LOCUS       NZ_CP091694             6222 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KMi006 plasmid pKMi006_3, complete sequence.
ACCESSION   NZ_CP091694
VERSION     NZ_CP091694.1
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 6222)
  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  JOURNAL   Unpublished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 6222)
  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
            CP091694.1.
            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..6222
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi006"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi006_3"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            265..423
                     /locus_tag="L6L65_RS25280"
     CDS             265..423
                     /locus_tag="L6L65_RS25280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            883..1698
                     /gene="sul2"
                     /locus_tag="L6L65_RS24950"
                     /old_locus_tag="L6L65_24955"
     ARG             884..1695
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1759..2562
                     /gene="aph(3'')-Ib"
                     /locus_tag="L6L65_RS24955"
                     /old_locus_tag="L6L65_24960"
     ARG             1760..2559
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2562..3398
                     /locus_tag="L6L65_RS24960"
                     /old_locus_tag="L6L65_24965"
     CDS             2562..3398
                     /locus_tag="L6L65_RS24960"
                     /old_locus_tag="L6L65_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(<3505..3909)
                     /locus_tag="L6L65_RS24965"
                     /old_locus_tag="L6L65_24970"
                     /pseudo=""
     CDS             complement(<3505..3909)
                     /locus_tag="L6L65_RS24965"
                     /old_locus_tag="L6L65_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3953..4342)
                     /locus_tag="L6L65_RS24970"
                     /old_locus_tag="L6L65_24975"
     CDS             complement(3953..4342)
                     /locus_tag="L6L65_RS24970"
                     /old_locus_tag="L6L65_24975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4560..5000
                     /locus_tag="L6L65_RS24975"
                     /old_locus_tag="L6L65_24980"
     CDS             4560..5000
                     /locus_tag="L6L65_RS24975"
                     /old_locus_tag="L6L65_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(5767..5916)
                     /locus_tag="L6L65_RS24980"
                     /old_locus_tag="L6L65_24985"
     CDS             complement(5767..5916)
                     /locus_tag="L6L65_RS24980"
                     /old_locus_tag="L6L65_24985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             2563..3395
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(5952..6125)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          4..432
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.743"
                     /coverage="99.0"
                     /evalue="1.93e-167"
ORIGIN
        1 agaagagata aggccacggc gaagccgttt ttccataggc tccgcccccc tgacaagcat
       61 cgcaaaatct gacgctcaaa tcagtggtgg cgaaacccga caggactata aagatcccag
      121 gcgtttcccc ctggtagctc cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt
      181 gtcattccgc tgttatggcc gcggtttctc attccacgcc tgacactcag ttccgtgaag
      241 gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccgctgcgcc
      301 ttgtccggta actatcaact tgagtccaac ccggaaagac acgacaaaac gccactggca
      361 gcagccatta gtaacaggag tgcacgagaa gatagattaa gaggtcttga agtagaggcc
