LOCUS       NZ_CP147113             4906 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_4, complete sequence.
ACCESSION   NZ_CP147113
VERSION     NZ_CP147113.1
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 4906)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4906)
  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
            CP147113.1.
            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..4906
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_4"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            complement(join(4593..4906,1..19))
                     /locus_tag="WAZ84_RS24425"
                     /old_locus_tag="WAZ84_24420"
     CDS             complement(join(4593..4906,1..19))
                     /locus_tag="WAZ84_RS24425"
                     /old_locus_tag="WAZ84_24420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_064184160.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKIRMATGNQGKSGSVRVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKNEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(175..420)
                     /locus_tag="WAZ84_RS24430"
                     /old_locus_tag="WAZ84_24425"
     CDS             complement(175..420)
                     /locus_tag="WAZ84_RS24430"
                     /old_locus_tag="WAZ84_24425"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_306293335.1"
                     /translation="MTKTMTEMEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATS
                     QALTHSDRVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(469..954)
                     /locus_tag="WAZ84_RS24435"
                     /old_locus_tag="WAZ84_24430"
     CDS             complement(469..954)
                     /locus_tag="WAZ84_RS24435"
                     /old_locus_tag="WAZ84_24430"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_095841943.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMLRASVSTAMAWIFICFALLIGILSGIIWFQGTIITSRLSEMD
                     SYSQQLESLKAKSGAGVAIYSDDKHRNTYMVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            complement(<1001..1423)
                     /locus_tag="WAZ84_RS24440"
                     /old_locus_tag="WAZ84_24435"
                     /pseudo=""
     CDS             complement(<1001..1423)
                     /locus_tag="WAZ84_RS24440"
                     /old_locus_tag="WAZ84_24435"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1632..1958)
                     /locus_tag="WAZ84_RS24445"
                     /old_locus_tag="WAZ84_24440"
     CDS             complement(1632..1958)
                     /locus_tag="WAZ84_RS24445"
                     /old_locus_tag="WAZ84_24440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_042014476.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHISRK
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDSLTPAERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(2174..2899)
                     /locus_tag="WAZ84_RS24450"
                     /old_locus_tag="WAZ84_24445"
     CDS             complement(2174..2899)
                     /locus_tag="WAZ84_RS24450"
                     /old_locus_tag="WAZ84_24445"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004193434.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_223526271.1"
                     /translation="MDLFNVDAVEWLKTLPSGSVDMVVTDPPYESLEKHRKIGTTTRLK
                     VSKSSSNEWFSIFPNDRFESLLSEIHRVLKNNRHFYIFCDQETMFLLKPIGEKVGFKFW
                     KPIVWDKKAIGMGYHYRAKYEFILFFEKGKRKLNNLGIPDILESKRIRNGYPTEKPVEL
                     LELLIQQSTERGELVIDPFFGSGSALKAALNQGRLCAGNDISASAHAYFRDTHLPDDLK
                     SAALTPALPVEQAARICTK"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(3221..4114)
                     /locus_tag="WAZ84_RS24455"
