LOCUS       NZ_AP022094             3137 bp    DNA     linear   CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S18-ESBL-07 plasmid pWP4-S18-ESBL-07_7
            map unlocalized.
ACCESSION   NZ_AP022094
VERSION     NZ_AP022094.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194481
            Sequence Read Archive: DRR199317
            Assembly: GCF_014171015.1
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-07
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3137)
  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                   :: 166x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:36:35
            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)                     :: 5,281
            CDSs (total)                      :: 5,159
            Genes (coding)                    :: 4,963
            CDSs (with protein)               :: 4,963
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 196
            CDSs (without protein)            :: 196
            Pseudo Genes (ambiguous residues) :: 0 of 196
            Pseudo Genes (frameshifted)       :: 84 of 196
            Pseudo Genes (incomplete)         :: 130 of 196
            Pseudo Genes (internal stop)      :: 43 of 196
            Pseudo Genes (multiple problems)  :: 49 of 196
            Pseudo Genes (short protein)      :: 4 of 196
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022094.1.
            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/
FEATURES             Location/Qualifiers
     source          1..3137
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S18-ESBL-07"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /map="unlocalized"
                     /plasmid="pWP4-S18-ESBL-07_7"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-08-06"
     gene            101..253
                     /locus_tag="H7R53_RS26060"
                     /old_locus_tag="WP4S18E07_P70010"
     CDS             101..253
                     /locus_tag="H7R53_RS26060"
                     /old_locus_tag="WP4S18E07_P70010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015986836.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024046379.1"
                     /translation="MANEVRRTKRLDTRRKPKMTNEQLLAFLAAGINASKNRDYQADIT
                     LEAHH"
                     /name="hypothetical protein"
     gene            290..808
                     /locus_tag="H7R53_RS26065"
                     /old_locus_tag="WP4S18E07_P70020"
     CDS             290..808
                     /locus_tag="H7R53_RS26065"
                     /old_locus_tag="WP4S18E07_P70020"
                     /inference="COORDINATES: protein motif:HMM:NF025323.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YafO family toxin"
                     /protein_id="WP_024046380.1"
                     /translation="MSHMPLDTTRIFVHVHPNLQEYPNASLFVEEFEEYKKQAFDYAKE
                     NGCLAADFLPALTEEDQKSLPPDQYLFGRDRLFYRGAAANDPLYHVHIFKPDDEKCVWH
                     DDNGISVNQWWCRSDAALIYAHMDTHSNDFHFLLLEIIDPGAHERYEEKGAIEHWRKLV
                     IAYRAVNDI"
                     /name="type II toxin-antitoxin system YafO family toxin"
     gene            1713..1862
                     /locus_tag="H7R53_RS26070"
                     /old_locus_tag="WP4S18E07_P70040"
     CDS             1713..1862
                     /locus_tag="H7R53_RS26070"
                     /old_locus_tag="WP4S18E07_P70040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001442891.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(2651..3049)
                     /locus_tag="H7R53_RS26075"
                     /old_locus_tag="WP4S18E07_P70050"
     CDS             complement(2651..3049)
                     /locus_tag="H7R53_RS26075"
                     /old_locus_tag="WP4S18E07_P70050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_024046378.1"
                     /translation="MSEKNPEAALEAKWGKSALAMGWTAVPSALFFLQGTLSISPVAFN
                     VLLNLLTHWWKAHEWPHPSQESIAVRMSVSVRTVQRGLAELENMGLITRRKTSKEHPKY
                     RGRNVYDLTNLVESLNNLAPNIKEKLSQ"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1506..1720
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.0"
                     /coverage="100.0"
