LOCUS       NZ_CP055085             3171 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHIN_116 plasmid unnamed10, complete
            sequence.
ACCESSION   NZ_CP055085
VERSION     NZ_CP055085.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925605
            Assembly: GCF_022354205.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3171)
  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 3171)
  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_022354205.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:17:39
            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)                     :: 4,956
            CDSs (total)                      :: 4,829
            Genes (coding)                    :: 4,546
            CDSs (with protein)               :: 4,546
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 81 of 283
            Pseudo Genes (incomplete)         :: 200 of 283
            Pseudo Genes (internal stop)      :: 45 of 283
            Pseudo Genes (multiple problems)  :: 44 of 283
            Pseudo Genes (short protein)      :: 4 of 283
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055085.1.
            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..3171
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_116"
                     /isolation_source="Shek Wu Hui WWTPs_116 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed10"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(857..1252)
                     /locus_tag="HUZ90_RS24600"
                     /old_locus_tag="HUZ90_24365"
     CDS             complement(857..1252)
                     /locus_tag="HUZ90_RS24600"
                     /old_locus_tag="HUZ90_24365"
                     /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_001222910.1"
                     /translation="MRISNIDWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNELQAQENARKQANQKRMEGKTQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELRYPKDNILQKLKAIRLDLETSPDHH"
                     /name="hypothetical protein"
     gene            1431..2384
                     /locus_tag="HUZ90_RS24605"
                     /old_locus_tag="HUZ90_24370"
     CDS             1431..2384
                     /locus_tag="HUZ90_RS24605"
                     /old_locus_tag="HUZ90_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235474.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001360358.1"
                     /translation="MATYHLNVKFGGKGQAGNHADYIERKGEYEKRKDLEYSEHGNMPG
                     WARDNPSHFWQAADQFERANGSTYREIEIALPRELTPDQRIELVQDFVRQVAGERHAYS
                     FAIHNPKASIDGGEQPHAHIMMSQRINDGMERSPEQYFRRYNAKNPERGGAKKDSGNLT
                     PTQQKEQLRTLRASWSALQNEHLARHGHRVRVDHRSLEERGIKRTPERHFGFAASSRLD
                     HAQRREILQNRAQPLEHFLEKAHSVRHQFDAQVQQKELVKTLLQDVARERGHALTARIN
                     KTGEVEFERAPTRTRSNTRGHGMGIRDNSRGYDYER"
                     /name="MobA/MobL family protein"
     gene            2396..2926
                     /locus_tag="HUZ90_RS24610"
                     /old_locus_tag="HUZ90_24375"
     CDS             2396..2926
                     /locus_tag="HUZ90_RS24610"
                     /old_locus_tag="HUZ90_24375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168768.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168766.1"
                     /translation="MASTEEGLLTLLLSVEHLKNTAIEQQKAVADTLAVARETLRGYRD
                     ISDSVVKQVSDEVRKGVQKTDIAGLMGERMTQDFQRLEETVAKMRANAEALNKDIATIH
                     HNVVKEYNTLNKYSLKWFIGVTVSFLVMFSLLGWFTKTLIDRNYTATEVVYQKIVDIEK
                     KLDKPATGKSRKN"
                     /name="hypothetical protein"
     Typing          1432..2381
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.685"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tattgtgctt gcgatctttc gtcagggagc gtagaacgaa aaaagcccgc cgttaggcga
