LOCUS       NZ_CP151332             4044 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella flexneri strain R20.0053 plasmid pR20.0053_4k, complete
            sequence.
ACCESSION   NZ_CP151332
VERSION     NZ_CP151332.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735798
            Assembly: GCF_038361275.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4044)
  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  JOURNAL   Unpublished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 4044)
  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_038361275.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:35:12
            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)                     :: 5,219
            CDSs (total)                      :: 5,089
            Genes (coding)                    :: 4,288
            CDSs (with protein)               :: 4,288
            Genes (RNA)                       :: 130
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 101
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 801
            CDSs (without protein)            :: 801
            Pseudo Genes (ambiguous residues) :: 0 of 801
            Pseudo Genes (frameshifted)       :: 290 of 801
            Pseudo Genes (incomplete)         :: 465 of 801
            Pseudo Genes (internal stop)      :: 182 of 801
            Pseudo Genes (multiple problems)  :: 133 of 801
            Pseudo Genes (short protein)      :: 5 of 801
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151332.1.
            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..4044
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="R20.0053"
                     /db_xref="taxon:623"
                     /plasmid="pR20.0053_4k"
                     /collected_by="Taiwan CDC"
     gene            join(3689..4044,1..175)
                     /locus_tag="AADX64_RS26050"
                     /old_locus_tag="AADX64_26050"
     CDS             join(3689..4044,1..175)
                     /locus_tag="AADX64_RS26050"
                     /old_locus_tag="AADX64_26050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067502.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLSDEFRKLEESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            182..415
                     /locus_tag="AADX64_RS26055"
                     /old_locus_tag="AADX64_26055"
     CDS             182..415
                     /locus_tag="AADX64_RS26055"
                     /old_locus_tag="AADX64_26055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137443.1"
                     /translation="MTELESHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVLHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(963..1430)
                     /locus_tag="AADX64_RS26060"
                     /old_locus_tag="AADX64_26060"
     CDS             complement(963..1430)
                     /locus_tag="AADX64_RS26060"
                     /old_locus_tag="AADX64_26060"
                     /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_014526575.1"
                     /translation="MRIDISHQTRHTPPNMLPREQNCVAMALSACFRQQLNPVVNSLLK
                     ERIIHSPKELEHDNAVIRVLQKLQIQEVCNSTLWETAKQQLLQKSDGRYFAINSKHLAF
                     PGPGESHAFCCIKYKNAIGINGNNAETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(1672..1830)
                     /locus_tag="AADX64_RS26065"
                     /old_locus_tag="AADX64_26065"
     CDS             complement(1672..1830)
                     /locus_tag="AADX64_RS26065"
                     /old_locus_tag="AADX64_26065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005093880.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="hypothetical protein"
     gene            complement(2432..2623)
                     /locus_tag="AADX64_RS26070"
                     /old_locus_tag="AADX64_26070"
     CDS             complement(2432..2623)
                     /locus_tag="AADX64_RS26070"
                     /old_locus_tag="AADX64_26070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165994.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLYDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2688..3011
                     /locus_tag="AADX64_RS26075"
                     /old_locus_tag="AADX64_26075"
     CDS             2688..3011
                     /locus_tag="AADX64_RS26075"
                     /old_locus_tag="AADX64_26075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956004.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQAARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3220..>3651
                     /locus_tag="AADX64_RS26080"
                     /old_locus_tag="AADX64_26080"
                     /pseudo=""
     CDS             3220..>3651
                     /locus_tag="AADX64_RS26080"
                     /old_locus_tag="AADX64_26080"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          2327..2413
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(1759..2316)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.032"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..519
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.532"
                     /coverage="100.0"
                     /evalue="7.32e-69"
