LOCUS       NZ_CP091689             4077 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KKo003 plasmid pKKo003_5, complete sequence.
ACCESSION   NZ_CP091689
VERSION     NZ_CP091689.1
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 4077)
  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  JOURNAL   Unpublished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 4077)
  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
            CP091689.1.
            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..4077
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KKo003"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKKo003_5"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            join(2006..4077,1..88)
                     /gene="mobQ"
                     /locus_tag="L6L54_RS25355"
                     /old_locus_tag="L6L54_25355"
     CDS             join(2006..4077,1..88)
                     /gene="mobQ"
                     /locus_tag="L6L54_RS25355"
                     /old_locus_tag="L6L54_25355"
                     /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_001029343.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(334..1041)
                     /locus_tag="L6L54_RS25360"
                     /old_locus_tag="L6L54_25360"
     CDS             complement(334..1041)
                     /locus_tag="L6L54_RS25360"
                     /old_locus_tag="L6L54_25360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1573..1827)
                     /gene="mobC"
                     /locus_tag="L6L54_RS25365"
                     /old_locus_tag="L6L54_25365"
     CDS             complement(1573..1827)
                     /gene="mobC"
                     /locus_tag="L6L54_RS25365"
                     /old_locus_tag="L6L54_25365"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(1829..2005)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2006..2364
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(336..1041)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.717"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1920..4075
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.861"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taatcgtacc tgggacgaat ggcggcgcga ggaagatgca cgaacacacg ccaccgagag
       61 gagacatgat cgcggttggt cacagtgaat gtgaacaata ttttgttttg tttaacatcg
      121 tgttatgttc ttcgatgttc atcgacaggg atgaatgcaa gaagcacaca cataatgcaa
      181 gcatagtttt gtttttccgc ccccaaaaaa tgggggttct tttttcgctg cattagagcg
      241 cttttgacgc aatttttcac ttcaatagta ccttcgcact actaacacaa aaaaaacgcg
      301 gcagggagcg ttttaggtgc cttaaaatcg attttagatc gtcatcttga tttgtttgtc
      361 ttccttgaag cgaaaatgca gggctacaac cgtgcgcccc tttttgatcg tctcaaccgt
      421 tacagccagg tcgctttttt tgttcagttc gtcaacacag ggttttatta gatccctgtt
      481 taacgttttg aaatctttat atttaccatc aagcatcagt gatgatttaa aatcatcgag
      541 ggcgataata cgttccccag tactgcggaa ttgctggaga atttcgtata ttcttatgct
      601 gtaacttctt gataaattgg aaatattttt aatgacgact ctggtgaatt gccccttcaa
      661 ctgtgtcaga taaggcatta ccgcgtcaga aaaagtgatt tgtgctttcc cctctcccct
      721 cgcgtactgt gcccgatact gaatccagcg gaactcctcg cgcttctcgt cgtccttgag
      781 aatgatcgac ctgtcccaca aacgatcgat cgcttcctgt agctgaacct cggcattttt
      841 ccgccccata tcagggaatg aatcaaaata ttccgcagct gtaatggtca ttgtcttttg
      901 caattcaggt gaagctacgt cagtaccgga gttaagtcgg cttatgcaga gcaataagaa
      961 acgctgttct tgtaaagtta gcttgtaact ggcctcaacc agcgcattgg acttataggc
     1021 tatcagaggg tttgatgtca ttttaaccac caggccaaaa atgaggtgag ataaaaacct
     1081 atcaccttta gcattggtga gcaattatat ttccaccccc cattttcctg tgaatattac
