LOCUS       NZ_CP135464             1433 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain isolateI plasmid pIsolateI_F, complete
            sequence.
ACCESSION   NZ_CP135464
VERSION     NZ_CP135464.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529180
            Assembly: GCF_032345195.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1433)
  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  JOURNAL   Unpublished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 1433)
  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                     :: isolateI
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 159X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:43:00
            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)                     :: 4,979
            CDSs (total)                      :: 4,866
            Genes (coding)                    :: 4,663
            CDSs (with protein)               :: 4,663
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 65 of 203
            Pseudo Genes (incomplete)         :: 152 of 203
            Pseudo Genes (internal stop)      :: 36 of 203
            Pseudo Genes (multiple problems)  :: 43 of 203
            Pseudo Genes (short protein)      :: 3 of 203
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135464.1.
            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..1433
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="isolateI"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIsolateI_F"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2017"
     gene            complement(join(1223..1433,1..11))
                     /locus_tag="RRL07_RS24890"
                     /old_locus_tag="RRL07_24890"
     CDS             complement(join(1223..1433,1..11))
                     /locus_tag="RRL07_RS24890"
                     /old_locus_tag="RRL07_24890"
                     /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="hypothetical protein"
                     /protein_id="WP_158414302.1"
                     /translation="MCKCNTVTRDDIPFAVWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGVTSRMLSVIPLLFFRG"
                     /name="hypothetical protein"
     gene            345..776
                     /locus_tag="RRL07_RS24895"
                     /old_locus_tag="RRL07_24895"
     CDS             345..776
                     /locus_tag="RRL07_RS24895"
                     /old_locus_tag="RRL07_24895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233485.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_063269671.1"
                     /translation="MRRVTQIDQESGEELGGFVAVIRPKQKSSFQRHFTMNQAALITIA
                     NELNHDQIRVLMALLADLDYENYIQVAQIDIADALKMQKTNVSRAIKNLIDFGIIIEGP
                     RIGRSKTYRLNPQFGWKGTVSNHRKALKNGLSVIQGGRV"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(1012..1270)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="99.0"
                     /evalue="1.09e-111"
ORIGIN
        1 catttgcaca tcctgtcccg atttctgagg cgttttagcg gtgaacggac ggcaaaacca
       61 tgatggagct gttgagcgtt gagagcgtga aatctggcaa aaatcacggc tggcgaggct
      121 tgtagcggaa taagccagta tacactccgc tggcgctacg tgactgggtc agggcttcgc
      181 cccgacaccc catgaaaact ttgttttggt tgcgagagta ataagataca gaagggggtc
      241 ttctggaagc cgcgccagaa gcgggatctt ttgacaaata gttatcttga gagataactt
      301 agttatcttg agagataact attttctcta gaacggagga agccgtgaga agagttacac
      361 agatagacca agagtcagga gaggagttgg gcggatttgt tgcagttatt cgtcccaagc
      421 aaaaatcgtc atttcagagg cattttacga tgaatcaggc tgcgttaatc acgattgcaa
      481 acgaacttaa tcatgatcaa attcgtgttt taatggcttt gctagctgat cttgactacg
      541 aaaactacat ccaagttgcg caaatcgata ttgcggatgc attgaaaatg caaaaaacga
      601 acgtcagtcg cgcaataaaa aacttgattg attttgggat catcatcgaa ggaccaagga
      661 tcgggcgtag taaaacctat cgcttgaatc ctcagttcgg atggaaaggg acggtaagca
      721 atcacaggaa agcactcaag aatggtctta gcgtcattca gggtggcagg gtttaaagag
      781 ccagcggcag gcggacaatc aggggctacg tgttaacgtt ttgaccatga ttgtctatcc
      841 tgcattgctc ttttgccgcc tcaaaatccc ttgcttgttt ttgctccccg atccccagaa
      901 cgaccgcgcc gccacggttc cggcagcgcc ttgagcgcaa ccggaaaccg tctggggaga
      961 accccagacc cccatcgctg taacaccgac ggtctacgac caccaaccag ccgaatagct
     1021 gcctgtgccg tgcaaatagg ctttgcaggg ggctgacgcg gttcctagcg acctgaaagc
     1081 ccctggttag gggtatcggc gcgcctgacc tcctgagagc ctctgtaagc gtttttcgcg
     1141 ccttccatgc cctgacgggc atttaaaacc cgtttcgtgt gtctgagagc ttctgagcgc
     1201 gtttgagggg ctatctggcg actcatcccc gaaagaacaa caacggaatc accgacaaca
     1261 tgcgagaggt gacaccgctc gccgcagccc cagcgaccga acgtagtgag cgagtgggcg
     1321 aggaagcgga agagaaccgg aaaccacatt gagcacgtac gcactgatgc ggggtgtcgg
     1381 ggcgaagccc tgaccagacg gcaaacggaa tatcgtcgcg ggtgacggta tta
//
