LOCUS       NZ_CP151387             6015 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R15.0763 plasmid pR15.0763_6k, complete
            sequence.
ACCESSION   NZ_CP151387
VERSION     NZ_CP151387.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735791
            Assembly: GCF_038368245.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 6015)
  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  JOURNAL   Unpublished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 6015)
  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_038368245.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:34:36
            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)                     :: 5,050
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,282
            CDSs (with protein)               :: 4,282
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 640
            CDSs (without protein)            :: 640
            Pseudo Genes (ambiguous residues) :: 0 of 640
            Pseudo Genes (frameshifted)       :: 168 of 640
            Pseudo Genes (incomplete)         :: 445 of 640
            Pseudo Genes (internal stop)      :: 113 of 640
            Pseudo Genes (multiple problems)  :: 84 of 640
            Pseudo Genes (short protein)      :: 3 of 640
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151387.1.
            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..6015
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R15.0763"
                     /db_xref="taxon:624"
                     /plasmid="pR15.0763_6k"
                     /collected_by="Taiwan CDC"
     gene            1..144
                     /locus_tag="AADX53_RS25170"
                     /old_locus_tag="AADX53_25155"
     CDS             1..144
                     /locus_tag="AADX53_RS25170"
                     /old_locus_tag="AADX53_25155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001419703.1"
                     /translation="MKKITGIILLLLAAIILAACQANYIRDVQGGTVSPSSSAELTGVE
                     TQ"
                     /name="colicin release lysis protein"
     gene            642..1577
                     /locus_tag="AADX53_RS25175"
                     /old_locus_tag="AADX53_25160"
     CDS             642..1577
                     /locus_tag="AADX53_RS25175"
                     /old_locus_tag="AADX53_25160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_001271369.1"
                     /translation="MSAALQYFEENLPLRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDLNAPAPNITIKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSTSA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTAETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(1771..2169)
                     /locus_tag="AADX53_RS25180"
                     /old_locus_tag="AADX53_25165"
     CDS             complement(1771..2169)
                     /locus_tag="AADX53_RS25180"
                     /old_locus_tag="AADX53_25165"
                     /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_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            2345..3271
                     /locus_tag="AADX53_RS25185"
                     /old_locus_tag="AADX53_25170"
     CDS             2345..3271
                     /locus_tag="AADX53_RS25185"
