LOCUS       NZ_AP022073             5219 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-W18-ESBL-09 plasmid pWP4-W18-ESBL-09_4,
            complete sequence.
ACCESSION   NZ_AP022073
VERSION     NZ_AP022073.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194468
            Sequence Read Archive: DRR199304
            Assembly: GCF_014169115.1
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-W18-ESBL-09
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5219)
  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                   :: 114x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:58:42
            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)                     :: 5,455
            CDSs (total)                      :: 5,329
            Genes (coding)                    :: 5,078
            CDSs (with protein)               :: 5,078
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 0 of 251
            Pseudo Genes (frameshifted)       :: 100 of 251
            Pseudo Genes (incomplete)         :: 165 of 251
            Pseudo Genes (internal stop)      :: 41 of 251
            Pseudo Genes (multiple problems)  :: 50 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022073.1.
            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..5219
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-W18-ESBL-09"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-W18-ESBL-09_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-02-13"
     gene            570..755
                     /locus_tag="H7R28_RS26900"
     CDS             570..755
                     /locus_tag="H7R28_RS26900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001508823.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_151313534.1"
                     /translation="MSVSEEAEKRLDVHFLLTHLCGISHPVWRTFHTIRTDGAWLSQYT
                     LRYRYVTGSWLRPDTR"
                     /name="hypothetical protein"
     gene            complement(841..1032)
                     /locus_tag="H7R28_RS26905"
                     /old_locus_tag="WP4W18E09_P40010"
     CDS             complement(841..1032)
                     /locus_tag="H7R28_RS26905"
                     /old_locus_tag="WP4W18E09_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_042634456.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENH"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1097..1420
                     /locus_tag="H7R28_RS26910"
                     /old_locus_tag="WP4W18E09_P40020"
     CDS             1097..1420
                     /locus_tag="H7R28_RS26910"
                     /old_locus_tag="WP4W18E09_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_052895110.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNCGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1629..>2060
                     /locus_tag="H7R28_RS27470"
                     /pseudo=""
     CDS             1629..>2060
                     /locus_tag="H7R28_RS27470"
                     /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..2628
                     /locus_tag="H7R28_RS26920"
                     /old_locus_tag="WP4W18E09_P40030"
     CDS             2098..2628
                     /locus_tag="H7R28_RS26920"
                     /old_locus_tag="WP4W18E09_P40030"
                     /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_011666801.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            2635..2868
                     /locus_tag="H7R28_RS26925"
                     /old_locus_tag="WP4W18E09_P40040"
     CDS             2635..2868
                     /locus_tag="H7R28_RS26925"
                     /old_locus_tag="WP4W18E09_P40040"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3413..3709)
