LOCUS       NZ_CP091710             3009 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KGu016 plasmid pKGu016_6, complete sequence.
ACCESSION   NZ_CP091710
VERSION     NZ_CP091710.1
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 3009)
  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  JOURNAL   Unpublished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 3009)
  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
            CP091710.1.
            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..3009
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KGu016"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKGu016_6"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.8 E"
                     /collection_date="2011"
                     /collected_by="Kyoto University"
     gene            275..469
                     /locus_tag="L6L59_RS26105"
                     /old_locus_tag="L6L59_26105"
     CDS             275..469
                     /locus_tag="L6L59_RS26105"
                     /old_locus_tag="L6L59_26105"
                     /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_001041619.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            940..1086
                     /locus_tag="L6L59_RS26110"
                     /old_locus_tag="L6L59_26110"
     CDS             940..1086
                     /locus_tag="L6L59_RS26110"
                     /old_locus_tag="L6L59_26110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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_077251022.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKAPLAAAIGKRVYKILLT
                     QSS"
                     /name="replication initiation protein"
     gene            1432..1740
                     /locus_tag="L6L59_RS26115"
                     /old_locus_tag="L6L59_26115"
     CDS             1432..1740
                     /locus_tag="L6L59_RS26115"
                     /old_locus_tag="L6L59_26115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017134632.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_072842281.1"
                     /translation="MKNSFELISTDPVKFNTWSIKSKLIIIIRKLMIDNNWSQSEAAEK
                     LGISQPRVSNMLNGKLDKFSIDTLLEMVFKMGYKLDMDFNPLKTESPLTMVVKKAMV"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(1757..2089)
                     /locus_tag="L6L59_RS26120"
                     /old_locus_tag="L6L59_26120"
     CDS             complement(1757..2089)
                     /locus_tag="L6L59_RS26120"
                     /old_locus_tag="L6L59_26120"
                     /inference="COORDINATES: protein motif:HMM:NF017757.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_072842283.1"
                     /translation="MSNDDTEYTFKPVNAQALKALRSLPEWVQVAFVHALDSVFYGVDP
                     GMPIVHLTSIGPGVVELKINGRPAYRCVYRSKAPGQVDLLHAFVKTCQGPDKKNMATAT
                     SRYKLL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(2676..2999)
                     /gene="mobA"
                     /locus_tag="L6L59_RS26125"
                     /old_locus_tag="L6L59_26125"
     CDS             complement(2676..2999)
                     /gene="mobA"
                     /locus_tag="L6L59_RS26125"
                     /old_locus_tag="L6L59_26125"
                     /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"
     Typing          complement(2..240)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="99.0"
                     /evalue="2.77e-117"
     Typing          505..1009
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.742"
                     /coverage="95.0"
                     /evalue="4.94e-158"
     Typing          complement(2680..2999)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.98e-62"
ORIGIN
