LOCUS       NZ_CP091681             5448 bp    DNA     circular CON 20-MAY-2024
DEFINITION  Escherichia coli strain KFu022 plasmid pKFu022_4, complete sequence.
ACCESSION   NZ_CP091681
VERSION     NZ_CP091681.1
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 5448)
  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  JOURNAL   Unpublished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 5448)
  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
            CP091681.1.
            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..5448
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFu022"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKFu022_4"
                     /geo_loc_name="Japan"
                     /lat_lon="34.6 N 135.7 E"
                     /collection_date="2012"
                     /collected_by="Kyoto University"
     gene            join(3929..5448,1..172)
                     /locus_tag="L6L66_RS24045"
                     /old_locus_tag="L6L66_24045"
     CDS             join(3929..5448,1..172)
                     /locus_tag="L6L66_RS24045"
                     /old_locus_tag="L6L66_24045"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_171867119.1"
                     /translation="MLSKERLSAIRAKVNRADSSTNKKNATLSSVSVNGDRITERKKES
                     FKTANSFIIRGKIEENETLTKRGERSLNCAQQRYIVVVNGKAHTVFTHRCRSRHCQNCQ
                     RIKAFVWQEKMKEIFPDLISKYPNHKYLFITFTVKNPKLKNLKSVLICMSRAYAKMFQR
                     KAFKKWFVGDIRSTEITRGNSGEDEAHPHFHALICVHPTYFKGSNYMSADVWGKNWGEC
                     LESEFKKEGLEYNAADYPKGFPRVDIRLAKSADRKTDITNQNISEHGEQLINYVLKYSV
                     KGSDLLKNGKADKWFWEFDKQVKNIRMIAASGDIKKSLAKLERDQFDYYKEQEKIEKLI
                     SDDVNFKADKAVFKKEDEYNYYLESKKDKFQYIIEAIEAKAYNYQCYYKALLSDHLLAF
                     RSGIDGIIENFRKINKTKTREDFEILEAAEQELVKIQCERIERLRFICDALVRVGLYKK
                     MSDFVYINIHTNEKTVIVKNNIVDILKAAEQKLLTDFNQSFMRLESAKTQDVFNAIVEN
                     VNEKSALIKLVRNEILAAGAYAYDADNLEYIDLETNERLEVIATIE"
                     /name="protein rep"
     gene            complement(189..1343)
                     /gene="mobQ"
                     /locus_tag="L6L66_RS24050"
                     /old_locus_tag="L6L66_24050"
     CDS             complement(189..1343)
                     /gene="mobQ"
                     /locus_tag="L6L66_RS24050"
                     /old_locus_tag="L6L66_24050"
                     /inference="COORDINATES: protein motif:HMM:NF041496.1"
                     /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_240752887.1"
                     /translation="MAIFHMSAQTISRSKGHSSVAAAAYRHGEKMTDEHTGEIHDYSKK
                     KGVSDGVVLIPDGADKRFLKPEYLWNTIEKSEKRKDAQLAREFNIALPVEMTDEQKKAL
                     AIDFCNENFVKNGMIADIAFHKLDSDNPHFHVMLTTRSLTPDGSGFGQKVREWNSKEQL
                     EAWRKGWADTANEHLQAAGIDARIDHRSLKDQKAELDAIPSPTVEQQAQAISLDRPATI
                     HRGHSGNPERLERFDALQEVKMSQEAKALDHIGQNTLKPSPAAPASSPTASLPDAKQGG
                     KKTGSAAATVSGSNINLADETTDKNLHLTEAQREELEDAENKEAAAKKKAYLTGGAGVP
                     EISETNKIQSNTDFKNKLRKVKTAINKEDEEEENNHKINRPRLK"
