LOCUS       NZ_AP021967             4072 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP3-W18-CRE-03 plasmid pWP3-W18-CRE-03_4,
            complete sequence.
ACCESSION   NZ_AP021967
VERSION     NZ_AP021967.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194405
            Sequence Read Archive: DRR199241
            Assembly: GCF_014168775.1
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-CRE-03
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  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                   :: 413x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 04:55:48
            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)                     :: 5,126
            CDSs (total)                      :: 5,007
            Genes (coding)                    :: 4,770
            CDSs (with protein)               :: 4,770
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 90 of 237
            Pseudo Genes (incomplete)         :: 163 of 237
            Pseudo Genes (internal stop)      :: 41 of 237
            Pseudo Genes (multiple problems)  :: 52 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP021967.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP3-W18-CRE-03"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP3-W18-CRE-03_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-02-13"
     gene            101..2248
                     /gene="mobQ"
                     /locus_tag="H7R02_RS25310"
                     /old_locus_tag="WP3W18C03_P40010"
     CDS             101..2248
                     /gene="mobQ"
                     /locus_tag="H7R02_RS25310"
                     /old_locus_tag="WP3W18C03_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_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2506..3207)
                     /locus_tag="H7R02_RS25315"
                     /old_locus_tag="WP3W18C03_P40020"
     CDS             complement(2506..3207)
                     /locus_tag="H7R02_RS25315"
                     /old_locus_tag="WP3W18C03_P40020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3740..3994)
                     /gene="mobC"
                     /locus_tag="H7R02_RS25320"
                     /old_locus_tag="WP3W18C03_P40030"
     CDS             complement(3740..3994)
                     /gene="mobC"
                     /locus_tag="H7R02_RS25320"
                     /old_locus_tag="WP3W18C03_P40030"
                     /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_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2..100)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.29e-44"
     Typing          101..459
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2507..3207)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          15..2245
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggcaaatcac gaagtgcgca cttatacaat ctccactccg tttcgattgt gtgcgccctg
       61 cggggctgaa agaaaactac aaaaaggcat tacggcagaa atggcgattt atcatctcag
      121 catgaaaatt atctccagaa gcagcggcta cagcgccgta gcttccgctg cctatcgttc
      181 cggttcactg atgcttgatg agcgtaccgg actgactcac gactacaccc gcaaaagcgg
      241 tgtggctgag gctgtgattc tgacccccgc caccgcccct gcctggtgta cgaaccgtgc
      301 cgaactctgg aatgccgttg agaaggccga acgccggaag aactcacaac ttgcgcggga
      361 aattgaactc gccatccccc acgaactgcc gcaggatgcc gcacgggaaa ccgttctcgc
      421 ctttgtcaga gaaaactttg tcagtcaggg catgattgct gatgtggcgt tccatcacat
      481 ggataaaaca aatccccatg cgcacatcat gctgaccacg agggctatcg gacctgctgg
      541 gttcagcgga aaggtcaggg actggaacga ccggacacat gccgagacgt ggcgggcatc
      601 atgggctgac catgcaaaca gggcactggc gaacgccggt tatcaggaag agatagacca
      661 tcgttcatac gagcgacagg ggcttgagaa aacgcctggt attcacctcg gaaagtctgc
      721 ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcggc gaacagaatc gtctgattaa
      781 caggcttaac ctggaaatac agatttcccg caccgaactc aggaacggag ggctgacaga
      841 gcctgcccgc cgtgtggctg accttctgaa tatcgggctt cctgacaacg caacttcgta
