LOCUS       NZ_CP147058             2257 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain 1002W03 plasmid p1002W03_4, complete
            sequence.
ACCESSION   NZ_CP147058
VERSION     NZ_CP147058.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992801
            Assembly: GCF_038396515.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2257)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2257)
  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                   :: Flye v. 2.9.1
            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_038396515.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:21:10
            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)                     :: 4,843
            CDSs (total)                      :: 4,731
            Genes (coding)                    :: 4,582
            CDSs (with protein)               :: 4,582
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 149
            CDSs (without protein)            :: 149
            Pseudo Genes (ambiguous residues) :: 0 of 149
            Pseudo Genes (frameshifted)       :: 60 of 149
            Pseudo Genes (incomplete)         :: 96 of 149
            Pseudo Genes (internal stop)      :: 29 of 149
            Pseudo Genes (multiple problems)  :: 32 of 149
            Pseudo Genes (short protein)      :: 3 of 149
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147058.1.
            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..2257
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="1002W03"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="p1002W03_4"
                     /geo_loc_name="Japan"
                     /collection_date="2010"
                     /collected_by="Fumie Adachi"
     gene            join(2158..2257,1..890)
                     /locus_tag="WAZ54_RS24210"
                     /old_locus_tag="WAZ54_24215"
     CDS             join(2158..2257,1..890)
                     /locus_tag="WAZ54_RS24210"
                     /old_locus_tag="WAZ54_24215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_052923600.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRLKDRKEFRPVQGWIRTTEVTRSS
                     DGSAHPHFHTLMMVPPSMLSGDGYVKHARWVELWRECLRVSYDPNVDVRAVKPRKPKDG
                     ESLAGATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESD"
                     /name="protein rep"
     gene            1386..1613
                     /locus_tag="WAZ54_RS24215"
                     /old_locus_tag="WAZ54_24220"
     CDS             1386..1613
                     /locus_tag="WAZ54_RS24215"
                     /old_locus_tag="WAZ54_24220"
                     /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_109475618.1"
                     /translation="MYSRHTVGTPNILVRAAPRHPANASRHAKKFRVPLTVPELVKQKI
                     AGSRAFGVGSDFVIDDVTGKTLGMVVGVTQ"
                     /name="hypothetical protein"
     Typing          894..974
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="89.0"
                     /evalue="5.64e-30"
     Typing          complement(617..808)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.891"
                     /coverage="100.0"
                     /evalue="2.88e-86"
ORIGIN
        1 tgcttgcggc cgaatatgag cgctacgggg cgcgtatggc cctctgtggc ggtttattgc
       61 gtttcgggtg gtctaccctc aaggaaaccg gagaaacgcg tctgaggctg cgtgaggcgc
      121 atttctgccg tgtccggcac tgtcctgtct gccagtggag gcgctccctg atgtggcaag
      181 cccgtttcta ccagtccctg ccgcgtatcg tggcggatta ccctgatgcc cgctggatgt
      241 tcctgaccct gaccgtgcgc aactgtgcga tcggggagct gggcgagatg ctgaaccgga
      301 tgaatgcagc tttccagcga ctgaaggatc gcaaggagtt ccggcctgtt cagggctgga
      361 tacgcaccac ggaagtcacc cgcagcagtg acggcagcgc acatccccac ttccacaccc
      421 tgatgatggt gccgccctca atgctatctg gtgacggtta cgtaaaacat gctcgctggg
      481 ttgaactctg gcgggagtgc ctgcgggtca gttacgaccc gaatgttgat gtccgggcag
      541 taaaaccccg taagccaaag gatggcgaat cgctggccgg tgccactgcc gaactggtgc
      601 gcggtgcggt ggccgaaacc ctgaaatatt ccacgaagcc ggctgacatg gtggccgatc
      661 ctgaatggtt cctcgaactg acccgccaga cgcacaagcg ccgctttgtg gcgaccggcg
      721 gtgcactcaa agacgtactg aagctcgatc aggaaaccga tgccgacatg gtgattgggg
      781 atgatatttc cgagggtgac gatgacggtt cacgcatcgc gttcgagtgg aaaaccgagg
      841 tcagaaagta ccgtcgctca ccgacgaaag ataaaactga atcagactag cagggtgtcg
      901 gggtgcagcc ctgaccagat ggcaattgtg atagcgtcgc gtgtgacggt attacaattg
      961 cacatcctgt cccgaaaatt cccgtcccga aaattcccgc cgtttctcgg ttttttgagc
     1021 atcgcagatc gcacgacaaa cgaaacgaag tgaagtttgt ataagtgcgc acttcgtggg
     1081 tgttctgtgc cgccagcttg tcgaacgcgt ggcggagctg cgcgacaaaa atggcaaaat
     1141 aattcgctgt ccgttcgcca gaattttgca cggccgtggt agctgcagga gcgcagaacg
     1201 gcagaaaatt gccagcgttc cggcaaaaaa atcggaacaa gaaatccccg tgttttactc
     1261 cgatgcagga tagggcaaac gccgcaaagt gacgtctctg acgccatttc gcaacgtttg
     1321 cccggtgacc tacagtcggt tcaacaaaca aaaaaaccgc tgcggagtcg ggacaagata
     1381 catgtttgta ttcccgccac acggtcggta ctccaaacat cctggtcagg gctgcgcccc
     1441 gacaccccgc caacgcctca cggcacgcga aaaaattccg cgtaccgctc accgttcccg
     1501 aactcgtcaa acagaaaatc gcggggtccc gcgcctttgg cgtgggttcc gattttgtga
     1561 ttgacgacgt cacggggaaa acactgggga tggtggttgg tgtcacgcag tgagaccaac
     1621 cacctgcgag gcggtttgaa agatctgctg ctggatatgg ttttaacgta tgaaattaaa
     1681 ttggcagtac tgcaaaacga aaacacggat gcgaaaatca caaaccagat agatttataa
     1741 aactttgtgg gaggtgaaga tgttttttga ggcttttgat cgcattgatg cggcgcttag
     1801 cattgcgatc ccgcttctgg tgttgttgag gtttttggtt gtgaaaaagc gctgattttg
     1861 cgtttatttt ttgctcaaag ctcgcgcgcg ttccttgtat ttatacttaa gggataactc
     1921 tgggattcaa attggcctcc agcccttgtc ccgcaaggct tgagggcaca tttgctccga
     1981 aatgggtttg gaagtattct gtcggaagtg gtcgcgttaa aagcgacccc cgcaacgacg
     2041 ggcatcgttc gggggcgtga ccacctgtag agattcgaat tggtgatacg gctaacacag
     2101 gtgatatggc aatgataaca cgtcagatga gccatcgccc acaatcgggt ggtgtgcatg
     2161 aaaaatcctg aactccagaa cctcacggac tattccccct cagatgcgcc ctgggacgct
     2221 cacagaagcg tttctgacga cgtgggaggg atttacc
//
