LOCUS       NZ_AP022099             5344 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S18-ESBL-09 plasmid pWP4-S18-ESBL-09_1,
            complete sequence.
ACCESSION   NZ_AP022099
VERSION     NZ_AP022099.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194483
            Sequence Read Archive: DRR199319
            Assembly: GCF_014169175.1
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-09
            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  JOURNAL   Unpublished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                   :: 224x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:00:21
            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)                     :: 5,009
            CDSs (total)                      :: 4,894
            Genes (coding)                    :: 4,728
            CDSs (with protein)               :: 4,728
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 63 of 166
            Pseudo Genes (incomplete)         :: 106 of 166
            Pseudo Genes (internal stop)      :: 35 of 166
            Pseudo Genes (multiple problems)  :: 35 of 166
            Pseudo Genes (short protein)      :: 5 of 166
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022099.1.
            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-09"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S18-ESBL-09_1"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-08-06"
     gene            complement(101..2260)
                     /gene="mobQ"
                     /locus_tag="H7R19_RS24645"
                     /old_locus_tag="WP4S18E09_P10010"
     CDS             complement(101..2260)
                     /gene="mobQ"
                     /locus_tag="H7R19_RS24645"
                     /old_locus_tag="WP4S18E09_P10010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_182913544.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILSPATAPAWCTNRTELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIELPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMTDMQATRRRWEELNTERKDAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRAQL
                     LKREEELRRKELEDTERRRAERRAEQLRKNDNAVIDSGVLRAVVTGYGVAPMPDDGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPTADNSQLVINALTDKG
                     LRFAGYGEAVNHDANSHISPAPELMEFHLKTREAPLLAAIHTPEKQPDHLFCLLGFNRT
                     WNEWRREEDARTHVSERRNDRDWSQ"
                     /name="mobQ"
     gene            2438..2692
                     /gene="mobC"
                     /locus_tag="H7R19_RS24650"
                     /old_locus_tag="WP4S18E09_P10020"
     CDS             2438..2692
                     /gene="mobC"
                     /locus_tag="H7R19_RS24650"
                     /old_locus_tag="WP4S18E09_P10020"
                     /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            3224..3916
                     /locus_tag="H7R19_RS24655"
                     /old_locus_tag="WP4S18E09_P10030"
     CDS             3224..3916
                     /locus_tag="H7R19_RS24655"
                     /old_locus_tag="WP4S18E09_P10030"
                     /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(1903..2261)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.944"
                     /coverage="100.0"
                     /evalue="1.85e-170"
     Typing          2262..2431
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.767"
                     /coverage="97.0"
                     /evalue="4.47e-69"
