LOCUS       NZ_CP147091             4270 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KTa005 plasmid pKTa005_7, complete sequence.
ACCESSION   NZ_CP147091
VERSION     NZ_CP147091.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992792
            Assembly: GCF_038396305.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4270)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4270)
  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                   :: Unicycler v. 0.5.0
            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_038396305.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:14:53
            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)                     :: 5,001
            CDSs (total)                      :: 4,881
            Genes (coding)                    :: 4,637
            CDSs (with protein)               :: 4,637
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 244
            CDSs (without protein)            :: 244
            Pseudo Genes (ambiguous residues) :: 0 of 244
            Pseudo Genes (frameshifted)       :: 59 of 244
            Pseudo Genes (incomplete)         :: 183 of 244
            Pseudo Genes (internal stop)      :: 41 of 244
            Pseudo Genes (multiple problems)  :: 40 of 244
            Pseudo Genes (short protein)      :: 4 of 244
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147091.1.
            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..4270
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KTa005"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKTa005_7"
                     /geo_loc_name="Japan"
                     /collection_date="2013"
                     /collected_by="Ryota Gomi"
     gene            785..1429
                     /locus_tag="WAZ86_RS24935"
                     /old_locus_tag="WAZ86_24925"
     CDS             785..1429
                     /locus_tag="WAZ86_RS24935"
                     /old_locus_tag="WAZ86_24925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032495680.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrD1"
                     /protein_id="WP_012634451.1"
                     /translation="MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSF
                     YDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNM
                     ITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSS
                     FDWSLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrD1"
     gene            complement(2051..2437)
                     /locus_tag="WAZ86_RS24940"
                     /old_locus_tag="WAZ86_24930"
     CDS             complement(2051..2437)
                     /locus_tag="WAZ86_RS24940"
                     /old_locus_tag="WAZ86_24930"
                     /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_058671329.1"
                     /translation="MRISNVEWLKKRIGFIRKLGEKTTRQRQIIDLLDDEASLSETDRR
                     LLHVLATAEKNELQEQDAAQKKAVQARISGQKNRRERNHKLFLAAGLMIDAGLVDTKTG
                     ELNFDSEKLLTALKRVRCDLETSV"
                     /name="hypothetical protein"
     gene            2605..3540
                     /locus_tag="WAZ86_RS24945"
                     /old_locus_tag="WAZ86_24935"
     CDS             2605..3540
                     /locus_tag="WAZ86_RS24945"
                     /old_locus_tag="WAZ86_24935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235474.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_072206570.1"
