LOCUS       NZ_CP146297             5428 bp    DNA     linear   CON 11-MAY-2024
DEFINITION  Shigella sonnei strain R16.0823 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP146297
VERSION     NZ_CP146297.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123227
            Assembly: GCF_037043765.2
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5428)
  AUTHORS   Chiou,C.-S., Hong,Y.-P. and Chen,B.-H.
  TITLE     Shigella sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5428)
  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. 2.9.2
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 204.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037043765.2-RS_2024_05_10
            Annotation Date                   :: 05/10/2024 23:57:54
            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)                     :: 5,019
            CDSs (total)                      :: 4,890
            Genes (coding)                    :: 4,251
            CDSs (with protein)               :: 4,251
            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)              :: 639
            CDSs (without protein)            :: 639
            Pseudo Genes (ambiguous residues) :: 0 of 639
            Pseudo Genes (frameshifted)       :: 177 of 639
            Pseudo Genes (incomplete)         :: 435 of 639
            Pseudo Genes (internal stop)      :: 112 of 639
            Pseudo Genes (multiple problems)  :: 83 of 639
            Pseudo Genes (short protein)      :: 3 of 639
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP146297.1.
            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..5428
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R16.0823"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /collected_by="Taiwan CDC"
     gene            <1..411
                     /locus_tag="V8Z64_RS00695"
                     /old_locus_tag="V8Z64_00695"
                     /pseudo=""
     CDS             <1..411
                     /locus_tag="V8Z64_RS00695"
                     /old_locus_tag="V8Z64_00695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002889888.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(993..1178)
                     /locus_tag="V8Z64_RS00700"
                     /old_locus_tag="V8Z64_00700"
     CDS             complement(993..1178)
                     /locus_tag="V8Z64_RS00700"
                     /old_locus_tag="V8Z64_00700"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_338637963.1"
                     /translation="MLNALEQAATGLYAAAERMGERLRRIAENVFACATGQRDAERAVM
                     QLSQQVQHLSERHQNA"
                     /name="hypothetical protein"
     gene            complement(1446..1655)
                     /locus_tag="V8Z64_RS00705"
                     /old_locus_tag="V8Z64_00705"
     CDS             complement(1446..1655)
                     /locus_tag="V8Z64_RS00705"
                     /old_locus_tag="V8Z64_00705"
                     /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_338637964.1"
                     /translation="MLTETMLNDEFSRLDKVCKRGCDLNETKIKDAIALFTTSTENRWK
                     APKEVKEAMMQHRKDVLKLQGIRT"
                     /name="hypothetical protein"
     gene            complement(2147..2341)
                     /locus_tag="V8Z64_RS00710"
                     /old_locus_tag="V8Z64_00710"
     CDS             complement(2147..2341)
                     /locus_tag="V8Z64_RS00710"
                     /old_locus_tag="V8Z64_00710"
                     /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_338637965.1"
                     /translation="MACDPVDYLLEESVTGGATVLQDNAEEVREADGGHAICEEIHVRC
                     YVVRGEGAPPGGREGDGEL"
                     /name="hypothetical protein"
     gene            complement(2365..2707)
                     /locus_tag="V8Z64_RS00715"
                     /old_locus_tag="V8Z64_00715"
                     /pseudo=""
     CDS             complement(2365..2707)
