LOCUS       NZ_AP019680             3274 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain GSH8M-2 plasmid pGSH8M-2-5, complete
            sequence.
ACCESSION   NZ_AP019680
VERSION     NZ_AP019680.1
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 3274)
  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
            AP019680.1.
            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..3274
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GSH8M-2"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pGSH8M-2-5"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.631549 N 139.745949 E"
                     /collection_date="2018-08"
                     /note="replicon type: Col440I"
     gene            101..934
                     /locus_tag="GDK32_RS25115"
                     /old_locus_tag="ECGSH8M2_p50010"
     CDS             101..934
                     /locus_tag="GDK32_RS25115"
                     /old_locus_tag="ECGSH8M2_p50010"
                     /inference="COORDINATES: protein motif:HMM:NF027299.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_072775497.1"
                     /translation="MILLAGKKMKTNYFTHRLFPSDGAVICEPLKTSFDNMIATNRNTA
                     TLANEYHVIQHVSGDVYTFIKTNSRDVFRKLDTSSNICVDLSNILNQHEKIAFASFFIL
                     KGDVIGFSNTLYSPRVGKLAEIYDAAMYSRNGNHNINFEPITNIVTEQDVMNYAHVGKI
                     TMKIEKSQGIIGGLGTLFSGNVKYDDVDSFEIKIIPKRAKDIKDTFAGLMQARPQEVSS
                     VAVSAKEHIGDVATDLNVIMSNTVYDFVNPNDTTTIEVQMEKNYNNNTTLRSLGY"
                     /name="hypothetical protein"
     gene            945..1382
                     /locus_tag="GDK32_RS25120"
                     /old_locus_tag="ECGSH8M2_p50020"
     CDS             945..1382
                     /locus_tag="GDK32_RS25120"
                     /old_locus_tag="ECGSH8M2_p50020"
                     /inference="COORDINATES: protein motif:HMM:NF027298.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046597188.1"
                     /translation="MKLKGFWLSAIVIAACNGMGFLFLYLSKTYFFPMVTFKDNLGNLG
                     SSLVTYSTAMMALLIAMVVIIFGLDGPRLHNFKKSGYLHVTYFIYMITFFELGLTMALS
                     LLCLSNISSIKVASYSLTFAFITFLLIGCLGIQLLNIKKNL"
                     /name="hypothetical protein"
     gene            2369..2518
                     /locus_tag="GDK32_RS25325"
                     /old_locus_tag="ECGSH8M2_p50030"
     CDS             2369..2518
                     /locus_tag="GDK32_RS25325"
                     /old_locus_tag="ECGSH8M2_p50030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          2162..2376
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.908"
                     /coverage="100.0"
                     /evalue="7.28e-73"
     Typing          complement(1700..2186)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.081"
                     /coverage="93.0"
                     /evalue="5.84e-177"
ORIGIN
        1 cggtgacaga tcatttaata tgcaaaactt ggaattttaa agaagcattg ttcttccata
       61 agaaatagaa tataaaaaga agaaaatata atgcgtttct atgattttac tagctgggaa
      121 aaaaatgaaa acaaattact tcacacacag attgtttcct tcagatggcg ctgttatttg
      181 tgagccatta aaaactagtt ttgataatat gatcgctact aacagaaaca ctgcaacgct
      241 agccaatgag tatcatgtaa ttcagcatgt gtctggcgat gtatatacgt ttataaaaac
      301 aaatagcaga gacgttttta gaaaactaga tacgagtagt aatatatgtg tagatctctc
      361 aaacatctta aatcaacatg aaaaaatagc ctttgcatct tttttcatat tgaagggtga
      421 tgttataggg tttagtaata cgttgtactc tcctcgtgtt gggaagttgg cagaaatata
