LOCUS       NZ_AP022046             5210 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S17-ESBL-03 plasmid pWP4-S17-ESBL-03_2,
            complete sequence.
ACCESSION   NZ_AP022046
VERSION     NZ_AP022046.1
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  JOURNAL   Unpublished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 5210)
  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
            AP022046.1.
            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..5210
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S17-ESBL-03"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S17-ESBL-03_2"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2017-07-10"
     gene            complement(841..1032)
                     /locus_tag="H7R12_RS25405"
                     /old_locus_tag="WP4S17E03_P20010"
     CDS             complement(841..1032)
                     /locus_tag="H7R12_RS25405"
                     /old_locus_tag="WP4S17E03_P20010"
                     /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_000165988.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDSENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1097..1420
                     /locus_tag="H7R12_RS25410"
                     /old_locus_tag="WP4S17E03_P20020"
     CDS             1097..1420
                     /locus_tag="H7R12_RS25410"
                     /old_locus_tag="WP4S17E03_P20020"
                     /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_000956005.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1629..>2060
                     /locus_tag="H7R12_RS25940"
                     /pseudo=""
     CDS             1629..>2060
                     /locus_tag="H7R12_RS25940"
                     /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            2098..2616
                     /locus_tag="H7R12_RS25420"
     CDS             2098..2616
                     /locus_tag="H7R12_RS25420"
                     /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_023144181.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSC
                     GTLWYLGGMIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPHQ
                     GKDWVQLME"
                     /name="MbeB family mobilization protein"
     gene            2623..2856
                     /locus_tag="H7R12_RS25425"
     CDS             2623..2856
                     /locus_tag="H7R12_RS25425"
                     /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_001555310.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMKLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3403..3699)
                     /locus_tag="H7R12_RS25430"
                     /old_locus_tag="WP4S17E03_P20040"
     CDS             complement(3403..3699)
                     /locus_tag="H7R12_RS25430"
                     /old_locus_tag="WP4S17E03_P20040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            3911..4108
                     /locus_tag="H7R12_RS25435"
                     /old_locus_tag="WP4S17E03_P20050"
     CDS             3911..4108
                     /locus_tag="H7R12_RS25435"
                     /old_locus_tag="WP4S17E03_P20050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            4126..4410
                     /locus_tag="H7R12_RS25440"
                     /old_locus_tag="WP4S17E03_P20060"
     CDS             4126..4410
                     /locus_tag="H7R12_RS25440"
                     /old_locus_tag="WP4S17E03_P20060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(4474..4863)
