LOCUS       NZ_AP022219             4086 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP8-S17-ESBL-05 plasmid pWP8-S17-ESBL-05_4,
            complete sequence.
ACCESSION   NZ_AP022219
VERSION     NZ_AP022219.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194597
            Sequence Read Archive: DRR199433
            Assembly: GCF_014169595.1
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. WP8-S17-ESBL-05
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4086)
  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                   :: 271x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:44:22
            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)                     :: 4,918
            CDSs (total)                      :: 4,797
            Genes (coding)                    :: 4,658
            CDSs (with protein)               :: 4,658
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 47 of 139
            Pseudo Genes (incomplete)         :: 81 of 139
            Pseudo Genes (internal stop)      :: 39 of 139
            Pseudo Genes (multiple problems)  :: 27 of 139
            Pseudo Genes (short protein)      :: 4 of 139
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022219.1.
            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..4086
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP8-S17-ESBL-05"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP8-S17-ESBL-05_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6316 N 139.7460 E"
                     /collection_date="2017-08-23"
     gene            complement(101..2248)
                     /gene="mobQ"
                     /locus_tag="H7R13_RS24295"
                     /old_locus_tag="WP8S17E05_P40010"
     CDS             complement(101..2248)
                     /gene="mobQ"
                     /locus_tag="H7R13_RS24295"
                     /old_locus_tag="WP8S17E05_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_182913724.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            2427..2681
                     /gene="mobC"
                     /locus_tag="H7R13_RS24300"
                     /old_locus_tag="WP8S17E05_P40020"
     CDS             2427..2681
                     /gene="mobC"
                     /locus_tag="H7R13_RS24300"
                     /old_locus_tag="WP8S17E05_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_000091749.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            3212..3919
                     /locus_tag="H7R13_RS24305"
                     /old_locus_tag="WP8S17E05_P40030"
     CDS             3212..3919
                     /locus_tag="H7R13_RS24305"
                     /old_locus_tag="WP8S17E05_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(1891..2249)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          2250..2420
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="97.0"
                     /evalue="2.6299999999999998e-81"
     Typing          3213..3919
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(105..2335)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtgcttctt gcattcatcc ctgtcgatga acatcgaaga acatcgaaga acatcgacga
       61 acataacacg atgttaaaca aaacaaaata ttgttcacat tcactgtgac caaccgcgat
      121 catgtctcct ctcggtggtg tgtgttcttg catcttcctc gcgccgccat tcgtcccagg
      181 tacgattgaa 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 gtggcagacg tccctgcgta aaatccacct tccttgctgc cagtgatggc atggctggct
      601 ggcggtcttc tccaagacag aaagactccg gccatgtctt cggctggcgg agattgcggg
      661 tatgttgcgg ccatgtctgg caaacctgcg tcagcagttg ctcaaaggtt gcagaggaat
      721 aaacacgttg cagtggcgga cgttggccga tttcgcttcg gtcacagata taaccactcc
      781 tgtcacgcat taaatcaaca ctctcaaaga ttctggtgcg gtatttctcc agctcgttcc
      841 cccagagcgt atattctccg ttccggttgt gaagcagaag gtaacaggtc atttccccgt
      901 taccaggcat gggagcctcg ccataccccg taacgactgc tctcagcacc cctgaatcca
