LOCUS       NZ_CP094990             3182 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Shigella flexneri strain 3160_NCHU22 plasmid pS3160_3, complete
            sequence.
ACCESSION   NZ_CP094990
VERSION     NZ_CP094990.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27117281
            Assembly: GCF_022869845.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3182)
  AUTHORS   Hu,N.-J., Yang,J., Chen,Y.-T. and Li,R.-Y.
  TITLE     Shigella flexneri strain:3160_NCHU Genome sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3182)
  AUTHORS   Hu,N.-J., Yang,J., Chen,Y.-T. and Li,R.-Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-APR-2022) Institute of Genomics and Bioinformatics,
            National Chung Hsing University, 145 Xinda Rd., South Dist.,
            Taichung City 402, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 17-JAN-2022
            Assembly Method                   :: unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 147.0x
            Sequencing Technology             :: Illumina iSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022869845.1-RS_2024_06_02
            Annotation Date                   :: 06/02/2024 04:14:34
            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)                     :: 5,058
            CDSs (total)                      :: 4,926
            Genes (coding)                    :: 4,155
            CDSs (with protein)               :: 4,155
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 771
            CDSs (without protein)            :: 771
            Pseudo Genes (ambiguous residues) :: 0 of 771
            Pseudo Genes (frameshifted)       :: 288 of 771
            Pseudo Genes (incomplete)         :: 447 of 771
            Pseudo Genes (internal stop)      :: 176 of 771
            Pseudo Genes (multiple problems)  :: 134 of 771
            Pseudo Genes (short protein)      :: 1 of 771
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP094990.1.
            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="3160_NCHU22"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:623"
                     /plasmid="pS3160_3"
                     /geo_loc_name="Taiwan"
                     /lat_lon="23.87481812 N 121.08515853 E"
                     /collection_date="2000"
                     /collected_by="Nien-Jen Hu"
     gene            7..171
                     /locus_tag="MT485_RS25200"
                     /old_locus_tag="MT485_25200"
     CDS             7..171
                     /locus_tag="MT485_RS25200"
                     /old_locus_tag="MT485_25200"
                     /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"
     gene            817..951
                     /locus_tag="MT485_RS25455"
     CDS             817..951
                     /locus_tag="MT485_RS25455"
                     /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(1196..2305)
                     /gene="wzz(fepE)"
                     /locus_tag="MT485_RS25205"
                     /old_locus_tag="MT485_25205"
     CDS             complement(1196..2305)
                     /gene="wzz(fepE)"
                     /locus_tag="MT485_RS25205"
                     /old_locus_tag="MT485_25205"
                     /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)"
     Typing          complement(252..338)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(2637..2896)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.656"
                     /coverage="89.0"
                     /evalue="2.05e-109"
     Typing          complement(3021..3119)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          363..889
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 ctgaatatgg cgcgatgtat caaaagccag agcctgacac tgcttgaaaa actggatgct
       61 ctggatgccg acgaacaggc ggccatgtgc aaacgactgc acgaactcgc agaagaactc
