LOCUS       NZ_AP022093             5344 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S18-ESBL-07 plasmid pWP4-S18-ESBL-07_6,
            complete sequence.
ACCESSION   NZ_AP022093
VERSION     NZ_AP022093.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194481
            Sequence Read Archive: DRR199317
            Assembly: GCF_014171015.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Itokawa,K., Yatsu,K., Inamine,Y. and Kuroda,M.
  TITLE     complete genome sequences of Escherichia coli str. WP4-S18-ESBL-07
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5344)
  AUTHORS   Sekizuka,T., Itokawa,K., Yatsu,K., Inamine,Y. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2019) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v2.5; minimap v0.2-r124; racon v1.1.0;
            circlator v1.5.3; Pilon v1.18; SPAdes v3.11.1; A5-miseq v20140604
            Genome Coverage                   :: 166x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:36:35
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,281
            CDSs (total)                      :: 5,159
            Genes (coding)                    :: 4,963
            CDSs (with protein)               :: 4,963
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 196
            CDSs (without protein)            :: 196
            Pseudo Genes (ambiguous residues) :: 0 of 196
            Pseudo Genes (frameshifted)       :: 84 of 196
            Pseudo Genes (incomplete)         :: 130 of 196
            Pseudo Genes (internal stop)      :: 43 of 196
            Pseudo Genes (multiple problems)  :: 49 of 196
            Pseudo Genes (short protein)      :: 4 of 196
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022093.1.
            Annotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).
            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..5344
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S18-ESBL-07"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S18-ESBL-07_6"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-08-06"
     gene            complement(join(5187..5344,1..13))
                     /locus_tag="H7R53_RS26550"
     CDS             complement(join(5187..5344,1..13))
                     /locus_tag="H7R53_RS26550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001562855.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_251000596.1"
                     /translation="MKTREAPLLAAIHTPEKQPDHLFCLLGFNRTWNEWRREEDARTHV
                     SERRNDRDWSQ"
                     /name="hypothetical protein"
     gene            complement(101..2107)
                     /gene="mobQ"
                     /locus_tag="H7R53_RS26555"
                     /old_locus_tag="WP4S18E07_P60010"
     CDS             complement(101..2107)
                     /gene="mobQ"
                     /locus_tag="H7R53_RS26555"
                     /old_locus_tag="WP4S18E07_P60010"
                     /inference="COORDINATES: protein motif:HMM:NF015354.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_251000597.1"
                     /translation="MRKNHEVRTYTISTSFRLCAPCGAERKLQKGITAEMAIYHLSMKI
                     ISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRKSGVAEAVILSPATAPAWCTNRTEL
                     WNAVEKAERRKNSQLAREIELAIPRELPQDAARETVLAFVRENFVSQGMIADVAFHHMD
                     KTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAETWRASWADHANRALANAGYQEEIDH
                     RSYERQGLEKTPGIHLGKSACAMETRGIETERGEQNRLINRLNLEIQISRTELRNSGLT
                     EPARRVADLLNIELPDNATSYTLRDIIEALPKDSNAAWKLTSNAMSMMTDMQATRRRWE
                     ELNTERKDAMSHAASLKKSSPFSSGFSRIPLMQWAAPEYRSEQGKIQSLSQQMEKLRQH
                     YRKVEKQDIPASQTAFEKQWQQWGASGLAALRAQLLKREEELRRKELEDTERRRAERRA
                     EQLRKNDNAVIDSGVLRAVVTGYGVAPMPDDGEMTCYLLLHNRNGEYTLWGNELEKYRT
                     RIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQLLTQVCQTWPQHTRNLRQPK
                     TWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVMSSVDRETRQLQLLLVMGVDD
                     SLGGVVRLNGTLYPAFAVPTADNSQLVINALTD"
                     /name="mobQ"
