LOCUS       NZ_AP022048             3372 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S17-ESBL-03 plasmid pWP4-S17-ESBL-03_4,
            complete sequence.
ACCESSION   NZ_AP022048
VERSION     NZ_AP022048.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194451
            Sequence Read Archive: DRR199287
            Assembly: GCF_014169015.1
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-03
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3372)
  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                   :: 175x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:31:16
            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)                     :: 5,157
            CDSs (total)                      :: 5,046
            Genes (coding)                    :: 4,814
            CDSs (with protein)               :: 4,814
            Genes (RNA)                       :: 111
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 89 of 232
            Pseudo Genes (incomplete)         :: 166 of 232
            Pseudo Genes (internal stop)      :: 31 of 232
            Pseudo Genes (multiple problems)  :: 48 of 232
            Pseudo Genes (short protein)      :: 3 of 232
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022048.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S17-ESBL-03"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S17-ESBL-03_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2017-07-10"
     gene            complement(101..292)
                     /locus_tag="H7R12_RS25475"
                     /old_locus_tag="WP4S17E03_P40010"
     CDS             complement(101..292)
                     /locus_tag="H7R12_RS25475"
                     /old_locus_tag="WP4S17E03_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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            356..679
                     /locus_tag="H7R12_RS25480"
                     /old_locus_tag="WP4S17E03_P40020"
     CDS             356..679
                     /locus_tag="H7R12_RS25480"
                     /old_locus_tag="WP4S17E03_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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            888..>1328
                     /locus_tag="H7R12_RS25945"
                     /pseudo=""
     CDS             888..>1328
                     /locus_tag="H7R12_RS25945"
                     /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            1357..1917
                     /locus_tag="H7R12_RS25490"
                     /old_locus_tag="WP4S17E03_P40030"
     CDS             1357..1917
                     /locus_tag="H7R12_RS25490"
                     /old_locus_tag="WP4S17E03_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            1924..2157
                     /locus_tag="H7R12_RS25495"
                     /old_locus_tag="WP4S17E03_P40040"
     CDS             1924..2157
                     /locus_tag="H7R12_RS25495"
                     /old_locus_tag="WP4S17E03_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          670..2240
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggctgcgccc cgacacccgc actgacgcgc cctggcgggc ttgtctgctc ccggcatccg
       61 ctcacaggca agctgtgaac gtctccggga gctgcatgtt tcagttgctt tcaccgtcat
      121 cgccgaagcg tgcgaggcaa ctgcggtaga gttcgtcggc gtggtcgtga agtgattcgc
      181 agatgtctgc ctgttcgtcc gcgtccagat cgttgagttt ttccagcagg gttagcgtct
      241 ggcttctgat aaagcgagcc atgttaaggg ctgttttttc ctgtttggtc atggtcttaa
      301 ggctccttgt atgggggatt tgttaggggg aatgataccg atgaaacgcg agaagatgct
      361 cacgatacgg gttaccgatg aggagcacgc ccggttactg gaacgctgcg agggtaaacg
