LOCUS       NZ_CP055045             3962 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_59 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP055045
VERSION     NZ_CP055045.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925586
            Assembly: GCF_022354025.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3962)
  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 3962)
  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_022354025.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:08:02
            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)                     :: 4,691
            CDSs (total)                      :: 4,573
            Genes (coding)                    :: 4,317
            CDSs (with protein)               :: 4,317
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 256
            CDSs (without protein)            :: 256
            Pseudo Genes (ambiguous residues) :: 0 of 256
            Pseudo Genes (frameshifted)       :: 78 of 256
            Pseudo Genes (incomplete)         :: 175 of 256
            Pseudo Genes (internal stop)      :: 53 of 256
            Pseudo Genes (multiple problems)  :: 48 of 256
            Pseudo Genes (short protein)      :: 4 of 256
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055045.1.
            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..3962
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_59"
                     /isolation_source="Shek Wu Hui WWTPs_59 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            join(3331..3962,1..73)
                     /locus_tag="HUZ71_RS23275"
                     /old_locus_tag="HUZ71_23095"
     CDS             join(3331..3962,1..73)
                     /locus_tag="HUZ71_RS23275"
                     /old_locus_tag="HUZ71_23095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221000.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS26 family transposase"
                     /protein_id="WP_001067855.1"
                     /translation="MNPFKGRHFQRDIILWAVRWYCKYGISYRELQEMLAERGVNVDHS
                     TIYRWVQRYAPEMEKRLRWYWRNPSDLCPWHMDETYVKVNGRWAYLYRAVDSRGRTVDF
                     YLSSRRNSKAAYRFLGKILNNVKKWQIPRFINTDKAPAYGRALALLKREGRCPSDVEHR
                     QIKYRNNVIECDHGKLKRIIGATLGFKSMKTAYATIKGIEVMRALRKGQASAFYYGDPL
                     GEMRLVSRVFEM"
                     /name="IS6-like element IS26 family transposase"
     gene            79..294
                     /locus_tag="HUZ71_RS23280"
                     /old_locus_tag="HUZ71_23100"
     CDS             79..294
                     /locus_tag="HUZ71_RS23280"
                     /old_locus_tag="HUZ71_23100"
                     /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_152920530.1"
                     /translation="MNKTKGCLIANFATVPAQVHSAEIHTIQPGEVLFPAFFPSENGER
                     GRNLLRGREALPAQPENPLSARSGRG"
                     /name="hypothetical protein"
     gene            complement(777..926)
                     /locus_tag="HUZ71_RS23285"
     CDS             complement(777..926)
                     /locus_tag="HUZ71_RS23285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162846302.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(1867..2412)
                     /locus_tag="HUZ71_RS23290"
                     /old_locus_tag="HUZ71_23105"
     CDS             complement(1867..2412)
                     /locus_tag="HUZ71_RS23290"
                     /old_locus_tag="HUZ71_23105"
