LOCUS       NZ_CP091669             4315 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KOr019 plasmid pKOr019_4, complete sequence.
ACCESSION   NZ_CP091669
VERSION     NZ_CP091669.1
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 4315)
  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  JOURNAL   Unpublished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 4315)
  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
            CP091669.1.
            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..4315
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KOr019"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKOr019_4"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.5 E"
                     /collection_date="2013"
                     /collected_by="Kyoto University"
     gene            join(3477..4315,1..76)
                     /locus_tag="L6L58_RS26210"
                     /old_locus_tag="L6L58_26205"
     CDS             join(3477..4315,1..76)
                     /locus_tag="L6L58_RS26210"
                     /old_locus_tag="L6L58_26205"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243916.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_095516886.1"
                     /translation="MLNKIQLPDEIKKNTVTNGNSISLIKKLPSQYAHLILSDIPYGIG
                     AEDWDVLHNNSNNAYLGSSPAQKNAGAIFKKRGKPINGWSEADKKIPLEYQQWCEKWAT
                     EWFRVLKPGASAIIFAGRRFSHRCICAMEDAGFNLRDIIAWMRVKAPHRAQRLSCVYER
                     RGDTLNAEKWNGWRVGNLQPTFEPILWFSKPYKIGGTIADNAIIHGVGAYNQDAFVARN
                     GKPENVITAGFSSNESGLHPTQKPVALMKTLIELTTQKGQLVIDPFSGSGSTLVAAKDL
                     GRDYIGFEINPTYVETSIKRLNK"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(77..1072)
                     /locus_tag="L6L58_RS26215"
                     /old_locus_tag="L6L58_26210"
     CDS             complement(77..1072)
                     /locus_tag="L6L58_RS26215"
                     /old_locus_tag="L6L58_26210"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000362418.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HindIII family type II restriction endonuclease"
                     /protein_id="WP_024190213.1"
                     /translation="MEWACLYMMPGGMILFVTLEGCWNMDLTNIEFINDAAINRRRYWT
                     NEIVKLSGHFVNDSSRVEEEIIYEVSKSGSQALLDHLRLCTAIPESYEHDSSEEKLYSK
                     YTDALISECFKFFGLNSIVLTERADAADVEVVCDSYSFVADAKVFRLSRTAKNQKDFKV
                     QAMDGWRNTKDFAMVVCPIYQLPVKSSQIYQQAILRNVCVFTYTHLAVLVKYADIVGSD
                     VRILLEEIFRSVILMNPSKDSVQYWTMINRTMLNYDKRIEKLWIDERIATSEGIYVLKK
                     MAIEYLSSERGRILSMSREEAVRALIKMNKIESRIEQIKKVTDNNILSLK"
                     /name="HindIII family type II restriction endonuclease"
     gene            complement(1138..1365)
                     /locus_tag="L6L58_RS26220"
                     /old_locus_tag="L6L58_26215"
     CDS             complement(1138..1365)
                     /locus_tag="L6L58_RS26220"
                     /old_locus_tag="L6L58_26215"
                     /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_015059041.1"
                     /translation="MTKLDATRFSRHEGYEVLDLINSFQAKGGGALTLKSQQIIEWMLH
                     ERLPSNIQGRAQVKAWVVDNFSQMKDGYPF"
