LOCUS       NZ_CP055222             2275 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_12 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP055222
VERSION     NZ_CP055222.1
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 2275)
  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 2275)
  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
            CP055222.1.
            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..2275
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_12"
                     /isolation_source="Shatin WWTPs_12 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(1394..2275,1..129)
                     /locus_tag="HUZ41_RS25610"
                     /old_locus_tag="HUZ41_25370"
     CDS             join(1394..2275,1..129)
                     /locus_tag="HUZ41_RS25610"
                     /old_locus_tag="HUZ41_25370"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001681832.1"
                     /translation="MKNPDSPILSLRDYSTQDSKWDSDRARADQVAKIYASDQAFFRRG
                     ERMFDCSQRLQFAPQSSRLTGEMRLALRHGEFCHVPFCPVCSRRRSLRWMRRLWEALPK
                     LLAEHPTASWLFLTLTVKNPPVGELRETLRQMNAAWERLIKRKAFAPVLGWLRSTEITY
                     GNVRGCCHPHFHVVLWVPSSWFTRDYVKHERWVEIWSECLRVDYAAGAHIKRVRPKRGK
                     VPEGASFAEVQRAALEAGVIETLKYTVKSSEIVRDPAWFLELARQTYGLRMIATGGRFR
                     EILQVEKPETDEDLIGADMPAKPDEFEEMAFWLAFDWRRDEKRYKRNPKADRRKE"
                     /name="protein rep"
     Typing          731..813
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="93.0"
                     /evalue="1.53e-15"
ORIGIN
        1 ttgattggtg ctgatatgcc agcgaagccg gacgagttcg aggagatggc gttctggctg
       61 gcgtttgact ggagacgtga cgagaaacgc tacaagcgga atccaaaagc agacaggcgg
      121 aaggagtgag cgtgtttcag aggcacattg tgggaatagt gcggtagtgg aggtgaaacg
      181 cgctcagaag cgttctaacg cgattttcag aaacgggcaa gtatttgccc gttttttcgt
      241 tttaaggcgc tcagaagcgt tttgagcgcg tttctggcgt tgtcgactgt aactctctct
      301 ggacttccgg tttcctgggg tgccagaaac gcgcgtttgt cgttttagcg tgtcgctggc
      361 acggtgtcta gggtgtcggg gcgcagccct gaccagatgg tgtttgtttg atggcgcgtg
      421 cgcggtccga caaacacaca tcctgtcccg tttttgcttc cggttttttg gattttctcc
      481 ggcgtggtaa cggaacattt cggaaatgtg acggcaaatc attttgcggt ttttgcgaac
      541 gagttggacc tcacgagcgc cagattgctg cgcggaaaaa aatcatgaaa tgcgcactta
      601 tacaatctcc actccgttcc gattgtgtgc ggtctgcgac gctcaaagaa acggcaaaat
      661 gatttgttgt ccggtcgtcg aaaatgccga gcctcatctg cccatctgcc agcgttcagg
      721 cgaaaaaatc gggacaggat gtgtgtttgt cggaccgcgc acgcgccatc aaacaaacac
      781 catctggtca gggctgcgcc ccgacacccc gccaacgtct cacacagcca gattgaaatc
      841 tgtcagcgtt cgccgttccc tgactcgtca aacagaaaat cgcggggtcc cgcgcctccg
      901 gcgtgggttc cgattttgtg attgacgaca tggcggataa aaacactggg agtggtggtt
      961 ggtgtcacgc agtgaggcca accacctgcc ggacggtttt ttgttgttca cagattcggg
     1021 tgaaaaggtt gtggatgggg tgggtgtaac aggcgcgaaa aacggggttt tgcggtgctg
     1081 aaaatctgcg caaatattga gcgattttgg ggtgcgcctt gtatttatac tataggcaac
     1141 aactcgcgga tgcatttttg cctttcagcc cagtaatggc gcgggtttga ggggtttttt
     1201 agttgtagat ggttgttaaa ttgtttttac aacttttttt ggctacagtg tgagcaacag
     1261 gttggtgagg ttccccggca gtgtgctacc actccggggg cgaccacctg aaaggtaaaa
     1321 ttcggtaagc caagcacagg tggtaagaac atgctaacac aagatttctg cccctgccta
     1381 ctgagggcag gtcatgaaaa atccagatag tccgatcctc tcactgcgtg actacagcac
     1441 gcaggattca aaatgggaca gcgatcgcgc gagggctgac caggtggcaa agatttacgc
     1501 gtcagaccag gcatttttcc gtcgcggcga gaggatgttt gattgcagtc agcgtttaca
     1561 gttcgctcca cagagttccc gtcttacagg cgagatgcga cttgcactgc gtcatggtga
     1621 attctgtcat gtcccgtttt gtccggtgtg tagccgtcgc cgctcgttac gctggatgcg
     1681 tcgtctgtgg gaggcgctac cgaaactact ggctgagcac cctactgcga gttggttatt
     1741 cctgaccctg actgtaaaaa atcctcccgt tggtgagttg cgcgagacac tccggcagat
     1801 gaatgcggct tgggagcgtt taatcaagcg caaagcgttt gcgcctgttc tgggatggct
     1861 gcggagtacg gaaattacct acgggaatgt gcgcggatgt tgtcacccgc acttccatgt
     1921 ggtgctctgg gttccttcgt catggttcac gcgggattac gtgaaacatg agcgctgggt
     1981 ggaaatctgg agtgaatgcc tgcgggtgga ttacgcagct ggcgcgcaca tcaagcgcgt
     2041 gcggccaaaa cgggggaaag tgccggaagg ggcaagtttt gctgaggtgc agcgggcagc
     2101 gctggaagcg ggcgtgatcg agacgctgaa atacacggtg aaatcatcgg aaatcgtgcg
     2161 cgatccggcg tggtttctgg agctggcgag gcagacctac gggctgcgga tgattgccac
     2221 gggaggacgg tttcgggaga tcctccaggt cgagaagccg gaaacggacg aggat
//