                     /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="SHOCT domain-containing protein"
                     /protein_id="WP_039004747.1"
                     /translation="MRERYLNKISNFDTARIVLFIAIQIISCIFMFWGAIPALIVFFSY
                     LAMRKECNLKPIEKSKDYISVYMLLTAALVLFLFVYKAGMFRRGGDYFLLVFVFILLYV
                     YHLAFHKLWLRTIDENSSIIIENGIFNFNRKNASVGFSRKDVNNIDTLLKLNEARKEGI
                     ISEDEFNKLKKRLNILND"
                     /name="SHOCT domain-containing protein"
     gene            complement(2505..>2678)
                     /locus_tag="HUZ71_RS23295"
                     /old_locus_tag="HUZ71_23110"
                     /pseudo=""
     CDS             complement(2505..>2678)
                     /locus_tag="HUZ71_RS23295"
                     /old_locus_tag="HUZ71_23110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001389365.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS6 family transposase"
                     /name="IS6 family transposase"
     gene            complement(2680..3141)
                     /locus_tag="HUZ71_RS23300"
                     /old_locus_tag="HUZ71_23115"
     CDS             complement(2680..3141)
                     /locus_tag="HUZ71_RS23300"
                     /old_locus_tag="HUZ71_23115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014198269.1"
                     /GO_component="GO:0005886 - plasma membrane [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_196451626.1"
                     /translation="MQNILMNLAFYLLVVAAGASFSLQQAANNHLRAELLSPWWAGFIS
                     YVGGSLAMLVMALVCRGPGLSWDMLSRTSPFSWTGGILGAIYIATAIFMIPKLGATTVL
                     ALMVVGQMLLSLMLDHYGLLGIPVYPVTGIRLLGVVLLVLGVVLIRWQA"
                     /name="DMT family transporter"
     Typing          complement(962..1135)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="100.0"
                     /evalue="2.58e-81"
     Typing          1102..1606
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.097"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 ccaggcctca gcattttatt atggtgatcc cctgggcgaa atgcgcctgg taagcagagt
       61 ttttgaaatg taaggccttt gaataagaca aaaggctgcc tcatcgctaa ctttgcaaca
      121 gtgcccgcgc aagtgcatag cgcggaaatt cacaccattc agccagggga agtcctgttt
      181 ccggcgttct tcccatccga aaacggtgaa cggggacgca atttattgcg tggccgtgaa
      241 gcgttgccgg cgcagccgga aaacccgctg tcagcacgtt caggaagggg gtgatgtaca
      301 aatggcacag aggatgaaag tgacgtatga gctgaaggaa tgatgtaaaa gtgatgtata
      361 aatgatgtaa aagtgatgca aaagtgttgt aaaagtgatg tacaggccga aggagtgttg
      421 taaaagtgtt gtaaaagtga tgtatgaact gaaggagcga tgtaattctg tagtcaggaa
      481 gaataacccg ttcatgcagg catgaacgat acagtgagga acgctttttt ttgtcacgat
      541 ctccccttaa cctgcgtaaa tcacccgcca tggttgatta tttttcaacc tcaaaatggt
      601 catacaccta acgcagccgc gattttcatc gcaactgcat gaattaaaag aaaaaaaagg
      661 aatgtttcgt tttcacgagt aatacccagg tattaaaaac ccactgtaat tacatgaaaa
      721 taaagaaata aaaggtaata ccggcgtatt accacgtacg cgggcaagcg aaaaagctat
      781 aacgcttccc ggccgacagg cggcccagaa tccacagggg catgcaggat ctcttcagta
      841 accttcgcca ttaaatcaaa aaggtcatat tcgccgggaa gctgcgtatc agtcgaaccc
      901 cgttgttcat catactcaga tggcatgggg tgatatccag tagcagagag gttgttagcg
      961 ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat actggcttac
     1021 tatgttggca ctgatgagga tgtcagtgaa gtgcttcatg tggcaggaga aaaaaggctg
     1081 caccggtgcg tcagcagaat atgtgataca ggatatattc cgcttcctcg ctcactgact
     1141 cgctacgctc ggtcgttcga ctgcggcgag cggaaatggc ttacgaacgg ggcagggatt
