LOCUS       NZ_CP062856             4593 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli O20:H12 strain Res13-Lact-PEB17-18 plasmid
            unnamed259, complete sequence.
ACCESSION   NZ_CP062856
VERSION     NZ_CP062856.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304208
            Assembly: GCF_015571715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O20:H12
  ORGANISM  Escherichia coli O20:H12
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4593)
  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  JOURNAL   Unpublished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 4593)
  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                     :: 17-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: 4E4-2
            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 13:24:39
            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)                     :: 5,101
            CDSs (total)                      :: 4,981
            Genes (coding)                    :: 4,791
            CDSs (with protein)               :: 4,791
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 190
            CDSs (without protein)            :: 190
            Pseudo Genes (ambiguous residues) :: 0 of 190
            Pseudo Genes (frameshifted)       :: 76 of 190
            Pseudo Genes (incomplete)         :: 118 of 190
            Pseudo Genes (internal stop)      :: 38 of 190
            Pseudo Genes (multiple problems)  :: 41 of 190
            Pseudo Genes (short protein)      :: 5 of 190
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062856.1.
            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..4593
                     /organism="Escherichia coli O20:H12"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-PEB17-18"
                     /serotype="O20:H12"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:2778656"
                     /plasmid="unnamed259"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-05-08"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            complement(673..1512)
                     /locus_tag="IMP99_RS24105"
                     /old_locus_tag="IMP99_24105"
     CDS             complement(673..1512)
                     /locus_tag="IMP99_RS24105"
                     /old_locus_tag="IMP99_24105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(2523..2714)
                     /locus_tag="IMP99_RS24110"
                     /old_locus_tag="IMP99_24110"
     CDS             complement(2523..2714)
                     /locus_tag="IMP99_RS24110"
                     /old_locus_tag="IMP99_24110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2777..3100
                     /locus_tag="IMP99_RS24115"
                     /old_locus_tag="IMP99_24115"
     CDS             2777..3100
                     /locus_tag="IMP99_RS24115"
                     /old_locus_tag="IMP99_24115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3309..>3743
                     /locus_tag="IMP99_RS25580"
                     /pseudo=""
     CDS             3309..>3743
                     /locus_tag="IMP99_RS25580"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3778..4338
                     /locus_tag="IMP99_RS24125"
                     /old_locus_tag="IMP99_24125"
     CDS             3778..4338
                     /locus_tag="IMP99_RS24125"
                     /old_locus_tag="IMP99_24125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            4345..4578
                     /locus_tag="IMP99_RS24130"
                     /old_locus_tag="IMP99_24130"
     CDS             4345..4578
                     /locus_tag="IMP99_RS24130"
                     /old_locus_tag="IMP99_24130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2351..2435
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(1782..2340)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3091..4592
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtcaggcgca ggagcttgcc cggcgctggc atgaagagca ggaacccgaa gcgcggatct
       61 ggcgtggccc gtcaatgggg atgtgaccgg ggtaccccct gaaatcgagc cagtttgtgg
      121 cacgccctac ccggatggcg ccaatgttaa tgtacgtaca ttagcattaa caatatccaa
      181 acctccccat tttgccccgt tcgacggctg gaacgtgcga aactgatcgt cattcagttt
      241 cgcgcataac tatgcatgag gttaaaattt accaggcgcg atcgcggcag tttttcgggt
      301 ggtttgttgc tgtttttacc tgtctgctgc cgtgatcgcg ctgaacgcgt ttaagcggta
      361 cgcgcaatgc gacgttatgg taaatacgga gtattttaat tgcgggcctt tgttgtatat
      421 ctctgtcgtt tgtccccggg gggaagcatt actgctaaca agtcccgtga gaaaactgcg
      481 caatcgtatt gcgcaccatg aacctattct caaccgcaat ctggaggatg attttgctac
      541 gataaagaga attatcgcgt atcggtgtca gcattcattg gagtggatgc tgaaaaacca
      601 ggtgttactc cctctactta cacttaaacc tctctaaaaa tataagtaag tactatcgag
      661 ggctatcatg aactatggtg ccctctgagc atagctaccc attacttctt ctatgtcatt
