LOCUS       NZ_CP147119             3062 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_10, complete
            sequence.
ACCESSION   NZ_CP147119
VERSION     NZ_CP147119.1
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 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  JOURNAL   Unpublished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_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
            CP147119.1.
            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="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_10"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            complement(66..737)
                     /locus_tag="WAZ84_RS24595"
                     /old_locus_tag="WAZ84_24590"
     CDS             complement(66..737)
                     /locus_tag="WAZ84_RS24595"
                     /old_locus_tag="WAZ84_24590"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /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(1072..1203)
                     /locus_tag="WAZ84_RS24600"
                     /old_locus_tag="WAZ84_24595"
     CDS             complement(1072..1203)
                     /locus_tag="WAZ84_RS24600"
                     /old_locus_tag="WAZ84_24595"
                     /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            1916..2143
                     /locus_tag="WAZ84_RS24605"
                     /old_locus_tag="WAZ84_24600"
     CDS             1916..2143
                     /locus_tag="WAZ84_RS24605"
                     /old_locus_tag="WAZ84_24600"
                     /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(2191..2379)
                     /locus_tag="WAZ84_RS24610"
                     /old_locus_tag="WAZ84_24605"
     CDS             complement(2191..2379)
                     /locus_tag="WAZ84_RS24610"
                     /old_locus_tag="WAZ84_24605"
                     /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"
     gene            2639..3043
                     /locus_tag="WAZ84_RS24615"
                     /old_locus_tag="WAZ84_24610"
     CDS             2639..3043
                     /locus_tag="WAZ84_RS24615"
                     /old_locus_tag="WAZ84_24610"
                     /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"
     Typing          1565..1738
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.429"
                     /coverage="100.0"
                     /evalue="5.6200000000000006e-73"
     Typing          complement(1095..1641)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.182"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 tgccattatg gttcgaacaa cggatgttat ggtaaatcta ttaactatat agtcattgtg
       61 cttgtctaaa cactcacatc agcttcattc ggtattatta atgtgtcagg ttccttacca
      121 atagggaatg ctattatata aatggtttcc attgatatgt tattaccaat gtttgttatg
      181 ttcgtttttt tctttgcgta aacaagtgcc acccccagtt tgttcagttt gtctatatgt
      241 acctggattt cttttgcggc atcatttttc tgttctttgt tataaagatc atggcaatcc
      301 atgtattctt ttaaatagca tttgattaga tggtttgctt cctctgcatc atgactcata
      361 tcgaaggatg aatcgaagaa tgatgcgtga catccttcag ttgcgtctag aagaccaatg
      421 cttgtgttaa gtttggttgc cttgatttgt tcacaagaat cctcaatata atcttggtat
      481 ttttttaatt catccatcga tggtatatag gtttctttat tgaaagcatc aatgtcgttt
      541 gcaccaaaag aatttgctag gtttcttcgc gtatcaatag atgaaggctc tcctttttct
      601 actctttgaa tagttcttaa atttaatcca ctgattgcgg ccaattgttc ctgagaccat
      661 tttcggtcat gtcgaattaa cttgacgcaa ttagcaactt cctcatcagt cagcgcacgg
      721 aaatttgatt tgttcataat taatgtctca tgtgattaga gtgtacatga agtatgtgtt
      781 gaatttgatg gaaataaaac gacagtatta cgacactagc cccgctcact actgacggga
      841 ggatgtatgt tgctgataaa ggatcttctt gagatcgtct ttctctgcgg gtaatctctt
      901 gccttggaaa cgaaaaaacc accctggcag gtggtttttc gaaggttagt aaatcctggc
      961 agattttcta accgtggtaa ctggcttcag cagagcgcag atacctaaac tgtccttcca
     1021 gtgtagccgc actcaggcca ccacttcaag aactctgtag cactgcctac attatcccgc
     1081 tctgctaatc cagttaccaa tggctgctgc cagtggcgct ttgtcgtgtc tttccgggtt
     1141 ggactcaagt tgatagttac cggaaaaggc gcagcagtcg gactgaacgg ggggttcgtg
     1201 catacagtcc agcttggagc gaactgcctt cccggaaccg agtgtcaggc gtggaatgag
     1261 ataaacgcgg ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc
     1321 gcacgaggga gccaccaggg ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca
     1381 ccactgattt gagcgtcaga tttcgtgatg cttgtcaggg gggcggagcc tatggaaaaa
     1441 cggcttcgcc gtggccttct cgcttccctg ttaagtttct tcttggcatc ttccaggaaa
     1501 tttccgcccc gccagtaagc ccgcaccgct cgccgcagcc gaacgaccga gcgcagcgag
     1561 tcagtgagcg aggaagcgga atatatcctg tatcgcatat tctgctgacg cgccggagcc
     1621 gccttttttc tccttccaca tgaagcactt cactgatttt cgcatccgtg ccaacatagt
     1681 aagccagtat acactccgct agcgctacgt gactggttca gggctgcgcc ccgacacctg
     1741 ctaaaagcac tgacgcgcct gcggcttgcc caaccccgcg ccgtccggga aagaatttcc
     1801 cgatcgaccc gacgtttctg tttacctgtg atgttaacgt ttggatcttt ttcccgggtt
     1861 tacctatttt cttctaatga agcgttcaca gctgacgtta atagatgggt gcttcatgtt
     1921 tggtttttca ccaggagaac ttatgaacct ttgccccgat gaacgtctgc tctttgtgcg
     1981 gatgatttcc gctatgcttc gccgttcggg cggtgatgcg ggtgctttta tgtttgaggc
     2041 gtatcgccat attgtgtccg ataccaatca agctcgtcgt tcctacatgc tcgacctgct
     2101 cgaaagcgtc aggcatgact atgtacacgg tggatataca tagttgccct ggatacgctt
     2161 ttcgtctaag tgagcgttct tttcgtctct ttattcgccg tcctgtatac cgaagcgtgc
     2221 gctcagcttc tgataaagcg cttctgcctg ttcgtgcatt cgctcacagt cggctgcctc
     2281 gtcatcaaga tcgagcacgt cgagtttttc gagcagcagc agcgactgcg cccggataaa
     2341 ttttgccatg ttcagtgtgg ctgattcctg ttttgtcata cggctttttc ccggttttat
     2401 ggtgatcgca gactgaaatc ttacttcatt cacttgagtg catagccatg caggtacgca
     2461 gaaatcatca ggggcgtttt ttctcgatat gggcacagaa aggtgtatgt ttcaggcagg
     2521 aggccgcaga aacgccctca gaggctctga ggcggtgcac gcaacagatg ttatggtaaa
     2581 ttatccgctt gtctgaaagc tggctgccga agcaaccaag gaaaggagaa cagacctgat
     2641 gaccatttta gtgacgatac aggcccagct cgttgtcggg gaggaacagg ttataaagag
     2701 cctcgctcct gagggcatgc tggccgccgt gttcgaagac gatggccgga ccgggtattt
     2761 ctatgcgctc gatgagtccg tcgagggaaa cccgattatg gacgcagtac acatctacaa
     2821 tgccgaagac gtttcagacg gtcacattcc ttctgatgtt aaaattggct ggtcagaaga
     2881 cagtcagaag tgcgtactcc tgatcaatgg atacccgcac ggggcattcg atttcgtggg
     2941 aaaaaacggg tactgcagga gtggttatcc tccccctata aacaaggtgt ggtctctttc
     3001 cgggcatgag tggagcgact cggtggatga ttttttccgg tgaattacgg caggctatag
     3061 cc
//
