LOCUS       NZ_AP019541             2866 bp    DNA     circular CON 06-JUN-2024
DEFINITION  Escherichia coli strain THO-008 plasmid pTHO-008_3, complete
            sequence.
ACCESSION   NZ_AP019541
VERSION     NZ_AP019541.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00164371
            Sequence Read Archive: DRR170687, DRR170688
            Assembly: GCF_027943565.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Katagiri,M., Segawa,T., Yatsu,K., Inamine,Y. and
            Kuroda,M.
  TITLE     complete genome sequences of Escherichia coli THO-008 carrying
            multi-copy IS26-mediated composite transposons harboring multi
            antimicrobial resistance genes including blaCTX-M-27 isolated from a
            patient in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2866)
  AUTHORS   Sekizuka,T., Katagiri,M., Segawa,T., Yatsu,K., Inamine,Y. and
            Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-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                   :: 200x
            Sequencing Technology             :: Sequel; NextSeq500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_027943565.1-RS_2024_06_06
            Annotation Date                   :: 06/06/2024 03:35:37
            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)                     :: 5,067
            CDSs (total)                      :: 4,939
            Genes (coding)                    :: 4,733
            CDSs (with protein)               :: 4,733
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 67 of 206
            Pseudo Genes (incomplete)         :: 152 of 206
            Pseudo Genes (internal stop)      :: 28 of 206
            Pseudo Genes (multiple problems)  :: 37 of 206
            Pseudo Genes (short protein)      :: 1 of 206
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP019541.1.
            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..2866
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="THO-008"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pTHO-008_3"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018"
     gene            146..1120
                     /locus_tag="QMN35_RS25285"
                     /old_locus_tag="ECTHO008_p30010"
     CDS             146..1120
                     /locus_tag="QMN35_RS25285"
                     /old_locus_tag="ECTHO008_p30010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427687.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_200922428.1"
                     /translation="MERIDNKKIKVKFENLSDRSEKDGVWDLHRKDCDLVSGLYFQSAE
                     FERYFERMEDCSGRLEFNQLLDRETGEIKIKLTNAHFCRVRHCPVCQWRKSLMWKAKFY
                     KALPEIEAEYKSARWMFLTLTVENCEITDLKNTLAHMNKAFKKLIKRKHFLKNNLGFVK
                     TTEITRSKDGKAHPHFHILLMMKSTYFKGTEYMKTSDWAELWRDCLNVSYTPITDIRIV
                     KVKNGGDASRSALADAVAETLKYAVKPSDMTKDREWFHELTRQVFKLRFVSTGGVLKDL
                     FKEETSEEDLLLLTEEEETDKELGSLYFNWYKTKAKYRRKITE"
                     /name="protein rep"
     gene            1414..2580
                     /locus_tag="QMN35_RS25290"
                     /old_locus_tag="ECTHO008_p30020"
     CDS             1414..2580
                     /locus_tag="QMN35_RS25290"
                     /old_locus_tag="ECTHO008_p30020"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_050394550.1"
                     /translation="MSYQFIHIEDYGINISKKRSNNGTSEKYKKETKGRSVSQIISEAK
                     RDNGFCSHVEKPEDPIILYGKSLDEVEKLAMEYHSKTKIIDKNGKEKKLRSDANVLLAG
                     VISLNRENMEIWEDYKNDSIAYLKNKYGKKLISVIEHTDEEHPHIHFYCIQDIGKKFDL
                     IHDGKKALHENKDKKKHDQNIAYLDSMRAFQEDFFKVVSSNYGLSKDGPRRARMSRSDY
                     FKLGREVKLINQVKLKAKKDGYKFAIDEFESKNWLNKITASITFNKDSLNEAISRGNKY
