LOCUS       NZ_CP091701             4339 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KFu019 plasmid pKFu019_3, complete sequence.
ACCESSION   NZ_CP091701
VERSION     NZ_CP091701.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236398
            Assembly: GCF_022494785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4339)
  AUTHORS   Gomi,R.
  TITLE     Genome sequencing of blaCTX-M-carrying Escherichia coli isolates
            recovered from river water in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4339)
  AUTHORS   Gomi,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JAN-2022) Department of Environmental Engineering,
            Kyoto University, Kyotodaigakukatsura, Nishikyo-Ku, Kyoto-City
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022494785.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:36:48
            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)                     :: 5,000
            CDSs (total)                      :: 4,877
            Genes (coding)                    :: 4,650
            CDSs (with protein)               :: 4,650
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 227
            CDSs (without protein)            :: 227
            Pseudo Genes (ambiguous residues) :: 0 of 227
            Pseudo Genes (frameshifted)       :: 71 of 227
            Pseudo Genes (incomplete)         :: 141 of 227
            Pseudo Genes (internal stop)      :: 49 of 227
            Pseudo Genes (multiple problems)  :: 32 of 227
            Pseudo Genes (short protein)      :: 1 of 227
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091701.1.
            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..4339
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFu019"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKFu019_3"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            complement(join(4279..4339,1..134))
                     /locus_tag="L6L55_RS24865"
                     /old_locus_tag="L6L55_24860"
     CDS             complement(join(4279..4339,1..134))
                     /locus_tag="L6L55_RS24865"
                     /old_locus_tag="L6L55_24860"
                     /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="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001307203.1"
                     /translation="MMTKQQKAALNMAKFIQGQTLLLLEKLNELDLDVEADLCEKLHED
                     AEQLCRTLIIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(887..1555)
                     /locus_tag="L6L55_RS24870"
                     /old_locus_tag="L6L55_24865"
     CDS             complement(887..1555)
                     /locus_tag="L6L55_RS24870"
                     /old_locus_tag="L6L55_24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001427890.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_000257472.1"
                     /translation="MAVDDVVEVQEPPKKRVQCFIDGYNLYHAIDETRETKNHWVDLWK
                     LASKYISKNTCVLSDVFWFSAPPVHLTKRKQELHANYSAALQHCGVSVVSGKFKLKRVS
                     CNAGSGCGKSFDRHEEKESDVNLAIGLVSAACNDEFDIAIVITADSDLCPPIKYVRNRF
                     PNKQVWILIPPKRRSRANDLKAIANRDFEITNKDLRASCLLQFYRNNTGVVAQRPPEWS
                     "
                     /name="NYN domain-containing protein"
     gene            1889..2455
                     /locus_tag="L6L55_RS24875"
                     /old_locus_tag="L6L55_24870"
     CDS             1889..2455
