LOCUS       NZ_CP147100             4376 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KOr024 plasmid pKOr024_5, complete sequence.
ACCESSION   NZ_CP147100
VERSION     NZ_CP147100.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992791
            Assembly: GCF_038396315.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4376)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4376)
  AUTHORS   Gomi,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAR-2024) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038396315.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:14:33
            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)                     :: 5,098
            CDSs (total)                      :: 4,975
            Genes (coding)                    :: 4,778
            CDSs (with protein)               :: 4,778
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 197
            CDSs (without protein)            :: 197
            Pseudo Genes (ambiguous residues) :: 0 of 197
            Pseudo Genes (frameshifted)       :: 55 of 197
            Pseudo Genes (incomplete)         :: 139 of 197
            Pseudo Genes (internal stop)      :: 30 of 197
            Pseudo Genes (multiple problems)  :: 27 of 197
            Pseudo Genes (short protein)      :: 2 of 197
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147100.1.
            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..4376
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KOr024"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKOr024_5"
                     /geo_loc_name="Japan"
                     /collection_date="2013"
                     /collected_by="Ryota Gomi"
     gene            complement(join(3649..4376,1..55))
                     /locus_tag="WAZ79_RS25475"
                     /old_locus_tag="WAZ79_25465"
     CDS             complement(join(3649..4376,1..55))
                     /locus_tag="WAZ79_RS25475"
                     /old_locus_tag="WAZ79_25465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000140057.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_079948273.1"
                     /translation="MTERILFVFEGEKTEKTITDSLLKKFIENDKRVVLSSFKTDIYSL
                     YKLMSEDEDLDVFAVLKEKNPDLVDFDRDSFSQLFLFFDYDGHAPAASDEKIDKLLSFF
                     NEETENGKLFISYPMVESIKCISHIDAIEDFCRHTVKICDCSKFKGYVAEYAHKSLIHF
                     NLYSDEIWNDVVRMHCVKSNFIMKGNMIFPSNYFSQKDIFGMQKSKYIDPNGSVSTLSS
                     FPMLLLDFFGHQRLFVLVSGEQIEDGDVLSSEEAQRTI"
                     /name="hypothetical protein"
     gene            complement(48..1172)
                     /locus_tag="WAZ79_RS25480"
                     /old_locus_tag="WAZ79_25470"
     CDS             complement(48..1172)
                     /locus_tag="WAZ79_RS25480"
                     /old_locus_tag="WAZ79_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000640319.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_089592240.1"
                     /translation="MIYRFEVEGFKGFSDKLVFDLTHRKNYEFNQDCILDGVVKKSLVY
                     GKNGIGKSNLGLALFDIVAHLTEFNVNDGMYNNYINAVNNSGIARFKYDFKFGDNIVTY
                     LYGKRSVKELVFEELFINDRLVTKFNRVLDSNAYFSLSGTETLNTALAESKISIINYIK
                     NNAILNDGIEKDLFNQFIVFVEKMLYFRSLDSNNYLGLEMGRHLITPDIVERGNVDDFE
                     RFLNKAGVKCKLCVMKIQSNNGVVEDIGFDFGSKQIPFYGVASTGTKSLALFYYWLQRF
                     KDEKCVSFIFVDEFDAFYHHSLSMLIVKEMKKAGAQVIITTHNTNVMTNELLRPDCYFI
