LOCUS       NZ_AP022052             4170 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S17-ESBL-08 plasmid pWP4-S17-ESBL-08_3,
            complete sequence.
ACCESSION   NZ_AP022052
VERSION     NZ_AP022052.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194455
            Sequence Read Archive: DRR199291
            Assembly: GCF_014169035.1
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-S17-ESBL-08
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4170)
  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                   :: 177x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:32:47
            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)                     :: 5,014
            CDSs (total)                      :: 4,892
            Genes (coding)                    :: 4,678
            CDSs (with protein)               :: 4,678
            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)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 89 of 214
            Pseudo Genes (incomplete)         :: 145 of 214
            Pseudo Genes (internal stop)      :: 38 of 214
            Pseudo Genes (multiple problems)  :: 52 of 214
            Pseudo Genes (short protein)      :: 3 of 214
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022052.1.
            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..4170
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S17-ESBL-08"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S17-ESBL-08_3"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2017-07-10"
     gene            complement(101..295)
                     /locus_tag="H7R14_RS24730"
     CDS             complement(101..295)
                     /locus_tag="H7R14_RS24730"
                     /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            1389..1799
                     /locus_tag="H7R14_RS24735"
                     /old_locus_tag="WP4S17E08_P30020"
     CDS             1389..1799
                     /locus_tag="H7R14_RS24735"
                     /old_locus_tag="WP4S17E08_P30020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            2057..2620
                     /locus_tag="H7R14_RS24740"
                     /old_locus_tag="WP4S17E08_P30040"
     CDS             2057..2620
                     /locus_tag="H7R14_RS24740"
                     /old_locus_tag="WP4S17E08_P30040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749520.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(2649..3275)
                     /locus_tag="H7R14_RS24745"
                     /old_locus_tag="WP4S17E08_P30050"
     CDS             complement(2649..3275)
                     /locus_tag="H7R14_RS24745"
                     /old_locus_tag="WP4S17E08_P30050"
                     /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_223149424.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHINDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     Typing          332..440
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.0"
                     /coverage="100.0"
                     /evalue="2.2800000000000002e-29"
     Typing          565..820
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="89.0"
                     /evalue="1.25e-96"
     Typing          complement(3552..4065)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgcgccccga cacccgctaa aaccccctga cgcgccctga cgggcttgtc tgctgacgaa
       61 aacgcccacg ggaaagccgt gaccgcctcc gtcagcttcg ttatgttcct gtttcacttt
      121 cggcctcaaa gcgaatctgg atgctgttct ggagttcttc tgcgagttcg tgcagtcgtt
      181 cgcacatggc cgcctgttcg tcggcatcca gagcatccag tttttcaagc agtgtcaggc
      241 tctggctttt gataaatcgc gccatattca gcgcagtttg ttgttgtttg ttcaccttcc
      301 gttgttctcc gtcagttccg ggtgtcgggg ggaccctgag caggtggtaa ttgtaagacg
      361 ttgcgggcga cggtattaca attgcacatc ctgtcctgtc ctgtcctgtt tctttaggac
      421 gtatcatggc acagcatatc aactgataaa taatccctgt gcagtgcagc cgctgttgca
      481 taaaatttcg ctctgcgtcg agtgtttctt aatcaataat tccgctgata ctccggaaaa
      541 acgcgagtct gttctcatgc ctgaaatgcc cacaccccac gcaaaaacaa gtttttgctg
      601 atttttcttt ataaatagag agttatgaca aattagttct tcttgctctc tttgtgatat
      661 ttaaaaaagc ggtgttggcg cagctacaac accgcgccga caccgctttt taggggtggt
      721 actgactatt ttcataaaaa acatcatctt atattagggg tgctgctagc ggcgcggtgt
