LOCUS       NZ_AP022166             5277 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP5-S18-ESBL-08 plasmid pWP5-S18-ESBL-08_5,
            complete sequence.
ACCESSION   NZ_AP022166
VERSION     NZ_AP022166.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194534
            Sequence Read Archive: DRR199370
            Assembly: GCF_014169415.1
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. WP5-S18-ESBL-08
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5277)
  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                   :: 302x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:34:33
            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)                     :: 5,406
            CDSs (total)                      :: 5,284
            Genes (coding)                    :: 5,080
            CDSs (with protein)               :: 5,080
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 75 of 204
            Pseudo Genes (incomplete)         :: 137 of 204
            Pseudo Genes (internal stop)      :: 38 of 204
            Pseudo Genes (multiple problems)  :: 42 of 204
            Pseudo Genes (short protein)      :: 5 of 204
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022166.1.
            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..5277
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP5-S18-ESBL-08"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP5-S18-ESBL-08_5"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6538 N 139.5126 E"
                     /collection_date="2018-08-06"
     gene            complement(101..292)
                     /locus_tag="H7R36_RS26620"
                     /old_locus_tag="WP5S18E08_P50010"
     CDS             complement(101..292)
                     /locus_tag="H7R36_RS26620"
                     /old_locus_tag="WP5S18E08_P50010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            358..681
                     /locus_tag="H7R36_RS26625"
                     /old_locus_tag="WP5S18E08_P50020"
     CDS             358..681
                     /locus_tag="H7R36_RS26625"
                     /old_locus_tag="WP5S18E08_P50020"
                     /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_191215872.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVVRSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            890..>1321
                     /locus_tag="H7R36_RS27165"
                     /pseudo=""
     CDS             890..>1321
                     /locus_tag="H7R36_RS27165"
                     /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            1359..1877
                     /locus_tag="H7R36_RS26635"
     CDS             1359..1877
                     /locus_tag="H7R36_RS26635"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_115722884.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQDGRRKFLVLPYGKSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            1884..2117
                     /locus_tag="H7R36_RS26640"
     CDS             1884..2117
                     /locus_tag="H7R36_RS26640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_001448503.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2444..3268)
                     /locus_tag="H7R36_RS26645"
                     /old_locus_tag="WP5S18E08_P50040"
     CDS             complement(2444..3268)
                     /locus_tag="H7R36_RS26645"
                     /old_locus_tag="WP5S18E08_P50040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000213997.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000213997.1"
                     /translation="MTTTIYREFEFAACDSKWSVDGHLRRDVIEKKAIHIDFKGKEAIS
                     LMCGDHPMIVLMQAMQLKVITPEQYASLMSLYMDVEDFTFGMVVLDKHSGAILVGMYTP
                     PMIAIKSKQIVYDLGSTGGEFAAHCLYYAEKRLRKKKRHRGYSTSSVGCKITSAVKYAY
                     RRDRYSGGKVYKIIWKNNGIMYNNIPLSNNSVKNHYRRILKETLKIIHSRYEEKINMRQ
