LOCUS       NZ_AP027216             1546 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE131328 plasmid pJNE131328-4, complete
            sequence.
ACCESSION   NZ_AP027216
VERSION     NZ_AP027216.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00566111
            Assembly: GCF_030295525.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Kubomura,A., Lee,K., Iyoda,S. and Akeda,Y.
  TITLE     Complete Genome Sequence of Eight LEE-negative Shiga Toxin-producing
            Escherichia coli Strains Isolated from Hemolytic-Uremic Syndrome
            Patients in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1546)
  AUTHORS   Kubomura,A., Lee,K., Iyoda,S. and Akeda,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JAN-2023) Contact:Akiko Kubomura National Institute of
            Infectious Diseases, Deaprtment of Bacteriology I; 1-23-1,Toyama,
            Shinjuku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Unicycler v. 0.5.0; Trycycler v. 0.5.3
            Genome Coverage                   :: 162.5x
            Sequencing Technology :: Illumina MiSeq; PacBio Sequel IIe
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/22/2023 12:23:31
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,131
            CDSs (total)                      :: 5,003
            Genes (coding)                    :: 4,820
            CDSs (with protein)               :: 4,820
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 79 of 183
            Pseudo Genes (incomplete)         :: 99 of 183
            Pseudo Genes (internal stop)      :: 43 of 183
            Pseudo Genes (multiple problems)  :: 35 of 183
            Pseudo Genes (short protein)      :: 2 of 183
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027216.1.
            Annotated at DFAST https://dfast.nig.ac.jp/
            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..1546
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE131328"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE131328-4"
                     /geo_loc_name="Japan"
                     /collection_date="2013"
                     /note="National Institute of Infectious Diseases JNE131328"
     gene            1..477
                     /locus_tag="QUE42_RS25655"
                     /old_locus_tag="JNE131328_p40010"
     CDS             1..477
                     /locus_tag="QUE42_RS25655"
                     /old_locus_tag="JNE131328_p40010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1082..1163
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(1360..1468)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(710..967)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="99.0"
                     /evalue="8.44e-113"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgtttt gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcgtgttttt gctccccgat ccccagaacg
      601 accgcgccgc cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca ccaaccagcc gaatagctgc
      721 ctgtgccgtg caaataggct ttgcagggag ctgacgcggt tcctagcgac ctgaaagccc
      781 ctggttaggg gtatcggcgc gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tggcgggcat ttaaacccgt ttcgtgcgtc tgagagcttc tgagcgtgtt
      901 tgaagggcta tctgacgact catccccgaa agaacaacaa cgggatcacc gacaacatgc
      961 gagaggtgat cccgctcgcc gcaagtcgat gaccgagtgt agcgagcgaa tcgacgagga
     1021 agcggaagag aaccggaagt tacattgagc acttacgcac ggatgcgggg tgtcggggtg
     1081 aagccctgac caggtgggga atgtctgagt gcgcgtgcgc ggtccgacat tcccacatcc
     1141 tgtcccgatt tctgaggcgt tttaacggtg aacggacggc aaaaacatga tcgagctgtt
     1201 gaacgtggag agcgcgaaat cgggcaaaat cacggctgac gaggcttgca gaggagtaag
     1261 ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg acaccccaaa
     1321 agggcgttgc gttgcgcgca acacccttgc ctagaataga tcttttacgc cgatttgtaa
     1381 gttgttgttt ttttagtgtg ttttttgttt acctgtcgca tccagggtga cacaacgttg
     1441 tcgcatcctg gatgcgacaa cacgcaacaa ggtgttgcac agatgtgtca tgatggctta
     1501 gagttgaacc aacgttagtg catgggattt tcagagggaa aaaatc
//
