LOCUS       NZ_AP027253             1551 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE120393 plasmid pJNE120393-7, complete
            sequence.
ACCESSION   NZ_AP027253
VERSION     NZ_AP027253.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00566463
            Assembly: GCF_030295585.1
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  JOURNAL   Unpublished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 1551)
  AUTHORS   Kubomura,A., Lee,K., Iyoda,S. and Akeda,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-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
            Genome Coverage                   :: 157.4x
            Sequencing Technology             :: Illumina MiSeq; PacBio RS II
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/22/2023 13:48:49
            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)                     :: 5,202
            CDSs (total)                      :: 5,076
            Genes (coding)                    :: 4,886
            CDSs (with protein)               :: 4,886
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 190
            CDSs (without protein)            :: 190
            Pseudo Genes (ambiguous residues) :: 0 of 190
            Pseudo Genes (frameshifted)       :: 80 of 190
            Pseudo Genes (incomplete)         :: 98 of 190
            Pseudo Genes (internal stop)      :: 50 of 190
            Pseudo Genes (multiple problems)  :: 35 of 190
            Pseudo Genes (short protein)      :: 2 of 190
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027253.1.
            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..1551
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE120393"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE120393-7"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /note="National Institute of Infectious Diseases JNE120393"
     gene            1..477
                     /locus_tag="QUF33_RS26005"
                     /old_locus_tag="JNE120393_49850"
     CDS             1..477
                     /locus_tag="QUF33_RS26005"
                     /old_locus_tag="JNE120393_49850"
                     /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"
     gene            complement(922..1143)
                     /locus_tag="QUF33_RS26010"
     CDS             complement(922..1143)
                     /locus_tag="QUF33_RS26010"
                     /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_152921959.1"
                     /translation="MCKCNTVTRDDIPFAIWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGITSRMLSVIPVLFFWG"
                     /name="hypothetical protein"
     Typing          1071..1162
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.398"
                     /coverage="100.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(1365..1473)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.364"
                     /coverage="100.0"
                     /evalue="9.16e-44"
     Typing          complement(709..969)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaagc 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 aaattgagct
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccttt gcgtgttttt gctccccgtt ctccagaaaa
      601 aaccgagccg ccacggttcc ggcagcgcct tgagcgctac cggaaaccgt ctggggagaa
      661 ccccagaccc ccatcgctgc aacaccgacg gtctacgacc acctaccaac cgcatggctg
      721 cctgttccgt gcaaatgggc tttgcagggg gctggcgcgg ttcctggcga cctgaaagcc
      781 cctggttagg ggtatcggcg cgcttgacct cctgagagcc tctgtaagcg tttttcgcgc
      841 cttccatgcc ctggcgggca tctaaaaccc gtttcgtgcg tctgagagct tttgagcgcg
      901 tttgaggggc tatctggcga ctcatcccca aaagaacaac accgggatca ccgacaacat
      961 gcgagaggtg atcccgctcg ccgcagcccc agcgaccgaa cgtagtgagc gagtgggcga
     1021 ggaagcggaa gagaaccgga aaccacattg agcacgtacg cactgatgcg gggtgtcggg
     1081 gcgaagccct gaccagatgg caaacggaat atcgtcgcgg gtgacggtat tacatttgca
     1141 catcctgtcc cgatttttgg ggcgttttag cggtgaacgg aaggcaaaaa catgatcgag
     1201 ctgttgaacg tggagagcgc gaaatcgtgc aaaatcacgg ctgacgaggc ttgcagagga
     1261 gtaagccagt atacactccg ctatcgctac gtgactgggt cagggcttcg ccccgacacc
     1321 cccaaagggc gttgcgttgc acgcaacacc cttgcctaga atagatcttt tacgccgatt
     1381 tgtaagtgct tgttttttta gtgtgttttt tatttacctg tcgcatccag gatgacacaa
     1441 cgttgtcgca tccaggatgc gacaacacgc aacaaggtgt tgcacagatg tgtcatgatg
     1501 gcttagattt gaaccaacgt tagtgcatgg gattttcaga gggaaaaaat c
//
