LOCUS       NZ_CP151305             5163 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R22.1286 plasmid pR22.1286_5.1k, complete
            sequence.
ACCESSION   NZ_CP151305
VERSION     NZ_CP151305.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122667
            Assembly: GCF_038363105.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5163)
  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  JOURNAL   Unpublished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 5163)
  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_038363105.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:39:45
            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)                     :: 5,120
            CDSs (total)                      :: 4,990
            Genes (coding)                    :: 4,358
            CDSs (with protein)               :: 4,358
            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)              :: 632
            CDSs (without protein)            :: 632
            Pseudo Genes (ambiguous residues) :: 0 of 632
            Pseudo Genes (frameshifted)       :: 173 of 632
            Pseudo Genes (incomplete)         :: 436 of 632
            Pseudo Genes (internal stop)      :: 109 of 632
            Pseudo Genes (multiple problems)  :: 83 of 632
            Pseudo Genes (short protein)      :: 3 of 632
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151305.1.
            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..5163
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R22.1286"
                     /db_xref="taxon:624"
                     /plasmid="pR22.1286_5.1k"
                     /collected_by="Taiwan CDC"
     gene            complement(109..1023)
                     /locus_tag="AADX63_RS25485"
                     /old_locus_tag="AADX63_25470"
     CDS             complement(109..1023)
                     /locus_tag="AADX63_RS25485"
                     /old_locus_tag="AADX63_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271363.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            2756..2965
                     /locus_tag="AADX63_RS25490"
                     /old_locus_tag="AADX63_25475"
     CDS             2756..2965
                     /locus_tag="AADX63_RS25490"
                     /old_locus_tag="AADX63_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(3031..3564)
                     /locus_tag="AADX63_RS25495"
                     /old_locus_tag="AADX63_25480"
     CDS             complement(3031..3564)
                     /locus_tag="AADX63_RS25495"
                     /old_locus_tag="AADX63_25480"
                     /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_029364822.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISHDFQRLEESVANMKVNADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(3567..4493)
                     /locus_tag="AADX63_RS25500"
                     /old_locus_tag="AADX63_25485"
     CDS             complement(3567..4493)
                     /locus_tag="AADX63_RS25500"
                     /old_locus_tag="AADX63_25485"
                     /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_019842150.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4670..5068
                     /locus_tag="AADX63_RS25505"
                     /old_locus_tag="AADX63_25490"
     CDS             4670..5068
                     /locus_tag="AADX63_RS25505"
