LOCUS       NZ_CP091696             3461 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KMi006 plasmid pKMi006_5, complete sequence.
ACCESSION   NZ_CP091696
VERSION     NZ_CP091696.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236407
            Assembly: GCF_022494765.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3461)
  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  JOURNAL   Unpublished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 3461)
  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_022494765.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:35:35
            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)                     :: 5,041
            CDSs (total)                      :: 4,921
            Genes (coding)                    :: 4,646
            CDSs (with protein)               :: 4,646
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 93 of 275
            Pseudo Genes (incomplete)         :: 191 of 275
            Pseudo Genes (internal stop)      :: 52 of 275
            Pseudo Genes (multiple problems)  :: 55 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091696.1.
            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..3461
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi006"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi006_5"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            256..861
                     /locus_tag="L6L65_RS25010"
                     /old_locus_tag="L6L65_25015"
     CDS             256..861
                     /locus_tag="L6L65_RS25010"
                     /old_locus_tag="L6L65_25015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012537770.1"
                     /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_224706372.1"
                     /translation="MSGRRFGRLPNWWSRSANGDDFLLMSLKSNDTGTGIAAMKCLLAL
                     SVLIDFHSRIAEVSLSGMEELTGLSRPMVIRGLARLEELGVVVSDKDYRTNRYELTIKS
                     NDSYWAKVPVDTVRKRLKTISNRGIAPFTALKLYITILNLRYKDKTTVQVMHDTLRNYT
                     GIQTNQVRHGLDVLYSSALLHLMPREDRATNEYQILGL"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1295..1495)
                     /locus_tag="L6L65_RS25015"
                     /old_locus_tag="L6L65_25020"
     CDS             complement(1295..1495)
                     /locus_tag="L6L65_RS25015"
                     /old_locus_tag="L6L65_25020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_113418166.1"
                     /translation="MIDDRTRQLRVDGFRKAEASLRLEGMGPSGTPLYESVKARILSGE
                     ITYGEGRDEILAHYQKRGDRN"
                     /name="antitoxin VbhA family protein"
     gene            complement(2395..3048)
                     /locus_tag="L6L65_RS25020"
                     /old_locus_tag="L6L65_25025"
     CDS             complement(2395..3048)
                     /locus_tag="L6L65_RS25020"
                     /old_locus_tag="L6L65_25025"
                     /inference="COORDINATES: protein motif:HMM:NF014045.4"
                     /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_074581898.1"
                     /translation="MKKQRTIVYVDGFNLYYGALKDKAGCRWLNIEEMVKSILPSKPTP
                     INDIVAVKYFTAKISSRANHPNQVNHQNIYLKALKTIPNLEVVLGRYDTHIVRSKLAAP
                     IVGVGSYVDVYKTEEKGSDVNLATHLLHDAHTSAFDVAIVITNDSDLALPIEFVVSKLN
                     KKVGVISPYPKASMHLCKVSSFTRVIRRSNITSSQFADQITDSDGTVLVKPTGW"
                     /name="NYN domain-containing protein"
     Typing          1539..2205
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.76"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaattttatg aaaaatttca caaaaataaa atatcgctta atctagatta gtattgtagt
       61 gtggtgttaa aactttcagt ctcgacgatc accttaggag gctgaggttt atggaaactc
      121 taaacaacat aatttctact ttagcttcgg catcacctga agctttggtt gcaatagtat
      181 cgctaggtgc catgtttttt atattcatga taataaaggt atttttctcg tttttagaaa
      241 agaaatggaa ttaaaatgag tggcagacgt tttggcaggc ttccaaattg gtggtcgcgc
