LOCUS       NZ_CP147073             6863 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain JKHS004 plasmid pJKHS004_4, complete
            sequence.
ACCESSION   NZ_CP147073
VERSION     NZ_CP147073.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992797
            Assembly: GCF_038396485.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6863)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6863)
  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                   :: Flye v. 2.9.1
            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_038396485.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:20:08
            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)                     :: 5,152
            CDSs (total)                      :: 5,028
            Genes (coding)                    :: 4,836
            CDSs (with protein)               :: 4,836
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 78 of 192
            Pseudo Genes (incomplete)         :: 118 of 192
            Pseudo Genes (internal stop)      :: 39 of 192
            Pseudo Genes (multiple problems)  :: 43 of 192
            Pseudo Genes (short protein)      :: 2 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147073.1.
            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..6863
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JKHS004"
                     /isolation_source="hospital wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pJKHS004_4"
                     /geo_loc_name="Japan"
                     /collection_date="2015"
                     /collected_by="Ryota Gomi"
     gene            complement(join(5427..6863,1..546))
                     /locus_tag="WAZ93_RS25745"
                     /old_locus_tag="WAZ93_25745"
     CDS             complement(join(5427..6863,1..546))
                     /locus_tag="WAZ93_RS25745"
                     /old_locus_tag="WAZ93_25745"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966094.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006306 - DNA methylation [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_080069401.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGADIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCVLEGGMSKEDQGKSEVYYNEIIARDEIDNLFSPKVLKEVNRYSKEGVK
                     KERIFNRNDNLIIRGNNLIALHCIKNIYEKSVKLIYIDPPYNTDTDSFKYNDKFSHSTW
                     LTFMKNRLEVAKDLLCDDGLIAISIDDNELNYLASLADDIFGRKNRIAIFPRITKKGGK
                     SASIFAKNHDYILLYVRSLENKRMYAVSHDDDNFKYKDEYFAERGSYKLNQTLDYDSLQ
                     YSKSLDYIIEINGEKYYPGGDENLFNDRMNGKHNRADWAWRWSRKLFDFGFENGFIEIR
                     NGGQRPRIYTKTYQNAKISKDGNDYVITYFDRTKPLSTLEFTENKYSNDNATKHISSLL
                     GKNIFDYTKPETLLAKLIEITSTKNDLILDFNLGSGTTAAVAHKMGRRYIGIEQMEYIN
                     DITVPRLKKVIEGEQGGISKDVNWQGGGSFVYAELMELNAYFVHEIQKAQSTEELEKLF
                     TMMKTEAHLNYQVELENVLSAEYEVDGIFRKVAFSELELHEQKQLLIEILDKNKLYVNV
                     SDMEDSELSISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     gene            1414..1605
                     /locus_tag="WAZ93_RS25750"
                     /old_locus_tag="WAZ93_25750"
     CDS             1414..1605
                     /locus_tag="WAZ93_RS25750"
                     /old_locus_tag="WAZ93_25750"
                     /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_048228005.1"
                     /translation="MNKQQQTALNMARFIKSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFSDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2275..2388
