LOCUS       NZ_AP022101             4063 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP4-S18-ESBL-09 plasmid pWP4-S18-ESBL-09_3,
            complete sequence.
ACCESSION   NZ_AP022101
VERSION     NZ_AP022101.1
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  JOURNAL   Unpublished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 4063)
  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
            AP022101.1.
            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..4063
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP4-S18-ESBL-09"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP4-S18-ESBL-09_3"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6514 N 139.4813 E"
                     /collection_date="2018-08-06"
     gene            101..802
                     /locus_tag="H7R19_RS24685"
                     /old_locus_tag="WP4S18E09_P30010"
     CDS             101..802
                     /locus_tag="H7R19_RS24685"
                     /old_locus_tag="WP4S18E09_P30010"
                     /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(1050..3197)
                     /gene="mobQ"
                     /locus_tag="H7R19_RS24690"
                     /old_locus_tag="WP4S18E09_P30020"
     CDS             complement(1050..3197)
                     /gene="mobQ"
                     /locus_tag="H7R19_RS24690"
                     /old_locus_tag="WP4S18E09_P30020"
                     /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            3376..3630
                     /gene="mobC"
                     /locus_tag="H7R19_RS24695"
                     /old_locus_tag="WP4S18E09_P30030"
     CDS             3376..3630
                     /gene="mobC"
                     /locus_tag="H7R19_RS24695"
                     /old_locus_tag="WP4S18E09_P30030"
                     /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(2840..3198)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3199..3375
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          102..802
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1054..3284)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtaatccac agaaaaaggg ggttgcaaaa aaaaaacttc cacccatatg ataagtggcg
       61 tacagtaaaa aaacgccacc aatagcaacg agcaagcgaa atgtcagatc tgatagctta
      121 caaatcaaac gcccttatcg aggcaagcta caagctcact ttgcaggaac agcgcttcct
      181 gctggtctgt atcagccgcc taaaatccgg agaagattcc ccttcgccgg atgaacaaaa
      241 aaccatgacc atcacggctg cagagtttca tgatgccttt cctgacatgg gacggcagca
      301 cgctgaagct aggctcaagg aagcgataga tcgcctctgg gacaggtcag taatcatcaa
      361 gaacgaggaa aaacgagaag agttccgctg ggtgcagtac cgggcgcagt atttcaaagg
      421 tgaggcgaaa gtagatatca ccttctccga tgccatcatg ccgtatctga cacagctcaa
      481 ggggcagttt acgcgggtag tcgtgaagaa cgtctccagc ctttccagca cctacagcat
      541 ccgcatttac gagctgctcc agcagttccg cagcaccggt gacagaacga tagctatcga
      601 tgatttccga accatgcttg ccgttgaaga taaatatcaa caattcaaag acttgaataa
      661 gatgataatc aagccagcca tcgccgaact gaacgaaaaa agcgatctgg ttgtaactgt
      721 tgagacgatc aaaaaggggc gcacggttgt agccctgcat tttcgcttca aggaagacaa
      781 acagatcaag atgacgatct aaaatcgatt ttaaggcacc taaaacgctc cctgctgcgt
      841 tttttttgtg ttagtagtgc gaaggtacta ttgaagtgaa aaattgcgtc aaaagcgctc
      901 taatgcagcg aaaaaagaac ccccaatttt tgggggcgga aaaacaaaac tatgcttgca
      961 ttatgtgtgt gtgcttcttg cattcatccc tgtcgatgaa catcgaagaa cataacacga
     1021 tgttaaacaa aacaaaatat tgttcacatt cactgtgacc aaccgcgatc atgtctcctc
     1081 tcggtggtgt gtgttcgtgc atcttcctcg cgctgccatt cctcccaggt acgattaaaa
     1141 cccagcgagc ggaacagatg atccggctgt ttttctggtg tgttgacggc agcaaaaagc