                     /translation="MATYHLSVKFGGKGKALAHANYITREDKFSQRKDLEHTEHGNMPE
                     WAKDDPAHFWQAADAFERANGSTYREIEIALPRELNEAQRLELVRDFVKQETGGQHTYS
                     FAIHNPQASIDGGEQPHAHIMMSQRVDDGIKRSPEQYFRRYNAKFPARGGARKDSGHNL
                     TPTEQKQALKALRERWERTHNAHMKRYGFEQGFIDSRSLKAQGIDRKPEQHLGFEAAGR
                     LDDSQRQDIKDSRTFSVVDVPEQAKHIDHSDRSWMNASGIEVNRKELVRSLTHDISQQY
                     GREMAARVTKQGNVEIERVKSLSRGFSISR"
                     /name="MobA/MobL family protein"
     gene            3543..4073
                     /locus_tag="WAZ86_RS24950"
                     /old_locus_tag="WAZ86_24940"
     CDS             3543..4073
                     /locus_tag="WAZ86_RS24950"
                     /old_locus_tag="WAZ86_24940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168766.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012634455.1"
                     /translation="MASTEEKLLTLLLSAEHLKEAAKEQQKAVADSLAVARETLKGYRE
                     ISDSVAQQVRDEVRQEVQKMDVAGLIGERISADFQRLEKSVGNMKINADALDKEISIIR
                     SNIIAEYNTLRGYSWKWFAGVAVAFVVLIFATSWFVKTELQDNYNASAAVYQKVADLEK
                     LLTTEQKPEKKKN"
                     /name="hypothetical protein"
     ARG             786..1426
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          536..691
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
     Typing          2606..3537
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.678"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgggggttt ttatggctca ggacgtaaaa ccgccctgag cgcgtttcag cggtgcgcgt
       61 aatgacgcgt tatggtaaat cggtgccaca ggcgtaagta tctgctaagg atctttttgt
      121 tgattctttt ttaagagcat aatgagatta tataaattga ttttggggtc cgcttggaaa
      181 agggaaaata acctacgcta agactacttt ttaaccaatc ggctattgga tatcactcgg
      241 ttcgcggggc tacagcgttt ctgtgtccga aaccgaacga ttacgtacag catgtagaca
      301 acatgtccga aagtaagcaa aaccattaac ggacagccgg atcatttcgt acatccctta
      361 cggtcagggg ttcgcgctca atggaacgaa atcacccgtt agcttaaaac gcttaacgta
      421 ggataatttc ctttttccaa gcggacccgt actcggttgg tcaaatcgct tcttgccaca
      481 aaacaagttt gtgtctttca gcgatttcgc atcgttttac ttgtcagttt gaatgatgtt
      541 aaaaacgcac tcagaagctc gcaaaaccgt tctaaacttt cagcgtagat ttgggtgttt
      601 tatagggtga tagtgtctta aaatcgtttt gaggggcttt agtggggatg aacgggcggt
      661 tttcgctaac taactcgccc gtttaacata aaagggattg tatgaatcaa ttttagctag
      721 agtttaaggt tgttcaaatt aatgtacaat gattgcactg tataaataac caggtgtagc
      781 atgtatggaa aagcacttta tcaatgaaaa gttttcacga gatcaattta cggggaatag
      841 agttaaaaat attgcctttt caaattgtga tttttcaggg gttgatttaa ctgatactga
      901 atttgttgat tgtagttttt acgacaggaa tagcttggaa gggtgtgatt ttaatagagc
      961 caaactaaaa aacgctagct ttaaaagctg cgatttatca atgagtaatt ttaaaaacat
     1021 tagcgcctta ggtcttgaaa ttagtgagtg tttagctcaa ggagctgatt ttcgaggggc
     1081 taattttatg aatatgataa ctacaaggtc atggttttgt agtgcttata taaccaagac
     1141 aaatcttagt tacgctaatt tttctagagt catattagaa aagtgcgaac tgtgggaaaa
     1201 tcgctggaat ggcactgtga taactggcgc cgtgtttcgt ggctccgatc tttcttgtgg
     1261 ggagttttca tcgtttgatt ggtctttggc tgattttact ggttgtgatt taacgggtgg
     1321 ggcgcttggc gagcttgatg caaggcgaat taatttagat ggagtgaagt tggatggaga
     1381 gcaggcgctt cagcttgttg agagtttagg tgttattgtt caccgataaa atctaggtaa
     1441 aaaacgccta atgccccaat gtggtactaa tcaaaacgga gcgaagcgac atcttcatct