     Typing          3225..3915
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.676"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(105..2347)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.92"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggaagggaaa tcaactgatt gtgtatagaa ggttcatttc cataccgatg aatatcaaaa
       61 acataacacg atgttaaacg aaacaaaata ttgttcacat tcactgtgac cagtcgcgat
      121 cgtttctcct ctcggagacg tgtgttcgtg catcttcctc gcgccgccat tcgttccagg
      181 tgcggttaaa gcccagtaaa cagaacagat gatccggctg tttttctggc gtgtggatgg
      241 cagccaaaag cggagcctca cgggttttca aatgaaattc cataagttca ggtgcaggtg
      301 aaatgtggct gtttgcatcg tggtttaccg cttcaccata accggcaaat cgtaaacctt
      361 tgtcggtcag agcattgatt accagctggc tgttgtcggc tgtggggacg gcaaacgcgg
      421 gatatagcgt accattaagc cggacaacac cgcccagaga gtcatccacg cccatgacca
      481 gcaaaagctg aagctggcgg gtttcccggt cgacagaact cattacaggc atcagcgtcg
      541 gtggcagacg tccctgcgta aaatccacct tccttgctgc cagtgatggc atggctggct
      601 ggcggtcttc tccaagacag aaagactccg gccatgtctt cggctggcgg agattgcggg
      661 tatgttgcgg ccatgtctgg caaacctgcg tcagcagttg ctcaaaggtc gcagaggaat
      721 aaacacgttg cagtggtgga tgttgaccga tttcgcttcg gtcacagata taaccactcc
      781 tgtcacgcat taaatcaaca cgctcaaaga ttctggtgcg gtatttctcc agctcgttcc
      841 cccagagcgt atattctccg ttccggttgt gaagcagaag gtaacaggtc atttccccgt
      901 catcaggcat gggtgccact ccataccccg taacgactgc tctcagtacc cctgaatcta
      961 taacggcatt gtcatttttc ctgagctgtt ccgctcgtcg ctccgcgcga cgacgttctg
     1021 tatcctccag ctccttccgg cgcaattcct cttcacgttt aagcaactgg gctctgagag
     1081 ctgcaaggcc ggatgccccc cactgctgcc actgtttttc aaatgccgtc tgactcgcgg
     1141 gaatgtcctg tttctccacc ttccggtaat gctgtcgcaa tttttccatt tgctggctca
     1201 gagactgaat ttttccctgc tcactacggt attccggtgc agcccattgc atcaggggaa
     1261 tacgggaaaa accggacgaa aacggcgatg attttttcag gctggcagca tggctcatcg
     1321 cgtcctttcg ttcggtgttc agctcttccc agcgtctgcg cgtcgcctgc atatctgtca
     1381 tcattgacat ggcattactg gtgagtttcc atgccgcgtt actgtccttc ggcaacgctt
     1441 cgatgatgtc acgtagtgtg tacgaagttg cgttgtcagg aagctcaata ttcagaaggt
     1501 cagccacacg gcgggcaggc tctgtcagcc ctccgttcct gagttcggtg cgggaaatct
     1561 gtatttccag gttaagcctg ttaatcagac gattctgttc gccgcgttct gtttcgatac
     1621 cgcgtgtttc catcgcacag gcagactttc cgaggtgaat accaggcgtt ttctcaagcc
     1681 cctgtcgctc gtatgaacga tggtctatct cttcctgata accggcgttc gccagtgccc
     1741 tgtttgcatg gtcagcccat gatgcccgcc acgtctcggc atgtgtccgg tcgttccagt
     1801 ccctgacctt tccgctgaac ccagcaggtc cgatagccct cgtggtcagc atgatgtgcg
     1861 catggggatt tgttttatcc atgtgatgga acgccacatc agcaatcatg ccctgactga
     1921 caaagttttc tctgacaaag gcgagaacgg tttcccgtgc ggcatcctgc ggcagttcac
     1981 gggggatggc gagttcaatt tcccgcgcaa gttgtgagtt cttccgacgt tcggccttct
     2041 caacggcatt ccagagttcg gtacggttcg tacaccaggc aggggcggtg gcgggggaca
     2101 gaatcacagc ctcagccaca ccgcttttgc gggtgtagtc gtgagtcagt ccggtacgct
     2161 catcaagcat tagtgaaccg gaacgatagg cagcagaagc aacggcactg tagccgttgc
     2221 ttctggagat gattttcatg ctgagatgat aaatcgccat ttctgccgta atgccttttt
     2281 gcagttttct ttcagccccg cagggcgcac acaatcgaaa cgaagtggag attgtataag
     2341 tgcgcacttc gtggtttttt cgcattatgc cagctcattt tttaaactac cagtgacgcg
     2401 ctaaaatgcg atttttcacc gcgcacggag tcacggaatg agcagaacac tcgaacagaa
     2461 aattgccgaa gctgaagcca gattgcagcg cctgaaggca aagagccgga gcctggacac
     2521 agcgcagaag gtcgttgtgg gtgcagcatt actggcaaag gtcagaaagc cggaggaagt