      421 tgactgcggc tacactgaaa gaacagtttt ggtaatggcg gtctcgtgaa ccctgttacc
      481 gggttaagca gttccccaac tgacttaacc ttcgaacaaa ccgcctcccc aggcggtttt
      541 ttcgtttaca gagcaagaga ttacgattca ttgaaaagga tctcaagaag atcctttgta
      601 gattactatc aattaatctt ccgaacatga caccagtcac tgttgattac ggttaaaccg
      661 ctccgtaaca ggtttccctc gtattggtga cttgcagcac caaagaagca aaaaagataa
      721 atatatctac ttattgagag atgatatatt tatttccaaa atgctacaga tacatcatca
      781 tgaaacggat caccgcaaac aggttactcg cctggggatt ccctttcgac ccgagcatcc
      841 gtatgagact catgctcgat tattattatt atagaagccc ccatgaataa atcgctcatc
      901 attttcggca tcgtcaacat aacctcggac agtttctccg atggaggccg gtatctggcg
      961 ccagacgcag ccattgcgca ggcgcgtaag ctgatggccg agggggcaga tgtgatcgac
     1021 ctcggtccgg catccagcaa tcccgacgcc gcgcctgttt cgtccgacac agaaatcgcg
     1081 cgtatcgcgc cggtgctgga cgcgctcaag gcagatggca ttcccgtctc gctcgacagt
     1141 tatcaacccg cgacgcaagc ctatgccttg tcgcgtggtg tggcctatct caatgatatt
     1201 cgcggttttc cagacgctgc gttctatccg caattggcga aatcatctgc caaactcgtc
     1261 gttatgcatt cggtgcaaga cgggcaggca gatcggcgcg aggcacccgc tggcgacatc
     1321 atggatcaca ttgcggcgtt ctttgacgcg cgcatcgcgg cgctgacggg tgccggtatc
     1381 aaacgcaacc gccttgtcct tgatcccggc atggggtttt ttctgggggc tgctcccgaa
     1441 acctcgctct cggtgctggc gcggttcgat gaattgcggc tgcgcttcga tttgccggtg
     1501 cttctgtctg tttcgcgcaa atcctttctg cgcgcgctca caggccgtgg tccgggggat
     1561 gtcggggccg cgacactcgc tgcagagctt gccgccgccg caggtggagc tgacttcatc
     1621 cgcacacacg agccgcgccc cttgcgcgac gggctggcgg tattggcggc gctgaaagaa
     1681 accgcaagaa ttcgttaact gcacattcgg gatatttctc tatattcgcg cttcatcaga
     1741 aaactgaagg aacctccatt gaatcgaact aatatttttt ttggtgaatc gcattctgac
     1801 tggttgcctg tcagaggcgg agaatctggt gattttgttt ttcgacgtgg tgacgggcat
     1861 gccttcgcga aaatcgcacc tgcttcccgc cgcggtgagc tcgctggaga gcgtgaccgc
     1921 ctcatttggc tcaaaggtcg aggtgtggct tgccccgagg tcatcaactg gcaggaggaa
     1981 caggagggtg catgcttggt gataacggca attccgggag taccggcggc tgatctgtct
     2041 ggagcggatt tgctcaaagc gtggccgtca atggggcagc aacttggcgc tgttcacagc
     2101 ctatcggttg atcaatgtcc gtttgagcgc aggctgtcgc gaatgttcgg acgcgccgtt
     2161 gatgtggtgt cccgcaatgc cgtcaatccc gacttcttac cggacgagga caagagtacg
     2221 ccgcagctcg atcttttggc tcgtgtcgaa cgagagctac cggtgcggct cgaccaagag
     2281 cgcaccgata tggttgtttg ccatggtgat ccctgcatgc cgaacttcat ggtggaccct
     2341 aaaactcttc aatgcacggg tctgatcgac cttgggcggc tcggaacagc agatcgctat
     2401 gccgatttgg cactcatgat tgctaacgcc gaagagaact gggcagcgcc agatgaagca
     2461 gagcgcgcct tcgctgtcct attcaatgta ttggggatcg aagcccccga ccgcgaacgc
     2521 cttgccttct atctgcgatt ggaccctctg acttggggtt gatgttcatg ccgcctgttt
     2581 ttcctgctca ttggcacgtt tcgcaacctg ttctcattgc ggacaccttt tccagcctcg
     2641 tttggaaagt ttcattgcca gacgggactc ctgcaatcgt caagggattg aaacctatag
     2701 aagacattgc tgatgaactg cgcggggccg actatctggt atggcgcaat gggaggggag
     2761 cagtccggtt gctcggtcgt gagaacaatc tgatgttgct cgaatatgcc ggggagcgaa
     2821 tgctctctca catcgttgcc gagcacggcg actaccaggc gaccgaaatt gcagcggaac
     2881 taatggcgaa gctgtatgcc gcatctgagg aacccctgcc ttctgccctt ctcccgatcc
     2941 gggatcgctt tgcagctttg tttcagcggg cgcgcgatga tcaaaacgca ggttgtcaaa
     3001 ctgactacgt ccacgcggcg attatagccg atcaaatgat gagcaatgcc tcggaactgc
     3061 gtgggctaca tggcgatctg catcatgaaa acatcatgtt ctccagtcgc ggctggctgg
     3121 tgatagatcc cgtcggtctg gtcggtgaag tgggctttgg cgccgccaat atgttctacg
     3181 atccggctga cagagacgac ctttgtctcg atcctagacg cattgcacag atggcggacg
     3241 cattctctcg tgcgctggac gtcgatccgc gtcgcctgct cgaccaggcg tacgcttatg
