LOCUS       NZ_CP147093             3062 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KTa005 plasmid pKTa005_9, complete sequence.
ACCESSION   NZ_CP147093
VERSION     NZ_CP147093.1
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 3062)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3062)
  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
            CP147093.1.
            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..3062
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KTa005"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKTa005_9"
                     /geo_loc_name="Japan"
                     /collection_date="2013"
                     /collected_by="Ryota Gomi"
     gene            join(2955..3062,1..297)
                     /locus_tag="WAZ86_RS24970"
                     /old_locus_tag="WAZ86_24965"
     CDS             join(2955..3062,1..297)
                     /locus_tag="WAZ86_RS24970"
                     /old_locus_tag="WAZ86_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016529521.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2251 domain-containing protein"
                     /protein_id="WP_008321396.1"
                     /translation="MTILVTIQAQLVVGEEQVIKSLAPEGMLAAVFEDDGRTGYFYALD
                     ESVEGNPIMDAVHIYNAEDVSDGHIPSDVKIGWSEDSQKCVLLINGYPHGAFDFVGKNG
                     YCRSGYPPPINKVWSLSGHEWSDSVDDFFR"
                     /name="DUF2251 domain-containing protein"
     gene            complement(382..1053)
                     /locus_tag="WAZ86_RS24975"
                     /old_locus_tag="WAZ86_24970"
     CDS             complement(382..1053)
                     /locus_tag="WAZ86_RS24975"
                     /old_locus_tag="WAZ86_24970"
                     /inference="COORDINATES: protein motif:HMM:NF013540.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_048230210.1"
                     /translation="MNKSNFRALTDEEVANCVKLIRHDRKWSQEQLAAISGLNLRTIQR
                     VEKGEPSSIDTRRNLANSFGANDIDAFNKETYIPSMDELKKYQDYIEDSCEQIKATKLN
                     TSIGLLDATEGCHASFFDSSFDMSHDAEEANHLIKCYLKEYMDCHDLYNKEQKNDAAKE
                     IQVHIDKLNKLGVALVYAKKKTNITNIGNNISMETIYIIAFPIGKEPDTLIIPNEADVS
                     V"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(1388..1519)
                     /locus_tag="WAZ86_RS24980"
                     /old_locus_tag="WAZ86_24975"
     CDS             complement(1388..1519)
                     /locus_tag="WAZ86_RS24980"
                     /old_locus_tag="WAZ86_24975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032159035.1"
                     /translation="MHEPPVQSDCCAFSGNYQLESNPERHDKAPLAAAIGNWISRAG"
                     /name="hypothetical protein"
     gene            2232..2459
                     /locus_tag="WAZ86_RS24985"
                     /old_locus_tag="WAZ86_24980"
     CDS             2232..2459
                     /locus_tag="WAZ86_RS24985"
                     /old_locus_tag="WAZ86_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_206282062.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAFMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(2507..2695)
                     /locus_tag="WAZ86_RS24990"
                     /old_locus_tag="WAZ86_24985"
     CDS             complement(2507..2695)
                     /locus_tag="WAZ86_RS24990"
                     /old_locus_tag="WAZ86_24985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_048230211.1"
                     /translation="MTKQESATLNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1881..2054
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.429"
                     /coverage="100.0"
                     /evalue="5.6200000000000006e-73"
     Typing          complement(1411..1957)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.182"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 cggaccgggt atttctatgc gctcgatgag tccgtcgagg gaaacccgat tatggacgca
