LOCUS       NZ_CP062835             3256 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PER04-33 plasmid unnamed34,
            complete sequence.
ACCESSION   NZ_CP062835
VERSION     NZ_CP062835.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304231
            Assembly: GCF_015571635.1
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  JOURNAL   Unpublished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                     :: 30-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-22-B
            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 15:44:03
            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)                     :: 5,036
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            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)              :: 312
            CDSs (without protein)            :: 312
            Pseudo Genes (ambiguous residues) :: 0 of 312
            Pseudo Genes (frameshifted)       :: 98 of 312
            Pseudo Genes (incomplete)         :: 228 of 312
            Pseudo Genes (internal stop)      :: 49 of 312
            Pseudo Genes (multiple problems)  :: 54 of 312
            Pseudo Genes (short protein)      :: 3 of 312
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062835.1.
            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-PER04-33"
                     /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            293..487
                     /locus_tag="IMQ22_RS23380"
                     /old_locus_tag="IMQ22_23400"
     CDS             293..487
                     /locus_tag="IMQ22_RS23380"
                     /old_locus_tag="IMQ22_23400"
                     /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(1484..1780)
                     /locus_tag="IMQ22_RS23385"
                     /old_locus_tag="IMQ22_23405"
     CDS             complement(1484..1780)
                     /locus_tag="IMQ22_RS23385"
                     /old_locus_tag="IMQ22_23405"
                     /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            2124..2405
                     /locus_tag="IMQ22_RS23390"
                     /old_locus_tag="IMQ22_23410"
     CDS             2124..2405
                     /locus_tag="IMQ22_RS23390"
                     /old_locus_tag="IMQ22_23410"
                     /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(159..257)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(561..643)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          656..1210
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.614"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 caaaaaattg tttttgcgtg gggtgtgggc atttcaggca tgagaacaga ctcgcgtttt
       61 tccggagtat cagcggaatt attgattaag aaacactcga cgcagagcga aattttatgc
      121 aacagcggct gcactgcaca gggattattt atcagttgat atgctgtgcc atgatacgtc
      181 ctaaaaaaac aggacaggat gtgcaattgt aataccgtcg cccgcaacgt cttacaatta
      241 ccacctggtc agggtccacc cgacacccgg tactgacgga gaacaacgga aggtgaacaa
      301 acagcaacaa actgcgctga atatggcgcg atttatcaaa agccagagcc tgacactgct
      361 tgaaaaactg gatgctctgg atgccgacga acaggcggcc atgtgcgaac gactgcacga
      421 actcgcggaa gaactccaga acagcatcca ggttcgcttt gagaccgaaa gtgaaacagg
      481 aacataacga agctgacgga ggcgctcacg gcttgtccgc gagcgttttc ggcagcagac
      541 aagcccgcca gggcgcgtca gcgggtgtcg gggcgaagcc ctgacccagt cacgtagcga