     1501 tgtctttgct tttctccatg atcagttatt gggtcatggt ctcttagctc gttaatctgg
     1561 ctaagtttgg ttaggttggg cttctttcga cacttcgcaa tccaagaaat ccctagtccg
     1621 ttgattggtg ctcttatcag gtacgcactg taatctttcg ataccgcagc gtgattcgga
     1681 ggcagagccg gaatttcgtt ttccggtacg ttttactacc acaatttgcc tgtttatcct
     1741 ttcggagacc gggctaagtc cgagtcaatc aagtggtgca tttgagttaa tgtcgttgaa
     1801 tggttttaag gaagtagtga caagctagct tcccattgct aagattggat tgtctaggtc
     1861 tgatcttagc aacgaatgca ccgaatcaga ttagcagagc cggagtgatg tcacaatcat
     1921 ttcggctctg cgctttctga acttaagcaa aaaatcccct cgtatttcaa tctgcaacgc
     1981 tcgccgcaag atgcaaactg gttttgcatc gaggaagcgt catatcactg aatccttgca
     2041 gaatgcacgg tcacaccgat gtttccagat cacagcgtac ccgtttcagc gcggtcagta
     2101 atttttcaga gtcaaaattc aactcacccg tttttgtatc aaccagtccc gcgtcaatca
     2161 tcagtccggc agccaagaac agtttgtgat tacgttccct gcggtttttc tgacctgaaa
     2221 tccgtgcctg aaccgccttt ttctgcgcgg catcctgttc ctgcaactcg tttttttcag
     2281 cggttgccag aacgtggagc agtcgcctgt cagtctcact gagcgaagcc tcatcatcca
     2341 gcaggtcgat aatctgccgt tgccgtgttg ttttctcccc cagttttctg atgaagccta
     2401 tgcgcttttt aagccattcg acgttactga tccgcatcgt ttaacttccc catcccgata
     2461 tttccgatgg tgaaagtata taacttgcgg tcagaagtcg catgacttat ctttactcat
     2521 aattcttcaa attagagtaa agcgcactta tatgtttctc cctgcgggca gaaacacgtg
     2581 cgtaaaacca agggcaaaaa catcatggca acctatcatc tcagcgtgaa atttggcggc
     2641 aagggtaaag cccttgctca tgccaattac atcacgcggg aagataagtt cagtcagcga
     2701 aaagatctcg aacacaccga gcacggcaat atgccggaat gggcgaaaga tgaccccgcc
     2761 catttctggc aggctgcgga tgcgttcgaa cgtgccaacg gttcaacgta ccgggaaatc
     2821 gagatagcac taccccgtga actgaacgaa gcgcagcggc tggagcttgt cagggatttt
     2881 gtgaagcagg aaacgggcgg tcaacatacg tattcgtttg cgattcacaa tccgcaagcc
     2941 agcattgacg gcggcgaaca gccgcacgcc catatcatga tgagccagcg tgttgatgac
     3001 ggtattaagc gcagcccaga gcagtatttc aggcgctata acgccaaatt tccggcgcgt
     3061 ggcggcgcgc gcaaggactc agggcataat ttaaccccta cagaacaaaa acaggcactg
     3121 aaagccctgc gggagcgctg ggagcgtacg cacaacgcgc atatgaaacg atatggcttt
     3181 gagcagggtt ttattgatag ccggtcactg aaagcacagg gtatagaccg gaaaccggaa
     3241 cagcatctcg gttttgaagc agccggacga ctggacgaca gccagaggca ggatattaaa
     3301 gacagccgga cgttttcagt cgtggatgtg cctgaacagg cgaagcatat cgaccacagc
     3361 gaccgtagct ggatgaatgc cagcggtatc gaggtaaacc ggaaggaact ggtcagatct
     3421 ctgacgcatg atatctcgca gcagtacggg cgggagatgg ctgcacgggt cacaaaacag
     3481 ggaaatgttg aaatagagcg cgtgaaatcc ctgtcacgcg gattttccat aagcaggtaa
     3541 ctatggcgag caccgaagaa aaacttctca cactcctgct gtcggcggag catctgaaag
     3601 aggccgcaaa agagcagcag aaagccgtgg cggattcgct ggcggtggca agggaaaccc
     3661 tgaaaggcta ccgggaaata tcagacagtg tggcacagca ggtacgggat gaagtccggc
     3721 aggaagtgca gaaaatggat gttgcggggc tgattggcga gcgtatcagc gctgattttc
     3781 agcgtctgga aaaatccgtc gggaacatga aaatcaatgc ggacgcgctg gacaaggaaa
     3841 tttccattat ccgcagcaat atcatcgcgg agtacaacac gctgcggggt tacagctgga
     3901 agtggtttgc aggggttgcg gttgcctttg tcgtactgat atttgccaca agctggtttg
     3961 tgaaaacgga actacaggac aattacaacg cgtctgctgc cgtctatcag aaagtggcag
     4021 accttgaaaa gctgctgaca acggaacaga aaccggaaaa gaaaaagaac tgacgcgctg
     4081 cgcttgtcca acgcctcacg ttcgcacaat aaattgcgca cccgttcacc gttttcagcc
     4141 gggtttgggg cgtcttttga gacttccggc ctgaattcag gccggaagtt ctcgccagtc
     4201 agtcaggtgc atggttatgc atggggctga aaatcacggt atgcgattct gagcggtttt
     4261 cggtgagaag
//