     3301 ggtgcctttc cgcagcttgg aacgcggatg gagaagagga gcaacgcgat ctagctatcg
     3361 cggccgcgat caagcaggtg cgacagacgt catactagat atcaagcgac ttctcctatc
     3421 ccctgggaac acatcaatct caccggagaa tatcgctggc caaagcctta gcgtaggatt
     3481 ccgccccttc ccgcaaacga ccccaaacag gaaacgcagc tgaaacggga agctcaacac
     3541 ccactgacgc atgggttgtt caggcagtac ttcatcaacc agcaaggcgg cactttcggc
     3601 catccgccgc gccccacagc tcgggcagaa accgcgacgc ttacagctga aagcgaccag
     3661 gtgctcggcg tggcaagact cgcagcgaac ccgtagaaag ccatgctcca gccgcccgca
     3721 ttggagaaat tcttcaaatt cccgttgcac atagcccggc aattcctttc cctgctctgc
     3781 cataagcgca gcgaatgccg ggtaatactc gtcaacgatc tgatagagaa gggtttgctc
     3841 gggtcggtgg ctctggtaac gaccagtatc ccgatcccgg ctggccgtcc tggccgccac
     3901 atgaggcatg ttccgcgtcc ttgcaatact gtgtttacat acagtctatc gcttagcgga
     3961 aagttctttt accctcagcc gaaatgcctg ccgttgctag acattgccag ccagtgcccg
     4021 tcactcccac tcttacattg ttcgcagtat ctaggtacat gttattgcgt gcaccttcat
     4081 gatgtataat gttattaatg acagcagaaa gatcgacaga attaatattc ttcgtacctg
     4141 ggacagttat cgggtgtcgg ccagtgatga gaccaaagga tgcagtataa gatgaaccac
     4201 tactattatc atggccacca ttaccaccac cgttaaaact acctcccgaa cttccagagc
     4261 cgctatgacc atcattgtag gggtcatttg gtcccatgtg accaaaacca ccgacagtac
     4321 cgctatttaa ctctgtactc ataaaattat cctctttgac ttttaaaaac agcaaaaact
     4381 gtatttataa caatgtgttt atatacagta ttcgaaatac tacgcccgtc aaaaccacac
     4441 cgtcaacagg ttttttgtgt atttttcacg cctcacgggc agcctcagac cttttgtgtt
     4501 aaaacagtaa tatgttctgc tgttacaata cggtacacac aggagacact gtcactttta
     4561 tggcatggca cacagttcaa gagacactga aattaacagg aaagtcgcgc tcgcaattat
     4621 atcgtgacat ggctaaaggc cttgtcagct atcgcacagg aaaaaatgat cgccgggagt
     4681 tcgagaccag tgaactgatt cgggcctatg gcgagctgcg cacttctgag acaccaaaaa
     4741 ggcacaagga gggacactcc aaatctgtcg ttagccaggc ggaaaatgct cagctagacg
     4801 tcattcagca gaaactggac gctctgcagc agactgttac cctaatgctt gaagacaaga
     4861 tggcgcggga agcagaaaac cgcctgcgaa atgaggagag ggaacaacta caggccgaaa
     4921 ttagccgtct ggctgacgcg ctggcacagg aaaaaaagcg gggattctgg tcgcggctgt
     4981 ttcgctccgg ttcagagtaa cagtgcaggt gactctgatt taccataaca tctgttatca
     5041 gcaccgcctg agaggccctc agggcgtttc tgacgggaaa ccggtaaaac aggcaacaaa
     5101 ccacccgaaa acccgccaga aacgcgcagg ctctgttttt acggcatgca tgagtatgcg
     5161 cacaagtgca tagcgcggaa attcacacca ttcagccggg gtaagtcctg tttccggcgt
     5221 tcttcccatc cgaaaacggt gaacggggac gcaatttatt gcgtggccgt gaagcgttgc
     5281 cggcgcagcc ggaaaacccg ctgtcagcac gttcaggaag ggggtgatgt acaaatggca
     5341 cagaggatga aagtgacgta tgagctgaag gaatgatgta aaagtgatgt ataagtgatg
     5401 taaaagtgat gtataagtga tgtaaaagtg atgtatgaac tgaaggagcg atgtaattct
     5461 gtagtcagga agaataaccc gttcatgcag gcatgaacga tacagtgagg aacgcttttt
     5521 ttgtcacgat ctccccttaa cctgcgtaaa tcacccgcca tggttgatta tttttcaacc
     5581 tcaaaatggt catacaccta acgcagccgc gattttcatc gcaactgcat gaattaaaag
     5641 aaaaaaaagg aatatttcgt tttcacgagt aatacccggg tattaaaaat ccactgtaat
     5701 tacatgaaaa taaagaaata aaaggtaata ccggagtatt accacgtacg cgggcaagcg
     5761 aaaaagctat aacgcttccc ggccgacagg cgacccaaaa tccacagggg catgcaggtt
     5821 ctcttcagta acctgcgcca ttaaatcaaa aaggtcatat tcgccgggaa gctgcgtatc
     5881 agtcgaatcc agttgttcat catattcaga tggcatgggg tgatatccag tagctgagag
     5941 gttgttagcg ggtttcgggg cgcagccctg aaccagtcat gtagcgctag cggagtgtat
     6001 actggcttac tatgttgcca cgattgcgaa aatcagtgaa gtgcttcatg tggcaggaga
     6061 aaaaaggcag caccggcgcg tcagcagaat atgcgataca ggagatattc cgcttcctcg
     6121 ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag cggtaccggc ttacggacgg
     6181 ggacggaaat ttcctggaag ataccaggaa gacacttagc aa
//
