LOCUS       NZ_CP151317             6015 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R21.0552 plasmid pR21.0552_6k, complete
            sequence.
ACCESSION   NZ_CP151317
VERSION     NZ_CP151317.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735802
            Assembly: GCF_038364745.1
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  JOURNAL   Unpublished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_038364745.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:43:35
            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)                     :: 5,428
            CDSs (total)                      :: 5,299
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 739
            CDSs (without protein)            :: 739
            Pseudo Genes (ambiguous residues) :: 0 of 739
            Pseudo Genes (frameshifted)       :: 212 of 739
            Pseudo Genes (incomplete)         :: 527 of 739
            Pseudo Genes (internal stop)      :: 127 of 739
            Pseudo Genes (multiple problems)  :: 121 of 739
            Pseudo Genes (short protein)      :: 3 of 739
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151317.1.
            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="R21.0552"
                     /db_xref="taxon:624"
                     /plasmid="pR21.0552_6k"
                     /collected_by="Taiwan CDC"
     gene            1..399
                     /locus_tag="AADX62_RS27030"
                     /old_locus_tag="AADX62_27015"
     CDS             1..399
                     /locus_tag="AADX62_RS27030"
                     /old_locus_tag="AADX62_27015"
                     /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            complement(593..1528)
                     /locus_tag="AADX62_RS27035"
                     /old_locus_tag="AADX62_27020"
     CDS             complement(593..1528)
                     /locus_tag="AADX62_RS27035"
                     /old_locus_tag="AADX62_27020"
                     /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(2026..2169)
                     /locus_tag="AADX62_RS27040"
                     /old_locus_tag="AADX62_27025"
     CDS             complement(2026..2169)
                     /locus_tag="AADX62_RS27040"
                     /old_locus_tag="AADX62_27025"
                     /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            complement(2253..2510)
                     /locus_tag="AADX62_RS27045"
                     /old_locus_tag="AADX62_27030"
     CDS             complement(2253..2510)
                     /locus_tag="AADX62_RS27045"
                     /old_locus_tag="AADX62_27030"
                     /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"
     gene            complement(2520..4157)
                     /locus_tag="AADX62_RS27050"
                     /old_locus_tag="AADX62_27035"
     CDS             complement(2520..4157)
                     /locus_tag="AADX62_RS27050"
                     /old_locus_tag="AADX62_27035"
                     /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_039063724.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSV
                     TDVLTPAQVKQRQDEEKRLQQEWNDAHPVEVAERNYEQARAELNQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKEKSAADAALSSAMESRKKKEDKKRSAENKLNEEKNKRRKGTKDYGHDY
                     HPAPKTEDIKGLGELKEGRPKTPKQGGGGKRARWYGDKGRKIYEWDSQHGELEGYRASD
                     GQHLGSFDPKTGKQLKGPDPKRSIKKYL"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            complement(4378..4911)
                     /locus_tag="AADX62_RS27055"
                     /old_locus_tag="AADX62_27040"
     CDS             complement(4378..4911)
                     /locus_tag="AADX62_RS27055"
                     /old_locus_tag="AADX62_27040"
                     /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            complement(4914..5840)
                     /locus_tag="AADX62_RS27060"
                     /old_locus_tag="AADX62_27045"
