LOCUS       NZ_CP062818             3256 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Sevr-PER06-05-b-A plasmid unnamed34,
            complete sequence.
ACCESSION   NZ_CP062818
VERSION     NZ_CP062818.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304267
            Assembly: GCF_015571555.1
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  JOURNAL   Unpublished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                     :: 29-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-28-H
            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 15:40:21
            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)                     :: 5,038
            CDSs (total)                      :: 4,916
            Genes (coding)                    :: 4,613
            CDSs (with protein)               :: 4,613
            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)       :: 94 of 303
            Pseudo Genes (incomplete)         :: 225 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
            CP062818.1.
            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-Sevr-PER06-05-b-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="2017-04-11"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            join(3103..3256,1..128)
                     /locus_tag="IMQ58_RS23435"
                     /old_locus_tag="IMQ58_23455"
     CDS             join(3103..3256,1..128)
                     /locus_tag="IMQ58_RS23435"
                     /old_locus_tag="IMQ58_23455"
                     /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"
     gene            1272..1466
                     /locus_tag="IMQ58_RS23440"
                     /old_locus_tag="IMQ58_23460"
     CDS             1272..1466
                     /locus_tag="IMQ58_RS23440"
                     /old_locus_tag="IMQ58_23460"
                     /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(2463..2759)
                     /locus_tag="IMQ58_RS23445"
                     /old_locus_tag="IMQ58_23465"
     CDS             complement(2463..2759)
                     /locus_tag="IMQ58_RS23445"
                     /old_locus_tag="IMQ58_23465"
                     /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"
     Typing          complement(758..1013)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1138..1236)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1540..1622)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1635..2189
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.614"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgcgctgcca tccattgaag ggagaccgtc aaggagagta ttcgttagag gtcaatggaa
       61 actggcgcgt agtgtttaag ctcgaagaac ctaacgtctt tgacgtggat ctcgaggatt
      121 atcactaaga aggtccttaa agcatcaaag tgacagtatc gatgctttag ggtctcataa
      181 aaaagcaaaa cctcggggta agttatatga agtattttct gtaccagata gtccctatag
      241 cagccatcat ttgcgcagca attctagcgc taaaaggtat caatggctgg gggtggttct
      301 taactgttgg gttcctgctt gcaggggcag atacagtaaa ggctcagtta tctaagtagt
      361 aataaacact atcaatagtg gttggataat tgccaaaaaa gcctctatct gttctgaaac
      421 agacaacaag gaaaaatcgg tgtaagccac ctccataaga ggtggtattg atatcaacat
      481 agataaaacc atcccgtaaa tcacagcatt taccataacg tcgcattacg cgcaccgcta
      541 aaacgcgctg aacgcgattc tgccgcaaac accgcaaaaa gagatgtttt accaagcgaa
