LOCUS       NZ_AP022074             5167 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-W18-ESBL-09 plasmid pWP4-W18-ESBL-09_5,
            complete sequence.
ACCESSION   NZ_AP022074
VERSION     NZ_AP022074.1
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  JOURNAL   Unpublished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 5167)
  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
            AP022074.1.
            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..5167
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-W18-ESBL-09"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-W18-ESBL-09_5"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-02-13"
     gene            complement(101..1015)
                     /locus_tag="H7R28_RS26950"
                     /old_locus_tag="WP4W18E09_P50010"
     CDS             complement(101..1015)
                     /locus_tag="H7R28_RS26950"
                     /old_locus_tag="WP4W18E09_P50010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            2752..2961
                     /locus_tag="H7R28_RS26955"
                     /old_locus_tag="WP4W18E09_P50020"
     CDS             2752..2961
                     /locus_tag="H7R28_RS26955"
                     /old_locus_tag="WP4W18E09_P50020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(3027..3560)
                     /locus_tag="H7R28_RS26960"
                     /old_locus_tag="WP4W18E09_P50030"
     CDS             complement(3027..3560)
                     /locus_tag="H7R28_RS26960"
                     /old_locus_tag="WP4W18E09_P50030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(3563..4489)
                     /locus_tag="H7R28_RS26965"
                     /old_locus_tag="WP4W18E09_P50040"
     CDS             complement(3563..4489)
                     /locus_tag="H7R28_RS26965"
                     /old_locus_tag="WP4W18E09_P50040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4666..5064
                     /locus_tag="H7R28_RS26970"
                     /old_locus_tag="WP4W18E09_P50050"
     CDS             4666..5064
                     /locus_tag="H7R28_RS26970"
                     /old_locus_tag="WP4W18E09_P50050"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     Typing          complement(241..1015)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(3567..4489)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agccgcgcca ttgcagggct gaacggggaa aaacggcaaa aaacctgctg ctcaaaaaga
       61 cgccagaaag gcgctgttat ctgatatagg cttatttggt ctactctacg agacctcgtt
      121 ttttcagttg gtaataccag gcgcgactga tccctaatgc ctcccacggt ttcagcgtgc
      181 gtgcagatgt agctactgtg ctgcgcttag acttagaacc gcccttgcga ccgcgtgcag
      241 cctgaatttc tggcgtgtgc gtatcagcca catactgtgc gaaagtttcc ggcgtgaagt
      301 tcctgtgcgt gtatttcgca atgctcttgc caatagcccg acattcagcc agtgaaagcg
      361 gaacgggaag cgatgcattg tacatttcga cacgctggat caccgcttca agccactgtg
