LOCUS       NZ_CP062841             3256 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PER02-33 plasmid unnamed34,
            complete sequence.
ACCESSION   NZ_CP062841
VERSION     NZ_CP062841.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304229
            Assembly: GCF_015571655.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3256)
  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  JOURNAL   Unpublished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 3256)
  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                     :: 27-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-19
            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 15:52:52
            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)                     :: 5,045
            CDSs (total)                      :: 4,923
            Genes (coding)                    :: 4,618
            CDSs (with protein)               :: 4,618
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 305
            CDSs (without protein)            :: 305
            Pseudo Genes (ambiguous residues) :: 0 of 305
            Pseudo Genes (frameshifted)       :: 94 of 305
            Pseudo Genes (incomplete)         :: 227 of 305
            Pseudo Genes (internal stop)      :: 46 of 305
            Pseudo Genes (multiple problems)  :: 53 of 305
            Pseudo Genes (short protein)      :: 3 of 305
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062841.1.
            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..3256
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-PER02-33"
                     /serotype="O-untypeable:H4"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamed34"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-03-20"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            924..1118
                     /locus_tag="IMQ20_RS23455"
                     /old_locus_tag="IMQ20_23475"
     CDS             924..1118
                     /locus_tag="IMQ20_RS23455"
                     /old_locus_tag="IMQ20_23475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2115..2411)
                     /locus_tag="IMQ20_RS23460"
                     /old_locus_tag="IMQ20_23480"
     CDS             complement(2115..2411)
                     /locus_tag="IMQ20_RS23460"
                     /old_locus_tag="IMQ20_23480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            2755..3036
                     /locus_tag="IMQ20_RS23465"
                     /old_locus_tag="IMQ20_23485"
     CDS             2755..3036
                     /locus_tag="IMQ20_RS23465"
                     /old_locus_tag="IMQ20_23485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          complement(410..665)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(790..888)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1192..1274)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1287..1841
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.614"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tatctaagta gtaataaaca ctatcaatag tggttggata attgccaaaa aagcctctat
       61 ctgttctgaa acagacaaca aggaaaaatc ggtgtaagcc acctccataa gaggtggtat
      121 tgatatcaac atagataaaa ccatcccgta aatcacagca tttaccataa cgtcgcatta
      181 cgcgcaccgc taaaacgcgc tgaacgcgat tctgccgcaa acaccgcaaa aagagatgtt
      241 ttaccaagcg aaaaccggaa aaatgcgtca ggatcgcttt cagctcactg catagctatg
      301 catgaaagtg aatggcgatc ggtttgggcg catacggtgc ccatgagaca cattttcgga
      361 cattttcagt tcgtgaatcc ctgactcatt gctacatatc tgaacagaca cccctagcag
