LOCUS       NZ_AP022002             4087 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP3-W18-ESBL-07 plasmid pWP3-W18-ESBL-07_4,
            complete sequence.
ACCESSION   NZ_AP022002
VERSION     NZ_AP022002.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194413
            Sequence Read Archive: DRR199249
            Assembly: GCF_014168835.1
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. WP3-W18-ESBL-07
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4087)
  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                   :: 176x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:23:09
            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)                     :: 5,032
            CDSs (total)                      :: 4,919
            Genes (coding)                    :: 4,710
            CDSs (with protein)               :: 4,710
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 83 of 209
            Pseudo Genes (incomplete)         :: 146 of 209
            Pseudo Genes (internal stop)      :: 41 of 209
            Pseudo Genes (multiple problems)  :: 54 of 209
            Pseudo Genes (short protein)      :: 3 of 209
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022002.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP3-W18-ESBL-07"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP3-W18-ESBL-07_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-02-13"
     gene            complement(101..2260)
                     /gene="mobQ"
                     /locus_tag="H7Q99_RS24885"
                     /old_locus_tag="WP3W18E07_P40010"
     CDS             complement(101..2260)
                     /gene="mobQ"
                     /locus_tag="H7Q99_RS24885"
                     /old_locus_tag="WP3W18E07_P40010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_113527967.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSHAERRAEQLRKNDNAVMDSGVLSAVVTEYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLATL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            2439..2693
                     /gene="mobC"
                     /locus_tag="H7Q99_RS24890"
                     /old_locus_tag="WP3W18E07_P40020"
     CDS             2439..2693
                     /gene="mobC"
                     /locus_tag="H7Q99_RS24890"
                     /old_locus_tag="WP3W18E07_P40020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            3225..3932
                     /locus_tag="H7Q99_RS24895"
                     /old_locus_tag="WP3W18E07_P40030"
     CDS             3225..3932
                     /locus_tag="H7Q99_RS24895"
                     /old_locus_tag="WP3W18E07_P40030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1903..2261)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2262..2438
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3226..3932
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(105..2347)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.465"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcattatgtg tgtgcttctt gcattcatcc ctgtcgatga acatcgaaga acatcgacga
       61 acataacacg atgttaaaca aaacaaaata ttgttcacat tcactgtgac caaccgcgat
      121 catgtctcct ctcggtggcg tgtgttcgtg catcttcctc gcgccgccat tcgtcccagg
      181 tacgattaaa acccagcgag cggaacagat gatccggctg tttttctggt gtgttgacgg
      241 cagcaaaaag cggtgcctca cgggttttca gatgaaactc cataagttcc ggcgcaggtg
      301 atatgtggct gtctgcatcg tgatttacgg caacaccata ccctgcatac cgtaacccct
      361 tatcggtcag tgcactgatg accagctggc tgttatcggc tgagggaacg gcaaacgcgg
      421 gatacagcgt accattaagc cggacaacac cgcccagaga gtcatccacg cccatgacca
      481 gcaaaagctg aagctggcgg gtttcccggt cgacagaact cattaccggc atcagcgtcg
      541 ctagcagacg tccctgcgta aaatccacct tccttgctgc cagtgatggc atggctggct
      601 ggcggtcttc tccaagacag aaagactccg gccatgtctt cggctggcgg agattgcggg
      661 tatattgcgg ccatgtctgg caaacctgcg tcagaagttg ctcaaaggtc gcagaggaat
      721 aaacacgttg cagtggtgga tgttgaccga tttcgcttcg gtcacagata taaccactcc
      781 tgtcacgcat taaatcaaca cgctcaaaga ttctggtgcg gtatttctcc agctcgttcc