      421 agaacgctgg ccagccctga cgaatcgccc tgtaagccca tttgcgcgtc atttcgaaca
      481 ggtggcagtt tcgccccatc ccgtaatgtt tatcgatgct acgacgctct gaggcgctca
      541 aatcgagata atcagccagt tcatcgaggg tataggcttc ctcgcgccac tccatcacca
      601 gccattccag gtggaacgga tttttgcaaa tcaggccgct gtagttcaca tccgcacaaa
      661 gtttctcaca cagcgaacgt tcaaccgctg cggcatattt cagcgcctta accgaggcat
      721 caggcgcggt tctcacggcg atgttgagtg cgtagagcag gtgagcgtgt ccgttcacag
      781 gatttttaac ggtgatgttc ggcgcgggag cgttccggtc gctccagtca atcgcagccc
      841 cctcgcggtc aacgtcaaaa accagccaga actgcgcatg aggctggttc tgctgtatgt
      901 accgcgcaag aagcgcacgc cctttgccgg agatgcgaag accaaaagcg agatcatccg
      961 tgtgataggg acgatggggt aaattttcgt cgaagtattg aagcgcggcg ctcatgtgtt
     1021 acgattctct ccgggttatg cgacctacac gccctctgta tttcatgttg aatcttgccg
     1081 gatctggaca tgatttcagg ggcgtttgtt tttcagtcgc ttacactaca cccaacggca
     1141 aatcctgtcg aaccttcccg aaaacccgat ccatttacca taactcccgt tgtacgcccc
     1201 ccttaaaacg ccctcagtcg ctttctggcg caaaaaacgc aaaaagacaa gaaaacacca
     1261 ggccaaacca gaaaaacgcg tcagaatcgt tttcagggcg ttgcataact atgcacgaaa
     1321 gcgatgtgcg atcggtttcg tgcgttctga acaccgaacg gctcaaaacg acaagttttc
     1381 tcccctggtg cgtggcgctc tgacggggtt tcctgtttcc aaacttcaca tctcgccagg
     1441 acaaaaaaaa accgacctgg ggtcggtggc aagaatcaga gtctatggga aatattttag
     1501 ttatcggatg ctcaatattc acaaacgcaa aaaatgcctc agtgatgccc taaaacaacc
     1561 tttccagaag gagtccgcgc tttacgatgc acggaagaga taaaaaaccc cacaaaagtg
     1621 gggaaccaag agaaacaaca attacaggtt gttggttgtg ttcgaacaac gatgaagtag
     1681 ctacgctaaa taataattac cgtacaggcc ctacatattc aacactaaat ttaagatcct
     1741 gacgaaggat ttataaatgc acgaaaacac atagacagac aaattcacta aattcataca
     1801 caaaaacaag tgtagttttc taagtaaatt agattcgaca accaattagt ttatccacat
     1861 cgcattccac tcttgctaca ccaatcacat ttcttgatat gtaatagcag aaaaaataaa
     1921 accagacacc aatagaccaa aaaacaaaca ttcaacaaga aacattttga acaatatcac
     1981 aaaactgtca caaccatcat cagactattg aaaaaaactg gttgctgttt tataaaagcg
     2041 actgtaacaa cctccactct atagttccat tagtttaaag tgtcacacaa actgagcatc
     2101 catttgtttt ccttactttt gcccctgtat tccaaggggt ttttttataa cttaaagatt
     2161 agcacaccac acaaaaacaa taaaaaaaaa cgacaagtta tacaataaaa ccagtactat
     2221 ccatacagct aattacatat aaatactatt aaaccatctg gacattaaaa ataaactctt
     2281 ataacataaa attaatgcgg ttccggtacc atatgtcagg gataatgtgc aaatggaggt
     2341 atcggaactg catttcagtt cattattaat taatgacaaa aaaaacctct gcgagcgcag
     2401 agggggtaag gaatgttccc ggtcataata tgtcgatagt gtttatatac atacagaaca
     2461 agaacaacaa ccagccaact aataaatatt ttatttttta gagctgaaac cttaaagctc
     2521 acttccattc catacattgt tataaacctt atgttgaaaa ctgaaagtaa gtacggcaga
     2581 cttattaagt tgcgtgcagt cttttcacgt tatacaaaca agaacacctg cgaagttatt
     2641 tctccttaca tatcccccta tgccaacggg ggattttttc tggttcacta acgcataaat
     2701 aatagtgaca ccctatcatt cacaaaccgt gataatataa ggattatcat catggcaaaa
     2761 ttaggtgaaa acaccccaca tattatcgat gctactgtag attttatggc atcaagccag
