LOCUS       NZ_CP055040             2453 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_60 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP055040
VERSION     NZ_CP055040.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925587
            Assembly: GCF_022354005.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2453)
  AUTHORS   Che,Y., Xu,X., Yang,Y., Brinda,K., Hanage,W., Yang,C. and Zhang,T.
  TITLE     High-resolution genomic surveillance elucidates a multilayered
            hierarchical transfer of resistance between WWTP- and
            human/animal-associated bacteria
  JOURNAL   Microbiome 10 (1), 16 (2022)
   PUBMED   35078531
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2453)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: "Other" v. Unicycler
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022354005.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 04:54:20
            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)                     :: 4,864
            CDSs (total)                      :: 4,740
            Genes (coding)                    :: 4,494
            CDSs (with protein)               :: 4,494
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 246
            CDSs (without protein)            :: 246
            Pseudo Genes (ambiguous residues) :: 0 of 246
            Pseudo Genes (frameshifted)       :: 65 of 246
            Pseudo Genes (incomplete)         :: 170 of 246
            Pseudo Genes (internal stop)      :: 46 of 246
            Pseudo Genes (multiple problems)  :: 36 of 246
            Pseudo Genes (short protein)      :: 5 of 246
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055040.1.
            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..2453
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_60"
                     /isolation_source="Shek Wu Hui WWTPs_60 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(219..518)
                     /locus_tag="HUZ72_RS24165"
                     /old_locus_tag="HUZ72_23975"
     CDS             complement(219..518)
                     /locus_tag="HUZ72_RS24165"
                     /old_locus_tag="HUZ72_23975"
                     /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_016247612.1"
                     /translation="MKKILFCSLLLLSASSFAQQFHYQCEGRDLKIMLSPNAAFLDGKS
                     FEYKNGETNGETTKMTFFGPSGEVLKFLVNPVNNLYRMGLTSGATFEEINCTEI"
                     /name="hypothetical protein"
     gene            complement(542..781)
                     /locus_tag="HUZ72_RS24170"
                     /old_locus_tag="HUZ72_23980"
     CDS             complement(542..781)
                     /locus_tag="HUZ72_RS24170"
                     /old_locus_tag="HUZ72_23980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001560795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001560795.1"
                     /translation="MIKKICITVIVVFLLLVGYGAWIGSEQNQRGVSLFEVAYTYNAMN
                     PISRIGYTFMLKRNHALVERAGEVKKSIDSMSGE"
                     /name="hypothetical protein"
     gene            1014..1202
                     /locus_tag="HUZ72_RS24175"
                     /old_locus_tag="HUZ72_23985"
     CDS             1014..1202
                     /locus_tag="HUZ72_RS24175"
                     /old_locus_tag="HUZ72_23985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1250..1477)
                     /locus_tag="HUZ72_RS24180"
                     /old_locus_tag="HUZ72_23990"
     CDS             complement(1250..1477)
                     /locus_tag="HUZ72_RS24180"
                     /old_locus_tag="HUZ72_23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224019247.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     Typing          1950..2439
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.325"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ttagtcttga agtcatgcgc cggttaaggc taaactgaaa ggacaagttt tggtgactgc
       61 gctcctccaa gccagttacc tcggttcaaa gagttggtag ctcagagaac cttcgaaaaa
      121 ccgccctgca aggcggtttt ttcgttttca gagcaagaga ttacgcgcag accaaaacga
      181 tctcaagaag atcatcttat taatcagata aaatatttct agatttcagt gcaatttatc
      241 tcttcaaatg tagcacctga agtcagcccc atacgatata agttgttgac aggattaacc
      301 aaaaacttga gaacctcacc agaaggacca aagaaggtca tctttgtcgt ttccccattc
      361 gtctctccat tcttatattc gaatgattta ccatcaagaa aagctgcatt aggtgaaagc
      421 attatcttta aatctcgtcc ttcacactga taatggaatt gttgtgcaaa tgaacttgca
      481 gaaagaagaa gcagcgaaca aaaaagtatc tttttcatat cagtccttta aatttaaaaa
      541 atcactcacc actcatgcta tcaatagatt tcttaacctc tccagccctc tcgactaaag
      601 catgatttct cttcagcata aatgtatagc cgatccgact aattggattc attgcgttgt
      661 atgtatatgc aacctcaaat aaagatactc ctcgctgatt ttgctcagat ccaatccaag
      721 caccatagcc aaccaacagc aaaaaaacga cgataacagt aatgcagatt ttttttatca
      781 ttccctatcc agataatatg aagaaaacag aattgaacat aacatccgtt gcccgcacca
      841 cctcaggcgc cctcagggcg tttctgagga ctccggcctg aaacatacac ctttctgtgc
      901 ccatatcgag aaaaaacgcc cctgatgatt tctgcgtacc tgcatggcta tgcactcaag
      961 tgaatgaagt aagatttcag tctgcgatca ccataaaacc gggaaaaagc cgtatgacaa
     1021 aacaggaatc agccgcactg aacatggcaa aatttatccg ggcgcagtcg ctgctgctgc
     1081 tcgaaaaact cgacgtgctc gatcttgatg acgaggcagc cgactgtgag cgaatgcacg
     1141 aacaggcaga agcgctttat cagaagctga gcgcacgctt cggcatacag gacggcgaat
     1201 aaagagacga aaagaacgct cacttagacg aaaagcgtat ccagggcaac tatgtatatc
     1261 caccgtgtac atagtcatgc ctgacgcttt cgagcaggtc gagcatgtag gaacgacgag
     1321 cttgattggt atcggacaca atatggcgat acgcctcaaa cataacagca cccgcatcac
     1381 cgcccgaacg gcgaagcata gcggaaatca tccgcacaaa gagcagacgt tcatcggggc
     1441 aaaggttcat aagttctcct ggtgaaaaac caaacatgaa gcacccatct attaacgtca
     1501 gctgtgaacg cttcattaga agaaaatagg taaacccggg aaaaagatcc aaacgttaac
     1561 atcacaggta aacagaaacg tcgggtcgat cgggaaattc tttcccggac ggcgcggggt
     1621 tgggcaagcc gcaggcgcgt cagtgctttt agcgggtgtc ggggcgcagc cctgaaccag
     1681 tcacgtagcg ctagcggagt gtatactggc taaacttcag agatgccaag gaagggacag
     1741 gatatgtttt gtagcaccgc caccacggtg gcgatactcc aaaacgcctg gtcagggcac
     1801 agccccgaca ccccagagcc gactgtaggt cactggacga acgcggcgga atgatgtcgg
     1861 atgacgtcat tttgcggcgt ttgccctatc ctgcatcgta ttaaaaaatg cagctatggc
     1921 gcgtacggtg ccaaagataa gcccggagat attccgcttc ctcgctcact gactcgctcc
     1981 gctcggtcgt tcggctgcgg cgagcggtac cggcttactg gcggggcgga aatttcctgg
     2041 catcttccag gaagaagctt aacagggaag caagaaggcc acggcgaagc cgtttttcca
     2101 taggctccgc ccccctgaca agcatcacga aatctgacgc tcaaatcagt ggtggcgaaa
     2161 cccgacagga cttaaagata ccaggcgttt ccccctggtg gctccctcgt gcgctctcct
     2221 gttcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt atctcattcc
     2281 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
     2341 ccccgttcag tccgaccgct gcgccttgtc cggtaactat cgtcttgagt ccaacccgga
     2401 aagacatgca aaagcaccac tggcagcagc cactggtaat tgatttagag gag
//
