LOCUS       NZ_CP091686             5755 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KKo003 plasmid pKKo003_3, complete sequence.
ACCESSION   NZ_CP091686
VERSION     NZ_CP091686.1
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 5755)
  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  JOURNAL   Unpublished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 5755)
  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
            CP091686.1.
            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..5755
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KKo003"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKKo003_3"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            630..1148
                     /locus_tag="L6L54_RS25250"
                     /old_locus_tag="L6L54_25250"
     CDS             630..1148
                     /locus_tag="L6L54_RS25250"
                     /old_locus_tag="L6L54_25250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310049.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001445155.1"
                     /translation="MSEKAKKVGRRSLSKRRESLIKELWGDELSELNIWNRKEHDGFTT
                     IPRTLNYINRIIDYLAGAGSPVSQTYLSLWCRVFDEGFVEIRDKDALAFESGFSGQRAV
                     TTWLGRMKKLRELGLISTKPGTSGEFHYVIMLNPLYVIKKSYESNGWARDERYNALFSR
                     MQEVGAEWE"
                     /name="hypothetical protein"
     gene            1145..1708
                     /locus_tag="L6L54_RS25255"
                     /old_locus_tag="L6L54_25255"
     CDS             1145..1708
                     /locus_tag="L6L54_RS25255"
                     /old_locus_tag="L6L54_25255"
                     /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_000999222.1"
                     /translation="MNDMKAVRHRYKQRYDFAASEVVGAFDELRSLDWSLEIASLSDVE
                     MSKRWIGAVDPNGVARLPPNGGWDWVKLYNGYLKNPSAFVCAIKSEGKLCALIGGGVSD
                     SKVVTKLHYLESAPYDTALSGYALDISVTYVVTVANAMGSEYSAIYEPNSKVREIAIND
                     YGFSEDNLFGTSKDFALYLPMSRI"
                     /name="hypothetical protein"
     gene            complement(1718..1870)
                     /locus_tag="L6L54_RS25260"
                     /old_locus_tag="L6L54_25260"
     CDS             complement(1718..1870)
                     /locus_tag="L6L54_RS25260"
                     /old_locus_tag="L6L54_25260"
                     /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_023351545.1"
                     /translation="MLAHVVELKKATEPCSSGTAGAFRQRVKARRAEQGRSNQQPEKLY
                     GVLVG"
                     /name="hypothetical protein"
     gene            complement(2166..2312)
                     /locus_tag="L6L54_RS25265"
                     /old_locus_tag="L6L54_25265"
     CDS             complement(2166..2312)
                     /locus_tag="L6L54_RS25265"
                     /old_locus_tag="L6L54_25265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_050863271.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHAKAPLAAANGKRMYKRLLT
                     QSS"
                     /name="hypothetical protein"
     gene            2541..2744
                     /locus_tag="L6L54_RS25270"
                     /old_locus_tag="L6L54_25270"
     CDS             2541..2744