                     /locus_tag="WAZ93_RS25755"
                     /old_locus_tag="WAZ93_25755"
     CDS             2275..2388
                     /locus_tag="WAZ93_RS25755"
                     /old_locus_tag="WAZ93_25755"
                     /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_072071404.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLLPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2786..5422)
                     /locus_tag="WAZ93_RS25760"
                     /old_locus_tag="WAZ93_25760"
     CDS             complement(2786..5422)
                     /locus_tag="WAZ93_RS25760"
                     /old_locus_tag="WAZ93_25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 -
                     hydrolase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="WP_088365282.1"
                     /translation="MAKKPKSVGSEKLLFNRLKQFDEPGLFHDNYQTPDYIQENLKDAL
                     RPYQHGALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKELGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSQELEIDGEKITIEPIETFPSIPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILNLRPDNRLFEFTATIDLANKDIGQKYRGKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESVRRHLANKKLQLSSDTSIWHKVIQRYANSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTIEHARLKEDFKKSAVYQAGKLYFNEVEEIESSSRNWETYSLETRFEIPYQT
                     VCEESLDNLTGTKTGITKPELLVLDERFYRKAMQRISFYALDNLQRFFPKLTGIREFIR
                     SDAYLGKLKITVIVPQSLDFTTVPAKDKLHLLETVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVVINQKITAVPTIGKKWYVYDNAILNQLEHRLIKTLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     Typing          complement(1281..1378)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="2.25e-39"
     Typing          complement(1700..1780)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.73e-35"
     Typing          1800..2347
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.128"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aattaggtta tttcctctga taattaaatt atcattacgg ttaaatattc tttctttttt
       61 tactccttct ttagagtaac gatttacttc tttgagaact ttcggtgaga acaaattatc
      121 tatttcatct cgtgcgatga tttcattata gtaaacctct gattttcctt gatcttcttt
      181 cgacataccg ccttcaagaa cacaatcctt gaaaggaaaa tccagcacca catcagaact
      241 gtaatcaagg tatttacctt cgctagttaa tcccactttg ttccggtatt tagtgaagct
      301 attagcccaa tattctttgt attttagaag accacataat ttgtcaaagt caaagataaa
      361 aatgccatca atatccgcac cataaacaga gcggactttt tcattatcga ccaatgcctt
      421 gataaggtct ggctgctttt gactgatagc gtcactcacc attgaacgtt gtaattcctc
      481 tccgttccag aattgcggga atgcttttaa aaccttgtta agttctttta ttaattcggt
      541 ctgcatgtca tggccttatg actgttaaat attggaatga ttgtaaggta tagcgttcgg
      601 tgctggaacc cgacagctat gagttggatg cagttgcggg gaaatgcatc agaatgggtg
      661 gtatttaaca taaacgctct tgcgcgcacc actaaaacgc gctgaacgcg attctgacgc
      721 aaacaccgca aaaagagatg ttttaccagt gaaaaccaga aaaatgcgtc aggatcgttt
      781 tcagctcgat gcatagctat gcatgaaagt gaatgacgat cggtttgagt gcattcggtg
      841 ccaataaggc acattttcag acattttcag ttcgtgaatt ccaggcatat ctgagcagac
      901 acccctaggg gcgctgctag gggtgtcctg taaaaaaatg cgacgcgtcc ctagggacgc
      961 ccatacctta attaactgtt ttttataaag attgtcagta ctgaccctaa gtagggtcgc
     1021 catagcgtcg ccatagggtc gtcaacgacg tgcttttgca taaatctgaa aaagaaaata
     1081 catttttgaa accataacaa catgatttca aaagcaaatc agcaaaaaat tagttttgcg
     1141 tggggtgtgg gcatttcagg catgagaaca gactcgcgtt tttccggggt atctgcggaa
     1201 tttttgataa aaaaaacctc gacgcagagc gaaattttat gcaacagcgg ctgtacagca
