LOCUS       NZ_CP091688             3172 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KKo003 plasmid pKKo003_7, complete sequence.
ACCESSION   NZ_CP091688
VERSION     NZ_CP091688.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236405
            Assembly: GCF_022494745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3172)
  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  JOURNAL   Unpublished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 3172)
  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                   :: Unicycler v. 0.4.8
            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_022494745.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:45:38
            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)                     :: 5,102
            CDSs (total)                      :: 4,983
            Genes (coding)                    :: 4,757
            CDSs (with protein)               :: 4,757
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 226
            CDSs (without protein)            :: 226
            Pseudo Genes (ambiguous residues) :: 0 of 226
            Pseudo Genes (frameshifted)       :: 84 of 226
            Pseudo Genes (incomplete)         :: 158 of 226
            Pseudo Genes (internal stop)      :: 38 of 226
            Pseudo Genes (multiple problems)  :: 48 of 226
            Pseudo Genes (short protein)      :: 1 of 226
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091688.1.
            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..3172
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KKo003"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKKo003_7"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            complement(340..534)
                     /locus_tag="L6L54_RS25325"
                     /old_locus_tag="L6L54_25325"
     CDS             complement(340..534)
                     /locus_tag="L6L54_RS25325"
                     /old_locus_tag="L6L54_25325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041622.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            818..1141
                     /gene="mobA"
                     /locus_tag="L6L54_RS25330"
                     /old_locus_tag="L6L54_25330"
     CDS             818..1141
                     /gene="mobA"
                     /locus_tag="L6L54_RS25330"
                     /old_locus_tag="L6L54_25330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1530..1958)
                     /locus_tag="L6L54_RS25335"
                     /old_locus_tag="L6L54_25335"
     CDS             complement(1530..1958)
                     /locus_tag="L6L54_RS25335"
                     /old_locus_tag="L6L54_25335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_138581343.1"
                     /translation="MTYSIKNKWKAGGLSLGWTAVPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWSLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDRRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKKPVYTVRKTTA"
                     /name="helix-turn-helix domain-containing protein"
     gene            2116..2286
                     /locus_tag="L6L54_RS25340"
                     /old_locus_tag="L6L54_25340"
     CDS             2116..2286
                     /locus_tag="L6L54_RS25340"
                     /old_locus_tag="L6L54_25340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001531327.1"
                     /translation="MKTEQRHDLVKDIEVFGVSLSLLISRANEKSVTMPSGLSREQRRA
                     WAAEQARKIHN"
                     /name="hypothetical protein"
     gene            2250..2678
                     /locus_tag="L6L54_RS25345"
                     /old_locus_tag="L6L54_25345"
     CDS             2250..2678
                     /locus_tag="L6L54_RS25345"
                     /old_locus_tag="L6L54_25345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000534558.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRYSAKTLDKIDDFIEHFE
                     KYNLFGDPLKGYPAWTGKVSPSWKVPDHYENKEAIEKYARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMKLPQNFE"
                     /name="hypothetical protein"
     gene            complement(2894..3025)
                     /locus_tag="L6L54_RS25350"
                     /old_locus_tag="L6L54_25350"
     CDS             complement(2894..3025)
                     /locus_tag="L6L54_RS25350"
                     /old_locus_tag="L6L54_25350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023151671.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLATATGKQDVREM"
