LOCUS       NZ_AP022102             3855 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S18-ESBL-09 plasmid pWP4-S18-ESBL-09_4,
            complete sequence.
ACCESSION   NZ_AP022102
VERSION     NZ_AP022102.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194483
            Sequence Read Archive: DRR199319
            Assembly: GCF_014169175.1
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-S18-ESBL-09
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3855)
  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                   :: 224x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:00:21
            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)                     :: 5,009
            CDSs (total)                      :: 4,894
            Genes (coding)                    :: 4,728
            CDSs (with protein)               :: 4,728
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 63 of 166
            Pseudo Genes (incomplete)         :: 106 of 166
            Pseudo Genes (internal stop)      :: 35 of 166
            Pseudo Genes (multiple problems)  :: 35 of 166
            Pseudo Genes (short protein)      :: 5 of 166
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022102.1.
            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..3855
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S18-ESBL-09"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S18-ESBL-09_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-08-06"
     gene            join(3794..3855,1..91)
                     /locus_tag="H7R19_RS24700"
     CDS             join(3794..3855,1..91)
                     /locus_tag="H7R19_RS24700"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001341064.1"
                     /translation="MLAHAVELKKATEPCSSGTAGAFRQRVKARRAEQGRSNQQPEKLY
                     GVLVG"
                     /name="hypothetical protein"
     gene            complement(101..655)
                     /locus_tag="H7R19_RS24705"
                     /old_locus_tag="WP4S18E09_P40010"
     CDS             complement(101..655)
                     /locus_tag="H7R19_RS24705"
                     /old_locus_tag="WP4S18E09_P40010"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_137069257.1"
                     /translation="MKAVRHRYKQRYNFAASEVVGAFDELKSLDWSLEIASLSDVEMSK
                     RWIGAVDPNGVARLPPNGGWDWVKLYNGYLKNPSAFVCAIKSEGKLCALIGGGVSDSKV
                     VTKLHYLESAPYDTALSGYALDISVTYVVTVANAMGSEYTAIYEPNSKVREIAINDYGF
                     SEDNLFGTRKDFALYLPMSRI"
                     /name="hypothetical protein"
     gene            complement(661..1179)
                     /locus_tag="H7R19_RS24710"
                     /old_locus_tag="WP4S18E09_P40020"
     CDS             complement(661..1179)
                     /locus_tag="H7R19_RS24710"
                     /old_locus_tag="WP4S18E09_P40020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001290382.1"
                     /translation="MSEKAKKVGRRSLSKRRESLIKELWGDELSELNIWNRKEHDGFTT
                     IPRTLNYINRIIDYLAGAGSPVSQTYLSLWCRVFDEGFVEIRDKDALAFESGFSGQRAV
                     TTWLGRMKKLRELGLISTKPGTSGEFHYVIMLNPLYVIKNLYESNGWIKDERYNALFSR
                     MQEVGAEWE"
                     /name="hypothetical protein"
     gene            complement(1518..1649)
                     /locus_tag="H7R19_RS25175"
                     /old_locus_tag="WP4S18E09_P40030"
     CDS             complement(1518..1649)
                     /locus_tag="H7R19_RS25175"
                     /old_locus_tag="WP4S18E09_P40030"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_264294644.1"
                     /translation="MLKSQQIIEWMLHERLPSNIQGRAQVKAWVVDNFSQMKDGYPF"
                     /name="hypothetical protein"
     gene            complement(2096..2419)
                     /gene="mobA"
                     /locus_tag="H7R19_RS24720"
                     /old_locus_tag="WP4S18E09_P40050"
     CDS             complement(2096..2419)
                     /gene="mobA"
                     /locus_tag="H7R19_RS24720"
                     /old_locus_tag="WP4S18E09_P40050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_001341214.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRS
                     AALGKKVNSLTDDRVLKEVMRLGTLQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2691..2885
                     /locus_tag="H7R19_RS24725"
                     /old_locus_tag="WP4S18E09_P40060"
     CDS             2691..2885
                     /locus_tag="H7R19_RS24725"
                     /old_locus_tag="WP4S18E09_P40060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041640.1"
                     /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_001041625.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFEAERGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2429..2654)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.417"
                     /coverage="99.0"
                     /evalue="4.84e-80"
     Typing          2898..3421
