LOCUS       NZ_CP055029             2638 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_67 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP055029
VERSION     NZ_CP055029.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925590
            Assembly: GCF_022353945.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2638)
  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 2638)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-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_022353945.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:14:26
            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)                     :: 4,646
            CDSs (total)                      :: 4,527
            Genes (coding)                    :: 4,291
            CDSs (with protein)               :: 4,291
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 70 of 236
            Pseudo Genes (incomplete)         :: 148 of 236
            Pseudo Genes (internal stop)      :: 58 of 236
            Pseudo Genes (multiple problems)  :: 35 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055029.1.
            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..2638
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_67"
                     /isolation_source="Shek Wu Hui WWTPs_67 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            join(2627..2638,1..189)
                     /locus_tag="HUZ75_RS23085"
                     /old_locus_tag="HUZ75_22945"
     CDS             join(2627..2638,1..189)
                     /locus_tag="HUZ75_RS23085"
                     /old_locus_tag="HUZ75_22945"
                     /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="antitoxin VbhA family protein"
                     /protein_id="WP_023139298.1"
                     /translation="MARSPDPRQRTEGFRKAEASLRLEGMDPAGTPLYENIKERVISGD
                     ITYEQGRAEILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     gene            complement(763..1092)
                     /locus_tag="HUZ75_RS23090"
                     /old_locus_tag="HUZ75_22950"
     CDS             complement(763..1092)
                     /locus_tag="HUZ75_RS23090"
                     /old_locus_tag="HUZ75_22950"
                     /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_052909321.1"
                     /translation="MKILPAEPGLYFFASFESGAHVYKVVAWSENENGGLDPQCVLTAL
                     YDKSSSSQQWELHSTSASAYQHSNDGRPFMYFITYFTSNGGIPELYNAINTLAERWGYP
                     LIDLP"
                     /name="hypothetical protein"
     gene            complement(1176..1607)
                     /locus_tag="HUZ75_RS23095"
                     /old_locus_tag="HUZ75_22955"
     CDS             complement(1176..1607)
                     /locus_tag="HUZ75_RS23095"
                     /old_locus_tag="HUZ75_22955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003511628.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_001025244.1"
                     /translation="MNIPTHLKHKPIIAVENYDRIDGPYADDTDAMGLSVGIAQWNTPG
                     YTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICIAMDYSKHGRLSSSDDFPVSRSG
                     GNPELSRHIDLMKNELKENHEHLDESLKRLAAELKRLGY"
                     /name="DUF6530 family protein"
     Typing          complement(1886..2430)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.23"
                     /coverage="90.0"
                     /evalue="1.49e-173"
ORIGIN
        1 cccgatccac gacaacgtac tgagggtttc cgcaaagcgg aagcgtcgct gaggcttgaa
       61 ggcatggacc ccgccggaac gccgctgtac gaaaatatca aggagcgggt tatttccggg
      121 gatatcactt acgaacaggg acgggcagaa attctggctc attaccagaa gcgtgcgaac
      181 ggccactgac acggacagga aactaggtac catcgcttcc tcaaaaaaac aggcgtggcc
      241 tctctccggc caggcttttc ctgtatttgc tatctgtttg ctacttgttt gctatctttt
      301 tgctatctgt ttgctatctg tttgctactt gtttgctact tgtttgctac cgctgccctc
      361 tgctgtgaaa agagtaaggc acgttagcga tgtatacatc gccgcgccgc aagggttccc
      421 cttccgaatc ccgttcatca ctgcgtgctg attaatccac gttaaatccg acccccttag
      481 caataaattc agccatgcct gacggcctgg ccaacgcctc acggccgcac agtaaactgc
      541 gcacccgtga ggcgttattt gtgaggttaa gtggtgcttt tggacgtcct gccggatttt
      601 agccgctaaa atcccggcca tgcatgtgtg tgcatagcca tgcagactcg tagaaatcat
      661 caggcgcgtt ttttcacgat ataggtatag ggaagtgccg gaaacagtca tcccgccgca
      721 gaaatgcgct gagggcgtct gagggggtgc gggcaacgga tgttatggta aatcaattaa
      781 tgggtatccc catcgttcgg ctagtgtgtt tattgcgtta taaagttcag gtatcccgcc
      841 attgctggtg aagtaggtga taaaatacat aaatggtctg ccgtcattgc tgtgctgata
      901 tgcagatgct gaagttgagt gaagttccca ttgctggctg gaactgctct tgtcatataa
      961 ggccgttaac acacactgtg gatctaaacc accattctca ttttctgacc aggccactac
     1021 tttgtaaacg tgagcaccgg actcaaaaga tgcgaaaaaa tataatcccg gttcagctgg
     1081 taggatcttc attagctagc ttccttttgt ttattctgtc tgagaggcaa taactaccta
     1141 attccccgtg gtgggtataa aaaatcacgg ggaggttaat aacctaaacg ttttagttct
     1201 gctgctaaac gcttaagact ctcatctaaa tgctcgtgat tctcttttag ctcgtttttc
     1261 attaaatcaa tgtgacgaga taactcagga ttgcctcctg aacgactgac cggaaagtcg
     1321 tcgctggaag ataagcggcc atgtttactg taatccattg ctatgcagat aagcgttgcc
     1381 aagtcgataa cacgatgaag aggtaattct tctgattgcc gtgaccactt ttctccggtg
     1441 ttgcgccaca cttttgctga tagctcggta tacccggggg tgttccattg agcaattcca
     1501 acggaaagcc ccatagcatc agtgtcatca gcataaggtc catcaattcg atcatagttt
     1561 tctacagcga taatcggttt gtgtttcaga tgagtaggga tgttcatatc attctctttt
     1621 atgtgaattt aggttgttaa ttaacaaaat aacaaaacag cttattttac taattagtaa
     1681 gtgtaacatt ttgtgaattg atggatttga agttgttggc gtggatcttc ttgagatcat
     1741 ttatggcaga gcgtaatctc ttgctcagaa aacgaaaaaa ccaccctggc aggtggtttt
     1801 tcgaaggtta gttaatcctg gcagattctc taaccgtggt aacagtcttg tgcgagacat
     1861 gtcaccaaat ctgtcctttc agtgtagccg cagtcaggcc accacttcaa gaactctcga
     1921 tacatctctc gcacatcctg tttaccagtg gctgctgcca gtggcgcttt gtcgtgtctt
     1981 tccgggttgg actcaagttg atagttaccg gaaaaggcgc agcggtcgga ctgaacgggg
     2041 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
     2101 ggaatgagat aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa tggcaggaac
     2161 aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata gtcctgtcgg
     2221 gtttcgccac cactgatttg agcgtcagat tctgtgatgc ttgtcagggg ggcgaagcct
     2281 atggaaaaac ggcttcgccg cggccttttc tgttcccctc tttctccttc cgctaccccc
     2341 gaatctgtgg gtaactccag gtggactgcc ggtaccgctc gccgcagccg aacggccgag
     2401 cgtagcgagt cagtgagcga ggaagcggaa gatctgcgat gcctgattgg gcttgtgtcg
     2461 cgccgtaccc tctctttacc gccggattac acagtttcct gcaatacttt ccttccggtt
     2521 tacacattcg tctgcacgga taaacaacgg cagagtacgg gcaggatatg taaagtaggc
     2581 ctactttacc gcctgcctta ttcgcttaca gctcaaagga acatcgatgg ccaggtcc
//
