LOCUS       NZ_AP022075             3272 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-W18-ESBL-09 plasmid pWP4-W18-ESBL-09_6,
            complete sequence.
ACCESSION   NZ_AP022075
VERSION     NZ_AP022075.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194468
            Sequence Read Archive: DRR199304
            Assembly: GCF_014169115.1
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-W18-ESBL-09
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3272)
  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                   :: 114x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:58:42
            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)                     :: 5,455
            CDSs (total)                      :: 5,329
            Genes (coding)                    :: 5,078
            CDSs (with protein)               :: 5,078
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 0 of 251
            Pseudo Genes (frameshifted)       :: 100 of 251
            Pseudo Genes (incomplete)         :: 165 of 251
            Pseudo Genes (internal stop)      :: 41 of 251
            Pseudo Genes (multiple problems)  :: 50 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022075.1.
            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..3272
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-W18-ESBL-09"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-W18-ESBL-09_6"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-02-13"
     gene            71..265
                     /locus_tag="H7R28_RS26975"
                     /old_locus_tag="WP4W18E09_P60010"
     CDS             71..265
                     /locus_tag="H7R28_RS26975"
                     /old_locus_tag="WP4W18E09_P60010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1393..2232
                     /locus_tag="H7R28_RS26980"
                     /old_locus_tag="WP4W18E09_P60020"
     CDS             1393..2232
                     /locus_tag="H7R28_RS26980"
                     /old_locus_tag="WP4W18E09_P60020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000546749.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_052924426.1"
                     /translation="MHLEEEDLRALERAVELLAQDTITETLTQLVGTPIDYLMSKLPKG
                     AEKKIYSLVEKSLNKAANAALWSLDNEPNRIASTKTNKFFAALSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFDLDRIDTKLECLAVFSFGGPSEDDDAVNTAYYATRNLT
                     AEIVQDLSKEISNITVKNAASTQTGKWLASLIEKVATRFGIVITEKMAAQAAPVIGALA
                     GATLNTMFTDYYQDMARGHFIVKRLERKYGDELIKAEYIKISDKLTNQNQRKHLNSN"
                     /name="EcsC family protein"
     Typing          complement(339..423)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          complement(2829..3097)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.037"
                     /coverage="93.0"
                     /evalue="7.52e-94"
     Typing          443..992
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.652"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcaacgtct tacaattacc acctgctcag ggtccccccg acacccggaa ctgacggaga
       61 acaacggaag gtgaacaaac aacaacaaac tgcgctgaat atggcgcgat ttatcaaaag
      121 ccagagcctg acactgcttg aaaaactgga tgctctggat gccgacgaac aggcggccat
      181 gtgcgaacga ctgcacgaac tcgcagaaga actccagaac agcatccaga ttcgctttga
      241 ggccgaaagt gaaacaggaa cataacgaag ctgacggagg cggtcacggc tttcccgtgg
      301 gcgttttcgt cagcagacaa gcccgtcagg gcgcgtcagg gggtttcggg gcgaagccct
      361 gaaccagtca cgtagcgata gcggagtgta tactggctta actatgtagc atcagtacag