                     /old_locus_tag="AADX53_25170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001314449.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            3274..3807
                     /locus_tag="AADX53_RS25190"
                     /old_locus_tag="AADX53_25175"
     CDS             3274..3807
                     /locus_tag="AADX53_RS25190"
                     /old_locus_tag="AADX53_25175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021546188.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQRLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFSVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            4028..5665
                     /locus_tag="AADX53_RS25195"
                     /old_locus_tag="AADX53_25180"
     CDS             4028..5665
                     /locus_tag="AADX53_RS25195"
                     /old_locus_tag="AADX53_25180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like bacteriocin tRNase domain-containing
                     protein"
                     /protein_id="WP_341742780.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSV
                     TDVLTPAQVKQRQDEEKRFQQEWNDAHPVEVAERNYEQARAELNQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKEKSAADAALSSAMESRKKKEDKKRSAENKLNEEKNKRRKGTKDYGHDY
                     HPAPKTEDIKGLGELKEGRPKTPKQGGGGKRARWYGDKGRKIYEWDSQHGELEGYRASD
                     GQHLGSFDPKTGKQLKGPDPKRSIKKYL"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            5675..5932
                     /locus_tag="AADX53_RS25200"
                     /old_locus_tag="AADX53_25185"
     CDS             5675..5932
                     /locus_tag="AADX53_RS25200"
                     /old_locus_tag="AADX53_25185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891189.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cloacin immunity family protein"
                     /protein_id="WP_001419702.1"
                     /translation="MGLKLHIHWFDKKNEEFKGGEYSKDFGDDGSVIERLGMPLKDNIN
                     NGWFDVEKRWVPILQPYFKNVIDISKFDYFVSFDYRDGDW"
                     /name="cloacin immunity family protein"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          643..1577
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2346..3268
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaagaaaa taacagggat tattttgttg cttcttgcag ccattattct tgctgcatgt
       61 caggcaaact atatccgtga tgttcagggc gggactgtat caccgtcatc ctctgctgaa
      121 ctgaccggag tggaaacgca gtaacctgca atcctcattt gacaaggaca aagcgtgtca
      181 ggctgattct gacgcgcttt ttttgttgaa gtgccacaaa aattccatgt gggagatggg
      241 atctaaaatc tccgtgcaga accttccatc cggagggaga aaacttttcg ttttgagccg
      301 ttcggtgttc agaacgcacg aaaccgatcg cacatcgctt tcgtgcatag ttatgcaacg
      361 ccctgaaaac gattctgacg cgtttttctg gtttgtcctg gtgttttctt gtctttttgc
      421 gttttttgcg ccagaaagcg attgagggcg ttttaagggg tacgtacaac gggagttatg
      481 gtaaatggat cgggttttcg ggaaggatcg acaggatttg ccgttgggtg tagtgtaagc
      541 gactgaaaaa caaacgcccc tgaaattcgt gtctctccgc caagattgtc acgagaatac
      601 aggggcgagg tcggtcgata acctggaagg aatcgtaaca catgagcgcc gcgcttcaat
      661 acttcgaaga aaatttaccc ctccgcccct atcacacgga tgatctcgct ttcggccttc
      721 gtatctccgg taaagggcgc gcgcttcttg cacggtatat ccagcagaac caacctcatg
