LOCUS       NZ_AP027251             3373 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE120393 plasmid pJNE120393-5, complete
            sequence.
ACCESSION   NZ_AP027251
VERSION     NZ_AP027251.1
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  JOURNAL   Unpublished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 3373)
  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
            AP027251.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE120393"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE120393-5"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /note="National Institute of Infectious Diseases JNE120393"
     gene            11..571
                     /locus_tag="QUF33_RS25975"
     CDS             11..571
                     /locus_tag="QUF33_RS25975"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            578..811
                     /locus_tag="QUF33_RS25980"
                     /old_locus_tag="JNE120393_49800"
     CDS             578..811
                     /locus_tag="QUF33_RS25980"
                     /old_locus_tag="JNE120393_49800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2128..2319)
                     /locus_tag="QUF33_RS25985"
                     /old_locus_tag="JNE120393_49810"
     CDS             complement(2128..2319)
                     /locus_tag="QUF33_RS25985"
                     /old_locus_tag="JNE120393_49810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2368..2706
                     /locus_tag="QUF33_RS25990"
                     /old_locus_tag="JNE120393_49820"
     CDS             2368..2706
                     /locus_tag="QUF33_RS25990"
                     /old_locus_tag="JNE120393_49820"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_251302571.1"
                     /translation="MKREKMLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTG
                     KLPTLSPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVR
                     EQGVRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          1964..2047
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          2..894
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="88.779"
                     /coverage="100.0"
                     /evalue="3.97e-148"
     Typing          2697..3373
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.248"
                     /coverage="100.0"
                     /evalue="3.42e-142"
ORIGIN
        1 ggggcgctgt atgagcaatc ttttacaaat gggaacagac ttcgagaaga aactgaaaga
       61 gcgagccgct tctaccgaga acatgctgaa cagcgagttc aggaagctcg aagagtctgt
      121 agacaaggca ttgagcttaa acaggcagaa aatcagagac gctatcagcg aacatacaac
      181 atccgtgaaa aagcaactgg atacgctgag caccaccgtg agcatgcagt tcagcaccac
      241 agaggccgaa ctgtcccggc agcagaaaaa actgctctgg cgggtgatca aagggcggat
      301 actgtttccg gcgctgaccg cgctcagcgt cacgggcggc attttcctgg ggtgctgggg
      361 gctgatggag tggcaggaaa gcaagattgc gaaaaatatc ctgactatca gagagcagga
      421 aaacacgctg gcgaaactcg aggcaaaaac ctggggggtg acgttcgtca atggcgagaa
      481 cgggaaattt ctggtgttgc cggacggggt gaaaggggaa aacacctgga cggtgggcga
      541 caagaacgcc gtgaggctgg tcagggagta aacgagtatg acggaactgg aagggcattt
      601 gctgaacgcc ttagagcatt tgcaacagga ctatatgcgg cggctgaacg agtgggagag
      661 cgccttcgcg gaattgcaga agatgcacga ggttacgcaa cggaacaacg cgatactgaa
