LOCUS       NZ_CP091680             5658 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KFu022 plasmid pKFu022_3, complete sequence.
ACCESSION   NZ_CP091680
VERSION     NZ_CP091680.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25236399
            Assembly: GCF_022494725.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5658)
  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  JOURNAL   Unpublished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 5658)
  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_022494725.1-RS_2024_05_20
            Annotation Date                   :: 05/20/2024 03:51:24
            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)                     :: 4,839
            CDSs (total)                      :: 4,718
            Genes (coding)                    :: 4,476
            CDSs (with protein)               :: 4,476
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 58 of 242
            Pseudo Genes (incomplete)         :: 177 of 242
            Pseudo Genes (internal stop)      :: 41 of 242
            Pseudo Genes (multiple problems)  :: 32 of 242
            Pseudo Genes (short protein)      :: 1 of 242
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091680.1.
            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..5658
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFu022"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKFu022_3"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2012"
                     /collected_by="Kyoto University"
     gene            complement(join(5401..5658,1..36))
                     /locus_tag="L6L66_RS24015"
                     /old_locus_tag="L6L66_24015"
     CDS             complement(join(5401..5658,1..36))
                     /locus_tag="L6L66_RS24015"
                     /old_locus_tag="L6L66_24015"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_240532970.1"
                     /translation="MAYKNKNGQPRERAMVAAYSLVTQFGGKQQDVAKVLGCSPSTIHQ
                     WVKEIGYKKEIAGLKQELSDANEYIEELADNLGLEYHPDEPEENDYDDEDDR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1032..1418)
                     /locus_tag="L6L66_RS24020"
                     /old_locus_tag="L6L66_24020"
     CDS             complement(1032..1418)
                     /locus_tag="L6L66_RS24020"
                     /old_locus_tag="L6L66_24020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016162088.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_032328203.1"
                     /translation="MAKISISEAARLTGKSRTTLHRLIKTGELSTCHGARNARMVDISE
                     LIRVFGPLEHRPSEQFAAQVSEHSDTGVSAQTEQVIAQLRQEVEHLKTLVSAKDSHIDS
                     LKQAMLLIEHKHTGDSSWWKFWKR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1418..1609)
                     /locus_tag="L6L66_RS24025"
                     /old_locus_tag="L6L66_24025"
     CDS             complement(1418..1609)
                     /locus_tag="L6L66_RS24025"
                     /old_locus_tag="L6L66_24025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_001737777.1"
                     /translation="MTKQEKTALNMAKFIQGQSLLLLDKLNELNLDIEADMCEKLHEDA
                     EMLCRTLYGRLNALQDVG"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2033..2194
                     /locus_tag="L6L66_RS24290"
     CDS             2033..2194
                     /locus_tag="L6L66_RS24290"
