LOCUS       NZ_CP147122             2203 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_13, complete
            sequence.
ACCESSION   NZ_CP147122
VERSION     NZ_CP147122.1
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 2203)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2203)
  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
            CP147122.1.
            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..2203
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_13"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            163..309
                     /locus_tag="WAZ84_RS24650"
                     /old_locus_tag="WAZ84_24645"
     CDS             163..309
                     /locus_tag="WAZ84_RS24650"
                     /old_locus_tag="WAZ84_24645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_087777340.1"
                     /translation="MHEPPVQSDCCAFSGNYLLESNPERHDKTPLAAAIGKRVYKRLLM
                     QSS"
                     /name="replication initiation protein"
     gene            complement(513..1073)
                     /locus_tag="WAZ84_RS24655"
                     /old_locus_tag="WAZ84_24650"
     CDS             complement(513..1073)
                     /locus_tag="WAZ84_RS24655"
                     /old_locus_tag="WAZ84_24650"
                     /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_140415667.1"
                     /translation="MIKINHEFSTFLDIARYEKIVRNNDLISTVLNLALLMENFTNIYI
                     KEISPEEFHDIFLDKKQKQHFKLNVAKSLGLPRSLADAITKLSGIRNNFAHKLDYELKD
                     EEIIEFEQYVEKITAKEICRSGALNYNEVDSFLSSGVKIKGSDDYTSNKVIGRLVNTTY
                     MLANKAAFFSIDEFNRRGILSLG"
                     /name="hypothetical protein"
     gene            complement(1401..1637)
                     /locus_tag="WAZ84_RS24660"
                     /old_locus_tag="WAZ84_24655"
     CDS             complement(1401..1637)
                     /locus_tag="WAZ84_RS24660"
                     /old_locus_tag="WAZ84_24655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230891.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016230891.1"
                     /translation="MTRLTNLTPAEKKFIDDAIAAAERAAGKKLNQPNRHIVLNRARAQ
                     IESQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     Typing          complement(1796..1976)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.352"
                     /coverage="83.0"
                     /evalue="4.29e-85"
     Typing          2..441
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.59"
                     /coverage="86.0"
                     /evalue="6.38e-127"
ORIGIN
        1 ggacttaaag atccccaccg tttccgatgg gtcgctccct cgtgcgctct cctgttcctg
       61 cctttcggtt taccggtgtc attccgctgt tatggccgcg tttgtctcat tccacgcctg
      121 acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt
      181 cagtccgact gctgcgcctt ttccggtaac tatcttcttg agtccaaccc ggaaagacac
      241 gacaaaacgc cactggcagc agccattggt aagagggtgt acaagagatt actgatgcag
      301 agttcttgaa gtctgagcca aactacagct aaactggaag gacgcttttg gtggcagcgg
      361 tcttgtacac cctgttacca cggttcagaa acttgcaggt ctctgatcct tcaaaaaaac
      421 cgcctggcag ggcggttttt tttgttcttg gaataagaag ataccgccac agatagacaa
      481 tcacaagcag ataaaatcaa acctttgaaa aatcatccga ggctcaatat tcctctacgg
      541 ttaaattcat ctattgagaa aaaagcagct ttgttagcaa gcatatatgt ggtgttaacc
      601 aatctcccta tcactttgtt agaggtgtaa tcatcgctcc cttttatctt cactccagat
      661 gataaaaacg aatcgacttc attgtaattt agagcgcctg atctacatat ttctttcgcg
      721 gttatctttt ctacatactg ctcaaactca ataatttctt catctttaag ctcataatct
      781 aatttatgcg caaaattatt cctaatccct gataacttag tgattgcatc ggccaaggat
      841 ctaggcaaac caagcgattt agctacgttg agtttgaaat gttgtttttg ctttttgtct
      901 aaaaaaatat cgtgaaactc ttctggagaa atctccttta tataaatatt agtaaaattc
      961 tccataagaa gagctaaatt caagacagta gaaattaaat cattatttct aacaatcttt
     1021 tcatatctag caatatctaa gaaagttgaa aattcgtggt taattttaat caaaataccc
     1081 cctctcagct tcataaattt aaaatattac ttagtgcaaa ttactaattt aaaaaaatta
     1141 gcaactgaaa atcttatacg ccgtataaga ctctcttttg cacgttaggt aaatcgcatt
     1201 taccataaca tccgttggcc gcaccccctg acaggccctc agcgcaattc tggcgcatca
     1261 gagccgtttc cggcacattt cctcacccgc atcccggaaa aacgcccctg atgatttctg
     1321 cgcgactgca tggctatgca cgcgggtgaa tcgcaggtga tttcgcagcg tcagcaccac
     1381 taaaccgcca aaatccgcaa tcagcggcgc ggcgcgcgcg gacgtgacca ggcaaaatcg
     1441 gactgctgcc gctcatcctc acgtaatgca cgctggcggt cggcgtaacg ctgcgactca
     1501 atctgcgcac gcgctctgtt caggacgatg tgccggttag gctgattgag cttcttcccg
     1561 gccgcacgtt cggcagcggc tatagcgtcg tcgataaact ttttctcagc gggggtcagg
     1621 tttgtcagtc tcgtcatgtt tatctccgta tgagaatagt ccctgcagtc tgccagacac
     1681 agtaggaacg atgaagcgta agcgacggtg aaaggcagtc agaaacggtg aacgggagcg
     1741 gattttaatc cggtgccgtg aggcgttgga caagccgcag gcgcgtcagt ggatttagcg
     1801 ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat actggctaaa
     1861 tatgttacgg cggagtggta atttatgaaa gtgcttcatg tgacaaggga gaaaatgcgg
     1921 ctaccgggcg taagtgcaac atgcagttaa ggatgaaatg acgcctcctc gctcactcgg
     1981 tcgctacgct cctgccgtga gactgcggcg ggcgttaccg gctcacagat gacgggacat
     2041 gcaagcagta ctcaaatcag gaagggccgg agaaaggatg cggcgttgcc gttttttcat
     2101 aggctccgcc cccctgccgg aattcataaa cagacacttt ttcggtgcgt ctgtgggagc
     2161 ctgagctcaa ccatgaatcc gacagcggtg acgaaacccg aca
//
