LOCUS       NZ_CP146294             2690 bp    DNA     circular CON 19-MAY-2024
DEFINITION  Shigella sonnei strain R15.3427 plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP146294
VERSION     NZ_CP146294.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123130
            Assembly: GCF_037042485.2
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2690)
  AUTHORS   Chiou,C.-S., Hong,Y.-P. and Chen,B.-H.
  TITLE     Shigella sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2690)
  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
  REMARK    Nucleotide sequence updated by submitter
REFERENCE   3  (bases 1 to 2690)
  AUTHORS   Chiou,C.-S., Hong,Y.-P. and Chen,B.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-FEB-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_037042485.2-RS_2024_05_19
            Annotation Date                   :: 05/19/2024 13:20:58
            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)                     :: 5,324
            CDSs (total)                      :: 5,192
            Genes (coding)                    :: 4,465
            CDSs (with protein)               :: 4,465
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 727
            CDSs (without protein)            :: 727
            Pseudo Genes (ambiguous residues) :: 0 of 727
            Pseudo Genes (frameshifted)       :: 209 of 727
            Pseudo Genes (incomplete)         :: 519 of 727
            Pseudo Genes (internal stop)      :: 128 of 727
            Pseudo Genes (multiple problems)  :: 119 of 727
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP146294.2.
            On May 19, 2024 this sequence version replaced NZ_CP146294.1.
            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..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R15.3427"
                     /db_xref="taxon:624"
                     /plasmid="unnamed4"
                     /collected_by="Taiwan CDC"
     gene            165..488
                     /gene="mobA"
                     /locus_tag="V8Z63_RS26605"
                     /old_locus_tag="V8Z63_26625"
     CDS             165..488
                     /gene="mobA"
                     /locus_tag="V8Z63_RS26605"
                     /old_locus_tag="V8Z63_26625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(714..1337)
                     /locus_tag="V8Z63_RS26610"
                     /old_locus_tag="V8Z63_26620"
     CDS             complement(714..1337)
                     /locus_tag="V8Z63_RS26610"
                     /old_locus_tag="V8Z63_26620"
                     /inference="COORDINATES: protein motif:HMM:NF045398.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(1716..1877)
                     /locus_tag="V8Z63_RS26615"
                     /old_locus_tag="V8Z63_26635"
     CDS             complement(1716..1877)
                     /locus_tag="V8Z63_RS26615"
                     /old_locus_tag="V8Z63_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(2375..2569)
                     /locus_tag="V8Z63_RS26620"
                     /old_locus_tag="V8Z63_26630"
     CDS             complement(2375..2569)
                     /locus_tag="V8Z63_RS26620"
                     /old_locus_tag="V8Z63_26630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..156
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.35e-75"
     Typing          2605..2690
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="1.44e-35"
