LOCUS       NZ_CP058890             2117 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_33 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP058890
VERSION     NZ_CP058890.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925559
            Assembly: GCF_022494095.1
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_022494095.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:15:22
            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)                     :: 4,637
            CDSs (total)                      :: 4,516
            Genes (coding)                    :: 4,304
            CDSs (with protein)               :: 4,304
            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)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 71 of 212
            Pseudo Genes (incomplete)         :: 134 of 212
            Pseudo Genes (internal stop)      :: 40 of 212
            Pseudo Genes (multiple problems)  :: 34 of 212
            Pseudo Genes (short protein)      :: 4 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058890.1.
            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_33"
                     /isolation_source="Stanley WWTPs_33 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(610..933)
                     /gene="yecR"
                     /locus_tag="HZT25_RS23040"
                     /old_locus_tag="HZT25_22910"
     CDS             complement(610..933)
                     /gene="yecR"
                     /locus_tag="HZT25_RS23040"
                     /old_locus_tag="HZT25_22910"
                     /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"
     Typing          1570..1785
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.284"
                     /coverage="100.0"
                     /evalue="7.22e-78"
ORIGIN
        1 gaaaaataat caaccatggc gggtgattta cgcaggttaa ggggagatcg tgacaaaaaa
       61 aagcgttcct cactgtatcg ttcatgcctg catgaacggg ttattcttcc tgactacaga
      121 attacatcgc tccttcagtt catacatcac ttttacaaca cttttacaac actccttcgg
      181 cctgtacatc acttttacaa cacttttgca tcacttttac atcatttata catcactttt
      241 acatcattcc ttcagctcat acgtcacttt catcctctgt gccatttgta catcaccccc
      301 ttcctgaacg tgctgacagc gggttttccg gctgcgccgg caacgcttca cggccacgca
      361 ataaattgcg tccccgttca ccgttttcgg atgggaagaa cgccggaaac aggacttccc
      421 ctggctgaat ggtgtgaatt tccgcgctat gcacttgcgc gcatactcat gcatgccgta
      481 aaaacagagc ctgcgcgttt ctggcgggtt ttcgggtggt ttgttgcctg ttttaccggt
      541 ttcccgtcag aaacgccctc agagcctctc aggcggtgca cgcaagggat gttatggtaa
      601 atgttgaact tagttttctg aagctttccc accggtgcat tggtactcga ttgaaacgtt
      661 ggtcatctca caaccataag ccccgacctg tgcgcaggtg gatgtttggc cgccaaatgc
      721 ctcagcccca gtgtatcccc atgttttaca tttttgtcca gccagatctt tagctgagtt
      781 cagatcaaca acgggttttt caaacatccc aaaggtgtaa cccattttca ctgtaccatc
      841 agctttactc ccccccatcg gggtcatttg tttttgcgtt gcgcagcctg aaagaattaa
      901 aacgcctaaa ccgatcgcta ctagtttttt cattttttat ttcccggatg attgttcgga
      961 attatcttaa cgggaagttt acacaaggca acaccctctg taatcctctg attatttgag
     1021 gtatcccata aaaaaatcaa agaaagccta atgcccccgt ggtgggtata taaaaatacg
     1081 gggagcggag cgaccttcgt ctagctcttg ttttgttttt cttgccgcgc aactggcttg
     1141 attgtgtggg tgttgtgtcc gacgtctctc acatcaccgc gtactgctgc ctttttcgct
     1201 cattttatca ggtgcaagtt atcgtactgc gagacggggt agagcctaac tctttcgcgg
     1261 ttaagttacg ttcccaccaa tttgcctgtt tatcctgccg gagtccgggg cgtagacctg
     1321 agcgtctaag gtgcagatat gattttaatg tcgttgaatg gtattaagct ggtagtgaca
     1381 tggctagcca gccctgctaa gatttgattg cgacgtctaa tccagcaggt atctgcacga
     1441 attagagtac cgaagccctg tgattatgtc acggggcttt tgtacattta gcgcccgaga
     1501 atcaaaaaca tcccttcaga acttatgtaa cgcccgccgc agtctcacgg caggagcgca
     1561 gcgaccgagt gagcgaggag gcgacatttc atccttacct gcatgttgca cttacgcccc
     1621 gcagctacat ttttcccctg ccacatgaag cacttccctg aattcccact tcgctttacc
     1681 atattaagcc agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa
     1741 acccgctaac aacctctctg ctactggata tcaccccatg ccatctgaat atgatgaaca
     1801 acggggttcg actgatacgc agcttcccgg cgaatatgac ctttttgatt taatggcgaa
     1861 ggttactgaa gagatcctgc atgcccctgt ggattctggg ccgcctgtcg gccgggaagc
     1921 gttatagctt tttcgcttgc ccgcgtacgt ggtaatacgc cggtattacc ttttatttct
     1981 ttattttcat gtaattacag tgggttttta atacctgggt attactcgtg aaaacgaaac
     2041 attacttttt tttcttttaa ttcatgcagt tgcgatgaaa atcgcggctg cgttaggtgt
     2101 atgaccattt tgaggtt
//
