LOCUS       NZ_AP019681             3067 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain GSH8M-2 plasmid pGSH8M-2-6, complete
            sequence.
ACCESSION   NZ_AP019681
VERSION     NZ_AP019681.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00168435
            Sequence Read Archive: DRR174986, DRR174987
            Assembly: GCF_009176965.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Inamine,Y., Segawa,T. and Kuroda,M.
  TITLE     Characterization of NDM-5- and CTX-M-55-coproducing Escherichia coli
            GSH8M-2 isolated from the effluent of a wastewater treatment plant
            in Tokyo Bay
  JOURNAL   Infect Drug Resist 12, 2243-2249 (2019)
   PUBMED   31413601
  REMARK    DOI:10.2147/IDR.S215273 Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3067)
  AUTHORS   Sekizuka,T., Segawa,T., Yatsu,K., Tanaka,R., Inamine,Y. and
            Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAY-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 :: Canu v. 1.4; minimap v. 0.2-r124; racon v. 1.1.0;
            circlator v. 1.5.3; Pilon v. 1.18; SPAdes v. 3.11.1; A5-miseq v.
            20140604
            Genome Coverage                   :: 598x
            Sequencing Technology             :: Sequel; NextSeq500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009176965.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 03:38:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,010
            CDSs (total)                      :: 4,890
            Genes (coding)                    :: 4,646
            CDSs (with protein)               :: 4,646
            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)       :: 74 of 244
            Pseudo Genes (incomplete)         :: 171 of 244
            Pseudo Genes (internal stop)      :: 45 of 244
            Pseudo Genes (multiple problems)  :: 39 of 244
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP019681.1.
            Annotated by DFAST v.1.0.8 (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="GSH8M-2"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pGSH8M-2-6"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.631549 N 139.745949 E"
                     /collection_date="2018-08"
                     /note="replicon type: Col440I"
     gene            join(2658..3067,1..10)
                     /locus_tag="GDK32_RS25125"
     CDS             join(2658..3067,1..10)
                     /locus_tag="GDK32_RS25125"
                     /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            578..898
                     /locus_tag="GDK32_RS25130"
                     /old_locus_tag="ECGSH8M2_p60010"
     CDS             578..898
                     /locus_tag="GDK32_RS25130"
                     /old_locus_tag="ECGSH8M2_p60010"
                     /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(926..1255)
                     /locus_tag="GDK32_RS25135"
                     /old_locus_tag="ECGSH8M2_p60020"
     CDS             complement(926..1255)
                     /locus_tag="GDK32_RS25135"
                     /old_locus_tag="ECGSH8M2_p60020"
                     /inference="COORDINATES: protein motif:HMM:NF017757.4"
                     /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(1691..1803)
                     /locus_tag="GDK32_RS25820"
                     /pseudo=""
     CDS             complement(1691..1803)
                     /locus_tag="GDK32_RS25820"
                     /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"
     gene            2149..2505
                     /locus_tag="GDK32_RS25145"
                     /old_locus_tag="ECGSH8M2_p60030"
     CDS             2149..2505
                     /locus_tag="GDK32_RS25145"
                     /old_locus_tag="ECGSH8M2_p60030"
                     /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"
     Typing          complement(1696..2061)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.431"