     Typing          complement(1806..2332)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          166..485
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 aatactgtca ctgccaaaaa aactgccgtg cctttgtcgg taattcgaac ttgctgacag
       61 gacaggatgt gtaattgtta taccgcgcat acatgcacgc tattacaatt accctggtca
      121 gggcttcgcc ccgacacccc gtgtcagata cggagccatg ttttatgaca aaacgaagtg
      181 gaagtaatac gcgcaggcgg gctatcagtc gccctgttcg tctgacggca gaagaagacc
      241 aggaaatcag aaaaagggct gctgaatgcg gcaagaccgt ttctggtttt ttacgggcgg
      301 cagctctcgg taagaacgtt aactcactga ctgatgatcg ggtgctgaaa gaagttatga
      361 gactgggggc gttacagaaa aaactcttta tcgacggcaa gcgtatcggg gacagggagt
      421 atgcggaggt gctgatcgct attacggagt atcaccgtgc cctgttatcc aggcttatgg
      481 cagattagct tcccggggag aaaactgttg aaaacagacg gtatgaacac ggtaagctcc
      541 caaagtgatc tccattcgct ttcatgcata gctatgcagc gagctgaaaa cgatcctgac
      601 gcatccttcc tgtttttccg gggtaaaaca tctatttttg tggtgtctgc gtcagaatcg
      661 cgttcagcgc gtttcagtgg tgcgtacaat taagggatta tggtaaatga tgattatttc
      721 tcctctctat ttactcggca agcgccaaag tgaattacat catattttac tcctgattca
      781 tttattactt taaatatgtc agaaaggtgc ttcttatgat ttttatcagt tataaatgct
      841 atatcaatat ttttgtttcc taagccatct tgatgtcttt gtataatatt ttgggcttgt
      901 tcatggtaat atagagcata gttttttatc ttctcattac ttgttgcgta ttcttttcta
      961 tatatggctt gtgacatcat ttcttcttct aattttgatt gaggtatatt gcgcgcgttc
     1021 gctagaactt ttaggtcatc tttgcttatg tttagtgatg gtgttaaccc tttttgagct
     1081 tcagtatggc gtttgtttac ctctgaaaga acgcttagtc cctttgtgaa gtcgttgtct
     1141 tttgtataaa aatcaattct taggtttttg gggactacag tccatccatc gcctttttga
     1201 cgcgtgaata gtgtttgtgg atgggagatc tctttccatc caccatgcga cataatgaca
     1261 agttgtgttg cttttcctgt ttggctcaat cctattccgt ctttctggaa taaacgacga
     1321 tgacttgtta cgtccatgtt tggtgatggg tgtgttttta tatttttgga tgatgttaga
     1381 aggtgatttc ttattgttga tgatatgttt gttatgagat tcgaattgag tattttcatt
     1441 tgttaacaat ccatttttgc ggtgtttttt attgtttttt ttcttttgtt taagggtgtg
     1501 tcggtgtaag tgtttatttt atgggttaaa gtaggatacc aagtgtgaaa aaaaattaaa
     1561 ggttcttctt gagatccttt ttttctgcgc gtaatctgct gcctgtaaac gaaaaaaccg
     1621 ccctgcaagg cggtttttcg aaggttctca gagctaccaa ctctttgagc cgaggtaact
     1681 ggcttggagg agcgcagtca ccaaaacttg ttctttcagt ttagccttaa caggcgcatg
     1741 acttcaagtc ttactcctct aattcggtta tcagtggctg ctgccagtgg cgataattcg
     1801 tgtcttaccg ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga
     1861 acggggggtt cgtgcacaca gcccagcttg gagcgaacga cctacaccgg gccgagatac
     1921 caacagcgtg agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat
     1981 ccggtaaacg gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc
     2041 tggtatcttt atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga
     2101 tgctcgtcag gggggcggag cctatggaaa aacgccacct gcgcggcctt tgtccctgcc
     2161 ttcggctttt tgctcacatg ttctttccgg cgttatcccc tgattctgtg gataaccgca
     2221 ttaccgcctt tgagtgagct gacaccgctc gccgcagtcg aacgaccgag cgtagcgagt
     2281 cagtgagcga ggaagcggaa gagcgcctta tgtgacattt tctccttacg caccggtata
     2341 ccgttctgca tcctgtctgg agcaggatac actgttatac cccggtgcca ctttccgctt
     2401 caaagcgtgt ctgtatgctg ttctggagtt cttccgcgat ttcgtgcagc ttctcacaca
     2461 tggcggcctg ttcgtcggca tcgagtgcgt ccagcttttc gagcagcgtc aggctctggc
     2521 tttttatgaa tcccgccatg ttgagtacgg tttgctgctg cttgttcatc tttctgtttt
     2581 ctccgttctg tctgtcatct gcgttgtgtg attatatcgc gtaccacttt tcgactgttt
     2641 taccgccggt attctgccgt ctgacgcatt gacgggtatt tctgcctgac
//