                     /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_071996610.1"
                     /translation="MHEPPVQSDCCASSGNYQLESNPERHDKAPLAAATGNCSRGVGLE
                     VMRRLRLN"
                     /name="replication initiation protein"
     gene            2529..4034
                     /locus_tag="L6L66_RS24030"
                     /old_locus_tag="L6L66_24030"
     CDS             2529..4034
                     /locus_tag="L6L66_RS24030"
                     /old_locus_tag="L6L66_24030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001577354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_176321127.1"
                     /translation="MSKLDLEKILAANGPCLSSELADILVEQFGLTPAAARKRISRGSQ
                     NLKKLSYIIFPHRARFVYLKNDYASTKYWKALYSSLKKENSSYYMAIDSIRTRGGMIRK
                     DEFGIICGSPVRQKNHIPYESLMLSLMKAEILLETSNENGGNYLYLKECEGHEHLLIES
                     QNKKELINGIMIEQARTWLKQLGLVSYGKTKAMGDETKNPMVGTFEWHITGPSYIHPLT
                     KNSINEKKPGFIVCDLNTTPSATLDDIDTFIRKMDMTLSLKNIGDCFFVYISNAYTEKA
                     LYKAKSKGVLAITFSNIFGKRNTVAAERLGDILNNRDINQIQASEIIKLTKELNERNGI
                     TQNLKGKLFEFICADMKKKIDISSRILIGREYITSQGDKAEADITSIRDDISICFIECK
                     AIKRESTLDDEQVDRWLDVRIPRLLNYCKSHTDYKHLKKTFELWVTGNLSENSNHRIND
                     FISKNPKIKITIKKPRELLKDVKDINDRALKNLLFNYFLKREK"
                     /name="hypothetical protein"
     gene            complement(4112..4456)
                     /locus_tag="L6L66_RS24035"
                     /old_locus_tag="L6L66_24035"
     CDS             complement(4112..4456)
                     /locus_tag="L6L66_RS24035"
                     /old_locus_tag="L6L66_24035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014542127.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024167139.1"
                     /translation="MANSFNVTIAEAALWSLQDAESFKSNYTDSVQAASWADDLLASSV
                     KAISQDPARYRYNAMLADKGISIRERLDPDNQYRCLYDFDEQNGVIEILLFVSTKQDLE
                     KMLYRYLVVK"
                     /name="hypothetical protein"
     gene            complement(4471..4740)
                     /locus_tag="L6L66_RS24040"
                     /old_locus_tag="L6L66_24040"
     CDS             complement(4471..4740)
                     /locus_tag="L6L66_RS24040"
                     /old_locus_tag="L6L66_24040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822261.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024167138.1"
                     /translation="MSITMSQKSAREGLGNPELFQGGVYVTKNGLAELFVQTAEEREAE
                     LRERERERQSNALLKLVMAAKREIKNGRGMSPEDAMRRLREART"
                     /name="hypothetical protein"
     Typing          complement(448..529)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.235"
                     /coverage="92.0"
                     /evalue="2.54e-18"
     Typing          1787..2145
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.028"
                     /coverage="84.0"
                     /evalue="2.95e-159"
ORIGIN
        1 ctctcttggt tgaccatttt tgtttttgta agccatgcca gcctctttta aaatttaaaa
       61 ttcgaatttt aaattttaaa agaggctgat gataagcaca agtaagcgac acaataaaaa
      121 aaccgcattt accataacgc cgcattacgc gcaccgctca gacggcctca gcgcgtttct
      181 gacggcagaa cggtaaaaca ggcaacaaac cacccggaaa accgccagaa acgcagggga
      241 tgaattctgg cacagtgaat gcctatgcag ccaggtgaat ggctctgatt tcggctccgg
