LOCUS       NZ_CP147136             4075 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KFu015 plasmid pKFu015_6, complete sequence.
ACCESSION   NZ_CP147136
VERSION     NZ_CP147136.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992786
            Assembly: GCF_038396395.1
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  JOURNAL   Unpublished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_038396395.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:35:59
            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)                     :: 5,106
            CDSs (total)                      :: 4,987
            Genes (coding)                    :: 4,790
            CDSs (with protein)               :: 4,790
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 197
            CDSs (without protein)            :: 197
            Pseudo Genes (ambiguous residues) :: 0 of 197
            Pseudo Genes (frameshifted)       :: 59 of 197
            Pseudo Genes (incomplete)         :: 133 of 197
            Pseudo Genes (internal stop)      :: 38 of 197
            Pseudo Genes (multiple problems)  :: 35 of 197
            Pseudo Genes (short protein)      :: 5 of 197
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147136.1.
            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="KFu015"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKFu015_6"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            862..1011
                     /locus_tag="WAZ88_RS25495"
                     /old_locus_tag="WAZ88_25495"
     CDS             862..1011
                     /locus_tag="WAZ88_RS25495"
                     /old_locus_tag="WAZ88_25495"
                     /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_341857474.1"
                     /translation="MPSEYDEQPDATDALFPGEYDLFDLMAHVTEENLHAPVDSGPPFG
                     REAL"
                     /name="hypothetical protein"
     gene            1480..1671
                     /locus_tag="WAZ88_RS25500"
                     /old_locus_tag="WAZ88_25500"
     CDS             1480..1671
                     /locus_tag="WAZ88_RS25500"
                     /old_locus_tag="WAZ88_25500"
                     /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"
     gene            1671..2072
                     /locus_tag="WAZ88_RS25505"
                     /old_locus_tag="WAZ88_25505"
     CDS             1671..2072
                     /locus_tag="WAZ88_RS25505"
                     /old_locus_tag="WAZ88_25505"
                     /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_000135006.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVTRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            2882..4000
                     /gene="wzz(fepE)"
                     /locus_tag="WAZ88_RS25510"
                     /old_locus_tag="WAZ88_25510"
     CDS             2882..4000
                     /gene="wzz(fepE)"
                     /locus_tag="WAZ88_RS25510"
                     /old_locus_tag="WAZ88_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243311.1"
                     /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_024191316.1"
                     /translation="MFSMKISKISDEHFSNYNMLPNGNEEIDLFDLIRVLWAAKIKIVG
                     VILFFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAF
                     ALFIKKFQSVNSLNEYMRSSPYVMEIIKKKNISALELHRAIVGLSENMKSVDDNASKKN
                     DKSSLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNELEVKTNVEKEIL
                     ALDEIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATK
                     LNIKKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAI
                     IVILSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     Typing          655..869
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.091"
                     /coverage="100.0"
                     /evalue="3.48e-51"
     Typing          complement(146..674)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.545"
                     /coverage="89.0"
                     /evalue="1.2e-144"
ORIGIN
        1 cagccgtagt cttctactct agaaaacgaa aaaaccacct ggggaggtgg tttttcgaag
       61 gttcagtaag ttggggaact tctgaaccgt ggtaacagtc ttgtgcgaga catgtcacca
      121 aatctgtcct tctagtgtag cctcagtaag gctgccactt caagaactct caatacatct
      181 ctcgcacatc ctgtttacca gtggccgctg ccaatggcgt taagtcgtgt cttaccgggt
      241 tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttctt
      301 gcatacagcc cagcttggag cgaactgtct aaacggaacg gggcgtggtg atttaggtaa
      361 agcttccacc actacacgga tgccgcagga cgggaacagg agagcgcaag agggagccac