     2821 gcatttcgtg agtatctgaa aaaacttccc cctgataaca caataccgcc agctcttact
     2881 gatgagcacg taccgttata tatacgaagg ctggaatact atcgtctgct ttatcgacca
     2941 aagcagacag aatcatattg aaaaaaacgg tgaacggttc gcgaaattct ttcgcgggtc
     3001 gtgaggcgtt ggacaagcga agcgcgtcag tttttccggc tcttccccgt gacaggtttc
     3061 tccaccagtt tatcttccag tgtcacaact ttctgataca ccgccgctgt ggcgttgtag
     3121 ttcctgtcga gtattgtttt cattccccat ccgagcacac agaacataac cagaaaagcc
     3181 actgacaccc cacccagcca tttccagcta taccctttaa gggtgttgta ttcctgcacg
     3241 atattgctgt gaattgtcgc aatatccctg ttcagggcat ccgcgtttgc cttcatgttt
     3301 gcgactgact cttccagccg ctgaaaatcc tggctgatgc gctcacctat cagtcctgcc
     3361 acgtccagct tctgcacctc atttctgact tcatccctga cctgttttgc cacaccgtca
     3421 gaaatatccc gatatccgcg aagagtttcc cttgccacag ccagagaatc agcaacagct
     3481 ttctgttgct ccattgcggt atgttgcaga tgctccaccg ataacaggag cgtaagtaat
     3541 ttttcttctg tgctggccat gttcagaatc ccatagaaaa tccacgtgac ggtgatttaa
     3601 cccgttcagg tgcagttcgg ttctgtctgc tcactctgtc tctcatgtca aagccatgct
     3661 cccgcgcaac atcatgttgc agccttctga ccagttcatg ttgcttaacc ggagtgtcca
     3721 gccattccct gatgtcatgc ccgaccgttc gcgcctgttc aagatggcgg gaatagtccg
     3781 gttcagaccg tttttgcatg atgtcatgac gctgggcatc atcaagccgt ccggcagctt
     3841 caaaacccag atgcacttcg ggacgtcgtt caatgccctg ttctttcagc gtccggcagt
     3901 caatgaagcc cctttcaaag ccatgctttc tcatatgttc gttgtgcttc acctcccagc
     3961 gttttcgcaa ttcccgcaac tgctcttttt gctgagtgag agtcaggctt ccggaatcct
     4021 ttttcgcacc tccccgctcg ggatacctgg cgttatagcg ccggaaatac tgttccggtg
     4081 tacgttcaat gccatcattc acacgctgac tcatcatgat atgcgcatga ggctgttcgc
     4141 cgccgtcaat gctcgctttc ggattgtgaa tggcaaaact ccaggcgtgc cgttcgccag
     4201 cttcctgacg tacaaaatcc tgcaccagtt caaggcgctg ttccggtgtc agttcacggg
     4261 gtaatgcaat ttcaagttcc ctataggtcg aaccgttcgc acgttcaaac tggtcagccg
     4321 cctgccagaa atgggaagga ttatccctgg cccattccgg catgtttccg tgtgcggaat
     4381 attccaaatc ctgacggtcg cggtatttct ctttgcgctc gatgtaatcg gcgtggtttg
     4441 cagcctgccc cttgccacca aatttaacgc tgaggtgata ggttgccacg gtttcagccc
     4501 tctgcaggag cgcactgttt ctcgacgaag gagagaaaca tataagtgcg cttccttcta
     4561 attttacgaa ttagcacgga agataccccc tgcacccgcc gaccgcaagc gatatactgc
     4621 acgaccacaa cacaccgcaa aaaaacacca gggagcatca cgaacatgcg catcagcaac
     4681 atcgaatggc tgaagaaacg gatcggattc atcaggaagc tcggagaaca gaccgcacga
     4741 cagagacaga ttattgacct gatcgacaac gaagccggac tcacagaaca ggaacgcaaa
     4801 cttctccacg tactggcaac agcggaaaaa aacgacttac aggcacagga gagcgaacga
     4861 aaacaggcgg tccaaaaacg aatcgaggga aaaaaacaac gacgggaacg caatcaccgg
     4921 ctctttctcg cggctgggct actgatcgaa gcaggactgg tagacacaaa aacaggcgag
     4981 ctatgctata aaaaagacag gatattacaa gcacttaagg aacttaagta cgatctggag
     5041 acatccccaa acccagacgc gtaagtgcct ccatccgtgt tccgattccc tggtgcttcc
     5101 tcgctcattc gctcgctacg ctcggtcatg agactgcggc gagcactacc accacaatca
     5161 cgcggaa
//
