LOCUS       NZ_CP058783             4145 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_17 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP058783
VERSION     NZ_CP058783.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925572
            Assembly: GCF_022494355.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4145)
  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 4145)
  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_022494355.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:07:50
            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)                     :: 4,714
            CDSs (total)                      :: 4,591
            Genes (coding)                    :: 4,355
            CDSs (with protein)               :: 4,355
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 70 of 236
            Pseudo Genes (incomplete)         :: 162 of 236
            Pseudo Genes (internal stop)      :: 43 of 236
            Pseudo Genes (multiple problems)  :: 38 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            CRISPR Arrays                     :: 5
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058783.1.
            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..4145
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLIN_17"
                     /isolation_source="Stanley WWTPs_17 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(3117..4145,1..114)
                     /gene="wzz(fepE)"
                     /locus_tag="HZT03_RS23370"
                     /old_locus_tag="HZT03_23205"
     CDS             join(3117..4145,1..114)
                     /gene="wzz(fepE)"
                     /locus_tag="HZT03_RS23370"
                     /old_locus_tag="HZT03_23205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            complement(152..>394)
                     /locus_tag="HZT03_RS23375"
                     /old_locus_tag="HZT03_23210"
                     /pseudo=""
     CDS             complement(152..>394)
                     /locus_tag="HZT03_RS23375"
                     /old_locus_tag="HZT03_23210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            <391..573
                     /locus_tag="HZT03_RS23380"
                     /old_locus_tag="HZT03_23215"
                     /pseudo=""
     CDS             <391..573
                     /locus_tag="HZT03_RS23380"
                     /old_locus_tag="HZT03_23215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            1759..1872
                     /locus_tag="HZT03_RS23385"
                     /old_locus_tag="HZT03_23220"
     CDS             1759..1872
                     /locus_tag="HZT03_RS23385"
                     /old_locus_tag="HZT03_23220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            2180..>2311
                     /locus_tag="HZT03_RS23390"
                     /pseudo=""
     CDS             2180..>2311
                     /locus_tag="HZT03_RS23390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(2460..2922)
                     /locus_tag="HZT03_RS23400"
                     /old_locus_tag="HZT03_23225"
                     /pseudo=""
     CDS             complement(2460..2922)
                     /locus_tag="HZT03_RS23400"
                     /old_locus_tag="HZT03_23225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.2"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /name="transposase"
     Typing          1488..1876
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.153"
                     /coverage="91.0"
                     /evalue="1.04e-173"
ORIGIN
        1 gcagggattc tgggcggcct gtttgcctgc ggcagcgtgc tgctgcgtga ggcaatgctc
       61 tcgcgtaatc cgttgccaga gccgataacg gccgtaacgc cagcaacaga gtaacgacga
      121 tattaaaaag gcgctgattc agcgcctttt tttatttcag gaaatcgtcg cgcaccggcg
      181 taaaggtatc cagaagggtg ccgggcttca ggcaaatgca gccgtgcatc acgtgcggcg
      241 ctttatagag cgtatcgccc gccgtcacga tctgcttttc ttcacctatc gtaaactcga
      301 actccccgga gagcacatag gtaagctgtt catgcgggtg attgtgcatc gggccaatcg
      361 caccctgctc aaaattgacc tccaccgcca tcatctttct tagcattctt ccttggtgga
      421 tttggcgtac ataaatttta cttaggtaaa ataggacagg gattcctgta tctaattttt
      481 tgctggacat tcatacccgc gatcatcgcg tttattgagt ttattattta tctatgcgat
      541 tccgatgaaa aattcgcaag aaaatatggc taactcatag caaaaaagcc ctgcggggct
      601 ttttttgtac cagtctgtga ggcagattta ccataacatc cgttgcgtgc accgcctgag
