LOCUS       NZ_CP135493             1459 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain isolateD plasmid pIsolateD_E, complete
            sequence.
ACCESSION   NZ_CP135493
VERSION     NZ_CP135493.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529175
            Assembly: GCF_032351055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1459)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Do we still need Illumina sequencing data?: Evaluating Oxford
            Nanopore Technologies R10.4.1 flow cells and v14 library prep kits
            for Gram negative bacteria whole genome assemblies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1459)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-2023) National Microbiology Lab, Public Health
            Agency of Canada, 1015 Arlington Street, Winnipeg R3E3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-JUN-2023
            Assembly Method :: Trycycler v. v0.5.0; Flye v. v2.9.2; Raven v.
            v1.8.1; Miniasm/minipolish v. v0.3_r179
            Assembly Name                     :: isolateD
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 245X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:56:47
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,954
            CDSs (total)                      :: 4,833
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 84 of 275
            Pseudo Genes (incomplete)         :: 187 of 275
            Pseudo Genes (internal stop)      :: 46 of 275
            Pseudo Genes (multiple problems)  :: 40 of 275
            Pseudo Genes (short protein)      :: 4 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135493.1.
            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..1459
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="isolateD"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIsolateD_E"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2020"
     gene            296..736
                     /locus_tag="RRL15_RS24770"
                     /old_locus_tag="RRL15_24770"
     CDS             296..736
                     /locus_tag="RRL15_RS24770"
                     /old_locus_tag="RRL15_24770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000031238.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000031238.1"
                     /translation="MSKDVERITQINDQGEIIGGFVAVIRPKQKSAFQRHFTMNQDALR
                     ILAKELTGEQFKVLMLMLADLDYENFIQIAQADIAETLGMQKTNVSRAVRALLDVGVIF
                     EGPKVGRSKTYRLNEQFGWKGTVTNHKKALKNGFSVIQGGRI"
                     /name="hypothetical protein"
     Typing          1346..1426
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.902"
                     /coverage="87.0"
                     /evalue="4.46e-26"
     Typing          complement(971..1231)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.13"
                     /coverage="100.0"
                     /evalue="1.84e-104"
ORIGIN
        1 ggagctgttg aacgtggaga gcgagaaatc ggacaaaaat catggctgac gaggcttgca
       61 gaggagtaag ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg
      121 acaccccaaa gagcagctag gataaatatc taatggaatc aatgcgttag acgcctaata
      181 taaagataca gaaaggagaa taaaaacatt aataaaatct aagggttaca gttgacatag
      241 ttatcaataa tgataacact gttatcatta ttgataactc aaatagggtt caaagatgag
      301 taaggatgtc gagagaatca ctcagataaa tgaccagggt gagattatcg gcggcttcgt
      361 tgccgttatc cgccctaaac aaaaatcagc atttcagagg catttcacca tgaatcaaga
      421 cgcattacgg atcttggcta aggaattaac cggggagcaa ttcaaggtct taatgctgat
      481 gcttgcagat ctggattacg aaaacttcat tcagatcgcc caagcagata ttgctgaaac
      541 tttagggatg cagaaaacga atgttagtcg cgccgttcgc gcgctactgg atgttggggt
      601 gatctttgag ggacctaaag tcggcagatc aaaaacatac cggctgaatg aacaatttgg
      661 ttggaaaggc accgtaacca accacaaaaa ggcactcaaa aacggcttta gtgtcattca
      721 gggcggccgg atttaaagag ccagcggcag gcggacaatc cacagaacat tgcatgcaat
      781 ttctagtgga ttgtctatcc tgcattgctc ttttgccgcc tcaaaatccc ttgcgtgttt
      841 ttgctccccg atctccagaa cgaccgagcc gccacggttc cggcagcgcc ttgagcgcaa
      901 ccggaaaccg tctggggaga cccccagacc ccccatcgct gtaacaccga cggtctacga
      961 ccacctacca accgagtggc tgcttgtacc gtgcaaatgg gctttgcagg gggctggcgc
     1021 ggttcctggc gacctgaaag cccctggcta ggggtatcgg cgcgcctgac ctcctgaaac
     1081 gctctgtaag cgtttttcgc gccttccatg ccctgacggg catttaaacc ccgcctcgtg
     1141 cgtctgagag cttctgagcg cgtttgaagg gctatctgac gactcatccc cgaaagaaca
     1201 acagcggaat caccgacagc atgcgagagg tggcaccgct cgccgcagcc ccagcgaccg
     1261 aacgttagtg agcgagtggg cgaggaagcg gaagagaaca ggaaaccaca ttgagcacgt
     1321 acgcactgat acggggtgtc ggggcgaagc tctgaccaga tggcaaacgg aatatcgtcg
     1381 cgggtgacgg tattacattt gcacatcctg tcctgatttc tgaggcgttt taacggtgaa
     1441 cggacggcaa aaacatgat
//