      301 atatacccca taacccttct ttttcacact ttccgggcct gctggcgtgc atttctggca
      361 ggtgattttg cgcatgcgca aaatcacgct gagaaaaagg tagtggtgaa cgggcgcgca
      421 atttattgcg tgaccgtgaa gcgcttgcag ggtgtcgggg cggcgagccc tgacaggagc
      481 atttgccatg ccgcgagtgc gcggtattac aaatgcacat cctgtcccgt ggcgctgaca
      541 ccctcaaaaa aactgaagcc atgaaaagac cctgaaaatg ccggcaagcc acagtgccgg
      601 atccggcacc acactggata taaatcagtc acacaatccg gccacctgga taaatatcat
      661 gtgggcggat ccggcactgc tcgcggatat acaggtgtgt ggatccggca ccagtgccgg
      721 attgtgtgac atgtaaggca ctgaaaaata gcgatagcca caatccggcg atatgacagt
      781 gccggtaccg acacctggag gtgtgctaaa tgtgtgatac ttttcggggt aaatgtaaat
      841 cgactgaaat atttatactt atcattttga tataaaaaga taaatctgca aggcgaagtc
      901 ttgcgtgggg tgtgatgttt tgtccctatc cacacagagc ggctatcgcg ctgtgtggat
      961 agtccgaaaa aacaggtttg tgctaagtca ttcagtaaat cagacaagcc ccgccggcaa
     1021 ctgaggcgtt ctcagcgttt ccagaacttc caccaggatg aatccccggt atgcttgtgc
     1081 tcaatcaaca gcatcgcttg tttgaggctg tcgatgtgtg aatccttggc tgaaactaat
     1141 gttttcaggt gttccacttc ctgccgcagc tgcgcaatga cctgttcagt ctgcgcggaa
     1201 acacctgtgt cagagtgttc agagacctgt gcagcgaact gttcagacgg acgatgctcc
     1261 agagggccaa aaacacggat aagctccgaa atatctacca ttctggcgtt ccttgcacca
     1321 tgacaggtgg acagttcacc tgttttaatc aacctgtgca gcgttgtccg actcttccca
     1381 gtcagccgag cggcctcact gatcgatatc ttggccatta acccacatcc tgtagagcat
     1441 ttaaccgccc atataaagtc ctgcagagca tctctgcatc ctcatgaagt ttttcacaca
     1501 tgtccgcctc aatgtcgaga ttgagctcat tcagcttatc cagcaacaaa agggactgcc
     1561 cctggatgaa cttcgccata ttcagcgcgg ttttctcttg tttagtcatg aacaggcctc
     1621 agtacgtacg tgcttaatgt taagacaggc tccattctgc ttcctcgccc gttcgctcgc
     1681 aatgctcggt cacgggtctg cggcgagcag tacagactga caaagttagc cacagattca
     1741 ggaggtaacc tactaggaaa gatgtgagga aaaagggtaa ggtaacggcg ttgccgtttt
     1801 tccataggct tcgcccccct gacaagcatc acgaaatctg acgctcaaat cagtggtggc
     1861 gaaacccgac aggacttaaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc
     1921 tcctgttcct gcctttcggt ttgccggtgt cattccgcag ttatggccgc ggtttctcat
     1981 tccacgcctg acactcagtt ccgggaaggc agttcgctcc aagctggact gtatgcacga
     2041 accccccgtt cagtccgact gctgcgcctc ttccggtaac tatcaacttg agtccaaccc
     2101 ggaaagacac gacaaagcgc cactggcagc agccactggt aactgttcta gaggagttgg
     2161 tcttgaagtt atgcgccggt taaggctaaa ctgaaagaac aagttttggt gactgtgctc
     2221 ctccaagcca gttacctcgg ttcaaaacct gcaagttctt gaaccgttga aaaaaccgcc
     2281 ctgcaaggcg gttttttcgt atctgaggct aggttaatct catacctcaa ttcacgtcaa
     2341 gaaaacaaac ccacctcaac cacctcattt tcatcaacaa ttgatgtatt gtgacgtttt
     2401 tagggtttag acaaaaacag cctcccataa agccagccac agagcgactt tgcgagagag
     2461 ttttttcgct gctcatagcc agcacgatag tgctgattat aaatagcgta gtgtgacaag
     2521 gataaaaaat gagcaaacta gatctagaaa aaatcttggc cgctaatggg ccatgtttaa
     2581 gctcagagct ggctgacatt ttggttgagc aatttggtct tacgcctgct gctgctagaa
     2641 aaagaatatc cagaggttca caaaatttaa aaaagctttc atacataatt ttcccgcaca
     2701 gagccagatt cgtttatttg aaaaatgact acgcttcaac taaatattgg aaagccctat
     2761 actcatcatt aaaaaaagaa aactcctcat actatatggc gatagattcc attagaacaa
     2821 gaggaggaat gatcaggaaa gacgagtttg gaataatctg tggttctcca gtaaggcaaa
     2881 aaaaccacat tccttatgaa tcgttaatgt tatcattaat gaaagcggaa atacttttag
     2941 aaacatctaa tgaaaatggt ggtaattatt tataccttaa agagtgcgag ggtcatgaac
