LOCUS       NZ_CP147116             4075 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_7, complete sequence.
ACCESSION   NZ_CP147116
VERSION     NZ_CP147116.1
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 4075)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4075)
  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
            CP147116.1.
            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..4075
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_7"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            complement(373..522)
                     /locus_tag="WAZ84_RS24525"
                     /old_locus_tag="WAZ84_24520"
     CDS             complement(373..522)
                     /locus_tag="WAZ84_RS24525"
                     /old_locus_tag="WAZ84_24520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162852253.1"
                     /translation="MPSEYDEQPDATDALFPGEYDLFNLMAHVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(1459..2568)
                     /gene="wzz(fepE)"
                     /locus_tag="WAZ84_RS24530"
                     /old_locus_tag="WAZ84_24525"
     CDS             complement(1459..2568)
                     /gene="wzz(fepE)"
                     /locus_tag="WAZ84_RS24530"
                     /old_locus_tag="WAZ84_24525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_112037116.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFDLIRVLWAAKIKIVGVIL
                     FFACIGFLVSLVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEMIKKKNISALELHRAIVGLSENMKSVDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(3387..3788)
                     /locus_tag="WAZ84_RS24535"
                     /old_locus_tag="WAZ84_24530"
     CDS             complement(3387..3788)
                     /locus_tag="WAZ84_RS24535"
                     /old_locus_tag="WAZ84_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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 domain-containing protein"
                     /protein_id="WP_112891221.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVTRHLKQEIEHLNSLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3788..3979)
                     /locus_tag="WAZ84_RS24540"
                     /old_locus_tag="WAZ84_24535"
     CDS             complement(3788..3979)
                     /locus_tag="WAZ84_RS24540"
                     /old_locus_tag="WAZ84_24535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(516..730)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.091"
                     /coverage="100.0"
                     /evalue="3.48e-51"
     Typing          711..1239
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.727"
                     /coverage="89.0"
                     /evalue="2.57e-146"
ORIGIN
        1 tttgtagttt atctgtagtc atcgcactaa aacgcaggat taaatcatca acttttgtag
       61 tcttcctgta gtctggaaaa ataatccgtt catgcaagca tgaacgaagc agttaaagac
      121 gctttttcgt cgccgatgat ccttaacctg cgcatatcac ccagccagaa tgataatttt
      181 ttgcccctta aatggtcata cacctaacgc agccgcgatt tttatcgcaa ctgcatgaat
      241 taaatgaaaa aaatggagtt atttcgtgta ttagcgtaat acgcaacgta ttacaatcat
      301 ctgtaacaac atgaaaataa acaaataaca tgtaatacca gcgtattaca tgtacgctgg
      361 ccagcgaaaa agctataacg cttcccggcc gacaggcggg ccagaatcca ccggggcgtg
      421 caggttctct tcagtaacat gagccattaa gttaaaaagg tcatattcgc cgggaaacag
      481 agcatcagtc gcatccggtt gttcatcata ctcagatggc atggtgtgat atccagtagc
      541 tgaggggtgt tagcgggttt cggggcgcag ccctgaacca gtcacgtagc gctagcggag
      601 tgcatactgg ctaaatattt taaaccgaag tggtgatttg ccaaagtgct tcatgtggca
      661 ggagtgaaat gaggcttacc ggcgtcagga gaagatgctg gttcaggtga tattccgctt
      721 cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg caggcttact
      781 aatggggcgg aaatttattt cctggtggat gccaggaaga aacttaacag ggatacgata
      841 aggccgcggc aaagccgttt ttccataggc tccgcccccc tgacaagcat cacgaaatct
      901 gacgctcaaa tcagtggtgg cgaaacccga caggactata aagataccag gcgtttcccc
