LOCUS       NZ_CP091668             4677 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KOr019 plasmid pKOr019_3, complete sequence.
ACCESSION   NZ_CP091668
VERSION     NZ_CP091668.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236411
            Assembly: GCF_022494685.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4677)
  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  JOURNAL   Unpublished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 4677)
  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_022494685.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:36:36
            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)                     :: 5,259
            CDSs (total)                      :: 5,146
            Genes (coding)                    :: 4,949
            CDSs (with protein)               :: 4,949
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 197
            CDSs (without protein)            :: 197
            Pseudo Genes (ambiguous residues) :: 0 of 197
            Pseudo Genes (frameshifted)       :: 87 of 197
            Pseudo Genes (incomplete)         :: 137 of 197
            Pseudo Genes (internal stop)      :: 42 of 197
            Pseudo Genes (multiple problems)  :: 56 of 197
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091668.1.
            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..4677
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KOr019"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKOr019_3"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.5 E"
                     /collection_date="2013"
                     /collected_by="Kyoto University"
     gene            complement(join(3661..4677,1..282))
                     /locus_tag="L6L58_RS26190"
                     /old_locus_tag="L6L58_26185"
     CDS             complement(join(3661..4677,1..282))
                     /locus_tag="L6L58_RS26190"
                     /old_locus_tag="L6L58_26185"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_166732602.1"
                     /translation="MMINFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESGITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFISGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            2040..2234
                     /locus_tag="L6L58_RS26195"
                     /old_locus_tag="L6L58_26190"
     CDS             2040..2234
                     /locus_tag="L6L58_RS26195"
                     /old_locus_tag="L6L58_26190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2871..2984
                     /locus_tag="L6L58_RS26200"
                     /old_locus_tag="L6L58_26195"
     CDS             2871..2984
                     /locus_tag="L6L58_RS26200"
                     /old_locus_tag="L6L58_26195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072101919.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(3219..3656)
                     /locus_tag="L6L58_RS26205"
                     /old_locus_tag="L6L58_26200"
     CDS             complement(3219..3656)
                     /locus_tag="L6L58_RS26205"
                     /old_locus_tag="L6L58_26200"
                     /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_052918195.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     Typing          complement(1526..1794)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.668"
                     /coverage="93.0"
                     /evalue="3.5e-92"
     Typing          complement(1906..2004)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2308..2392)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          2403..2940
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.993"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctcatcaagt aaaaaaggga ctacattctt cgtaatgcca ctttcgatag cttgcacaga
       61 atgcaggaca atatctttca ttaaagatat tgtcttcatg agattagatt ttccgctagc
      121 gttagctccg aaaatcaaag cagacttcag tatccgctca tcccttactg acactacatt
      181 agccaagttt atatcgtctt tcgatgacga caccgccaac atgctcatat tttgagcttc
      241 catgaaggaa aatgcgtttg aaagactaaa gttaatcatc ataagaacac ccctaacaac
      301 acccttaaac tcaaaaattg cacaatattg acaaaattct agattaagaa tagcataacc
      361 ccgtactaaa acaacaaaag ggtccaatag acagcacatt atgagtagat aagttaacga
      421 ccagcttaaa aagaggtgta tatgaagttt tttctatacc aaatggtccc atttgcctca
      481 gtgattagct cagcagtgct ggcttttcac tcggtatctg ggtggggatg gttccttttt
      541 gtcgcgttta tgctcagtgg cgctgacact gtaaaaaaat acgtagggag tgaaacatga
      601 atgaggagaa gcaaaaattg ttgaagtaag tgggttagcc tgtaccacca gaactaaccc
      661 gtaacaaacc atacgcaaat gcggcgcttg agtaccacct caagtgcttt gataaagcca
      721 gccacaagat ctgttggttg ctacagtaca attttgatag caaaaatcaa cattcatgtg
      781 gcgaaaatag gaaatgcaac atgcagacgg acgagcctca ggcatacatt tttcgccctt