      781 cgcagttctg gctggttttt gacgttgacc gcgagggggc tgcgattgac tggagcgacc
      841 tgaacgcccc cgcaccgaac atcaccataa aaaatcccgt gaacggtcac gcccacctgc
      901 tctacgcact caatatcgcc gtgagaaccg cgcctgatgc ttcggttaag gcgctgaaat
      961 acgccgccgc gattgaacgt gcgttgtgtg aaaaactggg cgcagatgta aactacagcg
     1021 gactgatttg caaaaatccg ttccatctgg aatggcaggt gatggagtgg cgtgaggaag
     1081 cctataccct cgatgaactg gctgattatc tcgatttgag cacttcagcg cgccgtagca
     1141 tcgataaaca ttacggaatg gggagaaact gccatctgtt cgaaatgacg cgcaaatggg
     1201 cttacagggc gattcgtcag ggctggccag cattctcaca gtggcttgat gccgtgattc
     1261 agcgtgtcga aatgtacaac gcatcgcttc ccgttccgct ttcacctcct gaatgtcggg
     1321 ctattggcaa gagtattgcg aaatacacgc acaggaactt cacggcggaa actttcgcac
     1381 agtatgtggc tgatacgcac acgccagaaa tacaggccaa gagaggcagg aaaggtggca
     1441 tcgctaaagg cgaagcctac gatgacaagc gtttcatggc gctatgtatg ctggagaatg
     1501 gatattctca gaaagctatt gcggcgatgt tggaggtttc tactcgaacc attcgaaact
     1561 ggaaaagcgg aaaatagcct atatcagata acagcgcctt tctggcgttt ttttgagcct
     1621 taggtctttt gccgtttttc cccgttcagc cctgcaatgg tgctgttttc cgcatgattg
     1681 tgctggtagt gctcgccgca gtctcatgac cgagcgtagc gagcgaatga gcgaggaagc
     1741 accagggaac aggaacacgg atggaggcac ttacgcgtct gggtttgggg atgtctccag
     1801 atcgtactta atttccttaa gtgcctgtaa tatcctgtct tttttatagc atagctcgcc
     1861 tgtttttgtg tctaccagtc ctgcttcgat cagtagccca gccgcgagaa agagtcggtg
     1921 attgcgttct cgtcgttgtt tttttccctc gattcgtttt tggaccgcct gttttcgttc
     1981 gctctcctgt gcctgtaagt cgtttttttc cgctgttgcc agtacgtgga ggagtttgcg
     2041 ttcctgttct gtgagtcctg cttcgttgtc gagcaggtca ataatctgtc tctgtcgtgc
     2101 ggtctgttct ccgagcttcc tgatgaatcc gatccgtttc ttcagccatt cgatgttgct
     2161 gatgcgcatg ttcgtggtgc tccctggtgt tttttgctgt gtgttgtggt cgtgcagtat
     2221 atcgcttgcg gtcggtgggt gcagggggta tcttccgtgc taattcgtaa aattagaagg
     2281 aagcgcactt atatgtttct ctccttcgtc gagaaacagt gcgctcctgc ggagggctga
     2341 aaccgtggca acctatcacc tcagcgttaa atttggtggc aaggggcagg ctgcaaacca
     2401 cgccgattac atcgagcgca aagagaaata ccgcgaccgt caggatttgg aatattccgc
     2461 acacggaaac atgccggaat gggcgcgaga taatccctca catttctggc aggcggctga
     2521 ccagtttgaa cgtgcgaacg gttcgaccta tcgggaactt gaaattgcat taccccgtga
     2581 actgacagcg gaacagcgcc ttgaactggt gcaggatttt gtacgtcagg aagctggcga
     2641 acggcacgcc tggagttttg ccattcacaa tccgaaagcg agcattgacg gcggcgaaca
     2701 gcctcatgcg catatcatga tgagccagcg tgtgaatgat ggcattgaac gtacaccgga
     2761 acagtatttc cggcgctata acgccaggta tcccgagcgg ggaggtgcga aaaaggattc
     2821 cggaagcctg actctcactc agcaaaaaga gcagttgcgg gaattgcgaa aacgctggga
     2881 ggtgaagcac aacgaacata tgagaaagca tggctttgaa aggggcttca ttgactgccg
     2941 gacgctgaaa gaacagggca ttgaacgacg tcccgaagtg catctgggtt ttgaagctgc
     3001 cggacggctt gatgatgccc agcgtcatga catcatgcaa aaacggtctg aaccggacta
     3061 ttcccgccat cttgaacagg cgcgaacggt cgggcatgac atcagggaat ggctggacac
     3121 tccggttaag caacatgaac tggtcagaag gctgcaacat gatgttgcgc gggagcatgg
     3181 ctttgacatg agagacagag tgagcagaca gaaccgaact gaacctgaac gggttaaatc
     3241 accgtcacgt ggattttcta tgggattctg aacatggcca gcacagaaga aaaattactc
     3301 acgctcctgt tatcggtgga gcatctgcaa cataccgcaa tggagcaaca gaaagctgtt
     3361 gctgattctc tggctgtggc aagggaaaca cttcgcggat atcgggatat ttctgacggt
