LOCUS       NZ_CP055081             5631 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHIN_116 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP055081
VERSION     NZ_CP055081.1
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 5631)
  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 5631)
  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
            CP055081.1.
            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..5631
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_116"
                     /isolation_source="Shek Wu Hui WWTPs_116 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            join(5478..5631,1..80)
                     /locus_tag="HUZ90_RS24510"
                     /old_locus_tag="HUZ90_24275"
     CDS             join(5478..5631,1..80)
                     /locus_tag="HUZ90_RS24510"
                     /old_locus_tag="HUZ90_24275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            561..1613
                     /locus_tag="HUZ90_RS24515"
                     /old_locus_tag="HUZ90_24280"
     CDS             561..1613
                     /locus_tag="HUZ90_RS24515"
                     /old_locus_tag="HUZ90_24280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_217823355.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSIIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            1615..2481
                     /locus_tag="HUZ90_RS24520"
                     /old_locus_tag="HUZ90_24285"
     CDS             1615..2481
                     /locus_tag="HUZ90_RS24520"
                     /old_locus_tag="HUZ90_24285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(3684..3875)
                     /locus_tag="HUZ90_RS24525"
                     /old_locus_tag="HUZ90_24290"
     CDS             complement(3684..3875)
                     /locus_tag="HUZ90_RS24525"
                     /old_locus_tag="HUZ90_24290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3940..4263
                     /locus_tag="HUZ90_RS24530"
                     /old_locus_tag="HUZ90_24295"
     CDS             3940..4263
                     /locus_tag="HUZ90_RS24530"
                     /old_locus_tag="HUZ90_24295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4472..>4903
                     /locus_tag="HUZ90_RS24535"
                     /pseudo=""
     CDS             4472..>4903
                     /locus_tag="HUZ90_RS24535"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4941..5471
                     /locus_tag="HUZ90_RS24540"
                     /old_locus_tag="HUZ90_24305"
     CDS             4941..5471
                     /locus_tag="HUZ90_RS24540"
                     /old_locus_tag="HUZ90_24305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     Typing          3509..3590
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2865..3052
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          4254..5629
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgcagttgag tcagcaggtg cagcacttga gcgagcggac agaacgcttg agccagttat
       61 acagcgagaa caggagataa gggatgaacg gctgatgcag gaacgcgaac atgagttatc
      121 tctggagcgg gagcgtcagc cggaaatcca ggagcggaca ctggatggcc cttcgctggg
      181 atggtgaaac catgaaaaat gacgtgttca gtggattaag gcgggctaat gtggcctgta
      241 gcatctggtt gcataggtat tcatgcggtt aaaatttatc aggtgcgatc gcggcagttt