                     NAQLNTAAASLSQTGQPKTQSQPHNQAPSASADKSHQMTMSRAINYARLFSD"
                     /name="hypothetical protein"
     gene            complement(3324..3860)
                     /locus_tag="H7R36_RS26650"
                     /old_locus_tag="WP5S18E08_P50050"
     CDS             complement(3324..3860)
                     /locus_tag="H7R36_RS26650"
                     /old_locus_tag="WP5S18E08_P50050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001555327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024218429.1"
                     /translation="MKDDKAVVVFTGKDLNIMRAEGGSGYWLAKAERLNDAKYLIAVRN
                     RRETWAVKDLEHGTGFLIAKITGCFKNPDYDDRNVITFEEYAEISVKKAWKMLTGGQRY
                     PVAYLTAEEAFSRIGITLEQLEWKKLQTSTLSQPIPSAEAPKKLSLNEAVERAKQDISN
                     ATDIDVSSITITINI"
                     /name="hypothetical protein"
     Typing          complement(4656..5193)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.225"
                     /coverage="99.0"
                     /evalue="3.84e-164"
     Typing          672..2221
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.099"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cccgacaccc gctaaaacct gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg
       61 ctcacaggca agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat
      121 caccgaaacg cgcgaggcag ctgcggtaaa gctcatcagc gtggtcgtga agcgattcac
      181 agatgtctgc ctgttcatcc gcgtccagtt cgttgagttt ctccagcagc gttaatgtct
      241 ggcttctgat aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct
      301 ccgtgtaagg ggggatttct gttcatgggg gtaatgatac cgatgaaacg cgagaggatg
      361 cttacgatac gggttactga tgatgaacat gcccggttac tggaacgctg tgagggtaaa
      421 caactggcgg tatggatgcg gcgggtctgc ctgggtgagc cggttgtccg ttccgggaag
      481 ctgccgacac tggcaccgcc gttactgcgt cagctggctg ccatcgggaa taacctgaat
      541 cagacggcga ggaaggtgaa cagcgggcag tggtcttccg gcgaccgggt tcaggtggtg
      601 gccgcactga tggccatcga gagagagttg cgcagcttac ggcaggtcgt cagggaacag
      661 ggagcgcggg atgatagtta agtttcatgc ccggggaaaa ggtggtggca gtggtccggt
      721 tgattacctt ctggggaggg agcgtaaccg ggaaggtgca acggtacttc agggtaaccc
      781 ggaagaagtc cgggagctta ttgatgccac gccatttgcg aagaaataca cgtccggtgt
      841 tctgtcgttc gcagagaagg aactgccgcc gggaggacgt gaaaaagtga tggagagctt
      901 tgagcgcgta ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca
      961 ccaggacaag gggcggcttg agcttaattt tgtcattccg aacatggagc tacagagcgg
     1021 aaaacgcctc cagccgtact acgaccgggc agacaggccg agaattgatg cctggcagac
     1081 actggtgaat caccattacg ggctgcatga ccccaacgcc ccggagaacc gcagaacgct
     1141 gaccctccct gataacctgc cggaaacgaa acaggcgctt gctgagagcg ttacacgagg
     1201 cctagaggtg ctttaccatg ccggggagat aaaaggccgt caggatgtga ttcaggcgct
     1261 cacagaggcg gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc
     1321 gaacggcggg aggaatatca gactgaaagg agcgttttat gagcaatctt ttacggacgg
     1381 gcgcggagtt cgagaaaaag ctgaaagaga gagccgaatc tacagagaaa atgctgaacg
     1441 acgaattcag caggctcggc gaatctgtaa gcgaggctgt gacctcaaac gagacgaaaa
     1501 tcaaaggcgc tatagcccag tttacggcct cgacggagga atcgctgaaa aaacaccggg
     1561 aaggggtgaa agaggcgatg atgcagcacc ggaaggacat gttaaagctg gcagggagtt
     1621 cgggcatgag gttgctgggg atagtctttc tcctgtttac cgcgagtggc gggacgctct
     1681 ggtatctcgg cgggaggata cagacgaacc tggaagaaat cagggtacag gaagagacat
     1741 tgcggaaact gaacgcgaag acatggggcg tggagtttgt tcaggacggg agaaggaaat
     1801 ttctggtcct tccgtacggg aaatcagcag aggtgactca ctatcagggg aaggactgga
     1861 tacaactgac ggagtgatac ggaatgacag agctggaaac acatttgctg aacgccttag
     1921 agcagctgca acaggattat atgcagcggc tgaacgaatg ggagagcgcc ttcgtggaat
     1981 tgcagaagat gttttcgctt acgcaacggg acaacgcgat gctgaacgag cgggtcatgc
     2041 agttgagtca gcaggtgcag cacttgagcg agcggacaga acgcttgagc cagttataca
     2101 gcgagaactg gagataagag aggaacggct gatacaggag cgcgaacatg cgttatccct
