LOCUS       NZ_AP022331             1551 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Escherichia coli O25:H4 strain 18044 plasmid p18044_5, complete
            sequence.
ACCESSION   NZ_AP022331
VERSION     NZ_AP022331.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00199041
            Sequence Read Archive: DRR203158, DRR203159
            Assembly: GCF_016756455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O25:H4
  ORGANISM  Escherichia coli O25:H4
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Nagaoka,H., Hirai,S., Morinushi,H., Mizumoto,S., Suzuki,K.,
            Shigemura,H., Takahashi,N., Suzuki,F., Mochizuki,M., Asanuma,M.,
            Maehata,T., Ogawa,A., Ohkoshi,K., Sekizuka,T., Ishioka,T.,
            Suzuki,S., Kimura,H., Kuroda,M., Suzuki,M., Murakami,K. and Kanda,T.
  TITLE     Coinfection with Human Norovirus and Escherichia coli O25:H4
            Harboring Two Chromosomal blaCTX-M-14 Genes in a Foodborne Norovirus
            Outbreak in Shizuoka Prefecture, Japan
  JOURNAL   J Food Prot 83 (9), 1584-1591 (2020)
   PUBMED   32866241
  REMARK    DOI:10.4315/JFP-20-042
REFERENCE   2  (bases 1 to 1551)
  AUTHORS   Hirai,S., Shigemura,H. and Murakami,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JAN-2020) Contact:Hiroaki Shigemura Fukuoka Institute
            of Health and Environmental Sciences; Mukaizano 39, Dazaifu
            818-0135, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Coverage                   :: 56x
            Sequencing Technology             :: Sequel; GridION X5; MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016756455.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 02:44:44
            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)                     :: 5,234
            CDSs (total)                      :: 5,121
            Genes (coding)                    :: 4,896
            CDSs (with protein)               :: 4,896
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 225
            CDSs (without protein)            :: 225
            Pseudo Genes (ambiguous residues) :: 0 of 225
            Pseudo Genes (frameshifted)       :: 80 of 225
            Pseudo Genes (incomplete)         :: 166 of 225
            Pseudo Genes (internal stop)      :: 41 of 225
            Pseudo Genes (multiple problems)  :: 52 of 225
            Pseudo Genes (short protein)      :: 1 of 225
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022331.1.
            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 O25:H4"
                     /mol_type="genomic DNA"
                     /strain="18044"
                     /serovar="O25:H4"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:2067421"
                     /plasmid="p18044_5"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            101..577
                     /locus_tag="ECO25NV_RS25810"
                     /old_locus_tag="ECO25NV_49860"
     CDS             101..577
                     /locus_tag="ECO25NV_RS25810"
                     /old_locus_tag="ECO25NV_49860"
                     /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(1021..1242)
                     /locus_tag="ECO25NV_RS26235"
     CDS             complement(1021..1242)
                     /locus_tag="ECO25NV_RS26235"
                     /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_158414302.1"
                     /translation="MCKCNTVTRDDIPFAVWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGVTSRMLSVIPLLFFRG"
                     /name="hypothetical protein"
     Typing          1182..1262
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.122"
                     /coverage="87.0"
                     /evalue="9.59e-28"
     Typing          complement(1465..1551)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="80.0"
                     /evalue="3.32e-38"
     Typing          complement(810..1068)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="99.0"
                     /evalue="1.09e-111"
ORIGIN
        1 cctggatgcg acaacacgca acaaggtgtt gcacagatgt gtcatgatgg cttagatttg
       61 aaccaacgtt agtgcatggg attttcagag ggaaaaaatc atgtttattg attcagaaaa
      121 acgactgaaa caactttcag atgaggcaaa gaaaaacacc gaggatctcg aagaagcaaa
      181 gaagaattca aggtttacac aggtatcccc aaaaggttgg gaacgcgttc gagagctgct
      241 gaaggatagt caaggcatat cagcactgaa gctgtactca tttttagcgg agcatatcga
      301 tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta gctgaaaaac ttggagttag
      361 cagaagcaca attattcggt ggctcaatta cttagaatca aaaaatgcat tagttagaat
      421 ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca catgaagtct ggaagggata
      481 caacactacg aaaaaccatg cagcgtttgt cactaaaaca ctggtcaaca aagacggtga
      541 tattcagcgc cgaatcatgg ccatgttttc aaattgagcc agcggcaggc ggacaatcag
      601 gggctacgtg ttaacgtttt gaccatgatt gtctatcctg cattgctctt ttgccgcctc
      661 aaaatccctt gcttgttttt gctccccgat ccccagaacg accgcgccgc cacggttccg
      721 gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac cccagacccc catcgctgta
      781 acaccgacgg tctacgacca ccaaccagcc gaatagctgc ctgtgccgtg caaataggct
      841 ttgcaggggg ctgacgcggt tcctagcgac ctgaaagccc ctggttaggg gtatcggcgc
      901 gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc ttccatgccc tgacgggcat
      961 ttaaaacccg tttcgtgtgt ctgagagctt ctgagcgcgt ttgaggggct atctggcgac
     1021 tcatccccga aagaacaaca acggaatcac cgacaacatg cgagaggtga caccgctcgc
     1081 cgcagcccca gcgaccgaac gtagtgagcg agtgggcgag gaagcggaag agaaccggaa
     1141 accacattga gcacgtacgc actgatgcgg ggtgtcgggg cgaagccctg accagacggc
     1201 aaacggaata tcgtcgcggg tgacggtatt acatttgcac atcctgtccc gatttctgag
     1261 gcgttttagc ggtgaacgga cggcaaaacc atgatggagc tgttgagcgt tgagagcgtg
     1321 aaatctggca aaaatcacgg ctggcgaggc ttgtagcgga ataagccagt atacactccg
     1381 ctatcgctac gtgactgggt cagggcttcg ccccgacacc ccaaaagggc gttgcgttgc
     1441 gcgcaacacc cttgcctaga atagatcttt tacgccgatt tgtaagttgt tgttttttta
     1501 gtgtgttttt tgtttacctg tcgcatccag ggtgacacaa cgttgtcgca t
//
