LOCUS       NZ_CP091683             4074 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KKo003 plasmid pKKo003_6, complete sequence.
ACCESSION   NZ_CP091683
VERSION     NZ_CP091683.1
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 4074)
  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  JOURNAL   Unpublished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 4074)
  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
            CP091683.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KKo003"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKKo003_6"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            complement(join(3987..4074,1..2072))
                     /gene="mobQ"
                     /locus_tag="L6L54_RS24145"
                     /old_locus_tag="L6L54_24145"
     CDS             complement(join(3987..4074,1..2072))
                     /gene="mobQ"
                     /locus_tag="L6L54_RS24145"
                     /old_locus_tag="L6L54_24145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_240749175.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            2251..2505
                     /gene="mobC"
                     /locus_tag="L6L54_RS24150"
                     /old_locus_tag="L6L54_24150"
     CDS             2251..2505
                     /gene="mobC"
                     /locus_tag="L6L54_RS24150"
                     /old_locus_tag="L6L54_24150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            3037..3729
                     /locus_tag="L6L54_RS24155"
                     /old_locus_tag="L6L54_24155"
     CDS             3037..3729
                     /locus_tag="L6L54_RS24155"
                     /old_locus_tag="L6L54_24155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1715..2073)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          2074..2250
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3038..3729
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.821"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..2159)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.583"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaacccagcg agcggaacag atgatccggc tgtttttctg gtgtgttgac ggcagcaaaa
       61 agcggtgcct cacgggtttt cagatgaaac tccataagtt ccggcgcagg tgatatgtgg
      121 ctgtctgcat cgtgatttac ggcaacacca taccctgcat accgtaaccc cttatcggtc
      181 agtgcactga tgaccagctg gctgttatcg gctgagggaa cggcaaacgc gggatacagc
      241 gtaccattaa gccggacaac accgcccaga gagtcatcca cgcccatgac cagcaaaagc
      301 tgaagctggc gggtttcccg gtcgacagaa ctcattaccg gcatcagcgt cggtagcaga
      361 cgtccctgcg taaaatccac cttccttgct gccagtgatg gcatggctgg ctggcggtct
      421 tctccaagac agaaagactc cggccatgtc ttcggctggc ggagattgcg ggtatattgc
      481 ggccatgtct ggcaaacctg cgtcagaagt tgctcaaagg tcgcagagga ataaacacgt
      541 tgcagtggtg gatgttgacc gatttcgctt cggtcacaga tataaccact cctgtcacgc
      601 attaaatcaa cacgctcaaa gattctggtg cggtatttct ccagctcgtt cccccagagc
      661 gtgtattctc cgttccggtt gtgaagcaga aggtaacagg tcatttcccc gttaccaggc
      721 atgggggcct cgccataccc cgtaacgact gcgctcagta cccctgaatc cataacggca
      781 ttgtcatttt tcctgagctg ttccgctcgt cgctccgcgc gactacgttc tgtatcctcc
      841 tgctccttcc ggcgcaattc ctcttcacgt ttaagcaact ggactctgag agctgcaagg
      901 ccggatgccc cccactgctg ccactgtttt tcaaatgccg tctgactcgc gggaatgtcc
      961 tgtttctcca ccttccggta atgctgtcgc aatttttcca tttgctggct cagcgactgg
     1021 atttttccct gttcgctacg gtattccggt gccgcccatt gcatcagggg aatacgggaa
     1081 aaaccggacg aaaacggcga tgattttttc aggctggcag catggctcat cgcttccttt
     1141 cgttcggtgt tcagctcttc ccagcgtctg cgcgtcgcct gcatatctgc catcatcgac