                     /locus_tag="V8Z64_RS00715"
                     /old_locus_tag="V8Z64_00715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001312460.1"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            2747..2972
                     /locus_tag="V8Z64_RS00720"
                     /old_locus_tag="V8Z64_00720"
                     /pseudo=""
     CDS             2747..2972
                     /locus_tag="V8Z64_RS00720"
                     /old_locus_tag="V8Z64_00720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3590..>3699
                     /locus_tag="V8Z64_RS00725"
                     /old_locus_tag="V8Z64_00725"
                     /pseudo=""
     CDS             3590..>3699
                     /locus_tag="V8Z64_RS00725"
                     /old_locus_tag="V8Z64_00725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="frameshifted; 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="replication initiation protein"
                     /name="replication initiation protein"
     Typing          3125..3656
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.869"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaaaaagc gtcatcgtgg atactctaca tcgtcagtgg gatgtaagat caccagcgct
       61 gtcaaatatg catacagacg agatcgctac tccggtggta aagtatacaa aatcatttgg
      121 aaaaataacg gcatcatgta caacaacata ccgttatcta acaactcggt aaaaaaccat
      181 taccggcgga ttttaaaaga aacattaaag atcattcata gcaggtacga agagaaaata
      241 aacatgagac agaatgccca gttaaataca gcggcagcct cgctctctca gacgggtcag
      301 ccgaaaacac aaagtcagcc acataaccaa gcacctagtg cgagtgctga taaaagccat
      361 cagatgacta tgtctcgagc cattaactat gctcgccttt tttctgactg atactgtaca
      421 gctagattta ccataatccc ttattgcgtg caccgcagaa acgcgttcgg tgcgatcacg
      481 gcagctgacg gtaaaaatgg caacaaacca cccgaaaaac tgccgcgatc gcacccgata
      541 aatttaaacc acatgcatag ctatgagcca tgtgaatcac gcaggaattg ccggccagag
      601 ctaataaacg cgattatttt catacctttc ggaaaggcag aagacggaac cggagcggaa
      661 aaacagaagt tcaggggaat gagcgctatc tggcgataga ggcaaaacac agcacaaaag
      721 acatccagaa tcgcgcccgt atgcgtttta acgcgttcct gtgttccagc aaggtcgact
      781 gaagcgcgtt cccggtgccc cgaatcaatc attatcccaa aaaatgcacc ggaaacgcgc
      841 tgacaacatt tagcctgtct ctattaccat ccagcgaagg gccatccatg tgcgttctgc
      901 attccggttg gcactcatgc tccagggata gccatgttcg cgctcctgta tcagcgttcg
      961 tcccttatct cctgttctcg ctgtataact ggtcaagcgt tctggtgtcg ctcgctcaag
     1021 tgctgcacct gctgactcaa ctgcatgact gctcgttcag catcgcgttg tcccgttgcg
     1081 caagcaaaaa cattctctgc tattcgacga aggcgctctc ccattcgctc agccgctgca
     1141 tatagtcctg ttgcagcttg ctctaatgcg ttcagcaaat gtctttcagc tccgtcactc
     1201 ttgtcactcc gtcattgaat ccagtccttc ccctataggg actcacgttg ccgatttccc
     1261 gtacgggagc cagcaatttc cttctcccgt tctgcacaaa ctccacgccc atgtctacgc
     1321 gttcagtttc tgcaatgttt cttcctgtat cctgatttct tccaggttcg cctgtatccg
     1381 cccgccaaga aaccatagcg ttcccgccac tcgcggtaaa cataagaaaa actatcccag
     1441 caaaatcatg tccttattcc ctgcagcttt aacacgtcct tcctgtgctg catcatcgcc
     1501 tctttcacct ctttcggtgc tttccagcga ttctctgtcg acgttgtgaa cagggctata
     1561 gcgtctttga tcttcgtctc gttcaggtca cagcctcgct tacacacttt atccagcctg
     1621 ctgaactcgt cgttcagcat tgtctctgta agcatcggtt ctctctttca cttttctcga
     1681 actccgtacc gttctgtaaa agattgctca taaaatgctc cttcagcctg tattcttccg
     1741 ccgttcggct ctgcaatgct gatactgctt cgcgtcaccc gacagtttca agcccgcctc
     1801 gctaagcgcc tgaatcacat cctgacggcc ttttatctcc cgacatgata aagcgctatc
     1861 ccgcgttaac gcttcagcaa gcgctgttgc atttcggttg gttatcagag agagtcagta
     1921 tccggcggtt tccggggcgt tgggctcatg cagcccgtaa tggtgattca ccagcgttgt
     1981 catgcatcaa ttgtcggctt cgtcgccggt ctagtacgct ggaggcgttt tccgctctgt
     2041 agctcatgtt cggaatgacg agattaagct caagcctatc cttgtcctgg tgctccaccc
     2101 caggatgctg tactcattct tttcgagaac gggcatcaat acgcgctcaa agttcgccat
     2161 caccttcacg tccccccggc ggagcacctt ctccgcgaac gacataacac ctgacgtgta
     2221 tttcttcgca aatggcgtgg cctccatcag cttcccgaac ttcttccgca ttatcctgaa
