LOCUS       NZ_CP058852             2117 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_36 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP058852
VERSION     NZ_CP058852.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925562
            Assembly: GCF_022494155.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2117)
  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 2117)
  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_022494155.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:10:52
            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)                     :: 4,544
            CDSs (total)                      :: 4,423
            Genes (coding)                    :: 4,231
            CDSs (with protein)               :: 4,231
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 65 of 192
            Pseudo Genes (incomplete)         :: 118 of 192
            Pseudo Genes (internal stop)      :: 39 of 192
            Pseudo Genes (multiple problems)  :: 32 of 192
            Pseudo Genes (short protein)      :: 4 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058852.1.
            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..2117
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLEFF_36"
                     /isolation_source="Stanley WWTPs_36 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            144..467
                     /gene="yecR"
                     /locus_tag="HZT28_RS22585"
                     /old_locus_tag="HZT28_22400"
     CDS             144..467
                     /gene="yecR"
                     /locus_tag="HZT28_RS22585"
                     /old_locus_tag="HZT28_22400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000716773.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YecR family lipoprotein"
                     /protein_id="WP_016245705.1"
                     /translation="MKKLVAIGLGVLILSGCATQKQMTPMGGSKADGTVKMGYTFGMFE
                     KPVVDLNSAKDLAGQKCKTWGYTGAEAFGGQTSTCAQVGAYGCEMTNVSIEYQCTGGKA
                     SEN"
                     /name="yecR"
     gene            complement(1267..1416)
                     /locus_tag="HZT28_RS22590"
     CDS             complement(1267..1416)
                     /locus_tag="HZT28_RS22590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162846302.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(1410..1625)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.284"
                     /coverage="100.0"
                     /evalue="7.22e-78"
ORIGIN
        1 tttttatata cccaccacgg gggcattagg ctttctttga tttttttatg ggatacctca
       61 aataatcaga ggattacaga gggtgttgcc ttgtgtaaac ttcccgttaa gataattccg
      121 aacaatcatc cgggaaataa aaaatgaaaa aactagtagc gatcggttta ggcgttttaa
      181 ttctttcagg ctgcgcaacg caaaaacaaa tgaccccgat gggggggagt aaagctgatg
      241 gtacagtgaa aatgggttac acctttggga tgtttgaaaa acccgttgtt gatctgaact
      301 cagctaaaga tctggctgga caaaaatgta aaacatgggg atacactggg gctgaggcat
      361 ttggcggcca aacatccacc tgcgcacagg tcggggctta tggttgtgag atgaccaacg
      421 tttcaatcga gtaccaatgc accggtggga aagcttcaga aaactaagtt caacatttac
      481 cataacatcc cttgcgtgca ccgcctgaga ggctctgagg gcgtttctga cgggaaaccg
      541 gtaaaacagg caacaaacca cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg
      601 gcatgcatga gtatgcgcgc aagtgcatag cgcggaaatt cacaccattc agccagggga
      661 agtcctgttt ccggcgttct tcccatccga aaacggtgaa cggggacgca atttattgcg
      721 tggccgtgaa gcgttgccgg cgcagccgga aaacccgctg tcagcacgtt caggaagggg
      781 gtgatgtaca aatggcacag aggatgaaag tgacgtatga gctgaaggaa tgatgtaaaa
      841 gtgatgtata aatgatgtaa aagtgatgca aaagtgttgt aaaagtgatg tacaggccga
      901 aggagtgttg taaaagtgtt gtaaaagtga tgtatgaact gaaggagcga tgtaattctg
      961 tagtcaggaa gaataacccg ttcatgcagg catgaacgat acagtgagga acgctttttt
     1021 ttgtcacgat ctccccttaa cctgcgtaaa tcacccgcca tggttgatta tttttcaacc
     1081 tcaaaatggt catacaccta acgcagccgc gattttcatc gcaactgcat gaattaaaag
     1141 aaaaaaaagt aatgtttcgt tttcacgagt aatacccagg tattaaaaac ccactgtaat
     1201 tacatgaaaa taaagaaata aaaggtaata ccggcgtatt accacgtacg cgggcaagcg
     1261 aaaaagctat aacgcttccc ggccgacagg cggcccagaa tccacagggg catgcaggat
     1321 ctcttcagta accttcgcca ttaaatcaaa aaggtcatat tcgccgggaa gctgcgtatc
     1381 agtcgaaccc cgttgttcat catattcaga tggcatgggg tgatatccag tagcagagag
     1441 gttgttagcg ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat
     1501 actggcttaa tatggtaaag cgaagtggga attcagggaa gtgcttcatg tggcagggga
     1561 aaaatgtagc tgcggggcgt aagtgcaaca tgcaggtaag gatgaaatgt cgcctcctcg
     1621 ctcactcggt cgctgcgctc ctgccgtgag actgcggcgg gcgttacata agttctgaag
     1681 ggatgttttt gattctcggg cgctaaatgt acaaaagccc cgtgacataa tcacagggct
     1741 tcggtactct aattcgtgca gatacctgct ggattagacg tcgcaatcaa atcttagcag
     1801 ggctggctag ccatgtcact accagcttaa taccattcaa cgacattaaa atcatatctg
     1861 caccttagac gctcaggtct acgccccgga ctccggcagg ataaacaggc aaattggtgg
     1921 gaacgtaact taaccgcgaa agagttaggc tctaccccgt ctcgcagtac gataacttgc
     1981 acctgataaa atgagcgaaa aaggcagcag tacgcggtga tgtgagagac gtcggacaca
     2041 acacccacac aatcaagcca gttgcgcggc aagaaaaaca aaacaagagc tagacgaagg
     2101 tcgctccgct ccccgta
//