                     MDDKGITPLFEKTDKELREAHNIEKMYKAGTFND"
                     /name="ATP-binding protein"
     gene            2618..2821
                     /locus_tag="WAZ79_RS25485"
                     /old_locus_tag="WAZ79_25475"
     CDS             2618..2821
                     /locus_tag="WAZ79_RS25485"
                     /old_locus_tag="WAZ79_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041634.1"
                     /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_001041634.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQATMCERLHELA
                     EELQNSIQTHFEAQYGIGVEQP"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3372..3485
                     /locus_tag="WAZ79_RS25490"
                     /old_locus_tag="WAZ79_25480"
     CDS             3372..3485
                     /locus_tag="WAZ79_RS25490"
                     /old_locus_tag="WAZ79_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001712890.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLTPLAAAIGN"
                     /name="hypothetical protein"
     Typing          complement(2418..2496)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.5"
                     /coverage="83.0"
                     /evalue="7.81e-24"
     Typing          2954..3441
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.278"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 tgatagtctt ctccgttttc tccccctcaa aaacaaataa aatccgctca gtcattaaat
       61 gtacccgctt tatacatttt ctctatatta tgagcttctc gcaactcttt gtctgttttc
      121 tcgaaaagtg gagtaatccc tttatcatcc ataatgaagt aacaatcagg cctaagcaac
      181 tcattcgtca tgacatttgt attatgcgtt gtaattatca cctgggcgcc ggcttttttc
      241 atctccttaa caataagcat ggaaagcgag tgatgataaa aagcatcaaa ctcatctaca
      301 aagataaatg aaacacattt ttcatcttta aatcgttgca accagtaata aaaaagagct
      361 aatgattttg tacctgtgga cgcaactcca tagaatggga tttgcttact cccaaagtca
      421 aagccaatat cttcaacaac tccattatta ctttgaattt tcattacgca aagtttacat
      481 ttaacccctg ctttattcaa aaacctttca aaatcatcaa cattacctct ctccacgata
      541 tccggagtga ttaggtgtcg ccccatctct agtccaagat aattatttga atcaagagat
      601 ctgaagtaca acattttctc aacaaaaaca ataaactgat taaatagatc tttttcgata
      661 ccatcattaa ggatggcgtt attttttata taattaatga tcgatatttt agactccgca
      721 agagcagtgt ttaaagtttc tgttcctgat aatgagaaat aggcatttga atcaagcact
      781 ctattaaatt tagttacaag cctgtcattg ataaacaact cttcaaaaac aagctctttc
      841 acactccttt tcccatataa ataagttaca atattatcac caaatttaaa atcatactta
      901 aatctcgcaa taccagagtt gttaactgca tttatatagt tattatacat gccatcatta
      961 acattaaact cagttaagtg agcgacaata tcaaaaagag caagccctaa gttgcttttc
     1021 cctataccat ttttaccgta taccaatgat tttttgacaa caccatcaag tatacaatct
     1081 tgattaaatt cataattctt cctatgagta agatcaaaca ctaatttgtc tgaaaacccc
     1141 ttaaacccct caacttcaaa tctgtatatc ataaaagcct cacatcaaag atgccgtaac
     1201 tatatcatgg caccgtaaaa aaattacacc aaatatagat attgattttt cttatcgctg
     1261 caattaaagt tgcaagcgaa ggctctcgca gtcctatgaa actcagcatg cttgctgttt
     1321 tttataggtg tcagttccta caactgacga agacaggaga gtacaaaatg aaacgtaaaa
     1381 gcgtattcgt tcgtgcctac cgtcgctttc gctacggcga gtgggaagac gtatgcagtc
     1441 attaccgctc aatgcctcgc taaacgacct ggctgaccgc gaagagcctt caatgcgtaa
     1501 aagttttgta acttgccgtg ccataccgat ttaccataac gtcgcattac gcgcaccgct
     1561 taaacgcgct gagcacgatt ctgacgtaaa aaccacaaaa agagatgttt tccccttggc
