LOCUS       NZ_CP055074             2443 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHIN_97 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP055074
VERSION     NZ_CP055074.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925606
            Assembly: GCF_022354185.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2443)
  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 2443)
  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_022354185.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:14:19
            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)                     :: 4,972
            CDSs (total)                      :: 4,847
            Genes (coding)                    :: 4,557
            CDSs (with protein)               :: 4,557
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 290
            CDSs (without protein)            :: 290
            Pseudo Genes (ambiguous residues) :: 0 of 290
            Pseudo Genes (frameshifted)       :: 78 of 290
            Pseudo Genes (incomplete)         :: 197 of 290
            Pseudo Genes (internal stop)      :: 56 of 290
            Pseudo Genes (multiple problems)  :: 42 of 290
            Pseudo Genes (short protein)      :: 5 of 290
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055074.1.
            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..2443
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_97"
                     /isolation_source="Shek Wu Hui WWTPs_97 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(47..1015)
                     /gene="mobV"
                     /locus_tag="HUZ91_RS24705"
                     /old_locus_tag="HUZ91_24500"
     CDS             complement(47..1015)
                     /gene="mobV"
                     /locus_tag="HUZ91_RS24705"
                     /old_locus_tag="HUZ91_24500"
                     /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_000024818.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="mobV"
     gene            1763..2203
                     /locus_tag="HUZ91_RS24710"
                     /old_locus_tag="HUZ91_24505"
     CDS             1763..2203
                     /locus_tag="HUZ91_RS24710"
                     /old_locus_tag="HUZ91_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001565850.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000344119.1"
                     /translation="MDENGEVKQDSKIETFSIPAEPPYVKLYIADIAMIHGLSKSQNDV
                     LLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKNIIAALVDKQIFFRAGRGELEA
                     NPFLFARGDWPSIYERRKKIELKISYDTNGRTVQTKVMDDEC"
                     /name="hypothetical protein"
     gene            2193..2420
                     /locus_tag="HUZ91_RS24715"
                     /old_locus_tag="HUZ91_24510"
     CDS             2193..2420
                     /locus_tag="HUZ91_RS24715"
                     /old_locus_tag="HUZ91_24510"
                     /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_089455228.1"
                     /translation="MNAEDKLFKNVDRLMLHDSLKKNEVLTVWERTFLSSVYSIYRRTS
                     GNKYSTKGLSPKQKNAAFSILKKHGYHLND"
                     /name="hypothetical protein"
     Typing          complement(51..1063)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.491"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgacgtcac tttgcggcgt tagccctatc ctgcatcgca tcaaaactaa cgctccatac
       61 cacccatgcc acgcgatcgc gtctgtcgct gtttttcacg ttcaatacgc tgctgttttt
      121 ccttttcctg gttttgctgc ttaaaccgct gagccatcat caggatttcg gtcatctgct
      181 ctctggaaag ccccttaaaa ggctctgtga cgctctgtag gcgtttctgc tgcgcatcca
      241 tagtcttctg tagctcacgc gctctttttg cgttctgggc gctctgagag gccatagcga
      301 tggttcctgc aaagccatcg ttcactgcgt ggcttagacg tttggctatg gctgcctgat
      361 cttccacgtc tttggtgaaa atgcccttcc gcaatacacg cggctccagc gcctccggcg
      421 agatcgatac ctggctacgg gtgccacggt ttatcgattc gtagtagtgc tgaactgtct
      481 gatgcgtggc gcggcttccc tcgatgccgc gctcaagacc cagttttttt actgattcag
      541 cgtaggtgct ctgatcttca cgcatctttg accgcccgcc aataaactct ttcgcggaca
      601 gccgtccatc ctgcgtcaat ggcaccacga acgcagacag gtgcggggtg gcctcgtccc
      661 ggtgaaccac cgccgccaca acacgatcct tcccgtattt cttctccagc cattgctcag
      721 agcgggcgaa aaactccgcc tgctgccgtg gtgtggcctc tttccaccac tcagggcttg
      781 ctgtcataac gtattcaacg gccagtaccg catctttacg gcgtttttcc ggcagcagct
      841 cccgcacacg ccccattgcc tgatccgttg atttggacac agagcagtag ttttctggtg
      901 tccgttcagc gttagcgttc ggcgtctcac gctctcggta gcagtgctgc aacgcgctgg
      961 ccacgcttcc cattcccgtc agctttttgc agcgcattat cgcgtagttc gccatgttcc
     1021 ccccctgatt ccggcattca ttcagccagg cgggggagcg cattgcgata cctccggcgg
     1081 gccactatca agatgatagt gtactcacta gactttgcta cgcaaaatcg ttcgggcagc
     1141 aagctgccag aaggtcaaaa tcaacggcgg tctggcaggt ggaaggcgtc gcttcgcgcc
     1201 accccccacc actgccaagc ctgttttatc cggagtgtcg tcaagggtaa atggcactcg
     1261 ctacgctcgc ccttgacgaa atcaggcaat gaaatcgtct ttgaaagagc aggaaccgct
     1321 cgccgcagct ttggctgagg cgtaccgcag gagcaacgcg acgaggaacg aacagccaaa
     1381 gcgaggaagc ggaatttcca ctccccgtac atagaaatgc gtacactcct tgctaaaaaa
     1441 aggcagtttt tcagtgtcta aaaatgccgt ttttcagccc ttattttccc ccttaatata
     1501 tagatataga tatgggaacc cgcttgtacc aagggctaga gcgaagaatc gtactcacct
     1561 caagtaccaa tcgtactcac ctcaagtact aatcgtactc acctcaagga ctaatcgtac
     1621 tcacctcaag tactaatcgt acttgataca aaggacttga ctgtatgtct ctttagtact
     1681 taaatgcgag tactaaatca tggcgaaacg tggggctgga gtgaatacga aaaagatttc
     1741 taggcttgaa cggcatacat acatggatga aaacggtgag gtaaaacaag actctaagat
     1801 cgagaccttt tccatcccag ccgaacctcc ctacgtcaag ctatacattg cagacattgc
     1861 gatgattcat ggtttatcaa aatctcaaaa tgatgtgctt ttacaattgg caatgctgat
     1921 tggatgggat gggtttgtgt ctgtatcaaa aactagattt gaaaaaacca tacagcccag
     1981 ggttcatatt gaatatcaga cctttaaaaa cataattgcg gctcttgtag ataaacaaat
     2041 attcttccgg gcagggcgtg gggaacttga agctaacccc tttctttttg cacggggaga
     2101 ctggccatca atttacgaaa gaagaaagaa aattgagtta aagatcagtt atgacaccaa
     2161 tggaagaacc gtgcagacga aggtaatgga tgatgaatgc tgaagataaa ctttttaaaa
     2221 atgtagacag gctaatgctg catgattcac taaaaaagaa tgaggttctg actgtttggg
     2281 agcgtacttt tttaagcagt gtttacagca tatatcgtag aactagcggt aataaatact
     2341 caactaaggg tttgtcacca aagcagaaaa acgcagcttt ttctatttta aaaaaacatg
     2401 gttaccatct gaatgattaa ttttttcgtg gtgaatgccg caa
//