     1201 tcctggaaga tgccaggaag agacttaaca gggaagagat agggccgcgg caaagccgtt
     1261 tttccatagg ctccgccccc ctgacaagca tcacgaaatc tgacgctcaa atcagtggtg
     1321 gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggcggct ccctcgtgcg
     1381 ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttgtc
     1441 tcattccacg cctgacactc agttccgggt agacagttcg ctccaagctg gactgtatgc
     1501 acgaaccccc cgttcagtcc gaccgctgcg ccttatccgg taactatcgt cttgagtcca
     1561 acccggaaag acatgcaaaa gcaccactgg cagcagccac tggtaattga tttagaggag
     1621 ttagtcttga agtcatgcgc cggttaaggc taaactgaaa ggacaagttt tggtgactgt
     1681 gctcctccaa gccagttacc gcggttcaaa agagcgtcaa ctcttgcgaa ccttcgaaaa
     1741 accaccttgc cgggtggttt tttcgtttgc agggaagaag attacgacga taaaaaatca
     1801 atgacaagaa gatattcaat cttatcaaag attcataagc ttgctttacc tttagttagc
     1861 aaaaaatcag tcgttaagaa tatttagtct tttttttaat ttattaaact catcttcact
     1921 tataatacct tcttttctag cctcgtttaa tttaagaaga gtatcaatgt tatttacatc
     1981 tttccgacta aatcctacag atgcattttt acgattaaaa ttaaaaatcc cgttttcaat
     2041 tattattgat gagttttcat ctatcgttcg caaccataat ttatgaaaag cgagatggta
     2101 aacataaagc aaaataaaaa caaaaacgag aaggaaataa tcaccgcccc ttctaaacat
     2161 gccagcttta tacacgaaaa gaaacagtac caaagcggct gtaagaagca tgtaaacgga
     2221 tatgtaatcc ttagacttct ctatcggctt taaattacat tccttcctca tggccaaata
     2281 tgagaaaaaa acaatcaagg caggaatagc cccccagaac ataaaaatac aagagataat
     2341 ttgaatggct ataaacaaca ctattcttgc cgtatcaaaa ttagatattt tatttaaata
     2401 ccgttcgcgc ataaatcacc accattcaat catagttaat taatttaaaa ggctctgttg
     2461 caaagattgg cggcagtcag aggtaggctg tcgctctgcg ccgatcaggc ggctgctgcg
     2521 aaatggtggt tgagcatgcc catggcctcc gtcagcgccg agggcccaat gccaaaagct
     2581 ctctccacaa ggcgcacctc gcccctgatg ccgggctgca ggcaccaggg gcgagcctgt
     2641 cctttgcgca gggctcgcat gacttcgaat cccttgatct tatgcctgcc atctgatcag
     2701 cactacccca agaacaagca ggacaacgcc cagcaggcgg ataccggtga caggataaac
     2761 cgggatacca agaaggccat agtgatcgag catcagggaa agcagcattt gcccgaccac
     2821 catcaatgcc agaaccgttg ttgctcccag tttcgggatc atgaaaatgg ccgtggcaat
     2881 gtaaatcgcc cctaaaatac cgcctgtcca tgaaaacggg ctggtacgcg aaagcatatc
     2941 ccatgacagg ccagggccgc gacaaaccag cgccatgacc agcatggcca gggaaccgcc
     3001 gacataactg atgaaacctg cccaccatgg tgaaagcagt tctgcgcgaa gatggttgtt
     3061 ggccgcctgt tgcagggaaa agctggcgcc ggcagcaaca accaggagat aaaacgccag
     3121 attcatcaga atgttttgca tggtttttct cgtcgaagaa gtgaaccgcc ccgggtttgg
     3181 cggagggtat tttgtttaag ttaaggcgtg ttgacggata gttcgtcaag ttgccgatag
     3241 tagtcctgtt caagatattc gccgactggc actgttgcaa atagtcggtg gtgataaact
     3301 tatcatcccc ttttgctgat ggagctgcac atgaacccat tcaaaggccg gcattttcag
     3361 cgtgacatca ttctgtgggc cgtacgctgg tactgcaaat acggcatcag ttaccgtgag
     3421 ctgcaggaga tgctggctga acgcggagtg aatgtcgatc actccacgat ttaccgctgg
     3481 gttcagcgtt atgcgcctga aatggaaaaa cggctgcgct ggtactggcg taacccttcc
     3541 gatctttgcc cgtggcacat ggatgaaacc tacgtgaagg tcaatggccg ctgggcgtat
     3601 ctgtaccggg ccgtcgacag ccggggccgc actgtcgatt tttatctctc ctcccgtcgt
     3661 aacagcaaag ctgcataccg gtttctgggt aaaatcctca acaacgtgaa gaagtggcag
     3721 atcccgcgat tcatcaacac ggataaagcg cccgcctatg gtcgcgcgct tgctctgctc
     3781 aaacgcgaag gccggtgccc gtctgacgtt gaacaccgac agattaagta ccggaacaac
     3841 gtgattgaat gcgatcatgg caaactgaaa cggataatcg gcgccacgct gggatttaaa
     3901 tccatgaaga cggcttacgc caccatcaaa ggtattgagg tgatgcgtgc actacgcaaa
     3961 gg
//