      301 tccgcgaatg gagatgattt tctattaatg agcctaaaat ctaatgacac aggaacagga
      361 attgcggcaa tgaagtgtct gctagccttg tctgtgctca ttgattttca ttctcgaata
      421 gcagaagtct ctttaagcgg tatggaagag ctaaccgggc ttagtagacc aatggttatc
      481 cgcgggttag ctaggcttga agaactagga gttgttgtct ctgacaagga ttacagaaca
      541 aaccggtatg aacttacgat aaaaagtaat gacagttact gggcaaaagt tcctgtcgat
      601 acagtccgaa aaagacttaa aaccatatcc aatagaggga ttgcaccatt cactgcttta
      661 aaattgtaca taacaatatt gaatctaagg tacaaagata aaacaactgt tcaagtcatg
      721 cacgatacac tcagaaacta caccggaatt cagacaaacc aggtaagaca tggtcttgat
      781 gtgctataca gcagtgctct gcttcacctc atgccgcgtg aagaccgtgc gacaaatgag
      841 tatcaaatat taggcctata gcatccatat ttaccataac atcccttgcc cgcaccccct
      901 gagaggccct cagcgcgatc ctgacgcgtc cgggccgttt ccggcatctt tccctctcca
      961 gatccctaaa aagtgcccct gatgatttct gcgcgcctgc atggctatgc atacgagtga
     1021 atagcagccg atttcgggcg gatgctggca ctaaaggcgg attttcggtg attaacttcc
     1081 ccgataacgg tgaacgggtg cgcagtttac tgtgcgaccg tgaggcgttg gccaggccgt
     1141 caggcatggc tgagcaacat gaggagagca gatttaacgt gggtgatcag cacgcagaaa
     1201 tttcgacgcg tcgaaatttt tcagggtgtc gggcggagcc tgaccaagag gctttggcgt
     1261 gccggcggta ctccaaagac acatcttgtc cgcgtcagtt gcggtcaccg cgcttctggt
     1321 aatgagccag tatttcatca cggccttctc cataggtgat ctcaccggaa agaatacgcg
     1381 ccttaaccga ttcatagagc ggagttccgg aggggcccat gccttcaagc cggagagaag
     1441 cctcggcctt acggaatccg tctacacgaa gttgtcgtgt acgatcatca atcatgggtt
     1501 ttccgttgag cagtcatgcg aataaggcag gcgtaaagtg ggcccacttt acatatcctg
     1561 cccgaatctt gccgttgtat agctgtgcag acaaaagtgg aaaacgacag gaaaccgttg
     1621 caaccggata tgtaattgga gaggaaacag gagtaccgag cgatacgagc cctgttcagc
     1681 attacagaca ttacgcttcc tcggtcattc gctcacttcg ttcggtcatg acgctgcggc
     1741 gagcgttact tgtacttgct caggcagaag gccatggcgg agagtaaaag agaactggga
     1801 cgttgccggt tttccatagg cttcgccctc ctgacgagac tcacagaaat caggcaattt
     1861 ccggagctca aatcagaagt ggcgaaaccc gacaggactt aaagatcccc accgtttccg
     1921 atgggtcgct ccctcgtgcg ctctcctgtt cccaccctga ggtttacccg ttgcagaccg
     1981 ccgtaaggtg gcgttttctc attcctaccc gtgcaactga gttccttgta ggtggttcgc
     2041 tccaagctgg gctgtatgca cgaactcccc gttcaacccg actaccgcgc ctattcaggt
     2101 aactgtactc ttgaatccaa ccctgaaaga cacgacaaag cgccactggc ggtagccatt
     2161 ggtagctggt tcacggagcg ggaaagtaca tgcaagtaca catagagttc ttgaagtgtc
     2221 agcctaacta cagctacact gaaaggacag ttttggtgac tgcgctccgt taaagccagt
     2281 taccttggtt aagaatctgc caggattttt aaccttcgaa aaaaccacct gccagggtgg
     2341 ttttttcgtt tccatagaaa gatacgcgtt tcatcctcta aacgtcaagc gacgtcacca
     2401 tccagtaggt ttcactaaaa cggtaccatc actatccgta atttgatcag caaactgcga
     2461 gctagttata ttcgaacgtc ttataaccct agtaaaagaa gatactttgc ataaatgcat
     2521 gctagctttc gggtatgggg aaatcacccc aaccttcttg tttaatttgc taacaacaaa
     2581 ttcaataggc aatgctaaat cagagtcgtt ggtaataact atggcgacat caaaagcaga
     2641 agtatgagca tcatgtaata aatgcgttgc aaggtttaca tctgaacctt tttcttctgt
     2701 tttataaaca tcaacatatg accctacgcc tactatcggc gcagcaagct tagaacgcac
     2761 tatgtgggtg tcatagcggc ccaatacgac ttcaagatta ggaattgttt ttaaagcttt
     2821 aaggtatata ttttgatgat taacctgatt aggatggttt gctcttgatg atattttcgc
     2881 agtgaagtat ttaactgcaa ctatatcatt aataggtgta ggctttgatg gaagtattga
     2941 tttaaccatc tcttcgatat tcaaccagcg gcacccagct ttatctttta gagcaccata
     3001 atataagttg aatccgtcga cataaacaat cgttctttgt tttttcattt ttgttatgtc
     3061 catatatgct gaaacctcca ctagggaggt ttcgcggtcg caccgtagtg cgaggttgta
     3121 tattttttgc tgaggttgcc ctcgcgccag cgcagaacgc tgggtagtga tgcaaattct
     3181 atacggaagt ataaaacttg caaccaaaaa aattcaccat gctacaatta gacttggcga
     3241 gcttacttta gtaagctcgc caagtctaat tgtagcatgg tgatagaaaa aatcaacaac
     3301 ttacttgtag ccatgggatc taggacctct atcggccttg cttgtcattt accatgtgat
     3361 taattattaa gctaaaaaac accatctcaa cccgcattat ttggcattta tagctctccc
     3421 atttactagt aaaaaacatg gaaaacaatg attaagtatt t
//
