LOCUS       NZ_AP022125             2997 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP5-W18-ESBL-11 plasmid pWP5-W18-ESBL-11_5,
            complete sequence.
ACCESSION   NZ_AP022125
VERSION     NZ_AP022125.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194523
            Sequence Read Archive: DRR199359
            Assembly: GCF_014169275.1
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. WP5-W18-ESBL-11
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2997)
  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                   :: 241x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:26:39
            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)                     :: 4,879
            CDSs (total)                      :: 4,763
            Genes (coding)                    :: 4,580
            CDSs (with protein)               :: 4,580
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 77 of 183
            Pseudo Genes (incomplete)         :: 106 of 183
            Pseudo Genes (internal stop)      :: 42 of 183
            Pseudo Genes (multiple problems)  :: 38 of 183
            Pseudo Genes (short protein)      :: 2 of 183
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022125.1.
            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..2997
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP5-W18-ESBL-11"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP5-W18-ESBL-11_5"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6538 N 139.5126 E"
                     /collection_date="2018-02-13"
     gene            101..349
                     /locus_tag="H7R04_RS24105"
                     /old_locus_tag="WP5W18E11_P50010"
     CDS             101..349
                     /locus_tag="H7R04_RS24105"
                     /old_locus_tag="WP5W18E11_P50010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017096688.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_029793011.1"
                     /translation="MKNVRMQFDLPEDRLDELDSLMKKCGISTKKELFNYALTMLEWAV
                     DESESGHEIAAIDRDSKQFYALRMPILKRVNRTSTAN"
                     /name="hypothetical protein"
     gene            422..793
                     /locus_tag="H7R04_RS24110"
                     /old_locus_tag="WP5W18E11_P50020"
     CDS             422..793
                     /locus_tag="H7R04_RS24110"
                     /old_locus_tag="WP5W18E11_P50020"
                     /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_024242345.1"
                     /translation="MSDSLDGFTEGDTSKEKQAVKQPKKFFSDVDDSADRRHLRWTKSG
                     VTLAMTILVAVMNWMVISMLYHVVDEELSLIRSGFMQADARTVTTSVYLALIAGTVAEV
                     SALFLIIVKSVFKNNNNDI"
                     /name="hypothetical protein"
     gene            1586..1777
                     /locus_tag="H7R04_RS24115"
                     /old_locus_tag="WP5W18E11_P50030"
     CDS             1586..1777
                     /locus_tag="H7R04_RS24115"
                     /old_locus_tag="WP5W18E11_P50030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(863..1288)
                     /name="rep_cluster_2374"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.766"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttatttatag gtagagatat ataaatacca acggtcctaa tggtgaagaa tgtgcagcat
       61 agagtacaag gatgacatgc tggcccctcg gagattagtt atgaaaaatg tacgtatgca
      121 attcgatcta cctgaagata ggttggatga actcgattct ttaatgaaga agtgcggcat
      181 aagtactaaa aaagagttgt tcaactacgc gttaacaatg cttgagtggg ctgtggacga
