LOCUS       NZ_AP022053             3373 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S17-ESBL-08 plasmid pWP4-S17-ESBL-08_4,
            complete sequence.
ACCESSION   NZ_AP022053
VERSION     NZ_AP022053.1
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  JOURNAL   Unpublished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 3373)
  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
            AP022053.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S17-ESBL-08"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S17-ESBL-08_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2017-07-10"
     gene            complement(708..899)
                     /locus_tag="H7R14_RS24750"
                     /old_locus_tag="WP4S17E08_P40010"
     CDS             complement(708..899)
                     /locus_tag="H7R14_RS24750"
                     /old_locus_tag="WP4S17E08_P40010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            963..1286
                     /locus_tag="H7R14_RS24755"
                     /old_locus_tag="WP4S17E08_P40020"
     CDS             963..1286
                     /locus_tag="H7R14_RS24755"
                     /old_locus_tag="WP4S17E08_P40020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1495..>1935
                     /locus_tag="H7R14_RS25205"
                     /pseudo=""
     CDS             1495..>1935
                     /locus_tag="H7R14_RS25205"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1964..2524
                     /locus_tag="H7R14_RS24765"
                     /old_locus_tag="WP4S17E08_P40030"
     CDS             1964..2524
                     /locus_tag="H7R14_RS24765"
                     /old_locus_tag="WP4S17E08_P40030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2531..2764
                     /locus_tag="H7R14_RS24770"
                     /old_locus_tag="WP4S17E08_P40040"
     CDS             2531..2764
                     /locus_tag="H7R14_RS24770"
                     /old_locus_tag="WP4S17E08_P40040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          544..627
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="95.0"
                     /evalue="4.11e-16"
     Typing          1277..2847
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acacctgatg agttgccaca aaaaccgtat gtagcgcggc tagattggtt gagttagacc
       61 ttggcggcag ttcccggtat gtggtggcgt gacgggtgag atggtgcggc gaagacgcat
      121 acgtcacgca ggcgcgggtt cttccactga cgcgccccgt gatcgatggc cttggctccg
      181 tccggcatat cgagagcggc aaactacccg tcccttcact gggaggggtg agttgttgcc
      241 gttccctccg accttccacc atccagcata tcgcacgatc ccatgtgcac cgctactcct
      301 gataactcca gtgcaaaaaa aaaaacggat ctgcatcaca acgagagtga tcccaccgct
      361 cgccgcagcc ccagcgaccg aacgtagtga gcgagtgggc gaggaagcgg aagagtcaca
      421 gaggcaagca ttgtgcactt acgcgcctgt gccagtgtcc gcgtgtgtgt tgtttatcgg
      481 gcgcgctgtt tttacgcatc tgtgcggctt tttactcctg acatggtgca cttcccatcc
      541 actctgcacc gatgcaaaat gaggaaagcc agtatacaca tcgctatcgc tctgtgaact
      601 gggtcagggc tgcgccccga cacccgcact gacgcgccct ggcgggcttg tctgctcccg
      661 gcatccgctc acaggcaagc tgtgaacgtc tccgggagct gcatgtttca gttgctttca
      721 ccgtcatcgc cgaagcgtgc gaggcaactg cggtagagtt cgtcggcgtg gtcgtgaagt