       61 gtacacatct acaatgccga agacgtttca gacggtcaca ttccttctga tgttaaaatt
      121 ggctggtcag aagacagtca gaagtgcgta ctcctgatca atggataccc gcacggggca
      181 ttcgatttcg tgggaaaaaa cgggtactgc aggagtggtt atcctccccc tataaacaag
      241 gtgtggtctc tttccgggca tgagtggagc gactcggtgg atgatttttt ccggtgaatt
      301 acggcaggct atagcctgcc attatggttc gaacaacgga tgttatggta aatctattaa
      361 ctatatagtc attgtgcttg tctaaacact cacatcagct tcattcggta ttattaatgt
      421 gtcaggttcc ttaccaatag ggaatgctat tatataaatg gtttccattg atatgttatt
      481 accaatgttt gttatgttcg tttttttctt tgcgtaaaca agtgccaccc ccagtttgtt
      541 cagtttgtct atatgtacct ggatttcttt tgcggcatca tttttctgtt ctttgttata
      601 aagatcatgg caatccatgt attcttttaa atagcatttg attagatggt ttgcttcctc
      661 tgcatcatga ctcatatcga aggatgaatc gaagaatgat gcgtgacatc cttcagttgc
      721 gtctagaaga ccaatgcttg tgttaagttt ggttgccttg atttgttcac aagaatcctc
      781 aatataatct tggtattttt ttaattcatc catcgatggt atataggttt ctttattgaa
      841 agcatcaatg tcgtttgcac caaaagaatt tgctaggttt cttcgcgtat caatagatga
      901 aggctctcct ttttctactc tttgaatagt tcttaaattt aatccactga ttgcggccaa
      961 ttgttcctga gaccattttc ggtcatgtcg aattaacttg acgcaattag caacttcctc
     1021 atcagtcagc gcacggaaat ttgatttgtt cataattaat gtctcatgtg attagagtgt
     1081 acatgaagta tgtgttgaat ttgatggaaa taaaacgaca gtattacgac actagccccg
     1141 ctcactactg acgggaggat gtatgttgct gataaaggat cttcttgaga tcgtctttct
     1201 ctgcgggtaa tctcttgcct tggaaacgaa aaaaccaccc tggcaggtgg tttttcgaag
     1261 gttagtaaat cctggcagat tttctaaccg tggtaactgg cttcagcaga gcgcagatac
     1321 ctaaactgtc cttccagtgt agccgcactc aggccaccac ttcaagaact ctgtagcact
     1381 gcctacatta tcccgctctg ctaatccagt taccaatggc tgctgccagt ggcgctttgt
     1441 cgtgtctttc cgggttggac tcaagttgat agttaccgga aaaggcgcag cagtcggact
     1501 gaacgggggg ttcgtgcata cagtccagct tggagcgaac tgccttcccg gaaccgagtg
     1561 tcaggcgtgg aatgagataa acgcggccat aacagcggaa tgacaccggt aaaccgaaag
     1621 gcaggaacag gagagcgcac gagggagcca ccagggggaa acgcctggta tctttaagtc
     1681 ctgtcgggtt tcgccaccac tgatttgagc gtcagatttc gtgatgcttg tcaggggggc
     1741 ggagcctatg gaaaaacggc ttcgccgtgg ccttctcgct tccctgttaa gtttcttctt
     1801 ggcatcttcc aggaaatttc cgccccgcca gtaagcccgc accgctcgcc gcagccgaac
     1861 gaccgagcgc agcgagtcag tgagcgagga agcggaatat atcctgtatc gcatattctg
     1921 ctgacgcgcc ggagccgcct tttttctcct tccacatgaa gcacttcact gattttcgca
     1981 tccgtgccaa catagtaagc cagtatacac tccgctagcg ctacgtgact ggttcagggc
     2041 tgcgccccga cacctgctaa aagcactgac gcgcctgcgg cttgcccaac cccgcgccgt
     2101 ccgggaaaga atttcccgat cgacccgacg tttctgttta cctgtgatgt taacgtttgg
     2161 atctttttcc cgggtttacc tattttcttc taatgaagcg ttcacagctg acgttaatag
     2221 atgggtgctt catgtttggt ttttcaccag gagaacttat gaacctttgc cccgatgaac
     2281 gtctgctctt tgtgcggatg atttccgcta tgcttcgccg ttcgggcggt gatgcgggtg
     2341 cttttatgtt tgaggcgtat cgccatattg tgtccgatac caatcaagct cgtcgttcct
     2401 acatgctcga cctgctcgaa agcgtcaggc atgactatgt acacggtgga tatacatagt
     2461 tgccctggat acgcttttcg tctaagtgag cgttcttttc gtctctttat tcgccgtcct
     2521 gtataccgaa gcgtgcgctc agcttctgat aaagcgcttc tgcctgttcg tgcattcgct
     2581 cacagtcggc tgcctcgtca tcaagatcga gcacgtcgag tttttcgagc agcagcagcg
     2641 actgcgcccg gataaatttt gccatgttca gtgtggctga ttcctgtttt gtcatacggc
     2701 tttttcccgg ttttatggtg atcgcagact gaaatcttac ttcattcact tgagtgcata
     2761 gccatgcagg tacgcagaaa tcatcagggg cgttttttct cgatatgggc acagaaaggt
     2821 gtatgtttca ggcaggaggc cgcagaaacg ccctcagagg ctctgaggcg gtgcacgcaa
     2881 cagatgttat ggtaaattat ccgcttgtct gaaagctggc tgccgaagca accaaggaaa
     2941 ggagaacaga cctgatgacc attttagtga cgatacaggc ccagctcgtt gtcggggagg
     3001 aacaggttat aaagagcctc gctcctgagg gcatgctggc cgccgtgttc gaagacgatg
     3061 gc
//