      241 gtccgaaagt ggtcacgaaa tcgcagctat cgatagagac agtaagcaat tttatgctct
      301 acgaatgcct attcttaagc gagtgaaccg tacatctact gcaaattaac ttatcacttg
      361 atgtgttaag gagaaggcca gcttaaactg gccttctttt tttattcaag agggtttgat
      421 tgtgtccgat agcctagatg gatttactga aggcgatacc tcaaaagaaa aacaagcggt
      481 aaaacaaccc aagaagttct ttagtgacgt cgacgattca gcagatagac ggcatctgag
      541 atggacaaaa agtggcgtta ctctggctat gacaattttg gttgctgtaa tgaactggat
      601 ggtcataagc atgctatatc acgtagttga tgaagagctt tctctgatac gaagtggctt
      661 tatgcaagca gacgcaagga ctgtaactac tagtgtttat ttggctttga ttgctggaac
      721 agttgctgag gtatctgctt tatttttgat aattgtaaag tcagttttta agaacaataa
      781 caatgatata tgaagttgat tccagtcgtt agatgtagtg tcacacatgg ttttgttctg
      841 tctgtcttga gatcactcta atcaaaatgt aatctcttgg gactgaaacg aaaaaaccac
      901 ccggcaaggt ggttttttcg aaggttcatt aaccggcaag tttctgaacc gtggtaactg
      961 gctttcgcag agcacagaaa ccgaattcgt tttaacagtg tagccgtagt ctgccttaca
     1021 cttcaacacc tcaacgcttc tttgttctgc gaatctgtta cctgtggctg ctgccattgg
     1081 cgttttaacg cgttttttcc gggttggact caaggtgata gttactggaa aaaacgcagc
     1141 agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gccttcccgg
     1201 atctgagtgt caggcgtgga gtgagaaaac gcggccataa cagcggaatg acaccggtaa
     1261 accgaaaggc aggaacagga gagcgcacga gggagccacc agggggaaac gcctggtatc
     1321 tttatagtcc tgtcgggttt cgccaccact gatttgagcg tccgattctg tgatgcttgt
     1381 caggggggcg gagcctatgg aaaaacgccc cgccggggcg ttgcctttta gcccttgtcc
     1441 ttagctttcg ttatgcttac cgttacgtta tctgcttatc ttccctccgc tcgccgcaga
     1501 ctcatgaccg aacggagtga gcgaatgagc gaggaagcgg aaaaccatca gaacgtacag
     1561 taagcacttt cgcgccgggg ctttcatgaa caaacaacaa aagactgccg ttaacatggc
     1621 taaattcatc caggatcagt ccctgcttct tctggacagg cttaatgagc tggatctgga
     1681 tcatgaggct gatttctgcg agaaactcca tgaggatgcg gaacgccttt accgaagcct
     1741 gtcagcgcgc ctgaatgagc agcaggacgg tgcgtaatgg ctccgttctg ggtattaccg
     1801 gagtaatacc ggcatcgcct taattttcat tgtcttagcg cttaacatta ttaccccggt
     1861 aatacccaga atccctgtat tttttctttt ttatttattt ttcatgcagt tgcgatgaaa
     1921 gtcgcggctg cgttaggtgt atgaccattt tgaggttgaa aaataatcaa ccatggcggg
     1981 tgatttacgc aggttaaggg gagatcgtga caaaaaaagc gttcctcact gtatcgttca
     2041 tgcctgcatg aacgggttat tcttcctgac tacagaatta tatcgctcct tcagttcata
     2101 catcactttt acaacacttt tacaacactc cttcagtctg tacatcgctt ttacaacact
     2161 tttgcatcac ttttacatca tttgtacatc acttttacat cattccttca gctcatacgt
     2221 cacttttacg tcagttccat cctctgtgcc atttgtacat ccgaccccct tcctgaacgt
     2281 gctgaaaacg gtttttccgg ctgtgccggc aacgcctcac ggccacgcaa taaattgcgt
     2341 ccccgttcac cgttttcgga taagaagaac atcggaaaca ggacttaccc cggctgaatg
     2401 gcgtgaattt ccgcgctatg cacttgcgcg catactcatg catgccgtaa aaacagagcc
     2461 tgcgcgtttc tggcgggttt tcgggtggtt tgttgcctgt tttaccggtt ttccgtcaga
     2521 aacgccctga ggccgtttta gcggtgcgta caatacttga gttatgttaa atgcacctaa
     2581 gatttggatg attgtttcat ctcgttacaa ctactgttgt ctttttaacc tatatcgttt
     2641 tatactcgta atatgctcca attacactcg acaatggaga tgtttgagtg taagatacaa
     2701 tctggagccc attacgaggt gtggtgggta aactggagat ttcacctgtg agcgagttaa
     2761 ctcaaaactg ctcctcgacc tccaggaaca gtgaggactg caccgacttc gaagaactgc
     2821 ctcctaaaga gctttctttg aaggattggt tctcagtctt tactgaggtc gatgagtaat
     2881 aaccaccatg gaggagtttt cacaacctcc tccatggtgg ggataacctg cttgcggaga
     2941 agagataagg ctaagcctta tccaaattag gagtatcata agtatatgaa acttaat
//