                     /name="hypothetical protein"
     gene            2262..2456
                     /locus_tag="L6L58_RS26225"
                     /old_locus_tag="L6L58_26220"
     CDS             2262..2456
                     /locus_tag="L6L58_RS26225"
                     /old_locus_tag="L6L58_26220"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3112..3273
                     /locus_tag="L6L58_RS26230"
                     /old_locus_tag="L6L58_26225"
     CDS             3112..3273
                     /locus_tag="L6L58_RS26230"
                     /old_locus_tag="L6L58_26225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_071779772.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNGFMGVGLE
                     VSCQLRLN"
                     /name="replication initiation protein"
     Typing          complement(1748..2003)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(2128..2226)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2530..2614)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          2625..3184
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.204"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttaggtagg gattatattg gtttcgaaat aaaccctaca tatgtagaga ccagtataaa
       61 gagattaaac aaataattat ttaagtgaca gaatattatt atctgtcact tttttaatct
      121 gctcaattct actttcaatt ttattcattt taatcaaagc tcttacagcc tcttctctgc
      181 tcatgcttag aattctacct ctctcggaag agaggtattc tattgccatc tttttcagca
      241 catagatacc ctctgatgta gcaattcgct catcaatcca aagtttttct attctcttat
      301 cataattcaa catcgttcta ttaatcatag tccagtactg cacactatcc ttacttggat
      361 tcatgagtat gacagatctg aatatttcct ctaacaatat cctaacatca ctaccaacaa
      421 tgtcagcata ctttaccaga acagctaaat gagtataagt aaacacacac acattgcgaa
      481 gaatagcttg ttgatatatt tgacttgatt taactggaag ctgatatatt ggacaaacaa
      541 ccatggcgaa atctttagta ttcctccaac catccattgc ttgaacttta aaatctttct
      601 gatttttagc tgttcgactt aaccgaaaaa ctttagcatc agcaacaaaa gaataactat
      661 cacatacaac ttctacatct gccgcatcag ccctctcagt taacacaatg ctattcaaac
      721 caaaaaactt aaaacattca gaaatcaatg cgtctgtata ctttgaatat aacttttctt
      781 cgcttgaatc atgctcatat gattcaggaa tggctgtgca taatcgaagg tggtccaata
      841 aagcctgaga tccagatttg gaaacttcat aaataatttc ctcctcaacc ctactggagt
      901 cattaacaaa atgcccactt aatttgacaa tttcattagt ccagtaacgc ctcctattta
      961 ttgcggcatc attaataaat tcaatatttg ttaaatccat attccaacaa ccttccagtg
     1021 ttacaaacaa aatcatacca ccaggcatca tatacagaca tgcccactcc ataacaattt
     1081 accataatgc ctcattgagc acagctcatg aaaaagcccg ctgtagcggg ctttttatca
     1141 gaatggataa ccatccttca tttgcgagaa gttatcaacc acccacgctt taacctgagc
     1201 tcgcccctgg atattggatg gcaggcgttc atgtagcatc cactcgataa tctgctgtga
     1261 ttttagcgtc agagcacccc cccctttggc ctggaaggaa ttaatcaaat ctaacacctc
     1321 ataaccctca tgacggctaa agcgcgtggc atctagctta gtcattcgtg gattatctcc
     1381 ttgtacagcc gtccatgagt aatcatggta attcatatca gatctattca tcttttctca
     1441 tcttcgcctg aattatatac gtacattacg acataacatt aataactcaa cagcctcatt
     1501 taccataacg tcgcattacg cgcaccgcta aaacgcgctg aacgcgattc tgccgcgaac
     1561 accgcaaaaa gagatgtttt accaagcgaa aaccggaaaa atgcgtcagg atcgctttca
     1621 gctcactgca tagctatgca tgaaagtgaa tggcgatcgg tttgggcgca tacggtgccc
