LOCUS       NZ_CP062898             3256 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-ER02-39 plasmid unnamed34,
            complete sequence.
ACCESSION   NZ_CP062898
VERSION     NZ_CP062898.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304147
            Assembly: GCF_015571875.1
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  JOURNAL   Unpublished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                     :: 13-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-17
            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 14:40:58
            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)                     :: 5,033
            CDSs (total)                      :: 4,914
            Genes (coding)                    :: 4,610
            CDSs (with protein)               :: 4,610
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 304
            CDSs (without protein)            :: 304
            Pseudo Genes (ambiguous residues) :: 0 of 304
            Pseudo Genes (frameshifted)       :: 94 of 304
            Pseudo Genes (incomplete)         :: 226 of 304
            Pseudo Genes (internal stop)      :: 46 of 304
            Pseudo Genes (multiple problems)  :: 53 of 304
            Pseudo Genes (short protein)      :: 3 of 304
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062898.1.
            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-ER02-39"
                     /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            193..489
                     /locus_tag="IMP38_RS23405"
                     /old_locus_tag="IMP38_23425"
     CDS             193..489
                     /locus_tag="IMP38_RS23405"
                     /old_locus_tag="IMP38_23425"
                     /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            complement(1486..1680)
                     /locus_tag="IMP38_RS23410"
                     /old_locus_tag="IMP38_23430"
     CDS             complement(1486..1680)
                     /locus_tag="IMP38_RS23410"
                     /old_locus_tag="IMP38_23430"
                     /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(2824..3105)
                     /locus_tag="IMP38_RS23415"
                     /old_locus_tag="IMP38_23435"
     CDS             complement(2824..3105)
                     /locus_tag="IMP38_RS23415"
                     /old_locus_tag="IMP38_23435"
                     /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          1331..1413
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1717..1815
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1940..2195
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(761..1318)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.464"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcgctgta caatgccggg gccttgaatt tcacatcaag tacccacatc ataaggaatg
       61 attagacgca ccaatgtgca tcataatgtc attctttttt tagtcaacaa tgagttgcgt
      121 tatgcgcaat gcgcaatctg aaaacgcaat aggcctatct ttttaaaact aatataggct
      181 tcagaggaag gtatgattaa tcttgtcgat ccagtacatc caggggtttt tatccgtgag
      241 atgtttatgg aaccgtttga aatatcagcc gcggacctgt ctgaaaaact gcatgtatca
      301 ccttccactc taagtagagt gctgaatgga aaagctgatt taagtgttga gatggcatta
      361 aggctttctc gagttcttgg tcgcagtgcc gagtcgtgga taaacatgca gactcaatac
      421 agtcttaacg cgagcaggaa gtcacctaat gtcattaagg aattagatga attggttcct