                     /locus_tag="L6L55_RS24875"
                     /old_locus_tag="L6L55_24870"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /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_000658210.1"
                     /translation="MKEHSVLSTFWGEDATSMGWTGLPNTLLILQSDLGISSAEMCVLI
                     NILMHQWPQKEKNISFPSIELLAKRIGVSERSIQRTIRSLEKKGFISIFPTERSNQLTK
                     GANIYDSSRLKAILNEKSIEAKKKNQGTKKQIPGIKIPFLCRVCLESKANNVIEFRKLF
                     GFTRTIAGNIPNKICKKCVNKNDVF"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3848..4279)
                     /locus_tag="L6L55_RS24880"
                     /old_locus_tag="L6L55_24875"
     CDS             complement(3848..4279)
                     /locus_tag="L6L55_RS24880"
                     /old_locus_tag="L6L55_24875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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_214142656.1"
                     /translation="MARVSISEAARLASVSRPTIYKLLKSGELSYTSVVKHGKNVKVID
                     TTELIRVFGSLAFDSERDNAVVKFDDHSTGVNSDFLQDLQHQVALLQAENAGLKDAVNA
                     RDEHINSLRQAIQLLEHKQGTADPQHVPAKSWWQFWKSR"
                     /name="helix-turn-helix domain-containing protein"
     Typing          311..666
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.179"
                     /coverage="82.0"
                     /evalue="8.43e-140"
ORIGIN
        1 tcctcatgga gcttttcgca aagatccgcc tcaacatcga gatcgagttc attaagcttt
       61 tccagcagaa gcagagtctg cccctggata aacttcgcca tattaagcgc agctttctgt
      121 tgtttcgtca tcacagcgtc agtgctccat gttaactctg gttcttttcc gcttcctcga
      181 ccgttcgctc gctacgctcg gtcacttgtc tgcggcgagc ggacggggcg ttctaaaaga
      241 caagcaagaa agtggataac cgtaagagga agcagccaaa aagccaagag aaggccacgc
      301 cccctgggcg ttttaccata ggcttcgccc ccctgacgag catctcaaaa atcgacgctc
      361 aagtcagaag tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggcgg
      421 ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcactc cgctgttatg
      481 gccgcggttc tctcattcca cgcctgacac tcagttccgg gaaggcagtt cgctccaagc
      541 tgggctgtat gcacgaaccc cccgttcagc ccgactgctg cgtcttaccc ggtaactatc
      601 atcttgagtc caacccggaa agacacgact aagcgccact ggcagcagcc attggtaact
      661 gatttagagg agttggtctt gaagttatgc gccagttaag gctaaactga aagaacaagt
      721 tttggtgact gtgctcctct actagccagt taccgcggtt cagaaacttg ccggttactg
      781 aaccttagaa aaaaccacct tgccgggtgg ttttttcttt tgcaattatg caactaaaag
      841 catattcgtc aacacgtttt cgagcacatc acgtttttcg ttagggctac gaccattcag
      901 gtgggcgctg agcaacaact ccagtattgt ttctataaaa ctggagaagg caggacgccc
      961 gcaaatcctt attagttatt tcaaaatctc tattagcaat cgcttttaga tcattggcgc
     1021 gagatcgtct tttaggtggt attaaaatcc agacttgctt gtttgggaat ctatttctga
     1081 catattttat tggcggacat aaatcagaat cagccgtgat gacgattgca atatcaaatt
     1141 catcattaca tgcagcacta accaatccaa tagctaaatt tacatcagat tctttttctt
     1201 catgacgatc aaatgacttc ccacaaccac ttcccgcatt acaagagact ctctttaact
     1261 taaacttccc agagactaca ctaacaccac aatgctgtaa tgccgcggag taattcgcat
     1321 ggagctcttg ttttctttta gttaagtgta ctgggggagc agaaaaccaa aaaacatcac
     1381 ttaaaacaca agtgttttta gaaatgtatt tagatgccaa tttccacaga tccacccaat
     1441 gattttttgt ttctctagtt tcatcaatgg cgtgataaag attgtatcca tcaatgaaac
     1501 actgaactct cttttttggt ggttcctgca cttccactac atcatctaca gccatgtgca
     1561 atctctctgt tttagatagc aaaaagggtc tgcaattgca gacccttttt gcgccaacga