     1261 cagggattat ttatcagttg atatgctgtg ccatgatacc tcctaaaaaa caggacagga
     1321 tgtgcaattg taataccgtc gcgcgcaacg tcttacaatt accacctggt cagggtccac
     1381 ccgacacccg gtactgacgg agaacaaccg aaggtgaaca aacagcaaca aactgcgctg
     1441 aatatggcgc gatttatcaa aagccagacg ctaaccctgc tagaaaaact caacgagctg
     1501 gacgcggacg aacaggcgga catctgcgaa tcacttcacg accacgccga cgaactctac
     1561 cgcagttgcc tcgctcgctt cagtgatgat ggtgaaaacc tctgacacat acagctcccg
     1621 gagacggcca cagcttgcct gtgagcggat gccgggagca gacaagcccg tcagggcgcg
     1681 tcaggccgtg gaccttgcgg gtgtcggggc gcagccatga cccagtcacg tagcgatagc
     1741 ggagtgtata ctggcttaac tgtgcggaat cagtgcgatt gtaagaaaac agcggcatat
     1801 gcggtgtgaa atatcgcata gatgcgtaag gagaacatgc ctgttcaggc actcttccgc
     1861 ttcctcgctc actgactcgc tacgctcggc cgttcggctg cggcgagcgg tatcagccca
     1921 ctcaaaaacg gtaatgcggt gatccacaga atcaggggat aaagccaaaa ggagcatgtg
     1981 agcaaaaaac aagaaccagg aaaaggccgc gccgatggcg tttttccata ggctccgccc
     2041 ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact
     2101 taaagatacc aggagtttcc ccctggtggc tccctcgtgc gctctcctgt tccgaccctg
     2161 ccgattaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc
     2221 tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac
     2281 gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac
     2341 ccggtaagac acgacttatt gccactggca gcagccactg gtaactgatt tagaggagtt
     2401 tgtcttgaag ttatgcacct gttaaggcta aactgaaaga acagattttg gtgactgcgc
     2461 tcctccaagc cagttacccg gttagataat ctgccaggat tagctaacct tcgaaaaacc
     2521 acctgccagg gtggtttttt cgtttacagg cagcagatta cgcgcagaaa aaaaggatca
     2581 caagaggatc cttgaatctt ttccccctca tccccctagg cataaacata gcgaacggtt
     2641 tttaaccaca attcaaaact aatgattcgc aacagcaaga acaaacaatg caaccattac
     2701 aggagcaatc atcaactccc ggggaggtgg ttagggataa caataaaata acggagcgta
     2761 atgctccgtt atttattgtc gtgatttaca gtggtaggga aagcgaggag gtttcgagcg
     2821 attctccatc attcagcttg ttctgcatgt cgctgacaaa aacgtccatc tggctgttgg
     2881 caaagaattt aatcccaacc agtctgacgt gctcattttc atcaattaca atgcgctccc
     2941 tatcattcag ggtttcgagc atccgttctt tccatgcgtc atccagcaaa cgatcatccc
     3001 ccttcggttc aaggaacacc tgccagtaag tgttgtccga atggcgcgtc agtatcatga
     3061 tgaaatctgg cataaacccg cgcacgccgc cgaactccgt gagcttaaag cgcgttgact
     3121 gctcgtcgtt acgcagtacg taaatatcgt cataacgcgc ttttagcttc ggcatgaatg
     3181 cttccagcgt tttaattagg cgatgctcaa gctgattcag tatcgcatta tcgtacacgt
     3241 accatttttt accaatggtg ggtacagcag tgattttctg attaataact accgacgggt
     3301 caatgtgcaa actgtaatct ttaataacct ctttcaccgg ctggctgata aagcggtacg
     3361 tgccttttac cttctgatca ttgcggcgaa cgttctctga gatacgcagc agaacggttt
     3421 ccagtaggtg cagcttatct tttgccggta cggtggtgaa atccagtgac tgcggtacga
     3481 tgactgtaat tttcagctta ccaagatagg cgtcactgcg gatgaactca cggatgcctg
     3541 tcagtttcgg gaagaaacgc tgcaggttat caagtgcgta aaagctgatc ctttgcatcg
     3601 ccttgcggta aaaacgctcg tccagtacca gtagttccgg ttttgtgatt ccagtctttg
     3661 tgcctgtcag gttgtccagc gactcctcgc agacggtctg atacggtatc tcaaagcgtg
     3721 tttccagcga gtaggtttcc cagtttctgc tgctgctctc aatctcctcc acttcgttga
     3781 agtacagctt acccgcctga tacacggcgg actttttaaa atcttctttc agtctggcgt
     3841 gttcaatcgt accgccgcca tcctgatgca catcaatgtc cgcctgctcc aaagaggcat
     3901 gcagtgtttt gatgtacgcc ggttcattga tggtgtgata gtgcagttgc tccagtacgc
     3961 tcaaatcctt cgtactgtta tcaaaacggc gggtgaagct tcgttgaccg tcataaatga
     4021 acgggtagta acgcgcgcct cgcccgataa gctgcgcttc gctgtccgtg ctggttttgc