     Typing          3002..4044
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.402"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agaaatcagg aagcagaacg agagtctgga gaagctgaac gcgaagacat ggggcgtgcg
       61 ttatcacgag gggagcaacg gacgttttct ggtgttgccc gaggggatga aagccgaaac
      121 gaactggacg atggaaaacg ggaaacagaa tgccgtaagg ctggtacagg agtgacagag
      181 catgacggag ctggaaagcc atttgctgaa cgcattagag cagctgcaac aggactatat
      241 gcagcggctg aacgaatggg agagcgcctt cgtggaattg cagaaaatgt tttcgcttac
      301 gcaacgggac aacgcgatgc tgaacgagcg ggtcatgcag ttgagtcagc aggtgctgca
      361 cttgagcgag cagacagaac gcttgagcca gttatacagc gagaactgga gataagagag
      421 gaacggttga tacaggagcg cgaacatgcg ttattcctgg aacgggaacg ccagccggaa
      481 atacaggaac ggacactgga tggcccttcg ctgggatggt aatcagagac aggctaaaat
      541 gttgtcagcg cgtttccggt gcattttttg ggataatggt tggttcgggg gcaccgggaa
      601 cgcgcttcag tcagaccttg ctgaaaacac aggaacgagt taaaacgcat acgggcgcga
      661 ttctggtgtg tcttttgtcg ctgtgttttg cctctattgc cagatcgcgc tcattcccct
      721 gaacttctgt tttcccgctc aggtccccgt cttcttcgct tccgaaagca tgaataaaat
      781 ccgtttcagc tgtctctggc tggcaattcc tgcgtgattc acatggctgc atagctatgc
      841 atgtggttaa aatttaccgg gtgcgatcgc ggcagttttt cgggtggttt gttgccattt
      901 ttacctgtct gctgccgtga tcgcgccgaa cgcgtttcag cggtgcgtac aattttaaga
      961 tattacgtta aattgtgagg gaatggtccc catatactga ctttatcata gggatagggt
     1021 tggtagtggg tcgattgggt ttcggcattg tttccgttaa tgccaattgc atttttgtat
     1081 ttgatgcaac agaaggcgtg agattctcct gggcctggaa aggctaagtg tttagaattg
     1141 atggcaaaat atcttccgtc cgatttttga agtagttgtt gtttggctgt ctcccaaagg
     1201 gtgctgttac aaacttcttg aatttgtagt ttttgcagga ctcttattac tgcgttgtca
     1261 tgttccaatt ctttagggga gtgtattatt ctctctttta ataagctgtt taccacaggg
     1321 tttagttgtt gtctaaagca cgcagataat gccattgcta cacaattttg ttcccgagga
     1381 agcatgtttg gcggggtatg ccgtgtttga tgtgatatgt ctattctcat agaaggtctc
     1441 tggcttatag catcaacaaa tacggctata aaacaaaatt ttcatagagt gattcaagat
     1501 cttcttgaga tccttttttg cggcgcgtaa tctgctgcct gcaaacaaaa aaaccaccgc
     1561 taccaacggt ggtttgtttg ccggaatcta gagttaccaa ctctttcttc cgaaggtaac
     1621 tggcttggtg gagcacagat accaaatgct gtccttctag tgtagccgca gttaggccac
     1681 cacttcaaga actcttaata tctcaatcca ccttgtccag ttaccaatgg ctgctgccag
     1741 tggcgttaag tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca
     1801 gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac
     1861 cgaactgaga taccaacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa
     1921 ggcggacagg tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc
     1981 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg
     2041 tcggtttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcca tcggcgcggc
     2101 cttcttcctg ttcctggtct tttgctcaca tgttctttcc ggcgttatcc cctgattctg
     2161 tggataacag catttcgttt ttgagtgagt agataccgct cgccgcagtc gaacgaccga
     2221 gcgtagcgag tcagtgagcg aggaagcgga aaagcgcctg gacgtgcatt ttctccttac
     2281 gcatctgtgc ggcatttcac acccggtatg gcgcactttt catacaatcc gcactgatgc
     2341 cgcatggtta agccagtata cactccgcta tcgctacgtg actgggtcat ggctgcgccc
     2401 cgacacccgc taacacccgc tgacaagccc gtcagaggtt ttcaccgtca tccccgaagc
     2461 gagcgaggca actgcggtaa agctcatcgg cgtggtcgta aagcgattca cagatgtctg
     2521 cctgttcatc cgcgtccagt tcgttgagct tctccagcag cgttaatgtc tggcttctga
     2581 taaagcgggc catgttaagg gcggtttttt cctgtttggt cactgatgcc tccgtgtaag
     2641 ggggatttct gttcatgggg gtaatgatac cgatgaaacg cgagaggatg ctcacgatac
     2701 gggttactga tgatgaacat gcccggttac tggaacgctg tgagggtaaa cagctggcgg
     2761 tatggatgcg gcgggtctgc ctgggtgagc cggttgcccg ttccgggagg ctgccgacac
     2821 tggcaccgcc gttactgcgt cagctggccg ccatcgggaa taacctgaat caggcagcga
     2881 ggaaggtgaa cagcgggcag tggtcttccg gtgaccgggt tcaggtggtg gccgcactga
     2941 tggccatcgg ggatgagctg cgccggctgc gtctggccgt cagggaacag gggacgcggg
     3001 atgatagtta agtttcatgc caggggaaaa ggcggtggca gtggtccggt tgattacctg
     3061 ctgggaaggg agcgtaaccg ggaaggggca acggtgcttc agggtaatcc ggaagaagtc
     3121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtccggtgt tctctcgttc
     3181 gcggagaagg agctgccgcc gggagggcgt gaaaaagtga tggcgagctt tgagcgtgta
     3241 ctgatgcccg gtctcgaaaa aaatcagtac agcattctgt gggtggagca ccaggacaag
     3301 gggcggcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
     3361 cagccgtact acgaccgcgc agacaggccg agaattgatg cctggcagac gctggtgaat
     3421 caccattacg ggctgcatga cccgaacgcc ccggagaacc gccggacgct gactctccct
     3481 gataacctgc cggaaacgaa acaggcgctt gctgagagca ttacacggtg gatagacgct
     3541 ctttatcatg tcggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggcg
     3601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
     3661 aagaatatca gactgaaagg agcattctat gagcaatctt ttacagacgg gcgcggagtt
     3721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaaa atgctgagcg acgagttcag
     3781 gaagctcgaa gaatctgtaa gcaaggctgt gacatcaaac gagacgaaaa tcaaagacgc
     3841 tatagccctg ttcacagctt cgacagagga atcactgaaa aaacatcggg aaggggtgaa
     3901 agaggcgatg atgcagcaca ggaaggacgt gttaaagctg gcagggaata cgggcatgat
     3961 gttactgggg atggtcattt tcctgtttac cgtgagtggc gggacgctct ggtatcttgg
     4021 cgggatgata caggcgaacc tgga
//
