LOCUS       NZ_CP147114             4696 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain KMi029 plasmid pKMi029_5, complete sequence.
ACCESSION   NZ_CP147114
VERSION     NZ_CP147114.1
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 4696)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4696)
  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
            CP147114.1.
            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..4696
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KMi029"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="pKMi029_5"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Ryota Gomi"
     gene            complement(<61..645)
                     /locus_tag="WAZ84_RS24465"
                     /old_locus_tag="WAZ84_24460"
                     /pseudo=""
     CDS             complement(<61..645)
                     /locus_tag="WAZ84_RS24465"
                     /old_locus_tag="WAZ84_24460"
                     /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(587..910)
                     /locus_tag="WAZ84_RS24470"
                     /old_locus_tag="WAZ84_24465"
     CDS             complement(587..910)
                     /locus_tag="WAZ84_RS24470"
                     /old_locus_tag="WAZ84_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_078206222.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMTIGDELRRLRLAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            976..1167
                     /locus_tag="WAZ84_RS24475"
                     /old_locus_tag="WAZ84_24470"
     CDS             976..1167
                     /locus_tag="WAZ84_RS24475"
                     /old_locus_tag="WAZ84_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_078206223.1"
                     /translation="MTKQEKTALNMARFIKSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1818..1976
                     /locus_tag="WAZ84_RS24480"
                     /old_locus_tag="WAZ84_24475"
     CDS             1818..1976
                     /locus_tag="WAZ84_RS24480"
                     /old_locus_tag="WAZ84_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_277107729.1"
                     /translation="MHEPPVQPDRCAFSGNYRLESNPVRHDLTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(2343..2486)
                     /locus_tag="WAZ84_RS24485"
                     /old_locus_tag="WAZ84_24480"
     CDS             complement(2343..2486)
                     /locus_tag="WAZ84_RS24485"
                     /old_locus_tag="WAZ84_24480"
                     /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_170872253.1"
                     /translation="MIKVLCDADKNIDKRLLSHLSPLGWERISLTDDYIWHQNKQVEQC
                     KF"
                     /name="hypothetical protein"
     gene            complement(2541..3308)
                     /locus_tag="WAZ84_RS24490"
                     /old_locus_tag="WAZ84_24485"
     CDS             complement(2541..3308)
                     /locus_tag="WAZ84_RS24490"
                     /old_locus_tag="WAZ84_24485"
                     /inference="COORDINATES: protein motif:HMM:NF024242.4"
                     /GO_function="GO:0003700 - DNA-binding transcription factor
                     activity [Evidence IEA]; GO:0043565 - sequence-specific DNA
                     binding [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [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_078206224.1"
                     /translation="MTQVCSIAFVKQSFSAEINNKIVCIRQNSLILFDQKVKSEISKNR
                     ERIIIIDIDLNTCMSFFTNTYNNAPLKCVTDECGLLIKENILPSLTATLFEFIEKTDHY
