LOCUS       NZ_AP022001             5167 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP3-W18-ESBL-07 plasmid pWP3-W18-ESBL-07_3,
            complete sequence.
ACCESSION   NZ_AP022001
VERSION     NZ_AP022001.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194413
            Sequence Read Archive: DRR199249
            Assembly: GCF_014168835.1
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. WP3-W18-ESBL-07
            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  JOURNAL   Unpublished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                   :: 176x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:23:09
            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)                     :: 5,032
            CDSs (total)                      :: 4,919
            Genes (coding)                    :: 4,710
            CDSs (with protein)               :: 4,710
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 83 of 209
            Pseudo Genes (incomplete)         :: 146 of 209
            Pseudo Genes (internal stop)      :: 41 of 209
            Pseudo Genes (multiple problems)  :: 54 of 209
            Pseudo Genes (short protein)      :: 3 of 209
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022001.1.
            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="WP3-W18-ESBL-07"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP3-W18-ESBL-07_3"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-02-13"
     gene            complement(101..499)
                     /locus_tag="H7Q99_RS24860"
                     /old_locus_tag="WP3W18E07_P30010"
     CDS             complement(101..499)
                     /locus_tag="H7Q99_RS24860"
                     /old_locus_tag="WP3W18E07_P30010"
                     /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"
     gene            676..1602
                     /locus_tag="H7Q99_RS24865"
                     /old_locus_tag="WP3W18E07_P30020"
     CDS             676..1602
                     /locus_tag="H7Q99_RS24865"
                     /old_locus_tag="WP3W18E07_P30020"
                     /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            1605..2138
                     /locus_tag="H7Q99_RS24870"
                     /old_locus_tag="WP3W18E07_P30030"
     CDS             1605..2138
                     /locus_tag="H7Q99_RS24870"
                     /old_locus_tag="WP3W18E07_P30030"
                     /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(2204..2413)
                     /locus_tag="H7Q99_RS24875"
                     /old_locus_tag="WP3W18E07_P30040"
     CDS             complement(2204..2413)
                     /locus_tag="H7Q99_RS24875"
                     /old_locus_tag="WP3W18E07_P30040"
                     /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            4150..5064
                     /locus_tag="H7Q99_RS24880"
                     /old_locus_tag="WP3W18E07_P30060"
     CDS             4150..5064
                     /locus_tag="H7Q99_RS24880"
                     /old_locus_tag="WP3W18E07_P30060"
                     /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"
     Typing          4151..4925
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          677..1599