     CDS             complement(4914..5840)
                     /locus_tag="AADX62_RS27060"
                     /old_locus_tag="AADX62_27045"
                     /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"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          complement(594..1528)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4918..5840)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcgcatca gcaacatcga atggctgaag aaacggatcg gattcatcag gaagctcgga
       61 gaacagaccg cacgacagag acagattatt gacctgctcg acaacgaagc aggactcaca
      121 gaacaggaac gcaaactcct ccacgtactg gcaacagcgg aaaaaaacga cttacaggca
      181 caggagagcg aacgaaaaca ggcggtccaa aaacgaatcg agggaaaaaa acaacgacga
      241 gaacgcaatc accgactctt tctcgcggct gggctactga tcgaagcagg actggtagac
      301 acaaaaacag gcgagctatg ctataaaaaa gacaggatat tacaggcact taaggaaatt
      361 aagtacgatc tggagacatc cccaaaccca gacgcgtaag tgcctccatc cgtgttcctg
      421 ttccctggtg cttcctcgct cattcgctcg ctacgctcgg tcatgagact gcggcgagca
      481 ctaccagcac aatcatgcgg aaaacagcac cattgcaggg ctgaacgggg aaaaacggca
      541 aaagacctaa ggctcaaaaa aacgccagaa aggcgctgtt atctgatata ggctattttc
      601 cgcttttcca gtttcgaatg gttcgagtag aaacctccaa catcgccgca atagctttct
      661 gagaatatcc attctccagc atacatagcg ccatgaaacg cttgtcatcg taggcttcgc
      721 ctttagcgat gccacctttc ctgcctctct tggcctgtat ttctggcgtg tgcgtatcag
      781 ccacatactg tgcgaaagtt tccgccgtga agttcctgtg cgtgtatttc gcaatactct
      841 tgccaatagc ccgacattca ggaggtgaaa gcggaacggg aagcgatgcg ttgtacattt
      901 cgacacgctg aatcacggca tcaagccact gtgagaatgc tggccagccc tgacgaatcg
      961 ccctgtaagc ccatttgcgc gtcatttcga acagatggca gtttctcccc attccgtaat
     1021 gtttatcgat gctacggcgc gctgaagtgc tcaaatcgag ataatcagcc agttcatcga
     1081 gggtataggc ttcctcacgc cactccatca cctgccattc cagatggaac ggatttttgc
     1141 aaatcagtcc gctgtagttt acatctgcgc ccagtttttc acacaacgca cgttcaatcg
     1201 cggcggcgta tttcagcgcc ttaaccgaag catcaggcgc ggttctcacg gcgatattga
     1261 gtgcgtagag caggtgggcg tgaccgttca cgggattttt tatggtgatg ttcggtgcgg
     1321 gggcgttcag gtcgctccag tcaatcgcag ccccctcgcg gtcaacgtca aaaaccagcc
     1381 agaactgcgc atgaggttgg ttctgctgga tataccgtgc aagaagcgcg cgccctttac
     1441 cggagatacg aaggccgaaa gcgagatcat ccgtgtgata ggggcggagg ggtaaatttt
     1501 cttcgaagta ttgaagcgcg gcgctcatgt gttacgattc cttccaggtt atcgaccgac
     1561 ctcgcccctg tattctcgtg acaatcttgg cggagagaca cgaatttcag gggcgtttgt
     1621 ttttcagtcg cttacactac acccaacggc aaatcctgtc gatccttccc gaaaacccga
     1681 tccatttacc ataactcccg ttgtacgtac cccttaaaac gccctcaatc gctttctggc
     1741 gcaaaaaacg caaaaagaca agaaaacacc aggacaaacc agaaaaacgc gtcagaatcg
     1801 ttttcagggc gttgcataac tatgcacgaa agcgatgtgc gatcggtttc gtgcgttctg
     1861 aacaccgaac ggctcaaaac gaaaagtttt ctccctccgg atggaaggtt ctgcacggag
     1921 attttagatc ccatctccca catggaattt ttgtggcact tcaacaaaaa aagcgcgtca
     1981 gaatcagcct gacacgcttt gtccttgtca aatgaggatt gcaggttact gcgtttccac
     2041 tccggtcagt tcagcagagg atgacggtga tacagtcccg ccctgaacat cacggatata
     2101 gtttgcctga catgcagcaa gaataatggc tgcaagaagc aacaaaataa tccctgttat
     2161 tttcttcata cgattccctg tatatatgga ttcaggaatt catccttgaa cacctgaatc
     2221 aaacacttta ttactcgtcc ctgatagttt aattaccagt caccatcacg ataatcgaaa
     2281 gaaacaaagt aatcgaactt actaatatca ataacatttt taaagtatgg ctgtaatatt
     2341 ggcacccatc tcttttcaac atcaaaccaa ccgttattaa tattatcctt taaaggcatt
     2401 ccaagacgtt caataaccga accatcatca ccgaaatcct ttgaatactc accaccttta
     2461 aattcctcat tcttcttatc aaaccaatga atgtgtaatt taagtcccat aacatcacct
     2521 taaagatact ttttaatact tcgtttcgga tctggacctt tcaactgctt accggtttta
     2581 gggtcaaatg aaccaagatg ctgaccatca ctggctcgat agccctcaag ctcaccatgc
     2641 tgagagtccc actcataaat tttacgcccc ttatctccat accatctggc acgcttacct
     2701 ccaccacctt gctttggagt ttttggcctc ccctctttta attcccccaa acctttaata
     2761 tcctcagttt taggagctgg atgataatca tggccataat ctttagtgcc ttttcggcgt