                     /name="mobQ"
     gene            1684..2025
                     /locus_tag="L6L66_RS24055"
                     /old_locus_tag="L6L66_24055"
     CDS             1684..2025
                     /locus_tag="L6L66_RS24055"
                     /old_locus_tag="L6L66_24055"
                     /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_100112215.1"
                     /translation="MAFNIEKYNKVKKELEQKANLLNRMEQEMKAEKRKEDAARKIKVG
                     AELIRIVRENNIETLDFANDISLLVGALTNNLILKRIHDQREFLRVEGDKRLNEWKLKN
                     NKKRSKTNE"
                     /name="hypothetical protein"
     gene            2018..2431
                     /locus_tag="L6L66_RS24060"
                     /old_locus_tag="L6L66_24060"
     CDS             2018..2431
                     /locus_tag="L6L66_RS24060"
                     /old_locus_tag="L6L66_24060"
                     /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_117250889.1"
                     /translation="MNNIRPNPNPRKEGTADMMNRLNFYDTSFACLHFLMIDFDNDMQE
                     MKRKKDFHPLQLLNKHDRASLDLEVRNIIRVSLASKMLDIQSDELLDADLYFEKQDELD
                     IGEDARIIAYVFRDFVKQRIEAAIKTIEEEKSI"
                     /name="hypothetical protein"
     gene            2428..2664
                     /locus_tag="L6L66_RS24065"
                     /old_locus_tag="L6L66_24065"
     CDS             2428..2664
                     /locus_tag="L6L66_RS24065"
                     /old_locus_tag="L6L66_24065"
                     /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_085480193.1"
                     /translation="MSILSLLAKAKPAVDDGGASFMGPAMGFFVAAFLVAIIASVVSSA
                     FRSAKNSADVSINNAKKYHVALIKEQYRRKGGG"
                     /name="hypothetical protein"
     gene            2693..3115
                     /locus_tag="L6L66_RS24070"
                     /old_locus_tag="L6L66_24070"
     CDS             2693..3115
                     /locus_tag="L6L66_RS24070"
                     /old_locus_tag="L6L66_24070"
                     /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_187790392.1"
                     /translation="MVIFFIACMLSVIYAAEIYQWQHYNAYKFKRWLKSGSIKNDEEQE
                     KIKKEVKKMTIDNILRLLKKYKIDFDANELVKNDFNIKMKYYKLILAEKERLKENKRLD
                     EAVKQKIKIETDTFDAEKFQKEAEERFKIFMKNRNK"
                     /name="hypothetical protein"
ORIGIN
        1 tcaagacgta ttcaatgcta ttgttgagaa tgtaaatgaa aaatcagcac tgattaaact
       61 tgtaagaaat gagattttag ccgctggcgc gtatgcttat gacgctgata atctcgaata
      121 tatagatctt gaaactaacg agcgtttaga agttatagca accatagagt aatagctcgc
      181 aagagctatt attttaaacg tggtctattt attttgtgat tgttttcttc ctcttcatct
      241 tctttattta tcgctgtttt aaccttcctg agcttatttt taaaatcagt attagactgt
      301 attttgtttg tttcgctgat ttcaggaacg ccagcgccgc ccgtcagata tgcttttttc
      361 ttcgctgctg cttctttatt ttctgcgtct tctaactctt cgcgctgcgc ttctgttaga
      421 tgtagatttt tgtctgttgt ttcatctgcg agattgatat tagatcctga aactgtagcc
      481 gctgctgaac ctgttttttt gcctccctgt ttagcatctg gtaaagatgc ggtaggggag
