LOCUS       NZ_CP055208             2351 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed9, complete
            sequence.
ACCESSION   NZ_CP055208
VERSION     NZ_CP055208.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925527
            Assembly: GCF_022354345.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2351)
  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 2351)
  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_022354345.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:20:11
            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)                     :: 5,236
            CDSs (total)                      :: 5,112
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 252
            CDSs (without protein)            :: 252
            Pseudo Genes (ambiguous residues) :: 0 of 252
            Pseudo Genes (frameshifted)       :: 84 of 252
            Pseudo Genes (incomplete)         :: 172 of 252
            Pseudo Genes (internal stop)      :: 54 of 252
            Pseudo Genes (multiple problems)  :: 51 of 252
            Pseudo Genes (short protein)      :: 2 of 252
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055208.1.
            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..2351
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed9"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(join(2007..2351,1..624))
                     /gene="mobV"
                     /locus_tag="HUZ39_RS26000"
                     /old_locus_tag="HUZ39_25845"
     CDS             complement(join(2007..2351,1..624))
                     /gene="mobV"
                     /locus_tag="HUZ39_RS26000"
                     /old_locus_tag="HUZ39_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_025766223.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRVEREKQRQMRSRGMGGMER"
                     /name="mobV"
     gene            1617..1943
                     /locus_tag="HUZ39_RS26005"
                     /old_locus_tag="HUZ39_25850"
     CDS             1617..1943
                     /locus_tag="HUZ39_RS26005"
                     /old_locus_tag="HUZ39_25850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001614210.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_001070513.1"
                     /translation="MNQAALITIANELNHDQMRVLMALLAELDYENYIQVAQIDIAEAL
                     TMQKTNVSRAVKNLIDFGIILEGPKIGRSKTYRLNPQFGWKGTVSNHKKALKNGLSVIQ
                     GGRT"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2011..2351)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.737"
                     /coverage="96.0"
                     /evalue="4.91e-44"
ORIGIN
        1 caatacacgc ggctccagcg cctccggcga gatcgatacc tggctacggg tgccacggtt
       61 tatcgattcg tagtagtgct gaactgtctg atgcgtggcg cggcttccct cgatgccgcg
      121 ctcaagaccc agttttttta ctgattcagc gtaggtgctc tgatcttcac gcatctttga
      181 ccgcccgcca ataaactctt tcgcggacag ccgtccatcc tgcgtcaatg gcaccacgaa
      241 cgcagacagg tgcggggtgg cctcgtcccg gtgaaccacc gccgccacaa cacgatcctt
      301 cccgtatttc ttctccagcc attgctcaga gcgggcgaaa aactccgcct gctgccgtgg
      361 tgtggcctct ttccaccact cagggcttgc tgtcataacg tattcaacgg ccagtaccgc
      421 atctttacgg cgtttttccg gcagcagctc ccgcacacgc cccattgcct gatccgttga
      481 tttggacaca gagcagtagt tttctggtgt ccgttcagcg ttagcgttcg gcgtctcacg
      541 ctctcggtag cagtgctgca acgcgctggc cacgcttccc attcccgtca gctttttgca
      601 gcgcattatc gcgtagttcg ccatgttccc ccctgattcc ggcattcatt cagccaggcg
      661 ggggagcgca ttgcgatacc tccggcgggc cactatcaag atgatagtgt ataataactc
      721 actagacttt gcttcgcaaa atcgttcggg aagctgcgct tccaaaggtc aaaatcaacg
      781 gcggtctggc aggtggaagg cgtcgctccg cgtcacctcc caccactgcc aagcctgttt
      841 tatccggtga gtcgtcaagg gtaaatggca ctcgctacgc tcgcccttga cgaaatcagg
      901 caatgaatat cgtttttgaa agagcaggaa ccgctcgccg caagaacgga ttagggagcg
      961 gcatcgccgc gagtctgtcc gttcgaggaa gcggaatttc cactccccgg acatagaaat
     1021 ccgtacgctc cagactcaaa aaagctcgtt tttcgatgtt taaaaatggc gtttttcagc
     1081 ctttattttc ccccttaata tatagatata gatacgggaa cccgcgcaca ccaagggcta
     1141 gagagaagaa tcgtactcac ctcaagtact aatcgtactt acctcaagta ctaatcgtac
     1201 ttacctcaag tactaatcgt actcacctca agtactaatc gtacttttcg ccgcagactc
     1261 atgaccgaac gtagtgagcg aatgagcgag gaagcggaat ttccacttcc cgtacataga
     1321 aattcgttcg caccgaacgg gcagaaaaac gcctgatttt gccgatgtat gagtacggag
     1381 agtaataaga tacagaaggg gatgtctcgg aagccgcgcc acaagcggaa agtttttgac
     1441 aatagttatc tctagagata acttagttat cttgagagat aactattttt cctgaaattg
     1501 gagattttta gatgcggaga atcacgcagg tagaccaaag tacaggggag gaattaggtg
     1561 gttttgtagc agtgattcgt cccaaacaaa agtcatcatt ccagaggcac tttactatga
     1621 atcaagccgc gctaattacc attgccaatg agctaaacca tgaccagatg cgtgtactga
     1681 tggccttgct cgcagagctg gattacgaga actacatcca ggtcgcgcag atagatattg
     1741 cagaagcgct gactatgcaa aaaacaaatg tcagtcgtgc ggtaaaaaac ctgattgatt
     1801 tcgggatcat actggaagga ccgaagattg ggcggagcaa aacgtaccgc ctaaatcccc
     1861 agttcggctg gaaaggtact gtcagcaacc acaaaaaagc actgaaaaac ggcctcagcg
     1921 ttatacaggg cggcagaacc tgatctctgg aatgccgcaa atggcgtcat tttgcggcgt
     1981 tagccctatc ctgcatcgca tcaaaactaa cgctccatac cgcccatgcc acgcgatcgc
     2041 atctgtcgct gtttctcacg ttcaacacgc tgctgtttct ccttctcctg gttttgctgc
     2101 ttaaaccgct gagccatcat caggatttcg gtcatctgct ctctggaaag ccccttaaaa
     2161 ggctctgtga cgctctgtag gcgtttctgc tgcgcatcca tagtcttctg tagctcacgc
     2221 gctctttttg cgttctgggc gctctgagag gccatagcga tggttcctgc aaagccatcg
     2281 ttcactgcgt ggcttagacg tttggctatg gctgcctgat cttccacgtc tttggtgaaa
     2341 atgcccttcc g
//