     1201 ggtgcctcac gggttttcag atgaaactgc atcagttctg gtgcaggtga tatgtggctg
     1261 tctgcatcgt gatttacggc aacaccatac cctgcatacc gtaacccctt atcggtcagc
     1321 gcactgatga ccagatgcct gttatcggct gagggaacgg caaacgcggg atacagcgta
     1381 ccattaagcc ggataacacc gcccagagag tcatccacgc ccatgaccag caaaagctga
     1441 agctggcggg tttcccggtc gacagaactc atgaccggca tcagcgtcgg tggcagacgt
     1501 ccctgcataa aatccacctt ccttgccgct ggtgatggca tggctggctg gcggtcttct
     1561 ccaagacaga aagactccgg ccatgtcttc ggctggcgga gattgcgggt atgttgcggc
     1621 catgtctggc aaacctgcgt cagcagttgc tcaaaggttg cagaggaata aacacgttgc
     1681 agtggcggac gttggccgat ttcgcttcgg tcacagatat aaccactcct gtcacgcatt
     1741 aaatcaacac tctcaaagat tctggtgcgg tatttctcca gctcgttccc ccagagcgta
     1801 tattctccgt tccggttgtg aagcagaagg taacaggtca tttccccgtt accaggcatg
     1861 ggagcctcgc cataccccgt aacgactgct ctcagcaccc ctgaatccat aacggcattg
     1921 tcatttttcc tgagctgctc cgcgcgacta cgttcagtat cttcctgttc cttccggcgc
     1981 aattcctctt cacgtttaag caactgggct ctgagagctg caaggccgga ttccccccac
     2041 tgctgccact gtttttcaaa tgccatctga ctcgcgggaa tgtcctgttt ctccaccttc
     2101 cggtaatgct gtcgtaattt ttccatttgc tggctcagag actggatttt tccctgctca
     2161 ctacggtatt ccggtgccgc ccattgcatc aggggaatac gggaaaaacc ggacgaaaac
     2221 ggcgatgatt ttttcaggct ggcagcatgg ctcatcgctt cctttcgttc ggtgttcagc
     2281 tcttcccagc gtctgcgcgt cgcctgcata tctgccatca tcgacatggc attactggtg
     2341 agtttccatg ccgagttact gtccttcggc aacgcttcga taatgtcacg tagtgtgtac
     2401 gaagttgcgt tgtcaggaag cccgatattc agaaggtcag ccacacggcg ggcaggctct
     2461 gtcagccctc cgttcctgag ttcggtgcgg gaaatctgta tttccaggtt aagcctgtta
     2521 atcagacgat tctgttcgcc gcgttctgtt tcgataccgc gtgtttccat cgcacaggca
     2581 gactttccga ggtgaatacc aggcgttttc tcaagcccct gtcgctcgta tgaacgatgg
     2641 tctatctctt cctgataacc ggcgttcgcc agtgccctgt ttgcatggtc agcccatgat
     2701 gcccgccacg tctcggcatg tgtccggtcg ttccagtccc tgacctttcc gctgaaccca
     2761 gcaggtccga tagccctcgt ggtcagcatg atgtgcgcat ggggatttgt tttatccatg
     2821 tgatggaacg ccacatcagc aatcatgccc tgactgacaa agttttctct gacaaaggcg
     2881 agaacggttt cccgtgcggc atcctgcggc agttcgtggg ggatggcgag ttcaatttcc
     2941 cgcgcaagtt gtgagttctt ccggcgttcg gccttctcaa cggcattcca gagttcggca
     3001 cggttcgtac accaggcagg ggcggtggcg ggggtcagaa tcacagcctc agccacaccg
     3061 cttttgcggg tgtagtcgtg agtcagtccg gtacgctcat caagcatcag tgaaccggaa
     3121 cgataggcag cggaagctac ggcgctgtag ccgctgcttc tggagataat tttcatgctg
     3181 agatgataaa tcgccatttc tgccgtaatg cctttttgta gttttctttc agccccgcag
     3241 ggcgcacaca atcgaaacgg agtggagatt gtataagtgc gcacttcgtg atttgccgtg
     3301 cattatgcca gctcagtttt taaactacca gtgacgcgct aaaatgcgat ttttcatcgc
     3361 gcacggagtt acatcatgag cagaacgctc gaacagaaga ttgctgatgc tgaggcgaga
     3421 ttacagcgcc tgaaggcgaa gagccggagc ctggacacag cgcagaaggt tgttgtgggt
     3481 gctgcattgc tggcaaaggt cagaaagccg gaggaggtgc agttgcgtgc ctggttactc
     3541 cagttcctga aggcagaggt gacacgacag gctgatgtga cgcgcatact gccgctgatt
     3601 aacgagctgg aggcgctgcc agaacagtga ttgtatcgtc cgctcgccgc agccccagcg
     3661 accgagcgtt agcgagcgag tgggcgagga agcggaagtg aatcagtcgc caggttgagc
     3721 acatacgcac ggtttttcgg caggtgatat gcgctgaacc cgcatgaata ctgggtttcc
     3781 acagggttgg agggggtgta ttcgaaactt gcaattctgc tttattgcaa cgcattgttt
     3841 ttattggttt tttgttttca gcaccccaag ttatccacag gctcgccgtt aagtttttaa
     3901 gatcttattt ttagatcttt ttttttaaaa cctttttagg tcttgtaaca ccatgatttt
     3961 aaagatgttc tggcaagata agtggagctt ttgggggtga aaggtggagc ttttgggggt
     4021 gaaaggtgga gcttttgggg gtgaaaggtg gagcttttgg ggg
//