      481 atattttgag aaaagaaaag gccgctatat gcggcctttt tctgtcttga ctctcaggca
      541 actggatcgt atcgtttctc gtaaacgaaa aaaccacccg gcaaggtggt tttttcgaag
      601 gttcagtaac cggcaagttt ctgaaccagg gtaactggct tggaggagcg cagtcaccaa
      661 aacttgttct ttcagtttag ccttaactgg cgcataactt caagactaac tcctctaaat
      721 cagttaccag tggctgctgc caatggtgtt ttgcatgtct ttccgggttg gactcaagat
      781 gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca
      841 gcttggagcg aacgacctac actgaaccga gatacctaca gcgtgagcta tgagaaagcg
      901 ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag
      961 gagagcgcac gagggagcca ccagggggaa acgtctggta tctttaagtc ctgtcgggtt
     1021 tcgccacctc tgacttgagc gtcgatttct gtgatgctcg tcaggggggc ggagcctatg
     1081 gaaaaacgcc tgcggcgcgg ccttcttcct gttcttggtc ttttgctcac atgttctttc
     1141 cggccttatc ccctgattct gtggataacc gtgctgccgt ttttgtgtaa gtcagtaccg
     1201 ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaaaagcgcc
     1261 tggacgcgca ttttctcctt acgcatctgt gcggaatttc acacccggca tggggcactt
     1321 ttcatacaat ctgcactgat gccgcatagt taagccagta tacactccgc tatcgctacg
     1381 tgactgggtc agggcttcgc cccgacaccc gctgacgcgc cctggcgggc ttgtctgctg
     1441 ccgaaaacgc tcgcggacaa gccgtgagcg cctccgtcag cttcgttatg ttcctgtttc
     1501 actttcggtc tcaaagcgaa cctggatgct gttctggagt tcttccgcga gttcgtgcag
     1561 tcgttcgcac atggccgcct gttcgtcggc atccagagca tccagttttt caagcagtgt
     1621 caggctctgg cttttgataa atcgcgccat attcagcgca gtttgttgct gtttgttcac
     1681 cttccgttgt tctccgtcag taccgggtgt cgggtggacc ctgaccaggt ggtaattgta
     1741 agacgttgcg ggcgacggta ttacaattgc acatcctgtc ctgttttttt aggacgtatc
     1801 atggcacagc atatcaactg ataaataatc cctgtgcagt gcagccgctg ttgcataaaa
     1861 tttcgctctg cgtcgagtgt ttcttaatca ataattccgc tgatactccg gaaaaacgcg
     1921 agtctgttct catgcctgaa atgcccacac cccacgcaaa aacaattttt tgctgatttt
     1981 tctttataaa tagagagtta tgacaaatta gttcttcttg ctctctttgt gatatttaaa
     2041 aaagcggtgt cggcgcggtg ttgtagctgc gccaacaccg ctttttaggg gtggtactga
     2101 ctattttcat aaaaaacatc attttatatt aggggtgctg ctagcggcgc ggtgtgtttt
     2161 tttacaggac gcccctgggg gcgctgctag gggtgtctgt tcagatatgt agcaatgagt
     2221 cagggattca cgaactgaaa atgtccgaaa atgtgtctca tgggcaccgt atgcgcccaa
     2281 accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga tcctgacgca
     2341 tttttccggt tttcgcttgg taaaacatct ctttttgcgg tgtttgcggc agaatcgcgt
     2401 tcagcgcgtt ttagcggtgc gcgtaatgcg acgttatggt aaatgctgtg atttacggga
     2461 tggttttatc tatgttgata tcaataccac ctcttatgga ggtggcttac accgattttt
     2521 ccttgttgtc tgtttcagaa cagatagagg cttttttggc aattatccaa ccactattga
     2581 tagtgtttat tactacttag ataactgagc ctttactgta tctgcccctg caagcaggaa
     2641 cccaacagtt aagaaccacc cccagccatt gatacctttt agcgctagaa ttgctgcgca
     2701 aatgatggct gctataggga ctatctggta cagaaaatac ttcatataac ttaccccgag
     2761 gttttgcttt tttatgagac cctaaagcat cgatactgtc actttgatgc tttaaggacc
     2821 ttcttagtga taatcctcga gatccacgtc aaagacgtta ggttcttcga gcttaaacac
     2881 tacgcgccag tttccattga cctctaacga atactctcct tgacggtctc ccttcaatgg
     2941 atggcagcgc aatgccttta aatccatcat atcctgcaag ttcgtcgctg tgcttaaggc
     3001 tgttaggatc agcttcagac gttgagtaaa ctgttgcgga attcctgcgt tgttacctgt
     3061 ttcggcaaac ttacgcaaac ctttatgctt gatatttatg atcattaatc accatcccat
     3121 atttgtttag atagaaacat cgcagtttat ttttccggtt catccgtatt tccattgcaa
     3181 accccttgct ctatttgaat aaatgacgta ggttttactt aaccaagtcg cattttaatc
     3241 tgttgacatt ggtttg
//