      481 tgatgctgca atgtattccc gaaatgggaa ccacaacata aattttgagc cgataacaaa
      541 catagttacc gagcaagatg ttatgaatta tgcccatgtt ggtaaaataa cgatgaaaat
      601 agagaagtct caaggcatta ttggtgggct tggtacgctt ttctctggga acgtaaagta
      661 tgacgatgtg gattcgtttg agataaagat aatccctaaa cgggctaaag acataaagga
      721 tacctttgca ggtttgatgc aggctaggcc tcaagaggtt agctcggtcg ctgtgtcagc
      781 taaagaacac attggtgacg ttgcaacaga tttgaatgtt ataatgtcta ataccgtata
      841 tgattttgta aatccaaatg acactactac tatcgaggtt cagatggaaa aaaattataa
      901 taacaataca acattaagaa gtttaggtta ctgaggattg cattgtgaag cttaagggtt
      961 tttggttgag cgctatagtt atagctgcat gtaatggcat gggcttttta tttctatacc
     1021 tttcaaaaac ctatttcttc ccgatggtaa cgtttaagga taatttaggt aaccttggtt
     1081 cttccttggt tacttattcg acagcgatga tggcgttgct tattgctatg gttgttataa
     1141 tctttggctt ggatggacct cgcttgcata actttaaaaa aagcggctat ctccatgtta
     1201 catattttat ttatatgata acgtttttcg agctcggctt aaccatggct ctttcgttac
     1261 tttgtttgtc caatatctca agtattaagg tggcttctta ttcattgact tttgcattta
     1321 ttactttttt gttgatagga tgtttaggta ttcaactctt aaatataaaa aagaatcttt
     1381 aatcaaccaa actgtgatgt tcatcacagg tgaaacggtt tgtgaccatt tttggtgagt
     1441 tgataaaatg cagaatgtgt aaggatcgtc ttgagatttt tgagagtgca gcgtagtctc
     1501 ttgctctgta aacaaaaaaa ccaccgctac caacggtggt ttgtttgccg gaagtgagag
     1561 ctaccaactc tttctcccga aggtaactgg ctttcacgga gcgcagatac caaaactgtc
     1621 cttttagtgt agccgtagtc aggccaccac ttcaagaact ccatagaaat actctactac
     1681 tctgctccgt gaatcctctt accaatggct gctgccaatg gcgcgttgtc gtgtctttcc
     1741 gggttggact caagaagaca gttaccggaa aggcgcagta gtcggactga acggggggtt
     1801 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
     1861 tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
     1921 gagcgcacga gggagctacc agggggaaac gcctgggatc tttatagtcc tgtcgggttt
     1981 cgccgccact gatttgagcg tcagattttg tgatgcttgt caggggggcg gagcctatgg
     2041 aaaaacggca gcgccgtatc ctttttccgg cctttcctga cttgagagcc atctttttat
     2101 cttgtcattc gtgagcaggt aacgcccgcc gcagtctcac ggcaggagcg tagcgaccga
     2161 gtgagcgagg aggcgtcatg tcaccgttac ctgcattttg cacttacgtc ctatagccgc
     2221 attttccctt gcaacatgaa taacttccct gaattaccac tccgacctaa catattcagc
     2281 ctgtatacac tccgctagcg ctacgtgact ggttcagggc tgcgccccga aacccgctaa
     2341 caacctctca gctactggat atcaccccat gccatctgaa tatgatgaac aactggattc
     2401 gactgatacg cagcttcccg gcgaatatga cctttttgat ttaatggcgc aggttactga
     2461 agagaacctg catgcccctg tggattttgg gtcgcctgtc ggccgggaag cgttatagct
     2521 ttttcgcttg cccgcgtacg tggtaatact ccggtattac cttttatttc tttattttca
     2581 tgtaattaca gtggattttt aatacccggg tattactcgt gaaaacgaaa tattcctttt
     2641 ttttctttta attcatgcag ttgcgatgaa aatcgcggct gcgttaggtg tatgaccatt
     2701 ttgaggttga aaaataatca accatggcgg gtgatttacg caggttaagg ggagatcgtg
     2761 acaaaaaagc gttcctcact gtatcgttca tgcctgcatg aacgggttat tcttcctgac
     2821 tacagaatta catcaaaagt acatcaaaat tacatcactt ttacatcact tttacatcac
     2881 ttttacatca ttccttcagc tcatacgtca ctttcatcct ctgtgccatt tgtacatcac
     2941 ccccttcctg aacgtgctga cagcgggttt tccggctgcg ccggcaacgc ttcacggcca
     3001 cgcaataaat tgcgtccccg ttcaccgttt tcggatggga agaacgccgg aaacaggact
     3061 taccccggct gaatggtgtg aatttccgcg ctatgcactt gtgcgcatac tcatgcatgc
     3121 cgtaaaaaca gagcctgcgc gtttctggcg ggttttcggg tggtttgttg cctgttttac
     3181 cggtttcccg tcagaaacgc gctgagggcc tctgcggcgg tgcacgcaac ggatgttatg
     3241 gtaaatagag ttggtggcct agctttacga cctt
//