      841 acataacggt aaagggcaaa cggataaccc gtcctaacgg gggaatgttt aagatcccaa
      901 ttaatcggga aaagaaaaaa caataaccac cgaagcatgc aagcttcggt ccctaactta
      961 gtttatgtaa ggaaagcaac atggcctttt atgtagatag cacagcgaaa tttttaacaa
     1021 aaacaaccga gcctgaaggg agtgtatggc ggtattacta taagccggga aatacttgtc
     1081 cggcttccgg catttaccgc tgcacgaact gtggtgatga agtgacgtgc aataaagatg
     1141 atcctttgcc accgcaaaat cataggcagc ataatgtccc aggtgacatc cgatgggaat
     1201 tggtagtgat gacaaagacg aagtaactta ctaggccgtc tacggacggc ttttttatac
     1261 ctgccaatca gctggattta ccataacatc cgattgcgcg caccgctaaa acgcgctgaa
     1321 cgcgattctg ccgcaaacac cgcaaaaaga gatgttttcc ccggggtaaa ccggaaaaat
     1381 gcgtcaggct cgctttcagc tcactgcata gctatgcatg aaagtgaatg acgatcggtt
     1441 tgggcgcata cagtgcccat gagacacatt ttcggacatt ttcagttcgt gaatccctga
     1501 ctcattgcta catatctgaa cagacacccc tggcagcgcc cccaggggcg tcctgtaaaa
     1561 aaacacaccg cgcagctagc agcaccccta atataagatg atgtttttta tgaaaatagt
     1621 cagtaccacc cctaaaaagc ggtgtcggcg cggtgttgta gctgcgccaa caccgctttt
     1681 ttaaatatca caaagagagc aagaagaact aatttgtcat aactctctat ttataaagaa
     1741 aaatcagtaa aaaattgttt ttgcgtgggg tgtgggcatt tcgggcatga gaacagactc
     1801 gcgtttttcc ggagtatcag cggaattatt gattaagaaa cactcgacgc agagcgaaat
     1861 tttatgcaac agcggctgca ctgcacaggg attatttatc agttgatatg ctgtgccatg
     1921 atacgtccta aagaaacagg acaggatgtg caattgtaat accgtcgccc gcaacgtctt
     1981 acaattacca cctgctcagg gtccccccga cacccggaac tgacggagaa caacggaagg
     2041 tgaacaaaca acaacaaact gcgctgaata tggcgcgatt tatcaaaagc cagagcctga
     2101 cactgcttga aaaactggat gctctggatg ccgacgaaca ggcggccatg tgcgaacgac
     2161 tgcacgaact cgcagaagaa ctccagaaca gcatccagat tcgctttgag gccgaaagtg
     2221 aaacaggaac ataacgaagc tgacggaggc ggtcacggct ttcccgtggg cgttttcgtc
     2281 agcagacaag cccgtcaggg cgcgtcaggg ggtttcgggg cgaagccctg aaccagtcac
     2341 gtagcgatag cggagtgtat actggcttaa ccatgcggca tcagtgcgga ttgtatgaaa
     2401 agtacgccat gccgggtgtg aaatgccgca cagatgcgta aggagaaaat gcatgtccag
     2461 gcgcttttcc gcttcctcgc tcactgactc gctacgctcg gtcgttcgac tgcggcgagc
     2521 ggtactgact cacacaaaaa cggtaacaca gttatccaca gaatcagggg ataaggccgg
     2581 aaagaacatg tgagcaaaag accaggaaca ggaggaaggc cgcgccgctg gcgtttttcc
     2641 ataggctccg cccccctgac gagcatcaca aaaaccgacg ctcaagtcag aggtggcgaa
     2701 acccgacagg acttaaagat accaggcgtt tccccctggt gactccctcg tgcgctctcc
     2761 tgttcctgcc attcggttta ccggtgtcac tccgctgtta tggccgcgtt tgtctcattc
     2821 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
     2881 cccccgttca gtccgaccgc tgcgcctttt ccggtaacta tcaacttgag tccaacccgg
     2941 aaagacacga caaaacgcca atggcagcag ccactggtaa ctgatttaga ggagttagtc
     3001 ttgaagttat gcgcctgtta aggctaaact gaaagaacag atttggttac tgcgctcctc
     3061 ataagccagt taccttggtt cacagagcgc caactcttag aaccgtcgaa aaaccgcccg
     3121 ccaaggcggt tttttcgttt acagagcaag agattacgac gagagcatca caatctcaag
     3181 aagatctttt cttaacatac aatacaactg tatctcatct atttttgact cttccagaag
     3241 cgatgatctc tatcaaaaaa cacgatatag aacacattat ctctcagaaa tccggcgact
     3301 cttcttttct gcccgccaat gttttttata accccccaat cctcatcaga ggatatctca
     3361 tctgggcatc taaaatcgtt tacagctgac tcaggaaatc gagtgtagtt agtaaacaca
     3421 ccgtcagaaa tcactttagt gattccattc gccgttagat aaaccaattt ttcaatgaga
     3481 tcaggtaggc taccatcatc tttccatgta tttatggact gcccaacatc atcgacgtta
     3541 tgaaaatgct taaaactaat agatataaat ctatcagtcg ttttcgctgt gctctttgaa
     3601 ggttttgttt cctcattcct cgaagagctt cgaatgcttt tgcctctctt tggcatataa
     3661 tcatccctca ggcattagct tttcaaattc attaagatta tcaaataacg ggattgcatc
     3721 aaaagcacct gataaataat cattcccata tgatggcttc aatgatcttt gtttctcttt
     3781 gtactcaacc aaagaataaa gatggctact ccctgacttt acatccttgt caacaaacca
     3841 aatttggtct cgtctaaagc aatcagtatt cattaaatta acatcctgaa ctgcagcgat
     3901 tacttggcta aacccttcac tttgcgcatg aaatatccta aataaaaact tagataaaag
     3961 ggtatggaac tttgaatcga actcatcaac caataataag ttattgttaa tcatggcgtt
     4021 ataaataggc ccaaggagat agactatctt tttggtcccc tctgattcaa aatcaatggg
     4081 aaccgaaatc tccccattag cagttttttt cacgactcta agagaaaata ctttttgatt
     4141 ttttgcaaaa ttctgaatcg agctgaataa attttttaaa ttatcatcat ctgtttttat
     4201 gttgccaaac gggaattcag gcgcaacttc atcaagataa atatcattaa tctgaaaggc
     4261 tggtaatatt ttttttagcc aagctttaaa atcttcagat tcatttataa gcttcatggt
     4321 aattccagta aacattcctt cgttagaacc agaaataaat accacattac taaaccaatt
     4381 cacaacacgc tttgagtgct ccccattaaa tccagcaaca acagaaacaa agggaacatc
     4441 ttctcttgtc ttctgaatga ccccatcctt tataaaaaga tttgactcgc taaatgctgc
     4501 tttatttatt tcaataagtt gaccatctcg ctcaaagaga atagtctccc ttgtttttgg
     4561 cgtgtagtac aaccactctt cttttatctt cccttgaaat aaagataatc cgtatctgta
     4621 tttaatccca tccgcaataa aagtcatttc catttcagat ggtttagtag gccccgc
//
