LOCUS       NZ_AP027252             2257 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE120393 plasmid pJNE120393-6, complete
            sequence.
ACCESSION   NZ_AP027252
VERSION     NZ_AP027252.1
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  JOURNAL   Unpublished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 2257)
  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
            AP027252.1.
            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..2257
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE120393"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE120393-6"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /note="National Institute of Infectious Diseases JNE120393"
     gene            join(1362..2257,1..94)
                     /locus_tag="QUF33_RS25995"
     CDS             join(1362..2257,1..94)
                     /locus_tag="QUF33_RS25995"
                     /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_052923600.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRLKDRKEFRPVQGWIRTTEVTRSS
                     DGSAHPHFHTLMMVPPSMLSGDGYVKHARWVELWRECLRVSYDPNVDVRAVKPRKPKDG
                     ESLAGATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESD"
                     /name="protein rep"
     gene            590..817
                     /locus_tag="QUF33_RS26000"
                     /old_locus_tag="JNE120393_49830"
     CDS             590..817
                     /locus_tag="QUF33_RS26000"
                     /old_locus_tag="JNE120393_49830"
                     /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          98..178
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="89.0"
                     /evalue="5.64e-30"
     Typing          complement(2078..2257)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.238"
                     /coverage="94.0"
                     /evalue="2.9e-81"
ORIGIN
        1 tgacgatgac ggttcacgca tcgcgttcga gtggaaaacc gaggtcagaa agtaccgtcg
       61 ctcaccgacg aaagataaaa ctgaatcaga ctagcagggt gtcggggtgc agccctgacc
      121 agatggcaat tgtgatagcg tcgcgtgtga cggtattaca attgcacatc ctgtcccgaa
      181 aattcccgtc ccgaaaattc ccgccgtttc tcggtttttt gagcatcgca gatcgcacga
      241 caaacgaaac gaagtgaagt ttgtataagt gcgcacttcg tgggtgttct gtgccgccag
      301 cttgtcgaac gcgtggcgga gctgcgcgac aaaaatggca aaataattcg ctgtccgttc
      361 gccagaattt tgcacggccg tggtagctgc aggagcgcag aacggcagaa aattgccagc
      421 gttccggcaa aaaaatcgga acaagaaatc cccgtgtttt actccgatgc aggatagggc
      481 aaacgccgca aagtgacgtc tctgacgcca tttcgcaacg tttgcccggt gacctacagt
      541 cggttcaaca aacaaaaaaa ccgctgcgga gtcgggacaa gatacatgtt tgtattcccg
      601 ccacacggtc ggtactccaa acatcctggt cagggctgcg ccccgacacc ccgccaacgc
      661 ctcacggcac gcgaaaaaat tccgcgtacc gctcaccgtt cccgaactcg tcaaacagaa
      721 aatcgcgggg tcccgcgcct ttggcgtggg ttccgatttt gtgattgacg acgtcacggg
      781 gaaaacactg gggatggtgg ttggtgtcac gcagtgagac caaccacctg cgaggcggtt
      841 tgaaagatct gctgctggat atggttttaa cgtatgaaat taaattggca gtactgcaaa
      901 acgaaaacac ggatgcgaaa atcacaaacc agatagattt ataaaacttt gtgggaggtg
      961 aagatgtttt ttgaggcttt tgatcgcatt gatgcggcgc ttagcattgc gatcccgctt
     1021 ctggtgttgt tgaggttttt ggttgtgaaa aagcgctgat tttgcgttta ttttttgctc
     1081 aaagctcgcg cgcgttcctt gtatttatac ttaagggata actctgggat tcaaattggc
     1141 ctccagccct tgtcccgcaa ggcttgaggg cacatttgct ccgaaatggg tttggaagta
     1201 ttctgtcgga agtggtcgcg ttaaaagcga cccccgcaac gacgggcatc gttcgggggc
     1261 gtgaccacct gtagagattc gaattggtga tacggctaac acaggtgata tggcaatgat
     1321 aacacgtcag atgagccatc gcccacaatc gggtggtgtg catgaaaaat cctgaactcc
     1381 agaacctcac ggactattcc ccctcagatg cgccctggga cgctcacaga agcgtttctg
     1441 acgacgtggg agggatttac ctgcttgcgg ccgaatatga gcgctacggg gcgcgtatgg
     1501 ccctctgtgg cggtttattg cgtttcgggt ggtctaccct caaggaaacc ggagaaacgc
     1561 gtctgaggct gcgtgaggcg catttctgcc gtgtccggca ctgtcctgtc tgccagtgga
     1621 ggcgctccct gatgtggcaa gcccgtttct accagtccct gccgcgtatc gtggcggatt
     1681 accctgatgc ccgctggatg ttcctgaccc tgaccgtgcg caactgtgcg atcggggagc
     1741 tgggcgagat gctgaaccgg atgaatgcag ctttccagcg actgaaggat cgcaaggagt
     1801 tccggcctgt tcagggctgg atacgcacca cggaagtcac ccgcagcagt gacggcagcg
     1861 cacatcccca cttccacacc ctgatgatgg tgccgccctc aatgctatct ggtgacggtt
     1921 acgtaaaaca tgctcgctgg gttgaactct ggcgggagtg cctgcgggtc agttacgacc
     1981 cgaatgttga tgtccgggca gtaaaacccc gtaagccaaa ggatggcgaa tcgctggccg
     2041 gtgccactgc cgaactggtg cgcggtgcgg tggccgaaac cctgaaatat tccacgaagc
     2101 cggctgacat ggtggccgat cctgaatggt tcctcgaact gacccgccag acgcacaagc
     2161 gccgctttgt ggcgaccggc ggtgcactca aagacgtact gaagctcgat caggaaaccg
     2221 atgccgacat ggtgattggg gatgatattt ccgaggg
//