       61 gcttcttcgg gttcattgag gttttcgacc tcctcaatgt tcctgtggag tctgttgcgg
      121 cgacaacgga aaccagttca ttcagtttgc atgaaccttc tgtattcttc aagcattacc
      181 gaccgcacag cctccccaga atcccgaaaa aatcctgttt ttgcagatga ttgcgtgttt
      241 gcaaagaccg tttgcggttg ggggagctgt gacgacggca accgcacgcg tgagagttcc
      301 gctaccggcg cagagagttt catcgacagc ggacacctga tgagttgcca caaaaaccgt
      361 atgtagcgcg gctagattgg ttgagttaga ccttggcggc agttcccggt atgtggtggc
      421 gtgacgggtg agatggtgcg gcgaagacgc atacgtcacg caggcgcggg ttcttccacc
      481 gacgcgcccc gtgatcgatg gccttggctc cgtccggcat atcgagagcg gcaaactacc
      541 cgtcccttca ctgggagggg tgagttgttg ccgttccctc cgaccttcca ccatccagca
      601 tatcgcacga tcccatgagc accgcaacaa ctgataactc cagagcaaaa aaaaaaagga
      661 tctgcatcat gtgagagtga tcccaccgct cgccgcagcc ccagcgaccg aacgtagtga
      721 gcgagtgggc gaggaagcgg aagtgaaccg gaaaccacat tgagcacgta cgcacctatg
      781 ccagatccgc gcgtagcgcg tcgcgaaatc gaaaacattg aacaccggca ggcaaacgca
      841 ccaccacgca gcggaattaa tgatgatctg ggcttgtttc aagatcgagc ctgattgcct
      901 taagtttctg taatatattg tcttttgggt atctcagttc gcctgttttt gtgtccacta
      961 gtccggcctc gatcagtaac cccgccgcaa gaaacaggcg gtgattgcgt tcccgtcgtt
     1021 gtgttttccc ctccatccgt ttttggttgg cctgtttgcg tgcgttctcc tgtgcctgta
     1081 gctcgttttt ttctgcggtt gccaggacgt ggagtagttt gcgctcctgt tctgttagtc
     1141 cggcttcgtt atcgagcagg tcaatgatct gcctctgtcg tgcggtctgt tctccgagct
     1201 tcctgataaa gccgattcgt ttcttcaacc agtcgatgtt gctgatgcgc atgtttggga
     1261 tgctccctgg tgttttttgc ggtgtgttgg ggttgtgcag tatatcgctt gcggtcggtg
     1321 ggtgcagggg gtatcttccg tgctaattcg taaaattaga aggaagcgca cttatatgtt
     1381 tcttcgccgt tggctcagaa acatgtgcgc tcctgcggag ggctaacacc gtggcaacct
     1441 atcacctcaa tgtaaaattt ggcggcaagg gacaggccgg aaaccatgcc gattacatcg
     1501 aacgcaaagg cgagtacgag aaacgaaaag atctggaata ctcagagcac gggaatatgc
     1561 caggctgggc gcgagataat ccctcccatt tctggcaagc ggctgatcag tttgaacgtg
     1621 cgaatggttc gacttatcgg gagatcgaaa tcgccttgcc gcgtgaactg acaccggatc
     1681 agcgcattga actggtgcag gattttgtgc gtcaggtagc tggagaacgg cacgcctata
     1741 gctttgccat tcacaatcca aaagcgagca ttgacggagg ggaacagcct catgcgcata
     1801 tcatgatgag ccagcgtatt aacgatggta tggaacgttc gccggaacag tatttccggc
     1861 gttataacgc caagaatccc gaacggggag gcgcaaaaaa agattcaggc aatctgacac
     1921 cgactcagca aaaagagcaa ttgcggacgt tacgggcgag ctggtcagcg ttacagaacg
     1981 agcatttagc gcgtcatggt cacagggtgc gcgttgacca tcgctcactg gaagaacgcg
     2041 gaattaaacg cacgccagaa cggcatttcg gatttgccgc ctcatcacgg cttgatcatg
     2101 cgcagcgccg cgaaatcctg caaaaccgag cgcagccgct cgaacatttt ctagagaaag
     2161 cgcattcggt tcgccatcaa tttgatgcac aagttcagca aaaagagtta gttaaaacgc
     2221 ttttacagga cgtcgcacgg gagcgagggc acgcgcttac ggcaagaata aataaaacag
     2281 gtgaagttga atttgaacgt gcgccaacgc ggacgcggag taacacgcga gggcacggca
     2341 tgggcattcg tgacaactca cgcgggtacg actacgaacg ttaaaagggg actgtatggc
     2401 gagtacagaa gaggggttgc tcacgctctt gttgtccgtt gagcatttga aaaacactgc
     2461 gatagaacaa cagaaagcgg ttgcagacac gctggcggtc gcaagggaaa cactgcgggg
     2521 gtatcgggat atttctgaca gtgttgtaaa acaggttagc gatgaagtca gaaaaggggt
     2581 acagaaaacg gacattgcgg ggctgatggg tgagcgcatg acccaggatt ttcagcgtct
     2641 tgaagagact gtggcaaaga tgagagccaa cgcggaggcg cttaacaagg acattgcgac
     2701 aattcatcac aatgttgtta aagaatacaa cacgctcaat aaatacagtc tgaaatggtt
     2761 tatcggtgtt acggtcagtt ttctggtcat gttctcgttg cttggctggt ttaccaaaac
     2821 gttgatcgac aggaactaca ccgcgacgga ggtcgtgtat cagaaaattg ttgatattga
     2881 aaagaaactg gacaaaccag caacagggaa gagccggaaa aactgacgcg cttcgcttgt
     2941 ccaacgcctc acgggacgcg aaaaaattcc gcgtcccgtt caccgttttc tgatgagaaa
     3001 gtttgccgtt ttgacccgtt cggtgctcag atttggcgaa attgattccg aatcactttt
     3061 gtgaatagtt atgcaagccc ctggaaacgt ttctgacgcg ttttttgagg taggggtggg
     3121 ggaaagcatg gttttttgat gttttgagcg taaaagcgtg aaaaatcgcg t
//