                     /locus_tag="L6L54_RS25270"
                     /old_locus_tag="L6L54_25270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001347451.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000415556.1"
                     /translation="MEKRQRRILFQPFLISAKSLYPAIRELATPAAVSRQERSDRVSEE
                     ASYHRNLHFLLYALQLHFSPAT"
                     /name="hypothetical protein"
     gene            2953..3276
                     /locus_tag="L6L54_RS25275"
                     /old_locus_tag="L6L54_25275"
     CDS             2953..3276
                     /locus_tag="L6L54_RS25275"
                     /old_locus_tag="L6L54_25275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_001445156.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3485..>3919
                     /locus_tag="L6L54_RS25280"
                     /old_locus_tag="L6L54_25280"
                     /pseudo=""
     CDS             3485..>3919
                     /locus_tag="L6L54_RS25280"
                     /old_locus_tag="L6L54_25280"
                     /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            3954..4439
                     /locus_tag="L6L54_RS25285"
                     /old_locus_tag="L6L54_25285"
     CDS             3954..4439
                     /locus_tag="L6L54_RS25285"
                     /old_locus_tag="L6L54_25285"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_015059929.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            4443..4658
                     /locus_tag="L6L54_RS25290"
                     /old_locus_tag="L6L54_25290"
     CDS             4443..4658
                     /locus_tag="L6L54_RS25290"
                     /old_locus_tag="L6L54_25290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137421.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4857..5408)
                     /locus_tag="L6L54_RS25295"
                     /old_locus_tag="L6L54_25295"
     CDS             complement(4857..5408)
                     /locus_tag="L6L54_RS25295"
                     /old_locus_tag="L6L54_25295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     Typing          2665..2849
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.638"
                     /coverage="86.0"
                     /evalue="2.7100000000000003e-47"
     Typing          complement(2204..2719)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.211"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3267..4762
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtaaatggtt tctgaggtgt aagcgaaaac tcgagttttg acgccattct gagtaggtaa
       61 tttgcagacg gaataaatac tggcgagcaa taagctcatc aacaaaaaat ggagatccta
      121 agatggatag agaaacccta tacctactca aaacgttaga ccataacaat gccttgcttg
      181 acgatattat ccgaagaaag atgggtaggt actacaacac gaagattttg cgtgattcct
      241 gtgatgctat tgaagccgaa ctacgacgtc gaggaatcat ttaaaaagac gaagcccgct
      301 tatgtgggct ttttcattgc gcattcaggg caccccttcc ccccccttaa accccctaag
      361 aaccccattc agcacagcga gcacaacgat tacattagag tacattgaga acagcgagta
      421 caaaatagcg cataactaat tgaaaaataa aaccgtaatt gtaaaaaata ttacatctca
      481 atatttgtat tgacaaaaaa aaagaatcat atcaaatgag atgttggtta atgatgtgct
      541 tggtttttgt gttattacac ataactcatt gaatataata ggttttttgt tgataatatt
