LOCUS       NZ_CP147115             4270 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_6, complete sequence.
ACCESSION   NZ_CP147115
VERSION     NZ_CP147115.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992787
            Assembly: GCF_038396365.1
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  JOURNAL   Unpublished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_038396365.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:15:29
            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)                     :: 4,937
            CDSs (total)                      :: 4,819
            Genes (coding)                    :: 4,584
            CDSs (with protein)               :: 4,584
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 56 of 235
            Pseudo Genes (incomplete)         :: 161 of 235
            Pseudo Genes (internal stop)      :: 45 of 235
            Pseudo Genes (multiple problems)  :: 31 of 235
            Pseudo Genes (short protein)      :: 4 of 235
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147115.1.
            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="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_6"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            complement(join(3752..4270,1..417))
                     /locus_tag="WAZ84_RS24505"
                     /old_locus_tag="WAZ84_24500"
     CDS             complement(join(3752..4270,1..417))
                     /locus_tag="WAZ84_RS24505"
                     /old_locus_tag="WAZ84_24500"
                     /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            585..971
                     /locus_tag="WAZ84_RS24510"
                     /old_locus_tag="WAZ84_24505"
     CDS             585..971
                     /locus_tag="WAZ84_RS24510"
                     /old_locus_tag="WAZ84_24505"
                     /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            complement(1593..2237)
                     /locus_tag="WAZ84_RS24515"
                     /old_locus_tag="WAZ84_24510"
     CDS             complement(1593..2237)
                     /locus_tag="WAZ84_RS24515"
                     /old_locus_tag="WAZ84_24510"
                     /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(3219..3749)
                     /locus_tag="WAZ84_RS24520"
                     /old_locus_tag="WAZ84_24515"
     CDS             complement(3219..3749)
                     /locus_tag="WAZ84_RS24520"
                     /old_locus_tag="WAZ84_24515"
                     /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             complement(1597..2237)
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2332..2487)
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
     Typing          complement(2..417)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.281"
                     /coverage="100.0"
                     /evalue="1.51e-88"
ORIGIN
        1 ctctgggctg cgcttaatac cgtcatcaac acgctggctc atcatgatat gggcgtgcgg
       61 ctgttcgccg ccgtcaatgc tggcttgcgg attgtgaatc gcaaacgaat acgtatgttg
      121 accgcccgtt tcctgcttca caaaatccct gacaagctcc agccgctgcg cttcgttcag
      181 ttcacggggt agtgctatct cgatttcccg gtacgttgaa ccgttggcac gttcgaacgc
      241 atccgcagcc tgccagaaat gggcggggtc atctttcgcc cattccggca tattgccgtg
      301 ctcggtgtgt tcgagatctt ttcgctgact gaacttatct tcccgcgtga tgtaattggc
      361 atgagcaagg gctttaccct tgccgccaaa tttcacgctg agatgatagg ttgccatgat
      421 gtttttgccc ttggttttac gcacgtgttt ctgcccgcag ggagaaacat ataagtgcgc
      481 tttactctaa tttgaagaat tatgagtaaa gataagtcat gcgacttctg accgcaagtt
      541 atatactttc accatcggaa atatcgggat ggggaagtta aacgatgcgg atcagtaacg
      601 tcgaatggct taaaaagcgc ataggcttca tcagaaaact gggggagaaa acaacacggc
      661 aacggcagat tatcgacctg ctggatgatg aggcttcgct cagtgagact gacaggcgac
      721 tgctccacgt tctggcaacc gctgaaaaaa acgagttgca ggaacaggat gccgcgcaga
      781 aaaaggcggt tcaggcacgg atttcaggtc agaaaaaccg cagggaacgt aatcacaaac
      841 tgttcttggc tgccggactg atgattgacg cgggactggt tgatacaaaa acgggtgagt
      901 tgaattttga ctctgaaaaa ttactgaccg cgctgaaacg ggtacgctgt gatctggaaa