      661 aggctctcag ggcgtttctg ggtcttcctg cctgtttccg acacttccct gtgcctatat
      721 cgtgaaaaaa cgcgcctgat gattctggcg cgtctgcatg gctatgcaca cacatgcatg
      781 gccgggattt tagcggctaa aatccggctg gacgcccaaa agcaccactg aacctcacga
      841 ataacgcctc acgggtgtgc agtttactgt gcggccgtga ggcgttggcc aggccgtcag
      901 gcatggctgg atttattgct aagggggtcg gatttaacgt ggatgaatca gcacgcagtg
      961 atgaacggga ttcggaaggg gcacccttgc ggcgcggcga tgtatacatc gctaacgtgc
     1021 cttggtcatt tattgcaaga agggagaggt agcattttga tagcaaaaaa gtagcaaaag
     1081 gatagcaacc gaaagaccag aagactctgg agatagcaaa aaagtagcaa aatggtagca
     1141 aaaagatagc aaacatgcgg gagctaacca ggagtcttta gcgggccggc ggtactccaa
     1201 aaacacatct tgtcccgctg ttttgtgaat aagccagcat agctgtgggc acaaaacatt
     1261 tcctgtccgc tgctttaacc tttgtaatcc aggaacgtca ggtgacgtca ctttgcggcg
     1321 ttagccctat cctgcatcgt attaaaaaat gcagcactgg cgcgtacggt gccgaagata
     1381 agtccgggga tattccgctt cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg
     1441 gcgagcggag ggaacggaga cattaaggca caggcaatga gagaggatcg agaggcaaaa
     1501 gaaaaggccg cggcgttgcc ggttttccat aggctccgcc cccctgacaa gcatcacaga
     1561 atctgacgct caaatcagtg gtggcgaaac ccgacaggac ttaaagatac caggcgtttc
     1621 cccctggtgg ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc
     1681 cgctgttatg gccgcgttta tctcattcca cgcctgacac tcagttccgg gtaggcagtt
     1741 cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgaccgctg cgtcttctcc
     1801 ggtaactatc gacttgagtc caagccggaa agacacgaca aagcgccact ggcagcagcc
     1861 actggtaact gatttagagg agttagtctt gaagttatgc gcctgttaag gctaaactga
     1921 aagaacagat ttggttactg cgctcctcat aagccagtta ccacggttca aagagttgca
     1981 gctctgagaa ccttcgaaaa accgccttgc tgggcggttt tttcgtttac tgagcaagag
     2041 attacgacgc tacagaaagg atctcaagaa gatccttcac cataatggaa atctatccca
     2101 cccgagcata taggatgcat atcgttataa aacatcggat attatgcatc ccaactaaaa
     2161 ataagctcga ggataaaaaa tgagttcaat ggtttactgc cgaggatgcg gcaaggaaat
     2221 acacgaaaca gcaaagtcat gcccacactg cggagccaca aacgcctctt caggttcagg
     2281 tgaaaaaagt agaatcgcag ccgcgctatt agggaaggtg cgaataagcg gggaaattct
     2341 tctcggttga ctcagtcatt tcatttcttc atgtttgagc cgattttttt ctcccgtaaa
     2401 tgccttgaat cagcctattt agaccgtttc ttcgccattt aaggcgttat tcccagtttt
     2461 tagtgagatc tctcccactg acgtatcatt tggtccgccc gaaacaggtt ggccagcgtg
     2521 aataacatcg ccagttggtt atcgtttttc agcaacccct tgtatctggc tttcacgaag
     2581 ccgaactgtc gcttgatgat gcgaaatggg tgctccacct tggcccggat gctggctttc
     2641 atgtaaccgg gcaaacagac gcatggaggc gatttcgtac agagcatctt cgatcgcgcc
     2701 atcgctcagg ttgtaccaat gctgcatgca gtgaatgcgt agcatggttt ccagcggata
     2761 aggtcgccgg ccattaccag ccttggggta aaacggctcg atgacttcca ccatgttttg
     2821 ccatggcaga atctgctcca tgcgggacaa gaaaatctct tttctggtct gacggcgctt
     2881 actgctgaat tcactgtcgg cgaaggtaag ttgatgactc atgatgaacc ctgttccatg
     2941 gctccagatg acaaacatga tctcatatca gggacttgtt cgcaccttcc ctaaatctga
     3001 tagtcggtct acagatagat caatctggcg ttcagattat tcttactttc ttgtatcatc
     3061 cgaccactgc aaccaatcag gcagaaattt actgcgctcc aaaaagaaga acggttatgt
     3121 cagcgatgga tttcaagaaa aacacggacc tcgattttcc ccgttatgcc actccggcgg
     3181 taagcaccaa agagatagat ctcctggggt tgttagacgt acttctggca gccaaaaaac
     3241 gtattgtgac gatcgtcctg gcgttcgccg tagtagggtt ggccattgcg tttttaatcc
     3301 cgcaaaaatg gaccagtaaa gccgtgatca cgccggccga gcagacgcag tggaacacgc
     3361 tgcgccagat gatggtgacg ctgcaggtgc tggacgtcga cgcgaaggtg agccgtggag
     3421 acgtgtttaa cctgttcatc aaaaagtttc agtcgcagtc gctgctcgaa gagtacatga
     3481 aaacctcccc gtacgtgatg tctcagctgg aaggcaccga ggtagacccg ctggagctgc
     3541 atcgcgcggt ggtgaatatt gctgagaaaa tgaaagcgac agataacacg caggttaaag
     3601 acgcagacaa agcgccgtat acctcatgga cgctgagctt taccgccccg acggcgggag
     3661 acgcgcagac ggttctggaa ggttacatca actatatctc ccgcattgtt gagcaggaga
     3721 cgatggaaaa tatccgtaac cagatcacgc tgaaaacgaa agtcgttcag cagcagctgg
     3781 agctggatcg cgtgcgtctg accaatatcc acaacaccaa cctgcagcgc ctcaactatt
     3841 cgctggaagt ggcgaacgcg gcaggcatta agaagccggt ttacagcaac ggacaggcgg
     3901 taaaagacga tcctgactac tccgtggcgc tgggtgctga cggtattgcg caaaagctgc
     3961 agattgaaaa gaatctgaag gacgtggccg agctgaatgc ggatttccag aaccgtgaat
     4021 actatctgac tcagttgcaa aaactgtccg tggaagacgt gaagcttgaa cccttcaggt
     4081 atcagctttc accgtcactg ccggtgaaaa aagacggtcc gggcaaagcc ctgattgtgc
     4141 tgctg
//