                     /locus_tag="H7R28_RS26930"
                     /old_locus_tag="WP4W18E09_P40060"
     CDS             complement(3413..3709)
                     /locus_tag="H7R28_RS26930"
                     /old_locus_tag="WP4W18E09_P40060"
                     /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            3921..4118
                     /locus_tag="H7R28_RS26935"
                     /old_locus_tag="WP4W18E09_P40070"
     CDS             3921..4118
                     /locus_tag="H7R28_RS26935"
                     /old_locus_tag="WP4W18E09_P40070"
                     /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            4136..4420
                     /locus_tag="H7R28_RS26940"
                     /old_locus_tag="WP4W18E09_P40080"
     CDS             4136..4420
                     /locus_tag="H7R28_RS26940"
                     /old_locus_tag="WP4W18E09_P40080"
                     /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(4484..4873)
                     /locus_tag="H7R28_RS26945"
                     /old_locus_tag="WP4W18E09_P40090"
     CDS             complement(4484..4873)
                     /locus_tag="H7R28_RS26945"
                     /old_locus_tag="WP4W18E09_P40090"
                     /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          670..755
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="99.0"
                     /evalue="4.06e-36"
     Typing          complement(102..658)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.104"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1411..2972
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.232"
                     /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 tgttcttggt cttttgctca catgtctttt
      481 ccggtgttat cccctgattc tgtggataac agcatttcgt ttttgagtga gtagataccg
      541 ctcgccgcag tcgaacgacc gagcgtagcg tgtcagtgag cgaggaagcg gaaaagcggc
      601 tggacgtgca ttttctcctt acgcatctgt gcggcatttc acacccggta tggcgcactt
      661 ttcataccat ccgcactgat ggcgcatggt taagccagta tacactccgc tatcgctacg
      721 tgactgggtc atggctgcgc cccgacaccc gctaaaaccc gctgacgcgc cctgacgggc
      781 ttgtctgctc ccggcatccg ctcacaggca agctgtgacc gtctccggga gctgcatgtg
      841 tcagtggttt tcaccgtcat ccccgaaacg tgcgaggcag ctgcggtaaa gctcatcggc
      901 gtggtcgtga agcgattcac agatatctgc ctgttcatct gcgtccagtt cgttgagctt
      961 ctccagcagc gttaatgtct ggcttctgat aaagcgggcc atgttaaggg cggttttttc
     1021 ctgtttagtc actgatgcct ccgtgtaagg gggatttctg ttcatggggg taatgatacc
     1081 gatgaaacgc gagaggatgc tcacgatacg ggttactgat gatgaacatg ctcgtttgct
     1141 ggaacgttgt gagggtaaac aactggcggt atggatgcgg cgggtctgcc tgggggagcc
     1201 ggttgcccgt tccgggaggc tgccgacact ggcaccgccg ttactgcgtc agctggccgc
     1261 catcgggaat aacctgaatc agacagcgag gaaggtgaac tgcgggcagt ggtcttccgg
     1321 tgaccgggtt caggtggtgg ccgcactgat ggccatcggg gacgagctgc gccggctgcg
     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 aaaaagtgat ggcgagcttt gagcgtgtac tgatgcccgg tctcgaaaaa aatcagtaca
     1681 gcatcctgtg ggtggagcac caggacaagg gacggcttga gctgaatttt gtcattccga
     1741 acatggagct acagaccgga aaacgcctcc agccgtacta cgaccgggca gacaggccga
     1801 gaattgatgc ctggcagacg ttggtgaatc accattacgg gctgcatgac cccaacgccc
     1861 cggagaaccg ccagatactg actctccctg ataacctgcc ggaaacgaaa caggcgcttg
     1921 cagagagcgt cacacgcggg atagacgctc tttatcatgt cggggagata aaaggccgtc
     1981 aggatgtgat tcaggcgctc acagaggcag ggcttgaagt ggtcagggtg acgcgaagca
     2041 gtctcagcat tgcagacccg aacggcggga agaatatcag actgaaagga gcattctatg
     2101 agcaatcttt tacagacggg cgcggagttc gagaaaaagc tgaaagagag agccgaatct
     2161 acagagacaa tgctgaacga cgagttcagg aagctcgaaa aatctgtaag caaggctgtg