     3421 gtggcaaaac aggtcaggga tgaagtcaga aacgaagtgc agaggctgga tgttgcaggg
     3481 ctgataggtg agcgcatcag tcaggatttt cagcggctgg aagagtcagt cgcaaacatg
     3541 aaggcaaacg cggatgccct gaacagggat attgcgacaa ttcacagcaa tatcgtgcag
     3601 gaatacaaca cccttaaagg gtatagctgg aaatggctgg gtggggtgtc agtggccttt
     3661 ctggttatgt tcagtgtgct cggatggggg atgaaaacaa ttctcgacag gaactacaac
     3721 gccacagcgg cggtgtatca gaaagttgtg acactggaag ataaactggt ggagaaacct
     3781 gtcacgggta agagccggaa aaactgacgc gcttcgcttg tccaacgcct cacgacccgc
     3841 gaaaggattt cgcgttccgt tcaccgtttt catgagtgat tcctccgaac tgccaaaaaa
     3901 tatccccccc tgacttgaca gaaaaaataa tggcgagtac tttttggtct gtacataaaa
     3961 ccagtggttt tatgtacagt atcaactata taatcaattg ttttaacgct taaaagaggg
     4021 aatttttatg agcggtggag atggacgcga ccacaacagt ggcgcacata acacaggtgg
     4081 taacattaat ggcggcccta cggggcttgg tggaaatggt ggggcttctg acggttcagg
     4141 atggagttcg gaaaataacc catggggtgg cggttccggt agtggtgttc actggggagg
     4201 tggctccggc aatggtaatg gcggggggaa tggtaattcc ggtggtggca gcaattcatc
     4261 cgtagcagca gtggcatttg gttttcctgc tttggcaact cctggtgccg gaacgctggg
     4321 tatcgccgtc tctggtgagg ctttatctgc ggcaatagcg gatatctttg cagccctgaa
     4381 aggcccgttt aaattcagcg catggggtat tgcgctttac ggcattctgc catctgaaat
     4441 agcaaaagat gacccgaata tgatgtcaaa gattgtgacg tcattaccgg cagaaacagt
     4501 gacgaatgtt caggtcagta cacttccgct ggaccaggca actgtcagcg tgacgaaacg
     4561 tgtgacagat gttgtgaagg acacacgaca gcatattgcc gtagttgcag gtgtgcctat
     4621 gagtgtgcct gttgtgaatg ccaaaccaac acgtactcca ggtgtatttc acgcatcatt
     4681 tcctggtgtc ccttctctga cagtcagcac tgtcaaaggc cttccggtgt caacaaccct
     4741 tccccgtggt attacggagg ataaaggccg gactgccgtt cctgcgggat ttacctttgg
     4801 tggtggttca catgaagcgg tgattcgctt tccgaaagaa agtgggcaga agccggttta
     4861 tgtatcagtg acagatgttc ttaccccagc acaggtaaaa caacgtcagg atgaggaaaa
     4921 acgcttccag caggaatgga atgacgcaca tccggtggaa gtggctgaac gcaattatga
     4981 acaggcccgc gcagaactga atcaggctaa taaagatgtt gccagaaacc aggaacgaca
     5041 ggctaaagct gttcaggttt ataattctcg taaaagtgaa cttgatgcag cgaataaaac
     5101 tcttgctgat gcaaaggctg aaataaaaca attcgagcga tttgcccgag aaccaatggc
     5161 tgctggtcac agaatgtggc aaatggcagg gcttaaggcc cagcgggcac agacggatgt
     5221 aaataataag aaggctgcat ttgatgctgc cgcaaaagag aagtcagcag cagatgctgc
     5281 attgagttct gcgatggaaa gcaggaagaa gaaagaagat aagaaaagga gtgctgaaaa
     5341 taaattaaac gaagagaaaa ataaacgccg aaaaggcact aaagattatg gccatgatta
     5401 tcatccagct cctaaaactg aggatattaa aggtttgggg gaattaaaag aggggaggcc
     5461 aaaaactcca aagcaaggtg gtggaggtaa gcgtgccaga tggtatggag ataaggggcg
     5521 taaaatttat gagtgggact ctcagcatgg tgagcttgag ggctatcgag ccagtgatgg
     5581 tcagcatctt ggttcatttg accctaaaac cggtaagcag ttgaaaggtc cagatccgaa
     5641 acgaagtatt aaaaagtatc tttaaggtga tgttatggga cttaaattac acattcattg
     5701 gtttgataag aagaatgagg aatttaaagg tggtgagtat tcaaaggatt tcggtgatga
     5761 tggttcggtt attgaacgtc ttggaatgcc tttaaaggat aatattaata acggttggtt
     5821 tgatgttgaa aagagatggg tgccaatatt acagccatac tttaaaaatg ttattgatat
     5881 tagtaagttc gattactttg tttctttcga ttatcgtgat ggtgactggt aattaaacta
     5941 tcagggacga gtaataaagt gtttgattca ggtgttcaag gatgaattcc tgaatccata
     6001 tatacaggga atcgt
//
