LOCUS       NZ_CP062861             4067 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PEB14-36 plasmid unnamed471,
            complete sequence.
ACCESSION   NZ_CP062861
VERSION     NZ_CP062861.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304205
            Assembly: GCF_015571815.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4067)
  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  JOURNAL   Unpublished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 4067)
  AUTHORS   Poulin-Laprade,D. and Brouard,J.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-OCT-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-13
            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 15:47:59
            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)                     :: 4,899
            CDSs (total)                      :: 4,779
            Genes (coding)                    :: 4,550
            CDSs (with protein)               :: 4,550
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 63 of 229
            Pseudo Genes (incomplete)         :: 152 of 229
            Pseudo Genes (internal stop)      :: 46 of 229
            Pseudo Genes (multiple problems)  :: 33 of 229
            Pseudo Genes (short protein)      :: 4 of 229
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062861.1.
            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..4067
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-PEB14-36"
                     /serotype="O-untypeable:H11"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamed471"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-03-13"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            complement(33..740)
                     /locus_tag="IMP96_RS00540"
                     /old_locus_tag="IMP96_00540"
     CDS             complement(33..740)
                     /locus_tag="IMP96_RS00540"
                     /old_locus_tag="IMP96_00540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1274..1525)
                     /gene="mobC"
                     /locus_tag="IMP96_RS00545"
                     /old_locus_tag="IMP96_00545"
     CDS             complement(1274..1525)
                     /gene="mobC"
                     /locus_tag="IMP96_RS00545"
                     /old_locus_tag="IMP96_00545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091744.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_195714405.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPE"
                     /name="mobC"
     gene            1704..3857
                     /gene="mobQ"
                     /locus_tag="IMP96_RS00550"
                     /old_locus_tag="IMP96_00550"
     CDS             1704..3857
                     /gene="mobQ"
                     /locus_tag="IMP96_RS00550"
                     /old_locus_tag="IMP96_00550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029350.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPEDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     Typing          complement(1530..1703)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="98.0"
                     /evalue="2.6299999999999998e-81"
     Typing          1704..2062
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          complement(34..740)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1618..3848
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.46"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagtgagcgt tttaggtgcc ttaaaatcga ttctagatcg tcatcttgat ctgtttgtct
       61 tccttgaagc gaaaatgcag ggctacaacc gtgcgcccct ttttgatcgt ctcaaccgtt
      121 acagccaggt cgcttttttt gttcagttcg tcaacacagg gttttattag atccctgttt
      181 aacgttttga aatctttata tttaccatca agcatcagtg atgatttaaa atcatcgagg
      241 gcgataatac gttccccagt actgcggaat tgctggagaa tttcgtatat tcttatgctg
      301 taacttcttg ataaattaga aatattttta atgacgactc tggtgaattg ccccttcaac
      361 tgtgtcagat aaggcattac cgcgtcagaa aaagtgattt gtgctttccc ctctcccctc
      421 gcgtactgtg cccgatactg aatccagcgg aactcctcgc gcttctcgtc gtccttgaga
      481 atgatcgacc tgtcccacaa acgatcgatc gcttcctgta gctgaacctc ggcatttttc
      541 cgccccatat cagggaatga atcaaaatat tccgcagctg taatggtcat tgtcttttgc