      541 gaagcaggag ccgctggcga gggcttaagc gtgttttgtc cgatgtggtc aagtgcttta
      601 gcctcttgtg acattttcac ttcttgaagc gcgtcaaagc gttctaaacg ctccgggttg
      661 ccgctgtggc ctctgtggat ggttgcgggg cggtctaagc tgatagcctg cgcctgttgc
      721 tccacggtgg gggaggggat agcgtcaagc tctgctttct ggtctttcag tgaacggtga
      781 tcaatacgcg catcgatgcc agcggcctgc aggtgctcgt tcgctgtatc cgcccatccc
      841 ttgcgccacg cttcgagctg ctccttgctg ttccattccc tgactttttg cccgaaccct
      901 gaaccgtccg gcgtaaggct gcgagtagtt agcattacgt gaaaatgtgg gttgtcgcta
      961 tcgagcttgt gaaaagctat atctgcaatc attccatttt ttacaaagtt ctcattacag
     1021 aaatctattg ctaacgcctt tttttgttcg tctgtcatct ccacgggtag cgcaatatta
     1081 aactcgcgtg ctaactgcgc atcttttctt ttttcgcttt tttcgatagt gttccacaag
     1141 tattcaggtt tcaaaaatct tttatctgcg ccgtcgggga ttaataccac accatcagaa
     1201 actccctttt ttttgctgta gtcgtggatc tctcctgtat gctcatctgt cattttttca
     1261 ccgtggcgat acgccgccgc agctacgcta ctatgtcctt ttgagcggct tattgtttgg
     1321 gcgctcatat gaaatattgc cattgttttt tctcctacta ttggaagcac atatattaaa
     1381 aaataagtaa aactattttt gcattataaa aaatcaataa tgtaatatga gcataaagcg
     1441 agtattcatt attatttttt gattgcagta aatccccatg aaatggggcg cacacattcg
     1501 aagaatgtat aagtgcgcta ttgtagtttt tagcaaaact aaaatagccg ctgcacgtaa
     1561 accttttatc tataaaatcg cgctcggaaa ataaaaatac atatatcgcg ctttacttaa
     1621 ataaataaat atattaccta aaatatatat aacagaaatc gcaaaaaata aaagaggtga
     1681 aacatggcgt ttaatataga aaaatacaat aaagtaaaaa aagagcttga gcaaaaagca
     1741 aacttactaa acaggatgga gcaagaaatg aaagctgaaa aaaggaaaga agatgcagcg
     1801 cgtaaaataa aagttggcgc tgaactaata aggatagtta gagaaaataa tatagagaca
     1861 ttggattttg ctaatgatat ttctttattg gttggagctt taactaataa tctaatatta
     1921 aaaagaatac acgatcaacg cgagtttttg agagttgagg gcgataaaag acttaacgag
     1981 tggaagttaa aaaacaacaa aaaaaggagc aagacgaatg aataacataa gacctaaccc
     2041 gaaccctcga aaagagggaa cggcggacat gatgaaccgc ttaaacttct atgatacgtc
     2101 ttttgcttgt ttgcattttc taatgataga ttttgataat gacatgcaag aaatgaaaag
     2161 aaaaaaagat tttcatccgc tccagctttt gaataaacat gatagagcaa gtttagattt
     2221 agaagtgcgc aatattatta gagtatcact tgcaagtaaa atgttagata ttcaaagcga
     2281 tgagctttta gacgctgatt tatattttga aaaacaagat gagttagata ttggcgagga
     2341 tgcaagaata atagcttatg tatttagaga ctttgtaaaa cagaggatag aagcagcgat
     2401 taaaactatt gaagaagaga aaagtatatg agcatattat cattgttagc aaaagcaaaa
     2461 ccggcagtag atgatggtgg ggctagtttc atggggccag caatgggttt ttttgttgct
     2521 gctttcttag ttgctattat tgcgtcagtt gtttcgagtg cttttcgttc tgctaaaaac
     2581 tctgctgatg tgagtataaa taatgcaaaa aaatatcacg tagcactaat aaaagagcag
     2641 tatcgaagaa aaggcggggg ctgatatgta ttatttaata tgcggccttt ttatggttat
     2701 attttttatt gcttgcatgc tttctgttat atatgctgct gagatctacc agtggcagca
     2761 ttacaacgct tataagttta agcgttggct taaaagtgga agtataaaaa atgatgagga
     2821 gcaagaaaaa ataaaaaagg aagtgaagaa aatgactata gataatattt taaggctcct
     2881 caagaaatac aaaatagatt ttgacgctaa cgagttagtg aaaaatgatt ttaatattaa
     2941 aatgaaatat tacaaactta tattagctga gaaagaaaga ctgaaagaaa ataaaagatt