      781 gtttttttac aggacgcccc tgggggcgct gccaggggtg tctgttcaga tatgtagcaa
      841 tgagtcaggg attcacgaac tgaaaatgtc cgaaaatgtg tctcatgggt actgtatgcg
      901 cccaaaccga tcgtcattca ctttcatgca tagctatgca gtgagctgaa agcgatcctg
      961 acgcattttt ccggtttacc ccggggaaaa catctctttt tgcggtgttt gcggcagaat
     1021 cgcgttcagc gcgttttagc ggtgcgcgca agaactctta tgttaaattc atctcatcgg
     1081 caacctatac aggcataaaa atcagtttct ataagcggct ttcttgcacc tacttggtga
     1141 tttttttgga tgcgctgacg ttgctcgact ttaaatcacc atagaaaaat accctttact
     1201 tacataaaga tcgatctgga tgtgtatctt gacgaggttc aatacgagca attgtttttg
     1261 tatttaaggt ttcttatcgc cgttttttgc ggctctagaa aaatcaatac aaaagatctt
     1321 gaaagtcacc tcgctccctg ggtacacttt cgtataagaa ctgatcgatg tctaaaacgg
     1381 attgtattat ggcctttatc tctctatcga acttggcagc gaagactgga aggataatcc
     1441 agtcgcagtg tgttacggcc acgcaaacga aaaaaagcac gggcgctgtc gagctgggat
     1501 tccgcttgag caagagcgct atggacgaga ctggtattac cattggggat cgtgtcgaca
     1561 ttctttacga caaagaagaa aaccagtgga tgattaagaa aattagtgaa ggtggctttg
     1621 gtgtgtctgg gcaaaaaaac aagcacggcg gttactcatc gtgtgctgtt agattgacct
     1681 tgcgaccagg ttttcctcgc ctttctgagg atgaagagga caacaagaag ctactttccg
     1741 atgattcatt cactcagcta agtgaaggtg taatcgtctt caggctggat gatgaatagg
     1801 aaggaccaaa aaggaaaggc agagttagtg agcgtcgcca aacaatcgac taactccgcc
     1861 ttctggtcaa cacatcacta cctttggaag ggtggagtgt tatgggcggc attatgttca
     1921 taaacttgca ttctaataaa gaaaaaatcg tttcttttga gggatgtgaa cacgacattt
     1981 tctattctga taggtgcgat gctattggct ttggtctctt aagtttatgt ttttaaaaac
     2041 atatgaggct atacatatgc acgctttatc aatactacct tcagttgccc gcgctaacct
     2101 ggcaactaaa ttctcgtctc atttgaaggt gatcgagctc ttcaacacga tgcaggattc
     2161 ccaagttgtt gtcttgtcat cactgatcga aggccatcac ctcaccagtt ctggtaacag
     2221 tgtcaaagcc gactttgagg tcactcgctt accggcgatt atcgagatgt tagagaaaaa
     2281 atattttttc cctattcgtc atctaaatgt atctgttaaa tctgtaacta caggaaggat
     2341 gactggacaa actgtctatt tcatagagcc tgaacacatc gagcaacttc tcgctgatcc
     2401 tgagcttgtg tttgctaatc aggaaaggag cctcttcttt cgttctctcg aaaaagaagg
     2461 gaaaaatctc ggcaagctta tcgagaaaaa aggtagtgtt tctcaagccg tcttaagcct
     2521 tctacatcac gcctacaaag ataaacctct ttctgacgag atgtggaagg agatagaaga
     2581 taagttcacc catatgctgg atgaattgag cgcggcgtaa aggcaagggc ggtcgttaga
     2641 ccgccttttt agtcttctaa acctaattct ttgtgatagt ttttcagcgt agagtaacga
     2701 tagtttctga gtatgttttc atctttcttg acgttcgctt ctatgtatct gtttacgaat
     2761 ttgttgaaat cttcttgtat tttttctttg ttatcattga tatgggtaaa ttcaggagtt
     2821 ggtatcttat aggctcgcga tacatactct tctttcttaa ttagcaacgc tttggtgtaa
     2881 tccagtcctt tcttaacacc ttctgatcgc tccgaaacga atccaaattt atggtttaaa
     2941 tggcttcgta agggtatccc gaacaccaat ccgttgagat caataactac gattccgtag
     3001 cctcttactt ttccatcatt actgccgtcg agagcctctt gtaggccttt gttatcagca
     3061 taaaactggt ctgtaagggt tcttaactgt atgtaatcct gtttgctcat ttttgatgtc
     3121 cattggcatt ttcctgtaac caatgtacaa aaaaagcaaa gccctctgta agagagggct
     3181 ttgcttttct ttcgttgagt cttggatttt ttacgtgtgg cgaactctac cgcacatctt
     3241 tctttggaag cttgtttgtt taacgtgggg ctcattccta ccgccacttc tagatttact
     3301 tatatcaaaa attatatgtg aagtcaattt cgtagctgtt cttgactgga cttactttgc
     3361 cagcgtaatc ttctcctgaa acgaaaaaac caccctggca ggtggttttt cgaaggttat
     3421 ttaatcctgg cagattatct aaccgtggta acagtcttgt gcgagacgtg tcaccaaatt
     3481 cgtccttcca gtgtagcctc agtaaggcca ccacttcaag aactctcaat acatctctcg
     3541 cacatcatgt ttaccagtgg ccgttgccaa tggcgattag tcgtgtcttt ccgggttgga
     3601 ctcaagtcga tagttaccgg aaaaggcgca gcggtcggac tgaacggggg gttcgtgcat
     3661 acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg gaatgagata
     3721 aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca
     3781 cgagggagcc accaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc
     3841 actgatttga gcgtcagatt tcgtgatgct tgtcaggggg gcggagccta tggaaaaacg
     3901 gcagcgccgc atccttttct tgccctgttt gtcatgccgt atgcctttgc tcttatccgt
     3961 gtgcaggtaa cgcccgccgc agccgaacgg caggagcgga agcgaccgag tgagcgagga
     4021 ggcgtaatgt caccgcaacc tccatgttct cccgtacgcc ctgcagctgc attttcccct
     4081 gccacatgaa gcacttttat aaagtgttac tccgccgtaa catattaagc cagtatacac
     4141 tccgctatcg ctacgtgact gggtcatggc
//