      601 tagcggagtg tatactggct taactatgcg gcatcagtgc agattgtatg aaaagtgccc
      661 catgccgggt gtgaaattcc gcacagatgc gtaaggagaa aatgcgcgtc caggcgcttt
      721 tccgcttcct cgctcactga ctcgctacgc tcggtcgttc ggctgcggcg agcggtactg
      781 acttacacaa aaacggcagc acggttatcc acagaatcag gggataaggc cggaaagaac
      841 atgtgagcaa aagaccaaga acaggaagaa ggccgcgccg caggcgtttt tccataggct
      901 ccgcccccct gacgagcatc acagaaatcg acgctcaagt cagaggtggc gaaacccgac
      961 aggacttaaa gataccagac gtttccccct ggtggctccc tcgtgcgctc tcctgttccg
     1021 accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct
     1081 catagctcac gctgtaggta tctcggttca gtgtaggtcg ttcgctccaa gctgggctgt
     1141 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcatcttgag
     1201 tccaacccgg aaagacatgc aaaacaccat tggcagcagc cactggtaac tgatttagag
     1261 gagttagtct tgaagttatg cgccagttaa ggctaaactg aaagaacaag ttttggtgac
     1321 tgcgctcctc caagccagtt accctggttc agaaacttgc cggttactga accttcgaaa
     1381 aaaccacctt gccgggtggt tttttcgttt acgagaaacg atacgatcca gttgcctgag
     1441 agtcaagaca gaaaaaggcc gcatatagcg gccttttctt ttctcaaaat ataggaacca
     1501 attcatctaa ttccttaatg acattaggtg acttcctgct cgcgttaaga ctgtattgag
     1561 tctgcatgtt tatccacgac tcggcactgc gaccaagaac tcgagaaagc cttaatgcca
     1621 tctcaacact taaatcagct tttccattca gcactctact tagagtggaa ggtgatacat
     1681 gcagtttttc agacaggtcc gcggctgata tttcaaacgg ttccataaac atctcacgga
     1741 taaaaacccc tggatgtact ggatcgacaa gattaatcat accttcctct gaagcctata
     1801 ttagttttaa aaagataggc ctattgcgtt ttcagattgc gcattgcgca taacgcaact
     1861 cattgttgac taaaaaaaga atgacattat gatgcacatt ggtgcgtcta atcattcctt
     1921 atgatgtggg tacttgatgt gaaattcaag gccccggcat tgtacagcgc atcaaaccaa
     1981 tgtcaacaga ttaaaatgcg acttggttaa gtaaaaccta cgtcatttat tcaaatagag
     2041 caaggggttt gcaatggaaa tacggatgaa ccggaaaaat aaactgcgat gtttctatct
     2101 aaacaaatat gggatggtga ttaatgatca taaatatcaa gcataaaggt ttgcgtaagt
     2161 ttgccgaaac aggtaacaac gcaggaattc cgcaacagtt tactcaacgt ctgaagctga
     2221 tcctaacagc cttaagcaca gcgacgaact tgcaggatat gatggattta aaggcattgc
     2281 gctgccatcc attgaaggga gaccgtcaag gagagtattc gttagaggtc aatggaaact
     2341 ggcgcgtagt gtttaagctc gaagaaccta acgtctttga cgtggatctc gaggattatc
     2401 actaagaagg tccttaaagc atcaaagtga cagtatcgat gctttagggt ctcataaaaa
     2461 agcaaaacct cggggtaagt tatatgaagt attttctgta ccagatagtc cctatagcag
     2521 ccatcatttg cgcagcaatt ctagcgctaa aaggtatcaa tggctggggg tggttcttaa
     2581 ctgttgggtt cctgcttgca ggggcagata cagtaaaggc tcagttatct aagtagtaat
     2641 aaacactatc aatagtggtt ggataattgc caaaaaagcc tctatctgtt ctgaaacaga
     2701 caacaaggaa aaatcggtgt aagccacctc cataagaggt ggtattgata tcaacataga
     2761 taaaaccatc ccgtaaatca cagcatttac cataacgtcg cattacgcgc accgctaaaa
     2821 cgcgctgaac gcgattctgc cgcaaacacc gcaaaaagag atgttttacc aagcgaaaac
     2881 cggaaaaatg cgtcaggatc gctttcagct cactgcatag ctatgcatga aagtgaatgg
     2941 cgatcggttt gggcgcatac ggtgcccatg agacacattt tcggacattt tcagttcgtg
     3001 aatccctgac tcattgctac atatctgaac agacacccct agcagcgccc ccaggggcgt
     3061 cctgtaaaaa aacacaccgc gccgctagca gcacccctaa tataaaatga tgttttttat
     3121 gaaaatagtc agtaccaccc ctaaaaagcg gtgttggcgc agctacaaca ccgcgccgac
     3181 accgcttttt taaatatcac aaagagagca agaagaacta atttgtcata actctctatt
     3241 tataaagaaa aatcag
//