      601 aaccggaaaa atgcgtcagg atcgctttca gctcactgca tagctatgca tgaaagtgaa
      661 tggcgatcgg tttgggcgca tacggtgccc atgagacaca ttttcggaca ttttcagttc
      721 gtgaatccct gactcattgc tacatatctg aacagacacc cctagcagcg cccccagggg
      781 cgtcctgtaa aaaaacacac cgcgccgcta gcagcacccc taatataaaa tgatgttttt
      841 tatgaaaata gtcagtacca cccctaaaaa gcggtgttgg cgcagctaca acaccgcgcc
      901 gacaccgctt ttttaaatat cacaaagaga gcaagaagaa ctaatttgtc ataactctct
      961 atttataaag aaaaatcagc aaaaaattgt ttttgcgtgg ggtgtgggca tttcaggcat
     1021 gagaacagac tcgcgttttt ccggagtatc agcggaatta ttgattaaga aacactcgac
     1081 gcagagcgaa attttatgca acagcggctg cactgcacag ggattattta tcagttgata
     1141 tgctgtgcca tgatacgtcc taaaaaaaca ggacaggatg tgcaattgta ataccgtcgc
     1201 ccgcaacgtc ttacaattac cacctggtca gggtccaccc gacacccggt actgacggag
     1261 aacaacggaa ggtgaacaaa cagcaacaaa ctgcgctgaa tatggcgcga tttatcaaaa
     1321 gccagagcct gacactgctt gaaaaactgg atgctctgga tgccgacgaa caggcggcca
     1381 tgtgcgaacg actgcacgaa ctcgcggaag aactccagaa cagcatccag gttcgctttg
     1441 agaccgaaag tgaaacagga acataacgaa gctgacggag gcgctcacgg cttgtccgcg
     1501 agcgttttcg gcagcagaca agcccgccag ggcgcgtcag cgggtgtcgg ggcgaagccc
     1561 tgacccagtc acgtagcgat agcggagtgt atactggctt aactatgcgg catcagtgca
     1621 gattgtatga aaagtgcccc atgccgggtg tgaaattccg cacagatgcg taaggagaaa
     1681 atgcgcgtcc aggcgctttt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg
     1741 gctgcggcga gcggtactga cttacacaaa aacggcagca cggttatcca cagaatcagg
     1801 ggataaggcc ggaaagaaca tgtgagcaaa agaccaagaa caggaagaag gccgcgccgc
     1861 aggcgttttt ccataggctc cgcccccctg acgagcatca cagaaatcga cgctcaagtc
     1921 agaggtggcg aaacccgaca ggacttaaag ataccagacg tttccccctg gtggctccct
     1981 cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct ttctcccttc
     2041 gggaagcgtg gcgctttctc atagctcacg ctgtaggtat ctcggttcag tgtaggtcgt
     2101 tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct gcgccttatc
     2161 cggtaactat catcttgagt ccaacccgga aagacatgca aaacaccatt ggcagcagcc
     2221 actggtaact gatttagagg agttagtctt gaagttatgc gccagttaag gctaaactga
     2281 aagaacaagt tttggtgact gcgctcctcc aagccagtta ccctggttca gaaacttgcc
     2341 ggttactgaa ccttcgaaaa aaccaccttg ccgggtggtt ttttcgttta cgagaaacga
     2401 tacgatccag ttgcctgaga gtcaagacag aaaaaggccg catatagcgg ccttttcttt
     2461 tctcaaaata taggaaccaa ttcatctaat tccttaatga cattaggtga cttcctgctc
     2521 gcgttaagac tgtattgagt ctgcatgttt atccacgact cggcactgcg accaagaact
     2581 cgagaaagcc ttaatgccat ctcaacactt aaatcagctt ttccattcag cactctactt
     2641 agagtggaag gtgatacatg cagtttttca gacaggtccg cggctgatat ttcaaacggt
     2701 tccataaaca tctcacggat aaaaacccct ggatgtactg gatcgacaag attaatcata
     2761 ccttcctctg aagcctatat tagttttaaa aagataggcc tattgcgttt tcagattgcg
     2821 cattgcgcat aacgcaactc attgttgact aaaaaaagaa tgacattatg atgcacattg
     2881 gtgcgtctaa tcattcctta tgatgtgggt acttgatgtg aaattcaagg ccccggcatt
     2941 gtacagcgca tcaaaccaat gtcaacagat taaaatgcga cttggttaag taaaacctac
     3001 gtcatttatt caaatagagc aaggggtttg caatggaaat acggatgaac cggaaaaata
     3061 aactgcgatg tttctatcta aacaaatatg ggatggtgat taatgatcat aaatatcaag
     3121 cataaaggtt tgcgtaagtt tgccgaaaca ggtaacaacg caggaattcc gcaacagttt
     3181 actcaacgtc tgaagctgat cctaacagcc ttaagcacag cgacgaactt gcaggatatg
     3241 atggatttaa aggcat
//