                     /locus_tag="H7R12_RS25445"
                     /old_locus_tag="WP4S17E03_P20070"
     CDS             complement(4474..4863)
                     /locus_tag="H7R12_RS25445"
                     /old_locus_tag="WP4S17E03_P20070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     Typing          669..756
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          complement(102..658)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1411..2960
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.555"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcagtgtag ccgctataag gcttcaactt caagagttct gcgtatctaa atccactttt
       61 tagttaccaa tggctgctgc cagtggcgtt aagtcgtgtc ttaccgggtt ggactcaaga
      121 cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc
      181 agcttggagc gaacgaccta caccgaactg agatacctac agcgtgagct atgagaaagc
      241 gccacgcttc ccgaagggag aaaggcggac aggtatccgg taaacggtaa ggtcggaaca
      301 ggagagcgca cgagggagct tccgggggga aacgcctggt atctttaagt cctgtcgggt
      361 ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat
      421 ggaaaaacgc cagcggcgcg gccttcttcc tgttcctggt cttttgctca catgtttttt
      481 ccggtgttat cccctgattc tgtggataac agcatttcgt ttttgagtga gtagataccg
      541 ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaaaagcgcc
      601 tggacgtgca ttttctcctt acgcatctgt gcggcatttc acacccggta tggcgcacgt
      661 ttcatacaat ccgcactgat gctgcatagt taagccagta tacactccgc tatcgctacg
      721 tgactggttc agggctgcgc cccgaaaccc gctaaaacac cctgacgcgc cctggcgggc
      781 ttgtctgctc ccggcatccg ctcacaggca agctgtgacc gtctccggga gctgcatatg
      841 tcagaggttt tcactgtcat ccccgaagcg cgcgaggcag ctgcggtaaa gctcatcggc
      901 gtggtcgtga agcgattcac agatatctgc ctgttcatcc gcgtccagtt cgttgagctt
      961 ctccagcagc gttaatgtct ggcttctgat aaagcgggcc atgttaaggg cggttttttc
     1021 ctgtttagtc actgatgcct ccgtgtaagg gggatttctg ttcatggggg taatgatacc
     1081 gatgaaacgc gagaggatgc tcacgatacg ggttactgat gatgaacatg cccggttact
     1141 ggaacgctgt gagggtaaac aactggcggt atggatgcgg cgggtctgcc tgggtgagcc
     1201 ggttgcccgt tccgggaggc tgccgacact ggcaccgccg ttactgcgtc agctggcagc
     1261 catcgggaat aacctgaacc agacagcccg taaggtgaac agcggacagt ggtcttccgg
     1321 cgaccgggtt caggtggtgg ccgcactgat ggccatcggg gatgagctgc gccggttgcg
     1381 tctggccgtc agggaacagg ggacgcggga tgatagttaa gtttcatgcc cggggaaaag
     1441 gtggtggcag tggtccggtt gattacctgc tgggaaggga gcgtaaccgg gaaggggcaa
     1501 cggtgcttca gggtaatccg gaagaagtac gggaactcat cgatgccacg ccatttgcga
     1561 agaaatacac gtccggtgtg ctgtcgttcg cggagaagga gctgccaccg ggaggacgtg
     1621 aaaaggtgat ggcgagcttt gagcgtgtac tgatgcccgg tctcgaaaaa aatcagtaca
     1681 gcatcctgtg ggtggagcac caggacaagg gacggcttga gctgaatttt gtcattccga
     1741 acatggagct acagaccgga aaacgcctcc agccgtacta cgaccgggca gacaggccga
     1801 gaattgatgc ctggcagacg ctggtgaatc accattacgg gctgcatgac cccaacgccc
     1861 cggagaaccg ccggatactg actctctctg ataacctgcc ggaaacgaaa caggcgcttg
     1921 cagagagcgt cacacgcggg atagacgctc tttatcatgt cggggagata aaaggccgtc
     1981 aggatgtgat tcaggcgctc acagaggcag ggcttgaagt ggtcagggtg acgcgaagca
     2041 gtatcagcat tgcagacccg aacggtggga agaatatcag gctgaaagga gcattttatg
     2101 agcaatcttt tacagacggg cgcggagttc gagaaaaagc tgaaagagag agccgaatct
     2161 acagagacaa tactgaacga cgagttcagg aagctcgaaa aatctgtaag caaggctgtg
     2221 acatcaaacg agacgaaaat caaagacgct atagccctgt tcacagcttc gacagaggaa
     2281 tcactgaaaa agcaccggga aggggtgaaa gaggcgatga tgcagcacag gaaggacgtg
     2341 ttaaagctgg cagggaatac gggcatgatg ttactgggga tggtcatttt cctgtttacc
