNNGIMYNNIPLSNNSVKNHYRRILKETLKIIHSRYEEKINMRQ
                     NAQLNTAAASLSQTGQPKTQSQPHNQAPSASADKSHQMTMSRAINYARLFSD"
                     /name="hypothetical protein"
     gene            complement(2963..3196)
                     /locus_tag="V8Z64_RS00020"
                     /old_locus_tag="V8Z64_25173"
     CDS             complement(2963..3196)
                     /locus_tag="V8Z64_RS00020"
                     /old_locus_tag="V8Z64_25173"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3203..3721)
                     /locus_tag="V8Z64_RS00025"
                     /old_locus_tag="V8Z64_25175"
     CDS             complement(3203..3721)
                     /locus_tag="V8Z64_RS00025"
                     /old_locus_tag="V8Z64_25175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015059036.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3759..4421)
                     /locus_tag="V8Z64_RS00030"
                     /old_locus_tag="V8Z64_25180"
                     /pseudo=""
     CDS             complement(<3759..4421)
                     /locus_tag="V8Z64_RS00030"
                     /old_locus_tag="V8Z64_25180"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4399..4722)
                     /locus_tag="V8Z64_RS00035"
                     /old_locus_tag="V8Z64_25182"
     CDS             complement(4399..4722)
                     /locus_tag="V8Z64_RS00035"
                     /old_locus_tag="V8Z64_25182"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_024185675.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLSEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAVLMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4787..4978
                     /locus_tag="V8Z64_RS00040"
                     /old_locus_tag="V8Z64_25183"
     CDS             4787..4978
                     /locus_tag="V8Z64_RS00040"
                     /old_locus_tag="V8Z64_25183"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(5071..5152)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="95.0"
                     /evalue="1.44e-35"
     Typing          complement(3..201)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="99.0"
                     /evalue="8.38e-87"
     Typing          5178..5532
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.365"
                     /coverage="96.0"
                     /evalue="4.01e-134"
     Typing          complement(2860..4409)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca
       61 cgctgttggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
      121 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcaacttga gtccaacccg
      181 gaaagacacg acaaaacgcc actggcagcg gccattggta aacaggatgt gcgagagatg
      241 tatcgagagt tcttgaagtg gtgcccttag tgcggctaca ctggaaggac agatttggtg
      301 gcatgtctcg cacaagactg ttaccacggt tagagaatct gccaggatta actaaccttc
      361 gaaaaaccac ctgccagggt ggttttttcg ttttcagagc tagagattac gcgtagaaaa
      421 aaaggatctc aagaagatcc tttttgtaga tagcttatag atgattcccg tgaactgaac
      481 gcgtatatcc aatagctata ttaaacattt cagcttgacc tggattcaga tagcacgttc
      541 tcagatctac tctcacaagc aacccattac cttcccgctc agcatagata ccacgagacc