      961 ctggtggctc cctcttgcgc tctcctgttc ccgtcctgcg gcatccgtgt agtggtggaa
     1021 gctttaccta aatcaccacg ccccgttccg tttagacagt tcgctccaag ctgggctgta
     1081 tgcaagaacc ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt
     1141 ccaacccggt aagacacgac ttaacgccat tggcagcggc cactggtaaa caggatgtgc
     1201 gagagatgta ttgagagttc ttgaagtggc agccttactg aggctacact agaaggacag
     1261 atttggtgac atgtctcgca caagactgtt accacggttc agaagttccc caacttactg
     1321 aaccttcgaa aaaccacctc cccaggtggt tttttcgttt tctagagtag aagactacgg
     1381 ctgtaaggga atgatctcaa gaagatcctt tgaacttttt ataaaagttg cttataaaat
     1441 gatgcatcag cacaactttt actcaatcac actcatcttt ctggcctcca tggcatgacg
     1501 taaaagtata tagccacatg caagcatccc tccaatgaca gaagaaagaa ttacaattat
     1561 ggcattactt ggcccatcct ttctgaccgg taacgttggg ctcaattgat actgaaacgg
     1621 cataaaatca acatccccca ctttcgccac aaccaattga ttcacaacat attgacgatt
     1681 tcgcaactcc ccactcaatt ccgaaacatc cttgattgat tttttgatgt tcaatttagt
     1741 tgctatacca tcagaaccga gagccacagg aaaatctgga tcatccttca taatctgacc
     1801 attgctgtat acaggttttt ttattccagc cgcattagca acctccagtg aataattgag
     1861 gcgtcgaata tctgcattca gctggtttct aatttttatc tcatccagtg caagaatttc
     1921 tttttcaaca ttagttttaa cttctagttt atttcttata tcttccatca aatcccttac
     1981 aacaagggaa gaaacataat taatataccc agacaacaca tcgtgagctt ctttacttgt
     2041 tggagcagta aaactcagag tccatgatac atacaatgat gacttgtcgt ttttcttact
     2101 ggcattatca tcaaccgact tcatattttc actcaaccca acaattgcac gatgcagttc
     2161 gagagcgcta atgttcttct ttttaatcat ctccataaca taaggagatg atctcatata
     2221 ctcattcaac gaattaacgg actgaaattt cttaataaac agagcaaatg cgctatcacg
     2281 attgatatca aaatccactc ccagaacatg aagcttggaa agctccttat ttaattcact
     2341 ccattgaaca gactcagcag gagtaaccac agcagaacta gtccattttt gtggcaaaac
     2401 aagagaaaca agaaagccaa tacaagcaaa aaatagaatc accccaacaa tttttatttt
     2461 tgctgcccat aaaactctaa tcaagtcaaa aaggtcaatt tcttcattac cattcggcaa
     2521 catgttgtaa ttagaaaaat gttcgtcaga tacctttgag attttcattg aaaaaacaca
     2581 atatattaac atatggtttt tttattctat catatgttag gaaaaaacct aaaaaccatt
     2641 cagcagacat ttaacataac attttaattg tacgcaccac taaaacggcc tcagggcgtt
     2701 tctgacggga aactggtaaa acaggcaaca aaccacccga aaacccgcca gaaacgcgca
     2761 ggctctgttt ttacggcatg catgagtatg cacgcaagtg catagcgcga aaattcacgc
     2821 cattcagcca gggtaagtcc tgtttccggc gttcttccta tccgaaaacg gtgaacgggg
     2881 acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag ccggaaaacc ggttttcagc
     2941 acgatcagga atcgggttcg tcgacggccg gcaatcacgt tatggcaagt cgccggacga
     3001 ctcaccagac aattcaccgg cgattcgact cgtgacttga ctctagagtc gtcaaggtca
     3061 aaaaaacacc aaaatgacga ttcaactcta gagtcaagtc gtcataagtt actgatattc
     3121 ttaagtgagt cgtcgatgac tctatgacga gtcgtcagca agtcgtacac gaatcgccga
     3181 cgacttggat tcaccttaca gaaagtaata ctgcgtaatt taataaccca caactaactg
     3241 atattaatga gttatcttca aaattttaat tttgcgtggg gtgtgggtat ttttagtggt
     3301 gaggagcgtt cagagatctg acgatttttg ggaaggttca ggaactcccc gggatggccg
     3361 gagaggaaaa ctgaagcatg acggggtcag gattttttcc agaatttcca ccatggcgcg
     3421 ggggattcag ttaattttgc ctggtgattt tcaagaagga gcatggcctg tttcaggctg
     3481 tcaatgtgcg aatccttgga caaaagtaag gagttcaggt gttcaatctc ctgtttcaga
     3541 tgacgagtca cctgttcact ctggtcagca gaggctgtat cacgctgttc agagacctgt
     3601 ccagaatggt gttcaccctt cggttgttca aagggaccaa agacacgtaa aagctctgaa
     3661 gtatctacca tttttgcatt gcgttcaccg ctacaggtgg acaggtcacc tgctttaatt
     3721 aacctgtgca gtgttgttct actcttaccc gtcagtcggg cagcctcact aatagacact
     3781 ctggccatca gttaccatcc tgtaatgcat ccagtctcga ggacagtgta cggaaaagat
     3841 gctccgcatc atcgtggagt ttctcacaaa ggtccgcctc aacatcgaga tcaagctcgt
     3901 tgagcttctc cagcaggagc agagactgat tctggatgaa tttagccatg ttcagcgctg
     3961 ttttctgttg tttcgtcata agggccctca gagcatcagt gctcagtgta aaccggtaag
     4021 ggggtcggat gtacgaatgg ttcagagaac ggatctgagg ttatcctgta gttat
//