      961 taacggcatt gtcatttttc ctgagctgct ccgcgcgact acgttcagta tcttcctgtt
     1021 ccttccggcg caattcctct tcacgtttaa gcaactgggc tctgagagct gcaaggccgg
     1081 attcccccca ctgctgccac tgtttttcaa atgccatctg actcgcggga atgtcctgtt
     1141 tctccacctt ccggtaatgc tgtcgtaatt tttccatttg ctggctcaga gactggattt
     1201 ttccctgctc actacggtat tccggtgccg cccattgcat aaggggaata cgggaaaaac
     1261 cggacgaaaa cggcgatgat tttttcaggc tggcagcatg gctcatcgct tcctttcgtt
     1321 cggtgttcag ctcttcccag cgtctgcgcg tcgcctgcat atctgccatc atcgacatgg
     1381 cattactggt gagtttccat gccgcattac tgtccttcgg caacgcttcg atgatgtcac
     1441 gtagtgtgta cgaagttgcg ttgtcaggaa gcacgatatt cagaaggtca gccacacggc
     1501 gggcaggctc tgtcagcccg ctgttcctga gttcagtgcg ggaaatctgt atttccaggt
     1561 taagcctgtt aatcagacga ttctgttcgc cgcgttctgt ttcgataccg cgtgtttcca
     1621 tcgcacaggc agactttccg aggtgaatac caggcgtttt ctcaagcccc tgtcgctcgt
     1681 atgaacgatg gtctatctct tcctgataac cggcgttcgc cagtgctctg tttgcatggt
     1741 cagcccatga tgcacgccac gtctcggcat gtgtccggtc gttccagtcc ctgacctttc
     1801 cgccgaaccc agcaggtccg acagccctcg tggtcagcat gatgtgcgca tggggatttg
     1861 ttttatccat gtgatggaac gccacatcag caatcatgcc ctgactgaca aagttttctc
     1921 tgacaaaggc gagaacggtt tcccgtgcgg catcctgcgg cagttcacgg gggatagcga
     1981 gttcaatttc ccgcgcaagt tgtgagttct tccggcgttc ggccttctca acggcattcc
     2041 agagttcggc acggttcgta caccaggcag gggctgtcgc gggggtcaga atcacagcct
     2101 cagccacacc gcttttgcgg gtgtagtcgt gagtcagtcc ggtacgctca tcaagcatta
     2161 gtgaaccaga acgataggca gcagaagcaa cggcgctgta gccgttgctt ctggagatga
     2221 ttttcatact gagatgataa atcgccattt ctgccgtaat gcctttttgc agttttcttt
     2281 cagccccgca gggcgcacac aatcgaaacg gagtggagat tgtataagtg cgcacttcgt
     2341 gatttgccgt gcattatgcc agctcagttt ttaaactacc agtgacgcgc taaaatgcga
     2401 tttttcaccg cgcacggagt cacgaaatga gcagaacact cgaacagaag attgccgaag
     2461 ctgaggccag attacagcgc ctgaaggcga agagccggag cctggacaca gcgcagaagg
     2521 tcattgtggg tgcagcattg ctggcaaagg tcagaaagcc ggaggaagtg cagttgcgag
     2581 cttggttact ccagttcctg aaggcagagg tgacacggca ggctgatgtg acgcgaatac
     2641 tgccgctgat taacgagctg gaggcgctgc cagagcagtg attgtatcgt ccgctcgccg
     2701 cagcccagcg accgaacgtt agcgagcgag tgggcgagga agcggaagtg aatcagtcgc
     2761 caggttgagc acatacgcac ggtttttcga caggtgatat gcgctgaacc cgcatgaata
     2821 ctggatttcc acagggttgg agggggtgta ttcggaattt tcaatcctga ttttttgcaa
     2881 tacattgttt ttatttgatt tttattttca gcaccccaag ttatccacag gctcgccgtt
     2941 aagtttttag atcttgtttt taagatcttg tttttaatac ttgttttagg gtcgaaattc
     3001 ctgattaaaa acaatgcgtt acacgtgcat aggtggggga atttaaggta aaggtgatat
     3061 aatttaaggt gcttgggtga ggtaatttaa ggtaaaggtg aggagattta aggtaatatt
     3121 cacaggaaaa tggggggtga aaatataatt gctcaccaat gctaaaggtg ataggttttt
     3181 atttcacctc atttttggcc tggtggttaa aatgacatca aaccctctga tagcctataa
     3241 gtccaatgcg ctggttgagg ccagttacaa gctaacttta caagaacagc gtttcttatt
     3301 gctctgcata agccgactta actccggtac tgacgtagct tcacctgaat tgcaaaagac
     3361 aatgaccatt acagctgcgg aatattttga ttcattccct gatatggggc ggaaaaatgc
     3421 cgaggttcag ctacaggaag cgatcgatcg tttgtgggac aggtcgatca ttctcaagga
     3481 cgacgagaag cgcgaggagt tccgctggat tcagtatcgg gcacagtacg cgaggggaga
     3541 ggggaaagca caaatcactt tttctgacgc ggtaatgcct tatctgacac agttgaaggg
     3601 gcaattcacc agagtcgtca ttaaaaatat ttctaattta tcaagaagtt acagcataag
     3661 aatatacgaa attctccagc aattccgcag tactggggaa cgtattatcg ccctcgatga
     3721 ttttaaatca tcactgatgc ttgatggtaa atataaagat ttcaaaacgt taaacaggga
     3781 tctaataaaa ccctgtgttg acgaactgaa caaaaaaagc gacctggctg taacggttga
     3841 gacgatcaaa aaggggcgca cggttgtagc cctgcatttt cgcttcaagg aagacaaaca
     3901 gatcaagatg acgatctaga atcgatttta aggcacctaa aacgctcact gtcgcgtttt
     3961 tcttgtgtca ggaatacgaa ggtaccattg aagtgaaaag ttgcgtcaaa aacgctctga
     4021 tgcagcaaaa aaagaacccc caatttttgg gggcggaaaa acaaaactat gcttgcatta
     4081 tgtgag
//
