LOCUS       NZ_CP091709             4072 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KGu016 plasmid pKGu016_5, complete sequence.
ACCESSION   NZ_CP091709
VERSION     NZ_CP091709.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236402
            Assembly: GCF_022494825.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  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  JOURNAL   Unpublished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 4072)
  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_022494825.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 04:03:20
            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)                     :: 5,248
            CDSs (total)                      :: 5,124
            Genes (coding)                    :: 4,913
            CDSs (with protein)               :: 4,913
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 80 of 211
            Pseudo Genes (incomplete)         :: 151 of 211
            Pseudo Genes (internal stop)      :: 43 of 211
            Pseudo Genes (multiple problems)  :: 54 of 211
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091709.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KGu016"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKGu016_5"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            complement(join(3482..4072,1..111))
                     /locus_tag="L6L59_RS26090"
                     /old_locus_tag="L6L59_26090"
     CDS             complement(join(3482..4072,1..111))
                     /locus_tag="L6L59_RS26090"
                     /old_locus_tag="L6L59_26090"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(644..898)
                     /gene="mobC"
                     /locus_tag="L6L59_RS26095"
                     /old_locus_tag="L6L59_26095"
     CDS             complement(644..898)
                     /gene="mobC"
                     /locus_tag="L6L59_RS26095"
                     /old_locus_tag="L6L59_26095"
                     /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"
     gene            1077..3236
                     /gene="mobQ"
                     /locus_tag="L6L59_RS26100"
                     /old_locus_tag="L6L59_26100"
     CDS             1077..3236
                     /gene="mobQ"
                     /locus_tag="L6L59_RS26100"
                     /old_locus_tag="L6L59_26100"
                     /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"
     Typing          complement(900..1076)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1077..1435
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3483..4072)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.831"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          991..3233
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.866"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cccagacttc aatcgaccga tgcaaagtaa caaaaatcgc tgttcctgta gggtcaattt
       61 ataactggct tcaaccagcg cattggattt ataggcaatt agatccgaca tagagcatcc
      121 ctccccaaaa ggtaatgaat aaaagataaa cataccctca acgaaaggca atgccttttt
      181 attttaatat ccctttttct gtgaatatta ccttaaatca tattgccttt accttaaatt
      241 cccccaccta aacaccttaa atcatattac ctttacctta aatcacatta cctatagcat
      301 tgtaacattt tgttttctat aaggaatttt ggcgctaaaa caagtattaa aaacaagatc
      361 ttaaaaacaa gatctaaaaa cttaacgacg agcctgtgga taacttggag tgctgaaaac
      421 aaaaaaccaa taaaaacaat gcgttgcaaa aaagcagaat tgcaagttcc gaatacaccc
      481 cctccaaccc tgtggaaatc cagtattcat gcgggttcag cgcatatcac ctcccgaaaa
      541 accgtgcgta tgtgctcaat caggcgacgg attcacttcc gcttcctcgc ccactcgctc
      601 gctaacgctc ggtcgctggg actgcggcga gcggacgata caatcactgt cctggcagcg
      661 cttccagctc gttaatcagc ggcagtatgc gcgtcacatc agcctgtcgt gtcacctctg
      721 ccttcaggaa ctggagtaac caggcacgca actgcacctc ctccggcttt ctgacctttg
      781 ccagcaatgc tgcacccaca atgaccttct gcgctgtgtc cagactcctg ctcttcgcct
      841 tcaggcgctg taatctggcc tcagcatcag caatcttctg ttcgagtgtt ctgctcatga