      301 ttcgggtggt ttgttgccat ttttacctgt ctgctgccgt gatcgcaccg aacgcgtttt
      361 ggcggtgcgt acaatgcgac gttatggtaa atggagcgga ttttcaggaa ggagtgatac
      421 taacaactcg aacactgtgc aaataatgat ttttttaaaa tatcggtaac gataataaat
      481 tatttcgttt tacgccggta ataaatataa tgtagtttca gtatataaaa aaatatatga
      541 ggtgtcttgt gggagctttc atgaatcttc aacaacgtat aaataaacta ccacaattat
      601 catccagttt ttcatttgga aaagatattg ataatattca ttcaattatc tttaacgaaa
      661 cttctaaaga taaaattgaa gatttactaa gaaaatgggt gtcaggcaat cagccctgtg
      721 tatttggtaa attggcaagc aagaaaatta aagggcttga tttccattta tctattgtaa
      781 atagccccca actatataat gatgatggtc atttgtttga ttttttgcgt aatgaaagag
      841 ttcgttttaa agaacgcgca agaagaggag aggtcagtgc gcatctcatt tattttattc
      901 atccacaact tgcctttgct cgtccatcag aagagttagt ggacatacaa aaatatattt
      961 gttcgctgca tatgccagag tgctatccaa taaaagagga tgttatttat actgaaagcg
     1021 taccatttca ggataaagat gggctaaaaa tatataaggc tggtgttaat gttttttact
     1081 cttctgctca tagaacaaga aatcatgata gaagaatacc agggggaata cttatttctg
     1141 taaatgcccc ggggcatttt atgaggctgg cgatagaaaa aggtttctat aaagatcaag
     1201 aacaagcgtt agcggatatt cgtaacatga ctattcagtc tgttggtaag ggtgggtatt
     1261 cacatccgga agggatttct acaacatggc attcagaatc taatttggat cgttttggat
     1321 gcccagtgca caccggtaat agttcttatt acagcggttt ttatcatact gatgtattaa
     1381 ttccaggaga attaactaag gatgaaagat tgctccatga aatagaaaat agtgatccaa
     1441 tgatcttcaa ctggaatgta ttgttttatg tttcattaga agagtttcct atagatgatc
     1501 cttattatgg agagtttatt ggtattcctg tagatgatgc atctatgttt tttaactcct
     1561 ttcaaccaag gaaatttgaa aacaaacccc tttatgagaa agaggatgat taatatgatt
     1621 aaaggaatgc tttttgcttt tttagcagcg ttctcatggg gggcagctat cgtaatgagc
     1681 aaaaaaggag ttgaagaact agatgccgga ggggtgtttt tctggcagat ttgtagtgca
     1741 gtaatactat cttggatagt tctttttata aaaagaaaaa aactcccatt aaactcaaaa
     1801 gcgatacttg cttatgcgac aggcgttttt gaaccattct tagcgtatac ttttacactc
     1861 tacggacttt attttatttc agcaggaagc gcatcaatta ttttttcact tgaatcagtg
     1921 tttatattgg tgttgtctgt tcttatttgc tcagttaaaa ttaattcccc gcaatatttt
     1981 atattgttcc ttataggtgc aattgttggc agtattttgg tagccttgcc agacatcagt
     2041 aatggatcga ataatattgt tggatattgt cttgttgttg ccggtgtgtt atcggcagca
     2101 ttttatgttg ttatatcgtc tcgccttatt aaatcgtttg agcctatcac attattgagc
     2161 ggacagttga cattctccct tatactgtca tcgctcttta tttttatatc taaatcatca
     2221 atttatcttc cgttggaatc cgtgattatt gttttttcat ctggaatatt acaatatttt
     2281 ttagcttttt gtttttactt gaactccttg cgttggctcc cagttcattt ggcagggata
     2341 atgttgtact ttattccgct agttgcatta tttttgtcat ggttgttttt ggatgaacaa
     2401 ttcacattct tacagggggt aggatttatt gtaactgtgc taagtgtata ttttcttaac
     2461 agaaaatact cagaggagta acattctgtt caggattgcc ccccggcctc catcgatacc
     2521 gtgccaaatg cacgtaaaaa acgggagcgt ttctggtgtc ggaatgtaac caagggggtc
     2581 agaggcgcgc taaaacgctc tcaggggagt caaatagaga cgtttgtaac aaaaagatca
     2641 aaggatcctc ttgagatcct ttttttctgc gcgtaatctg ctgcctgtaa acgaaaaaac
     2701 cgccttgcag ggcggtttga tcgaaggtta agtcagcttg cagactgctt aaccaggtaa
     2761 ctgtcttatg cgagacgagt caccaaaatt gttcttctag tgtagccgca ctccggcagc
     2821 cacttcaagt actctctaaa tatctcgcac atgactttta ccaatggctg ctgccagtgg
     2881 cgctttgtgg tgtcttttcc gggttggacc caagagaaca gttaccggag aaggcgcagc
     2941 agtcgggctg aacggggggt tcctgcatac agcccagccc ggagcgaact gcctaagtcg
