LOCUS       NZ_CP151327             3182 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella flexneri strain R20.0210 plasmid pR20.0210_3k, complete
            sequence.
ACCESSION   NZ_CP151327
VERSION     NZ_CP151327.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735799
            Assembly: GCF_038366275.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3182)
  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  JOURNAL   Unpublished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 3182)
  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_038366275.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:43:36
            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)                     :: 5,201
            CDSs (total)                      :: 5,075
            Genes (coding)                    :: 4,289
            CDSs (with protein)               :: 4,289
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 786
            CDSs (without protein)            :: 786
            Pseudo Genes (ambiguous residues) :: 0 of 786
            Pseudo Genes (frameshifted)       :: 286 of 786
            Pseudo Genes (incomplete)         :: 452 of 786
            Pseudo Genes (internal stop)      :: 182 of 786
            Pseudo Genes (multiple problems)  :: 131 of 786
            Pseudo Genes (short protein)      :: 5 of 786
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151327.1.
            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..3182
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="R20.0210"
                     /db_xref="taxon:623"
                     /plasmid="pR20.0210_3k"
                     /collected_by="Taiwan CDC"
     gene            join(2783..3182,1..710)
                     /gene="wzz(fepE)"
                     /locus_tag="AADX61_RS25995"
                     /old_locus_tag="AADX61_26000"
     CDS             join(2783..3182,1..710)
                     /gene="wzz(fepE)"
                     /locus_tag="AADX61_RS25995"
                     /old_locus_tag="AADX61_26000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_005065596.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(955..1089)
                     /locus_tag="AADX61_RS26000"
                     /old_locus_tag="AADX61_26005"
     CDS             complement(955..1089)
                     /locus_tag="AADX61_RS26000"
                     /old_locus_tag="AADX61_26005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606675.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     gene            complement(1735..1899)
                     /locus_tag="AADX61_RS26005"
                     /old_locus_tag="AADX61_26010"
     CDS             complement(1735..1899)
                     /locus_tag="AADX61_RS26005"
                     /old_locus_tag="AADX61_26010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_000090200.1"
                     /translation="MARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQIR
                     FEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1569..1655
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          1970..2068
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2193..2452
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.656"
                     /coverage="89.0"
                     /evalue="2.05e-109"
     Typing          complement(1018..1544)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 gcgctctcga actgcatcgt gcaattgttg agttgagtaa aaatatgaag tcgattgatg
       61 ataatgccag taagaaaaac gacaagtcat cattgtatgt atcatggact ctgagtttta
      121 ctgctccaac aagtaaagaa gctcacgatg tgttgtctgg gtatattaat tatgtttctt
      181 cccttgttgt aagggatttg atggaagata taagaaataa actagaagtt aaaactaatg
