LOCUS       NZ_AP027211             1552 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE082640 plasmid pJNE082640-5, complete
            sequence.
ACCESSION   NZ_AP027211
VERSION     NZ_AP027211.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00566112
            Assembly: GCF_030295505.1
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  JOURNAL   Unpublished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 1552)
  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                   :: 53.4x
            Sequencing Technology :: Illumina MiSeq; PacBio Sequel IIe
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/22/2023 12:16:24
            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)                     :: 4,993
            CDSs (total)                      :: 4,869
            Genes (coding)                    :: 4,669
            CDSs (with protein)               :: 4,669
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 100 of 200
            Pseudo Genes (incomplete)         :: 101 of 200
            Pseudo Genes (internal stop)      :: 42 of 200
            Pseudo Genes (multiple problems)  :: 39 of 200
            Pseudo Genes (short protein)      :: 3 of 200
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027211.1.
            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..1552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE082640"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE082640-5"
                     /geo_loc_name="Japan"
                     /collection_date="2008"
                     /note="National Institute of Infectious Diseases JNE082640"
     gene            1..477
                     /locus_tag="QUE04_RS24965"
                     /old_locus_tag="JNE082640_p50010"
     CDS             1..477
                     /locus_tag="QUE04_RS24965"
                     /old_locus_tag="JNE082640_p50010"
                     /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          1071..1156
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="95.0"
                     /evalue="4.39e-26"
     Typing          complement(1366..1474)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(708..968)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="3.95e-106"
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 attattcgtt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcatttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcgtgttttt gctccccgat ctccagaacg
      601 accgagccgc cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca cctaccaacc gagtgactgc
      721 ctgtaccgtg caaatgggct ttgcaggggg ctggcgcggt tcctggcgac ctgaaagccc
      781 ctggctaggg gtatcggcgc gcctgacctc ctgaaacgct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tgacgggcat ttaaaccccg cctcgtgcgt ctgagagctt ctgagcgcgt
      901 ttgaagggct atctgacgac tcatccccga aagaacaaca gcggaatcac cgacaacatg
      961 cgagaggtgg caccgctcgc cgcagcccca gcgaccgaac gttagtgagc gagtgggcga
     1021 ggaagcggaa gagaaccgga aaccacattg agcacgtacg cactgatacg gggtgtcggg
     1081 gcgaagccct gaccagatgg caaacggaat atcgtcgcgg gtgacggtat tacatttgca
     1141 catcctgtcc cgatttctgc gggggttaac ggtgaacgga cggcaaaaaa cgtgcaggag
     1201 ctgttgaacg tgaaaaccac gaaatctggc aaaaatcacg gctggcgagg cttgcagagg
     1261 agtaagccag tatacactcc gctatcgcta cgtgactggg tcagggcttc gccccgacac
     1321 ccccaaaggg cgttgcgttg cgcgcaacac ccttgcctag aatagatctt ttacgccgat
     1381 ttgtaagttg ttgttttttt agtgtgtttt ttgtttacct gtcgcatcca gggtgacaca
     1441 acgttgtcgc atcctggatg cgacaacacg caacaaggtg ttgcacagat gtgtcatgat
     1501 ggcttagatt tgaaccaacg ttagtgcatg ggatttttag agggaaaaaa tc
//