     3001 ccccgagata ccagaagacg tgagctatga gaaagcgcca cgtgtcccgt aagggagaaa
     3061 ggcggaaaag gtatccggta atcgatatgg cgggaacgtg ggggcgcagg agggagcgat
     3121 tcaccggaaa cggtgatgat ctttaagcca cgtcgggttt cgccaccgct ggcggatttc
     3181 atggttgagc cgcaaggctc ccacagatgc accgaaaaag tgtctgtttt gtgaagtccg
     3241 tcaggggggc ggagcctatg gaaaaagcgc ctccggcgcg gcctttcccg gggtttcgtt
     3301 ttttgcgcac atgttctttc ctggtttatc cccgggttct gtggataaca gggttagcgt
     3361 ttttgagaaa ggagagtccg ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag
     3421 cgaggaagcg gaagagcgcc tgaactggca ttttctcctt acgcatctgt gcggcatttc
     3481 acaccggaca tggcgcactt ttcatacaat ccgcactgat gccgaatggt taagccagta
     3541 tacactccgc tatcgctacg tgactgggtc agggcttcgc cccgacaccc caaaggtcaa
     3601 cggcctgacg cgccctggcg ggcttgtctg ctcccggcat ccgctcacag acaagctgtg
     3661 accgtctccg ggagctgcat gtgtcagcgg ttttcaccgt catccccgaa gcgtgcgagg
     3721 caactgcggt aaagctcatc ggcgtggtcg tgaagcgatt cacagatgtc tgcctgttca
     3781 tccgcgtcca gttcgttgag cttctccagc agcgttaatg tctggcctct gatgaagcgg
     3841 gccatgttaa gggcggtttt ttcctgtttg gtcactgatg cctccgtgta agggggggtt
     3901 ctgttcatgg gggtaatgat accgatgaaa cgcgagagga tgctcacgat acgggttact
     3961 gatgatgaac atgcccggtt actggaacgc tgtgagggta aacaactggc ggtatggatg
     4021 cggcgggtct gcctgggtga gccggttgcc cgttccggga agctgccgac actggcaccg
     4081 ccgttactgc gtcagctggc cgccatcggg aataacctta accagacagc gaggaaggtg
     4141 aacagcgggc agtggtcttc cggtgaccgg gttcaggtgg tggccgcact gatggccatc
     4201 ggggatgagc tgcgccggct gcgtctggcg gtcagggaac agggggcgcg ggatgatagt
     4261 taagtttcat gccaggggaa aaggtggtgg cagtggtccg gttgattacc tgctgggaag
     4321 ggagcgtaac cgggaagggg caacggtgct tcaggggaat ccggaagagg tccgggaact
     4381 catcgatgcc acgccatttg cgaagaaata cacgtcaggt gttctgtcgt tcgcggagaa
     4441 ggagctgccg cctggagggc gtgaaaaagt gatggcgagc tttgagcgtg tactgatgcc
     4501 cggtctcgag aaaaatcagt acagcatcct gtgggtggag caccaggaca agggacggct
     4561 tgagctgaat tttgtcattc cgaacatgga gctacagacc ggaaaacgcc tccagccgta
     4621 ctacgaccgg gcagacaggc cgagaattga tgcctggcag acgctggtga atcaccatta
     4681 cggtctgcat gaccccaacg ccccggagaa ccgccggacg ctgacccttc ctgataacct
     4741 gccggaaacg aaacaggcgc ttgctgaggg cgtcacacgc gggatagacg cgctttacca
     4801 tgccggagag ataaaaggcc gtcaggatgt gattcaggcg ctcacagagg cggggcttga
     4861 agtggtcagg gtgacgcgaa gcagtatcag cattgcagac ccgaacggcg ggaggaatat
     4921 cagactgaaa ggagcgtttt atgagcaatc ttttacagac gggcgcggag ttcgagaaaa
     4981 agctgaaaga gagagccgaa tctacagaga aaatgctgaa cgacgagttc aggaagctcg
     5041 aagaatctgt aaacagggaa ctgacctcaa acgaatcttt aatcaggaac gctatcaacg
     5101 accatacaac agccctgaaa gaactgctgg agaggtatca gaaaacgacc gtcgatacga
     5161 tggacgcgca ctggaaaacc gtactgaaaa tgagcgtgaa acgctggctg tggctgatta
     5221 tcgtctcagt actgatgttt gccacgaccg ggagtctgct gtggtaccag ggcatgaaga
     5281 taaacgcgaa tatgaatatt ctccgcgagc agaaagagag tctggagaag ctgaacgcga
     5341 agacatgggg cgtgcgttat cacgaggaca gcaacggacg ttttctggtg ttgccgaagg
     5401 ggatgaaagc cgaaacgaac tggacgaagg acaacggcaa actgaacgca gtgagactgg
     5461 tgcaggagtg acagagcatg acggagctgg aaagacattt gctgaacgca ttagagcaac
     5521 tgcaacagga ctatatgcag cggctgaacg aatgggagaa cgccttcgtg gaattgcaga
     5581 aaatgttttc gcttacgcaa cgggacaacg cgatgctgaa cgggcgagtc a
//