      241 ttgaaaaaga aattcttgca ctggatgaga taaaaattag aaaccagctg aatgcagata
      301 ttcgacgcct caattattca ctggaggttg ctaatgcggc tggaataaaa aaacctgtat
      361 acagcaatgg tcagattatg aaggatgacc cagattttcc tgtggctctc ggttctgatg
      421 gtatagcaac taaattgaac atcaaaaaat caatcaagga tgtttcggaa ttgagtgggg
      481 agttgcgaaa tcgtcaatat gttgtgaatc aattggttgt ggcgaaagtg ggggatgttg
      541 attttatgcc atttcagtat caattgagcc caacgttacc ggtcagaaag gatgggccaa
      601 gtaatgccat aattgtaatt ctttcttctg tcattggagg gatgcttgca tgtggctata
      661 tacttttacg tcatgccatg gaggccagaa agatgagtgt gattgagtaa aagttgtgct
      721 gatgcatcat tttataagca acttttataa aaagttcaaa ggatcttctt gagatcattc
      781 ccttacagcc gtagtcttct actctagaaa acgaaaaaac cacctgggga ggtggttttt
      841 cgaaggttca gtaagttggg gaacttctga accgtggtaa cagtcttgtg cgagacatgt
      901 caccaaatct gtccttctag tgtagcctca gtaaggctgc cacttcaaga actctcaata
      961 catctctcgc acatcctgtt taccagtggc cgctgccaat ggcgttaagt cgtgtcttac
     1021 cgggttggac tcaagacgat agttaccgga taaggcgcag cggtcgggct gaacgggggg
     1081 ttcgtgcaca cagcccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg
     1141 aatgagacga acgcggccat aacagcggaa tgacaccggt aaaccgaaag gcaggaacag
     1201 gagagcgcac gagggagcca ccagggggaa acgcctggta tctttaagtc ctgtcgggtt
     1261 tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg
     1321 gaaaaacgcc accggcgcgg ccttttttcg gggcctcttt tttgctcaca tgttttttct
     1381 ggtgttatcc cctgattctg tggataaccg tatatccgtc tttgcgtgag cagacaccgc
     1441 tcgccgcagc cgaacgaccg agcgcagcga gtcagtgagc gaggaagcgg aagagcgccg
     1501 gaagctgcat tttctcctta cgtatctgtg cagcatttca cacctcatat gtcgctgttc
     1561 tctcaccatc tgctctgccg cctcataatt aagccagtat acactccgtt atcgctacgt
     1621 gactgggtca tggctgcgcc ccgacacccg ctaaaacccc ctgacgcgcc ctgacgggct
     1681 tgtctgctga cgaaaacgcc cacgggaaag ccgtgaccgc ctccgtcagc ttcgttatgt
     1741 tcctgtttca ctttcggcct caaagcgaat ctggatgctg ttctggagtt cttctgcgag
     1801 ttcgtgcagt cgtttgcaca tggccgcctg ttcgtcggca tccagagcat ccagtttttc
     1861 aagcagtgtc aggctctggc ttttgataca tcgcgccata ttcagcgcag tttgttgtta
     1921 tttgttcacc ttccgttgtt ctccgtcagt tccgggtgtc gggggggggg accctgagca
     1981 ggtggtaatt gtaagacgtt gcgggcgacg gtattacaat tgcacatcct gtcctgtttc
     2041 tttaggacgt atcatggcac agcatatcaa ctgataaata atccctgtgc agtgcagccg
     2101 ctgttgcata aaatttcgct ctgcgtcgag tgtttcttaa tcaataattc cgctgatact
     2161 ccggaaaaac gcgagtctgt tctcatgcct gaaatgccca caccccacgc aaaaacaagt
     2221 ttttgctgat ttttctttat aaatagagag ttatgacaaa ttagttcttc ttgctctctt
     2281 tgtgatattt aaaaaagcgg tgtcggcgcg gtgttgtagc tgcgccaaca ccgcttttta
     2341 ggggtggtac tgactatttt cataaaaaaa aaacattatc ttatattagg ggtgctgcta
     2401 gcggcgcggt gtgttttttt acaggacgcc cctgggggcg ctgctagggg tgtctgttca
     2461 gatatgtagc aatgagtcag ggattcacga actgaaaatg tccgaaaatg tgtctcatgg
     2521 gcactgtatg cgcccaaacc gatcgtcatt cactttcatg catagctatg cagtgagctg
     2581 aaagcgatcc tgacgcattt ttccggttta ccccggggaa aacatctctt tttgcggtgt
     2641 ttgcggcaga atcgcgttca gcgcgtttta gcggtgcgcg caataaaatg ttatgttaaa
     2701 tgtctgctga atggttttta ggttttttcc taacatatga tagaataaaa aaaccatatg
     2761 ttaatatatt gtgttttttt caatgaaaat ctcaaaggtc tctgacgaac atttttctaa
     2821 ttacaacatg ttgccgaatg gtaatgaaga aattgacctt tttggcttga ttagcgtttt
     2881 atgggcagca aaaataaaaa ttgttggggt gattctattt tttgcttgta ttggctttct
     2941 tgtttctttt gttttgccac aaaaatggac tagttctgct gtggttactc ctgctgagtc
     3001 tgttcaatgg agtgaattaa ataaggagct ttccaagctt catgttctgg gagtggattt
     3061 tgatatcaat cgtgatagcg catttgctct gtttattaag aaatttcagt ccgttaattc
     3121 gttgaatgag tatatgagat catctcctta tgttatggag attattaaaa agaataacat
     3181 ta
//
