LOCUS       NZ_CP062886             3256 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PEA06-10 plasmid unnamed34,
            complete sequence.
ACCESSION   NZ_CP062886
VERSION     NZ_CP062886.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304175
            Assembly: GCF_015571775.1
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  JOURNAL   Unpublished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                     :: 21-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-32
            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 13:28:07
            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)                     :: 5,044
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,617
            CDSs (with protein)               :: 4,617
            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)         :: 226 of 305
            Pseudo Genes (internal stop)      :: 47 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
            CP062886.1.
            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-PEA06-10"
                     /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            complement(130..411)
                     /locus_tag="IMP66_RS23445"
                     /old_locus_tag="IMP66_23465"
     CDS             complement(130..411)
                     /locus_tag="IMP66_RS23445"
                     /old_locus_tag="IMP66_23465"
                     /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            755..1051
                     /locus_tag="IMP66_RS23450"
                     /old_locus_tag="IMP66_23470"
     CDS             755..1051
                     /locus_tag="IMP66_RS23450"
                     /old_locus_tag="IMP66_23470"
                     /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(2048..2242)
                     /locus_tag="IMP66_RS23455"
                     /old_locus_tag="IMP66_23475"
     CDS             complement(2048..2242)
                     /locus_tag="IMP66_RS23455"
                     /old_locus_tag="IMP66_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"
     Typing          1893..1975
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          2279..2377
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          2502..2757
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1323..1880)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.464"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgcgcaaatg atggctgcta tagggactat ctggtacaga aaatacttca tataacttac
       61 cccgaggttt tgctttttta tgagacccta aagcatcgat actgtcactt tgatgcttta
      121 aggaccttct tagtgataat cctcgagatc cacgtcaaag acgttaggtt cttcgagctt
      181 aaacactacg cgccagtttc cattgacctc taacgaatac tctccttgac ggtctccctt
      241 caatggatgg cagcgcaatg cctttaaatc catcatatcc tgcaagttcg tcgctgtgct
      301 taaggctgtt aggatcagct tcagacgttg agtaaactgt tgcggaattc ctgcgttgtt
      361 acctgtttcg gcaaacttac gcaaaccttt atgcttgata tttatgatca ttaatcacca
      421 tcccatattt gtttagatag aaacatcgca gtttattttt ccggttcatc cgtatttcca
      481 ttgcaaaccc cttgctctat ttgaataaat gacgtaggtt ttacttaacc aagtcgcatt
      541 ttaatctgtt gacattggtt tgatgcgctg tacaatgccg gggccttgaa tttcacatca
      601 agtacccaca tcataaggaa tgattagacg caccaatgtg catcataatg tcattctttt
      661 tttagtcaac aatgagttgc gttatgcgca atgcgcaatc tgaaaacgca ataggcctat
      721 ctttttaaaa ctaatatagg cttcagagga aggtatgatt aatcttgtcg atccagtaca
      781 tccaggggtt tttatccgtg agatgtttat ggaaccgttt gaaatatcag ccgcggacct
      841 gtctgaaaaa ctgcatgtat caccttccac tctaagtaga gtgctgaatg gaaaagctga
      901 tttaagtgtt gagatggcat taaggctttc tcgagttctt ggtcgcagtg ccgagtcgtg
      961 gataaacatg cagactcaat acagtcttaa cgcgagcagg aagtcaccta atgtcattaa
     1021 ggaattagat gaattggttc ctatattttg agaaaagaaa aggccgctat atgcggcctt
     1081 tttctgtctt gactctcagg caactggatc gtatcgtttc tcgtaaacga aaaaaccacc
     1141 cggcaaggtg gttttttcga aggttcagta accggcaagt ttctgaacca gggtaactgg
     1201 cttggaggag cgcagtcacc aaaacttgtt ctttcagttt agccttaact ggcgcataac
     1261 ttcaagacta actcctctaa atcagttacc agtggctgct gccaatggtg ttttgcatgt
     1321 ctttccgggt tggactcaag atgatagtta ccggataagg cgcagcggtc gggctgaacg
     1381 gggggttcgt gcacacagcc cagcttggag cgaacgacct acactgaacc gagataccta
     1441 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     1501 gtaagcggca gggtcggaac aggagagcgc acgagggagc caccaggggg aaacgtctgg
     1561 tatctttaag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ctgtgatgct
     1621 cgtcaggggg gcggagccta tggaaaaacg cctgcggcgc ggccttcttc ctgttcttgg
     1681 tcttttgctc acatgttctt tccggcctta tcccctgatt ctgtggataa ccgtgctgcc
     1741 gtttttgtgt aagtcagtac cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg
     1801 agcgaggaag cggaaaagcg cctggacgcg cattttctcc ttacgcatct gtgcggaatt
     1861 tcacacccgg catggggcac ttttcataca atctgcactg atgccgcata gttaagccag
     1921 tatacactcc gctatcgcta cgtgactggg tcagggcttc gccccgacac ccgctgacgc
     1981 gccctggcgg gcttgtctgc tgccgaaaac gctcgcggac aagccgtgag cgcctccgtc
     2041 agcttcgtta tgttcctgtt tcactttcgg tctcaaagcg aacctggatg ctgttctgga
     2101 gttcttccgc gagttcgtgc agtcgttcgc acatggccgc ctgttcgtcg gcatccagag
     2161 catccagttt ttcaagcagt gtcaggctct ggcttttgat aaatcgcgcc atattcagcg
     2221 cagtttgttg ctgtttgttc accttccgtt gttctccgtc agtaccgggt gtcgggtgga
     2281 ccctgaccag gtggtaattg taagacgttg cgggcgacgg tattacaatt gcacatcctg
     2341 tcctgttttt ttaggacgta tcatggcaca gcatatcaac tgataaataa tccctgtgca
     2401 gtgcagccgc tgttgcataa aatttcgctc tgcgtcgagt gtttcttaat caataattcc
     2461 gctgatactc cggaaaaacg cgagtctgtt ctcatgcctg aaatgcccac accccacgca
     2521 aaaacaattt tttgctgatt tttctttata aatagagagt tatgacaaat tagttcttct
     2581 tgctctcttt gtgatattta aaaaagcggt gtcggcgcgg tgttgtagct gcgccaacac
     2641 cgctttttag gggtggtact gactattttc ataaaaaaca tcattttata ttaggggtgc
     2701 tgctagcggc gcggtgtgtt tttttacagg acgcccctgg gggcgctgct aggggtgtct
     2761 gttcagatat gtagcaatga gtcagggatt cacgaactga aaatgtccga aaatgtgtct
     2821 catgggcacc gtatgcgccc aaaccgatcg ccattcactt tcatgcatag ctatgcagtg
     2881 agctgaaagc gatcctgacg catttttccg gttttcgctt ggtaaaacat ctctttttgc
     2941 ggtgtttgcg gcagaatcgc gttcagcgcg ttttagcggt gcgcgtaatg cgacgttatg
     3001 gtaaatgctg tgatttacgg gatggtttta tctatgttga tatcaatacc acctcttatg
     3061 gaggtggctt acaccgattt ttccttgttg tctgtttcag aacagataga ggcttttttg
     3121 gcaattatcc aaccactatt gatagtgttt attactactt agataactga gcctttactg
     3181 tatctgcccc tgcaagcagg aacccaacag ttaagaacca cccccagcca ttgatacctt
     3241 ttagcgctag aattgc
//
