LOCUS       NZ_CP062875             1546 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PEA14-20 plasmid unnamednovel_1,
            complete sequence.
ACCESSION   NZ_CP062875
VERSION     NZ_CP062875.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304185
            Assembly: GCF_015571755.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1546)
  AUTHORS   Poulin-Laprade,D., Brouard,J.-S., Gagnon,N., Turcotte,A.,
            Langlois,A., Matte,J.J., Carrillo,C.D., Zaheer,R., McAllister,T.,
            Topp,E. and Talbot,G.
  TITLE     Resistance determinants and their genetic context in bacteria from a
            longitudinal study of pigs reared under conventional and
            antibiotic-free husbandry practices
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1546)
  AUTHORS   Poulin-Laprade,D. and Brouard,J.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-SEP-2020) Sciences and Technology, Agriculture and
            Agri-Food Canada, 2000 College, Sherbrooke, Quebec J1M 0C8, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 28-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-34
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.00x
            Sequencing Technology :: Oxford Nanopore MinION and Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/16/2023 13:27:08
            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)                     :: 5,207
            CDSs (total)                      :: 5,084
            Genes (coding)                    :: 4,837
            CDSs (with protein)               :: 4,837
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 76 of 247
            Pseudo Genes (incomplete)         :: 161 of 247
            Pseudo Genes (internal stop)      :: 53 of 247
            Pseudo Genes (multiple problems)  :: 42 of 247
            Pseudo Genes (short protein)      :: 4 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062875.1.
            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..1546
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-PEA14-20"
                     /serotype="O-untypeable:H16"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamednovel_1"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-04-24"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            1..477
                     /locus_tag="IMP76_RS25690"
                     /old_locus_tag="IMP76_25685"
     CDS             1..477
                     /locus_tag="IMP76_RS25690"
                     /old_locus_tag="IMP76_25685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1082..1163
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.59"
                     /coverage="100.0"
                     /evalue="2.9e-32"
     Typing          complement(1360..1468)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(710..967)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.615"
                     /coverage="99.0"
                     /evalue="1.83e-109"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgtttt gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcgtgttttt gctccccgat ccccagaacg
      601 accgcgccgc cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca ccaaccagcc gaatagctgc
      721 ctgtgccgtg caaataggct ttgcagggag ctgacgcggt tcctagcgac atgaaagccc
      781 ttggttaggg gtatcggcgc gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tggcgggcat ttaaacccgt ttcgtgcgtc tgagagcttc tgagcgtgtt
      901 tgaagggcta tctgacgact catccccgaa agaacaacaa cgggatcacc gacaacatgc
      961 gagaggtgat cccgctcgcc gcaagtcgat gaccgagcgt agcgagcgaa tcgacgagga
     1021 agcggaagag aaccggaagt tacattgagc acttacgcac ggatgcgggg tgtcggggtg
     1081 aagtcctgac caggtgggga atgtctgagt gcgcgtgcgc ggtccgacat tcccacatcc
     1141 agtcccgatt tctgaggcgt tttaacggtg aacggacggc aaaaacatga tcgagctgtt
     1201 gaacgtggag atcgcgaaat cgggcaaaat catggctgac gaggcttgca gaggagtaag
     1261 ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg acaccccaaa
     1321 agggcgttgc gttgcgcgca acacccttgc ctagaataga tcttttacgc cgatttgtaa
     1381 gttgttgttt ttttagtgtg ttttttgttt acctgtcgca tccagggtga cacaacgttg
     1441 tcgcatcctg gatgcgacaa cacgcaacaa ggtgttgcac agatgtgtca tgatggctta
     1501 gatttgaacc aacgttagtg catgggattt tcagagggaa aaaatc
//
