LOCUS       NZ_CP091676             3372 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KKo009 plasmid pKKo009_4, complete sequence.
ACCESSION   NZ_CP091676
VERSION     NZ_CP091676.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236406
            Assembly: GCF_022494705.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3372)
  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  JOURNAL   Unpublished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 3372)
  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_022494705.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:58:57
            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)                     :: 5,067
            CDSs (total)                      :: 4,947
            Genes (coding)                    :: 4,740
            CDSs (with protein)               :: 4,740
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 92 of 207
            Pseudo Genes (incomplete)         :: 133 of 207
            Pseudo Genes (internal stop)      :: 42 of 207
            Pseudo Genes (multiple problems)  :: 52 of 207
            Pseudo Genes (short protein)      :: 1 of 207
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091676.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KKo009"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKKo009_4"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2012"
                     /collected_by="Kyoto University"
     gene            complement(1077..1310)
                     /locus_tag="L6L68_RS25180"
                     /old_locus_tag="L6L68_25175"
     CDS             complement(1077..1310)
                     /locus_tag="L6L68_RS25180"
                     /old_locus_tag="L6L68_25175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_074149632.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMYEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1317..1877)
                     /locus_tag="L6L68_RS25185"
                     /old_locus_tag="L6L68_25180"
     CDS             complement(1317..1877)
                     /locus_tag="L6L68_RS25185"
                     /old_locus_tag="L6L68_25180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1909..2565)
                     /locus_tag="L6L68_RS25190"
                     /old_locus_tag="L6L68_25185"
                     /pseudo=""
     CDS             complement(<1909..2565)
                     /locus_tag="L6L68_RS25190"
                     /old_locus_tag="L6L68_25185"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2555..2878)
                     /locus_tag="L6L68_RS25195"
                     /old_locus_tag="L6L68_25190"
     CDS             complement(2555..2878)
                     /locus_tag="L6L68_RS25195"
                     /old_locus_tag="L6L68_25190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2942..3133
                     /locus_tag="L6L68_RS25200"
                     /old_locus_tag="L6L68_25195"
     CDS             2942..3133
                     /locus_tag="L6L68_RS25200"
                     /old_locus_tag="L6L68_25195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3215..3295)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.585"
                     /coverage="93.0"
                     /evalue="4.04e-16"
     Typing          complement(995..2565)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acacacgcgg acactggcac aggcgcgtaa gtgcacaatg cttgcctctg tgactcttcc
       61 gcttcctcgc ccactcgctc actacgttcg gtcgctgggg ctgcggcgag cggtgggatc
      121 actctcgttg tgatgcagat ccgttttttt tttgcactgg agttatcagg agtagcggtg
      181 cacatgggat cgtgcgatat gctggatggt ggaaggtcgg agggaacggc aacaactcac
      241 ccctcccagt gaagggacgg gtagtttgcc gctctcgata tgccggacgg agccaaggcc
      301 atcgatcacg gggcgcgtca gtggaagaac ccgcgcctgc gtgacgtatg cgtcttcgcc