     gene            2180..2434
                     /gene="mobC"
                     /locus_tag="H7R53_RS26050"
                     /old_locus_tag="WP4S18E07_P60020"
     CDS             2180..2434
                     /gene="mobC"
                     /locus_tag="H7R53_RS26050"
                     /old_locus_tag="WP4S18E07_P60020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_033816893.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            2966..3658
                     /locus_tag="H7R53_RS26055"
                     /old_locus_tag="WP4S18E07_P60030"
     CDS             2966..3658
                     /locus_tag="H7R53_RS26055"
                     /old_locus_tag="WP4S18E07_P60030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_182913543.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYELLQQFRSTGERIIAL
                     NDFRSMLGIENKYKKFRDLNKILIKPCITELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1645..2003)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.944"
                     /coverage="100.0"
                     /evalue="1.85e-170"
     Typing          2004..2173
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.767"
                     /coverage="97.0"
                     /evalue="4.47e-69"
     Typing          2967..3657
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.676"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..2089)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.121"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cacgggtttt caaatgaaat tccataagtt caggtgcagg tgaaatgtgg ctgtttgcat
       61 cgtggtttac cgcatcacca taaccggaaa atcgtaaacc ttagtcggtc agagcattga
      121 ttaccagctg gctgttgtcg gctgtgggga cggcaaacgc gggatatagc gtaccattaa
      181 gccggacaac accgcccaga gagtcatcca cgcccatgac cagcaaaagc tgaagctggc
      241 gggtttcccg gtcgacagaa ctcattacag gcatcagcgt cggtggcaga cgtccctgcg
      301 taaaatccac cttccttgct gccagtgatg gcatggctgg ctggcggtct tctccaagac
      361 agaaagactc cggccatgtc ttcggctggc ggagattgcg ggtatgttgc ggccatgtct
      421 ggcaaacctg cgtcagcagt tgctcaaagg tcgcagagga ataaacacgt tgcagtggtg
      481 gatgttgacc gatttcgctt cggtcacaga tataaccact cctgtcacgc attaaatcaa
      541 cacgctcaaa gattctggtg cggtatttct ccagctcgtt cccccagagc gtatattctc
      601 cgttccggtt gtgaagcaga aggtaacagg tcatttcccc gtcatcaggc atgggtgcca
      661 ctccataccc cgtaacgact gctctcagta cccctgaatc tataacggca ttgtcatttt
      721 tcctgagctg ttccgctcgt cgctccgcgc gacgacgttc tgtatcctcc agctccttcc
      781 ggcgcaattc ctcttcacgt ttaagcaact gggctctgag agctgcaagg ccggatgccc
      841 cccactgctg ccactgtttt tcaaatgccg tctgactcgc gggaatgtcc tgtttctcca
      901 ccttccggta atgctgtcgc aatttttcca tttgctggct cagagactga atttttccct
      961 gctcactacg gtattccggt gcagcccatt gcatcagggg aatacgggaa aaaccggacg
     1021 aaaacggcga tgattttttc aggctggcag catggctcat cgcgtccttt cgttcggtgt
     1081 tcagctcttc ccagcgtctg cgcgtcgcct gcatatctgt catcattgac atggcattac
     1141 tggtgagttt ccatgccgcg ttactgtcct tcggcaacgc ttcgatgatg tcacgtagtg
     1201 tgtacgaagt tgcgttgtca ggaagctcaa tattcagaag gtcagccaca cggcgggcag
     1261 gctctgtcag cccgctgttc ctgagttcgg tacgggaaat ctgtatttcc aggttaagcc
     1321 tgttaatcag acgattctgt tcgccgcgtt ctgtttcgat accgcgtgtt tccatcgcac
     1381 aggcagactt tccgaggtga ataccaggtg ttttctcaag cccctgtcgc tcgtatgaac
     1441 gatggtctat ctcttcctga taaccggcgt tcgccagtgc cctgtttgca tggtcagccc
     1501 atgatgcccg ccacgtctcg gcatgtgtcc ggtcgttcca gtccctgacc tttccaccga
     1561 accccgcagg tccgacagcc ctcgtggtca gcatgatgtg cgcatgggga tttgttttat
     1621 ccatgtgatg gaacgccaca tcagcaatca tgccctgact gacaaagttt tctctgacaa
     1681 aggcgagaac ggtttcccgt gcggcatcct gcggcagttc acgggggatg gcgagttcaa
     1741 tttcccgcgc aagttgtgag ttcttccgac gttcggcctt ctcaacggca ttccagagtt
     1801 cggtacggtt cgtacaccag gcaggggcgg tggcggggga cagaatcaca gcctcagcca
     1861 caccgctttt gcgggtgtag tcgtgagtca gtccggtacg ctcatcaagc attagtgaac
     1921 cggaacgata ggcagcagaa gcaacggcac tgtagccgtt gcttctggag atgattttca
     1981 tgctgagatg ataaatcgcc atttctgccg taatgccttt ttgcagtttt ctttcagccc
     2041 cgcagggcgc acacaatcga aacgaagtgg agattgtata agtgcgcact tcgtggtttt