      901 cacactacgt gacattatcg aagcgttgcc gaaggacagt aactcggcat ggaaactcac
      961 cagtaatgcc atgtcgatga tggcagatat gcaggcgacg cgcagacgct gggaagagct
     1021 gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc ctgaaaaaat catcgccgtt
     1081 ttcgtccggt ttttcccgta ttcccctgat gcaatgggcg gcaccggaat accgtagtga
     1141 gcagggaaaa atccagtctc tgagccagca aatggaaaaa ttacgacagc attaccggaa
     1201 ggtggagaaa caggacattc ccgcgagtca gatggcattt gaaaaacagt ggcagcagtg
     1261 gggggaatcc ggccttgcag ctctcagagc ccagttgctt aaacgtgaag aggaattgcg
     1321 ccggaaggaa caggaagata ctgaacgtag tcgcgcggag cagctcagga aaaatgacaa
     1381 tgccgttatg gattcagggg tgctgagagc agtcgttacg gggtatggcg aggctcccat
     1441 gcctggtaac ggggaaatga cctgttacct tctgcttcac aaccggaacg gagaatatac
     1501 gctctggggg aacgagctgg agaaataccg caccagaatc tttgagagtg ttgatttaat
     1561 gcgtgacagg agtggttata tctgtgaccg aagcgaaatc ggccaacgtc cgccactgca
     1621 acgtgtttat tcctctgcaa cctttgagca actgctgacg caggtttgcc agacatggcc
     1681 gcaacatacc cgcaatctcc gccagccgaa gacatggccg gagtctttct gtcttggaga
     1741 agaccgccag ccagccatgc catcaccagc ggcaaggaag gtggatttta tgcagggacg
     1801 tctgccaccg acgctgatgc cggtcatgag ttctgtcgac cgggaaaccc gccagcttca
     1861 gcttttgctg gtcatgggcg tggatgactc tctgggcggt gttatccggc ttaatggtac
     1921 gctgtatccc gcgtttgccg ttccctcagc cgataacagg catctggtca tcagtgcgct
     1981 gaccgataag gggttacggt atgcagggta tggtgttgcc gtaaatcacg atgcagacag
     2041 ccacatatca cctgcaccag aactgatgca gtttcatctg aaaacccgtg aggcaccgct
     2101 ttttgctgcc gtcaacacac cagaaaaaca gccggatcat ctgttccgct cgctgggttt
     2161 taatcgtacc tgggaggaat ggcagcgcga ggaagatgca cgaacacaca ccaccgagag
     2221 gagacatgat cgcggttggt cacagtgaat gtgaacaata ttttgttttg tttaacatcg
     2281 tgttatgttc gtcgatgttc ttcgatgttc atcgacaggg atgaatgcaa gaagcacact
     2341 cacataacgc aagcatagtt ttgtttttcc gcccccaaaa attggggggt cttttttcgc
     2401 tgcatcagag cgtttttgac gcaatttttc acttcaatag taccttcgca ctactaacac
     2461 aaaaaaaacg cagcagggag cgttttaggt gccttaaaat cgattttaga tcgtcatctt
     2521 gatctgtttg tcttccttga agcgaaaatg cagggctaca accgtgcgcc cctttttgat
     2581 cgtctcaaca gttacaacca gatcgctttt ttcgttcagt tcggcgatgg ctggcttgat
     2641 tatcatctta ttcaagtctt tgaattgttg atatttatct tcaacggcaa gcatggttcg
     2701 gaaatcatcg atagctatcg ttctgtcacc ggtgctgcgg aactgctgga gcagctcgta
     2761 aatgcggatg ctgtaggtgc tggaaaggct ggagacgttc ttcacgacta cccgcgtaaa
     2821 ctgccccttg agctgtgtca gatacggcat gatggcatcg gagaaggtga tatctacttt
     2881 cgcctcacct ttgaaatact gcgcccggta ctgcacccag cggaactctt ctcgtttttc
     2941 ctcgttcttg atgattactg acctgtccca gaggcgatct atcgcttcct tgagcctagc
     3001 ttcagcgtgc tgccgtccca tgtcaggaaa ggcatcatga aactctgcag ccgtgatggt
     3061 catggttttt tgttcatccg gcgaagggga atcttctccg gatttcaggc ggctgataca
     3121 gaccagcagg aagcgctgtt cctgcaaagt gagcttgtag cttgcctcga taagggcgtt
     3181 tgatttgtaa gctatcagat ctgacatttc gcttgctcgt tgctattggt ggcgtttttt
     3241 tactgtacgc cacttatcat atgggtggaa gttttttttt tgcaaccccc tttttctgtg
     3301 gattacaccc ccaaaagctc cacctttcac ccccaaaagc tccacctttc acccccaaaa
     3361 gctccacctt tcacccccaa aagctccact tatcttgcca gaacatcttt aaaatcatgg
     3421 tgttacaaga cctaaaaagg ttttaaaaaa aagatctaaa aataagatct taaaaactta
     3481 acggcgagcc tgtggataac ttggggtgct gaaaacaaaa aaccaataaa aacaatgcgt
     3541 tgaaataaag cagaattgca agtttcgaat acaccccctc caaccctgtg gaaacccagt
     3601 attcatgcgg gttcagcgca tatcacctgc cgaaaaaccg tgcgtatgtg ctcaacctgg
     3661 cgactgattc acttccgctt cctcgcccac tcgctcgcta acgctcggtc gctggggctg
     3721 cggcgagcgg acgatacaat cactgttctg gcagcgcctc cagctcgtta atcagcggca
     3781 gtatgcgcgt cacatcagcc tgtcgtgtca cctctgcctt caggaactgg agtaaccagg
     3841 cacgcaactg cacctcctcc ggctttctga cctttgccag caatgcagca cccacaacaa
     3901 ccttctgcgc tgtgtccagg ctccggctct tcgccttcag gcgctgtaat ctcgcctcag
     3961 catcagcaat cttctgttcg agcgttctgc tcatgatgta actccgtgcg cgatgaaaaa
     4021 tcgcatttta gcgcgtcact ggtagtttaa aaactgagct ggcataatgc ac
//