        1 tccgtatctg acatggggtg tcggggcgaa gccctgacca gggtaattgt aatagcgtgc
       61 atgtatgcgc ggtataacaa ttgcacatcc tgtcctgtca gcaagttcga attaccgaca
      121 aaggcacggc agttttttgg cagtgacagt attgtcaggc agaaatgccc gtcaaagagt
      181 cagacggcag aataccggcg gtaaaacagt cgaaaagtgg tacgcgatat aatcacacaa
      241 cgcagatgac agacagaacg gagaaaacga aaagatgaac aagcagcagc aagccgtact
      301 caacatggcc ggattcataa aaagccagag cctgacgctg ctcgaaaaac tggacgcact
      361 cgatgctgac gaacaggccg ccatgtgtga gaagctgcac gaactcgcgg aagaacttca
      421 gaacagcata cagacacgct ttgaagcgga aaatcgcacc gggatataac gcatccggac
      481 aggatgcaga acggcataga ggagcgtaag gagaaaatgt cacataaggc gctcttccgc
      541 ttcctcgctc actgactcgc tacgctcggt cgttcgactg cggcgagcgg tgtcagctca
      601 ctcaaaagcg gtaatacggt tatccacaga atcaggggat aaagccggaa agaacatgtg
      661 agcaaacagc aaagcaccgg aagaagccag cgccgcaggc gtttttccat aggctccgcc
      721 cccctgacga gcatcacaaa aaccgacgct caagtcagag gtggcgaaac ccgacaggac
      781 tataaagata ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttcctgcct
      841 ttcggtttac caatgtcatt ccgctgttat ggccgcgttt gtctcattcc acgcctgaca
      901 ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag
      961 tccgaccgct gcgccttgtc cggtaactat caacttgagt ccaacccgga aagacacgac
     1021 aaagcgccac tggcagcagc cattgggaag agggtgtaca agatattact gacgcagagt
     1081 tcttgaagtc agagccaaac tacagctaaa ctaaaaagac agaatttggt ttcagcggtc
     1141 ttgtacaccc tgttaccatg gttcagaagt tccccaactc actgaaccct caaaaaaacc
     1201 gcctccccag gcggtttttt tgtttcttga acaagactac tctttgctta agagtcacgt
     1261 caataccatc attgttactt gcaagatcaa atgcaattca catctttttc tcttgaaaga
     1321 gatatcatta cttgtataat gccccgccca tatatatata tatatatata aggagttcct
     1381 tgtcggaact tttatcatcg aggtacaggt aatccaacat ggagctgttc tatgaaaaat
     1441 tcatttgagc tgataagtac cgacccggtg aaattcaaca catggtcgat aaaatcaaaa
     1501 ctcataataa taatcagaaa gttaatgatc gataacaatt ggtctcaatc tgaagcagct
     1561 gaaaagttag gtatcagtca gccccgagta agtaacatgc tgaacgggaa gctagacaaa
     1621 ttctccatcg acacattgtt agaaatggtg ttcaagatgg gttacaagct agatatggat
     1681 ttcaacccat taaaaacaga atcaccactc acaatggttg taaaaaaggc gatggtgtaa
     1741 gcatcgcctt tatggattac aacaacttgt agcgtgatgt tgcggttgcc atattcttct
     1801 tatcgggtcc ttgacacgtt ttcacgaacg catgcagcaa gtccacttga cctggagctt
     1861 tgctgcgata aacgcaacga taagcagggc gaccattgat tttcaactca acaacaccgg
     1921 gtccgatgga cgtcaagtgc acgatgggca tccccggatc cactccgtag aaaactgaat
     1981 ccaatgcgtg cacgaatgca acctgaaccc actcagggag tgatctcaat gcctttaaag
     2041 cctgggcatt aacaggtttg aacgtatatt cagtgtcgtc gtttgacata gcaatcctct
     2101 cttaggttat tgatgtttaa caaattaact accgtattga tatttcgcat aaatactccg
     2161 attaattgat ctgtgagcat aaaaaaacca caccgcccta ttttttaggt cagtgcgcgt
     2221 atggtcatta gctcgtagaa ccaataatta ttggcaatct cgccaacact gacacagtat
     2281 acaaatactt atatgcaatc aagttttatc aaaggtatac aaaactaacc gctcaaaaaa
     2341 aaagcggttt accttaagtc atgacactaa agagggttat ttaggcaaac agaactgtag
     2401 ccagagaagc ccgattgcta gataaaaacc aatgaagaaa cctcgccaat gatagattta
     2461 ccataatccc ttaattgtac gcaccgcaga aacgcgctga acgggattct gccgcagaca
     2521 ccgcaaaaag agatgtgtta ccaagcgaaa accggaaaaa tgcgtcagga tcgttttcag
     2581 ctcgctgcat agctatgcat gaaagcgaat ggtgatcact ttgggagctt acggtgttca
     2641 taccgtctgt tttcgacagt tttctctccg ggaagctaat ctgccataag cctggataac
     2701 agggcacggt gatactccgt aatagcgatc agcacctccg catactccct gtccccgaca
     2761 cgcttgccgt cgataaagag ttttttctgt aacgccccca gtctcataac ttctttcagt
     2821 acccgatcat cagtcagtga gttaactttc ttaccgagag ctgccgcccg taaaaaaccg
     2881 gaaacggtct tgccgcattc agcagccctt tttctgattt cctggtcttc ttctgccgtc
     2941 agacgaacag ggcgactgat agcccgcctg cgcgtattac ttccacttcg ttttgtcata
     3001 aaacatggc
//