     2401 gtgagttgcg ggacgctctg gtatcttggc gggatgatac aggcgaacct ggaagatatc
     2461 aggaagcagg aagagacatt gcagaaactg aacgcgaaga catggggcgt ggagttcgta
     2521 caggacggga acaggaaatt tctggtcctt ccgtacggga aatcagcaga ggtgattccc
     2581 catcagggga aggactgggt acaactgatg gagtgacaca gagtgacgga gctggaaaga
     2641 catttgctga acgcattaga gcaactgcaa caggactata tgcagcggct gaacgaatgg
     2701 gagagcgcct tcgtggaatt gcagaaaatg ttttcgctta cgcaacggga caacgcgatg
     2761 ctgaacgagc gggtcatgaa gttgagtcag caggtgcagc acttgagcga gcggacagaa
     2821 cgcttgagcc agttatacag cgagaacagg agataaggga cgaacggctg atacaggaac
     2881 gcgaacatga gttatccctg gagcgtgagc gccagctgga aatacaggaa cggacactgg
     2941 atggcccttc gctgggatgg taatcagaga caggctaaaa tgttgtcagc gcgtttccgg
     3001 tgcatttttt gggataatgg ttggttcggg gcaccgggaa cgcgcttcag tcataaacct
     3061 tgctgaaaac acaggaacgc gttaaaacgc atacgggcgc gattctggtg tgtctttcat
     3121 agtcgtgttt ttgcctctat tgccagatcg cgctcattcc cctgaacttc tgttttcctg
     3181 ctcaaatccc cgtcttcttc gcttccgaaa gtatgaaaaa aatccgtttc agcggtctct
     3241 gactggcaat tcctgcgtga ttcacctggc tgcataggta tgcatgtggt taaaatttac
     3301 cgggtgcgat cgcggcagtt ttccgggtgg tttgttgcca tttttacctg tctgctgccg
     3361 tgatcgcacc gaacgcgttt cggcggtgcg tacaataagt gattatggta aatcaccctt
     3421 ccaggcgttc agcccttctt ccggtttttt tccgttcagg aatttacggg cgagacgaat
     3481 gcgtcttgcc tggtaaatcg catcgtaggc ctgtgactgt cccacaccgt tactgatttc
     3541 actgaccaga tggcgcaggt cggcctgtgt cagtgtgtaa acgtgtttct ggatgaggtc
     3601 acgggctgtc cgctcttcgt atccggcagc gataagtgca gccagcaggc gtttgtctgt
     3661 tttgctcagt cggtggcgac cagattttgt tttgctcacg ttatctcctc tctgtttttt
     3721 ctcctgatgt tatccggtgc tgtttttctg ctgcgaatct tcccttcctg atttttataa
     3781 gggtgattca gatcacaaaa atgaaaattc atatcattga caggaaaaat aatgcggcgt
     3841 aatttatact gtatataaaa ctagtattta tatatacagt atattctgtg taaataaagg
     3901 gagggataaa atgaaagaag aaaaagtatt gcttcaccgt ttcttatttg tagttaggaa
     3961 taagaatggt tgtgaactat catgttcggc agaccttatg ggaacaaggg atgatgttta
     4021 taagtatttc tctgattctg ttagtgggct agatgttgag cttatagatg tttcttgcga
     4081 gagtgaatgg gaagaacatt cgcattgaac taatcaggag attatatgat ttctcaaaat
     4141 gtttgggctc ctcctttctt ttttggtcct tgggttgaac ttgaaaatca tactggtgat
     4201 atcgcgtaca ctgtctattt tgatacattg tctaatgtac ccggtccatt tattgctttt
     4261 atctggtatg cccctaatgg gccaagaaca gttaacgtta ttggtccagc atcttatcag
     4321 atctcttgca agggcgctgg tgttgataaa attaaattta aaagtgtcag tgggacaggg
     4381 cagattattc atgtatacac taccttataa taagagctga ataaatataa tcctgcctaa
     4441 gctatacctt aagcaggatt atatctatta atattatttt gaatatgctt ttatgatttc
     4501 catcactgtt gtttcatcgt tcacaggttg ataataatgg gttggattta gtgcagaatg
     4561 aatgattgca ggttgggata ttacttttcc atcaaaatat gaaatcaggg gtttccctat
     4621 atttttacta gttatttcgt ttagtttttt cttacataaa ctatctgtgt ttacttctat
     4681 tatgacgcct ttgttttttt ctgattggga agggtacatt ttaagtatgc aatatttatt
     4741 cagaatgatg ctgtcaccac caactttgta aacaatgttt ttgtttgttt cagtacttga
     4801 acatcctata agtaaggtca gtatagtact cgatgttatt gactttactg atgatttgaa
     4861 catattaact ccattttatt ttgttaaaat tccaatctat aaatacatat acacgtaaaa
     4921 ataaacaatg cgaacgtttt cacttatatt atccccatga tgtgattgaa tggtggttcc
     4981 atataagaga gggcaattat actatctttc tctcctgaac tgatgggatt gcagtttaga
     5041 gaaaaaaaga tcaaaggatc ttcttgagat cctttttttc tgcgcgtaat ctgctgcctg
     5101 taaacgaaaa aaccaccctg gcaggtggtt tttcgaaggt tagctaatcc tggcagatta
     5161 cctaaccggg tagctggctt aagtggagca cagataccaa aagatgtcct
//