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcgtgattg tggtggtagt gctcgccgca gtctcatgac cgagcgtagc gagcgaatga
       61 gcgaggaagc accagggaat cggaacacgg atggaggcac ttacgcgtct gggtttgggg
      121 atgtctccag atcgtactta agttccttaa gtgcttgtaa tatcctgtct tttttatagc
      181 atagctcgcc tgtttttgtg tctaccagtc ctgcttcgat cagtagccca gccgcgagaa
      241 agagccggtg attgcgttcc cgtcgttgtt tttttccctc gattcgtttt tggaccgcct
      301 gttttcgttc gctctcctgt gcctgtaagt cgtttttttc cgctgttgcc agtacgtgga
      361 gaagtttgcg ttcctgttct gtgagtccgg cttcgttgtc gatcaggtca ataatctgtc
      421 tctgtcgtgc ggtctgttct ccgagcttcc tgatgaatcc gatccgtttc ttcagccatt
      481 cgatgttgct gatgcgcatg ttcgtgatgc tccctggtgt ttttttgcgg tgtgttgtgg
      541 tcgtgcagta tatcgcttgc ggtcggcggg tgcagggggt atcttccgtg ctaattcgta
      601 aaattagaag gaagcgcact tatatgtttc tctccttcgt cgagaaacag tgcgctcctg
      661 cagagggctg aaaccgtggc aacctatcac ctcagcgtta aatttggtgg caaggggcag
      721 gctgcaaacc acgccgatta catcgagcgc aaagagaaat accgcgaccg tcaggatttg
      781 gaatattccg cacacggaaa catgccggaa tgggccaggg ataatccttc ccatttctgg
      841 caggcggctg accagtttga acgtgcgaac ggttcgacct atagggaact tgaaattgca
      901 ttaccccgtg aactgacacc ggaacagcgc cttgaactgg tgcaggattt tgtacgtcag
      961 gaagctggcg aacggcacgc ctggagtttt gccattcaca atccgaaagc gagcattgac
     1021 ggcggcgaac agcctcatgc gcatatcatg atgagtcagc gtgtgaatga tggcattgaa
     1081 cgtacaccgg aacagtattt ccggcgctat aacgccaggt atcccgagcg gggaggtgcg
     1141 aaaaaggatt ccggaagcct gactctcact cagcaaaaag agcagttgcg ggaattgcga
     1201 aaacgctggg aggtgaagca caacgaacat atgagaaagc atggctttga aaggggcttc
     1261 attgactgcc ggacgctgaa agaacagggc attgaacgac gtcccgaagt gcatctgggt
     1321 tttgaagctg ccggacggct tgatgatgcc cagcgtcatg acatcatgca aaaacggtct
     1381 gaaccggact attcccgcca tcttgaacag gcgcgaacgg tcgggcatga catcagggaa
     1441 tggctggaca ctccggttaa gcaacatgaa ctggtcagaa ggctgcaaca tgatgttgcg
     1501 cgggagcatg gctttgacat gagagacaga gtgagcagac agaaccgaac tgcacctgaa
     1561 cgggttaaat caccgtcacg tggattttct atgggattct gaacatggcc agcacagaag
     1621 aaaaattact tacgctcctg ttatcggtgg agcatctgca acataccgca atggagcaac
     1681 agaaagctgt tgctgattct ctggctgtgg caagggaaac tcttcgcgga tatcgggata
     1741 tttctgacgg tgtggcaaaa caggtcaggg atgaagtcag aaatgaggtg cagaagctgg
     1801 acgtggcagg actgataggt gagcgcatca gccaggattt tcagcggctg gaagagtcag
     1861 tcgcaaacat gaaggcaaac gcggatgccc tgaacaggga tattgcgaca attcacagca
     1921 atatcgtgca ggaatacaac acccttaaag ggtatagctg gaaatggctg ggtggggtgt
     1981 cagtggcttt tctggttatg ttctgtgtgc tcggatgggg aatgaaaaca atactcgaca
     2041 ggaactacaa cgccacagcg gcggtgtatc agaaagttgt gacactggaa gataaactgg
     2101 tggagaaacc tgtcacgggg aagagccgga aaaactgacg cgcttcgctt gtccaacgcc
     2161 tcacgacccg cgaaagaatt tcgcgaaccg ttcaccgttt ttttcaatat gattctgtct
     2221 gctttggtcg ataaagcaga cgatagtatt ccagccttcg tatatataac ggtacgtgct
     2281 catcagtaag agctggcggt attgtgttat cagggggaag ttttttcaga tactcacgaa
     2341 atgcctggct tgatgccata aaatctacag tagcatcgat aatatgtggg gtgttttcac
     2401 ctaattttgc catgatgata atccttatat tatcacggtt tgtgaatgat agggtgtcac
     2461 tattatttat gcgttagtga accagaaaaa atcccccgtt ggcatagggg gatatgtaag
     2521 gagaaataac ttcgcaggtg ttcttgtttg tataacgtga aaagactgca cgcaacttaa
