LOCUS       NZ_CP147117             4018 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_8, complete sequence.
ACCESSION   NZ_CP147117
VERSION     NZ_CP147117.1
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 4018)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4018)
  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
            CP147117.1.
            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..4018
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_8"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            604..927
                     /locus_tag="WAZ84_RS24545"
                     /old_locus_tag="WAZ84_24540"
     CDS             604..927
                     /locus_tag="WAZ84_RS24545"
                     /old_locus_tag="WAZ84_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_024191642.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1136..>1570
                     /locus_tag="WAZ84_RS24550"
                     /old_locus_tag="WAZ84_24545"
                     /pseudo=""
     CDS             1136..>1570
                     /locus_tag="WAZ84_RS24550"
                     /old_locus_tag="WAZ84_24545"
                     /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            1605..2090
                     /locus_tag="WAZ84_RS24555"
                     /old_locus_tag="WAZ84_24550"
     CDS             1605..2090
                     /locus_tag="WAZ84_RS24555"
                     /old_locus_tag="WAZ84_24550"
                     /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_061390563.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2094..2309
                     /locus_tag="WAZ84_RS24560"
                     /old_locus_tag="WAZ84_24555"
     CDS             2094..2309
                     /locus_tag="WAZ84_RS24560"
                     /old_locus_tag="WAZ84_24555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_072048928.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2438..2965
                     /locus_tag="WAZ84_RS24565"
                     /old_locus_tag="WAZ84_24560"
     CDS             2438..2965
                     /locus_tag="WAZ84_RS24565"
                     /old_locus_tag="WAZ84_24560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016246513.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            3220..3432
                     /locus_tag="WAZ84_RS24570"
                     /old_locus_tag="WAZ84_24565"
     CDS             3220..3432
                     /locus_tag="WAZ84_RS24570"
                     /old_locus_tag="WAZ84_24565"
                     /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_034169353.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(3861..3974)
                     /locus_tag="WAZ84_RS24575"
                     /old_locus_tag="WAZ84_24570"
     CDS             complement(3861..3974)
                     /locus_tag="WAZ84_RS24575"
                     /old_locus_tag="WAZ84_24570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072035093.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     Typing          314..491
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          complement(2..198)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.477"
                     /coverage="86.0"
                     /evalue="1.12e-83"
     Typing          complement(3658..4018)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.282"
                     /coverage="99.0"
                     /evalue="1.15e-74"
     Typing          918..2401
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggcgtggaat tagataaacg cggccataac agcggaatga caccggtaaa ccgaaaggca
       61 ggaacaggag agcgcacgag ggagctacca gggggaaacg cctgggatct ttatagtcct
      121 gtcgggtttc gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg
      181 agcctatgga aaaacggcaa cgccgcatcc tttttccgcc ctttctgatt gatttccgct
      241 tagtctcttt atccagccat tcgtaagctg gcaacgcccg ccgcagtctc acggcaggag
      301 cgcagcgacc gagtgagcga ggaggcgtca tttcaccggg atctgcattt cgcacttacg
      361 ccccacagca gcattttctc cctgccacat gaagcacttt cctgaatccc cactccgatt
      421 taccatgtta agccagtata cactccgcta gcgctacgtg actggttcag ggctgcgccc
      481 cgaaacccgc tgaaaagtac tgccgcgccc tgcgggcttg cccaacaccg ctccggacag
      541 gaaaaaattt cccgcccgaa ccggtgttat ccggaggatg gtttggcaga aaagcgcaac