     2101 ttcgcattat gccagctcat tttttaaact accagtgacg cgctaaaatg cgatttttca
     2161 ccgcgcacgg agtcacggaa tgagcagaac actcgaacag aaaattgccg aagctgaagc
     2221 cagattgcag cgcctgaagg caaagagccg gagcctggac acagcgcaga aggtcgttgt
     2281 gggtgcagca ttactggcaa aggtcagaaa gccggaggaa gtgcagttgc gtgcctggtt
     2341 gctccagttc ctgaaggcag aggtgacacg gcaggctgat gtgacgcgaa tactgccgct
     2401 gattaacgag ctggaggcgc tgccagaaca gtgattgtat cgtctgctcg ccgcagcccc
     2461 agcgaccgag cgttagcgag cgagtgggcg aggaagcgga agtgacctcg tagccaggtt
     2521 gagcacatat gcacagtttt tcggcaggcg atatgcgctg aacccgcatg aatactggat
     2581 ttccacaggg ttggaggggg ggcattcgga atttgcaaat ccgctttttc acaacatatt
     2641 gtttttattg aatttttgtt tttagcatcc caatttatcc acaggcccgc cgttaagttt
     2701 ttagatcttg tttttaagat cttgttttta atacttgttt taggggtgaa attcattaat
     2761 aaaatcaatg cgttgcagtg gtatatgtgg agggatttaa ggtatatgtg gaggaattta
     2821 aggtgtttag gtggaggaat ttaaggtata tgtggaggaa tttaaggtgt tattcacaga
     2881 aatgcgcgga tataaaaaaa atcattccac atttcttatt tgtggggcac attaaatcat
     2941 caccacattt gaacgggatc tttgtatgtc ggacttgatt gcctacaagt cgaacgctct
     3001 ggttgaggcc agctacaagc tgaccctaca ggaacaacgt tttctgttgc tgtgtatcag
     3061 tcgattgaaa tctggtgctg atgctgaatt gcaaaagaca atgaccatta ccgccgcgga
     3121 atattttgat tcattccctg acatggggcg gaaaaatgcc gaggttcagt tacaggaagc
     3181 gatcgatcgt ttatgggaca ggtcgatcat tctcaaggat gacgagaagc gtgaggagtt
     3241 ccgctggatc cagtatcggg cacagtacgc taaaggtgag gccaaggctc gaataacctt
     3301 ttctgacgcg gtaatgcctt atctaacgca actgaagggg caattcacgc gcgttgttat
     3361 aaaaaacata tcaggtttat caagcagtta cagtataaga atatacgagc ttctccagca
     3421 attccgcagt acgggagaga gaattattgc tcttaatgac tttcgttcaa tgttaggtat
     3481 tgaaaataaa tacaaaaaat tcagagactt aaacaagata ctaataaaac cttgtatcac
     3541 ggaactgaac aaaaaaagcg acctggctgt aacggttgag acgatcaaga agggacgtac
     3601 agtcgtagcc ctgcattttc gcttcaagga agacaaacag atcaagatga cgatctagaa
     3661 tcgattttaa ggcacctaaa acgctctctg aagcgttttt tttgtatcag gtatgggatt
     3721 gtaccagtca aataaaaaaa cacctcagaa gcgctatgag gcgttttagc gcgtttctga
     3781 cgagggtttt gtcggctatg taacggagac actgataagg agtcgtcagt tctgccagaa
     3841 acgcgcacta atttttaatg cgtatccagc gttgtgtcca gacgaacgaa ttgtttttcc
     3901 ggtcggtttg cggcaaattt aactcactga gtagtgtagt taacgatcac ataactgttt
     3961 tggttacccg ctcttccagg cgggtttttt ttgtccgtaa attcgcttcg ggtcagggga
     4021 ggcaaacagc tcaggacacc gtcaagaaac ggcgtggttt ggcaggacag aaaccgtgac
     4081 ggttgagcac atttctgacc ccaagtgatt agttccgcca tcacaggtta attacgccag
     4141 aaacgtactc aggcgctttg taacgtgatt tcactcattg ggcaagtgtt tacccagtat
     4201 ttctttcccc ggaaacatgt tgcacagcac acaacacttt tgggggggag agggattcac
     4261 tctcccccaa aaaaaacccc cgggtcttgg ggggagaaac tatgctgaat attgatttgt
     4321 gttatgtatg tgtgcttctt gtattcatcc cttccgatga acatcagaaa catagcatga
     4381 tgttatgcag agaaaaatat gctgttcgca ttggttctgt gaagtaactc acacagcgtt
     4441 tgtgcatgca aagttccata tctacatgac taaaaaaaaa cccgccggtg tgtgcgggta
     4501 atttatagcc aatgaagttt tattacatac gttgaggtat aactgcggac cgttgccccg
     4561 caattaataa aacctgccat attcctgcat gagaaacaac caccacctct gcgcaaatgc
     4621 attgtgccat gatatatgca gcgcataact atgcattcta tttgcaaaag aactcgcttg
     4681 ttcgtaataa agaggagtta agattttgct tgcatatcac aaaaaaaaca gccagaacag
     4741 gatggagaat atctccgctg gtgtatttca accgtgcaaa caagtaatca gggtggcagg
     4801 gatattctca tttatcctgc gcgccataac cccccatcct tcagggcgtg aggatgtcaa
     4861 taggaggtta aaatccattg attaagatgc gcaggtaaat ttaaattaac aggtgcgcac
     4921 cccgtggttg atttaattaa cggcatggat gattcgattg cgctaaggga ggggtgcgca
     4981 tctcacaaac gattatctga ggcgttatag ccccccattg tttaatatca ggcatctccg
     5041 gttgacagca actccctctt ttctaaaaaa aatccccgaa aaacggggaa gggaaatcaa
     5101 ctgattgtgt atagaaggtt catttccata ccgatgaata tcaaaaacat aacacgatgt
     5161 taaacgaaac aaaatattgt tcacattcac tgtgaccagt cgcgatcgtt tctcctctcg
     5221 gagacgtgtg ttcgtgcatc ttcctcgcgc cgccattcgt tccaggtgcg gttaaagccc
     5281 agtaaacaga acagatgatc cggctgtttt tctggcgtgt ggatggcagc caaaagcgga
     5341 gcct
//