      421 attataagaa aagagcacca tatgcgatgt gaaataccgc acagatgcgt aaggagaaaa
      481 tgccgcatca ggcgctcttc cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg
      541 ctgcggcgag cggtgccggc tcactcaaag gcggtaatac ggttatccac agaatcaggg
      601 gataaggccg gaaagaacat gtgagcaaaa aggcaaaagg caacgaaagg ccgcgccgct
      661 ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac gctcaagtca
      721 gaggtggcga aacccgacag gactataaag ataccaggcg tttccccctg gaagctccct
      781 cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct ttctcccttc
      841 gggaagcgtg gcgctttctc atagctcacg ctgttggtat ctcagttcgg tgtaggtcgt
      901 tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct gcgccttatc
      961 cggtaactat cgtcttgagt ccaacccggt aagacacgac aaagcgccac tggcagcagc
     1021 cactggtaac tggacaaggt ggattgagat attaagagtt cttgaagtgg tggcctaact
     1081 gcggctacac tagaaggaca gtatttggta tctgtgctcc accaagccag ttacccggtt
     1141 aagcagtccc caactgactt aaccttcgac taaaccgcct ccccaggcgg ttttttcgtt
     1201 tactggcagc agattacgcg cagaaaaaaa ggatctcaag aggatccttt gatcttttca
     1261 tcactcctac ttcacggaca acaatgatat cggcatctcg cccgttgaat cactgaattc
     1321 tcccaaggta agatcccaaa acagaccact tacaaaaagt aggctacaga ttgattcata
     1381 agggattttt acatgcatct tgaagaagaa gatctgcgcg ctttagaaag agccgtagaa
     1441 ttattagcac aagatacaat tacagaaaca ctaacccaat tagttggaac cccaatagat
     1501 tacttaatga gtaaacttcc caaaggagca gaaaagaaaa tttatagcct agtagaaaaa
     1561 tctctcaaca aagctgctaa tgcagcctta tggagcctag acaatgaacc taaccgaata
     1621 gcatcaacta agacaaataa gttctttgct gccttatctg gagccattgg tggtgctttt
     1681 ggcttttctg cattagcaat tgagttacca gtttcaacga caattatgct tcgttcaatt
     1741 gcggacatag caagaagtga aggttttgat ctagatagga ttgatacaaa actagagtgt
     1801 ttagcggtgt tttccttcgg aggaccatct gaggacgatg atgcagttaa tactgcatac
     1861 tatgcaacaa ggaatttgac tgctgagatc gtacaagatt tatccaaaga aatttctaac
     1921 attactgtca agaacgctgc ttcaacacaa acaggaaaat ggttagcttc gttaatagaa
     1981 aaagttgcga caagatttgg tatagttatt acagaaaaaa tggcagctca agctgctcct
     2041 gttattggag cactggctgg agccacatta aacacgatgt ttaccgacta ttatcaagat
     2101 atggctcgag gtcattttat tgtcaaaaga cttgagagaa aatatggtga tgaattgata
     2161 aaggctgaat atataaaaat ctcagataaa ctcaccaatc agaaccaacg gaagcatttg
     2221 aacagcaact aacggtttca ctaagtgcat agcaccgtta tggccaggtg ctatggaggg
     2281 tgtcaactca cgaacaatca cacaaacaac aaaattattt atgattttat tttaaacatt
     2341 atattcgcaa caactgcatt aatgaaattg gctttttttg aatcaactaa aacagagtca
     2401 caatttgggc actgactaaa agcattcccc ccatcaacta aaacatcgct acatttaggc
     2461 acagttttac accaatggca tgataaacat ttataggtca tagccattct aatcattacc
     2521 aatttcaact ccacgcacaa aataaatagt taacccagca tctacgaata tcaatcatat
     2581 ttaccataat cccgtattgc gcgcaccgct aaaacgcgct gaacgcgatt ctgccgcaaa
     2641 caccgcaaaa agagatgttt tccccggggt aaaccgaaaa aatgcgtcag gctcgctttc
     2701 agctcactgc atagctatgc atgaaagtga atgacgatcg gtttgggcgc atacagtgcc
     2761 catgagacac attttcggac attttcagtt cgtgaatccc tgactcattg ctacatatct
     2821 gaacagacac ccctggcagc gcccccaggg gcgtcctgta aaaaaacaca ccgcgcagct
     2881 agcagcaccc ctaatataag atgatgtttt ttatgaaaat agtcagtacc acccctaaaa
     2941 agcggtgtcg gcgcggtgtt gtagctgcgc caacaccgct tttttaaata tcacaaagag
     3001 agcaagaaga actaatttgt cataactctc tatttataaa gaaaaatcag caaaaaattg
     3061 tttttgcgtg gggtgtgggc atttcgggca tgagaacaga ctcgcgtttt tccggagtat
     3121 cagcggaatt attgattaag aaatactcga cgcagagcga aattttatgc aacagcggct
     3181 gcactgcaca gggattcttt atcagttgat atgctgtgcc atgatacgtc ctaaagaaac
     3241 aggacaggat gtgcaattgt aataccgtcg cc
//
