LOCUS       NZ_CP055209             1551 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed10, complete
            sequence.
ACCESSION   NZ_CP055209
VERSION     NZ_CP055209.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925527
            Assembly: GCF_022354345.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1551)
  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 1551)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-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_022354345.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:20:11
            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)                     :: 5,236
            CDSs (total)                      :: 5,112
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 252
            CDSs (without protein)            :: 252
            Pseudo Genes (ambiguous residues) :: 0 of 252
            Pseudo Genes (frameshifted)       :: 84 of 252
            Pseudo Genes (incomplete)         :: 172 of 252
            Pseudo Genes (internal stop)      :: 54 of 252
            Pseudo Genes (multiple problems)  :: 51 of 252
            Pseudo Genes (short protein)      :: 2 of 252
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055209.1.
            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..1551
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed10"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            1..477
                     /locus_tag="HUZ39_RS26010"
                     /old_locus_tag="HUZ39_25860"
     CDS             1..477
                     /locus_tag="HUZ39_RS26010"
                     /old_locus_tag="HUZ39_25860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(921..1142)
                     /locus_tag="HUZ39_RS26015"
     CDS             complement(921..1142)
                     /locus_tag="HUZ39_RS26015"
                     /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_158414302.1"
                     /translation="MCKCNTVTRDDIPFAVWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGVTSRMLSVIPLLFFRG"
                     /name="hypothetical protein"
     Typing          1082..1162
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.122"
                     /coverage="87.0"
                     /evalue="9.59e-28"
     Typing          complement(1365..1473)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(710..968)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.615"
                     /coverage="99.0"
                     /evalue="5.080000000000001e-110"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagt caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgtttt gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcttgttttt gctccccgat ccccagaacg
      601 accgcgccgc cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca ccaaccagcc gaatagctgc
      721 ttgtgccgtg caaataggct ttgcaggggg ctgacgcggt tcctagcgac ctgaaagccc
      781 ctggttaggg gtatcggcgc gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tgacgggcat ttaaaacccg tttcgtgtgt ctgagagctt ctgagcgcgt
      901 ttgaggggct atctggcgac tcatccccga aagaacaaca acggaatcac cgacaacatg
      961 cgagaggtga caccgctcgc cgcagcccca gcgaccgaac gtagtgagcg agtgggcgag
     1021 gaagcggaag agaaccggaa accacattga gcacgtacgc actgatgcgg ggtgtcgggg
     1081 cgaagccctg accagacggc aaacggaata tcgtcgcggg tgacggtatt acatttgcac
     1141 atcctgtccc gatttctgag gcgttttagc ggtgaacgga cggcaaaacc atgatggagc
     1201 tgttgagcgt tgagagcgtg aaatctggca aaaatcacgg ctggcgaggc ttgtagcgga
     1261 ataagccagt atacactccg ctatcgctac gtgactgggt cagggcttcg ccccgacacc
     1321 ccaaaagggc gttgcgttgc gcgcaacacc cttgcctaga atagatcttt tacgccgatt
     1381 tgtaagttgt tgttttttta gtgtgttttt tgtttacctg tcgcatccag ggtgacacaa
     1441 cgttgtcgca tcctggatgc gacaacacgc aacaaggtgt tgcacagatg tgtcatgatg
     1501 gcttagattt gaaccaacgt tagtgcatgg gattttcaga gggaaaaaat c
//