                     /old_locus_tag="WAZ84_24450"
     CDS             complement(3221..4114)
                     /locus_tag="WAZ84_RS24455"
                     /old_locus_tag="WAZ84_24450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517860.1"
                     /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_094158691.1"
                     /translation="MNNAVLELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERASAYNLQFAVPLD
                     DKEVNDIAKSIAKWTLKRLDESTFKQYVLDTHSPEIQSVRGKRSKRGASLCSERTLEPW
                     VELGISRRKYYYDKKK"
                     /name="replication initiation protein"
     gene            complement(4307..4591)
                     /gene="nadS"
                     /locus_tag="WAZ84_RS24460"
                     /old_locus_tag="WAZ84_24455"
     CDS             complement(4307..4591)
                     /gene="nadS"
                     /locus_tag="WAZ84_RS24460"
                     /old_locus_tag="WAZ84_24455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     Typing          1633..1825
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.513"
                     /coverage="100.0"
                     /evalue="1.87e-33"
     Typing          complement(84..1642)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.51"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actcaatcgc gtgactcacg gctgtctcct gtttttaacg gagtacatag tacacttaat
       61 tctgatttcg gaaaagcggt cacatcgagg ggccatagta acgagtcgtt tttttctgcg
      121 gctccggctg ctgctcgcgc agcttctcct cactggcgcg gtcatgctgt gcaatcagcg
      181 catcaagcgg ctgacgttcc tgctcaagct ctcgacctgc gcgcgcaagc tctctacctg
      241 actgctcaag tgctgacaca cccggtcgct gtgcgtcagc gcctgtgaag tagcctcgaa
      301 catgtgctgc aagctgctgt agctgtcctg ccacgcctgc tgctgttgct cgtagcttgt
      361 ctgtaagctc tctaaggcgc tcagaagctg tttttccatc tcggtcatcg ttttggtcat
      421 cctcggtgtt aaaaacgcgc tgtgtcgttt cagggcgctc tgacggggtt atttcgccgt
      481 gtatttcact acggtgttgt cggtcgtcga tgtataggtt tccacgccgt gcgcctgctt
      541 cggcagcacc accatgtagg tgttccggtg cttgtcgtcg ctgtagatcg ccacgcccgc
      601 gccgcttttc gctttcaggc tctccagctg ttggctgtag ctgtccatct cgctcaggcg
      661 cgaggtgatg atcgtgccct gaaaccagat tatcccgctc aggatgccga tcagcagggc
      721 gaagcagatg aatatccacg ccatcgccgt tgagacagag gctctgagca tgcccgtcag
      781 tctgccgttc tgctcgcgga tagcgttgct gatgctctgc gagcttgatt gcagttccgc
      841 gctgatagac gtctccagcc tcgcgaactc gcgcttcacg ctctgctcgg tatcctgcgc
      901 ctgctgcttc gatttctcct cgaagccctt cgccaaattt aaaatctcgc tcataaatca
      961 ttcctttcag ccggatattt cggccgccgt ccggatcggc aatgctgatg ctgcttttcg
     1021 tttcccgcgc cacggtcagg ccgtagcttt ccagctgcgt caccacgtcc tgccggctgc
     1081 ggatcacgcc ctgctgcatc aggttcatca ggccggcggt gattttctct gccgcctgct
     1141 gtttgtcgcg gggcagatcg ctggcctgcg tcagcggacg gcggtagatc gggtcgttcg
     1201 ggtcgcgcag ccccagccgg tcgttggtca gggtctgcca ggcgttgacg cggggacggt
     1261 cggcgcggtc aaagtagggt tgcaggcgtt ttccactctg caattcgatg ttcgggatga
     1321 caaaattcag ctcaagccgt cccttgtcgc gatgctctac ccacaggcag gcgtactggt
     1381 cgcggtcgag gccggtcagc agcgtgtgct cccattcgtc catcaggcgc gatttctcca
     1441 cgtctgcaat gtcaggttcc tggaatgaaa gcacgccgga agtataggcg cgggcaaagt
     1501 cgcagccgtc gatcagctcc cgcacatgtt caggattgcc gcgcagtacg gtggcctgtt
     1561 cgcgctgccg gtcttttccc agcaggtaat ccacaggacc gctacccgaa cccgcacccc
     1621 gcgagtgaat tttaacgatc acggttctgc tccagcaggt cgccaagctg acggtcaagg
     1681 ctggtcagta cgacgagcag cgaggcacgt tcagcaggcg tcagggaatc agtctgattc
     1741 aggcgacggg cgatctggtt caggttattg ccaatcccgc tgacctgtcg cagcagttcg
     1801 ggcgccacat caggcacacg gcgcttgcgt gagatgtgtt cacccagacc gagctgacgt
     1861 aaccattcgg caaggtgagt acggtcacag cggtcaagca gccgctgatg ctcagtttcg