      841 cccagagcgt gtattctccg ttccggttgt gaagcagaag gtaacaggtc atttccccgt
      901 taccaggcat gggggcctcg ccatactccg taacgactgc gctcagtacc cctgaatcca
      961 taacggcatt gtcatttttc ctgagctgtt ccgctcgtcg ctccgcgtga ctacgttctg
     1021 tatcctcctg ctccttccgg cgcaattcct cttcacgttt aagcaactgg actctgagag
     1081 ctgcaaggcc ggatgccccc cactgctgcc actgtttttc aaatgccgtc tgactcgcgg
     1141 gaatgtcctg tttctccacc ttccggtaat gctgtcgcaa tttttccatt tgctggctca
     1201 gcgactggat ttttccctgt tcgctacggt attccggtgc cgcccattgc atcaggggaa
     1261 tacgggaaaa accggacgaa aacggcgatg attttttcag gctggcagca tggctcatcg
     1321 cttcctttcg ttcggtgttc agctcttccc agcgtctgcg cgtcgcctgc atatctgcca
     1381 tcatcgacat ggcattactg gtgagtttcc atgccgcatt actgtccttc ggcaacgctt
     1441 cgatgatgtc acgtagtgtg tacgaagttg cgttgtcagg aagcacgata ttcagaaggt
     1501 cagccacacg gcgggcaggc tctgtcagcc cgctgtttct gagttcggta cgggaaatct
     1561 gtatttccag gttaagtctg ttaatcagac gattctgttc gccgcgttct gtttcgatac
     1621 cgcgtgtttc catcgcacag gcagactttc cgaggtgaat accaggcgtt ttctcaagcc
     1681 cctgtcgctc gtatgaacga tggtctatct cttcctgata accggcgttc gccagtgccc
     1741 tgttcgcatg gtcagcccat gatgcacgcc acgtctcggc atgtgtccgg tcgttccagt
     1801 ccctgacctt tccaccgaat ccagcaggtc cgacagctct cgtggtcagc atgatgtgcg
     1861 catggggatt tgttttatcc atgtgatgga acgccacatc agcaatcatg ccctgactga
     1921 caaagttttc tctgacaaag gcgagaacgg tttcccgtgc ggcatcctgc ggtagttcgc
     1981 gggggatggc gagttcaatt tcccgcgcaa gttgtgagtt cttccggcgt tcggccttct
     2041 caacggcatt ccagagttcg gcacggttcg tacaccaggc aggggctgtc gcgggagtca
     2101 gaatcacagc ttcagccaca ccgcttttgc gggtgtagtc gtgagtcagt ccggtacgct
     2161 catcaagcat cagtgaaccg gaacgatagg cagcagaagc aacggcgctg tagccgctgt
     2221 ttctggagat gattttcatg ctgagatgat aaatcgccat ttctgccgta atgccttttt
     2281 gtggttttct ttcagccccg cagggcgcac acaatcgaaa cggagtggag attgtataag
     2341 tgcgcacttc gtgattttcc gtgcattatg ccagctcagt ttttaaacta ccagtgacgc
     2401 gctaaaatgc gatttttcat cgcgcacgga gttacatcat gagcagaaca ctcgaacaga
     2461 agattgctga tgctgaggcc agattacagc gcctgaaggc gaagagcagg agtctggaca
     2521 cagcgcagaa ggtcattgtg ggtgcagcat tgctggcaaa ggtcagaaag ccggaggagg
     2581 tgcagttgcg tgcctggtta ctccagttcc tgaaggcaga ggtgacacga caggctgatg
     2641 tgacgcgcat actgccgctg attaacgagc tggaagcgct gccaggacag tgattgtatc
     2701 gtccgctcgc cgcagtccca gcgaccgagc gttagcgagc gagtgggcga ggaagcggaa
     2761 gtgaatccgt cgcctgattg agcacatacg cacggttttt cgggaggtga tatgcgctga
     2821 acccgcatga atactggatt tccacagggt tggagggggt gtattcggaa cttgcaattc
     2881 tgcttttttg caacgcattg tttttattgg ttttttgttt tcagcactcc aagttatcca
     2941 caggctcgtc gttaagtttt tagatcttgt ttttaagatc ttgtttttaa tacttgtttt
     3001 agcgccaaaa ttccttatag aaaacaaaat gttacaacgc tataggtgat atgatttaag
     3061 gtaaaggtga tataatttaa ggtgcttggg tgaggtaatt taaggtaaag gtgaggagat
     3121 ttaaggtaat attcacagga aaatgggggg tgaaaatata attgctcacc aatgctaaag
     3181 gtgataggtt tttatttcac ctcatttttg gcctggtggt taaaatgaca tcaaaccctc
     3241 tgatagccta taagtccaat gcgctggttg aggccagtta caagctaact ttacaagaac
     3301 agcgtttctt attgctctgc ataagccgac ttaactccgg tactgacgta gcttcacctg
     3361 aattgcaaaa gacaatgacc attacagctg cggaatattt tgattcattc cctgatatgg
     3421 ggcggaaaaa tgccgaggtt cagctacagg aagcgatcga tcgtttgtgg gacaggtcga
     3481 tcattctcaa ggacgacgag aagcgcgagg agttccgctg gattcagtat cgggcacagt
     3541 acgcgagggg agaggggaaa gcacaaatca ctttttctga cgcggtaatg ccttatctga
     3601 cacagttgaa ggggcaattc accagagtcg tcattaaaaa tatttctaat ttatcaagaa
     3661 gttacagcat aagaatatac gaaattctcc agcaattccg cagtactggg gaacgtatta
     3721 tcgccctcga tgattttaaa tcatcactga tgcttgatgg taaatataaa gatttcaaaa
     3781 cgttaaacag ggatctaata aaaccctgtg ttgacgaact gaacaaaaaa agcgacctgg
     3841 ctgtaacggt tgagacgatc aaaaaggggc gcacggttgt agccctgcat tttcgcttca
     3901 aggaagacaa acagatcaag atgacgatct agaatcgatt ttaaggcacc taaaacgctc
     3961 cctgctgcgt tttttttgtg ttagtagtgc gaaggtacta ttgaagtgaa aaattgcgtc
     4021 aaaagcgctc taatgcagcg aaaaaagaac ccccattttt cgggggcgga aaaacaaaac
     4081 tatgctt
//