      601 tgcaaagatc tattgattgc tctaccagct tttcagtaat gcgctgtcta ccgggagagc
      661 gcaggtcaag atagaaatta ctaaccatcg taccagcttc gctagaaaga cgattgatgg
      721 tcgtttcaat acatgaatct atttgctgca tagatatcga catataaccc ccaaaaagaa
      781 taacatcaaa ataagataca cataaaaaaa tataaaatca aataaaaaca acttaagcac
      841 aaaataagca aaaataagaa agagataagc acagaatttg taggcttgct tttatcgcat
      901 aaataaaacc acacccctaa tttaatcgta tataattaaa atcatgacga taaaaaacta
      961 aagcatggga tttctatatg aaagataata aagcagttgt cgtatttaca ggcaaagatc
     1021 taaacataat gagagctgag ggaggttcag gttattggct agcaaaagca gaacggctta
     1081 atgacgccaa atatctcatc gcagtaagaa accggagaga aacatgggcg gtgaaagacc
     1141 tcgaacacgg aactggcttt ctgattgcaa agatcaccgg atgctttaaa aaccctgatt
     1201 acgacgacag aaacgtaatt acatttgagg aatatgctga aatttcagtg aaaaaggcat
     1261 ggaaaatgct aactggcggt cagcgttatc cggttgctta tctgacagca gaggaagctt
     1321 tttcccgtat agggataacg ctagagcagc tggagtggaa aaaactccag acttcaacac
     1381 tatctcagcc aatcccctct gcagaagcgc cgaaaaaact aagcctcaac gaggcagttg
     1441 aaagagctaa gcaagatata agcaatgcaa ctgatatcga tgtatcttct attacgataa
     1501 ctatcaacat ctgatttttt cgtatatctg gtatcttaac gatagtcgaa aaagaattaa
     1561 gccattgata tgacaacaac aatatacaga gagtttgaat ttgctgcttg tgatagcaaa
     1621 tggtcagttg atggacatct tcgaagagat gttattgaaa aaaaagcaat acatatagat
     1681 ttcaaaggaa aagaagcaat atcccttatg tgtggtgatc atccgatgat cgtccttatg
     1741 caagctatgc agctgaaagt cataactcca gagcagtacg ctagcttaat gagtctctac
     1801 atggatgtag aagacttcac cttcggcatg gtggtcctcg ataaacactc aggtgctata
     1861 ttagtaggta tgtatacccc cccgatgatt gcgataaaaa gcaaacaaat agtttacgat
     1921 ttaggttcaa ctggcggcga atttgcagca cattgtctct actatgcgga aaaaaggctt
     1981 agaaaaaaaa agcgtcatcg tggatactct acatcgtcag tgggatgtaa gatcaccagc
     2041 gctgtcaaat atgcatacag acgagatcgc tactccggtg gtaaagtata caaaatcatt
     2101 tggaaaaata acggcatcat gtacaacaac ataccgttat ctaacaactc ggtaaaaaac
     2161 cattaccggc ggattttaaa agaaacatta aagatcattc atagcaggta cgaagagaaa
     2221 ataaacatga gacagaatgc ccagttaaat acagcggcag cctcgctctc tcagacgggt
     2281 cagccgaaaa cacaaagtca gccacataac caagcaccta gtgcgagtgc tgataaaagc
     2341 catcagatga ctatgtctcg agccattaac tatgctcgcc ttttttctga ctgatactgt
     2401 acagctagat ttaccataat cccttattgc gtgcaccgca gaaacgcgtt cggtgcgatc
     2461 acggcagcag acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcaccc
     2521 gataaatttt aaccacatgc atagctatgc agccatgtga atcacgcagg aattgccagc
     2581 cagagactgc tgaaacggat ttttttcata ctttcggaaa ggcagaagac ggaaccggag
     2641 cggaaaaaca gaagttcagg ggaatgagcg cgatctggca atagaggcaa aacacagcaa
     2701 caaaagacac accagaatcg cgcccgtatg cgttttaacg cgttcctgtg ttttcagcaa
     2761 ggtctgactg aagcgcgttc ccggtgcccc cgaaccaacc attatcccaa aaaatgcacc
     2821 ggaaacgcgc tgacaacatt ttagcctgtc tctgattacc atcccagcga agggccatcc
     2881 agtgtgcgtt cctgtatttc cggctggcgc tcacgctcca gggataacgc atgttcgcgc
     2941 tcctgtatca gccgttcgtc ccttatctcc tgttctcgct gtataactgg ctcaagcgtt
     3001 ctgtccgctc gctcaagtgc tgcacctgct gactcaactg catgacctgc tcgttcagca