      361 gcaccatctc acccgtcacg ccaccacata ccgggaactg ccgccaaggt ctaactcaac
      421 caatctagcc gcgctacata cggtttttgt ggcaactcat caggtgtccg ctgtcgatga
      481 aactctctgc gccggtagcg gaactctcac gcgtgcggtc gccgtcgtca cagctccccc
      541 aaccgcaaac gattctcgca aatacgcaag tatctgcaaa aacaggtttt tttcggggtt
      601 cctgggagac tgtgctgttg aaaaactctt gaagaataca gaaggctcat gcaaactgaa
      661 tgaactggtt tctgttgtgg atctcaacag tttccacagg aacattgagg aggtcagaga
      721 cctcaatgaa cccgaaacag ctcgccttcc tggcgagctg ttttcgttct acgcccaccg
      781 acgaaagatc gcaagtgcaa taacgagatt tttcacgtct ttacgctcaa aaagtaaaaa
      841 aaccatgttt tcccctggct gaatccccaa aaacgcgtga aatgcgtttt caggatgttg
      901 catagctatg cacaaatacg gcacacgatt tgtttcgctc gccccagccg tcgaacgggt
      961 caaaatggca agatttcgtc acttctccgg tcacatctcc attgatggcc cactccgaac
     1021 ccgtgccgcg cgttcctgta cctcatgtct gtaccgggca cgctcctgtt catcccttag
     1081 ctgttgttcg cgataaataa ccgactcaag cgatccactt gcccggctaa tctctgcacc
     1141 tgctgactca atatcacgac gcgctcgttc agtatcgcgt tgttccgttg cgtaacctcg
     1201 tacatcttct gcaattccgc gaaggcgctc tcccactcgt tcagccgccg catatagtcc
     1261 tgttgcaaat gctctaaggc gttcagcaaa tgcccttcca gttccgtcat actcgtttac
     1321 tccctgacca gcctcacggc gttcttgtcg cccaccgtcc aggtgttttc ccctttcacc
     1381 ccgtccggca acaccagaaa tttcccgttc tcgccattga cgaacgtcac cccccaggtt
     1441 tttgcctcga gtttcgccag cgtgttttcc tgctctctga tagtcaggat atttttcgca
     1501 atcttgcttt cctgccactc catcagcccc cagcacccca ggaaaatccc gcccgtgacg
     1561 ctgagcgcgg tcagcgccgg aaacagtatc cgccctttga tcacccgcca gagcagtttt
     1621 ttctgctgcc gggacagttc ggcctctgtg gtgctgaact gcatgctcac ggtggtgctc
     1681 agcgtatcca gttgcttttt cacggatgtt gtatgttcgc tgatagcgtc tctgattttc
     1741 tgcctgttta agctcaatgc cttgtctaca gactcttcga gcttcctgaa ctcgctgttc
     1801 agcatgttct cggtagaagc ggctcgctct ttcagtttct tctcgaagtc tgttcccatt
     1861 tgtaaaagat tgctcataca gcgccccctt tagcctgaga ttccgccccc cctccgggtc
     1921 ggcaatactg atgctgcttt tggttgtcct caccacctca aaacctgccg ctgtaagcgc
     1981 ctctgtgaca tcctgacgcg tttttattgc tccggcatgg taaagagcct caagaccccg
     2041 tgtaatcgct tctgcggcct cctgtttcgc ttttggcaga ttatttggcg tgacaagcgt
     2101 ccgtctgttc tccggtgcgt tcgggtcacg cagcccgtaa tgatgattaa ccagcgtctg
     2161 ccaggcattt atcctcggcc tgtccgcacg gtcgtagtac ggctggaggc gcttaccgct
     2221 ctgtagctcc atgttcggga tgacaaaatt cagttcgagc cgccccttat cctggtgttc
     2281 cacccagaga atgctgtact ggtctttttc gagaccgggc ataagaacac gctcaaagct
     2341 cgtcatcact ctttcgcgtt cacccggtgg tagctccttc tccgcgaacg acagaacgcc
     2401 tgacgtgtat ttcttcgaaa atggcgtgga atcaatgagt tcccgcactt cttccgggtt
     2461 accccggagc accgttgcgc cttcgcggtt acgctcccgc cccagcaggt aatcgaccgg
     2521 gccacttcca ccgcctttcc ccctggcatg aaatttaact atcatcccgt accccctgtt
     2581 ccctgacagc ctgccgcaac tggcgcaatt caccctcgat ggccatcagt gcggccacca
     2641 catgaacccg gtcaatcgaa gaccactggc cgctgttcac cttccgggct gtctggttca
     2701 ggttgttccc gatggcagcc agatgccgca gcaatggcgg tgccagtgtc ggcagttttc
     2761 ctgtgcgtgc aaccggctcc cccagacaga cccgccgcat ccattccgcc agtcgtttac
     2821 cctcgcagcg ttccagtaac cgggcgtgct cctcatcggt aacccgtatc gtgagcatct
     2881 tctcgcgttt catcggtatc attcccccta acaaatcccc catacaagga gccttaagac
     2941 catgaccaaa caggaaaaaa cagcccttaa catggctcgc tttatcagaa accagacgct
     3001 aaccctgctg gaaaaactca acgatctgga cgcggacgaa caggcagaca tctgcgaatc
     3061 acttcacgac cacgccgacg aactctaccg cagttgcctc gcacgcttcg gcgatgacgg
     3121 tgaaagcaac tgaaacatgc agctcccgga gacgttcaca gcttgcctgt gagcggatgc
     3181 cgggagcaga caagcccgcc agggcgcgtc agtgcgggtg tcggggcgca gccctgaccc
     3241 agttcacaga gcgatagcga tgtgtatact ggctttcctc attttgcatc ggtgcagagt
     3301 ggatgggaag tgcaccatgt caggagtaaa aagccgcaca gatgcgtaaa aacagcgcgc
     3361 ccgataaaca ac
//