     1621 gccgtagctc aaattgacca ccgctagata aatcttcgcg ggaagaattt ttaacttcat
     1681 gctcagagcc gtagcttcaa gagccactga gagtactcgc ctctcaggta gtgagcagag
     1741 cttatgccat atgaagtgaa actagcaaaa ggatgacatt tatgtcaccc tataagataa
     1801 atagtaacta cagtagtaga gataaatctc tactactgta gttactatat tgtgattttt
     1861 tgattttttt acttttaagg ctaaccacat gaaagaacat agtgtactca gtacgttctg
     1921 gggggaagat gctacatcga tggggtggac tggcctaccc aacacgctgt tgattcttca
     1981 aagtgacttg ggtatttcaa gcgctgaaat gtgtgttctc attaatattt tgatgcatca
     2041 atggccacaa aaagaaaaaa acatatcctt tccatcaatt gagttattgg cgaaaagaat
     2101 aggcgtaagc gagagaagca tacagcgaac aataaggagc cttgaaaaga aagggttcat
     2161 aagtatattt ccaaccgaaa ggagtaacca gctaactaaa ggtgcgaata tctatgactc
     2221 atccagatta aaagcaattc ttaatgaaaa aagcattgag gcaaagaaaa aaaaccaagg
     2281 aactaaaaaa caaataccag gtataaaaat accattttta tgccgcgtct gcttagaatc
     2341 aaaggctaat aatgttattg aatttagaaa attatttggt ttcacaagaa caattgctgg
     2401 taatatccca aataaaatat gcaaaaaatg cgtaaacaaa aacgatgttt tttagaagaa
     2461 gatgattctc ttaccatgta atggtcaacc attagacgat acagaggtat ttactccaaa
     2521 atctcattgc ccgcgccata aagcaggtcc gcagtctgtg gacctgctca tgtcaattcc
     2581 ctcggatata aagttcgaca atgattgcag tcatagcctt ctccacaatg gccgtatcac
     2641 taaccttgtc cattccctca cgtttcatat ggtcgattag gcggcgatta tggtttaaat
     2701 ccctgattag ggcgctagta gtcttttgca tcggggttac cctccttttg gttatgagct
     2761 catggctcac tcttatttat ccctcgtttt atgagcccat gaataattgg cggtaaaggt
     2821 tggttttcgt cgctatttac cataacgcct cattacgcgc accgctgaaa cgcgctgagt
     2881 gcgatttcag cgcgaagacg atgaaatcca catcttaccc ggcaaaaacg cgccagaatc
     2941 gatctgagcg cgtttacggc ctgtgaatga ttatgcagcg cagtgaatga tctcagacct
     3001 ggcaccaaaa agctggtgaa accgcgattt ttcccggttt tcctgcccgg atttccgggc
     3061 ggaagccaac catttcgttt tcatgccata acaggtcagt accccgtccc tgatttgcaa
     3121 aatcaccccg ggataacttc ccggctacgg tgtaacggcg catttcagct attctctgct
     3181 gatgttgctc ggccgttaca gggggggact ccccagatcc gaaaactctc tcttaaactc
     3241 cgcccacaga aacttcaggt catcgataag ggtcgcaagc cattttttca ccgttcagcc
     3301 tccacatcat ttaaaccatt cagataacag actggcgaaa gaaagcggtg aacgggcacg
     3361 caatttattg cggggtcgtg agacgctggc agggtgtcgg ggcgcagcca tgacagttat
     3421 tttatccatc acacgcaaag tgggagatac aggcattgca tcgtgcaaac agaaaacggg
     3481 tataccagaa gcaatacctt atcaggaaag gcattgccgc catcataaag acctttcagg
     3541 tataccatgc aattcaccat ctggtatacc gccttcaggc ctcaccacga ctggctttga
     3601 cggcataaaa acactctctt gtataccatt tcatacatga gggtgtatac ccccgtaagc
     3661 cttgccagca aaggcttccg gcagagcagt gtatactgcg tggggtgtga cacgattttc
     3721 tggcctttct cagccataag aagtcaaaaa tgcaggaaaa tcagcaggac gaaagaatac
     3781 aaaaatccat atccggcaga aactgagtgg aaggccgaac gctatggccg gaatgcgtgg
     3841 taatgactca gcgtgatttc cagaactgcc accaggactt tgcagggaca tgctgcggat
     3901 cagcagtgcc ctgtttatgc tccagcagct gtatggcctg acgaagggag ttgatatgtt
     3961 catcccgggc attcactgca tctttcagcc cggcgttttc tgcctgcaaa agtgccacct
     4021 gatgctgtaa atcctgtaaa aaatcgctgt taacaccagt agaatggtcg tcaaatttta
     4081 caacggcatt gtcacgttca ctgtcaaaag caagagaacc aaaaacacga ataagttctg
     4141 tagtatcaat tactttgacg tttttaccat gctttacaac agaggtgtaa cttaactcac
     4201 cagatttgag taacttgtaa atagtcggac gactgacact ggcaaggcgt gccgcttcgc
     4261 taatagatac ccgagccatt ataaatcccc ctgatgacca tccagacgaa taatcagagt
     4321 gcgacagagt tgttccgca
//