                     KKSLSSKTKKLKELEDIETKYNDLRKDFKLRVNNQTENLRNKNNTLEYENENIKNKNKE
                     LEEENKKLKTTLEETSPLYELLKNKFGDQFEEWKNNLFKSFRSKIKPK"
                     /name="plasmid recombination protein"
ORIGIN
        1 ccataaaaca ggctctaagc cttgtgtagc aagggtttca gggggtttag aaggtgggat
       61 tttggtataa cgttgacaaa aaaaatcccc gtgttaagtt ttgagtgtcg aagtcaaaaa
      121 ctataatacg gggatcggta tatctatgga gagaatagat aataaaaaaa taaaagtcaa
      181 gtttgaaaat ttaagtgata gatcggaaaa ggatggtgtt tgggatttac accgtaaaga
      241 ctgcgatctt gtatctggtt tatattttca atcagcagag ttcgaaagat attttgaaag
      301 aatggaagac tgctcaggtc gtttagagtt taatcaactg ttagaccgtg aaacgggcga
      361 aataaaaata aaattaacta atgctcattt ctgtcgtgta agacattgcc cggtatgtca
      421 gtggagaaaa tcgcttatgt ggaaagctaa attttataaa gcacttccag aaatagaagc
      481 agaatataaa tctgctcgtt ggatgttttt aactctaaca gtagaaaact gcgaaataac
      541 tgatttaaaa aatactcttg ctcatatgaa taaagctttt aaaaagctga taaagagaaa
      601 gcatttttta aaaaataatc tcggtttcgt taagactacg gaaataacaa gatcaaaaga
      661 cgggaaagct catccacact ttcatatatt gctaatgatg aaaagtacct attttaaagg
      721 aacggaatat atgaagacca gtgattgggc tgagttatgg agagattgcc ttaatgtctc
      781 atatacccct ataacagaca ttaggatcgt taaggtcaag aacggtggtg atgccagccg
      841 ttcggctctt gctgatgctg tagctgaaac tttgaagtat gccgtaaaac caagcgatat
      901 gactaaggat cgtgaatggt ttcacgagct gacaaggcaa gtttttaaat taaggttcgt
      961 atcaactggt ggagtattga aagatttatt caaggaagaa acttccgaag aagatttatt
     1021 attactaaca gaagaagaag aaacagacaa agaacttgga tcgttatatt ttaactggta
     1081 taaaacaaaa gcaaaataca gaagaaaaat aacagaatga taaatagtag tgattataaa
     1141 aaataatata aggagaatat tatgatcact gctataactg taatatctat tttatcaaac
     1201 atactaacga ttatagtttg tataaaaaca ctaatcggga agtaataaaa aaggcacctg
     1261 taagggtgct ttttttatgc ctttgacttt tccccgtagg ggccggcgtt tattgcgaag
     1321 caataaacat agtcggttcc tatgtattta caaaaacggg aaatatgcta aaaaatatat
     1381 ataggaaaaa atataaaagc aggggtaaat ataatgtcat atcagtttat acatattgaa
     1441 gattacggga taaatatatc taaaaaaagg agtaataacg gaacgagtga aaaatacaaa
     1501 aaagaaacaa aaggaagatc cgttagccaa ataatatcag aagcaaaaag agacaatggg
     1561 ttttgttctc atgttgaaaa gccagaagat ccgattattt tatatggtaa gagtttagat
     1621 gaagttgaaa aactcgctat ggaataccat agtaaaacaa agataataga taaaaacggg
     1681 aaagagaaaa aattaagatc tgatgctaat gttttactcg ctggggttat ttctttaaat
     1741 cgtgaaaata tggaaatatg ggaagattat aaaaatgatt cgatagctta tttgaaaaat
     1801 aagtatggta aaaagcttat atcagttatt gaacacactg acgaggaaca tcctcacata
     1861 catttttatt gtattcagga tataggtaag aagtttgatt tgatacacga cggaaaaaaa
     1921 gcattgcatg aaaataaaga taagaaaaaa cacgatcaaa atatagctta cttggattca
     1981 atgagagcct ttcaagagga ttttttcaaa gttgtaagct ctaactatgg cttgtcgaaa
     2041 gacggcccca gaagggctag aatgagtcgt tctgactact tcaagcttgg tagagaagta
     2101 aagttgatta atcaagtaaa gttaaaagca aaaaaagatg gttataaatt tgcaatagac
     2161 gaattcgaaa gtaagaactg gttaaataaa ataacagcaa gtattacttt taataaagac
     2221 tcattaaatg aagctatttc tcgtggtaat aaatacaaaa aatcgcttag tagtaaaact
     2281 aaaaaactaa aagaacttga agatatagaa actaaatata atgatctgag aaaggatttt
     2341 aaacttaggg ttaataatca aactgaaaac ctaagaaata aaaataacac tcttgaatat
     2401 gaaaatgaaa atataaagaa caaaaacaaa gaacttgagg aagaaaataa aaaactaaaa
     2461 accactcttg aagaaacttc cccactctac gagctattaa aaaataagtt tggggatcag
     2521 tttgaggaat ggaaaaataa cttgtttaaa tcttttagat ccaaaataaa acctaaatag
     2581 ttaaatagtc aataagaatg gcggggggtc ccctctgggg ttccgctatt gttgttgact
     2641 acacacccac gaatacactt ccaatggtgt aaggagagca aagcgaccct tacacctgtt
     2701 aagccggttt taagctctta gaagccctct ggaagcctca gaaggcttct ggcttgtggt
     2761 ttggtgggtt tgttccagtg gtggttttgg gtgttaaaaa cagcctcgca gagggtgatt
     2821 ttcctttact tgatacctta ggcataacgg tcggataaag gaaaag
//