                     /evalue="1.6099999999999998e-54"
     Typing          complement(989..1525)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.882"
                     /coverage="89.0"
                     /evalue="0.0"
ORIGIN
        1 gacacgtacg cgctaaacta aaagttgttt tcttctatac ttcacttaac gacaggcatt
       61 ttccctagcc acacacaagc gtgaagctta aggtttcgat atggctaatg aagttagaag
      121 aacgaagcgt ttagatacgc gtcgtaagcc aaaaatgaca aacgaacagt tactggcttt
      181 tttggctgca ggcattaatg cgtcaaaaaa tcgtgactac caagctgata tcactttaga
      241 agcccaccat taaaacgtgg tagaatccct gtaaaaaccg cagggattca tgagccacat
      301 gcctcttgat acaactcgta tttttgtaca tgtgcatcct aaccttcagg agtatccaaa
      361 cgcctctctt tttgtagaag agttcgaaga atacaaaaaa caggcttttg attacgcaaa
      421 agagaacggg tgcctagctg ctgattttct tcccgccttg actgaagaag atcaaaaatc
      481 attacctcct gatcagtatc tatttggtag ggataggctt ttttatagag gggctgctgc
      541 aaatgatccc ctatatcatg ttcatatctt caagccggat gatgaaaagt gtgtctggca
      601 tgatgataat ggtattagcg ttaatcaatg gtggtgtcgc agtgatgcgg cattgattta
      661 tgctcatatg gatacgcata gcaatgactt ccacttcctt ttgcttgaaa tcattgatcc
      721 cggcgctcac gagagatatg aggaaaaagg tgcaatagag cactggagaa agctggttat
      781 cgcctaccga gcagtgaatg atatctaggc aatgaaaaat gagttgttga cgtattgctt
      841 tggtaagtat taccctcaat ccaaacgaaa aaaccacccg gcaaggtggt ttttcgaagg
      901 atcagtaaac cggcaagttt ctgaaccgtg gtaacagtct tgtgcgagac atgtcaccaa
      961 atctgtcctt ccagtgtagc ctcactaagg cctccacttc aagaactctc gatacatctc
     1021 tcgcacatcc tgcttaccag tggccgctgc cagtggcgtt aagtcgtgtc tttccgggtt
     1081 ggactcaaga tgatagttac cggacaaggc gcagcggtcg gactgaacgg ggggttcgtg
     1141 catacagtcc agcttggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag
     1201 acaaacgcgg ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc
     1261 gcacgaggga gctaccaggg ggaaacgcct gggatcttta tagtcctgtc gggtttcgcc
     1321 gccactgatt tgagcgtcag atttcgtgat gcttgtcagg ggggcggagc ctatggaaaa
     1381 acggcagcgc cgcggccttc tcgtttccct gttaagttcg ctcctggcat ctacccggaa
     1441 atttccgccc catttgtaag ccggtaccgc tcgccgcagc cgaacgaccg agcgtagcga
     1501 gtcagtgagc gaggaagcgg aatatctcct gtattgcatc ttctgctgac gcgccggtgc
     1561 cacctttttc tcctgccaca tgaagcactt tcataaagtg ttactccacc gtagcatatt
     1621 gagcccatat acactccgct agtgctacgt gactggttca gggctgcgcc ccaaaacccg
     1681 ctaacaacct ctccgctact ggatatcacc ccatgccatc tgaatatgat gaacaactgg
     1741 attcgactga tacgcagctt cccggcgaat atgacctttt tgatttaatg gcgcaggtta
     1801 ctgaagagaa cctgcacgcc ccggtggatt ttgggccgcc tgtcggccgg gaagcgttat
     1861 agctttttcg cttacccgcg tacgtgtaat acgccggtat tacatcttat ttctttattt
     1921 tcatgtgatt acaggtggtt gtaatacgtt gcgtattaca taaataaacg ggaacttcag
     1981 tttttacctt ttaattcatg caattgcgat gaaaatcgcg gttgcgtatg gtgtatggcc
     2041 atttaaggga taaagaatca tctccttacc gggctgagct ttgcctattc tgaggagatc
     2101 tgtgaaaaaa agcgtccata actagctcgt tcatacttgt atgaacgagc ttattcctcc
     2161 tgactactaa taaactacag cgtcactact gatttactac tgatttacta caaaccggag
     2221 ggggggacta cagaaacact actgatttac tactgattta ctacaaatcg gaggaggatg
     2281 actacttatc tactactgat ttactactga attacgtcat aacagttctc tgaaccattc
     2341 gtacatccga cccccttctc ttcatgcttg atgctcttgc caacgcttca cggtcacgca
     2401 ataaattgcg tccccgttca ccgttttcgg atgagaagaa cgtcgaaaac aggacttcca
     2461 ctggctgcac ggcgtgaaat tctgcgctat gcacttgcgc gcatactcat gcatgccgta
     2521 aaaacagagc ctgcgcgttt ctggcgggtt ttcgggtggt ttgttgcctg ttttaccggt
     2581 ttcccgtcag aaacgccctg agagcctctc aggcggtgca cgcaacggat gttatggtaa
     2641 ataactaccc ttattgtgat aatttttctt ttatatttgg cgctaaattg ttcagcgatt
     2701 ccaccagatt agttaaatcg tacacgtttc tccccctgta tttggggtgc tctttactag
     2761 tttttcttct ggttattaag cccatatttt ccaattcagc caacccacgt tgaactgttc
     2821 ttacagagac actcatcctt acagctatgc tttcttgaga tggatgaggc cactcatggg
     2881 ccttccacca atgagtcaaa agattcagta agacattaaa agctacagga gatatggata
     2941 gagtaccttg aagaaagaac aacgcagaag gaacggcagt ccatcccata gctaatgcgc
     3001 ttttccccca tttcgcttct aatgcggctt ctggattttt ttctgacatg acagtactca
     3061 caatgctaag atgacgggaa tcctaaagga ttcccgtcat cttagcattg tgagtattat
     3121 aattatataa ttagtac
//