     1621 taaaccggaa aaatgcgtca ggaaggtttt cagcacgttg catgactatg catggaactg
     1681 aatggtgatc ggtttgggcg cgtccggtgt ctcaaaggct tattttcgga tgttttcgtc
     1741 ctccggcgtc gtttttccgg ctcctccagg tggccatacg cagcaccgta agcagcactc
     1801 ccccccataa aatcaggcac tgtaagcagc accgtaaagg gaaaatccag ccacaatcca
     1861 gcaccataac aggcaccgtt acagtgcctg ttgttgatta acgccatgat taataaggat
     1921 tagcactgta acagtgccgg ttacagtgcc tgatccagcc acaatccggc accgttgcgg
     1981 tgctgcgtat ggaggaaaaa cgtaaatttt gctacctgaa ataattttaa tgcactgatt
     2041 ctaaagataa atcatgcaaa acgcagtttt gcgacaggtg tgggaaatgc aggtcagagg
     2101 agaggggaat ttcaggcgcg gatccggtcc tggttcaggc tacagggctc tcagaaaaag
     2161 cgaataaatt tgcgctagcc gtcatggcgt tacgccgggg tatcggggtg aaaccctgag
     2221 cagggagtaa ttgtaatagc gtcacgtgtg acggtattac aattacacat cctgtcctgt
     2281 gacaggcagc cggatacggt cgtccaggtg gcaacagtac ggcagggggg tacaactgta
     2341 ccccgtcaca tccgcaaaag atttacggca cgaaaccgga gcgacgcaac aactgccggt
     2401 aacacgaccc catgaacggg acaggatgtg taatcgtata accgcgcacg cacgttcatc
     2461 cgattacaac ctggtcaggg ctttaccccg acacccacga tgtgatgaac ggatgaacat
     2521 aaaacaaccg gaaaaacgcg cactgtccag gcaaagaacg gaacacggca taatcacatg
     2581 acgctgaata cagagacaga acggagaacg acagaaggtg aacaaacagc agcaaaccgc
     2641 acttaacatg gcgcgattca tcaaaagcca gagtctgaca ctgcttgaaa agctggatgc
     2701 ccttgatgcc gacgaacagg caaccatgtg tgaacggctg cacgaactgg cggaagaact
     2761 gcagaacagc atacagacgc attttgaagc gcagtacggc attggagtag aacaaccata
     2821 aagacgcagg cgaaagcggt cgcggcttgt ccgtgagcgt tttcgcctgc agacaagccc
     2881 gcagggcgcg tcaggacagt gacctgagaa aaacactggc gcgtaagtgc tcaaagcaaa
     2941 cgggcggaga aattccgctt cctcgcccac tcgctcacta cgttcggtcg ctggggctgc
     3001 ggcgagcggt ggcggctctc taataacggc aggcagttta tccacagaat cgggggataa
     3061 ccaggacaga acatgtgggc aaaagagcac gaccgtaaaa ggctgcgacg atgccgtttt
     3121 tccataggct ccgcccccct gacgagcatc acaaaaatcg acgctcaagt cagaggtggc
     3181 gaaacccgac aggactataa agataccagg cgtttccccc tggaagctcc ctcgtgcgct
     3241 ctcctgttcc gaccctgccg tttaccggat acctgtccgc ctttctcctt tcaggaagcg
     3301 tggcgctttc tcatagctca cgctgttggt atctcagttc ggtgtaggtc gttcgctcca
     3361 agctgggctg tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta tccggtaact
     3421 atcgtcttga gtccaacccg gaaagacacg acttaacgcc actggcagca gccattggta
     3481 actgatttag aggagttagt cttgatgtta tgcgccggtt aaggctaaac tgaaagaaca
     3541 agttttggtg actgagctcc tctattctat tagccagtta cctcggttca gaaacttgcc
     3601 ggttactgaa ccttcgaaaa aaccaccttg ccgggtggtt ttttcttttc aaatagtacg
     3661 ctgggcttcc tccgaactca atacgtctcc atcctcaatt tgttcaccgc tgaccagcac
     3721 aaacaatctt tggtgcccaa aaaagtctaa aagtaacatc gggaatgaac ttaatgtaga
     3781 tacagagcca tttggatcta tatattttga cttctgcata ccgaatatat ctttctgtga
     3841 aaaataatta gaaggaaaaa tcatattccc cttcattatg aaattagatt tcacacaatg
     3901 catcctaacc acatcattcc aaatctcatc agaatacaaa ttaaagtgaa tcaatgactt
     3961 atgagcatat tctgcaacat accccttaaa cttagaacaa tcacatattt ttactgtatg
     4021 cctacaaaaa tcctcaatcg catcaatatg cgagatacat tttatagact caaccatagg
     4081 ataactgata aataatttac cgttttcagt ttcctcatta aaaaaactta gtagcttatc
     4141 tatcttttcg tcagaagcag ctggagcatg cccatcataa tcaaagaaca gaaaaagctg
     4201 agagaaagaa tctctatcaa aatctactaa gtcaggattt ttttccttca acacggcaaa
     4261 tacatcaaga tcttcatcct cactcatcaa cttataaagt gaatatatat ctgtcttaaa
     4321 tgaagaaaga acaaccctct tatcattctc aatgaatttt tttaaaagac tatcag
//