     1201 atggcattac tggtgagttt ccatgccgca ttactgtcct tcggcaacgc ttcgatgatg
     1261 tcacgtagtg tgtacgaagt tgcgttgtca ggaagcacga tattcagaag gtcagccaca
     1321 cggcgggcag gctctgtcag cccgctgttt ctgagttcgg tacgggaaat ctgtatttcc
     1381 aggttaagtc tgttaatcag acgattctgt tcgccgcgtt ctgtttcgat accgcgtgtt
     1441 tccatcgcac aggcagactt tccgaggtga ataccaggcg ttttctcaag cccctgtcgc
     1501 tcgtatgaac gatggtctat ctcttcctga taaccggcgt tcgccagtgc cctgttcgca
     1561 tggtcagccc atgatgcacg ccacgtctcg gcatgtgtcc ggtcgttcca gtccctgacc
     1621 tttccaccga atccagcagg tccgacagct ctcgtggtca gcatgatgtg cgcatgggga
     1681 tttgttttat ccatgtgatg gaacgccaca tcagcaatca tgccctgact gacaaagttt
     1741 tctctgacaa aggcgagaac ggtttcccgt gcggcatcct gcggcagttc acgggggata
     1801 gcgagttcaa tttcccgcgc aagttgtgag ttcttccggc gttcggcctt ctcaacggca
     1861 ttccagagtt cggcacggtt cgtacaccag gcaggggctg tcgcgggggt cagaatcaca
     1921 gcttcagcca caccgctttt gcgggtgtag tcgtgagtca gtccggtacg ctcatcaagc
     1981 attagtgaac cggaacgata ggcagcggaa gctacggcgc tgtagccgct gcttctggag
     2041 ataattttca tgctgagatg ataaatcgcc atttctgccg taatgccttt ttgtagtttt
     2101 ctttcagccc cgcagggcgc acacaatcga aacggagtgg agattgtata agtgcgcact
     2161 tcgtgatttg ccgtgcatta tgccagctca gtttttaaac taccagtgac gcgctaaaat
     2221 gcgatttttc atcgcgcacg gagttacatc atgagcagaa cgctcgaaca gaagattgct
     2281 gatgctgagg cgagattaca gcgcctgaag gcgaagagcc ggagcctgga cacagcgcag
     2341 aaggttgttg tgggtgcagc attgctggca aaggtcagaa agccggagga ggtgcagttg
     2401 cgtgcctggt tactccagtt cctgaaggca gaggtgacac gacaggctga tgtgacgcgc
     2461 atactgccgc tgattaacga gctggaggcg ctgccaggac agtgattgta tcgtccgctc
     2521 gccgcagccc cagcgaccga gcgttagcga gcgagtgggc gaggaagcgg aagtgaatcc
     2581 gtcgccaggt tgagcacata cgcacggttt ttcggcaggt gatatgcgct gaacccgcat
     2641 gaatactgga tttccacagg gttggaaggg gagtattcgg aacttgcaat tctgctttct
     2701 tgcaacacat tgtttttatt ggttttttgt tttcatcccc ccaagttatc cacaggctcg
     2761 ccgttaagtt tttagatctt gtttttaaga tcttgttttt aatacttgtt ttaggggtga
     2821 aattcattaa taaaatcaat atgttatagt ggtatatgtg gaggaattta aggtaaaggt
     2881 ggaggaattt aaggtgttta ggtggaggaa tttaaggtaa aggtggagga atttaaggtg
     2941 ttattcacag aaatgtgagg atataaaaaa aaacattcca catttcttat ttgtggggca
     3001 cattaaagca tcaccacatt tgaacgggat ctttgtatgt cggacttgat tgcctacaag
     3061 tcgaatgctt tggttgaggc cagctacaag ttgaccctac aggaacaacg ttttctgttg
     3121 ctgtgtatca gtcgattgaa atctggtgct gatgctgaat tgcaaaagac aatgaccatt
     3181 accgctgcgg aatattttga ttcattccct gacatggggc ggaaaaatgc cgaggttcag
     3241 ttacaggaag cgatcgatcg tttatgggac aggtcgatca ttctcaagaa tgacgagaag
     3301 cgtgaggagt tccgctggat ccagtatcgg gcacagtacg ctaaaggtga ggccaaggct
     3361 cgaataacct tttctgacgc ggtaatgcct tatctgacgc aactgaaggg gcaattcacg
     3421 cgcgttgtta taaaaaacat atcaggttta tcaagtagtt acagtataag aatatacgag
     3481 ttcctccagc aattccgcag tacgggagag agaattattg ctcttaatga ctttcgttca
     3541 atgttaggga ttgaaaataa atacaaacaa ttcagagact taaataaaat actaataaaa
     3601 ccctgtgttg acgaactgaa caaaaaaagc gacctggctg taacggttga gacgatcaaa
     3661 aaggggcgca cggttgtagc cctgcatttt cgcttcaagg aagataaaca gatcaagatg
     3721 acgatctaaa atcgatttta aggcacctaa aacgctccct gctgcgtttt ttttgtgtta
     3781 gtagtgcgaa ggtactattg aagtgaaaaa ttgcgtcaaa aacgctctga tgcagcgaaa
     3841 aaagaacccc caatttttgg gggcggaaaa acaaaactat gcttgcatta tgtgagtgtg
     3901 cttcttgcat tcatccctgt cgatgaacat cgaagaacat cgaagaacat aacacgatgt
     3961 taaacaaaac aaaatattgt tcacattcac tgtgaccaac cgcgatcatg tctcctctcg
     4021 gtggtgtgtg ttcttgcatc ttcctcgcgc cgccattcgt cccaggtacg attg
//
