LOCUS       NZ_CP151348             3182 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella flexneri strain R19.0876 plasmid pR19.0876_3k, complete
            sequence.
ACCESSION   NZ_CP151348
VERSION     NZ_CP151348.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735796
            Assembly: GCF_038367165.1
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  JOURNAL   Unpublished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_038367165.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:53:55
            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)                     :: 5,205
            CDSs (total)                      :: 5,075
            Genes (coding)                    :: 4,283
            CDSs (with protein)               :: 4,283
            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)              :: 792
            CDSs (without protein)            :: 792
            Pseudo Genes (ambiguous residues) :: 0 of 792
            Pseudo Genes (frameshifted)       :: 287 of 792
            Pseudo Genes (incomplete)         :: 459 of 792
            Pseudo Genes (internal stop)      :: 182 of 792
            Pseudo Genes (multiple problems)  :: 133 of 792
            Pseudo Genes (short protein)      :: 5 of 792
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151348.1.
            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="R19.0876"
                     /db_xref="taxon:623"
                     /plasmid="pR19.0876_3k"
                     /collected_by="Taiwan CDC"
     gene            1..1110
                     /gene="wzz(fepE)"
                     /locus_tag="AADX54_RS26015"
                     /old_locus_tag="AADX54_26020"
     CDS             1..1110
                     /gene="wzz(fepE)"
                     /locus_tag="AADX54_RS26015"
                     /old_locus_tag="AADX54_26020"
                     /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(1355..1489)
                     /locus_tag="AADX54_RS26020"
                     /old_locus_tag="AADX54_26025"
     CDS             complement(1355..1489)
                     /locus_tag="AADX54_RS26020"
                     /old_locus_tag="AADX54_26025"
                     /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(2135..2299)
                     /locus_tag="AADX54_RS26025"
                     /old_locus_tag="AADX54_26030"
     CDS             complement(2135..2299)
                     /locus_tag="AADX54_RS26025"
                     /old_locus_tag="AADX54_26030"
                     /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          1969..2055
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2370..2468
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2593..2852
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.656"
                     /coverage="89.0"
                     /evalue="2.05e-109"
     Typing          complement(1418..1944)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 atgaaaatct caaaggtctc tgacgaacat ttttctaatt acaacatgtt gccgaatggt
       61 aatgaagaaa ttgacctttt tggcttgatt agcgttttat gggcagcaaa aataaaaatt
      121 gttggggtga ttctattttt tgcttgtatt ggctttcttg tttcttttgt tttgccacaa
      181 aaatggacta gttctgctgt ggttactcct gctgagtctg ttcaatggag tgaattaaat
      241 aaggagcttt ccaagcttca tgttctggga gtggattttg atatcaatcg tgatagcgca
      301 tttgctctgt ttattaagaa atttcagtcc gttaattcgt tgaatgagta tatgagatca
      361 tctccttatg ttatggagat tattaaaaag aataacatta gcgctctcga actgcatcgt