      421 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccaccac tgatttgagc
      481 gtcagatttc gtgatgcttg tcaggggggc ggagcctatg gaaaaacggc tttgccgcgg
      541 ccttatcgta tccctgttaa gtttcttcct ggcatccacc aggaaataaa tttccgcccc
      601 attcgtaagc ctgcaccgct cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg
      661 aggaagcgga atatcacctg aaccagcatc ttctcctgac gccggtaagc ctcatttcac
      721 tcctgccaca tgaagcactt tggcaaatca ccacttcggt ttaaaatatt tagccagtat
      781 gcactccgct agcgctacgt gactggttca gggctgcgcc ccgaaacccg ctaacacccc
      841 tcagctactg gatatcacac catgccatct gagtatgatg aacaaccgga tgcgactgat
      901 gctctgtttc ccggcgaata tgaccttttt gacttaatgg ctcatgttac tgaagagaac
      961 ctgcacgccc cggtggattc tggcccgcct ttcggccggg aagcgttata gctttttcgc
     1021 tggccagcgt acatgtaata cgctggtatt acatgttatt tgtttatttt catgttgtta
     1081 cagatgattg taatacgttg cgtattacgc taatacacga aataactcca tttttttcat
     1141 ttaattcatg cagttgcgat aaaaatcgcg gctgcgttag gtgtatgacc atttaagggg
     1201 caaaaaatta tcattctggc tgggtgatct gcgcaggtta aggatcatcg gcgacgaaaa
     1261 agcgtcttta actgcttcgt tcatgcaagc atgaacggat tatttttcca gactacagga
     1321 agactacaaa agttgatgat ttaatcctgc gttttagtgc gatgactaca gataaactac
     1381 aaaataacta caggataacc tcagatccgt tctctgaacc attcgtacat ccgaccccct
     1441 taccggttta tactgagcac tgatgctctg agggccctta tgacgaaaca acagaaaaca
     1501 gcgctgaaca tggctaaatt catccagaat cagtctctgc tcctgctgga gaagcttaac
     1561 gagcttgatc tcgatgttga ggcggacctt tgtgagaaac tccacgatga tgcggagcat
     1621 cttttccgta cactgtcctc gagattggat gcattacagg atggtaactg atggccagag
     1681 tatctattag tgaggctgcc cgactgacgg gtaagagtag aacaacactg cacaggttaa
     1741 ttaaagcagg tgacctgtcc acctgtagcg gtgaacgcaa tgcaaaaatg gtagatactt
     1801 cagagctttt acgtgtcttt ggtccctttg aacaaccgaa gggtgaacac cattctggac
     1861 aggtctctga acagcgtgat acagcctctg ctgaccagag tgaacaggtg actcgtcatc
     1921 tgaaacagga gattgaacac ctgaacacct tacttttgtc caaggattcg cacattgaca
     1981 gcctgaaaca ggctatgctc cttcttgaaa atcaccaggc aaaattaact gaatccccgg
     2041 cgccatggtg gaaattctgg aaaaaatcct gaccccgtca tgcttcagtt ttcctctccg
     2101 gccatcccgg ggagttcctg aaccttccca aaaatcgtca gatctctgaa cgctcctcac
     2161 cactaaaaat acccacaccc tacgcaaaat taaaattttg aagataactc attaatatca
     2221 gttagttgtg ggttattaaa ttacgcagta ttactttctg taaggtgaat ccaagtcgtc
     2281 ggcgattcgt gtacgacttg ctgacgactc gtcatagagt catcgacgac tcacttaaga
     2341 ctatcagtaa cttatgatga cttgactcta gagttgaatc gtcattttgg tgtttttttg
     2401 acctttacga ctctagagtc aagtcacgag tcgaatcgcc ggtgaattgt cttgtgagtc
     2461 gtccggcgac ttgccataac gtgattgccg gccgtcgacg aacccgattc ctgatcgtgc
     2521 tgaaaaccgg ttttccggct gcgccggcaa cgcttcacgg ccacgcaata aattgcgtcc
     2581 ccgttcaccg ttttcggata ggaagaacgc cggaaacagg acttaccctg gctgaatggc
     2641 gtgaattttc gcgctatgca cttgcgtgca tactcatgca tgccgtaaaa acagagcctg
     2701 cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt taccggtttc ccgtcagaaa
     2761 cgccctgagg ccgttttagt ggtgcgtaca attaaaatgt tatgttaaat gtctgctgaa
     2821 tggtttttag gatttttcct aacatatgat agaataaaaa aaccatatgt taatatattg
     2881 tattttttca atgaaaatct caaagatatc tgacgaacat ttttctaatt acaacatgtt
     2941 gccgaatggt aatgaagaaa ttgacctttt tgacttgatt agagttttat gggcagcaaa
     3001 aataaaaatt gttggggtga ttctattttt tgcttgtatt ggctttcttg tttcttttgt
     3061 tttgccacaa aaatggacta gttctgctgt ggttactcct gctgagtctg ttcaatggag
     3121 tgaattaaat aaggagcttt ccaagcttca tgttctggga gtggattttg atatcaatcg
     3181 tgatagcgca tttgctctgt ttattaagaa atttcagtcc gttaattcgt tgaatgagta
     3241 tatgagatca tctccttatg ttatggagat aattaaaaag aagaacatta gcgctctcga
     3301 actgcatcgt gcaattgttg ggttgagtga aaatatgaag tcggttgatg ataatgccag
     3361 taagaaaaac gacaagtcat cattgtatgt atcatggact ctgagtttta ctgctccaac
     3421 aagtaaagaa gctcacgatg tgttgtctgg gtatattaat tatgtttctt cccttgttgt
     3481 aagggatttg atggaagata taagaaatga actagaagtt aaaactaatg ttgaaaaaga
     3541 aattcttgca ctggatgaga taaaaattag aaaccagctg aatgcagata ttcgacgcct
     3601 caattattca ctggaggttg ctaatgcggc tggaataaaa aaacctgtat acagcaatgg
     3661 tcagattatg aaggatgatc cagattttcc tgtggctctc ggttctgatg gtatagcaac
     3721 taaattgaac atcaaaaaat caatcaagga tgtttcggaa ttgagtgggg agttgcgaaa
     3781 tcgtcaatat gttgtgaatc aattggttgt ggcgaaagtg ggggatgttg attttatgcc
     3841 gtttcagtat caattgagcc caacgttacc ggtcagaaag gatgggccaa gtaatgccat
     3901 aattgtaatt ctttcttctg tcattggagg gatgcttgca tgtggctata tacttttacg
     3961 tcatgccatg gaggccagaa agatgagtgt gattgagtaa aagttgtgct gatgcatcat
     4021 tttataagca acttttataa aaagttcaaa ggatcttctt gagatcattc cctta
//
