LOCUS       NZ_CP062829             3256 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PER12-33-A plasmid unnamed34,
            complete sequence.
ACCESSION   NZ_CP062829
VERSION     NZ_CP062829.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304239
            Assembly: GCF_015571615.1
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  JOURNAL   Unpublished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                     :: 19-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-26-F
            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 15:10:08
            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)                     :: 5,039
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,614
            CDSs (with protein)               :: 4,614
            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)              :: 303
            CDSs (without protein)            :: 303
            Pseudo Genes (ambiguous residues) :: 0 of 303
            Pseudo Genes (frameshifted)       :: 93 of 303
            Pseudo Genes (incomplete)         :: 226 of 303
            Pseudo Genes (internal stop)      :: 46 of 303
            Pseudo Genes (multiple problems)  :: 53 of 303
            Pseudo Genes (short protein)      :: 3 of 303
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062829.1.
            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-PER12-33-A"
                     /serotype="O-untypeable:H4"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamed34"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-03-27"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            947..1141
                     /locus_tag="IMQ30_RS23420"
                     /old_locus_tag="IMQ30_23440"
     CDS             947..1141
                     /locus_tag="IMQ30_RS23420"
                     /old_locus_tag="IMQ30_23440"
                     /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(2138..2434)
                     /locus_tag="IMQ30_RS23425"
                     /old_locus_tag="IMQ30_23445"
     CDS             complement(2138..2434)
                     /locus_tag="IMQ30_RS23425"
                     /old_locus_tag="IMQ30_23445"
                     /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            2778..3059
                     /locus_tag="IMQ30_RS23430"
                     /old_locus_tag="IMQ30_23450"
     CDS             2778..3059
                     /locus_tag="IMQ30_RS23430"
                     /old_locus_tag="IMQ30_23450"
                     /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(433..688)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(813..911)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1215..1297)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1310..1864
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.614"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggcagataca gtaaaggctc agttatctaa gtagtaataa acactatcaa tagtggttgg
       61 ataattgcca aaaaagcctc tatctgttct gaaacagaca acaaggaaaa atcggtgtaa
      121 gccacctcca taagaggtgg tattgatatc aacatagata aaaccatccc gtaaatcaca
      181 gcatttacca taacgtcgca ttacgcgcac cgctaaaacg cgctgaacgc gattctgccg
      241 caaacaccgc aaaaagagat gttttaccaa gcgaaaaccg gaaaaatgcg tcaggatcgc
      301 tttcagctca ctgcatagct atgcatgaaa gtgaatggcg atcggtttgg gcgcatacgg
      361 tgcccatgag acacattttc ggacattttc agttcgtgaa tccctgactc attgctacat
      421 atctgaacag acacccctag cagcgccccc aggggcgtcc tgtaaaaaaa cacaccgcgc