     1921 gtgagccgga ttttgatctc tttcgttcgc ttttccatag gctccgctga gaaaaaattc
     1981 gcaccaccgt gagaattttt cgcagtggat gccgggggtt tcggggggcg gcgagccccc
     2041 tgaaccagtc acggtggcac ctcgttagag gggacgctgt gtgtactggc ttaggggaaa
     2101 gtgcagtatg acagattcag tgctggttgc aaaaaaaagc cctctgctag agagggctgt
     2161 tatctgatat aggttatttg gtgcaaattc tcgcagcctg ctcaacggga agcgctggag
     2221 tgagtgctgc tgattttaga tcgtcaggga gatgggtatc tctaaagtaa gcgtgtgccg
     2281 atgctgatat atcattacca gcgcaaagac gcccctgatt gagagctgct tttagtgctg
     2341 agccggaccc aaagaaaggg tctatcacaa gctctccacg ctctgtactt tgctgtatca
     2401 atagctccag caactcgaca ggtttctccg ttgggtaccc atttctaatt cttttacttt
     2461 ctaatatatc tggtatccct aaattattta gctttctttt acccttttca aaaaatagaa
     2521 taaactcata cttcgctctg tagtgatagc ccatcccgat agccttttta tcccaaacta
     2581 taggcttcca aaatttaaat cctactttct ctccaatggg ttttaaaaga aacattgttt
     2641 cttggtcaca aaatatataa aaatgcctat tatttttaag caccctatga atttcagaaa
     2701 gcaacgattc aaacctatcg tttgggaaaa tactgaacca ttcattgcta gatgatttac
     2761 tcaccttaag ccttgttgta gtacctatct tcctgtgttt ctctaacgat tcatacgggg
     2821 ggtctgtgac caccatatcg acgctcccgc tagggagcgt ctttaaccat tcaactgcat
     2881 caacattaaa caaatcaatc acgctttagc taccatattg cacttaatct catgagataa
     2941 atcgacagaa gatggttcac caggcccttt attacgacaa tcaatgcaat ggctatgtac
     3001 accatctggg ttatttgccg ttactcgacg gtcagtaaaa ccgaagtctt caacaagcct
     3061 acgaaaaata tgaagtgaac cgtgagtttg agaacaccta gggcatgatt ttaacgtatt
     3121 atcagcactt ctaatagcaa tgcttaaatc aacaccacaa caggtacaag aactcatata
     3181 aacctccaaa ttaacaatgc tgtgaatcaa attaaaaaca tcattttttc ttgtcgtagt
     3241 agtattttct acgactaata ccaagctcaa cccaaggctc taaagttctt tcagaacata
     3301 atgatgcgcc tcttttcgac ctctttcccc ttactgattg aatctcaggg gaatgagtat
     3361 ctaatacata ctgcttaaaa gtagactcgt cgagtctttt aagagtccat ttggcgatac
     3421 tctttgcaat atcattgacc tctttatcat ccaaaggcac agcaaattgc agattgtagg
     3481 cgctggcacg ctcatagcag gcttgcagcc actgctcata ctcaggccag ccctgacgga
     3541 tggcgcggta tgcccacttg cgggttttgt cgaacaacgt gcagttacgg cctaagccgt
     3601 agtcggcaac gatttctttg tcgttcgcag cgttcaggtc gagaaagtca gccagccagt
     3661 ccagtgtgta gagttctggc tgccacaccg caattttcca gtggccgtgg ttcggatttt
     3721 tgcagattaa ccccgaatac cccgcgtcag cctctaattt tttacgcagc gcgttctcca
     3781 cggcggcagc gtagcgcagc ggcttcattt tcccgtcagg tgcggtgcgt atcgaggttt
     3841 ccagcgcgta cagcaggtgc gcgtgtccgt tttccgggtt ggtgatggtc agcgtgggcg
     3901 cgggcgcgtt gcgatcgctc cagtcgatgg cggcaccggc gcgatcgacg tcgaatccca
     3961 gccagaacat ggcgtgaggc tgattgaact ggatgtattt cgccaaaatg gcgcgttctt
     4021 tccctgcaat gcgtacacca aagtgtaaat catccgagaa gtacggcttg tgcggtaagc
     4081 ggtcgttgaa aagttcgagt actgcgttat tcaattcgcc ctgcgcttat ggcgggctgt
     4141 tgtctggcac gtttcatgtg ctaatatcct ttcaaggttt cgacctggcc ctggttatca
     4201 tgtgcatccg ccaagattga gcatgatttc cggggctttg ttttttctgt tgccgttaaa
     4261 ttacacgcga acggcctcgc ctgtcgaatc cttctgtcac aacggcttag tgcgccgcca
     4321 gttcctggaa gaatttcggg ttcgcctgga tggttgccag taccttcgcc gccagtccgg
     4381 tcgggttacg gcgtccggtt tcccagctct tgatggtgtc gaggctggtt cccagcactt
     4441 ttgccatctc gctctgagat acgttcagct gtgccctgat ggctttcacg tctgccagct
     4501 cgtaacgggt gacgcgggca ggctctctga cgccgttttt gatttcaacg gcttcttcca
     4561 gcgatgcttt cagctcgtca aaaaaactca tgtcacacct cgtttttcag ttgttgggtc
     4621 agcgtcttca gcgcggcttt ttccgcgtcc gtcaggctgt ctttggtgct tttcgggtag
     4681 gccatcacca gatagatcac ctcggcggtg gccagaaagt aaatcaccct cacgctgccg
     4741 ctttttccct ggttgcccgt cgccatcctg attttgcgca gcccgccggt tttctgaatg
     4801 agatcgcctt tgtccggcga ctcaatcagc gtcttttgca gttccctgag ttcttcatcc
     4861 gtggcgatct gttttatctg acgggtaaac atcggggtct cgataa
//