                     /name="hypothetical protein"
     Typing          573..809
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          complement(2..305)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.387"
                     /coverage="98.0"
                     /evalue="1.4599999999999999e-98"
     Typing          complement(2954..3172)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.636"
                     /coverage="95.0"
                     /evalue="8.879999999999999e-106"
     Typing          819..1138
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.23e-62"
ORIGIN
        1 tccaggggga aacgcctggt atctttaagt cctgtcgggt ttcgccacct ctgacttgag
       61 cgtcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc ctcccgcgcg
      121 cccttcttct gggtctttgt cttttgctca catgttcttt ccggttttat cccccgattc
      181 tgtggataac cgtattaccg cctttgagtg agctgacacc gctcgccgca gtcgaacgac
      241 cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc cttatgtgac attttctcct
      301 tacgctcctc tatgccgttc tgcatcctgt ccggatgcgt tatatcccgg taagattttc
      361 cgcttcaaag cgtgtctgta tgctgttctg gagttcttct gcgagttcgt gcagtttctc
      421 acacatggcg gcctgttcgt cggcattgag tgcgtccagt ttttcgagca gcgtcaggct
      481 ctgacttttt atgaatcccg ccatgttgag tacggcttgc tgctgcttat tcatcttttc
      541 gttttctccg ttctgtctgt catctgcgtt gtgtgattat atcgcgtacc acttttcgac
      601 tgttttgctg ccgctattct gccgcttggc tttttgacgg gcatttctgt cagacaacac
      661 tgtcactgcc aaaaaactgc cgtgcctttg tcggtaattc gagcttgctg acaggacagg
      721 atgtgcaatt gttataccgc gcatacatgc acgctattac aattgccctg gtcagggctt
      781 tgccccgaca cccatgtcag atacggagcc atgttttatg acaaaacgaa gtggaagtaa
      841 tacgcgcagg cgggctatca gtcgccctgt tcgtctgacg gcagaagaag accaggaaat
      901 cagaaaaagg gctgctgaat gcggcaagac cgtttccggt tttttacggg cggcagctct
      961 cggtaagaaa gttaactcac tgactgatga tcgggtactg aaagaagtta tgagactggg
     1021 ggcgttacag aaaaaactct ttatcgacgg caagcgtgtc ggggacaggg agtatgcgga
     1081 ggtgctgatc gctattacgg agtatcaccg tgccctgtta tccaggctta tggcagatta
     1141 gcttcccgga gagaaaactg tcgaaaactg acggtatgaa caccgtaagc tcccaaagtg
     1201 atcaccattc gctttcatgc atagctatgc agcgagctga aaacgatcct gacgcatcct
     1261 tcctgttttt ccggggtaaa acatctcttt ttgcggtgtc tgcgtcagaa tcgcgttcag
     1321 cgcgtttcag tggtgcgtac aattaaggga ttatggtaaa tatatgagct atgcgataac
     1381 tttaactgtg aagcgatgaa cccattacag gcaaagccaa ttactcctga cagtggttta
     1441 gccagaagca gggctaccaa gaccaatgca ataagtaata tatcgttttg ctatcgtgca
     1501 tcgctcgcgc tcagttccat tgtgcttttt taagctgtcg tttttcttac ggtatatacc
     1561 ggttttttat ggcgtggttt cttaacttgt tcagctactg atggacccat tgtatctagg
     1621 tagtcaacta gctttgttag atcataaata ttgcgaccac catatcggcg atcactcttc
     1681 gatgttggtt tcttgtccaa gagattagct ttttcaagat cattgatagc tctctgaaca
     1741 gtccgtacag aaacccccat acgtatggct agactttcca ttgacggatg cggccactct
     1801 tgcaaactcc accagtgaac gatcaggtta agtagtgtgt taaaggccac tgaagttagc
     1861 tttttctcgt tttgtataaa aaacaatacg gtaggcactg ctgtccagcc aagagacaaa
     1921 ccgccagctt tccatttatt cttaatggag taagtcattg attttcctaa gccccaaaat
     1981 atttaaagta tatattatat ggtatattca tatgaatagg gtgacactgg cgccattatt
     2041 gtgcaaccaa aaaagactac tctgaaaacg aggaaaagat tttttcctgc ctgaattaga
     2101 tacggagtta gcgatatgaa aaccgaacaa cgtcatgatc ttgttaaaga tattgaggtt
     2161 tttggcgtat ccttgtctct gttgatttcc agagcgaatg agaagtctgt tacaatgcca
     2221 tctggtctaa gtcgggagca gagaagagca tgggcagcgg agcaggcgcg caaaatccac
     2281 aattgaatat tgtctcattc tctgagacct tcaaccttta ttacacatcc agatattctg
     2341 caaaaacact cgataaaatc gatgatttca ttgagcattt tgaaaaatac aatctctttg
     2401 gcgatccttt aaaaggatat ccagcttgga ctggcaaagt atcgccatcg tggaaagtgc
     2461 ctgatcatta cgaaaacaaa gaagctattg agaagtatgc tagagctaac aaattatggc
     2521 atgctcattt aggcgatccg gtttttaaag atacgtttca tgggaaatac aaggtttctg
     2581 actgggttat tcatttccag cggctgacac cgaaccatat aaagctttta gagcttggat
     2641 accatgaccc aatgaagcta cctcaaaact ttgaatgatc gagcggcagg ctaaatgaaa
     2701 tcttgagatt cattcagtct cgtcgtaatc tcactattgt aaaaacgaaa aaaccaccct
     2761 ggcaggtggt ttttcgaagg ttagttaatc ctggcagatt ctctaaccgt ggtaacagtc
     2821 ttgtgcgaga catgtcacca aatactgtcc tttcagtgta gcctcagtta ggccgccact
     2881 tcaagaactc tcgttacatc tctcgcacat cctgcttacc agtggccgtt gccagtggcg
     2941 ttaagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt
     3001 cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac
     3061 cgagatacca acagcgtgag ctatgagaaa gcgccacgct tccctaaggg agaaaggcgg
     3121 acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag ct
//