     3001 acctgttaat agaaagccaa aacaaaaaag aactcattaa cgggataatg attgagcaag
     3061 ctagaacatg gctaaaacaa ttaggcttag tgagttatgg gaaaacaaaa gccatgggtg
     3121 atgaaacaaa aaacccaatg gttggaactt tcgaatggca tataacaggc ccctcataca
     3181 ttcatccatt gactaaaaac agcatcaatg aaaaaaaacc agggtttatt gtctgtgatt
     3241 taaacacaac accatcagcc acattggatg atatcgacac attcataaga aagatggata
     3301 tgacattatc attaaaaaat ataggtgatt gtttttttgt ttacatatca aatgcataca
     3361 ccgaaaaagc attatacaaa gctaaatcaa aaggcgtgct ggctataact ttcagcaata
     3421 tatttggaaa aagaaacaca gtcgctgcgg aaaggttagg agatatatta aataatagag
     3481 atattaacca aatacaggcg tcagaaataa taaagcttac aaaggaatta aatgagagga
     3541 atgggataac tcaaaattta aaaggaaaac tttttgagtt tatctgtgcg gacatgaaga
     3601 aaaaaattga catctcctca aggatactga taggcagaga atatattaca agccaaggag
     3661 ataaagccga ggctgatatc acgtctatca gagatgacat ttctatatgt ttcatagaat
     3721 gtaaggcaat aaaaagagaa agtactcttg atgacgaaca ggttgataga tggcttgatg
     3781 tcaggatccc aagacttttg aactattgca agtcacacac ggattacaaa cacttaaaaa
     3841 aaacattcga gctttgggta actggtaact taagcgaaaa ttcaaatcat aggataaatg
     3901 attttataag taaaaacccc aaaataaaaa taacaataaa aaaacctaga gaacttctta
     3961 aagatgtaaa ggatataaac gacagggctc ttaaaaacct actctttaac tattttttaa
     4021 aaagagagaa ataaaaagct tggctttacc ataatgcctc gctataagaa ccacacgaaa
     4081 atgcccacta taaaagtggg cattttcaca attacttaac aacaaggtat cgataaagca
     4141 ttttctcaag gtcttgctta gtactaacga aaagcaatat ctcaatgaca ccattttgct
     4201 catcaaaatc atataaacaa cggtactggt tatcagggtc caagcgctca cggatcgata
     4261 ttcccttatc tgctaacata gcattgtagc gataacgagc aggatcttga gaaatggcct
     4321 ttaccgatga tgctaaaaga tcatcagccc acgaagcagc ttgaacacta tccgtgtagt
     4381 ttgatttgaa ggattctgca tcttgcaggg accatagtgc cgcttccgcg atcgttacat
     4441 tgaatgaatt tgccaagttg gctccttata ttaagttcgc gcttcacgta acctccgcat
     4501 agcatcttcg ggggacattc cacgaccatt ttttatctct ctttttgcag ccattactag
     4561 cttcaaaaga gcatttgatt gccgttctct ttctctttca cgcagctcgg cctctctctc
     4621 ttctgcggtc tgtacgaaca gttctgctaa accatttttc gtaacataaa cgcctccttg
     4681 gaatagttca gggttgccaa gaccttcgcg ggctgacttc tgagacatag ttatagacat
     4741 atgtatacct ttagttaaaa cagtcactta cacgcaagat taagcataag caactaactc
     4801 ctgaataaaa aaagaggtca aaaaaacctc atatcttgct gccacttagg gtgagtagca
     4861 tttacattgt atcaaaaccc atattggtgt acaaatttat gttgaatttg tacaccaaca
     4921 tttaagcata aactttctga gcttcaacta accactattg cttgaaaaaa atcgattaaa
     4981 cccacataag agaagtggat acagtaccga ctgtatcttc caaaaacggg gagatgggta
     5041 tgccgtatga aatgggcgct gaatgtccgt gttgcaaagt aaccgcaggt agggatgtta
     5101 aagagataga cgagatcttc ggctttagag agatgtctga cggcagaaaa atccctcagt
     5161 catactgccg taaatgcaga agcgcacatt gttcaaaact tgaaaaacgt tgcagctaac
     5221 ctacaaaaac cagcacaaaa cggagttaat taatgaaaat caataagata cagaaaaagg
     5281 acgctctctt ttgcccaata tgcggaaggc ctgttgaaaa ctgcaatggt catcccttaa
     5341 atggttaatt gaaaaggccc gcacttgcgg gccttttcat agcgagaacg aaaggatgag
     5401 ctaacggtca tcctcatcgt cataatcatt ctcttccggt tcatctggat ggtattcaag
     5461 tccgagatta tcagctagct cttcgatgta ttcattcgca tcactaagtt cttgcttcag
     5521 tcccgcgatc tcttttttat aaccaatctc ttttacccac tgatgaatcg tagatggtga
     5581 acaaccaagt actttagcta catcctgctg tttgccacca aactgcgtta ccaaagaata
     5641 cgcggcaacc atggctcg
//
