LOCUS       NZ_CP091656             2460 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KMi025 plasmid pKMi025_4, complete sequence.
ACCESSION   NZ_CP091656
VERSION     NZ_CP091656.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236410
            Assembly: GCF_022494605.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2460)
  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  JOURNAL   Unpublished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 2460)
  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_022494605.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:48:27
            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)                     :: 5,058
            CDSs (total)                      :: 4,937
            Genes (coding)                    :: 4,636
            CDSs (with protein)               :: 4,636
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 301
            CDSs (without protein)            :: 301
            Pseudo Genes (ambiguous residues) :: 0 of 301
            Pseudo Genes (frameshifted)       :: 98 of 301
            Pseudo Genes (incomplete)         :: 221 of 301
            Pseudo Genes (internal stop)      :: 49 of 301
            Pseudo Genes (multiple problems)  :: 58 of 301
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091656.1.
            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..2460
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi025"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi025_4"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2013"
                     /collected_by="Kyoto University"
     gene            complement(join(2383..2460,1..153))
                     /locus_tag="L6L63_RS25130"
                     /old_locus_tag="L6L63_25135"
     CDS             complement(join(2383..2460,1..153))
                     /locus_tag="L6L63_RS25130"
                     /old_locus_tag="L6L63_25135"
                     /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_140430389.1"
                     /translation="MMNAEDKLFKNVDRLMLHDSLKKNEVLTVWERTFLSSVYSIYRRT
                     SGNKYSTKGLSPKQKNAAFSILKKYNYHLMD"
                     /name="hypothetical protein"
     gene            complement(140..580)
                     /locus_tag="L6L63_RS25135"
                     /old_locus_tag="L6L63_25140"
     CDS             complement(140..580)
                     /locus_tag="L6L63_RS25135"
                     /old_locus_tag="L6L63_25140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001565850.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000344119.1"
                     /translation="MDENGEVKQDSKIETFSIPAEPPYVKLYIADIAMIHGLSKSQNDV
                     LLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKNIIAALVDKQIFFRAGRGELEA
                     NPFLFARGDWPSIYERRKKIELKISYDTNGRTVQTKVMDDEC"
                     /name="hypothetical protein"
     gene            1268..2284
                     /gene="mobV"
                     /locus_tag="L6L63_RS25140"
                     /old_locus_tag="L6L63_25145"
     CDS             1268..2284
                     /gene="mobV"
                     /locus_tag="L6L63_RS25140"
                     /old_locus_tag="L6L63_25145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_109879960.1"
                     /translation="MRSPDWLDVRQNEGVSMANYAIMRCKKLTGMGSVASALQHCYRER
                     ETPNADAERTPENYCSVSQSADEAMGKLRELLPEKRRKDAVLAVEYVMTASPEWWNEAT
                     PRQQAEFFARSEQWLEKKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGG
                     RSKMREDQSTYAESVKKLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPR
                     VLRKGIFTKDVEDQAAIAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKR
                     LQSVTEPFKGLSREQMTEILMMAQRFKQQNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="mobV"
     Typing          1269..2281
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.337"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgagtattta ttaccgctag ttctacgata tatgctgtaa acactgctta aaaaagtacg
       61 ctcccaaaca gtcagaacct cattcttttt tagtgaatca tgcagcatta gcctgtctac
      121 atttttaaaa agtttatctt cagcattcat catccattac cttcgtctgc accgttcttc
      181 cattggtgtc ataactgatc tttaactcaa ttttctttct tctttcgtaa attgatggcc
      241 agtctccccg tgcaaaaaga aaggggttag cttcaagttc cccacgccct gcccggaaga
      301 atatttgttt atctacaaga gccgcaatta tgtttttaaa ggtctgatat tcaatatgaa
      361 ccctgggctg tatggttttt tcaaatctag tttttgatac agacacaaac ccatcccatc
      421 caatcagcat tgccaattgt aaaagcacat cattttgaga ttttgataaa ccatgaatca
      481 tcgcaatgtc tgcaatgtat agcttgacgt agggaggttc ggctgggatg gaaaaggtct
      541 cgatcttaga gtcttgtttt acctcaccgt tttcatccat gtatgtatgc cgttcaagcc
      601 tagaaatctt tttcgtattc actccagccc cacgtttcgc catgatttag tactcgcatt
      661 taagtactaa agagacatac agtcaagtcc tttgcatcaa gtacgattag tacttgaggt
      721 gagtacgatt agtccttgag gtgagtacga ttagtacttg aggtgagtac gattggtact
      781 tgaggtgagt acgattcttc gctctagccc ttggtacaag cgggttccca tatctatatc
      841 tatatattaa gagggaaaat aaaggctgaa aaacgccatt tttaaacatc gaaaaacgag
      901 cttttttgag tctggagcgt acggatttct atgtccgggg agtggaaatt ccgcttcctc
      961 gaacggacag actcgcggcg atgccgctcc ctaatccgtt cttgcggcga gcggttcctg
     1021 ctctttcaaa aacgatattc attgcctgat ttcgtcaggg gcgagcgaag cgagtgccat
     1081 ttacccttga cgactcaccg gataaaacag gcttggcagt ggtggggggt ggcgcggagc
     1141 gacgccttcc acctgccaga ctgccgttga ttttgacctt ctggcagctt gctgcccgaa
     1201 cgattttgcg tagcaaagtc tagtgagtac actatcatcc tgatagtggc ccgccggagg
     1261 catcgcaatg cgatcccccg actggctgga tgtacgccag aacgaggggg taagcatggc
     1321 gaattacgcg ataatgcgct gcaaaaagct gacgggaatg ggcagtgtgg ccagcgcttt
     1381 gcagcactgc tacagggagc gtgagacgcc gaatgctgac gctgaacgga caccagaaaa
     1441 ctactgctct gtgtctcagt cggcagatga ggcgatggga aagctgcggg agctgttgcc
     1501 ggaaaaacgc cgtaaagatg cggtactggc tgttgaatac gttatgacgg caagccctga
     1561 gtggtggaac gaggccacac cgcggcagca ggcggagttt ttcgcccgct ctgagcaatg
     1621 gctggagaag aaatacggga aggatcgtgt tgtggcggcg gtggttcacc gggacgaggc
     1681 caccccgcac ctgtctgcgt tcgtggtgcc attgacgcag gatggacggc tgtccgcgaa
     1741 agagtttatt ggcgggcggt caaagatgcg tgaagatcag agcacctacg ctgaatcagt
     1801 aaaaaaactg ggtcttgagc gcggcatcga gggaagccgc gccacgcatc agacagttca
     1861 gcactactac gaatcgataa accgtggcac ccgtagccag gtatcgatct cgccggaggc
     1921 gctggagccg cgtgtattgc ggaagggcat tttcaccaaa gacgtggaag atcaggcagc
     1981 catagccaaa cgtctaagcc acgcagtgaa cgatggcttt gcaggaacca tcgctatggc
     2041 ctctcagagc gcccagaacg caaaaagagc gcgtgagcta cagaagacta tggatgcgca
     2101 gcagaaacgc ctacagagcg ttacagagcc ttttaagggg ctttccagag agcagatgac
     2161 cgaaatcctg atgatggctc agcggtttaa gcagcaaaac caggaaaagg aaaaacagca
     2221 gcgtattgaa cgtgaaaaac agcgacagac gcgatcgcgt ggcatgggtg gtatggagcg
     2281 ttagttttga tgcgatgcag gatagggcta acgccgcaaa gtgacgtcat ttgcggcatt
     2341 ccagagatca ggttctgccg ccctgtataa cgctgaggcc agctaatcca tcagatggta
     2401 attgtatttt ttcaaaatag aaaaagctgc gtttttctgc tttggtgaca aacccttagt
//