      121 cagaacagca tccagattcg ctttgaggcc gaaagtgaaa caggaacata acgaagctga
      181 cggaggcggt cacggctttc ccgtgggcgt tttcgtcagc agacaagccc gtcagggcgc
      241 gtcagggggt tttagcgggt gtcggggcgc agccatgacc cagtcacgta gcgataacgg
      301 agtgtatact ggcttaatta tgaggcggca gagcagatgg tgagagaaca gcgacatatg
      361 aggtgtgaaa tgctgcacag atacgtaagg agaaaatgca gcttccggcg ctcttccgct
      421 tcctcgctca ctgactcgct gcgctcggtc gttcggctgc ggcgagcggt gtctgctcac
      481 gcaaagacgg atatacggtt atccacagaa tcaggggata acaccagaaa aaacatgtga
      541 gcaaaaaaga ggccccgaaa aaaggccgcg ccggtggcgt ttttccatag gctccgcccc
      601 cctgacgagc atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggactt
      661 aaagatacca ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc
      721 ggtttaccgg tgtcattccg ctgttatggc cgcgttcgtc tcattccacg cctgacactc
      781 agttccgggt aggcagttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
      841 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta
      901 acgccattgg cagcggccac tggtaaacag gatgtgcgag agatgtattg agagttcttg
      961 aagtggcagc cttactgagg ctacactaga aggacagatt tggtgacatg tctcgcacaa
     1021 gactgttacc acggttcaga agttccccaa cttactgaac cttcgaaaaa ccacctcccc
     1081 aggtggtttt ttcgttttct agagtagaag actacggctg taagggaatg atctcaagaa
     1141 gatcctttga actttttata aaagttgctt ataaaatgat gcatcagcac aacttttact
     1201 caatcacact catctttctg gcctccatgg catgacgtaa aagtatatag ccacatgcaa
     1261 gcatccctcc aatgacagaa gaaagaatta caattatggc attacttggc ccatcctttc
     1321 tgaccggtaa cgttgggctc aattgatact gaaatggcat aaaatcaaca tcccccactt
     1381 tcgccacaac caattgattc acaacatatt gacgatttcg caactcccca ctcaattccg
     1441 aaacatcctt gattgatttt ttgatgttca atttagttgc tataccatca gaaccgagag
     1501 ccacaggaaa atctgggtca tccttcataa tctgaccatt gctgtataca ggttttttta
     1561 ttccagccgc attagcaacc tccagtgaat aattgaggcg tcgaatatct gcattcagct
     1621 ggtttctaat ttttatctca tccagtgcaa gaatttcttt ttcaacatta gttttaactt
     1681 ctagtttatt tcttatatct tccatcaaat cccttacaac aagggaagaa acataattaa
     1741 tatacccaga caacacatcg tgagcttctt tacttgttgg agcagtaaaa ctcagagtcc
     1801 atgatacata caatgatgac ttgtcgtttt tcttactggc attatcatca atcgacttca
     1861 tatttttact caactcaaca attgcacgat gcagttcgag agcgctaatg ttattctttt
     1921 taataatctc cataacataa ggagatgatc tcatatactc attcaacgaa ttaacggact
     1981 gaaatttctt aataaacaga gcaaatgcgc tatcacgatt gatatcaaaa tccactccca
     2041 gaacatgaag cttggaaagc tccttattta attcactcca ttgaacagac tcagcaggag
     2101 taaccacagc agaactagtc catttttgtg gcaaaacaaa agaaacaaga aagccaatac
     2161 aagcaaaaaa tagaatcacc ccaacaattt ttatttttgc tgcccataaa acgctaatca
     2221 agccaaaaag gtcaatttct tcattaccat tcggcaacat gttgtaatta gaaaaatgtt
     2281 cgtcagagac ctttgagatt ttcattgaaa aaaacacaat atattaacat atggtttttt
     2341 tattctatca tatgttagga aaaaacctaa aaaccattca gcagacattt aacataacat
     2401 tttattgcgc gcaccgctaa aacgcgctga acgcgattct gccgcaaaca ccgcaaaaag
     2461 agatgttttc cccggggtaa accggaaaaa tgcgtcagga tcgctttcag ctcactgcat
     2521 agctatgcat gaaagtgaat gacgatcggt ttgggcgcat acagtgccca tgagacacat
     2581 tttcggacat tttcagttcg tgaatccctg actcattgct acatatctga acagacaccc
     2641 ctagcagcgc ccccaggggc gtcctgtaaa aaaacacacc gcgccgctag cagcacccct
     2701 aatataagat aatgtttttt ttttatgaaa atagtcagta ccacccctaa aaagcggtgt
     2761 tggcgcagct acaacaccgc gccgacaccg cttttttaaa tatcacaaag agagcaagaa
     2821 gaactaattt gtcataactc tctatttata aagaaaaatc agcaaaaact tgtttttgcg
     2881 tggggtgtgg gcatttcagg catgagaaca gactcgcgtt tttccggagt atcagcggaa
     2941 ttattgatta agaaacactc gacgcagagc gaaattttat gcaacagcgg ctgcactgca
     3001 cagggattat ttatcagttg atatgctgtg ccatgatacg tcctaaagaa acaggacagg
     3061 atgtgcaatt gtaataccgt cgcccgcaac gtcttacaat taccacctgc tcagggtccc
     3121 cccccccgac acccggaact gacggagaac aacggaaggt gaacaaataa caacaaactg
     3181 cg
//
