LOCUS       NZ_CP091657             1888 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KMi025 plasmid pKMi025_5, complete sequence.
ACCESSION   NZ_CP091657
VERSION     NZ_CP091657.1
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 1888)
  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  JOURNAL   Unpublished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 1888)
  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
            CP091657.1.
            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..1888
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi025"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi025_5"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2013"
                     /collected_by="Kyoto University"
     gene            1089..1229
                     /locus_tag="L6L63_RS25445"
     CDS             1089..1229
                     /locus_tag="L6L63_RS25445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240737.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042863642.1"
                     /translation="MDCKHEPPVQSDRCALPGNYRLESNPERHDKTPLAAAIGRGCTRD
                     Y"
                     /name="hypothetical protein"
     gene            1457..1885
                     /locus_tag="L6L63_RS25145"
                     /old_locus_tag="L6L63_25150"
     CDS             1457..1885
                     /locus_tag="L6L63_RS25145"
                     /old_locus_tag="L6L63_25150"
                     /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_162522475.1"
                     /translation="MSLNMTFSITEVREGRIGSLVITKELYDKLEKYSCSNGLITSTYN
                     HGHGVVRYYTVKYCLQMNYHGQNHPQKYLIKRGGRYPSKYAMVKKTVEELEYSTPTFDA
                     ICRNIAIKYPHMVKFANYISETPLKGFAATFNNSVGND"
                     /name="hypothetical protein"
     Typing          856..1206
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.591"
                     /coverage="81.0"
                     /evalue="2.93e-164"
ORIGIN
        1 ttatttacca taacatccct tgcccgcacc ccctgagagg ccctcagcgc gtttctgccg
       61 cgtcctctgc gtttccggca cctttccctg tccatatcgt gaaaaaacgc gcctgatgat
      121 ttctgcgcgc ctgcatggct atgcacagaa gtgaatggcg gccggtttcg gacgaatgct
      181 ggcactaaag gcgaattttg aacaaaaaaa acggacatcg agggtcagga tgtccgacaa
      241 aatttgcaca aacagtcagc cggtaccgat cagagagccg gcaaataagt atgacagtaa
      301 aaagtggtta tcaactgccc ccgcgctgct gattgcgcag ttttagggct ttggccagtg
      361 caggcaggcc cggccggaat caggggatct ggtaacggtg aacgggtgca cagttgactg
      421 tgcggccgtg aggcgttggc caagccgcca ggtgcggcag cttccggtgg gtacaaacgc
      481 cagcactttg cgaatcctgc cctagatctc aacagcagag aaatttcgta cgcacgaaac
      541 tcagcgtatc gggcggcgcc tgatgaaaca ttctggagtg tcggcggtac tccaaaaaca
      601 catcttgtcc cgctgatttt gtcactggcg caaagcggcg gtaatgacaa gacatttcct
      661 gtccgcatca atacgtgcag aaaacgtaag tggtgaaaga tgatagtacg gagcgacagg
      721 agcctaagca gccaccggag aaattacgct tcctcggtca ttcgctcact gcgttcggtc
      781 atgactctgc ggcgagcgtt acgggatcaa tcaaagggcg tggaggtatg aagtgtgaga
      841 agagacttaa gggctgccgg ttttccatag gctccgcccc cctgacaagc atcacgaaat
      901 ctgacgctca aatcagcggt ggcgaaaccc gacaggacta taaagatccc aggcgtttcc
      961 ccctggtagc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc
     1021 gctgttatgg ccgcgtttat ctcattccac gcctgacact cagttccggg taggcagttc
     1081 gctccaagct ggactgtaag cacgaacccc ccgttcagtc cgaccgctgc gccttacccg
     1141 gtaactatcg tcttgagtcc aacccggaaa gacacgacaa aacgccactg gcagcagcca
     1201 ttggtagagg gtgtacaaga gattactgat gcagagttct tgaagttaga gccaaactac
     1261 ggctaaactg gaaggacaaa tttggtggca gcggtcttgt acaccctgtt accacggttc
     1321 agaagttccc cagcttactg aaccttcgaa aaaccacctc cccaggtggt tttttcgttt
     1381 ctggataaga gactacgacg acagacggat gatctcaaga aaatcctctc taacaggtta
     1441 tattcagagt aaaaaagtga gcttaaatat gactttttca ataacagaag tgcgtgaggg
     1501 gcgtatcggt tctttagtta ttacaaaaga gctttacgat aaattagaaa aatactcttg
     1561 ctcaaatgga ttaataacat ccacatacaa ccatggtcat ggcgttgtta gatactacac
     1621 cgtgaaatat tgcctccaga tgaactatca cggacaaaat catcctcaaa aatatcttat
     1681 taaaagaggg gggagatatc ccagcaagta tgcaatggtc aaaaaaaccg ttgaagagtt
     1741 agagtattca acaccgacat ttgacgcaat atgtaggaac atagcaataa aatacccaca
     1801 catggtcaag tttgctaatt acatatcaga aaccccatta aaaggcttcg ccgcaacctt
     1861 taataactcc gttggtaatg attaagtg
//
