LOCUS       NZ_CP055047             2458 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_59 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP055047
VERSION     NZ_CP055047.1
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 2458)
  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 2458)
  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
            CP055047.1.
            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..2458
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_59"
                     /isolation_source="Shek Wu Hui WWTPs_59 WWTPs effluent"
                     /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(64..177)
                     /locus_tag="HUZ71_RS23500"
     CDS             complement(64..177)
                     /locus_tag="HUZ71_RS23500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_058670733.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHDKAPLAAATGN"
                     /name="hypothetical protein"
     gene            597..788
                     /locus_tag="HUZ71_RS23320"
                     /old_locus_tag="HUZ71_23135"
     CDS             597..788
                     /locus_tag="HUZ71_RS23320"
                     /old_locus_tag="HUZ71_23135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1652..2077)
                     /locus_tag="HUZ71_RS23325"
                     /old_locus_tag="HUZ71_23140"
     CDS             complement(1652..2077)
                     /locus_tag="HUZ71_RS23325"
                     /old_locus_tag="HUZ71_23140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676030.1"
                     /GO_function="GO:0005515 - protein binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PH domain-containing protein"
                     /protein_id="WP_004884531.1"
                     /translation="MGSYVDQSLTRNESVISRAQTSWIPTIIPVIIGILLLPFYGLGLL
                     IIIPVLLRVWSTELALTNQRVIAKVGFIRRNTVELRIDKVESLGIHQGILGRIFNYGSI
                     VIKGTGGTNTPIPNIKAPMQFRSIVNNHIEEMNSKQQ"
                     /name="PH domain-containing protein"
     Typing          complement(61..415)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.348"
                     /coverage="82.0"
                     /evalue="2.93e-164"
ORIGIN
        1 accaaatctg tcctttcagt ttagccttaa ccggcgcata acttcaagac taactcctct
       61 aaatcagtta ccagtggctg ctgccagtgg cgctttgtcg tgtctttccg ggttggactc
      121 aagatgatag ttaccggaca aggcgcagca gtcggactga acggggggtt cgtgcataca
      181 gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagataaac
      241 gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga
      301 gggagctacc agggggaaac gcctgggatc tttatagtcc tgtcgggttt cgccaccact
      361 gatttgagcg tcagattttc gtgatgcttg tcaggggggc ggagcctatg gaaaaacgcc
      421 ccggcggggc gtggcctttt cgcccttgtc cttagctttc gttatgctta ccgttacgtt
      481 atctgcttat cctccctccg ctcgccgcag actcatgacc gaacggagtg agcgaatgag
      541 cgaggaagcg gaaaaccatc cgaacgtaca gtaagcactt tcgcgccggg gctttcatga
      601 acaaacaaca aaagactgcc gttaacatgg ctaaattcat ccaggatcag tccctgcttc
      661 ttctggacag gcttaatgag ctggatctgg atcatgaggc tgatttctgc gagaaactcc
      721 atgaggatgc ggaacgcctt taccgaagcc tgtcagcgcg cctgaatgag cagcaggacg
      781 gtgcgtaatg gctccgttct gggtattacc ggagtaatac cggcatcgcc ttaattttca
      841 ttgtgttagc gcttaacatt attaccccgg taatacccag aatccctgtg ttttttcttt
      901 tttatttatt tttcatgaag ttgcgatgaa aatcgcagct gcgttaggtg tatgtcattt
      961 tttagtatat aaaacgacca ctcccgagtg ctggcgccgc aggttaagga tgattctggc
     1021 taaaaagcgt ccttttccgg gaaagggtca tgctcgtatg accctatggg ttcagcgact
     1081 acacataaac tacaaaattg catctgcttt taccccagaa cgcgggtgta caacagaatt
     1141 acatcaaaag tacatcactt ttacgtcaga tcgcgggtgt acaacagaat tacatcaaaa
     1201 gtacatcact tttacgtcac ttttacatca tttttacgtc agatctgacc tctgaactat
     1261 tcgtacatcc gccccctctt cctgggcctc ctgcacgtgc tgaaaatggt ttttccggct
     1321 gtgccggcaa cgcctcacgg ccacgcaata aattgcgcat ccgttcaccg ttatcggggt
     1381 ggttcgtggt ggctttcagg gcgttcatcg gattttagcc gctaaaatcc cggccaggta
     1441 tgtccgtgca tagccatgca gtcgcgccag aatcatcagg ggcgtttttt ctcgatatgg
     1501 gcacagaaag gtgtgtgttt caggccggag gcctcagaaa cgccctgagg gcctctgagg
     1561 cggtgcgggc aacggatgtt atggtaaatc cagctgattg gcaggtacaa aaaaagcccc
     1621 gcagggcttt ttttgtaatg ctacgaggaa gctactgctg cttagaattc atttcctcga
     1681 tatgattgtt cacaatcgat ctgaattgca ttggcgcctt gatgtttgga attggagtgt
     1741 tggttccgcc agtgccttta atcacgatag acccatagtt aaagattcgt cccagtatcc
     1801 cttgatgtat gccaaggctt tcaactttat caatacggag ttccaccgta ttgcgtcgga
     1861 taaaacccac ttttgcgatg actctttggt tagttaatgc aagctccgtt gaccaaactc
     1921 taaggagcac agggattatt ataagtaacc ctaagccgta aaaaggcagc aacaagattc
     1981 cgataattac tgggatgatt gttggaatcc aggaggtttg agcgcgagat attacggatt
     2041 catttctcgt taatgattgg tctacgtagc ttcccataag gttatatcca tttagaaaaa
     2101 ataggatttt tcccttttta aggcgaatca gcaatagaaa ctttatgtct ccgtggtggg
     2161 tatacaaaat ttacggagag cgtagcgacc gtcgcacagt tcggttcttt cctttcgtga
     2221 cgcaactggc ttgattctgt ggtggtggtg gctgctgcta tgtctcacat actcttggcg
     2281 ttgcaatcct ttatcccata tctgtcgaat atcacagatg atcttcttga gatcctgtcc
     2341 gttgcgtcgt aatctctttc tctggaaacg aaaaaaccgc cttgcagggc ggtttttcga
     2401 aggttctcag agctaccaac tctttgaacc gcggtaactg gcttggagga gcgcagta
//