     1141 cttaaatctc ctcaccttta ccttaaatta cctcacccaa gcaccttaaa ttatatcacc
     1201 tttaccttaa attccctcac ctatacacgt gtaacgcatt gtttttaatc aggaatttcg
     1261 accctaaaac aagtattaaa aacaagatct taaaaacaag atctaaaaac ttaacggcga
     1321 gcctgtggat aacttggggt gctgaaaata aaaatccaat aaaaacaatg tgttgaaaaa
     1381 aatcaggatt gaagattccg aatacacccc ctccaaccct gtggaaatcc agtattcatg
     1441 cgggttcagc gcatatcacc tcccgaaaaa ccgtgcgtat gtgctcaatc aggcgacgga
     1501 ttcacttccg cttcctcgcc cactcgctcg ctaacgctcg gtcgctggga ctgcggcgag
     1561 cggacgatac aatcactgtc ctggcagcgc ttccagctcg ttaatcagcg gtagtatgcg
     1621 cgtcacatca gcctgtcgtg tcacctctgc cttcaggaac tggagtaacc aggcacgcaa
     1681 ctgcacctcc tccggctttc tgacctttgc cagcaatgct gcacccacaa tgaccttctg
     1741 cgctgtgtcc agactcctgc tcttcgcctt caggcgctgt aatctggcct cagcatcagc
     1801 aatcttctgt tcgagtgttc tgctcatgat gtaactccgt gcgcgatgaa aaatcgcatt
     1861 ttagcgcgtc actggtagtt taaaaactga gctggcataa tgcacggaaa atcacgaagt
     1921 gcgcacttat acaatctcca ctccgtttcg attgtgtgcg ccctgcgggg ctgaaagaaa
     1981 accacaaaaa ggcattacgg cagaaatggc gatttatcat ctcagcatga aaatcatctc
     2041 cagaaacagc ggctacagcg ccgttgcttc tgctgcctat cgttccggtt cactgatgct
     2101 tgatgagcgt accggactga ctcacgacta cacccgcaaa agcggtgtgg ctgaagctgt
     2161 gattctgact cccgcgacag cccctgcctg gtgtacgaac cgtgccgaac tctggaatgc
     2221 cgttgagaag gccgaacgcc ggaagaactc acaacttgcg cgggaaattg aactcgccat
     2281 cccccgcgaa ctaccgcagg atgccgcacg ggaaaccgtt ctcgcctttg tcagagaaaa
     2341 ctttgtcagt cagggcatga ttgctgatgt ggcgttccat cacatggata aaacaaatcc
     2401 ccatgcgcac atcatgctga ccacgagagc tgtcggacct gctggattcg gtggaaaggt
     2461 cagggactgg aacgaccgga cacatgccga gacgtggcgt gcatcatggg ctgaccatgc
     2521 gaacagggca ctggcgaacg ccggttatca ggaagagata gaccatcgtt catacgagcg
     2581 acaggggctt gagaaaacgc ctggtattca cctcggaaag tctgcctgtg cgatggaaac
     2641 acgcggtatc gaaacagaac gcggcgaaca gaatcgtctg attaacagac ttaacctgga
     2701 aatacagatt tcccgtaccg aactcagaaa cagcgggctg acagagcctg cccgccgtgt
     2761 ggctgacctt ctgaatatcg tgcttcctga caacgcaact tcgtacacac tacgtgacat
     2821 catcgaagcg ttgccgaagg acagtaatgc ggcatggaaa ctcaccagta atgccatgtc
     2881 gatgatggca gatatgcagg cgacgcgcag acgctgggaa gagctgaaca ccgaacgaaa
     2941 ggaagcgatg agccatgctg ccagcctgaa aaaatcatcg ccgttttcgt ccggtttttc
     3001 ccgtattccc ctgatgcaat gggcggcacc ggaataccgt agcgaacagg gaaaaatcca
     3061 gtcgctgagc cagcaaatgg aaaaattgcg acagcattac cggaaggtgg agaaacagga
     3121 cattcccgcg agtcagacgg catttgaaaa acagtggcag cagtgggggg catccggcct
     3181 tgcagctctc agagtccagt tgcttaaacg tgaagaggaa ttgcgccgga aggagcagga
     3241 ggatacagaa cgtagtcgcg cggagcgacg agcggaacag ctcaggaaaa atgacaatgc
     3301 cgttatggat tcaggggtac tgagcgcagt cgttacgggg tatggcgagg cccccatgcc
     3361 tggtaacggg gaaatgacct gttaccttct gcttcacaac cggaacggag aatacacgct
     3421 ctgggggaac gagctggaga aataccgcac cagaatcttt gagcgtgttg atttaatgcg
     3481 tgacaggagt ggttatatct gtgaccgaag cgaaatcggt caacatccac cactgcaacg
     3541 tgtttattcc tctgcgacct ttgagcaact tctgacgcag gtttgccaga catggccgca
     3601 atatacccgc aatctccgcc agccgaagac atggccggag tctttctgtc ttggagaaga
     3661 ccgccagcca gccatgccat cactggcagc aaggaaggtg gattttacgc agggacgtct
     3721 gctaccgacg ctgatgccgg taatgagttc tgtcgaccgg gaaacccgcc agcttcagct
     3781 tttgctggtc atgggcgtgg atgactctct gggcggtgtt gtccggctta atggtacgct
     3841 gtatcccgcg tttgccgttc cctcagccga taacagccag ctggtcatca gtgcactgac
     3901 cgataagggg ttacggtatg cagggtatgg tgttgccgta aatcacgatg cagacagcca
     3961 catatcacct gcgccggaac ttatggagtt tcatctgaaa acccgtgagg caccgctttt
     4021 tgctgccgtc aacacaccag aaaaacagcc ggatcatctg ttccgctcgc tgggttt
//
