LOCUS       NZ_AP027250             3904 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia coli strain JNE120393 plasmid pJNE120393-4, complete
            sequence.
ACCESSION   NZ_AP027250
VERSION     NZ_AP027250.1
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  JOURNAL   Unpublished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 3904)
  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
            AP027250.1.
            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..3904
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JNE120393"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJNE120393-4"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /note="National Institute of Infectious Diseases JNE120393"
     gene            complement(join(3596..3904,1..1242))
                     /locus_tag="QUF33_RS25960"
     CDS             complement(join(3596..3904,1..1242))
                     /locus_tag="QUF33_RS25960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_065336819.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARYGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNARDQDMER"
                     /name="MobA/MobL family protein"
     gene            1414..1860
                     /locus_tag="QUF33_RS25965"
                     /old_locus_tag="JNE120393_49780"
     CDS             1414..1860
                     /locus_tag="QUF33_RS25965"
                     /old_locus_tag="JNE120393_49780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184723.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(2121..3140)
                     /locus_tag="QUF33_RS25970"
                     /old_locus_tag="JNE120393_49790"
     CDS             complement(2121..3140)
                     /locus_tag="QUF33_RS25970"
                     /old_locus_tag="JNE120393_49790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_031603333.1"
                     /translation="MSAALQYFEENLPHRPYHTNDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKF"
                     /name="replication initiation protein"
     Typing          complement(2366..3140)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.426"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(2..1242)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.411"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttaaaagca gcgttttctt tgtcccactc ggattcagct tgctgtagct tgttcctgaa
       61 ttcattcctt tcatgttcag cggtttccag cacacttttt tgctccagaa tacgcgcatc
      121 aatctccctt ttatcagccc cccgaaacag gccacgaatc ccattcaaag cattgcgttg
      181 ttcctgtagc tcccgcagct ccctttgtgc ggaaacgaca ttacgcccca gtttgtctaa
      241 ataccgtgct ccttcatata ttcgcctgct ccattcggaa agagagtctt tttttgcttt
      301 cgcattctga agcagcttat gttctttgag cgcattggga ttggcatccc ctaaacgagc
      361 aagccttgct tctccctgaa tgaccgtttt cataaccttg cggtactgaa gcaataactc
      421 cggtgaacgg gctgaacgaa caggctcaac tgccttgatt ttttgctttt gctcctgttc
      481 ctgctgaatg gcatttgcgg catctctggc ggtcttgagt tcccgctcag cattcctccg
      541 ttcctggatt gcaacaatct gctcaccatt gagactggcg gcctgaacgg ggccaagatg
      601 aacttccggc gtgcgattga taccctgttc tttcagagaa cgatgatcta cgcgcgactc
      661 gtgaccgtat cgcgcaaggt gctcattctg cacatctgcc cagcgggaac gcagcgcaac
      721 aagggcggct tttcgctctc cggctgtctg gggaatactc gctttttttg cgcctccccg
      781 ttctggtgat ttgctgttgg cacgtttaaa aaattgctgc ggatcgcgtt caataccatc
      841 attaatccgc tcgcaaaaca tgatatgcgc gtgtggctgt tcctttccgt cgattgcacc
      901 tggcggattg tggatcgcgt actggtaggc atggcgatcg ccaagttcct tttgcacgaa
      961 atcttcaaca agttctatcc gttgttcgcg tgtcagttca cgcggtaacg cgatctcaat
