LOCUS       NZ_AP027210             2395 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE082640 plasmid pJNE082640-4, complete
            sequence.
ACCESSION   NZ_AP027210
VERSION     NZ_AP027210.1
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  JOURNAL   Unpublished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 2395)
  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
            AP027210.1.
            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..2395
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE082640"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE082640-4"
                     /geo_loc_name="Japan"
                     /collection_date="2008"
                     /note="National Institute of Infectious Diseases JNE082640"
     gene            complement(1..990)
                     /locus_tag="QUE04_RS24955"
                     /old_locus_tag="JNE082640_p40010"
     CDS             complement(1..990)
                     /locus_tag="QUE04_RS24955"
                     /old_locus_tag="JNE082640_p40010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_064550293.1"
                     /translation="MENPELQNLADYSPADKTWDEHRSISDDVGGIYLRAAGFERYGER
                     VEGCSGILRFGWSTNEETGETRLRLRDARFCRVRHCPICQWRRSLMWQARFYQSLPKIV
                     AEYPDARWLFLTLTVRNCPITELGDTLTVMNAAFQRLKDRKEFRGVLGWVRTTEVTRGK
                     DGSAHPHFHTLLMVSPSMLSGDGYVKHARWVELWRDCLRVEYDPNIDIRVVKSRKPKDG
                     ESLPCSVVDQLRGVVVETLKYSTKPADMLVDPEWFLELTRQVHKRRFVATGGVLKDVLQ
                     LERETNEDLIMADGMAEGADDGSRLAFSWRAVAKKYRRDRTMDKPKQK"
                     /name="protein rep"
     gene            complement(1528..1755)
                     /locus_tag="QUE04_RS24960"
                     /old_locus_tag="JNE082640_p40020"
     CDS             complement(1528..1755)
                     /locus_tag="QUE04_RS24960"
                     /old_locus_tag="JNE082640_p40020"
                     /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_109475618.1"
                     /translation="MYSRHTVGTPNILVRAAPRHPANASRHAKKFRVPLTVPELVKQKI
                     AGSRAFGVGSDFVIDDVTGKTLGMVVGVTQ"
                     /name="hypothetical protein"
     Typing          84..275
                     /name="Col(MP18)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.083"
                     /coverage="100.0"
                     /evalue="6.45e-58"
ORIGIN
        1 ttatttctgt tttggcttat ccattgtgcg atctcggcga tactttttag ccaccgcccg
       61 ccatgaaaac gccagacgcg atccgtcatc cgcaccctct gccatgccat ctgccataat
      121 caaatcctcg ttcgtttccc gctccagttg caaaacgtcc ttaagcacac cacccgtcgc
      181 cacaaaacgg cgcttgtgta cctggcgtgt taactctagg aaccattcag gatcgaccag
      241 catgtcggcg ggctttgtag aatatttcag tgtttcaacc accaccccgc gcagttgatc
      301 caccacagaa cagggcaacg attcaccgtc tttcggtttt ctggacttca caaccctgat
      361 gtcgatgttc gggtcatact ccacccgcag acagtcgcgc cacaactcca cccatcgggc
      421 atgtttcaca taaccatcac cggacaacat cgagggggaa accatcagca gggtgtggaa
      481 atgggggtga gcgctgccgt ccttgccgcg ggtgacttcc gtcgtgcgca cccagcccag
      541 cacgccgcga aactctttgc gatctttcag gcgctggaag gccgcattca tcacggtcag
      601 ggtgtcgcca agctccgtaa tcggacagtt acggacggtc agggtcagga acagccagcg
      661 tgcatcagga tattccgcaa cgatctttgg cagggactga tagaaacggg cttgccacat
      721 cagggaacgc ctccactgac agatcggaca gtgccggacc cgacagaacc gcgcatcacg
      781 taaccgcagg cgcgtttctc cggtttcctc gttggtggac cacccgaaac gcagaatgcc
      841 gctacaaccc tccacgcgtt cgccgtagcg ttcaaatccg gcagcccgca gataaattcc
      901 gcccacatca tcggaaatac tccggtgctc atcccacgtt ttgtccgcag gggagtaatc
      961 cgccagattc tgaagttcag ggttttccat gcctgccgct ccctagtgcg cgacaggcga
     1021 aattacgtgt tatcattcca atatcacctg tatatcgagt tatcaatcca atttcccagg
     1081 tggtcacccc cccgaacgac gcccatcgtt gcgggggttt attttttgac cgctaaaacc
     1141 aaaatacact caaaaccatt tcggagcaaa ttgccgttca gcccagtcct gacaaggcct
     1201 agaggcaaat ttgaatccca gagttatccc ttaagtataa atacaaggaa cgcgcgcgag
     1261 ctttgagcaa aaaataaacg caaaatcagc gctttttcac aaccaaaaac ctcaacaaca
     1321 ccagaagcgg gatcgcaatg ctaagcgccg cgtcaatgcg atcaaaagcc tcaaaaaaca
     1381 tcttcacctc ccacaaagtt ttataaaact atctgggttg tgattttcgc atccgtgttt
     1441 tcgttttgca gtactgccaa tttaatttca tgcgttaaaa ccatatccag cagcagatct
     1501 ttcaagccgc ctcgcaggtg gttggtctca ctgcgtgaca ccaaccacca tccccagtgt
     1561 tttccccgtg acgtcgtcaa tcacaaaatc ggaacccacg ccaaaggcgc gggaccccgc
     1621 gattttctgt ttgacgagtt cgggaacggt gagcggtacg cggaattttt tcgcgtgccg
     1681 tgaggcgttg gcggggtgtc ggggcgcagc cctgaccagg atgtttggag taccgaccgt
     1741 gtggcgggaa tacaaacatg tatcttgtcc cgattttttc gccagaacgc tggcagagca
     1801 tcggcagttc tgcgccgtta agccctccgc aggagcgcac agtttctctc cttcgtcgag
     1861 aaactactaa gtgcgcatcc gcacttaact cgcggatgat ttttggcacc gcagccacca
     1921 cagctacgca aaaatttcgg cgaccggaca gcaaatcatt ttgccgtttt cgtgacgcag
     1981 ccgttccgcg caatcgacaa actggcagta cagaaaactc acgaagtgcg cacttataca
     2041 aacttcactt cgtttcgttt gtcgtgcggt ctgcgacgct caaaaaaccg agaaacggcg
     2101 ggaattttcg ggacaggatg tgtaattgta ataccgtcac gcgcgacgct atcacaatta
     2161 ccacctggtc agggctgcgc ccgacaccct cgacaccgtg ccaaatgcac gttaaaaaaa
     2221 cgggcgcgtt tctggtgtcg gaatgcaact aaggggttag gtttgttagg ggatgccaga
     2281 agcgcgctaa aacgccacct gacgcattaa actggctcag ggtatacctg accgccaccg
     2341 aaacctaaaa cgcgcctgag cgcattttag aggtcttaaa atcgattttt agatg
//