                     /old_locus_tag="AADX63_25490"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     Typing          complement(110..1023)
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.909"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3571..4493)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgcggaaag ccgcgccatt gcagggctga acgggggaaa acggcaaaaa acctgctgct
       61 caaaaagacg ccagaaaggc gctgttatct gatataggct tatttggtct actctacgag
      121 acctcgtttt ttcagttggt aataccaggc gcgactgatc cctaatgcct cccacggttt
      181 cagcgtgcgt gcagatgtag ctactgtgct gcgcttagac ttagaaccgc ccttgcgacc
      241 gcgtgcagcc tgaatttctg gcgtgtgcgt atcagccaca tactgtgcga aagtttccgg
      301 cgtgaagttc ctgtgcgtgt atttcgcaat gctcttgcca atagcccgac attcagccag
      361 tgaaagcgga acgggaagcg atgcattgta catttcgaca cgctggatca ccgcttcaag
      421 ccactgtgag aacgctggcc agccctgacg aatcgccctg taagcccatt tgcgcgtcat
      481 ttcgaacagg tggcagtttc gccccatccc gtaatgttta tcgatgctac gacgctctga
      541 ggcgctcaaa tcgagataat cagccagttc atcgagggta taggcttcct cgcgccactc
      601 catcaccagc cattccaggt ggaacggatt tttgcaaatc aggccgctgt agttcacatc
      661 cgcacaaagt ttctcacaca gcgaacgttc aaccgctgcg gcatatttca gcgccttaac
      721 cgaggcatca ggcgcggttc tcacggcgat gttgagtgcg tagagcaggt gagcgtgtcc
      781 gttcacagga tttttaacgg tgatgttcgg cgcgggagcg ttccggtcgc tccagtcaat
      841 cgcagccccc tcgcggtcaa cgtcaaaaac cagccagaac tgtgcatgag gctggttctg
      901 ctggatatac cgtgcaagaa gcgcgcgccc tttgccggag atacgaaggc cgaaagcgag
      961 atcatccgtg tgatagggac ggtggggtaa attttcttcg aagtattgaa gcgcggcgct
     1021 catgtgttac gattccttcc aggttatcga ccgacatcgc ccctgtattt tcgtgaaagt
     1081 cttggcggat agacacgaat ttcaggggcg tttgtttttc agtcgcttac actaccccca
     1141 acgacaaaac ctgtcgagcc ttcccgcaaa tccgatccat ttaccataac tcccgttgta
     1201 cgtaccatgt aaaacgccct caatcgcttt ctggcgcaaa aaacgcaaaa agacaagaaa
     1261 acaccaggcc aaaccagaaa aacgcgtcag aatcgttttc agggcgttgc ataactatgc
     1321 acgaaagcga tgtgcgatcg gtttcgtgcg ttctgaacac cgaacggctc aaaacgacaa
     1381 gttttctccc ctggtgcgtg gcgctctgac ggggtttcct gtttccaaac ttcacatctc
     1441 gccaggacaa aaaaaaccga cctggggtcg gtggcaagaa tcagagtcta tgggaaatat
     1501 tttagttatc ggatgctcaa tattcacaaa cgcaaaaaat gcctcagtga tgccctaaaa
     1561 caacctttcc agaaggagtc cgcgctttac gatgcacgga agagataaaa aaccccacaa
     1621 aagtggggaa ccaagagaaa caacaattac aggttgttgg ttgtgttcga acaacgatga
     1681 agtagctacg ctaaataata attaccgtac aggccctaca tattcaacac taaatttaag
     1741 atcctgacga aggatttata aatgcacgaa aacacataga cagacaaatt cactaaattc
     1801 atacacaaaa acaagtgtag ttttctaagt aaattagatt cgacaaccaa ttagtttatc
     1861 cacatcgcat tccactcttg ctacaccaat cacatttctt gatatgtaat agcagaaaaa
     1921 ataaaaccag acaccaatag accaaaaaac aaacattcaa caaaaaacat tttgaacaat
     1981 atcacaaaac tgtcacaacc atcatcagac tattgaaaaa aactggttgc tgttttataa
     2041 aagcgactgt aacaacctcc actctatagt tccattagtt taaagtgtca cacaaactga
     2101 gcatccattt gttttcctta cttttgcccc tgtattccaa gggttttttt tataacttaa
     2161 agattagcac accacacaaa aacaataaaa aaaacgacaa gttatacaat aaaaccagta
     2221 ctatccatac agctaattac atataaatac tattaaacca tctggacatt aaaaataaac
     2281 tcttataaca taaaattaat gcggttccgg taccatatgt cagggataat gtgcaaatgg
     2341 aggtatcgga actgcatttc agttcattat taattaatgg caaaaaaaac ctctgcgagc
     2401 gcagaggggg taaggaatgt tcccggtcat aatatgtcga tagtgtttat atacatacag