     1021 ttcacggtac gcagtcccgt tttttcgttc aaattcatct gcggctttcc atagctctgc
     1081 gggatttttc ttcgcccatg atggcatgtt accggatgac gaaaattcca gatcctcccg
     1141 cgatttgtag ctcttatatt cgccggatct ggaaatgtaa tcagcatgtt ttaaggcact
     1201 gccttttgct ccagctttga cggtgcaatg gtagcttgcc atctgccttt tagccctccg
     1261 caggagcgca cagtttctcg acgaaggaga gaaactacta agtgcgcatc cctgaattaa
     1321 tcagggatga ttttacggtc tcacacgcag gcagacaagg tgatattatg cacaataaca
     1381 actcacatta acggcaaaag tgcagaggta agaatgacaa atcgtgaaga gtggttaagt
     1441 gcaaaaattg cctacatcaa cggactgaaa tcaccgtcag agcagcagag attacttgtg
     1501 ttactggcag agaaaaaaaa ccgaacaacg acggatgaaa aaacgttgtc cgcactgata
     1561 cgggcagaaa aaaccgcaga gaaagcagcc gcagcaaaag ccagggtaac ggcaatcata
     1621 gcggcagaac ggaaggcagc cgcaagggcg gaacgaaagg cgcgggatca tgaactctac
     1681 aaggccgcag gcctcatgat tgtggcagga ctggtggaca gcaaaaccgg aaaaccaaag
     1741 tttagtgctg ccgaactggt aggcgcactc gcaggaatcg cagagctacc gcgcaaccat
     1801 ccaaaatggc aggaatggga aagacgcggg aaggagctac taaccaaaga cagtgcgtaa
     1861 gagcctccgt tcacgttccg gttccctggt gcttcctcgc tcattcgctc gctacgctcg
     1921 gtcatgagac tgcggcgagc acaaccacct caatcatgcg gtaagccgca ccattgctgg
     1981 gctgacagga gaaaaccgcc ggaaagcccg ctgctcaaaa agacgccgaa aggcgctgtt
     2041 atctgatata ggcttgttca tgtccgcgaa tttaaccatc cattaacaaa aacagggggt
     2101 aattgtcatt tttctgttaa ttaaaattta attatttgtt tcttggttaa ccattctcca
     2161 gaattatcca tccagcgtcg aatagtccgg ctgctaacac caaccgccac tgcaatatct
     2221 tccgttgacg ctcccaagat atacatatca agcgccctac gacgtttgtc gtcgttagca
     2281 gtccaccgaa cagcggcgct ttttttccct ttgtccgact gattttctga cgaattggcc
     2341 ttcccgccct tgcgaccgcg tgctgcctga atttctggcg tgtgcgtatc agccacatac
     2401 tgtgcgaaag tttccggcgt gaagttcctg tgcgtgtatt tcgcaatgct cttgccaata
     2461 gcccgacatt caggcggaga aagcggaacg ggaagcgatg cgttgtacat ttcgacacgc
     2521 tgaatcacgg catcaagcca ctgtgagaat gctggccagc cctgacgaat cgccctgtaa
     2581 gcccatttgc gcgtcatttc aaacaggtgg cagtttcgcc ccatcccgta atgtttatcg
     2641 atgctacgac gctctgaggc gctcaaatcg agataatctg ccagttcatc gagggtatag
     2701 gcttcctcgc gccactccat cacctgccat tccaggtgga acggattttt gcaaatcagt
     2761 ccgctgtagt tcacatcagc acaaagtttc tcacacagcg aacgttcaat cgcggcggca
     2821 tatttcagcg ccttaaccga gctgtccggc gcggttctca cggcgatatt gagtgcgtag
     2881 agcaggtgag catgaccgtt cacaggattt tttacggtga tgttcggcgc gggggcgttc
     2941 cggtcgctcc agtcaatcgc ggccccctcg cggtcaacgt caaaaaccag ccagaactgc
     3001 gcatgaggct ggttctgctg gatgtaccgc gcaagaagcg cacgcccttt gccggagatg
     3061 cgaagaccaa aagcgagatc attcgtgtga tagggacggt ggggtaaatt ttcttcgaag
     3121 tattgaagcg cggcgctcat gtgttacgat tccttccagg ttatcgaccg acatcgcccc
     3181 tgtattttcg tgacaatctt ggcggagaga cacgaatttc aggggcgttt gtttttcagt
     3241 cgcttacact acccccaacg acaaaacctg tcgagccttc ccgcaaaacc gatccattta
     3301 ccataactcc cgttgtacgt accccataaa acgccctcaa tcgctttctg acgcaaaaaa
     3361 cgcaaaaaga caaggaaaca ccaggctgaa ccagaaaaat gcgtcagaat cgtttttagg
     3421 gcgctgcata actatgcacg aaagcgatgc gcgatcggtt tcgagcgttc agaagggcga
     3481 acgggtcaaa acagcaaact ttctcatcag aaaacggtga acgggacgcg gaattttttc
     3541 gcgttccgtg aaacgttggc ggggttcggg gcgcagtccc gatattgcta cattttcaac
     3601 gctccatatc ttgatcacgt gcgttactac gtgatgcctc cctggcccag gatcgctgta
     3661 tacgcagtgc cttttcctcc tgttgctgcc gttcctgcgc catttctgcc agtaactcat
     3721 gtcgcatttg agctttttca tctccagata tactgagttc aggctccaga gataacatct
     3781 ggctacgggc aacggatact tcttcagcaa ccttttgcct ggtattctct aaagatgccg
     3841 cggccagaat ctcacgttct ctgtacctgt ccagatcccc aacgtactta tatccctcgg
     3901 tacg
//
