LOCUS       NZ_AP022251             3067 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP8-S18-CRE-02 plasmid pWP8-S18-CRE-02_6,
            complete sequence.
ACCESSION   NZ_AP022251
VERSION     NZ_AP022251.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194621
            Sequence Read Archive: DRR199457
            Assembly: GCF_014169695.1
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-S18-CRE-02
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3067)
  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                   :: 573x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:11:20
            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)                     :: 5,006
            CDSs (total)                      :: 4,886
            Genes (coding)                    :: 4,642
            CDSs (with protein)               :: 4,642
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 244
            CDSs (without protein)            :: 244
            Pseudo Genes (ambiguous residues) :: 0 of 244
            Pseudo Genes (frameshifted)       :: 73 of 244
            Pseudo Genes (incomplete)         :: 167 of 244
            Pseudo Genes (internal stop)      :: 44 of 244
            Pseudo Genes (multiple problems)  :: 37 of 244
            Pseudo Genes (short protein)      :: 4 of 244
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022251.1.
            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..3067
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP8-S18-CRE-02"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP8-S18-CRE-02_6"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6316 N 139.7460 E"
                     /collection_date="2018-08-06"
     gene            101..457
                     /locus_tag="H7R30_RS24685"
                     /old_locus_tag="WP8S18C02_P60010"
     CDS             101..457
                     /locus_tag="H7R30_RS24685"
                     /old_locus_tag="WP8S18C02_P60010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019105480.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_057696257.1"
                     /translation="MAWHSVSQAQKLTGKSRRTLYRDMASGRVSWRNDGNGHRELETSE
                     LIRVYGALVDDGTTERHSVAHYDGTDSNNAMLDELRALRIEVADLKSMLLRLEHKEEKP
                     HSTSARWWCFWRKY"
                     /name="hypothetical protein"
     gene            610..1029
                     /locus_tag="H7R30_RS24690"
                     /old_locus_tag="WP8S18C02_P60020"
     CDS             610..1029
                     /locus_tag="H7R30_RS24690"
                     /old_locus_tag="WP8S18C02_P60020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001588168.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_057696256.1"
                     /translation="MAKQPDPQLRAEGFRKAEASLKLEGMDPCGTPLYESIKARIVSGD
                     LTYEQGRLEIMAHYTAVAGAVPVTVGDVITEEFLTPLNMSHEALAQMMGVSCQVVEDIV
                     YGRRRLTVVEASKLAVIFGTDEDFWSNLQALSDRR"
                     /name="HigA family addiction module antitoxin"
     gene            1597..1917
                     /locus_tag="H7R30_RS24695"
                     /old_locus_tag="WP8S18C02_P60030"
     CDS             1597..1917
                     /locus_tag="H7R30_RS24695"
                     /old_locus_tag="WP8S18C02_P60030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003341209.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_057696258.1"
                     /translation="MLHRVSEPYELFAKDAVELNMISLKSKLIIILTELIREQGWSQRV
                     AAEKLGVSQPRVSNLMNGQFSKFAIDTLLEILCRIGFVMDVSFRPHDKESPIDVKVKKA
                     VL"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(1945..2274)
                     /locus_tag="H7R30_RS24700"
                     /old_locus_tag="WP8S18C02_P60040"
     CDS             complement(1945..2274)
                     /locus_tag="H7R30_RS24700"
                     /old_locus_tag="WP8S18C02_P60040"
                     /inference="COORDINATES: protein motif:HMM:NF017757.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_057696255.1"
                     /translation="MKPVVYVGGSQKSLTGQKVFPKSLEDEVAVEINRLQYGLSPLRKT
                     KAMNGLGQGVIEWVKNGKPAYRMVYVVGKKAVYVLHAFSKTSDGTPKSEEDTIKLRYKM
                     LPKDF"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(2710..2822)