      601 ttcatgttga attgactttt gggggataaa tgtcagagaa ggcaaaaaaa gtaggtaggc
      661 gctctctatc aaaaagaaga gaaagtctaa taaaagagct ttggggggat gagctttccg
      721 aacttaatat atggaacagg aaagaacacg atggatttac aacaatccca agaacattga
      781 attatatcaa taggataatc gattaccttg ctggcgctgg atctcctgtg tcacagacat
      841 acctcagttt atggtgtcga gtttttgacg agggattcgt cgaaattagg gataaagatg
      901 ctctggcatt tgagtcaggg tttagtgggc agcgagcggt gactacttgg ctaggaagaa
      961 tgaaaaagct acgggagctg ggactgatat caacgaagcc tggtacttct ggcgagtttc
     1021 attatgtaat catgttgaat ccactttacg taattaaaaa gtcatatgaa tcaaatggat
     1081 gggcaaggga tgagcgttac aacgctctat tttctaggat gcaggaagtg ggggcggagt
     1141 gggaatgaac gacatgaaag ctgttcgtca ccgatataag cagagatatg attttgctgc
     1201 gtcagaagta gtgggggcgt ttgatgaact tagaagtttg gattggagtt tagaaatcgc
     1261 atctttaagt gacgtggaaa tgtcaaagag atggattggg gctgttgatc ctaacggtgt
     1321 tgcaagacta ccacctaacg gtggatggga ctgggttaag ctctacaacg gctatttgaa
     1381 gaaccctagc gcattcgtct gtgccattaa atcagaaggc aagctatgcg ctctgattgg
     1441 tggcggggtt tctgatagta aagtggtaac taagctgcat taccttgaat cagcccctta
     1501 tgacacggct ctttcaggat atgcactgga tatttctgtt acgtatgttg ttactgtcgc
     1561 gaatgcgatg ggaagcgaat actcagccat ctatgagcca aatagcaaag tcagagagat
     1621 agctataaat gattatggat ttagcgagga caacttgttt gggacaagta aagatttcgc
     1681 tctgtatcta ccaatgagcc ggatttaacc ggctcattta tcctaccagt acgccgtaga
     1741 gtttttctgg ctgttggttt gatcggcctt gctctgctcg tcttgctttc acgcgctggc
     1801 gaaatgctcc ggctgtgcca gaagagcatg gttccgtcgc ttttttaagt tcgaccacgt
     1861 gagctaacat attatttccg ttttttcgtg agttagtaca aagcatatga ggtgacggat
     1921 acgtcaactt catagtaact gtactgtatt gtagaagaga tgcgcaagtc gcagaattaa
     1981 tgcgaccctt cattgacgag gcgaagagta aacgcgtatc ttctttgaaa acgaaaaaac
     2041 cacccggcaa ggtggttttt cgaaggttca ttaaaccggc aagtttatga accgtggtaa
     2101 cagggtgtac aagaccactg ccaccaaatt cgtccttcca gtttagccgt agttgggctg
     2161 atacttcaag aactctgcgt tagtaatctc ttgtacatcc tcttaccgtt ggctgctgcc
     2221 agtggcgctt ttgcatgtct ttccgggttg gactcaagat gatagttacc ggataaggcg
     2281 cagcagtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac
     2341 ccggaactga gtgtcaggcg tggaatgaga aaccgcggcc ataacagcgg agtgacaccg
     2401 gtaaaccgaa aggcaggaac aggagagcgc acgagggagc taccaggggg aaacgcctgg
     2461 gatctttata gtcctgtcgg gtttcgccgc ctctgatttg agcgtcagat ttcgtgatgc
     2521 ttgtcagggg ggcggagcct atggaaaaac ggcaacgccg catccttttt cagcccttcc
     2581 tgatttccgc taagtctctt tatccagcca ttcgtgagct ggcaacgccc gccgcagtct
     2641 cacggcagga gcgcagcgac cgagtgagcg aggaggcgtc atatcaccgt aacctccatt
     2701 ttctcctgta cgccctgcag ctgcattttt cccctgccac atgaagcact ttcattaagt
     2761 gttactccgc cgtaacatac tgagccagta tacactccgc tagcgttacg tgactggttc
     2821 agggctgcgc cccgaaacct gctaaaacca ctgacgcgcc tgcggcttgt ccaacaccgc
     2881 gccgaccggg aaaagatttc ccgcccgtcc cggcgttatc aggaggctgg attggcagac
     2941 aaacgcagta aaatgctcac gatgtgggtg accgaagatg agcaccgccg tctgttggaa
     3001 cgctgcgacg gtaaacagct tgcagcctgg atgcgccaga cgtgcttgga cgagaaaccc
     3061 gcccgcgccg gcaagcttcc ctcgatctcg ccggcgctgc ttcgtcagct tgccggcatg
     3121 gggaacaacc tcaaccagat tgcccggcag gttaacgccg gtggtggcag cgggcacgac