      901 tgtaactccg tgcgcgatga aaaatcgcat tttagcgcgt cactggtagt ttaaaaactg
      961 agctggcata atgcacggaa aatcacgaag tgcgcactta tacaatctcc actccgtttc
     1021 gattgtgtgc gccctgcggg gctgaaagaa aaccacaaaa aggcattacg gcagaaatgg
     1081 cgatttatca tctcagcatg aaaatcatct ccagaaacag cggctacagc gccgttgctt
     1141 ctgctgccta tcgttccggt tcactgatgc ttgatgagcg taccggactg actcacgact
     1201 acacccgcaa aagcggtgtg gctgaagctg tgattctgac tcccgcgaca gcccctgcct
     1261 ggtgtacgaa ccgtgccgaa ctctggaatg ccgttgagaa ggccgaacgc cggaagaact
     1321 cacaacttgc gcgggaaatt gaactcgcca tcccccgcga actaccgcag gatgccgcac
     1381 gggaaaccgt tctcgccttt gtcagagaaa actttgtcag tcagggcatg attgctgatg
     1441 tggcgttcca tcacatggat aaaacaaatc cccatgcgca catcatgctg accacgagag
     1501 ctgtcggacc tgctggattc ggtggaaagg tcagggactg gaacgaccgg acacatgccg
     1561 agacgtggcg tgcatcatgg gctgaccatg cgaacagggc actggcgaac gccggttatc
     1621 aggaagagat agaccatcgt tcatacgagc gacaggggct tgagaaaacg cctggtattc
     1681 acctcggaaa gtctgcctgt gcgatggaaa cacgcggtat cgaaacagaa cgcggcgaac
     1741 agaatcgtct gattaacaga cttaacctgg aaatacagat ttcccgtacc gaactcagaa
     1801 acagcgggct gacagagcct gcccgccgtg tggctgacct tctgaatatc gtgcttcctg
     1861 acaacgcaac ttcgtacaca ctacgtgaca tcatcgaagc gttgccgaag gacagtaatg
     1921 cggcatggaa actcaccagt aatgccatgt cgatgatggc agatatgcag gcgacgcgca
     1981 gacgctggga agagctgaac accgaacgaa aggaagcgat gagccatgct gccagcctga
     2041 aaaaatcatc gccgttttcg tccggttttt cccgtattcc cctgatgcaa tgggcggcac
     2101 cggaataccg tagcgaacag ggaaaaatcc agtcgctgag ccagcaaatg gaaaaattgc
     2161 gacagcatta ccggaaggtg gagaaacagg acattcccgc gagtcagacg gcatttgaaa
     2221 aacagtggca gcagtggggg gcatccggcc ttgcagctct cagagtccag ttgcttaaac
     2281 gtgaagagga attgcgccgg aaggagcagg aggatacaga acgtagtcgc gcggagcgac
     2341 gagcggaaca gctcaggaaa aatgacaatg ccgttatgga ttcaggggta ctgagcgcag
     2401 tcgttacggg gtatggcgag gcccccatgc ctggtaacgg ggaaatgacc tgttaccttc
     2461 tgcttcacaa ccggaacgga gaatacacgc tctgggggaa cgagctggag aaataccgca
     2521 ccagaatctt tgagcgtgtt gatttaatgc gtgacaggag tggttatatc tgtgaccgaa
     2581 gcgaaatcgg tcaacatcca ccactgcaac gtgtttattc ctctgcgacc tttgagcaac
     2641 ttctgacgca ggtttgccag acatggccgc aatatacccg caatctccgc cagccgaaga
     2701 catggccgga gtctttctgt cttggagaag accgccagcc agccatgcca tcactggcag
     2761 caaggaaggt ggattttacg cagggacgtc tgctaccgac gctgatgccg gtaatgagtt
     2821 ctgtcgaccg ggaaacccgc cagcttcagc ttttgctggt catgggcgtg gatgactctc
     2881 tgggcggtgt tgtccggctt aatggtacgc tgtatcccgc gtttgccgtt ccctcagccg
     2941 ataacagcca gctggtcatc agtgcactga ccgataaggg gttacggtat gcagggtatg
     3001 gtgttgccgt aaatcacgat gcagacagcc acatatcacc tgcgccggaa cttatggagt
     3061 ttcatctgaa aacccgtgag gcaccgcttt ttgctgccgt caacacacca gaaaaacagc
     3121 cggatcatct gttccgctcg ctgggtttta atcgtacctg ggacgaatgg cggcgcgagg
     3181 aagatgcacg aacacacgcc accgagagga gacatgatcg cggttggtca cagtgaatgt
     3241 gaacaatatt ttgttttgtt taacatcgtg ttatgttctt cgatgttcat cgacagggat
     3301 gaatgcaaga agcacacaca taatgcaagc atagttttgt ttttccgccc ccaaaaaatg
     3361 ggggttcttt tttcgctgca ttagagtgct tttgacgcaa tttttcactt caatagtacc
     3421 ttcgcactac taacacaaaa aaaacgcagc agggagcgtt ttaggtgcct taaaatcgat
     3481 tttagatcgt catcttgatt tgtttgtctt ccttgaagcg aaaatgcagg gctacaaccg
     3541 tgcgcccctt tttgatcgtc tcaaccgtta cagccaggtc gctttttttg ttcagttcgt
     3601 caatgcaggg tcttaataat tgctggttaa gtgatttata tgtttgatat ttatgctcta
     3661 tatcaagcat tgagcgaaag tcatcgagag cgataatacg ttcgccagta ctgcggaact
     3721 gctggaggag ttcgtatatc cttatactgt aacttcttga taatctagat atattcttga
     3781 ttacaactct agtaaattgc ccttgtagtt gtgtcaaata aggcattact gcgtcagaaa
     3841 atgttatttg tgctctggcc tcgcctttag cgtactgtgc ccgatactgg atccagcgga
     3901 actcctcacg tttctcgtca tccttgagaa tgattgacct gtcccacaaa cgatcaattg
     3961 cttcctgtaa ctgaacctcg gcatttttcc gccccatgtc agggaatgaa tcgaaatatt
     4021 ccgcagctgt aatggtcatt gtcttttgca attttggaga ttctgcatca gc
//