     2281 gcaccgttgc ccctccggtt acgctctctt ccagcaggta atcaaccgga tcacatgcca
     2341 ccacctcttc ccctggcatg aaacttaact atcatcccgc gctccatgtt ccccgacgac
     2401 ctgccgtaag ctgcgcaact ctctctcgat ggccatcagt acgacaatca cctgaaccgg
     2461 tcacggaaga ccactgccgc tgttcacctc ctcgccgtct gattcaggta attcccgact
     2521 cccggcagcc agctggctca ataacggcgg tgccagtgtc ggcagcttcc cggaacgggc
     2581 aacggctcac tcaggcagac ccgccgcatc cataccgaca gttgttacca cccaacttcc
     2641 agcaaacggg catgttcatc atcagtaacc cgtatcgtga gcattcttgg cgtttcatcg
     2701 gtatcattac cccatgaaca gaaatccccc ttacacggag gcatcagtga ctgaacagga
     2761 aaaaaccgcc tcaacatggc ccgctttatc agaagccaga cattaacgct gctgcagaaa
     2821 ctcaacgaac tggacgcaga tgaacaggcc gatattgtga atcacttcac gacgatgccg
     2881 accagcttta ccgcagctgc ctcgcacgct tccgcgatga cggtgcaaac ctttgccaca
     2941 taagctccgg ggacggtcaa tgctgtctgt gagcggatgc cggggcagac aagtcgtcac
     3001 ggcgcgtcag gccgttaacc ttgcgggtgt cggggcgaag ccatgaccca gtcacgtagc
     3061 gatagtgagt gtatactcgg cgtaaccatg cggcatcagt gcagattata aaaaagagac
     3121 catatgcggt gtgaaatgct gcacaatgcg taaggagaaa ataccgcatt tggcgctctt
     3181 cgcttctcgc tcaccactcg ctacgctcgg tggttcggct gcggcgagcg gagtcggctc
     3241 actcaaaggc ggtaatacgg ttatccacga atcagggcat caggccggaa agaacatgtg
     3301 acagaaagga aaggaacaac aaaaggccgt gccgctggcg tttttccata ggctccgccc
     3361 cctgacgagc atcacaaaat cgacgctcaa gtcaaggtgg cgaaactcga caggactata
     3421 aacataccat gcgttttccc ctggaagctc cctcgtgcgc tctctgttcc gcccctgccg
     3481 cttaccggat acctgtccgc ctttcccctt cgggaagcgt ggcgctttct catagctcac
     3541 gctgttggca ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacggtcc
     3601 ccccgttcag cccgatcgtt gcgcttatcc ggtaactatc aacttgagtc cgaaccggaa
     3661 ggacatgaca aaacgcgact ggcagcgggc attgtaaaca ggattgcgcg agatgtatcg
     3721 agagttctga agtggtgcct aagtgcggct acatggaagg acaatttggt ggcatgtctg
     3781 gaacaagacg ttaccacggt taaagaatct gccaggatta actaaccttc gaaaaacccc
     3841 tgccagggtg ggtctctcgt tttctgagct aaagattacg cgtaagaaaa aaaggatccc
     3901 aaacaatatc ctttttgtaa tacagctata tgattcccgt gaactaaacg ctatatccaa
     3961 tacgataatc aacatttcag cttgacctgg atccagatca ccttttcaga tctactctac
     4021 aagcaaccca ttaccttccc gctcagcata ataccacgct accataaaaa tatctattga
     4081 ttgctctacc acttttcagt aatgcgctgt ctatcgagag agcgaggtca aagatagaaa
     4141 ttactaacca tcgtaccagc ttcgctagaa agacgattga tggtcgcttc aatacatgaa
     4201 tcattgctgc atagatatcg acatataacc cccaaaaaga ataacatcaa aataagatac
     4261 acataaaaaa atataaaatc aaatacaaac aacttaagca aaataagcaa aaataagaaa
     4321 gataagcaca gaatttgtag gtttgctttt atcgcataaa tcaaaccaca cccttaattt
     4381 aatctatata attaaaatca tgacgataaa aaactgaagc atgggacttc tatatgaaag
     4441 ataataaagc agttgtcgta ttaccggcaa aaatttagac ataatcagag ctgaggtagg
     4501 ttcaggttat tggctagcaa aagagaacgg attaatccgc caaatatctc atcgcagtaa
     4561 gaaaccggag agaaacatgg gcggtgaaag acctcgaaca cggagcctag ctttccctga
     4621 tcgcaaagat caccgaatgt ttcaacaacc tgattacgac gacagaaaag taattacatt
     4681 cgaggaatat gctgaaattt cagtgaaaaa ggcatggaaa atgctaatgg cggtcagcgt
     4741 tatccggttc ttatctgaca gcagaggaag cttcttcccg tatagggatg acgctagagc
     4801 agctgggagt ggaaaaaagt ccagacttca acactatctc agccgatccc ctctgcggaa
     4861 gagccgcaaa aactaagctc aacgagccag tagagctaag caagatataa gcaatgtacc
     4921 tgacatccat gtatcttcta ttacgataac tatcaacatc tgatctcttc gtatatctgg
     4981 tatcttaacc atagtcaaaa agaattaagc caatcatatg acaacaacaa tatacacaga
     5041 gtttgaattt gctgcttgtg atagcaaatg gtcagttcat ggacatcttg aagagatgtt
     5101 attgaaaaaa aagcaataca tatagatttc aaaggaaaag aagccatacc ccttacgtgt
     5161 ggtgatcatc cgatgatcgt cctaatgcta gctatgcagc tgaaattcat aagttccaga
     5221 gcagtacgtt agccttaatg gtctctacat ggatgtagaa gactctcacc ttcggcatgg
     5281 tggtccttga taaacactca ggtgctatat cagtaagtat gcacaccccc gatgattgcg
     5341 ataaaaagca aacaaatagt tacgatttag gttcaactgg cggtcgaatt tgagcacatt
     5401 gtctctacta tgcggaaaaa aggcttag
//