      421 actggcggaa tggatgcggc gggtctgtct gggggagccg gttgcacgca caggaaaact
      481 gccgacacta tcgccgccat tgctgcggca tctggctgcc atcgggaaca acctgaacca
      541 gacagcccgg aaggtgaaca gcggccagtg gtcttcgatt gaccgggttc atgtggtggc
      601 cgcactgatg gccatcgagg gtgaattgcg ccagttgcgg caggctgtca gggaacaggg
      661 ggtacgggat gatagttaaa tttcatgcca gggggaaagg cggtggaagt ggcccggtcg
      721 attacctgct ggggcgggag cgtaaccgcg aaggcgcaac ggtgctccgg ggtaacccgg
      781 aagaagtgcg ggaactcatt gattccacgc cattctcgaa gaaatacact tcaggcgttc
      841 tgtcgttcgc ggagaaggag ttaccgccgg gtgaacgcga aagagtgatg acgagctttg
      901 agcgtgttct tatgcccggt ctcgaaaaag accagtacag cattctctgg gtggaacacc
      961 aggataaggg gcggctcgaa ctgaattttg tcatcccgaa catggagcta cagagcggta
     1021 agcgcctcca gccgtactac gaccgcgcgg acaggccgag gataaatgcc tggcagacgc
     1081 tggttaatca tcattacggg ctgcgtgacc cgaacgcacc ggagaacaga cggacgcttg
     1141 tcacgccaaa taatctgcca aaagcgaaac aggaggccgc agaagcgatt acacggggtc
     1201 ttgaggctct ttaccatgcc ggagcaataa aaacgcgtca ggatgtcaca gaggcgctta
     1261 cagcggcagg ttttgaggtg gtgaggacaa ccaaaagcag catcagtatt gccgacccgg
     1321 agggggggcg gaatctcagg ctaaaggggg cgctgtatga gcaatctttt acaaatggga
     1381 acagacttcg agaagaaact gaaagagcga gccgcttcta ccgagaacat gctgaacagc
     1441 gagttcagga agctcgaaga gtctgtagac aaggcattga gcttaaacag gcagaaaatc
     1501 agagacgcta tcagcgaaca tacaacatcc gtgaaaaagc aactggatac gctgagcacc
     1561 accgtgagca tgcagttcag caccacagag gccgaactgt cccggcagca gaaaaaactg
     1621 ctctggcggg tgatcaaagg gcggatactg tttccggcgc tgaccgcgct cagcgtcacg
     1681 ggcggcattt tcctggggtg ctgggggctg atggagtggc aggaaagcaa gattgcgaaa
     1741 aatatcctga ctatcagaga gcaggaaaac acgctggcga aactcgaggc aaaaacctgg
     1801 ggggtgacgt tcgtcaatgg cgagaacggg aaatttctgg tgttgccgga cggggtgaaa
     1861 ggggaaaaca cctggacggt gggcgacaag aacgccgtga ggctggtcag ggagtaaacg
     1921 agtatgacgg aactggaagg gcatttgctg aacgccttag agcatttgca acaggactat
     1981 atgcggcggc tgaacgagtg ggagagcgcc ttcgcggaat tgcagaagat gcacgaggtt
     2041 acgcaacgga acaacgcgat actgaacgag cgcgtcgtga tattgagtca gcaggtgcag
     2101 agattagccg ggcaagtgga tcgcttgagt cggttattta tcgcgaacaa cagctaaggg
     2161 atgaacagga gcgtgcccgg tacagacatg aggtacagga acgcgcggca cgggttcgga
     2221 gtgggccatc aatggagatg tgaccgggga agtgacgaaa tcttgccatt ttgaccagtt
     2281 cgacggctgg ggcgagcgaa acaaatcgtg tgccgtattt gtgcatagct atgcaacatc
     2341 ctgaaaacgc atttcacgcg tttttgggga ttcagccagg ggaaaacatg gtttttttac
     2401 tttttgagcg taaagacgtg aaaaatctcg ttattgcact tgcgatcttt cgtcggcggg
     2461 cgtagaacga aaacagctcg ccaggaaggc gagctgtttc gggttcattg aggtctctga
     2521 cctcctcaat gttcctgtgg aaactgttga gatccacaac agaaaccagt tcattcagtt
     2581 tgcatgagcc ttctgtattc ttcaagaatt tttcaacagc acagtctccc aggaaccccg
     2641 aaaaaaacct gtttttgcag atacttgcgt atttgcgaga atcgtttgcg gttgggggag
     2701 ctgtgacgac ggcgaccgca cgcgtgagag ttccgctacc ggcgcagaga gtttcatcga
     2761 cagcggacac ctgatgagtt gccacaaaaa ccgtatgtag cgcggctaga ttggttgagt
     2821 tagaccttgg cggcagttcc cggtatgtgg tggcgtgacg ggtgagatgg tgcggcgaag
     2881 acgcatacgt cacgcaggcg cgggttcttc cactgacgcg ccccgtgatc gatggccttg
     2941 gctccgtccg gcatatcgag agcggcaaac tacccgtccc ttcactggga ggggtgagtt
     3001 gttgccgttc cctccaacct ttcaccatcc ggcatatcgc acgatcccat gtgcaccgca
     3061 actcctgata actccagtgc aaaaaaaaaa acggatctgc atcacaacga gagtgatccc
     3121 accgctcgcc gcagccccag cgaccgaacg tagtgagcga gtgggcgagg aagcggaaga
     3181 gtcacagatg caagcattgt gcacttacgc gcctgtgcca gtgtccgcgt gtgtgctgtt
     3241 tatcgggtgc gctgttttta catctgtgcg gctttttact cctgacatgg tgcacttccc
     3301 atccatgtct gcaccgatgc aaaatgagat aagccagtat acacatcgct atcgctctgt
     3361 gaactgggtc ag
//