      721 cgagcgcgtc gtgatattga gtcagcaggt gcagagatta gccgggcaag tggatcgctt
      781 gagtcggtta tttatcgcga acaacagcta agggatgaac aggagcgtgc ccggtacaga
      841 catgaggtac aggaacgcgc ggcacgggtt cggagtgggc catcaatgga gatgtgaccg
      901 gggaagtgac gaaatcttgc cattttgacc agttcgacgg ctggggcgag cgaaacaaat
      961 cgtgtgccgt atttgtgcat agctatgcaa catcctgaaa acgcatttca cgcgtttttg
     1021 gggattcagc caggggaaaa catggttttt ttactttttg agcgtaaaga cgtgaaaaat
     1081 ctcgttattg cacttgcgat ctttcgtcgg cgggcgtaga acgaaaacag ctcgccagga
     1141 aggcgagctg tttcgggttc attgaggtct ctgacctcct caatgttcct gtggaaactg
     1201 ttgagatcca caacagaaac cagttcattc agtttgcatg agccttctgt attcttcaag
     1261 aatttttcaa cagcacagtc tcccaggaac cccgaaaaaa acctgttttt gcagatactt
     1321 gcgtatttgc gagaatcgtt tgcggttggg ggagctgtga cgacggcgac cgcacgcgtg
     1381 agagttccgc taccggcgca gagagtttca tcgacagcgg acacctgatg agttgccaca
     1441 aaaaccgtat gtagcgcggc tagattggtt gagttagacc ttggcggcag ttcccggtat
     1501 gtggtggcgt gacgggtgag atggtgcggc gaagacgcat acgtcacgca ggcgcgggtt
     1561 cttccactga cgcgccccgt gatcgatggc cttggctccg tccggcatat cgagagcggc
     1621 aaactacccg tcccttcact gggaggggtg agttgttgcc gttccctcca acctttcacc
     1681 atccggcata tcgcacgatc ccatgtgcac cgcaactcct gataactcca gtgcaaaaaa
     1741 aaaaaaacgg atcagcatca caacgagagt gatcccaccg ctcgccgcag ccccagcgac
     1801 cgaacgtagt gagcgagtgg gcgaggaagc ggaagagtca cagatgcaag cattgtgcac
     1861 ttacgcgcct gtgccagtgt ccgcgtgtgt gctgtttatc gggtgcgctg tttttacatc
     1921 tgtgcggctt tttactcctg acatggtgca cttcccatcc attctgcacc gatgcaaaat
     1981 gagataagcc agtatacaca tcgctatcgc tctgtgaact gggtcagggc tgcgccccga
     2041 cacccgcact gacgcgccct ggcgggcttg tctgctcccg gcatccgctc acaggcaagc
     2101 tgtgagcgtc tccgggagct gcatgtttca gttgctttca ccgtcatcgc cgaagcgtgc
     2161 gaggcaactg cggtagagtt cgtcggcgtg gtcgtgaagt gattcgcaga tgtctgcctg
     2221 ttcgtccgcg tccagatcgt tgagtttttc cagcagggtt agcgtctggc ttctgataaa
     2281 gcgagccatg ttaagggctg ttttttcctg tttggtcatg gtcttaaggc tccttgtatg
     2341 ggggatttgt tagggggaat gataccgatg aaacgcgaga agatgctcac gatacgggtt
     2401 accgatgagg agcacgcccg gttactggaa cgctgcgagg gtaaacgact ggcggaatgg
     2461 atgcggcggg tctgtctggg ggagccggtt gcacgcacag gaaaactgcc gacactatcg
     2521 ccgccattgc tgcggcatct ggctgccatc gggaacaacc tgaaccagac agcccggaag
     2581 gtgaacagcg gccagtggtc ttcgattgac cgggttcatg tggtggccgc actgatggcc
     2641 atcgagggtg aattgcgcca gttgcggcag gctgtcaggg aacagggggt acgggatgat
     2701 agttaaattt catgccaggg ggaaaggcgg tggaagtggc ccggtcgatt acctgctggg
     2761 gcgggagcgt aaccgcgaag gcgcaacggt gctccggggt aacccggaag aagtgcggga
     2821 actcattgat tccacgccat tctcgaagaa atacacttca ggcgttctgt cgttcgcgga
     2881 gaaggagtta ccgccgggtg aacgcgaaag agtgatgacg agctttgagc gtgttcttat
     2941 gcccggtctc gaaaaagacc agtacagcat tctctgggtg gaacaccagg ataaggggcg
     3001 gctcgaactg aattttgtca tcccgaacat ggagctacag agcggtaagc gcctccagcc
     3061 gtactacgac cgcgcggaca ggccgaggat aaatgcctgg cagacgctgg ttaatcatca
     3121 ttacgggctg cgtgacccga acgcaccgga gaacagacgg acgcttgtca cgccaaataa
     3181 tctgccaaaa gcgaaacagg aggccgcaga agcgattaca cggggtcttg aggctcttta
     3241 ccatgccgga gcaataaaaa cgcgtcagga tgtcacagag gcgcttacag cggcaggttt
     3301 tgaggtggtg aggacaacca aaagcagcat cagtattgcc gacccggagg gggggcggaa
     3361 tctcaggcta aag
//