      961 catcggtgtg accgtgcatt ctgcaaggat tcagtgatat gacgcttcct cgatgcaaaa
     1021 ccagtttgca tcttgcggcg agcgttgcag attgaaatac gaggggattt tttgcttaag
     1081 ttcagaaagc gcagagccga aatgattgtg acatcactcc ggctctgcta atctgattcg
     1141 gtgcattcgt tgctaagatc agacctagac aatccaatct tagcaatggg aagctagctt
     1201 gtcactactt ccttaaaacc attcaacgac attaactcaa atgcaccact tgattgactc
     1261 ggacttagcc cggtctccga aaggataaac aggcaaattg tggtagtaaa acgtaccgga
     1321 aaacgaaatt ccggctctgc ctccgaatca cgctgcggta tcgaaagatt acagtgcgta
     1381 cctgataaga gcaccaatca acggactagg gatttcttgg attgcgaagt gtcgaaagaa
     1441 gcccaaccta accaaactta gccagattaa cgagctaaga gaccatgacc caataactga
     1501 tcatggagaa aagcaaagac aagatgaaga tgtcgcttcg ctccgttttg attagtacca
     1561 cattggggca ttaggcgttt tttacctaga ttttatcggt gaacaataac acctaaactc
     1621 tcaacaagct gaagcgcctg ctctccatcc aacttcactc catctaaatt aattcgcctt
     1681 gcatcaagct cgccaagcgc cccacccgtt aaatcacaac cagtaaaatc agccaaagac
     1741 caatcaaacg atgaaaactc cccacaagaa agatcggagc cacgaaacac ggcgccagtt
     1801 atcacagtgc cattccagcg attttcccac agttcgcact tttctaatat gactctagaa
     1861 aaattagcgt aactaagatt tgtcttggtt atataagcac tacaaaacca tgaccttgta
     1921 gttatcatat tcataaaatt agcccctcga aaatcagctc cttgagctaa acactcacta
     1981 atttcaagac ctaaggcgct aatgttttta aaattactca ttgataaatc gcagctttta
     2041 aagctagcgt tttttagttt ggctctatta aaatcacacc cttccaagct attcctgtcg
     2101 taaaaactac aatcaacaaa ttcagtatca gttaaatcaa cccctgaaaa atcacaattt
     2161 gaaaaggcaa tatttttaac tctattcccc gtaaattgat ctcgtgaaaa cttttcattg
     2221 ataaagtgct tttccataca tgctacacct ggttatttat acagtgcaat cattgtacat
     2281 taatttgaac aaccttaaac tctagctaaa attgattcat acaatccctt ttatgttaaa
     2341 cgggcgagtt agttagcgaa aaccgcccgt tcatccccac taaagcccct caaaacgatt
     2401 ttaagacact atcaccctat aaaacaccca aatctacgct gaaagtttag aacggttttg
     2461 cgagcttctg agtgcgtttt taacatcatt caaactgaca agtaaaacga tgcgaaatcg
     2521 ctgaaagaca caaacttgtt ttgtggcaag aagcgatttg accaaccgag tacgggtccg
     2581 cttggaaaaa ggaaattatc ctacgttaag cgttttaagc taacgggtga tttcgttcca
     2641 ttgagcgcga acccctgacc gtaagggatg tacgaaatga tccggctgtc cgttaatggt
     2701 tttgcttact ttcggacatg ttgtctacat gctgtacgta atcgttcggt ttcggacaca
     2761 gaaacgctgt agccccgcga accgagtgat atccaatagc cgattggtta aaaagtagtc
     2821 ttagcgtagg ttattttccc ttttccaagc ggaccccaaa atcaatttat ataatctcat
     2881 tatgctctta aaaaagaatc aacaaaaaga tccttagcag atacttacgc ctgtggcacc
     2941 gatttaccat aacgcgtcat tacgcgcacc gctgaaacgc gctcagggcg gttttacgtc
     3001 ctgagccata aaaacccccg tcttctcacc gaaaaccgct cagaatcgca taccgtgatt
     3061 ttcagcccca tgcataacca tgcacctgac tgactggcga gaacttccgg cctgaattca
     3121 ggccggaagt ctcaaaagac gccccaaacc cggctgaaaa cggtgaacgg gtgcgcaatt
     3181 tattgtgcga acgtgaggcg ttggacaagc gcagcgcgtc agttcttttt cttttccggt
     3241 ttctgttccg ttgtcagcag cttttcaagg tctgccactt tctgatagac ggcagcagac
     3301 gcgttgtaat tgtcctgtag ttccgttttc acaaaccagc ttgtggcaaa tatcagtacg
     3361 acaaaggcaa ccgcaacccc tgcaaaccac ttccagctgt aaccccgcag cgtgttgtac
     3421 tccgcgatga tattgctgcg gataatggaa atttccttgt ccagcgcgtc cgcattgatt
     3481 ttcatgttcc cgacggattt ttccagacgc tgaaaatcag cgctgatacg ctcgccaatc
     3541 agccccgcaa catccatttt ctgcacttcc tgccggactt catcccgtac ctgctgtgcc
     3601 acactgtctg atatttcccg gtagcctttc agggtttccc ttgccaccgc cagcgaatcc
     3661 gccacggctt tctgctgctc ttttgcggcc tctttcagat gctccgccga cagcaggagt
     3721 gtgagaagtt tttcttcggt gctcgccata gttacctgct tatggaaaat ccgcgtgaca
     3781 gggatttcac gcgctctatt tcaacatttc cctgttttgt gacccgtgca gccatctccc
     3841 gcccgtactg ctgcgagata tcatgcgtca gagatctgac cagttccttc cggtttacct
     3901 cgataccgct ggcattcatc cagctacggt cgctgtggtc gatatgcttc gcctgttcag
     3961 gcacatccac gactgaaaac gtccggctgt ctttaatatc ctgcctctgg ctgtcgtcca
     4021 gtcgtccggc tgcttcaaaa ccgagatgct gttccggttt ccggtctata ccctgtgctt
     4081 tcagtgaccg gctatcaata aaaccctgct caaagccata tcgtttcata tgcgcgttgt
     4141 gcgtacgctc ccagcgctcc cgcagggctt tcagtgcctg tttttgttct gtaggggtta
     4201 aattatgccc tgagtccttg cgcgcgccgc cacgcgccgg aaatttggcg ttatagcgcc
     4261 tgaaatactg
//