     3181 cgcgtgcagg tcgtcgccgc gctgatggcc atagatgccg gactcgagcg gctgcggcat
     3241 gccgtgctgg aaaagggtgc agacgatgat cgttaagttt cacccgcgag ggcgcggcgg
     3301 tggcgccggt ccggtggatt atctgctggg gaaagaccga cagcgcgacg gcgccaccgt
     3361 tttgcagggg aagccggaag aagtcaggga gcttatcgac gcctcgccct acgcaaaaaa
     3421 gtacacatcc ggcgtcctgt cctttgccga aaaggattta ccgcccgggc agcgcgaaaa
     3481 gctgatggcg agctttgaac gggttctgat gcccggactc gataaagacc agtacagcgt
     3541 gctgtgggtt gagcaccagg ataaggggcg gctggagctg aacttcctga tcccgaacat
     3601 ggagctgctg actggcaggc gtctccagcc gtattacgac cgcgccgacc gtccgcgcat
     3661 tgatgcctgg cagaccatcg tgaacggcag gctggggctg catgacccga acgcgcctga
     3721 aaaccggcgg gcgctggtca cgccgtccgc gctgccgaaa acgaagcagg aagccgctca
     3781 ggcaattaca cggggtttac tggccttagc ctcgtccggg gagctgaaaa cccgccagga
     3841 cgtcactgag gcgctggaaa gcgcaggttt tgaggtggta cgcaccacaa aaagcagcat
     3901 cagcattgcc gacccggacg gggggcgaaa catccgactg aagggagcca tctatgaaca
     3961 gtcttttaac gctggcaaag gacttagagc agaaatcgaa agcgcagcag cagagtaccg
     4021 gcgagatgct gaaagccgca ttcagcgagc acgagaagtc tgtcagagcg gaactgagcg
     4081 aaagcgagaa gagaatcagc gccgccatcc tcgaccacga ccggaagctg tcctcagcca
     4141 tgagccagcg cacgaaaggc atggtgcgta tggtcagcca gacgtggctg accatcgtcc
     4201 tggtgtctac actgctgaca gcatcgggcg caagcattct atggtggcag gggcagcaga
     4261 tactcgacaa ttacacgatc atccgggagc agaagagcac gcaggccatg ctgtccgaga
     4321 ggaacagcgg cgtgcagctc tcgacctgcg gagagcagag acgccgctgc gtgagggtga
     4381 acccggaagc gggacggttc ggagaggatt cgagctggat gatactggcg gggaaatagc
     4441 acatgacgga gctggaaaaa cagttgctga gcgcattaga gcagctacag caggactact
     4501 cgaaaaggct ggacgagtgg gagaacgcct tcgcggaatg gcggacgatg tctggtctta
     4561 tgcaacggga gaacgcggcg ctgagcgagc gcgtcacggg cttgagcagg caggtgcaga
     4621 gtttgagcga gcagctgcgc cggttgtcac aaggctgaac gtgatagagg cacatcgtga
     4681 gcaggaacgg gcggcgcagc atcagaaagc gctggagctg gaacgatctc agcgacagcg
     4741 aacgtacaac ggtccgtcac tttgaatctg tgcgccggaa aagcatgggc ttgctgtttc
     4801 tggcgtacag gttcagttct agaacatgag gctgctatct tgttgttcac gcttcatcag
     4861 atcttgatgc ttattgttat ggctgagcta tcaatccctg ttgcgttgct aatatccttt
     4921 ttggctcttt caattgcctc gttaagggag agtttttctg ttttctcttc agccagacca
     4981 ggaatcactg tattaggaac cgatggggat gaaggatgga atttcttcca ttccagttgt
     5041 tccggtgtta ccccaatacg taaaaaagct tcctgtgcgc tcaggtaagc aaccggatag
     5101 cgctgaccat cggttagcat tttccatgct tttggcgtgt gaatttctgc gtattcatca
     5161 aaggttatga cgttcctgtc gtcgtaatca gggcttttaa aacacccggt aattttggcg
     5221 atcaggaatg ctgtgccgtg ttctaggtct tttactgccc acgtttccct tctgtttctt
     5281 actgctatga ggtaatcggc atcgttgagc ctgtctgttc tggcatgcca gtagcctgac
     5341 cccccctcag ttctcattat gttcaaatcc ttcccggtaa aaaccacaac agctttcata
     5401 tctttcatat agaaaccctt aataggtgag taaatttcat ttttttatga aatctatacg
     5461 atagaattcg tgttgtaaat gttttttatg cgataaaata cagcccccta cctcttttac
     5521 tgttagtggt aaggctttct gtttgatttt ttgataaacc ggttaaaaca ggggcttgga
     5581 cgaggatata cattgaaagc atgagccatt cacgtggctg catggctatg cagtcgcgtg
     5641 aaatttatca ggcgcagaat gcgcggttta gcggggagtt tactgccggt tttaccgggc
     5701 taacgccgct ttcacgctga acccgtccgg agcggtgcgg gcaagggatg ttatg
//
