LOCUS       NZ_CP058795             1553 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_6 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP058795
VERSION     NZ_CP058795.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925576
            Assembly: GCF_022494435.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1553)
  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 1553)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUL-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. Unicycler 0.4.8
            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_022494435.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:11:09
            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)                     :: 4,890
            CDSs (total)                      :: 4,767
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 65 of 209
            Pseudo Genes (incomplete)         :: 135 of 209
            Pseudo Genes (internal stop)      :: 41 of 209
            Pseudo Genes (multiple problems)  :: 32 of 209
            Pseudo Genes (short protein)      :: 3 of 209
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058795.1.
            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..1553
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLIN_6"
                     /isolation_source="Stanley WWTPs_6 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            1..477
                     /locus_tag="HZT08_RS24325"
                     /old_locus_tag="HZT08_24110"
     CDS             1..477
                     /locus_tag="HZT08_RS24325"
                     /old_locus_tag="HZT08_24110"
                     /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            525..815
                     /locus_tag="HZT08_RS24330"
     CDS             525..815
                     /locus_tag="HZT08_RS24330"
                     /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_154304673.1"
                     /translation="MIVYPALLFCRLKILCVFLLPVLQKKPSRHGSGSALSATGNRLGR
                     TPDPHRCNTDGLRPPTNRMAACSVQMGFAGGWRGSWRPESPWLGVSARLTS"
                     /name="hypothetical protein"
     Typing          1084..1164
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="87.0"
                     /evalue="2.0600000000000002e-29"
     Typing          complement(1367..1475)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.091"
                     /coverage="100.0"
                     /evalue="9.09e-49"
     Typing          complement(709..969)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc 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 aaattgagct
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgttct gactatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccttt gcgtgttttt gctccccgtt ctccagaaaa
      601 aaccgagccg ccacggttcc ggcagcgcct tgagcgctac cggaaaccgt ctggggagaa
      661 ccccagaccc ccatcgctgc aacaccgacg gtctacgacc acctaccaac cgcatggctg
      721 cctgttccgt gcaaatgggc tttgcagggg gctggcgcgg ttcctggcga cctgaaagcc
      781 cctggttagg ggtatcggcg cgcttgacct cctgagagcc tctgtaagcg tttttcgcgc
      841 cttccatgcc ctggcgggca tctaaaaccc gtttcgtgcg tctgagagct tttgagcgcg
      901 tttgaggggc tatctggcga ctcatcccca aaagaacaac accgggatca ccgacaacat
      961 gcgagaggtg gcaccgctcg ccgcagcccc agcgaccgaa cgttagtgag cgagtgggcg
     1021 aggaagcgga agagaaccgg aaaccacatt gagcacgtac gcactgatgc ggggtgtcgg
     1081 ggcgaagccc tgaccagatg gcaaacggaa tatcgtcgcg ggtgacggta ttacatttgc
     1141 acatcctgtc ccgatttctg aggcgtttta gcggtgaacg gacggcaaaa ccatgatgga
     1201 gctgttgaac gttgagagcg tgaaatctgg caaaaatcac agctggtaag gcttgcagag
     1261 gagtaagcca gtatacactc cgctatcgct acgtgactgg gtcagggctt cgccccgaca
     1321 cccccaaagg gcgttgcgtt gcacgcaaca cccttgccta gaatagatct tttacgccga
     1381 tttgtaagtg gttgtttttt tagtgtgttt tttatttacc tgtcgcatcc aggatgacac
     1441 aacgttgtcg catcctggat gcgacaacac gcaacaaggt gttgcacaga tgtgtcatga
     1501 tggcttagat ttgaaccaac gttagtgcat gggattttca gagggaaaaa atc
//