                     /locus_tag="H7R30_RS25150"
                     /pseudo=""
     CDS             complement(2710..2822)
                     /locus_tag="H7R30_RS25150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          complement(2715..3067)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.045"
                     /coverage="82.0"
                     /evalue="2.41e-120"
ORIGIN
        1 ctatggaaaa acgggttccc gtcatcttcg tgctttcgct tgctgcccct gctagagttt
       61 cctccgtatt ctttggtgtc actttatcta tggggggctt atggcatggc acagtgtgtc
      121 acaggcacaa aaactaaccg gtaagagtag aagaacgctt taccgtgata tggcatcagg
      181 ccgtgtttcg tggcgaaatg atggcaatgg gcatcgggag cttgaaacgt cagagcttat
      241 tcgtgtctat ggtgcattag ttgatgatgg cacaactgaa cggcacagcg tggcacacta
      301 cgatggcaca gattctaaca acgctatgct ggatgaactg cgcgctttac gtattgaagt
      361 tgcggatttg aaatccatgt tgttgcgtct tgagcacaaa gaagagaaac cacattccac
      421 ctccgctcga tggtggtgct tctggcgtaa atactgattg tttccctttg aattacacag
      481 ttttctgcaa tttttcctcc acctttacac attagtctgc acagctaaac aacggcagaa
      541 tgcgggcagg acatgtaaag ttagctaact ttacgcctgc cttattcgct atcgctcaaa
      601 ggaacgccca tggctaagca acctgatcca caactacgcg cagaagggtt tcgtaaggcc
      661 gaagcttccc tgaaacttga gggaatggac ccttgtggga ctccgttata tgagtcgatt
      721 aaggcccgta tcgtttccgg tgatctgact tatgaacagg gacgtttaga aattatggcg
      781 cactataccg ctgtcgcagg tgctgttccg gttaccgtag gtgacgttat tactgaggaa
      841 tttttaacgc cactgaacat gagccatgaa gcgctggcgc agatgatggg ggtttcctgt
      901 caggttgttg aggatattgt ctacggtcgc cggcgcctca ctgttgtcga agcgtccaag
      961 ctggctgtta tcttcggaac cgacgaggat ttctggagca atcttcaggc cttgagcgat
     1021 cgcaggtagt gctacctacg aagcgcccct caagtgtcgt aatgttcctg aaaaatcttc
     1081 ccggacatca tttctaacgt ccaaaaaatc acgccagaaa tgggcgggtt tggtccccgt
     1141 aaacagatcc ttttgtcatg tatcgctgct tttctttatc aaatgggtgt acatgttgtt
     1201 ccgtgcatag ccatgcatgc gcttaaaact tatcaggggc gatttggtaa catacggcaa
     1261 tggaaaacca tggcttttgg ctggctggcc gcagaaacgc gctgagagcc tttcctgagg
     1321 ttcggtcaac gggtgttatg ttaaatgacc acttcttttc tattcattta ctatgaactt
     1381 cgatgaagtt agccgttttt ttttgtggtg aaaagtgcgg ttgtcacttg catcttggct
     1441 taaagaacat tatataaggg ggggggtata taaaaaatta tatttttttt gttgcctctt
     1501 tctaaggcgt gcgtataatg ccgcaccctg taaacgctcg aatgtttttt gagctgcatc
     1561 tactttttta cactcgcagg acttatgagg gcaaatatgc ttcaccgtgt aagtgaaccg
     1621 tacgaactct ttgctaagga cgctgttgag ctaaatatga tttcactgaa gtccaagctg
     1681 atcattattc ttacggagtt gatccgtgag caggggtggt cacaacgtgt cgcagcagag
     1741 aagctaggtg tcagtcagcc aagagtcagt aatcttatga acggtcaatt ttcaaagttc
     1801 gccatcgata cgctactgga gatcttgtgc cgcattggat tcgttatgga tgtttcattt
     1861 cgacctcacg acaaagagag tccaattgac gtgaaagtga aaaaagcagt gctgtgaaca
     1921 ctgctttggt taccgtctga tttatcagaa gtcttttgga agcatcttat accttagctt
     1981 gattgtatcc tcctcggact ttggtgtgcc atctgacgtt tttgagaatg catgtagtac
     2041 gtagactgcc tttttaccta ctacgtaaac catcctgtaa gctggtttac cattcttcac
     2101 ccactcgata acaccttgtc cgaggccatt catcgccttg gtctttcgca aaggtgacaa
     2161 gccatattgt aagcggttta tctccactgc cacttcgtct tcaagactct ttgggaacac
     2221 cttttggccg gttaggcttt tttgtgaacc cccaacatat actactggtt tcatgaacac
     2281 ctcctatcag tgtcgtcgtc gattcaaagc gcacatacgc atttcctctg ttggttgcta
     2341 ttacctgccc ctctctcctt gagacggcag aatttcaact ctggagtata aagtttttta
     2401 aggatgttcc gatagtgctt ttctatataa atttttgtat atcttgctaa ttgtttactt
     2461 tttgagcgat gtgtgttttt ttttggcttg gtagctgtgg ttcttgtagg cgtttcttga
     2521 cggggtggcc tgagagattt agtctggttc ggaaacaaaa aaaccacccg gcaaggtggt
     2581 tttttgaagg ttcagtaaac cggcaagttt ctgaaccgag gtaactggct tggaggagcg
     2641 cagtcaccaa aacttgttct ttcagtttag ccctatccgg cgcataactt caagactctc
     2701 tcctctaaat cagttaccag tggctgctgc cattggcgct ttgtcgtgct ttttcgggtt
     2761 ggactcaagt tgatagttac cgaaaaggcg cagcggtcgg gctgaacggg gggttcatgc
     2821 acacagccca gcttggagcg aacaacctac atcgaaccga gatgcctaca gtgtgagcta
     2881 tgagaaagcg ccacacttcc cgtaagggaa aaaggcggac aggtatccgg taagcgacaa
     2941 ggttggaaca ggagagcgca tgagggagca actaggggga aactcctggt atctttatag
     3001 tcctgtcggg tttcgcctct tctggcttga agtatcattt ttgtgatact cgccgggggg
     3061 gcggagc
//