     2821 ttatttttct cttcgtttaa tttattttca gcactccttt tcttatcttc tttcttcttc
     2881 ctgctttcca tcgcagaact caatgcagca tctgctgctg acttctcttt tgcggcagca
     2941 tcaaatgcag ccttcttatt atttacatcc gtctgtgccc gctgggcctt aagccctgcc
     3001 atttgccaca ttctgtgacc agcagccatt ggttctcggg caaatcgctc gaattgtttt
     3061 atttcagcct ttgcatcagc aagagtttta ttcgctgcat caagttcact tttacgagaa
     3121 ttataaacct gaacagcttt agcctgtcgt tcctggtttc tggcaacatc tttattagcc
     3181 tgattcagtt ctgcgcgggc ctgttcataa ttgcgttcag ccacttccac cggatgtgcg
     3241 tcattccatt cctgctggag gcgtttttcc tcatcctgac gttgttttac ctgtgctggg
     3301 gtaagaacat ctgtcactga tacataaacc ggcttctgcc cactttcttt cggaaagcga
     3361 atcaccgctt catgtgaacc accaccaaag gtaaatcccg caggaacggc agtccggcct
     3421 ttatcctccg taataccacg gggaagggtt gttgacaccg gaaggccttt gacagtgctg
     3481 actgtcagag aagggacacc aggaaatgat gcgtgaaata cacctggagt acgtgttggt
     3541 ttggcattca caacaggcac actcataggc acacctgcaa ctacggcaat atgctgtcgt
     3601 gtgtccttca caacatctgt cacacgtttc gtcacgctga cagttgcctg gtccagcgga
     3661 agtgtactga cctgaacatt cgtcactgtt tctgccggta atgacgtcac aatctttgac
     3721 atcatattcg ggtcatcttt tgctatttca gatggcagaa tgccgtaaag cgcaataccc
     3781 catgcgctga atttaaacgg gcctttcagg gctgcaaaga tatccgctat tgccgcagat
     3841 aaagcctcac cagagacggc gatacccagc gttccggcac caggagttgc caaagcagga
     3901 aaaccaaatg ccactgctgc tacggatgaa ttgctgccac caccggaatt accattcccc
     3961 ccgccattac cattgccgga gccacctccc cagtgaacac cactaccgga accgccaccc
     4021 catgggttat tttccgaact ccatcctgaa ccgtcagaag ccccaccatt tccaccaagc
     4081 cccgtagggc cgccattaat gttaccacct gtgttatgtg cgccactgtt gtggtcgcgt
     4141 ccatctccac cgctcataaa aattccctct tttaagcgtt aaaacaattg attatatagt
     4201 tgatactgta cataaaacca ctggttttat gtacagacca aaaagtactc gccattattt
     4261 tttctgtcaa gtcagggggg gatatttttt ggcagttcgg aggaatcact catgaaaacg
     4321 gtgaacggaa cgcgaaatcc tttcgcgggt cgtgaggcgt tggacaagcg aagcgcgtca
     4381 gtttttccgg ctcttacccg tgacaggttt ctccaccagt ttatcttcca gtgtcacaac
     4441 tttctgatac accgccgctg tggcgttgta gttcctgtcg agaattgttt tcatccccca
     4501 tccgagcaca ctgaacataa ccagaaaggc cactgacacc ccacccagcc atttccagct
     4561 atacccttta agggtgttgt attcctgcac gatattgctg tgaattgtcg caatatccct
     4621 gttcagggca tccgcgtttg ccttcatgtt tgcgactgac tcttccagcc gctgaaaatc
     4681 ctgactgatg cgctcaccta tcagccctgc aacatccagc ctctgcactt cgtttctgac
     4741 ttcatccctg acctgttttg ccacaccgtc agaaatatcc cgatatccgc gaagtgtttc
     4801 ccttgccaca gccagagaat cagcaacagc tttctgttgc tccattgcgg tatgttgcag
     4861 atgctccacc gataacagga gcgtgagtaa tttttcttct gtgctggcca tgttcagaat
     4921 cccatagaaa atccacgtga cggtgattta acccgttcag gttcagttcg gttctgtctg
     4981 ctcactctgt ctctcatgtc aaagccatgc tcccgcgcaa catcatgttg cagccttctg
     5041 accagttcat gttgcttaac cggagtgtcc agccattccc tgatgtcatg cccgaccgtt
     5101 cgcgcctgtt caagatggcg ggaatagtcc ggttcagacc gtttttgcat gatgtcatga
     5161 cgctgggcat catcaagccg tccggcagct tcaaaaccca gatgcacttc gggacgtcgt
     5221 tcaatgccct gttctttcag cgtccggcag tcaatgaagc ccctttcaaa gccatgcttt
     5281 ctcatatgtt cgttgtgctt cacctcccag cgttttcgca attcccgcaa ctgctctttt
     5341 tgctgagtga gagtcaggct tccggaatcc tttttcgcac ctccccgctc gggatacctg
     5401 gcgttatagc gccggaaata ctgttccggt gtacgttcaa tgccatcatt cacacgctgg
     5461 ctcatcatga tatgcgcatg aggctgttcg ccgccgtcaa tgctcgcttt cggattgtga
     5521 atggcaaaac tccaggcgtg ccgttcgcca gcttcctgac gtacaaaatc ctgcaccagt
     5581 tcaaggcgct gttccgctgt cagttcacgg ggtaatgcaa tttcaagttc ccgataggtc
     5641 gaaccgttcg cacgttcaaa ctggtcagcc gcctgccaga aatgtgaggg attatctcgc
     5701 gcccattccg gcatgtttcc gtgtgcggaa tattccaaat cctgacggtc gcggtatttc
     5761 tctttgcgct cgatgtaatc ggcgtggttt gcagcctgcc ccttgccacc aaatttaacg
     5821 ctgaggtgat aggttgccac ggtttcagcc ctccgcagga gcgcactgtt tctcgacgaa
     5881 ggagagaaac atataagtgc gcttccttct aattttacga attagcacgg aagatacccc
     5941 ctgcacccac cgaccgcaag cgatatactg cacgaccaca acacacagca aaaaacacca
     6001 gggagcacca cgaac
//