      601 aaaatgctca ctatgtgggt gacagaagac gagcaccgcc gacttctgga gcgctgtgag
      661 ggtaaacaac tcgcggcctg gatgcgccag atatgcctgg acgaaaagcc ctcgcgtgct
      721 ggcaaacttc catccatctc gccggcgctg cttcgtcagc ttgccggcat gggtaacaac
      781 ctcaaccaga ttgcccggca ggttaacgcc ggtggcggta ctgggcacga tcgcgtgcag
      841 gttgtcgccg tgctgatggc cattgatgcc ggactcgagc ggctgcggca cgccgtgctg
      901 gaaaaggggg cagacgatga tcgttaagtt tcatcccaga ggccgcggcg gtggcggcgg
      961 tccggtggat tatctgctgg ggaaagaccg gcagcgcgac ggcgccagcg ttctgcaggg
     1021 taagccggag gaagtgcggg agcttattga cgcctcgcct tacgccaaga aatacacctc
     1081 cggcgtgctg tcttttgccg aacaggattt gccgcccggc cagcgtgaaa agctgatggc
     1141 gagctttgag cgggttctga tgcccggact cgataaagac cagtacagcg tactgtgggt
     1201 tgagcaccgg gacaaagggc ggctggagct gaacttcctg atcccgaaca cggagctgct
     1261 gaccggcaga cgtctccagc cgtattacga ccgcgccgac cgtccgcgca ttgatgcctg
     1321 gcagaccata gtgaacggca gactggggct gcacgacccg aacgcgccgg aaaaccggcg
     1381 ggcgctggtt acaccgtccg cgctgccgga agcgaagcag gaagccgccc aggcgattac
     1441 gcgcggccta ctttcccttg cctcatccgg ggagctgaaa acccgtcagg acgtcactga
     1501 ggcgctggaa agtgcgggtt ttgaggtggt gcgcaccacg aaaagcagca tcagcattgc
     1561 cgaccctgac ggggggcgaa acatccgact gaagggagcc atctatgaac agtcttttaa
     1621 cgctggcgaa ggacttagag cagaaatcga aagcgcagca gcagactacc ggcgagatgc
     1681 tgaaagccgc attcagcgag cacgagaagt ctgtcagagc ggaactgagc gaaagcgaga
     1741 agagaatcag cgccgccatc ctcgaccacg accggaagct gtcctcagcc atgagccaac
     1801 gcacgaaagg gatgctgcgt atgatcagcc agacgtggct gaccatagtc ctggtctccg
     1861 cgctactgat cgcctcgagc gcgggcattc tgtggtggca ggggcaacag atactcgaca
     1921 actacacgac catccaggaa cagaagagca cgcaggccat gctttcagag aagaacaacg
     1981 gcgtccagct cacgacctgc ggggaggaga gacgccgctg cgtgagggtg aacccggaag
     2041 cgggaagatt cggagaggat tcgagctgga tgatactggc ggggaaatag cacatgacgg
     2101 aactggaaaa acagttgctg agcgcattag agcagctaca gcaggactac tcgaaaaggc
     2161 tggacgagtg ggagaacgcc ttcgcggaat ggcggacgat gtctgggctt atgcaacggg
     2221 agaacgcggc gctgagcgag cgcgtcacgg gcttgagcag gcaggtgcag agtttgagcg
     2281 atcagctgcg ccgattgtcg caaggctgaa tggcatcgag gcgcaccggg agcaggagcg
     2341 cgcggcgcag caccagaaag cgctggagct ggaacgatcg cagcggcaga aaggttttga
     2401 gcttggaatg tagttaatca atgaaaaggg atgcgttatg aaatgtttct gggcttgctc
     2461 agtctcggtg gttttggcta tgtcatttac agtcgctgct gcggagaata acgacaacgt
     2521 tacatataca aaaccgtcag ccgggaggga cttatatctt acctgtaaag gttatcaggt
     2581 gaagggggca tctgtaatta acgtcgagaa accttcttac cttgaaggta ctggtgagca
     2641 ggttgaattt gcaatcatta ctcctgttgg tgcgtctgac ggactcaagg tcttttttga
     2701 ttcatggggt ttttcttcat ttggattgat tgaaagccat gtgatgcatg agcactggtc
     2761 tttagttcat gttggggggc gtgcttcagt caaaggtgaa aagattgatt attcatttgt
     2821 agataaccag ccacaggagg gggggagcta taaacccaaa acaggtgtgt tcctgtacgg
     2881 ctgcatgaac tcggataaaa gaccatcttg ggtcgaaaag atctacacaa gaacaggtgt
     2941 gtttcgaggg ggcatagaag actaaaatac tgcttacagc atgaaaatcc attgaacaga
     3001 gtgtcagttc atttccgtgc ataactatgc ataccgtaag aacttacggg gggcatttat
     3061 cggcgttttt acgtggtaag aggtgctctt ttgcggttca tggcgcagaa cggtgctgag
     3121 gctgtctgcg gcggtgcgaa caagggatgt tatggtaaat aagagtgtct tttggatatt
     3181 ttaaatctgt ttttttatta aatttaatgg gggcagaaaa tgggggattt tgagcgtacc
     3241 tttggagctg gtgctgattt tgatcggata attgatgaga ataacagcga atattttcga
     3301 gaagatcgcc gaaaaactaa aaattcaaaa aaaaaattct cttcttttca agatgctttg
     3361 gtttgggcga aagctaatcc tggcaaaacg ataataagat ctccagacgg tgtggggttt
     3421 attgaaaaat gaaagagtgg attcactgta aaacaacagt cattttttgg acaacactgt
     3481 ctatatacgt actcatatgt ttcacagtgt cgtatgttgg agtctatgtt acgtacgttg
     3541 cagggcctat tttgttagtt acaggcattc ttgcatggct tacgaaacct agctgtaatc
     3601 caaagtgact gggctagacg aactttatcc ccccataaaa cccgcttttt taaacggatc
     3661 ttcttgagat cattcatgga gaatcgtaat ctcttagcac tgtaaacgaa aaaaccgccc
     3721 agcaaggcgg ttttttcgaa ggttctcaga gcagcaactc tttgaaccga ggtaactggc
     3781 ttggaggagc acagtcacca aaacttgtcc tttcagttta gccttaaccg gcgcataact
     3841 tcaagactaa ctcctctaaa tcagttacca gtggctgctg ccagtggcgt tttgtcgtgt
     3901 ctttccgggt tggactcaag tcgatagtta ccggataagg cgcagcggtc ggactgaacg
     3961 gggggttcgt gcatacagtc cagcttggag cgaactgcct acccggaact gagtgtca
//