     2461 aacaagaaca acaaccagcc aactaataaa tattttattt tttagagctg aaaccttaaa
     2521 gctcacttcc attccataca ttgttataaa ccttatgttg aaaactgaaa gtaagtacgg
     2581 cagacttatt aagttgcgtg cagtcttttc acgttataca aacaagaaca cctgcgaagt
     2641 tatttctcct tacatatccc cctatgccaa cgggggattt tttctggttc actaacgcat
     2701 aaataatagt gacaccctat cattcacaaa ccgtgataat ataaggatta tcatcatggc
     2761 aaaattaggt gaaaacaccc cacatattat cgatgctact gtagatttta tggcatcaag
     2821 ccaggcattt cgtgagtatc tgaaaaaact tccccctgat aacacaatac cgccagctct
     2881 tactgatgag cacgtaccgt tatatatacg aaggctggaa tactatcgtc tgctttatcg
     2941 accaaagcag acagaatcat attgaaaaaa acggtgaacg gttcgcgaaa tcctttcgcg
     3001 ggtcgtgagg cgttggacaa gcgaagcgcg tcagtttttc cggctcttcc ccgtgacagg
     3061 tttctccacc agtttatctt ccagtgtcac aactttctga tacaccgccg ctgtggcgtt
     3121 gtagttcctg tcgagtattg ttttcattcc ccatccgagc acacagaaca taaccagaaa
     3181 agccactgac accccaccca gccatttcca gctataccct ttaagggtgt tgtattcctg
     3241 cacgatattg ctgtgaattg tcgcaatatc cctgttcagg gcatccgcgt ttaccttcat
     3301 gtttgcgact gactcttcca gccgctgaaa atcatggctg atgcgctcac ctatcagccc
     3361 tgctacgtcc agcttctgca cctcgtttct gacttcatcc ctgacctgtt ttgccacacc
     3421 gtcagaaata tcccgatatc cgcgaagtgt ttcccttgcc acagccagag aatcagcaac
     3481 agctttctgt tgctccattg cggtatgttg cagatgctcc accgataaca ggagcgtgag
     3541 taatttttct tctgtgctgg ccatgttcag aatcccatag aaaatccacg tgacggtgat
     3601 ttaacccgtt caggttcagt tcggtcctgt ctgctcactc tgtctctcat gtcaaagcca
     3661 tgctcccgcg caacatcatg ttgaagcctt ctgaccagtt catgttgctt aaccggagtg
     3721 tccagccatt ccctgatgtc atgcccgacc gttcgcgcct gttcaagatg gcgggaatag
     3781 tccggttcag accgtttttg catgatgtca tgacgctggg catcatcaag ccgtccggca
     3841 gcttcaaaac ccagatgcac ttcgggacgt cgttcaatgc cctgttcttt cagcgtccgg
     3901 cagtcaatga agcccctttc aaagccatgc tttctcatat gttcgttgtg cttcacctcc
     3961 cagcgttttc gcaattcccg caactgctct ttttgctgag tgagagtcag gcttccggaa
     4021 tcctttttcg cacctccccg ctcgggatac ctggcgttat agcgccggaa atactgttcc
     4081 ggtgtacgtt caatgccatc attcacacgc tgactcatca tgatatgcgc atgaggctgt
     4141 tcgccgccgt caatgctcgc tttcggattg tgaatggcaa aactccaggc gtgccgttcg
     4201 ccagcttcct gacgtacaaa atcctgcacc agttcaaggc gctgttccgg tgtcagttca
     4261 cggggtaatg caatttcaag ttccctatag gtcgaaccgt tcgcacgttc aaactggtca
     4321 gccgcctgcc agaaatggga aggattatcc ctggcccatt ccggcatgtt tccgtgtgcg
     4381 gaatattcca aatcctgacg gtcgcggtat ttctctttgc gctcgatgta atcggcgtgg
     4441 tttgcagcct gccccttgcc accaaattta acgctgaggt gataggttgc cacggtttca
     4501 gccctctgca ggagcgcact gtttctcgac gaaggagaga aacatataag tgcgcttcct
     4561 tctaatttta cgaattagca cggaagatac cccctgcacc cgccgaccgc aagcgatata
     4621 ctgcacgacc acaacacacc gcaaaaaaac accagggagc atcacgaaca tgcgcatcag
     4681 caacatcgaa tggctgaaga aacggatcgg attcatcagg aagctcggag aacagaccgc
     4741 acgacagaga cagattattg acctgatcga caacgaagcc ggactcacag aacaggaacg
     4801 caaacttctc cacgtactgg caacagcgga aaaaaacgac ttacaggcac aggagagcga
     4861 acgaaaacag gcggtccaaa aacgaatcga gggaaaaaaa caacgacggg aacgcaatca
     4921 ccggctcttt ctcgcggctg ggctactgat cgaagcagga ctggtagaca caaaaacagg
     4981 cgagctatgc tataaaaaag acaggatatt acaagcactt aaggaactta agtacgatct
     5041 ggagacatcc ccaaacccag acgcgtaagt gcctccatcc gtgttccgat tccctggtgc
     5101 ttcctcgctc attcgctcgc tacgctcggt catgagactg cggcgagcac taccaccaca
     5161 atc
//