      781 gattcgcaga tgtctgcctg ttcgtccgcg tccagatcgt tgagtttttc cagcagggtt
      841 agcgtctggt ttctgataaa gcgagccatg ttaagggctg ttttttcctg tttggtcatg
      901 gtcttaaggc tccttgtatg ggggatttgt tagggggaat gataccgatg aaacgcgaga
      961 agatgctcac gatacgggtt accgatgagg agcacgcccg gttactggaa cgctgcgagg
     1021 gtaaacgact ggcggaatgg atgcggcggg tctgtctggg ggagccggtt gcacgcacag
     1081 gaaaactgcc gacactggca ccgccattgc tgcggcatct ggctgccatc gggaacaacc
     1141 tgaaccagac agcccggaag gtgaacagcg gccagtggtc ttcgattgac cgggttcatg
     1201 tggtggccgc actgatggcc atcgagggtg aattgcgcca gttgcggcag gctgtcaggg
     1261 aacagggggt acgggatgat agttaaattt catgccaggg ggaaaggcgg tggaagtggc
     1321 ccggtcgatt acctgctggg gcgggagcgt aaccgcgaag gcgcaacggt gctccggggt
     1381 aacccggaag aagtgcggga actcattgat tccacgccat tttcgaagaa atacacgtca
     1441 ggcgttctgt cgttcgcgga gaaggagcta ccaccgggtg aacgcgaaag agtgatgacg
     1501 agctttgagc gtgttcttat gcccggtctc gaaaaagacc agtacagcat tctctgggtg
     1561 gaacaccagg ataaggggcg gctcgaactg aattttgtca tcccgaacat ggagctacag
     1621 agcggtaagc gcctccagcc gtactacgac cgtgcggaca ggccgaggat aaatgcctgg
     1681 cagacgctgg ttaatcatca ttacgggctg cgtgacccga acgcaccgga gaacagacgg
     1741 acgcttgtca cgccaaataa tctgccaaaa gcgaaacagg aggccgcaga agcgattaca
     1801 cggggtcttg aggctcttta ccatgccgga gcaataaaaa cgcgtcagga tgtcacagag
     1861 gcgcttacag cggcaggttt tgaggtggtg aggacaacca aaagcagcat cagtattgcc
     1921 gacccggagg gggggcggaa tctcaggcta aagggggcgc tgtatgagca atcttttaca
     1981 aatgggaaca gacttcgaga agaaactgaa agagcgagcc gcttctaccg agaacatgct
     2041 gaacagcgag ttcaggaagc tcgaagagtc tgtagacaag gcattgagct taaacaggca
     2101 gaaaatcaga gacgctatca gcgaacatac aacatccgtg aaaaagcaac tggatacgct
     2161 gagcaccacc gtgagcatgc agttcagcac cacagaggcc gaactgtccc ggcagcagaa
     2221 aaaactgctc tggcgggtga tcaaagggcg gatactgttt ccggcgctga ccgcgctcag
     2281 cgtcacgggc gggattttcc tggggtgctg ggggctgatg gagtggcagg aaagcaagat
     2341 tgcgaaaaat atcctgacta tcagagagca ggaaaacacg ctggcgaaac tcgaggcaaa
     2401 aacctggggg gtgacgttcg tcaatggcga gaacgggaaa tttctggtgt tgccggacgg
     2461 ggtgaaaggg gaaaacacct ggacggtggg cgacaagaac gccgtgaggc tggtcaggga
     2521 gtaaacgagt atgacggaac tggaagggca tttgctgaac gccttagagc atttgcaaca
     2581 ggactatatg cggcggctga acgagtggga gagcgccttc gcggaattgc agaagatgca
     2641 cgaggttacg caacggaaca acgcgatact gaacgagcgc gtcgtgatat tgagtcagca
     2701 ggtgcagaga ttagccgggc aagtggatcg cttgagtcgg ttatttatcg cgaacaacag
     2761 ctaagggatg aacaggagcg tgcccggtac agacatgagg tacaggaacg cgcggcacgg
     2821 gttcggagtg ggccatcaat ggagatgtga ccggagaagt gacgaaatct tgccattttg
     2881 acccgttcga cggctggggc gagcgaaaca aatcgtgtgc cgtatttgtg catagctatg
     2941 caacatcctg aaaacgcatt tcacgcgttt ttggggattc agccagggga aaacatggtt
     3001 tttttacttt ttgagcgtaa agacgtgaaa aatctcgtta ttgcacttgc gatctttcgt
     3061 cggtgggcgt agaacgaaaa cagctcgcca ggaaggcgag ctgtttcggg ttcattgagg
     3121 tctctgacct cctcaatgtt cctgtggaaa ctgttgagat ccacaacaga aaccagttca
     3181 ttcagtttgc atgagccttc tgtattcttc aagagttttt caacagcaca gtctcccagg
     3241 aaccccgaaa aaaacctgtt tttgcagata cttgcgtatt tgcgagaatc gtttgcggtt
     3301 gggggagctg tgacgacggc gaccgcacgc gtgagagttc cgctaccggc gcagagagtt
     3361 tcatcgacag cgg
//