     2581 taagtctgcc gtacttactt tcagttttca acataaggtt tataacaatg tatggaatgg
     2641 aagtgagctt taaggtttca gctctaaaaa ataaaatatt tattagttgg ctggttgttg
     2701 ttcttgttct gtatgtatat aaacactatc gacatattat gaccgggaac attccttacc
     2761 ccctctgcgc tcgcagaggt tttttttgtc attaattaat aatgaactga aatgcagttc
     2821 cgatacctcc atttgcacat tatccctgac atatggtacc ggaaccgcat taattttatg
     2881 ttataagagt ttatttttaa tgtccagatg gtttaatagt atttatatgt aattagctgt
     2941 atggatagta ctggttttat tgtataactt gtcgtttttt tttattgttt ttgtgtggtg
     3001 tgctaatctt taagttataa aaaaacccct tggaatacag gggcaaaagt aaggaaaaca
     3061 aatggatgct cagtttgtgt gacactttaa actaatggaa ctatagagtg gaggttgtta
     3121 cagtcgcttt tataaaacag caaccagttt ttttcaatag tctgatgatg gttgtgacag
     3181 ttttgtgata ttgttcaaaa tgtttcttgt tgaatgtttg ttttttggtc tattggtgtc
     3241 tggttttatt ttttctgcta ttacatatca agaaatgtga ttggtgtagc aagagtggaa
     3301 tgcgatgtgg ataaactaat tggttgtcga atctaattta cttagaaaac tacacttgtt
     3361 tttgtgtatg aatttagtga atttgtctgt ctatgtgttt tcgtgcattt ataaatcctt
     3421 cgtcaggatc ttaaatttag tgttgaatat gtagggcctg tacggtaatt attatttagc
     3481 gtagctactt catcgttgtt cgaacacaac caacaacctg taattgttgt ttctcttggt
     3541 tccccacttt tgtggggttt tttatctctt ccgtgcatcg taaagcgcgg actccttctg
     3601 gaaaggttgt tttagggcat cactgaggca ttttttgcgt ttgtgaatat tgagcatccg
     3661 ataactaaaa tatttcccat agactctgat tcttgccacc gaccccaggt cggttttttt
     3721 ttgtcctggc gagatgtgaa gtttggaaac aggaaacccc gtcagagcgc cacgcaccag
     3781 gggagaaaac ttgtcgtttt gagccgttcg gtgttcagaa cgcacgaaac cgatcgcaca
     3841 tcgctttcgt gcatagttat gcaacgccct gaaaacgatt ctgacgcgtt tttctggttt
     3901 ggcctggtgt tttcttgtct ttttgcgttt tttgcgccag aaagcgactg agggcgtttt
     3961 aaggggggcg tacaacggga gttatggtaa atggatcggg ttttcgggaa ggttcgacag
     4021 gatttgccgt tgggtgtagt gtaagcgact gaaaaacaaa cgcccctgaa atcatgtcca
     4081 gatccggcaa gattcaacat gaaatacaga gggcgtgtag gtcgcataac ccggagagaa
     4141 tcgtaacaca tgagcgccgc gcttcaatac ttcgacgaaa atttacccca tcgtccctat
     4201 cacacggatg atctcgcttt tggtcttcgc atctccggca aagggcgtgc gcttcttgcg
     4261 cggtacatac agcagaacca gcctcatgcg cagttctggc tggtttttga cgttgaccgc
     4321 gagggggctg cgattgactg gagcgaccgg aacgctcccg cgccgaacat caccgttaaa
     4381 aatcctgtga acggacacgc tcacctgctc tacgcactca acatcgccgt gagaaccgcg
     4441 cctgatgcct cggttaaggc gctgaaatat gccgcagcgg ttgaacgttc gctgtgtgag
     4501 aaactttgtg cggatgtgaa ctacagcggc ctgatttgca aaaatccgtt ccacctggaa
     4561 tggctggtga tggagtggcg cgaggaagcc tataccctcg atgaactggc tgattatctc
     4621 gatttgagcg cctcagagcg tcgtagcatc gataaacatt acgggatggg gcgaaactgc
     4681 cacctgttcg aaatgacgcg caaatgggct tacagggcga ttcgtcaggg ctggccagcg
     4741 ttctcacagt ggcttgaagc ggtgatccag cgtgtcgaaa tgtacaatgc atcgcttccc
     4801 gttccgcttt cactggctga atgtcgggct attggcaaga gcattgcgaa atacacgcac
     4861 aggaacttca cgccggaaac tttcgcacag tatgtggctg atacgcacac gccagaaatt
     4921 caggctgcac gcggtcgcaa gggcggttct aagtctaagc gcagcacagt agctacatct
     4981 gcacgcacgc tgaaaccgtg ggaggcatta gggatcagtc gcgcctggta ttaccaactg
     5041 aaaaaacgag gtctcgtaga gtagaccaaa taagcctata tcagataaca gcgcctttct
     5101 ggcgtctttt tgagcagcag gttttttgcc gtttttcccc gttcagccct gcaatggcgc
     5161 ggctttc
//