                     AASSRVWLCMSLLSLFNEHNDVNSFIFTHMKSISYKVICIINAIPEKQWQLKDVSERIY
                     MSESLIKKKLKNEGTSFTLLLIDIRMRLAKKLLSSGLYSISETAIKCGYKNTSYFISSF
                     KKYYGVTPSHHIKNTINNVNPTKVQYSNLGELY"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3847..4080)
                     /locus_tag="WAZ84_RS24495"
                     /old_locus_tag="WAZ84_24490"
     CDS             complement(3847..4080)
                     /locus_tag="WAZ84_RS24495"
                     /old_locus_tag="WAZ84_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4087..4605)
                     /locus_tag="WAZ84_RS24500"
                     /old_locus_tag="WAZ84_24495"
     CDS             complement(4087..4605)
                     /locus_tag="WAZ84_RS24500"
                     /old_locus_tag="WAZ84_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_078206227.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMRQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     Typing          complement(1254..1339)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="1.8899999999999998e-34"
     Typing          1363..1890
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.322"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(2..597)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.46e-128"
ORIGIN
        1 ttccgtgagc gcctgaatca catcctgacg gccttttatc tccccgacat gataaagagc
       61 gtctatcccg cgtgtgacgc tctcagcaag cgcctgtttc gtttccggca ggttatcagg
      121 gagagtcagt atccggcggt tctccggggc gttggggtca tgcagcccgt aatggtgatt
      181 caccagcgtc tgccaggcat caattctcgg cctgtctgcc cggtcgtagt acggctggag
      241 gcgttttccg ctctgtaact ccatgttcgg aatgacaaaa ttcagctcaa gccgtccctt
      301 gtcctggtgc tccacccaca ggatgctgta ctgattcttt tcgagaccgg gcatcagtac
      361 acgctcaaag ctcgccatca ctttttcacg ccctccaggc ggcagctcct tctccgcgaa
      421 cgacagaaca cctgacgtat atttcttcgc aaatggcgtg gcatcgatga gttcccggac
      481 ttcttccgga ttaccctgaa gcaccgttgc cccttcccgg ttacgctccc ttcccagcag
      541 gtaatcaacc ggaccactgc caccaccttt ccccctggca tgaaacttaa ctatcatccc
      601 gccctccctg ttccctgacg gcaagacgca accggcgcag ctcatccccg atggtcatca
      661 gtgcggccac cacctgaacc cggtccccgg aagaccactg cccgctgttc accttcctcg
      721 ctgtctgatt caggttattt ccgatggcgg ccagctgacg cagtaacggc ggtgccagtg
      781 tcggcagctt cccggaacgg gcgacaggct cacccaggca gacccgccgc atccataccg
      841 ccagttgttt accctcacag cgctccagta accgggcatg ttcatcatca gtaacccgta
      901 tcgtgagcat cctctcgcgt ttcatcggta tcattacccc catgaacaga aatcccccct
      961 tacacggagg catcagtgac caaacaggaa aaaaccgccc ttaacatggc ccgctttatc
     1021 aaaagccaga cattaacgct gctggagaag ctcaacgaac tggacgcaga tgaacaggca
     1081 gacatctgtg aatcgcttca cgaccacgcc gatgagcttt accgcagctg cctagcacgc
     1141 ttcggggatg acggtgaaaa cctctgacac aggcagctcc cggagacggt cacagcttgt
     1201 ctgtgagcag atgccgggag cagataagcc cgccagggcg cgtcagcggg ttttagcggg
     1261 tgtcggggcg cagccatgac ccagtcacgt agcgatagcg gagtgtatac tggcttaacc
     1321 atgcggcatc gtgctgattg tatgaaaagc gcatcatggc cggtgtgaaa cgccgcacag
     1381 atgcgtaagg agaaaatgca catccgggca ctttcccgct tcctcgctca ctgactcgct
     1441 acgctcggtc gttcggctgc ggcgagcggt actgactcac tcagagacgg taatacggtt
     1501 atccacagaa tcaggggata aggccggaaa gaacatgtga gcaaaaaggc cgcgccactg
     1561 gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaaacgacg ctcaagtcag
     1621 aggtggcgaa acccgacagg acttaaagat accaggcgtt tccccctgga agctccctcg
     1681 tgcgctctcc tgttccgacc ctgccgttta ccggatacct gtccgccttt ctcccttcgg
     1741 gaagcgtggc gctttctcat agctcacgct gttggtatct cggctcggtg taggtcgttc
     1801 gctccaagct gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttttccg
     1861 gtaactatcg tcttgagtcc aacccggtaa gacacgactt aacgccactg gcagcagcca
     1921 ttggtaactg gacaaggtgg attgagatat taagagttct tgaagtggtg gcctaactga
     1981 ggctacacta gaaggactgt tttggtatct gcgctccacc taagccagtt accttcggaa
     2041 gaaagagttg gtagctctca attccggcaa acaaaccacc gttggtagcg gtggtttttt
     2101 tgtttacagg cagcagatta cgcgcaggaa aaaaggatct caagaagatc ctttgatctt
     2161 ttcatcactc cgacttcatg gacaacaata atgtcggcat ctcgcctata aaatcactga
     2221 actcattcag gcaaacttcc aagataaact acctagtaat gactctgatt tatcgtcaaa
     2281 taaggctcag ctcacgaaac ggaaaaaatc gtacgctagg cctcgccagg cattcgtaac
     2341 ggtcaaaact tgcattgctc gacctgcttg ttctggtgcc agatgtagtc atcagtcaga
     2401 ctgatgcgct cccagcccag cggcgaaaga tgcgataata gtcgcttgtc gatgttcttg
     2461 tccgcgtcgc acagcacctt gatcacccgt gcctgaaatc caaccggata cagagagaac
     2521 cacccgaaaa tctgatttat ttaataaagc tcgcctaggt tagaatattg aacctttgtt
     2581 ggattaacat tattaatagt gttttttata tggtgtgatg gtgttactcc ataatatttt
     2641 ttaaatgaag atataaaata tgacgtattt ttatacccac acttaattgc tgtctcgcta
     2701 atagaataca atcctgatga aagcaatttt ttggcgagac gcattcgaat gtcaattaat
     2761 agcaatgtga acgaagtacc ttcatttttt aactttttct ttatcaaact ttcactcata
     2821 tatattcgct cagaaacatc ttttaactgc cattgttttt ctggaattgc gttaatgata
     2881 caaataactt tatatgagat ggatttcata tgcgtaaaga taaagctatt aacgtcatta
     2941 tgttcattaa atagtgataa cagagacata cataaccaga cccttgaact cgcagcgtaa
     3001 tgatctgttt tttctataaa ttcaaagagg gttgccgtta atgatggcaa aatattctct
     3061 ttgataagca aaccacactc atctgtaacg cactttaacg gtgcgttatt gtacgtgtta
     3121 gtaaaaaatg acatacacgt attaagatcg atgtcgataa ttattatcct ttctctattc
     3181 ttcgaaattt cgctttttac tttttgatca aaaagaataa gtgaattttg tcttatacag
     3241 actatcttat tgtttatttc agcggaaaat gattgtttaa caaaggctat agagcaaact
     3301 tgtgtcataa tatctattcc ttgattattt tcgtgataat tataagcaac aaggattttt
     3361 aatccttata taaatagcta tttatacatc aactaattaa attagcatat ttaatactat
     3421 acatatagct cgatataatg attttgtcga tgttgttagt aaaatattta tcaatataca
     3481 aaaagtacaa aaaaaacagt ccagaacaaa cccaaaaata gagctaagcg gcgtatttac
     3541 cataacgtcg cattacgcgc accgctaaaa cgcgttcagc gcgatcacgg cagcagacag
     3601 gtaaaaatgg caacaaacca cccgaaaaac tgccgcgatc gcgcctgata aattttaacc
     3661 gtatgaatac ctatgcaacc agatggtaca ggccacatta ccccctctta atccactgaa
     3721 gctgccattt ttcatggttt caccatccca gcgaagggcc atccagcgtg cgttcctgta
     3781 tttccggctg acgctcccgt tccagggata acgcatgttc gcgctcctgt atcagccgtt
     3841 cctctcttat ctccagttct cgctgtataa ctgactcaag cgttctgtct gctcgctcaa
     3901 gtgctgcacc tgctgactca actgcatgac ccgctcgttc agcatcgcgt tgtcccgttg
     3961 cgtaagcgaa aacatcttct gcaattccac gaaggcgctc tcccattcgc tcagccgctg
     4021 catatagtcc tgttgcagct gctctaaggc gttcagcaaa tgtgtttcca gctctgtcac
     4081 tctgtgtcac tccttcagat gtacccattc cttcccctga aaggaaatca cctctgctga
     4141 cttcccgtaa ggaaggacca gaaatttcct gttcccgtcc tgcacaaact ccacgcccca
     4201 tgtcttcgcg ttcagtttct gcaatgtctc ttcctgcttc ctgatatctt ccaggttcgc
     4261 ctgtatcctc ccgccaagat accagagcgt cccgccactc gcggtaaaca ggagaaagac
     4321 tatccccagt aacatcatgc ccgtattccc tgccagcttt aacacgtcct tcctgtgctg
     4381 cctcatcgcc tctttcaccc cttcccggtg tttctccagc gattcctctg tcgaggctgt
     4441 gaacagggct atagcgtctc tgattttcgt ctcgtttgat gtcacagcct cgcttacaga
     4501 ttcgccgagc ctcctgaact cgttgttcag cattttctct gtagattcgg ctctctcttt
     4561 cagctttttc tcgaactccg cgcccgtctg taaaagattg ctcataaaac gctcctttca
     4621 gtctgatatt cctcccgccg ttcgggtctg caatgctgat actgcttcgc gtcaccctga
     4681 ccacttcaag ccccgc
//