                     /coverage="85.0"
                     /evalue="1.43e-127"
ORIGIN
        1 tcgcaggtag tgctacctac gaagcgcccc tcaagtgtcg taatgttcct gaaaaatctt
       61 cccggacatc atttctaacg tccaaaaaat cacgccagaa atgggcgggt ttggtccccg
      121 taaacagatc cttttgtcat gtatcgctgc ttttctttat caaatgggtg tacatgttgt
      181 tccgtgcata gccatgcatg cgcttaaaac ttatcagggg cgatttggta acatacggca
      241 atggaaaacc atggcttttg gctggctggc cgcagaaacg cgctgagagc ctttcctgag
      301 gttcggtcaa cgggtgttat gttaaatgac cacttctttt ctattcattt actatgaact
      361 tcgatgaagt tagccgtttt tttttgtggt gaaaagtgcg gttgtcactt gcatcttggc
      421 ttaaagaaca ttatataagg gggggggtat ataaaaaatt atattttttt tgttgcctct
      481 ttctaaggcg tgcgtataat gccgcaccct gtaaacgctc gaatgttttt tgagctgcat
      541 ctactttttt acactcgcag gacttatgag ggcaaatatg cttcaccgtg taagtgaacc
      601 gtacgaactc tttgctaagg acgctgttga gctaaatatg atttcactga agtccaagct
      661 gatcattatt cttacggagt tgatccgtga gcaggggtgg tcacaacgtg tcgcagcaga
      721 gaagctaggt gtcagtcagc caagagtcag taatcttatg aacggtcaat tttcaaagtt
      781 cgccatcgat acgctactgg agatcttgtg ccgcattgga ttcgttatgg atgtttcatt
      841 tcgacctcac gacaaagaga gtccaattga cgtgaaagtg aaaaaagcag tgctgtgaac
      901 actgctttgg ttaccgtctg atttatcaga agtcttttgg aagcatctta taccttagct
      961 tgattgtatc ctcctcggac tttggtgtgc catctgacgt ttttgagaat gcatgtagta
     1021 cgtagactgc ctttttacct actacgtaaa ccatcctgta agctggttta ccattcttca
     1081 cccactcgat aacaccttgt ccgaggccat tcatcgcctt ggtctttcgc aaaggtgaca
     1141 agccatattg taagcggttt atctccactg ccacttcgtc ttcaagactc tttgggaaca
     1201 ccttttggcc ggttaggctt ttttgtgaac ccccaacata tactactggt ttcatgaaca
     1261 cctcctatca gtgtcgtcgt cgattcaaag cgcacatacg catttcctct gttggttgct
     1321 attacctgcc cctctctcct tgagacggca gaatttcaac tctggagtat aaagtttttt
     1381 aaggatgttc cgatagtgct tttctatata aatttttgta tatcttgcta attgtttact
     1441 ttttgagcga tgtgtgtttt tttttggctt ggtagctgtg gttcttgtag gcgtttcttg
     1501 acggggtggc ctgagagatt tagtctggtt cggaaacaaa aaaaccaccc ggcaaggtgg
     1561 ttttttgaag gttcagtaaa ccggcaagtt tctgaaccga ggtaactggc ttggaggagc
     1621 gcagtcacca aaacttgttc tttcagttta gccctatccg gcgcataact tcaagactct
     1681 ctcctctaaa tcagttacca gtggctgctg ccattggcgc tttgtcgtgc tttttcgggt
     1741 tggactcaag ttgatagtta ccgaaaaggc gcagcggtcg ggctgaacgg ggggttcatg
     1801 cacacagccc agcttggagc gaacaaccta catcgaaccg agatgcctac agtgtgagct
     1861 atgagaaagc gccacacttc ccgtaaggga aaaaggcgga caggtatccg gtaagcgaca
     1921 aggttggaac aggagagcgc atgagggagc aactaggggg aaactcctgg tatctttata
     1981 gtcctgtcgg gtttcgcctc ttctggcttg aagtatcatt tttgtgatac tcgccggggg
     2041 ggcggagcct atggaaaaac gggttcccgt catcttcgtg ctttcgcttg ctgcccctgc
     2101 tagagtttcc tccgtattct ttggtgtcac tttatctatg gggggcttat ggcatggcac
     2161 agtgtgtcac aggcacaaaa actaaccggt aagagtagaa gaacgcttta ccgtgatatg
     2221 gcatcaggcc gtgtttcgtg gcgaaatgat ggcaatgggc atcgggagct tgaaacgtca
     2281 gagcttattc gtgtctatgg tgcattagtt gatgatggca caactgaacg gcacagcgtg
     2341 gcacactacg atggcacaga ttctaacaac gctatgctgg atgaactgcg cgctttacgt
     2401 attgaagttg cggatttgaa atccatgttg ttgcgtcttg agcacaaaga agagaaacca
     2461 cattccacct ccgctcgatg gtggtgcttc tggcgtaaat actgattgtt tccctttgaa
     2521 ttacacagtt ttctgcaatt tttcctccac ctttacacat tagtctgcac agctaaacaa
     2581 cggcagaatg cgggcaggac atgtaaagtt agctaacttt acgcctgcct tattcgctat
     2641 cgctcaaagg aacgcccatg gctaagcaac ctgatccaca actacgcgca gaagggtttc
     2701 gtaaggccga agcttccctg aaacttgagg gaatggaccc ttgtgggact ccgttatatg
     2761 agtcgattaa ggcccgtatc gtttccggtg atctgactta tgaacaggga cgtttagaaa
     2821 ttatggcgca ctataccgct gtcgcaggtg ctgttccggt taccgtaggt gacgttatta
     2881 ctgaggaatt tttaacgcca ctgaacatga gccatgaagc gctggcgcag atgatggggg
     2941 tttcctgtca ggttgttgag gatattgtct acggtcgccg gcgcctcact gttgtcgaag
     3001 cgtccaagct ggctgttatc ttcggaaccg acgaggattt ctggagcaat cttcaggcct
     3061 tgagcga
//