      481 cgctagcagc acccctaata taaaatgatg ttttttatga aaatagtcag taccacccct
      541 aaaaagcggt gttggcgcag ctacaacacc gcgccgacac cgctttttta aatatcacaa
      601 agagagcaag aagaactaat ttgtcataac tctctattta taaagaaaaa tcagcaaaaa
      661 attgtttttg cgtggggtgt gggcatttca ggcatgagaa cagactcgcg tttttccgga
      721 gtatcagcgg aattattgat taagaaacac tcgacgcaga gcgaaatttt atgcaacagc
      781 ggctgcactg cacagggatt atttatcagt tgatatgctg tgccatgata cgtcctaaaa
      841 aaacaggaca ggatgtgcaa ttgtaatacc gtcgcccgca acgtcttaca attaccacct
      901 ggtcagggtc cacccgacac ccggtactga cggagaacaa cggaaggtga acaaacagca
      961 acaaactgcg ctgaatatgg cgcgatttat caaaagccag agcctgacac tgcttgaaaa
     1021 actggatgct ctggatgccg acgaacaggc ggccatgtgc gaacgactgc acgaactcgc
     1081 ggaagaactc cagaacagca tccaggttcg ctttgagacc gaaagtgaaa caggaacata
     1141 acgaagctga cggaggcgct cacggcttgt ccgcgagcgt tttcggcagc agacaagccc
     1201 gccagggcgc gtcagcgggt gtcggggcga agccctgacc cagtcacgta gcgatagcgg
     1261 agtgtatact ggcttaacta tgcggcatca gtgcagattg tatgaaaagt gccccatgcc
     1321 gggtgtgaaa ttccgcacag atgcgtaagg agaaaatgcg cgtccaggcg cttttccgct
     1381 tcctcgctca ctgactcgct acgctcggtc gttcggctgc ggcgagcggt actgacttac
     1441 acaaaaacgg cagcacggtt atccacagaa tcaggggata aggccggaaa gaacatgtga
     1501 gcaaaagacc aagaacagga agaaggccgc gccgcaggcg tttttccata ggctccgccc
     1561 ccctgacgag catcacagaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact
     1621 taaagatacc agacgtttcc ccctggtggc tccctcgtgc gctctcctgt tccgaccctg
     1681 ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc
     1741 tcacgctgta ggtatctcgg ttcagtgtag gtcgttcgct ccaagctggg ctgtgtgcac
     1801 gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcatct tgagtccaac
     1861 ccggaaagac atgcaaaaca ccattggcag cagccactgg taactgattt agaggagtta
     1921 gtcttgaagt tatgcgccag ttaaggctaa actgaaagaa caagttttgg tgactgcgct
     1981 cctccaagcc agttaccctg gttcagaaac ttgccggtta ctgaaccttc gaaaaaacca
     2041 ccttgccggg tggttttttc gtttacgaga aacgatacga tccagttgcc tgagagtcaa
     2101 gacagaaaaa ggccgcatat agcggccttt tcttttctca aaatatagga accaattcat
     2161 ctaattcctt aatgacatta ggtgacttcc tgctcgcgtt aagactgtat tgagtctgca
     2221 tgtttatcca cgactcggca ctgcgaccaa gaactcgaga aagccttaat gccatctcaa
     2281 cacttaaatc agcttttcca ttcagcactc tacttagagt ggaaggtgat acatgcagtt
     2341 tttcagacag gtccgcggct gatatttcaa acggttccat aaacatctca cggataaaaa
     2401 cccctggatg tactggatcg acaagattaa tcataccttc ctctgaagcc tatattagtt
     2461 ttaaaaagat aggcctattg cgttttcaga ttgcgcattg cgcataacgc aactcattgt
     2521 tgactaaaaa aagaatgaca ttatgatgca cattggtgcg tctaatcatt ccttatgatg
     2581 tgggtacttg atgtgaaatt caaggccccg gcattgtaca gcgcatcaaa ccaatgtcaa
     2641 cagattaaaa tgcgacttgg ttaagtaaaa cctacgtcat ttattcaaat agagcaaggg
     2701 gtttgcaatg gaaatacgga tgaaccggaa aaataaactg cgatgtttct atctaaacaa
     2761 atatgggatg gtgattaatg atcataaata tcaagcataa aggtttgcgt aagtttgccg
     2821 aaacaggtaa caacgcagga attccgcaac agtttactca acgtctgaag ctgatcctaa
     2881 cagccttaag cacagcgacg aacttgcagg atatgatgga tttaaaggca ttgcgctgcc
     2941 atccattgaa gggagaccgt caaggagagt attcgttaga ggtcaatgga aactggcgcg
     3001 tagtgtttaa gctcgaagaa cctaacgtct ttgacgtgga tctcgaggat tatcactaag
     3061 aaggtcctta aagcatcaaa gtgacagtat cgatgcttta gggtctcata aaaaagcaaa
     3121 acctcggggt aagttatatg aagtattttc tgtaccagat agtccctata gcagccatca
     3181 tttgcgcagc aattctagcg ctaaaaggta tcaatggctg ggggtggttc ttaactgttg
     3241 ggttcctgct tgcagg
//