     4081 tgctgctcgc ctgctcgctg atgcggacaa tatcgtagag gttgagaacg tcccagcctt
     4141 cattcacctt cgcgacggca aagacggctc tcaccggatt atcgacttct tctagtgtat
     4201 tcagcaggac gggattctct tccagcagat ctgacttgtt gacgttcagc aggttaaagt
     4261 cgttaaagtc ctcctgaatt tgcccagtca ccgtcactaa atcactgtta gcgtaacgct
     4321 gaatcacttt atgccagata ctggtgtcag agctgagctg gagttttttg ttagctagat
     4381 gacgtctgac gctctcaggt gtcatggcgg ctatcagttg cgaaaactcc tcctgcttcg
     4441 cctttgatat cgcaatctta ttcgacttga acagaatgac cggtttgaag ccggtgatgc
     4501 cgtgatctgc tgccgtcagt ttacggtact ggcttaaaag taccgcatca agcatcttgt
     4561 cgctgtcatt ctggttggct tccagcagca tgactttctt cgagtaaccg tctgacatga
     4621 actgtttcag gtcatactga tacaccacct taccacggta tttctgcccg atatctttgt
     4681 tcgcaagatc aatggtggcg gtgaactcga acaggcggtt atccggtcgc aggttgagga
     4741 tgttctcaat cgtgcgttcc caggtctgct cctcgttctc cggtgaggtt ttcgacttgc
     4801 ctctagcttt agtaccggcg ttgaaatgat gtgcctcgtc accaagcagc acaaggggga
     4861 tttcttttaa atcctcgtag gtgatgctgt tctcacgata gctgttcagc tcgtcgtgca
     4921 tcttatggat agtagagagc ttgaggtaaa tcgtgttacg ttccggtatg gacgggaatg
     4981 tttctatcgg ttcgatggtg attttttccc cgtcgatttc cagctcctga ctgaacaggt
     5041 acttcggcga ttgcggatta agcaagttct ctcgcgtttt ctggataatc gcgtctgtat
     5101 gcacgaagaa aatgaagttc tgatacccta actctttaaa cagataaagt atcgttcctg
     5161 ccatcaccat cgttttccct gcaccggttg ccatgtgaaa cagcaggtgg cgataatgca
     5221 gcagcgcatc atcccgttta cgttgcgtgt aatgcaggta acgcagtgca ccatgctgat
     5281 aggggcgcag ggcatctttc aggttttcct gaatatagtc cggcgtctga tagttatcgt
     5341 ggaacagtcc tggttcatcg aactgcttca gcctgttaaa cagtagcttc tcactgccga
     5401 ctgacttcgg tttcttcgcc atgccgtcac tccattccgt agaagctgcg ggtaaaggct
     5461 ttatcgctct ccgaaatgct cagttcgctg tcctccatat cagagacatt cacgtagagt
     5521 ttatttttat cgaggatttc aatcagaagc tgcttctgct catgcagttc cagttcactg
     5581 aaagctacct tacggaagat gccatccact tcgtactcag cggacagcac attttccagc
     5641 tctacctgat agttgagatg ggcctctgtt ttcatcatgg taaagagttt ttcgagttct
     5701 tccgtggact gcgctttctg aatttcatgc acgaaatagg cgttcagctc catcaattct
     5761 gcgtagacaa agctgcctcc cccctgccag ttaacgtctt ttgagatccc cccctgttca
     5821 ccttcgatga cttttttcag gcgaggtacc gtaatgtcgt tgatgtactc catctgctca
     5881 ataccgatat agcgacgccc cattttgtga gcaacagcag ctgtagttcc actaccaaga
     5941 ttaaagtcta gaattaggtc atttttagta gatgttattt cgattagctt agccaatagg
     6001 gtttctggtt ttgtataatc aaatatattt ttccctaaga gggagctaat gtgttttgtc
     6061 gcattgtcgt tagaatactt gttttcagta aactcaagtg ttgacaatgg ctttgttcta
     6121 tcaaagtagg ttatgacata atcatttccg tcctttgata tctttgcatt ttgatatgtt
     6181 tttgtatata tccttggcct ttggccgcca tttcttattt caataaaccc attttcaaac
     6241 ccaaaatcga ataatttcct actccatctc caagcccagt ccgccctgtt atgcttgcca
     6301 ttcattctat cattaaataa attttcatca ccacctgggt aatatttctc accattgatt
     6361 tctattatat aatcaagtga tttgctgtat tgaaggctat cataatccaa ggtttggttg
     6421 agtttgtagc ttcctctctc agcaaagtac tcatctttat atttgaaatt atcgtcgtcg
     6481 tgcgaaactg catacatacg cttgttttct aaacttctaa cataaagcag tatgtaatca
     6541 tgattctttg cgaaaatgct ggcggatttc cctcctttct ttgttattct tgggaatata
     6601 gcaatcctat tttttcggcc aaaaatatca tcagccaacg aggccaaata atttaattca
     6661 ttatcatcaa tactaattgc aattaacccg tcatcgcaca acaaatcttt tgcaacttca
     6721 agtctgttct tcatgaaagt cagccacgta gagtgactaa atttatcatt atatttaaag
     6781 ctatctgtat cagtattata tggtggatct atataaatta atttaactga cttctcgtat
     6841 atatttttta tacagtgcaa cgc
//