      721 gaataattca tttcttaact ctaagtattc tagtaactcc atttctaatg actctgtcgt
      781 gaacttaaat ctagaaggat ctttgattga gtttactagt cttgataacg ctctatatgt
      841 tttgagtgaa ggttgcatta tagatggaaa gtatttgaaa acctcttcat ctctgttgaa
      901 attaactaaa aacttgtagt catcatttat aaatctcaag catacagcgt caagcttatc
      961 gccttttctt attattattt ctttatagga aagatatttt tcagaagata agtcccacat
     1021 caagcgaaaa tctctctttg cgaacgagtt cgcgtcatca ttgaaaagag atgatgtgat
     1081 ggctttggat agaccttctg tgtttatctc tttgttggat gggtagtaaa ttttattaat
     1141 tgctttcatt ctctcaaatg atgaatatag gtcattatgc caccttgttg aaatcactcc
     1201 tttagttata ttctccttgc taaaattaag ccctgtatca aaaataaatg cagccatcag
     1261 tgaatatgat atgtttttta ttaactcaga cttaaatggt tccgctatgg agtagtacag
     1321 tgataaaata actaaaaata aaaggtattg tcttaccttt cccgatgagt atatgtaaag
     1381 gcgatattta tttattgata gttttatttt gtatggaatg atctcatttc tgtcatatcc
     1441 tcttcgtggt ggagcaaaac aaaagaaaca tgcagctatt aataaaacaa aaaagatgaa
     1501 cagtgtaagc aagttcggct cctgtgtatg ctcactatgc atgattgtct tgagatctaa
     1561 cgatcctgaa ggtagtcttg tccgtaaacg aaaaaaccgc ccagcaaggc ggcttttcga
     1621 aggttctcag agcagcaact ctttgaacca aggtaactgg cttggaggag cacagccacc
     1681 aaatctgtcc tttcagttta gccttaaccg gcgcataact tcaagactaa ctcctctaaa
     1741 cggttaccaa tggctgctgc cagtggcgtt tttacgtgtc tttccgggtt ggactcaaga
     1801 cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc
     1861 agcttggagc gaacgaccta caccgggccg agataccaac agcgtgagct atgagaaagc
     1921 gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca
     1981 ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg
     2041 tttcgccacc tctgacttga gcatctgttt ttgtgatgct cgtcaggggg gcggagccta
     2101 tggaaaaacg ccagcggcgc ggccttcttc ctgttcctgg ccttttgctc acatgtttct
     2161 tttggcgtta tcccctgatt ctgtggataa ccgcatcacc gtctttgagt gagctgatac
     2221 cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg
     2281 cctgatgcgg cattttctcc ttacgcatct gtgcggtatt tcacaccgca tatggtgcac
     2341 ttttcttata atccgcactg atgccacata gttaagccag tatacactcc gctatcgcta
     2401 cgtgactggg tcagggctgc gccccgacac ccgctaaaac ccgctgacgc gccctgacgg
     2461 gcttgtctgc tcccggcatc cgctcacagg caagctgtga acgtctccgg gagctgcatg
     2521 tttcagttgc tttcaccgtc atcgccgaag cgtgcgaggc aactacggta gagttcgtcg
     2581 gcgtggtcgt gaagtgattc gcagatgtct gcctgttcgt ccgcgtccag ctcgttgagt
     2641 ttttccagca gggtcagcgt ctggcttctg ataaagcggg ccatgttaag ggctgttttt
     2701 tcctgtttgg tcatggtctt aaggctcctt aataggggat tttttagggg gaatgatacc
     2761 gatgaaacgc gagaagatgc tcacgatacg ggttagcgat gaggagcacg cccggttact
     2821 ggaacgctgc gagggtaaac gactggcaga atggatgcgg cgggtctgtc tgggggagcc
     2881 ggttgcgcgc acaggaaaac tgccgacact atcgccgcca ttgctgcggc atctggctgc
     2941 catcgggaac aatctgaacc agacagcccg gaaggtgaac agcggccact ggtcttcgat
     3001 tgaccgggtt catgtggtgg ccgctctgat ggccatcgag ggtgaattgc gccagttgcg
     3061 gcaggctgtc agggaacagg ggggacggga tgatagttaa atttcatgcc agggggaaag
     3121 gcggtggaag tggcccggtc gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa
     3181 cggtgctccg gggtaacccg gaagaaatcc gggaactcat tgatgccacg ccattttcga
     3241 agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga gttaccgccg ggtgaacgcg
     3301 aaagagtgat gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa gaccagtaca
     3361 gcattctctg ggtggaacac caggataagg ggcggctcga actgaatttt gtcattccga
     3421 acatggaact acagagcggt aagcgcctcc agccgtacta cgaccgtgcg gacaggccga
     3481 ggataaatgc ctggcagacg ctggttaatc atcattacgg gctgcgtgac ccgaacgcac
     3541 cggagaacag acggacgctt gtcacaccga ataatctgcc aaaagcgaaa caggaggccg
     3601 cagaagcgat tacacggggt cttgaggcgc tttaccgtgc cggagcaata aaaacgcgtc
     3661 aggatgtcac tgaggcgctc acagcggcag gttttgaggt ggtgaggaca accagaagca
     3721 gtatcagtat tgccgacccg gagggggggc ggaatctcag gctaaagggg gcgctgtatg
     3781 agcaatcttt tacaaatggg aacggacttc gagaagaaac tgaaagagcg agccgcttct
     3841 accgagaaca tgctgaacag cgagttcagg aagctagaag agtctgtaga caaggcactg
     3901 agcttaaaca ggcagaaaat cagagacgct atcagcgaac atacaacatc cgtgaaacag
     3961 caactggata cgctgagcac caccgtgagc acgcagctca gcaccacaga ggccgaactg
     4021 tcccggcagc agaaaaacct gctctggcag gtgatcaaag ggcgggtact gtttccggcg
     4081 ctgaccgcgc tcagcgtcac gggcggcatt ttcctggggt gctgggggct gattcagtgg
     4141 caggaaagca ggattgcgaa aaatatcttg accatcagag agcaggaaaa cacgctggcg
     4201 aaactcgagg caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg
     4261 gtgctgccgg acggggtgaa aggggaaaac acctggacgg tgggcgacaa gaacgccgtg
     4321 aggctggtca gggagtaaac gagtatgacg gaactggaag ggcatttgct gaacgcctta
     4381 gagcatttgc aacaggacta tatgcggcgg ctgaacgagt gggagagcgc cttcgcagaa
     4441 ttgcagaaga tgcacgcggt tacgcaacag aacaacgcga tactgaacga gcgtgtcgtg
     4501 aacttgagtc agcaggtgca gctattagcc ggacaagtcg accgcttgag tcggttattt
     4561 atcacgaaca acagataagg gatgaacagg agc
//
