LOCUS       NZ_CP055105             2460 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain SWHIN_107 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP055105
VERSION     NZ_CP055105.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925599
            Assembly: GCF_022354645.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2460)
  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 2460)
  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_022354645.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:15:51
            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)                     :: 5,106
            CDSs (total)                      :: 4,984
            Genes (coding)                    :: 4,806
            CDSs (with protein)               :: 4,806
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 65 of 178
            Pseudo Genes (incomplete)         :: 114 of 178
            Pseudo Genes (internal stop)      :: 25 of 178
            Pseudo Genes (multiple problems)  :: 26 of 178
            Pseudo Genes (short protein)      :: 3 of 178
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055105.1.
            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..2460
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_107"
                     /isolation_source="Shek Wu Hui WWTPs_107 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed6"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(join(1709..2460,1..217))
                     /gene="mobV"
                     /locus_tag="HUZ84_RS25435"
                     /old_locus_tag="HUZ84_25220"
     CDS             complement(join(1709..2460,1..217))
                     /gene="mobV"
                     /locus_tag="HUZ84_RS25435"
                     /old_locus_tag="HUZ84_25220"
                     /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            911..1393
                     /locus_tag="HUZ84_RS25440"
                     /old_locus_tag="HUZ84_25225"
     CDS             911..1393
                     /locus_tag="HUZ84_RS25440"
                     /old_locus_tag="HUZ84_25225"
                     /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_202974839.1"
                     /translation="MNTKKISKLERHTYMDESGEIKQDSKIETFSIPAEPPYVKLYIAD
                     IAMIHGLSKSQNDVLLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKNIIAALVD
                     KQIFLRAGRGELEANPFLFARGDWPSIYERRKKIELRISYDSNGRTVQTTVTDDER"
                     /name="hypothetical protein"
     Typing          complement(1713..2458)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.787"
                     /coverage="96.0"
                     /evalue="3.06e-149"
ORIGIN
        1 cggccagtac cgcatcttta cggcgttttt ccggcagcag ctcccgcaca cgccccattg
       61 cctgatccgt tgatttggac acagagcagt agttttctgg tgtccgttca gcgttagcgt
      121 tcggcgtctc acgctctcgg tagcagtgct gcaacgcgct ggccacgctt cccattcccg
      181 tcagcttttt gcagcgcatt atcgcgtagt tcgccatgtt cccccctgat tccggcattc
      241 attcagccag gcgggggagc gcattgcgat acctccggcg ggccactatc aagatgatag
      301 tgtactcact agactttgct tcgcaaaatc gttcgggaag ctgcgcttcc aaaggtcaaa
      361 atcaacggcg gtctgacagg tggaaggcgt cgctccgcgt cacctcccac cactgccaag
      421 cctgttttat ccggtgagtc gtcaagggta aatggcactc gctacgctcg cccttgacga
      481 aatcaggcaa tgaatatcgt ttttgaaaga gcaggaaccg ctcgccgcaa gaacggatta
      541 gggagcggca tcgccgcgag tctgtccgtt cgaggaagcg gaatttccac tccccggaca
      601 tagaaatccg tacgctccag actcaaaaaa gctcgttttt cgatgtttaa aaatggcgtt
      661 tttcagcctt tattttcccc cttaatatat agatatagat acgggaaccc gcgcacacca
      721 agggctagag agaagaatcg tactcacctc aagtactaat cgtacttacc tcaagtacta
      781 atcgtactta cctcaagtac taatcgtact cacctcaagt actaatcgta ctttaggtaa
      841 ggtacttgac taccggcatc tttagtactt aaatgtgagt actaaaaaca tgctgataca
      901 tggggctaga gtgaatacaa aaaagatttc taagcttgaa cggcatacat acatggacga
      961 gagcggagag attaaacaag actctaagat cgagactttt tctatcccgg ctgaaccgcc
     1021 ctacgtcaag ctttacatcg cagacattgc gatgattcat ggtttgtcaa aatctcaaaa
     1081 tgatgtgctt ttgcagttgg caatgctgat tggatgggat ggctttgtat ctgtatcaaa
     1141 aactagattt gagaagacca tacaacctag ggttcatatt gaatatcaga cgtttaaaaa
     1201 cataatcgct gcccttgttg ataaacaaat ctttctccgg gcagggcggg gagagcttga
     1261 agccaatccg tttctttttg ctcggggaga ctggccttca atttacgaaa gaagaaaaaa
     1321 aatagagtta agaatcagtt atgattccaa tggaaggaca gtacaaacaa cggtaacgga
     1381 tgatgaacgc tgaagataag ctattcaaaa aagtagatag attaatgctg catgactctc
     1441 taaaaaagaa tgaggttttg actgtttggg agcgtacttt tttaagtagt acatacagca
     1501 tatatcgcag aacaagcggt aatgaatttt caactaaggg attgtcacca aaacaaaaaa
     1561 gcaccgcttt ttctattttg aaaaaataca attaccatct gatggattag ctggactcag
     1621 cgttatacag ggcggcagaa cctgatctct ggaatgccgc aaatgacgtc actttgcggc
     1681 gttagcccta tcctgcatcg catcaaaact aacgctccat accacccatg ccacgcgatc
     1741 gcgtctgtcg ctgtttttca cgttcaatac gctgctgttt ttccttttcc tggttttgct
     1801 gcttaaaccg ctgagccatc atcaggattt cggtcatctg ctctctggaa agccccttaa
     1861 aaggctctgt aacgctctgt aggcgtttct gctgcgcatc catagtcttc tgtagctcac
     1921 gcgctctttt tgcgttctgg gcgctctgag aggccatagc gatggttcct gcaaagccat
     1981 cgttcactgc gtggcttaga cgtttggcta tggctgcctg atcttccacg tctttggtga
     2041 aaatgccctt ccgcaataca cgcggctcca gcgcctccgg cgagatcgat acctggctac
     2101 gggtgccacg gtttatcgat tcgtagtagt gctgaactgt ctgatgcgtg gcgcggcttc
     2161 cctcgatgcc gcgctcaaga cccagttttt ttactgattc agcgtaggtg ctctgatctt
     2221 cacgcatctt tgaccgcccg ccaataaact ctttcgcgga cagccgtcca tcctgcgtca
     2281 atggcaccac gaacgcagac aggtgcgggg tggcctcgtc ccggtgaacc accgccgcca
     2341 caacacgatc cttcccgtat ttcttctcca gccattgctc agagcgggcg aaaaactccg
     2401 cctgctgccg tggtgtggcc tctttccacc actcagggct tgctgtcata acgtattcaa
//