     2161 ggaacgggag cgtcagccgg aaatacagga acgcacgctg gatggtcctt cgctgggatg
     2221 gtgaagccat gaaaaatggc agcttcagtg gattaagagg ggttaatgtg gcctgtatca
     2281 tccggttgca taggtattca tgcggttaaa atttatcagg cgcgatcgcg gcagtttttc
     2341 gggtggtttg ttgccatttt tacctgtctg ctgccgtgat cgcgatgaac gcgttttagc
     2401 ggtgcgtaca ataagggatt atggtaaatc tagctgtaca gtatcagtca gaaaaaaggc
     2461 gagcatagtt aatggctcga gacatagtca tctgatggct tttatcagca ctcgcactag
     2521 gtgcttggtt atgtggctga ctttgtgttt tcggctgacc cgtctgagag agcgaggctg
     2581 ccgctgtatt taactgggca ttctgtctca tgtttatttt ctcttcgtac ctgctatgaa
     2641 tgatctttaa tgtttctttt aaaatccgcc ggtaatggtt ttttaccgag ttgttagata
     2701 acggtatgtt gttgtacatg atgccgttat ttttccaaat gattttgtat actttaccac
     2761 cggagtagcg atctcgtctg tatgcatatt tgacagcgct ggtgatctta catcccactg
     2821 acgatgtaga gtatccacga tgacgctttt tttttctaag ccttttttcc gcatagtaga
     2881 gacaatgtgc tgcaaattcg ccgccagttg aacctaaatc gtaaactatt tgtttgcttt
     2941 ttatcgcaat catcgggggg gtatacatac ctactaatat agcacctgag tgtttatcga
     3001 ggaccaccat gccgaaggtg aagtcttcta catccatgta gagactcatt aagctagcgt
     3061 actgctctgg agttatgact ttcagctgca tagcttgcat aaggacgatc atcggatgat
     3121 caccacacat aagggatatt gcttcttttc ctttgaaatc tatatgtatt gctttttttt
     3181 caataacatc tcttcgaaga tgtccatcaa ctgaccattt gctatcacaa gcagcaaatt
     3241 caaactctct gtatattgtt gttgtcatat caatggctta attctttttc gactatcgtt
     3301 aagataccag atatacgaaa aaatcagata ttgatagtta tcgtaataga agatacatcg
     3361 atatcagttg cattgcttat atcttgctta gctctttcaa ctgcctcgtt gaggcttagt
     3421 tttttcggcg cttctgcaga ggggattggc tgagatagtg ttgaagtctg gagttttttc
     3481 cactccagct gctctagcgt tatccctata cgggaaaaag cttcctctgc tgtcagataa
     3541 gcaaccggat aacgctgacc gccagttagc attttccatg cctttttcac tgaaatttca
     3601 gcatattcct caaatgtaat tacgtttctg tcgtcgtaat cagggttttt aaagcatccg
     3661 gtgatctttg caatcagaaa gccagttccg tgttcgaggt ctttcaccgc ccatgtttct
     3721 ctccggtttc ttactgcgat gagatatttg gcgtcattaa gccgttctgc ttttgctagc
     3781 caataacctg aacctccctc agctctcatt atgtttagat ctttgcctgt aaatacgaca
     3841 actgctttat catctttcat atagaaatcc catgctttag ttttttatcg tcatgatttt
     3901 gattatatac gattaaatga gggggtgggg ttttatttat gcgataaaag caagtctaca
     3961 aattctgtgc ttatctcttt cttatttttg cttattttgt gcttaagttg tttttatttg
     4021 attttatatt tttttatgtg tatcttattt tgatgttatt ctttttgggg gttatatgtc
     4081 gatatctatg cagcaaatag attcatgtat tgaaacgacc atcaatcgtc tttctagcga
     4141 agctggtacg atggttagta atttctatct tgacctgcgc tctcccggta gacagcgcat
     4201 tactgaaaag ctggtagagc aatcaataga tctttgcagg tctcgtggta tctatgctga
     4261 gcgggaaggt aatgggttgc ttgtgagagt agatctgaga acgtgctatc tgaatccagg
     4321 tcaagctgaa atgtttaata tagctattgg atatacgcgt tcagttcacg gaaatcatct
     4381 ataagctgtc tacaaaaagg atcttcttga gatccttttt ttctacgcgt aatctctagc
     4441 tctgaaaacg aaaaaaccac cctagcaggt ggtttttcga aggttagtta atcctggcag
     4501 attctctaac cgtggtaaca gtcttgtgcg agacatgcca ccaaatctgt ccttccagtg
     4561 tagccgcact aagggcacca cttcaagaac tctcgataca tctctcgcac atcctgttta
     4621 ccaatggccg ctgccagtgg cgttttgtcg tgtctttccg ggttggactc aagtcgatag
     4681 ttaccggata agacgcagcg gtcggactga acggggggtt cgtgcataca gtccagcttg
     4741 gagcgaactg ccttcccgga accgagtgtc aggcgtggaa tgagacaaac gcggccataa
     4801 cagcggagtg acaccagtaa accgaaaggt aggaacagga gagcgcacga gggagcttcc
     4861 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg
     4921 tcgattttgt gatgctcgtc aggggggcgg agcctatgga aaaacgccag cggcgtggcc
     4981 ttttccgggt tctcgttttt tgctcacatg tttcttttgg cgttatcccc tgattctgtg
     5041 gataaccgta ttaccgcctt tgagtgagcc gactccgctc gccgcagccg aacgaccgag
     5101 cgtagcgagt cagtgagcga ggaagcggaa gagcgccgga acgtgcattt tctccttacg
     5161 catctgtgcg gcatttcaca ccgcatatgg cgctcttttc ttacaatctg cactgatgcc
     5221 gcatgattaa gccagtatac actccgctat cgctacgtga ctgggtcatg gctgcgc
//