      421 gcaattgttg agttgagtaa aaatatgaag tcgattgatg ataatgccag taagaaaaac
      481 gacaagtcat cattgtatgt atcatggact ctgagtttta ctgctccaac aagtaaagaa
      541 gctcacgatg tgttgtctgg gtatattaat tatgtttctt cccttgttgt aagggatttg
      601 atggaagata taagaaataa actagaagtt aaaactaatg ttgaaaaaga aattcttgca
      661 ctggatgaga taaaaattag aaaccagctg aatgcagata ttcgacgcct caattattca
      721 ctggaggttg ctaatgcggc tggaataaaa aaacctgtat acagcaatgg tcagattatg
      781 aaggatgacc cagattttcc tgtggctctc ggttctgatg gtatagcaac taaattgaac
      841 atcaaaaaat caatcaagga tgtttcggaa ttgagtgggg agttgcgaaa tcgtcaatat
      901 gttgtgaatc aattggttgt ggcgaaagtg ggggatgttg attttatgcc atttcagtat
      961 caattgagcc caacgttacc ggtcagaaag gatgggccaa gtaatgccat aattgtaatt
     1021 ctttcttctg tcattggagg gatgcttgca tgtggctata tacttttacg tcatgccatg
     1081 gaggccagaa agatgagtgt gattgagtaa aagttgtgct gatgcatcat tttataagca
     1141 acttttataa aaagttcaaa ggatcttctt gagatcattc ccttacagcc gtagtcttct
     1201 actctagaaa acgaaaaaac cacctgggga ggtggttttt cgaaggttca gtaagttggg
     1261 gaacttctga accgtggtaa cagtcttgtg cgagacatgt caccaaatct gtccttctag
     1321 tgtagcctca gtaaggctgc cacttcaaga actctcaata catctctcgc acatcctgtt
     1381 taccagtggc cgctgccaat ggcgttaagt cgtgtcttac cgggttggac tcaagacgat
     1441 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     1501 tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagacga acgcggccat
     1561 aacagcggaa tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcca
     1621 ccagggggaa acgcctggta tctttaagtc ctgtcgggtt tcgccacctc tgacttgagc
     1681 gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc accggcgcgg
     1741 ccttttttcg gggcctcttt tttgctcaca tgttttttct ggtgttatcc cctgattctg
     1801 tggataaccg tatatccgtc tttgcgtgag cagacaccgc tcgccgcagc cgaacgaccg
     1861 agcgcagcga gtcagtgagc gaggaagcgg aagagcgccg gaagctgcat tttctcctta
     1921 cgtatctgtg cagcatttca cacctcatat gtcgctgttc tctcaccatc tgctctgccg
     1981 cctcataatt aagccagtat acactccgtt atcgctacgt gactgggtca tggctgcgcc
     2041 ccgacacccg ctaaaacccc ctgacgcgcc ctgacgggct tgtctgctga cgaaaacgcc
     2101 cacgggaaag ccgtgaccgc ctccgtcagc ttcgttatgt tcctgtttca ctttcggcct
     2161 caaagcgaat ctggatgctg ttctggagtt cttctgcgag ttcgtgcagt cgtttgcaca
     2221 tggccgcctg ttcgtcggca tccagagcat ccagtttttc aagcagtgtc aggctctggc
     2281 ttttgataca tcgcgccata ttcagcgcag tttgttgtta tttgttcacc ttccgttgtt
     2341 ctccgtcagt tccgggtgtc gggggggggg accctgagca ggtggtaatt gtaagacgtt
     2401 gcgggcgacg gtattacaat tgcacatcct gtcctgtttc tttaggacgt atcatggcac
     2461 agcatatcaa ctgataaata atccctgtgc agtgcagccg ctgttgcata aaatttcgct
     2521 ctgcgtcgag tgtttcttaa tcaataattc cgctgatact ccggaaaaac gcgagtctgt
     2581 tctcatgcct gaaatgccca caccccacgc aaaaacaagt ttttgctgat ttttctttat
     2641 aaatagagag ttatgacaaa ttagttcttc ttgctctctt tgtgatattt aaaaaagcgg
     2701 tgtcggcgcg gtgttgtagc tgcgccaaca ccgcttttta ggggtggtac tgactatttt
     2761 cataaaaaaa aaacattatc ttatattagg ggtgctgcta gcggcgcggt gtgttttttt
     2821 acaggacgcc cctgggggcg ctgctagggg tgtctgttca gatatgtagc aatgagtcag
     2881 ggattcacga actgaaaatg tccgaaaatg tgtctcatgg gcactgtatg cgcccaaacc
     2941 gatcgtcatt cactttcatg catagctatg cagtgagctg aaagcgatcc tgacgcattt
     3001 ttccggttta ccccggggaa aacatctctt tttgcggtgt ttgcggcaga atcgcgttca
     3061 gcgcgtttta gcggtgcgcg caataaaatg ttatgttaaa tgtctgctga atggttttta
     3121 ggttttttcc taacatatga tagaataaaa aaaccatatg ttaatatatt gtgttttttt
     3181 ca
//
