LOCUS       NZ_AP022539             2866 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain THO-008 plasmid pTHO-008-3, complete
            sequence.
ACCESSION   NZ_AP022539
VERSION     NZ_AP022539.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00196006
            Sequence Read Archive: DRR199811
            Assembly: GCF_015139155.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     complete genome sequences of Escherichia coli str. THO-008 isolated
            from a patient
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2866)
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-FEB-2020) 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 v. 2.5; 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                   :: 431x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/15/2023 04:34:51
            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)                     :: 5,058
            CDSs (total)                      :: 4,930
            Genes (coding)                    :: 4,729
            CDSs (with protein)               :: 4,729
            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)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 60 of 201
            Pseudo Genes (incomplete)         :: 146 of 201
            Pseudo Genes (internal stop)      :: 28 of 201
            Pseudo Genes (multiple problems)  :: 33 of 201
            Pseudo Genes (short protein)      :: 5 of 201
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022539.1.
            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..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="2018-06-07"
     gene            102..1268
                     /locus_tag="JLF34_RS24995"
                     /old_locus_tag="THOESC008_P30010"
     CDS             102..1268
                     /locus_tag="JLF34_RS24995"
                     /old_locus_tag="THOESC008_P30010"
                     /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"
     gene            1700..2674
                     /locus_tag="JLF34_RS25000"
                     /old_locus_tag="THOESC008_P30020"
     CDS             1700..2674
                     /locus_tag="JLF34_RS25000"
                     /old_locus_tag="THOESC008_P30020"
                     /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"
ORIGIN
        1 ttgcgaagca ataaacatag tcggttccta tgtatttaca aaaacgggaa atatgctaaa
       61 aaatatatat aggaaaaaat ataaaagcag gggtaaatat aatgtcatat cagtttatac
      121 atattgaaga ttacgggata aatatatcta aaaaaaggag taataacgga acgagtgaaa
      181 aatacaaaaa agaaacaaaa ggaagatccg ttagccaaat aatatcagaa gcaaaaagag
      241 acaatgggtt ttgttctcat gttgaaaagc cagaagatcc gattatttta tatggtaaga
      301 gtttagatga agttgaaaaa ctcgctatgg aataccatag taaaacaaag ataatagata
      361 aaaacgggaa agagaaaaaa ttaagatctg atgctaatgt tttactcgct ggggttattt
      421 ctttaaatcg tgaaaatatg gaaatatggg aagattataa aaatgattcg atagcttatt
      481 tgaaaaataa gtatggtaaa aagcttatat cagttattga acacactgac gaggaacatc
      541 ctcacataca tttttattgt attcaggata taggtaagaa gtttgatttg atacacgacg
      601 gaaaaaaagc attgcatgaa aataaagata agaaaaaaca cgatcaaaat atagcttact
      661 tggattcaat gagagccttt caagaggatt ttttcaaagt tgtaagctct aactatggct
      721 tgtcgaaaga cggccccaga agggctagaa tgagtcgttc tgactacttc aagcttggta
      781 gagaagtaaa gttgattaat caagtaaagt taaaagcaaa aaaagatggt tataaatttg
      841 caatagacga attcgaaagt aagaactggt taaataaaat aacagcaagt attactttta
      901 ataaagactc attaaatgaa gctatttctc gtggtaataa atacaaaaaa tcgcttagta
      961 gtaaaactaa aaaactaaaa gaacttgaag atatagaaac taaatataat gatctgagaa
     1021 aggattttaa acttagggtt aataatcaaa ctgaaaacct aagaaataaa aataacactc
     1081 ttgaatatga aaatgaaaat ataaagaaca aaaacaaaga acttgaggaa gaaaataaaa
     1141 aactaaaaac cactcttgaa gaaacttccc cactctacga gctattaaaa aataagtttg
     1201 gggatcagtt tgaggaatgg aaaaataact tgtttaaatc ttttagatcc aaaataaaac
     1261 ctaaatagtt aaatagtcaa taagaatggc ggggggtccc ctctggggtt ccgctattgt
     1321 tgttgactac acacccacga atacacttcc aatggtgtaa ggagagcaaa gcgaccctta
     1381 cacctgttaa gccggtttta agctcttaga agccctctgg aagcctcaga aggcttctgg
     1441 cttgtggttt ggtgggtttg ttccagtggt ggttttgggt gttaaaaaca gcctcgcaga
     1501 gggtgatttt cctttacttg ataccttagg cataacggtc ggataaagga aaagccataa
     1561 aacaggctct aagccttgtg tagcaagggt ttcagggggt ttagaaggtg ggattttggt
     1621 ataacgttga caaaaaaaat ccccgtgtta agttttgagt gtcgaagtca aaaactataa
     1681 tacggggatc ggtatatcta tggagagaat agataataaa aaaataaaag tcaagtttga
     1741 aaatttaagt gatagatcgg aaaaggatgg tgtttgggat ttacaccgta aagactgcga
     1801 tcttgtatct ggtttatatt ttcaatcagc agagttcgaa agatattttg aaagaatgga
     1861 agactgctca ggtcgtttag agtttaatca actgttagac cgtgaaacgg gcgaaataaa
     1921 aataaaatta actaatgctc atttctgtcg tgtaagacat tgcccggtat gtcagtggag
     1981 aaaatcgctt atgtggaaag ctaaatttta taaagcactt ccagaaatag aagcagaata
     2041 taaatctgct cgttggatgt ttttaactct aacagtagaa aactgcgaaa taactgattt
     2101 aaaaaatact cttgctcata tgaataaagc ttttaaaaag ctgataaaga gaaagcattt
     2161 tttaaaaaat aatctcggtt tcgttaagac tacggaaata acaagatcaa aagacgggaa
     2221 agctcatcca cactttcata tattgctaat gatgaaaagt acctatttta aaggaacgga
     2281 atatatgaag accagtgatt gggctgagtt atggagagat tgccttaatg tctcatatac
     2341 ccctataaca gacattagga tcgttaaggt caagaacggt ggtgatgcca gccgttcggc
     2401 tcttgctgat gctgtagctg aaactttgaa gtatgccgta aaaccaagcg atatgactaa
     2461 ggatcgtgaa tggtttcacg agctgacaag gcaagttttt aaattaaggt tcgtatcaac
     2521 tggtggagta ttgaaagatt tattcaagga agaaacttcc gaagaagatt tattattact
     2581 aacagaagaa gaagaaacag acaaagaact tggatcgtta tattttaact ggtataaaac
     2641 aaaagcaaaa tacagaagaa aaataacaga atgataaata gtagtgatta taaaaaataa
     2701 tataaggaga atattatgat cactgctata actgtaatat ctattttatc aaacatacta
     2761 acgattatag tttgtataaa aacactaatc gggaagtaat aaaaaaggca cctgtaaggg
     2821 tgcttttttt atgcctttga cttttccccg taggggccgg cgttta
//