     3001 agatgaagca gtaaaacaaa aaataaaaat agaaactgat acgtttgacg ctgaaaagtt
     3061 tcagaaagaa gcagaagaac gatttaaaat attcatgaaa aaccgcaata aataatctca
     3121 gatctcaact tgtcaaaaaa aatcaaggag gttccgcccg cagggtggat accttgattt
     3181 ttattgacaa ctcaccagat aaaaaaactt gtcatggtga aaggagagca aggcgagcct
     3241 ttcgcctgtt aagccgcctt tacgcccttc taagcccttt accgtccctc tctgtggtaa
     3301 tctctggccg ctggcctcct gccgttctgg gtgggtttgt taagtggtgg gagtgccagc
     3361 cctgcagctg agtccggggg catttgtcgc cccgcctttg ccctttggtt ttgggttttg
     3421 ggagtgagcg aagcgagtga tctacttccc ttgtttaata agaaacaaat cagatttttt
     3481 ttaccccaaa aatcggcctg tacgccttgg tgtgtctggc tttgctcgaa aagctgttgg
     3541 tcaatggcgg tagctaaaac gcccattttt taaccaaaaa atactcgcgc cggttcctgc
     3601 tgaaaatggg acgggtctgc ataaaatcgc cctttcctct cctgtattgg gatgtgatct
     3661 gcaaaaggtt tcggataaac ggctgaaggt gggatgacac cacaaaaaac cgccttttaa
     3721 cccatgcttt ttgggatgaa gcaaagcgga gcggcggaaa atgggcgcaa aaatgggacg
     3781 gggctgcact tttgggcggt tttaggtgtt cgggatgggc ggcgtaggtg ttcgatttgt
     3841 atgcaaagcg ggtgtaagtg attgacagaa ataaaaaacc ccttagattg gtagttgcga
     3901 cgctacacaa aaataagggg ttttttatat gctttcaaag gaaagattaa gcgcaatacg
     3961 cgcgaaagtc aatagagctg atagctctac aaataaaaaa aatgcaacac tttcaagcgt
     4021 ttctgtaaac ggtgatcgaa tcacagaacg caaaaaagaa agtttcaaaa cggcgaatag
     4081 ttttattatt cgcggcaaga ttgaagaaaa tgaaacgcta acaaaacgcg gtgaacgttc
     4141 tttgaactgc gctcaacagc gttatattgt cgtagttaat ggtaaagcac atactgtatt
     4201 tactcatcgc tgccgttctc gtcattgcca aaactgccag agaataaagg cttttgtatg
     4261 gcaagaaaaa atgaaagaga tatttcccga tctcatttct aaatatccaa atcacaaata
     4321 cttgtttatt acatttacag ttaaaaatcc aaagttaaaa aatcttaaat ctgtattgat
     4381 ttgtatgtct cgcgcttacg ctaaaatgtt tcaacgtaaa gcgtttaaaa aatggtttgt
     4441 gggtgatatt agatcgacag aaatcacgcg aggaaatagc ggagaggatg aagcgcaccc
     4501 gcattttcat gcgttgatct gtgttcatcc aacttatttt aaaggctcta actatatgag
     4561 cgccgatgtt tggggcaaga actggggcga gtgcttagag tctgaattca aaaaagaagg
     4621 cttagaatat aacgccgctg attatccaaa gggtttccct cgcgtggata ttcgtcttgc
     4681 taaatctgct gatagaaaaa cagacattac taatcaaaat atcagcgaac acggcgagca
     4741 gcttataaac tacgttttaa aatatagcgt caaaggttcg gacttgctga aaaatggaaa
     4801 ggctgataaa tggttttggg agttcgacaa gcaagtaaaa aatattagaa tgatagcggc
     4861 aagcggcgat attaaaaaat cactcgctaa acttgaacgc gatcagtttg attattataa
     4921 agaacaagaa aagatagaaa aactaatatc tgacgatgtg aactttaaag cagataaagc
     4981 agtatttaaa aaagaggatg aatataacta ttatttagaa agtaaaaaag ataagtttca
     5041 atatatcatt gaagcgattg aagctaaagc gtataactat cagtgctatt ataaggcgtt
     5101 attatctgac catcttttag cttttagatc tggtattgat ggcatcattg aaaactttcg
     5161 caaaataaat aaaacaaaaa cgagagaaga ttttgaaata ttggaagcag cagagcagga
     5221 gcttgtaaaa atacaatgcg aaagaataga acgcttgcgc tttatttgtg atgcgcttgt
     5281 aagagtcggt ttatataaaa agatgtctga ttttgtgtat ataaatatac atacaaatga
     5341 aaaaactgtt attgtaaaaa ataacattgt agatattttg aaagcagcag aacaaaaact
     5401 tttaaccgat tttaaccaaa gtttcatgag gcttgaaagc gcaaaaac
//