     2221 acatcaaacg agacgaaaat caaagacgct atagccctgt tcacagcttc gacagaggaa
     2281 tcactgaaaa aacaccggga aggggtgaaa gaggcgatga tgcagcacag gaaggacgtg
     2341 ttaaagctgg cagggaatac gggcatgatg ttactgggga tggtcatttt cctgtttacc
     2401 gtgagtggcg ggacgctctg gtatcttggc gggatgatac aggcgaacct ggaagaaatc
     2461 aggaagcaga acgagaatct ggagaagctg aacgcgaaga catggggcgt gcgttatcac
     2521 gaggggagca acggacgttt tctggtgttg cccgagggga tgaaagccga aacgaactgg
     2581 acgatggaaa acgggaaaca gaatgccgta aggctggtac aggagtaaca gagcatgacg
     2641 gagctggaaa gacatttgct gaacgcatta gagcaactgc aacaggacta tatgcagcgg
     2701 ctgaacgaat gggagagcgc cttcgtggaa ttgcagaaaa tgttttcgct tacgcaacgg
     2761 gacaacgcga tgctgaacga gcgggtcatg cagttgagtc agcaggtgca gcacttgagc
     2821 gagcagacag aacgcttgag ccagttatac agcgagaaca ggagataagg gacgaacggc
     2881 tgatacagga acgcgaacat gcgttatccc tggagcgtga gcgccagctg gaaatacagg
     2941 aacggacact ggatggccct tcgctgggat ggtaatcaga gacaggctaa aatgttgtca
     3001 gcgcgtttcc ggtgcatttt ttgggataat ggttggttcg ggggcaccgg gaacgcgctt
     3061 cagtcagacc ttgctgaaaa cacaggaacg cgttaaaacg catacgggcg cgattctggt
     3121 gtgtcttttg ttgctgtgtt ttgcctctat tgccagatcg cgctcattcc cctgaacttc
     3181 tgttttcctg ctccggtccc cgtcttcttc gcttccgaaa gcatgaaaaa aatccgtttc
     3241 agctgtctct ggctggcaat tcctgcatga ttcacatggc tgcatagcta tgcatgtggt
     3301 taaaatttac cgggtgcgat cgcggcagtt tttcgggtgg tttgttgcca tttttacctg
     3361 tctgctgccg tgatcgcgcc gaacgcgttt cagcggtgcg tacaataagt gattatggta
     3421 aatcaccctt ccaggcgttc agcccttctt ccggtttttt tccgttcagg aatttacggg
     3481 cgagacgaat gcgtcttgcc tggtaaatcg catcgtaggc ctgtgactgt cccacaccgt
     3541 tactgatttc actgaccaga tggcgcaggt cggcctgtgt cagtgtgtaa acgtgtttct
     3601 ggatgaggtc acgggctgtc cgctcttcgt atccggcagc gataagtgca gccagcaggc
     3661 gtttgtctgt tttgctcagt cggtggcgac cagattttgt tttgctcacg ttatctcctc
     3721 tctgtttttt ctcctgatgt tatccggtgc tgtttttctg ctgcgaatct tcccttcctg
     3781 atttttataa gggtgattca gatcacaaaa atgaaaattc atatcattga caggaaaaat
     3841 aatgcggcgt aatttatact gtatataaaa ctagtgttta tatacacagt atattctgtg
     3901 taaataaagg gagggataaa atgaaagaag aaaaagtatt gcttcaccgt ttcttatttg
     3961 tagttaggaa taagaatggt tgtgaactat catgttcggc agaccttatg ggaacaaggg
     4021 atgatgttta taagtatttc tctgattctg ttagtgggct agatgttgag cttatagatg
     4081 tttcttgcga gagtgaatgg gaagaacatt cgcattgaac taatcaggag attatatgat
     4141 ttctcaaaat gtttgggctc ctcctttctt ttttggtcct tgggttgaac ttgaaaatca
     4201 tactggtgat atcgcgtaca ctgtctattt tgatacattg tctaatgtac ccggtccatt
     4261 tattgctttt atctggtatg cccctaatgg gccaagaaca gttaacgtta ttggtccagc
     4321 atcttatcag atctcttgca agggcgctgg tgttgataaa attaaattta aaagtgtcag
     4381 tgggacaggg cagattattc atgtatacac taccttataa taagagctga atagatataa
     4441 tcctgcctaa gctatacctt aagcaggatt atatctatta atattatttt gaatatgctt
     4501 ttatgatttc catcactgtt gtttcatcgt tcacaggttg ataataatgg gttggattta
     4561 gtgcagaatg aatgattgca ggttgggata ttacttttcc atcaaaatat gaaatcaggg
     4621 gtttccctat atttttacta gttatttcgt ttagtttttt cttacataaa ctatctgtgt
     4681 ttacttctat tatgacgcct ttgttttttt ctgattggga agggtacatt ttaagtatgc
     4741 aatatttatt cagaatgatg ctgtcaccac caactttgta aacaatgttt ttgtttgttt
     4801 cagtacttga acatcctata agtaaggtca gtatagtact cgatgttatt gactttactg
     4861 atgatttgaa catattaact ccattttatt ttgttaaaat tccaatctat aaatacatat
     4921 acacgtaaaa ataaacaatg cgaacgtttt cacttatatt atccccatga tgtgattgaa
     4981 tggtggttcc atataagaga gggcaattat actatctttc tctcctgaac tgatgggatt
     5041 gcagtttaga gaaaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
     5101 tgctgcctgt aaacgaaaaa accaccctgg caggtggttt ttcgaaggtt agctaatcct
     5161 ggcagattac ctaaccgggt agctggctta agtggagcac agataccaaa agatgtcct
//