     1681 atgagacaca ttttcggaca ttttcagttc gtgaatccct gactcattgc tacatatctg
     1741 aacagacacc cctagcagcg cccccagggg cgtcctgtaa aaaaacacac cgcgccgcta
     1801 gcagcacccc taatataaaa tgatgttttt tatgaaaata gtcagtacca cccctaaaaa
     1861 gcggtgttgg cgcagctaca acaccgcgcc gacaccgctt ttttaaatat cacaaagaga
     1921 gcaagaagaa ctaatttgtc ataactctct atttataaag aaaaatcagc aaaaaattgt
     1981 ttttgcgtgg ggtgtgggca tttcaggcat gagaacagac tcgcgttttt ccggagtatc
     2041 agcggaatta ttgattaaga aacactcgac gcagagcgaa attttatgca acagcggctg
     2101 cactgcacag ggattattta tcagttgata tgctgtgcca tgatacgtcc taaagaaaca
     2161 ggacaggatg tgcaattgta ataccgtcgc ccgcaacgtc ttacaattac cacctgctca
     2221 gggtcccccc gacacccgga actgacggag aacaacggaa ggtgaacaaa caacaacaaa
     2281 ctgcgctgaa tatggcgcga tttatcaaaa gccagagcct gacactgctt gaaaaactgg
     2341 atgctctgga tgccgacgaa caggcggcca tgtgcgaacg actgcacgaa ctcgcggaag
     2401 aactccagaa cagcatccag gttcgctttg agactgaaag tgaaacagga acataacgaa
     2461 gctgacggag gcgctcacgg cttgtccgcg agcgttttcg gcagcagaca agcccgccag
     2521 ggcgcgtcag cgggtgtcgg ggcgaagccc tgacccagtc gcgtagcgac agcggagtgt
     2581 atactggctt aaccatgcgg catcagtgca gattgtatga aaagtgcccc atgccgggtg
     2641 tgaaatgccg cacagatgcg taaggagaaa atgcacgtcc aggcgctttt ccgcttcctc
     2701 gctcactgac tcgctacgct cggtcgttcg gctgcggcga gcggtactga ctcacacaaa
     2761 aacggtaaca cagttatcca cagaatcagg ggataaggcc ggaaagaaca tgtgagcaaa
     2821 aaggcaaagc caggacaaaa ggccgcgccg ctggcgtttt tccataggct ccgcccccct
     2881 gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa
     2941 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg
     3001 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca
     3061 cgctgttggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
     3121 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
     3181 gtaagacacg ccttaacgcc actggcagca gccactggta acggttttat gggagttggt
     3241 cttgaagttt cttgccagtt aaggctaaac tgaaagaaca gattttggtg actgcgctcc
     3301 cacaaagcca gttaccgtgg ttcaaaaacc tgcaagttct ttgaaccttg aaaaaaccgc
     3361 cctgcaaggc ggttttttct tttcagaaag gctacgatga aaggtaatcc tgcgtcaagg
     3421 tactttaacg tatactatca gcgtgttttt aaagctatga aagagcagga atttagatgt
     3481 taaacaagat ccaattacct gatgaaataa aaaagaatac cgttaccaat ggtaactcga
     3541 tatcattaat aaaaaaactc ccatcacaat atgcacattt aatactcagt gatatccctt
     3601 atgggatagg agcagaagac tgggatgtgc tacataataa ctcaaataac gcatacctag
     3661 gttcaagccc tgcgcagaaa aacgcaggtg ctatttttaa aaaaagagga aaaccaataa
     3721 atggatggtc agaggctgat aagaaaatac cattagaata tcagcaatgg tgtgaaaaat
     3781 gggctactga atggttcaga gtattaaaac caggtgccag tgcaattatt tttgcaggca
     3841 gaagattttc tcatcgatgc atatgtgcaa tggaagatgc tggattcaat cttcgcgata
     3901 taattgcatg gatgagagta aaagcccctc acagagccca aaggttgagt tgcgtttacg
     3961 aaaggcgcgg ggatacatta aacgcagaaa aatggaatgg atggcgagtt ggaaatctac
     4021 aaccaacctt tgaacccata ctatggttct ctaaaccata taaaattggc ggcacaattg
     4081 cagataatgc aattattcat ggtgtcggtg cttataatca agatgcattt gtagcaagaa
     4141 atggcaaacc tgaaaatgtc attacagctg gattttccag caatgaaagt ggattacacc
     4201 caacacaaaa acctgtagcc ttaatgaaaa cacttataga attaacaaca caaaaaggtc
     4261 aattagtcat tgaccctttt agtggcagtg gttctacatt ggtagcagcg aaaga
//
