LOCUS       NZ_CP055223             2052 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_12 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP055223
VERSION     NZ_CP055223.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925529
            Assembly: GCF_022354305.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2052)
  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 2052)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-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_022354305.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:26:11
            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)                     :: 5,154
            CDSs (total)                      :: 5,032
            Genes (coding)                    :: 4,774
            CDSs (with protein)               :: 4,774
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 258
            CDSs (without protein)            :: 258
            Pseudo Genes (ambiguous residues) :: 0 of 258
            Pseudo Genes (frameshifted)       :: 70 of 258
            Pseudo Genes (incomplete)         :: 186 of 258
            Pseudo Genes (internal stop)      :: 42 of 258
            Pseudo Genes (multiple problems)  :: 35 of 258
            Pseudo Genes (short protein)      :: 4 of 258
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055223.1.
            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..2052
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_12"
                     /isolation_source="Shatin WWTPs_12 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(join(1849..2052,1..348))
                     /locus_tag="HUZ41_RS25615"
                     /old_locus_tag="HUZ41_25375"
     CDS             complement(join(1849..2052,1..348))
                     /locus_tag="HUZ41_RS25615"
                     /old_locus_tag="HUZ41_25375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007182947.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_239637181.1"
                     /translation="MTKRKVYKTDLRTLDYSPSSNPLIKPTEVPVKRKRVRSSLAGKQL
                     VDANTGLLEATAVIHQIEDKDTDEFVKVFAAGIAASYELSRTGQRVFQAILQEYEQTPM
                     TRGYADSIYLAWFDGGLSGRKIDMSEYTFKRGLRELLDKGFIAPQAPNVFWVNPALFFK
                     GDRVMLIREYRKQKYLPENK"
                     /name="hypothetical protein"
     gene            complement(1128..1631)
                     /gene="ddp1"
                     /locus_tag="HUZ41_RS25620"
                     /old_locus_tag="HUZ41_25380"
     CDS             complement(1128..1631)
                     /gene="ddp1"
                     /locus_tag="HUZ41_RS25620"
                     /old_locus_tag="HUZ41_25380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000809479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_239637180.1"
                     /translation="MKQIKFRLTDEEYNVAHVNAISNGVNSVNAFAKRKVLDVSATPSK
                     VIVSNEPSVPVKTCLYPHELELIKRNAALHGMSVSREIAIRLRKSVLKNEVCLYPEEVQ
                     VLRKLSTTINRVGRNIHFIISGDRFCTVNDPHFRNEIKELTELCETVDKTIEQLVCSVN
                     NRFG"
                     /name="ddp1"
     Typing          635..885
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.048"
                     /coverage="96.0"
                     /evalue="6.62e-104"
ORIGIN
        1 ccaagctagg tagatcgaat ccgcataacc acgtgtcatt ggtgtttgct catactcctg
       61 caaaatagct tgaaatacac gttgtcctgt ccgagacaac tcgtaagagg ccgcaatacc
      121 ggccgcaaat actttcacaa actcgtcagt atctttgtct tcgatttgat gaattactgc
      181 tgttgcctct aacagcccag tatttgcatc tacaagctgt ttccctgcta acgaagaacg
      241 gactcgtttt ctcttcaccg gcacttctgt aggtttaatt aacgggttgc tcgaagggct
      301 ataatcgagc gttctcaagt cggttttata tacttttcgc ttagtcattc gagcatcctt
      361 tgagatatat ttgctcgata tactgaaggc ggcttcacta ttaatcaagc atttttttta
      421 tgttttttgc tcgatcgctc gcgcaaggtt gctcgatcgc tcttgcaaag ttgctcgatc
      481 ggtttcagca tttacgcggc ttagcagact ttcctttctc actcttatac ttataacgcg
      541 tgcgtaagtg ccctaatcaa cgccagttct cttccgcttc ctcgcccact cgctcactaa
      601 cgttcggtcg ctggggctgc ggcgagcggt gccacctctc gcatgttgtc ggtgattccg
      661 ttgttgttct ttcgggaatg agttgccaga tagcccctga aacgcgctca gaagctctca
      721 gacgcacgaa acggggttta aatgcccgtc agggcatgga aggcgcgaaa aacgcttaca
      781 gagcgtttca ggaggtcagg cgcgccgata cccctaacca ggggctttca ggtcgccagg
      841 aaccgcgcca gccccctgca aagcctattc gcacggaaca ggcagtcgct cggttggtag
      901 gtggtcgtag accgatgatg ttacagcggt gggggtctgg ggttctcccc agtcggtttc
      961 cggttgcgct caaggcgctg ccggaaccgt ggcggctcgg ttgttctgga gatcgggggc
     1021 taaaaatctt cgtgttttac tccgatgcag gataggcgta gccactacaa atgtgcacat
     1081 ttgagtgatt acgccagccg ctacacgggg ttctagttaa tacgttttca cccaaaacga
     1141 ttattaacac tacaaactaa ttgttctatt gttttatcga ctgtttcgca taattctgta
     1201 agttccttta tctcatttct gaaatgagga tcgtttactg tacaaaaacg atcgccgcta
     1261 attatgaaat gaatatttcg accaactcta ttaatcgtag ttgaaagttt tctgagcacc
     1321 tgtacttctt cggggtaaag acaaacttcg tttttcaaaa ctgatttacg taagcgtatt
     1381 gctatttctc gactaacact cattccgtgt aatgctgcat tacgctttat taactccagt
     1441 tcatgtgggt ataaacatgt ttttactggt acagatggtt cattcgatac aataacctta
     1501 gaaggtgttg cgctaacatc taaaaccttc ctctttgcaa aagcatttac actattaacg
     1561 ccatttgaaa tagcattaac atgagcaacg ttgtattcct cgtcggtcaa tctaaattta
     1621 atttgcttca tagtacctcc taagagcctg cagcaggcac aggcaaaaac cccgtttttg
     1681 gacaatcatg gaaaatggta cccatttgac catggttgtc tatcctgcat tgattacagc
     1741 ccatttaagc ggtcttgctc aaagattatc agtaaaagct cttacaggtt gttgtgatgt
     1801 agcgggcacc gaagctatca ccttccggtc gcccgcgttt gataatgctt atttattttc
     1861 tggtaaatat ttttgtttcc gatattctct aatcaacata actctatcac ctttaaaaaa
     1921 tagtgcagga ttaacccaaa atacattggg agcttgaggt gcaataaaac ctttatctag
     1981 caactctctc aatcctcgtt taaaagtgta ttcactcatg tcaattttgc gtccagataa
     2041 tcccccatca aa
//