     3061 tcgcgttgtc ccgttgcgta agcgaaaaca ttttctgcaa ttccacgaag gcgctctccc
     3121 attcgctcag ccgctgcata tagtcctgtt gcagttgctc taatgcgttc agcaaatgtc
     3181 tttccagctc cgtcactctg tgtcactccg tcagttgtac ccagtccttc ccctgatagg
     3241 gaatcaccgt tgccgatttc ccgtacggaa ggaccagaaa tttccttctc ccgtcctgca
     3301 caaactccac gccccatgtc ttcgcgttca gtttctgcaa tgtttcttcc tgtatcctga
     3361 tttcttccag gttcgcctgt atccgcccgc caagatacca gagcgtcccg ccactcgcgg
     3421 taaacaggag aaagactatc cccagcaacc tcatgcccgt attccctgcc agctttaaca
     3481 cgtccttcct gtgctgcatc atcgcctctt tcaccccttc ccggtgtttt tccagcgatt
     3541 cctctgtcga cgttgtgaac agggctatag cgtctttgat tttcgtctcg tttgaggtca
     3601 cagccttgct tacagatttt tcgagcttgc tgaactcgtc gttcagcatt gtctctgtag
     3661 attcggctct ctctttcagc tttttctcga actccgcgcc cgtctgtaaa agattgctca
     3721 taaaatgctc ctttcagcct gatattcttc ccgccgttcg ggtctgcaat gctgatactg
     3781 cttcgcgtca ccctgacaac ttcaagcccc gcctctgtga gcgcctgaat cacatcctga
     3841 cggcctttta tctccccgac atgataaaga gcgtctatcc cccgtgtaac gctctcagca
     3901 agcgcctgtt tcgtttccgg caggttatca gagagagtca gtatccggcg gttctccggg
     3961 gcgttggggt catgcagccc gtaatggtga ttcaccagcg tctgccaggc atcaattctc
     4021 ggcctgtctg cccggtcgta gtacggctgg aggcgttttc cgctctgtag ctccatgttc
     4081 ggaatgacaa aattaagctc aagccgtccc ttgtcctggt gctccaccca caggatgctg
     4141 tactgattct tttcgagacc gggcatcagt acgcgctcaa agctcgccat cactttttca
     4201 cgtcctcccg gcggcagcac cttctccgcg aacgacagaa cacctgacgt gtatttcttc
     4261 gcaaatggcg tggcatcgat gagttcccgg acttcttccg gattaccctg aagcaccgtt
     4321 gccccttccc ggttacgctc ccttcccagc aggtaatcaa ccggaccact gccaccacct
     4381 tttcccctgg catgaaactt aactatcatc ccgcgctcca tgttccctga cgacctgccg
     4441 taagctgcgc aactctctct cgatggccat cagtacggcc accacctgaa cccggtcacc
     4501 ggaagaccac tgcccgctgt tcaccttcct cgccgtctga ttcaggttat tcccgatggc
     4561 agccagctgg cgcagtaacg gcggtgccag tgtcggcagc ttcccggaac gggcaaccgg
     4621 ctcactcagg cagacccgcc gcatccatac cgccagttgt ttaccctcac aacgttccag
     4681 caaacgggca tgttcatcat cagtaacccg tatcgtgagc attctctcgc gtttcatcgg
     4741 tatcattacc cccatgaaca gaaatccccc ttacacggag gcatcagtga ctaaacagga
     4801 aaaaaccgcc cttaacatgg cccgctttat cagaagccag acattaacgc tgctggagaa
     4861 actcaacgaa ctggacgcag atgaacaggc cgatatttgt gaatcacttc acgaccacgc
     4921 cgacgagctt taccgcagct gcctcgcacg cttcggggat gacggtgaaa acctctgaca
     4981 catacagctc ccggagacgg tcactgcttg tctgtgagcg gatgccggga gcagacaagc
     5041 ccgtcagggc gcgtcaggcc gttgaccttg cgggtgtcgg ggcgcagcca tgacccagtc
     5101 acgtagcgat agcggagtgt atactggctt aaccatgcgg catcagtgca gattataaga
     5161 aaagagcacc atatgcggtg tgaaatgccg cacagatgcg taaggagaaa ataccgcatc
     5221 tggcgctctt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg gctgcggcga
     5281 gcggagtcgg ctcactcaaa ggcggtaata cggttatcca cagaatcagg ggataaggcc
     5341 ggaaagaaca tgtgagcaaa aaggcaaagg acaacaaaag gccgcgccgc tggcgttttt
     5401 ccataggctc cgcccccctg acgagcatca caaaatcgac gctcaagtca gaggtggcga
     5461 aacccgacag gactataaag ataccaggcg tttccccctg gaagctccct cgtgcgctct
     5521 cctgttccga ccctgccg
//