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.687"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(2100..2419)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="2.38e-61"
ORIGIN
        1 agcatttcgc caacgcgtga aagcaagacg agcagagcaa ggccgctcaa accaacagcc
       61 agaaaaactc tacggcgtac tggtaggata aatgagccgg ttaaatccgg ctcattggta
      121 gatacagagc gaaatctttc cttgtcccaa acaagttgtc ctcgctaaat ccataatcat
      181 ttatagctat ctctctgact ttgctatttg gctcatagat ggctgtatat tcgcttccca
      241 tcgcattcgc gacagtaaca acatacgtaa cagaaatatc cagtgcatat cctgaaagag
      301 ccgtgtcata aggggctgat tcaaggtaat gcagcttggt taccacttta ctatcagaaa
      361 ccccgccacc aatcagagcg catagcttgc cttctgattt tatggcacag acgaatgcgc
      421 tagggttctt caaatagccg ttatagagct taacccagtc ccatccaccg ttaggtggta
      481 gtcttgcaac accgttagga tcaacagccc caatccatct ctttgacatt tccacgtcac
      541 ttaaagatgc gatttctaaa ctccaatcca aacttttaag ttcatcaaac gcccccacaa
      601 cttctgacgc agcaaaatta tatctctgct tatatcgatg acgaacagct ttcatgtcac
      661 tcattcccac tcagccccca cttcctgcat cctagaaaat agagcgttgt aacgctcatc
      721 ttttatccat ccatttgatt catataagtt tttaattacg taaagtggat tcaacatgat
      781 tacataatga aactcgccag aagtaccagg cttcgttgat atcagtccca gctctcgtag
      841 ctttttcatt cttcctagcc aagtagtcac cgctcgctgc ccactaaacc ctgactcaaa
      901 tgccagagca tctttatccc taatttcgac gaatccctcg tcaaaaactc gacaccataa
      961 actgaggtat gtctgtgata caggagatcc agcgccagca aggtaatcga ttatcctatt
     1021 gatataattc aatgttcttg gaattgttgt aaatccatcg tgttctttcc tgttccatat
     1081 attcagttcg gaaagctcat ccccccaaag ctcttttatt agactttctc ttctttttga
     1141 tagagagcgc ctacctactt ttttggcctt ctctgacatt tatctatccc caaaaagtca
     1201 attcaacatg aaaacattat caacaaaaaa tcattatatt caatgagtta tgtgtaataa
     1261 cacaaaaact aagcacatca ttagccaaca tctcatttga tgtaattctt tttttttgtt
     1321 aatacaaaga ttgagatgca atatttattg caactatggt tttatttttc aattagttat
     1381 atacaatttt gtactcgctg ttctcaatgt gctctgtgta atcgttgtac tcgctgtgct
     1441 gaatggggtt attaggggat tttaaggggg ggaaggggtg ccattctgag aaaaagcccg
     1501 ctacagcggg ctttttctca gaatggataa ccatccttca tttgcgagaa gttatcaacc
     1561 acccacgctt taacctgagc tcgcccctgg atattggatg gcaagcgttc atgtagcatc
     1621 cactcgataa tctgctgtga ttttagcatc agagcccccc ccctttggcc tggaaggaat
     1681 taatcaaatc taacacctca taaccctcat gacggctaaa gcgcgtggca tctagcttcg
     1741 tcattcgtgg attatcgcct tgtacagccg tccatgagta atcatggtaa ttcatatcag
     1801 atctgttcat cttttctcat cttcgcttga attatatacg tacattacaa cataacatta
     1861 atgactcaac agcctcattt accataacgt cgcattacgc gcaccgctta aacgcgctga
     1921 acgcgattct gacgcagaca ccgcaaaaag agatgttttc cctggggtaa accggaaaaa
     1981 tgcgtcagga tcgttttcag ctcgcggcat agctatgcat gaaagtgaat ggcgatcggt
     2041 ttgggggctt acggcgttca ttccgtctgt tttcgacagt tttctctccg ggacgctaat
     2101 ctgccataag cctggataac agggcccggt gatactccgt aatagcgatc agcacctccg
     2161 catactccct gtccccgaca cgcttgccgt cgataaagag ttttttctgc aacgtcccca
     2221 agcgcataac ttctttaagc acccggtcat cagtcagtga gttaactttc ttaccgagag
     2281 ctgccgaccg taaaaaaccg gaaacggtct tgccgcattc agcagccctt tttctgattt
     2341 cctggtcttc ttctgccgtc agacgaacag ggcgactgat agcccgcctg cgcgtattac
     2401 ttccacttcg ttttgtcata aaacatggct ccgtatctga catggggtgt cggggcgaaa
     2461 ccctgaccag ggtaattgta atagcgtgca tgtatgcgcg gtataacaat tacacatcct
     2521 gtcctgtcag caagttcgaa ttaccgacaa aggcacggca gttttttggc agtgacagtg
     2581 ttgtcggacc gtcttaccgt cggcagaata ccgacggtaa gacggtcgaa aagtggtgcg
     2641 cgatataatc acacgacgca gatgacagac agaacggaga aagcagaaag atgaacaagc
     2701 agcagcaaac cgcactcaac atggcaaaat tcataaaaag ccagagcctg acgctgctcg
     2761 aaaaactgga ctcactcgat gctgatgcac aggccgccat gtgtgagaaa ctgcacgaac
     2821 tcgcagaaga actccagaac agcatacaga cacgctttga agcggaaagg ggcaccgggg
     2881 tataacggta tacctgtgcg taaggagaaa atgacacata aggcgctctt ccgcttcctc
     2941 gctcactgac tcgctacgct cggtcgttcg actgcggcga gcggactctc ctttctcaaa
     3001 ggcggtgata tggttatcca cagaatcagg ggataacgcc ggaaagaaca tgtgagcaaa
     3061 aagccgaagg cagggacaaa ggccgcgcag gtggcgtttt tccataggct ccgcccccct
     3121 gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa
     3181 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg
     3241 tttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca
     3301 cgctgttggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
     3361 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcaacttga gtccaacccg
     3421 gaaagacacg acaaagcgcc actggcagca gccaacggta agaggatgta caagagatta
     3481 ctaacgcaga gttcttgaag tatcagccca actacggcta aactggaagg gcgaatttgg
     3541 tggcagtggt cttgtacacc ctgttaccac ggttcataaa cttgccggtt taatgaacct
     3601 tcgaaaaacc accttgccgg gtggtttttt cgtttttaaa gaagatacgc gtttactctt
     3661 cgcctcgtca atgaagggtt gcattaattc tgtgacttgc gcatctcttc tacaatacag
     3721 tacagttact aggaagttga cgtatccgtc acctcatatg ctttatacta actcacgaaa
     3781 aaacggaaat aatatgttag ctcacgcggt cgaacttaaa aaagcgacgg aaccatgctc
     3841 ttctggcaca gccgg
//