     2581 gcagttgcgt gcctggttgc tccagttcct gaaggcagag gtgacacggc aggctgatgt
     2641 gacgcgaata ctgccgctga ttaacgagct ggaggcgctg ccagaacagt gattgtatcg
     2701 tctgctcgcc gcagccccag cgaccgagcg ttagcgagcg agtgggcgag gaagcggaag
     2761 tgacctcgta gccaggttga gcacatatgc acagtttttc ggcaggcgat atgcgctgaa
     2821 cccgcatgaa tactggattt ccacagggtt ggaggggggg cattcggaat ttgcaaatcc
     2881 gctttttcac aacatattgt ttttattgaa tttttgtttt tagcatccca atttatccac
     2941 aggcccgccg ttaagttttt agatcttgtt tttaagatct tgtttttaat acttgtttta
     3001 ggggtgaaat tcattaataa aatcaatgcg ttgcagtggt atatgtggag ggatttaagg
     3061 tatatgtgga ggaatttaag gtgtttaggt ggaggaattt aaggtatatg tggaggaatt
     3121 taaggtgtta ttcacagaaa tgcgcggata taaaaaaaat cattccacat ttcttatttg
     3181 tggggcacat taaatcatca ccacatttga acgggatctt tgtatgtcgg acttgattgc
     3241 ctacaagtcg aacgctctgg ttgaggccag ctacaagctg accctacagg aacaacgttt
     3301 tctgttgctg tgtatcagtc gattgaaatc tggtgctgat gctgaattgc aaaagacaat
     3361 gaccattacc gccgcggaat attttgattc attccctgac atggggcgga aaaatgccga
     3421 ggttcagtta caggaagcga tcgatcgttt atgggacagg tcgatcattc tcaaggatga
     3481 cgagaagcgt gaggagttcc gctggatcca gtatcgggca cagtacgcta aaggtgaggc
     3541 caaggctcga ataacctttt ctgacgcggt aatgccttat ctaacgcaac tgaaggggca
     3601 attcacgcgc gttgttataa aaaacatatc aggtttatca agcagttaca gtataagaat
     3661 atacgagctt ctccagcaat tccgcagtac gggagagaga attattgctc ttaatgactt
     3721 tcgttcaatg ttaggtattg aaaataaata caaaaaattc agagacttaa acaagatact
     3781 aataaaacct tgtatcacgg aactgaacaa aaaaagcgac ctggctgtaa cggttgagac
     3841 gatcaagaag ggacgtacag tcgtagccct gcattttcgc ttcaaggaag acaaacagat
     3901 caagatgacg atctagaatc gattttaagg cacctaaaac gctctctgaa gcgttttttt
     3961 tgtatcaggt atgggattgt accagtcaaa taaaaaaaca cctcagaagc gctatgaggc
     4021 gttttagcgc gtttctgacg agggttttgt cggctatgta acggagacac tgataaggag
     4081 tcgtcagttc tgccagaaac gcgcactaat ttttaatgcg tatccagcgt tgtgtccaga
     4141 cgaacgaatt gtttttccgg tcggtttgcg gcaaatttaa ctcactgagt agtgtagtta
     4201 acgatcacat aactgttttg gttacccgct cttccaggcg ggtttttttt gtccgtaaat
     4261 tcgcttcggg tcaggggagg caaacagctc aggacaccgt caagaaacgg cgtggtttgg
     4321 caggacagaa accgtgacgg ttgagcacat ttctgacccc aagtgattag ttccgccatc
     4381 acaggttaat tacgccagaa acgtactcag gcgctttgta acgtgatttc actcattggg
     4441 caagtgttta cccagtattt ctttccccgg aaacatgttg cacagcacac aacacttttg
     4501 ggggggagag ggattcactc tcccccaaaa aaaacccccg ggtcttgggg ggagaaacta
     4561 tgctgaatat tgatttgtgt tatgtatgtg tgcttcttgt attcatccct tccgatgaac
     4621 atcagaaaca tagcatgatg ttatgcagag aaaaatatgc tgttcgcatt ggttctgtga
     4681 agtaactcac acagcgtttg tgcatgcaaa gttccatatc tacatgacta aaaaaaaacc
     4741 cgccggtgtg tgcgggtaat ttatagccaa tgaagtttta ttacatacgt tgaggtataa
     4801 ctgcggaccg ttgccccgca attaataaaa cctgccatat tcctgcatga gaaacaacca
     4861 ccacctctgc gcaaatgcat tgtgccatga tatatgcagc gcataactat gcattctatt
     4921 tgcaaaagaa ctcgcttgtt cgtaataaag aggagttaag attttgcttg catatcacaa
     4981 aaaaaacagc cagaacagga tggagaatat ctccgctggt gtatttcaac cgtgcaaaca
     5041 agtaatcagg gtggcaggga tattctcatt tatcctgcgc gccataaccc cccatccttc
     5101 agggcgtgag gatgtcaata ggaggttaaa atccattgat taagatgcgc aggtaaattt
     5161 aaattaacag gtgcgcaccc cgtggttgat ttaattaacg gcatggatga ttcgattgcg
     5221 ctaagggagg ggtgcgcatc tcacaaacga ttatctgagg cgttatagcc ccccattgtt
     5281 taatatcagg catctccggt tgacagcaac tccctctttt ctaaaaaaaa tccccgaaaa
     5341 acgg
//