      421 cgcccccagg ggcgtcctgt aaaaaaacac accgcgccgc tagcagcacc cctaatataa
      481 aatgatgttt tttatgaaaa tagtcagtac cacccctaaa aagcggtgtt ggcgcagcta
      541 caacaccgcg ccgacaccgc ttttttaaat atcacaaaga gagcaagaag aactaatttg
      601 tcataactct ctatttataa agaaaaatca gcaaaaaatt gtttttgcgt ggggtgtggg
      661 catttcaggc atgagaacag actcgcgttt ttccggagta tcagcggaat tattgattaa
      721 gaaacactcg acgcagagcg aaattttatg caacagcggc tgcactgcac agggattatt
      781 tatcagttga tatgctgtgc catgatacgt cctaaaaaaa caggacagga tgtgcaattg
      841 taataccgtc gcccgcaacg tcttacaatt accacctggt cagggtccac ccgacacccg
      901 gtactgacgg agaacaacgg aaggtgaaca aacagcaaca aactgcgctg aatatggcgc
      961 gatttatcaa aagccagagc ctgacactgc ttgaaaaact ggatgctctg gatgccgacg
     1021 aacaggcggc catgtgcgaa cgactgcacg aactcgcgga agaactccag aacagcatcc
     1081 aggttcgctt tgagaccgaa agtgaaacag gaacataacg aagctgacgg aggcgctcac
     1141 ggcttgtccg cgagcgtttt cggcagcaga caagcccgcc agggcgcgtc agcgggtgtc
     1201 ggggcgaagc cctgacccag tcacgtagcg atagcggagt gtatactggc ttaactatgc
     1261 ggcatcagtg cagattgtat gaaaagtgcc ccatgccggg tgtgaaattc cgcacagatg
     1321 cgtaaggaga aaatgcgcgt ccaggcgctt ttccgcttcc tcgctcactg actcgctacg
     1381 ctcggtcgtt cggctgcggc gagcggtact gacttacaca aaaacggcag cacggttatc
     1441 cacagaatca ggggataagg ccggaaagaa catgtgagca aaagaccaag aacaggaaga
     1501 aggccgcgcc gcaggcgttt ttccataggc tccgcccccc tgacgagcat cacagaaatc
     1561 gacgctcaag tcagaggtgg cgaaacccga caggacttaa agataccaga cgtttccccc
     1621 tggtggctcc ctcgtgcgct ctcctgttcc gaccctgccg cttaccggat acctgtccgc
     1681 ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgtaggt atctcggttc
     1741 agtgtaggtc gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg
     1801 ctgcgcctta tccggtaact atcatcttga gtccaacccg gaaagacatg caaaacacca
     1861 ttggcagcag ccactggtaa ctgatttaga ggagttagtc ttgaagttat gcgccagtta
     1921 aggctaaact gaaagaacaa gttttggtga ctgcgctcct ccaagccagt taccctggtt
     1981 cagaaacttg ccggttactg aaccttcgaa aaaaccacct tgccgggtgg ttttttcgtt
     2041 tacgagaaac gatacgatcc agttgcctga gagtcaagac agaaaaaggc cgcatatagc
     2101 ggccttttct tttctcaaaa tataggaacc aattcatcta attccttaat gacattaggt
     2161 gacttcctgc tcgcgttaag actgtattga gtctgcatgt ttatccacga ctcggcactg
     2221 cgaccaagaa ctcgagaaag ccttaatgcc atctcaacac ttaaatcagc ttttccattc
     2281 agcactctac ttagagtgga aggtgataca tgcagttttt cagacaggtc cgcggctgat
     2341 atttcaaacg gttccataaa catctcacgg ataaaaaccc ctggatgtac tggatcgaca
     2401 agattaatca taccttcctc tgaagcctat attagtttta aaaagatagg cctattgcgt
     2461 tttcagattg cgcattgcgc ataacgcaac tcattgttga ctaaaaaaag aatgacatta
     2521 tgatgcacat tggtgcgtct aatcattcct tatgatgtgg gtacttgatg tgaaattcaa
     2581 ggccccggca ttgtacagcg catcaaacca atgtcaacag attaaaatgc gacttggtta
     2641 agtaaaacct acgtcattta ttcaaataga gcaaggggtt tgcaatggaa atacggatga
     2701 accggaaaaa taaactgcga tgtttctatc taaacaaata tgggatggtg attaatgatc
     2761 ataaatatca agcataaagg tttgcgtaag tttgccgaaa caggtaacaa cgcaggaatt
     2821 ccgcaacagt ttactcaacg tctgaagctg atcctaacag ccttaagcac agcgacgaac
     2881 ttgcaggata tgatggattt aaaggcattg cgctgccatc cattgaaggg agaccgtcaa
     2941 ggagagtatt cgttagaggt caatggaaac tggcgcgtag tgtttaagct cgaagaacct
     3001 aacgtctttg acgtggatct cgaggattat cactaagaag gtccttaaag catcaaagtg
     3061 acagtatcga tgctttaggg tctcataaaa aagcaaaacc tcggggtaag ttatatgaag
     3121 tattttctgt accagatagt ccctatagca gccatcattt gcgcagcaat tctagcgcta
     3181 aaaggtatca atggctgggg gtggttctta actgttgggt tcctgcttgc aggggcagat
     3241 acagtaaagg ctcagt
//