      601 aattcaggtg aagctacgtc agtaccggag ttaagtcggc ttatgcagag caataagaaa
      661 cgctgttctt gtaaagttag cttgtaactg gcctcaacca gcgcattgga cttataggct
      721 atcagagggt ttgatgtcat tttaaccacc aggccaaaaa tgaggtgaaa taaaaaccta
      781 tcacctttag cattggtgag caattatatt ttcacccccc attttcctgt gaatattacc
      841 ttaaatctcc tcacctttac cttaaattac ctcacccaag caccttaaat tatatcacct
      901 ttaccttaaa ttcccccacc tatgcacgtg taacgcattg tttttaatca ggaatttcga
      961 ccctaaaaca agtattaaaa acaagatctt aaaaacaaga tctaaaaact taacggcgag
     1021 cctgtggata acttggggtg ctgaaaataa aaatcaaata aaaacaatgt attgcaaaaa
     1081 atcaggattg aaaattccga atacaccccc tccaaccctg tggaaatcca gtattcatgc
     1141 gggttcagcg catatcacct gtcgaaaaac cgtgcgtatg tgctcaacct ggcgactgat
     1201 tcacttccgc ttcctcgccc actcgctcgc taacgttcgg tcgctgggct gcggcgagcg
     1261 gacgatacaa tcactactct ggcagcgcct ccagctcgtt aatcagcggc agtattcgcg
     1321 tcacatcagc ctgccgtgtc acctctgcct tcaggaactg gagtaaccaa gctcgcaact
     1381 gcacttcctc cggctttctg acctttgcca gcaatgctgc acccacaatg accttctgcg
     1441 ctgtgtccag gctccggctc ttcgccttca ggcgctgtaa tctggcctca gcttcggcaa
     1501 tcttctgttc gagtgttctg ctcatttcgt gactccgtgc gcggtgaaaa atcgcatttt
     1561 agcgcgtcac tggtagttta aaaactgagc tggcataatg cacggcaaat cacgaagtgc
     1621 gcacttatac aatctccact ccgtttcgat tgtgtgcgcc ctgcggggct gaaagaaaac
     1681 tgcaaaaagg cattacggca gaaatggcga tttatcatct cagtatgaaa atcatctcca
     1741 gaagcaacgg ctacagcgcc gttgcttctg ctgcctatcg ttctggttca ctaatgcttg
     1801 atgagcgtac cggactgact cacgactaca cccgcaaaag cggtgtggct gaggctgtga
     1861 ttctgacccc cgcgacagcc cctgcctggt gtacgaaccg tgccgaactc tggaatgccg
     1921 ttgagaaggc cgaacgccgg aagaactcac aacttgcgcg ggaaattgaa ctcgctatcc
     1981 cccgtgaact gccgcaggat gccgcacggg aaaccgttct cgcctttgtc agagaaaact
     2041 ttgtcagtca gggcatgatt gctgatgtgg cgttccatca catggataaa acaaatcccc
     2101 atgcgcacat catgctgacc acgagggctg tcggacctgc tgggttcggc ggaaaggtca
     2161 gggactggaa cgaccggaca catgccgaga cgtggcgtgc atcatgggct gaccatgcaa
     2221 acagggcact ggcgaacgcc ggttatcagg aagagataga ccatcgttca tacgagcgac
     2281 aggggcttga gaaaacgcct ggtattcacc tcggaaagtc tgcctgtgcg atggaaacac
     2341 gcggtatcga aacagaacgc ggcgaacaga atcgtctgat taacaggctt aacctggaaa
     2401 tacagatttc ccgcaccgaa ctcaggaaca gcgggctgac agagcctgcc cgccgtgtgg
     2461 ctgaccttct gaatatcggg cttcctgaca acgcaacttc gtacacacta cgtgacatca
     2521 tcgaagcgtt gccggaggac agtaacgcgg catggaaact caccagtaac gccatgtcga
     2581 tgatggcaga tatgcaggcg acgcgcagac gctgggaaga gctgaacacc gaacgaaagg
     2641 aagcgatgag ccatgctgcc agcctgaaaa aatcatcgcc gttttcgtcc ggtttttccc
     2701 gtattcccct gatgcaatgg gctgcaccgg aataccgtag tgagcaggga aaaatccagt
     2761 ctctgagcca gcaaatggaa aaattgcgac agcattaccg gaaggtggag aaacaggaca
     2821 ttcccgcgag tcagacggca tttgaaaaac agtggcagca gtggggggaa tccggccttg
     2881 cagctctcag atcccagttg cttaaacgtg aagaggaatt gcgccggaag gagctggagg
     2941 atacagaacg tagtcgcgcg gagcagctca gaaaaaatga caatgccgtt atggattcag
     3001 gggtgctgag agcagtcgtt acggggtatg gcgaggctcc catgcctggt aacggggaaa
     3061 tgacctgtta ccttctgctt cacaaccgga acggagaata tacgctctgg gggaacgagc
     3121 tggagaaata ccgcaccagg atctttgaga gtgttgattt aatgcgtgac aggagtggtt
     3181 atatctgtga ccgaagcgaa atcggtcaac atccaccact gcaacgtgtt tattcctctg
     3241 cgacctttga gcaacttctg acgcaggttt gccagacatg gccgcaacat acccgcaatc
     3301 tccgccaacc gaagacatgg ccggagtctt tctgtcttgg agaagaccgc cagccagcca
     3361 tgccatcact ggcagcaagg aaggtggatt ttacgcaggg acgtctgcca ccgacgctga
     3421 tgccggtcat gagttctgtc gaccgggaaa cccgccagct tcagcttttg ctggtcatgg
     3481 gcgtggatga ctctctgggc ggtgttgtcc ggcttaatgg tacgctgtat cccgcgtttg
     3541 ccgttccctc agccgataac agccagctgg tcatcagtgc actgaccgat aaggggttac
     3601 ggtatgcagg gtatggtgtt gccgtaaatc acgatgcaga cagccacata tcacctgcgc
     3661 cggaacttat ggagtttcat ctgaaaaccc gtgaggcacc gctttttgct gtcgtcaaca
     3721 caccagaaaa acagccggat catctgttcc gctcgctggg tttcaatcgt acctgggacg
     3781 aatggcggcg cgaggaagat gcacgaacac acgccaccga gaggagacct gatcgcggtt
     3841 ggtcacaggg aatgtgaaca atattttgtt ttgtttaaca tcgtgttatg ttcgtcgatg
     3901 ttcatcgaca gggatgaatg caagaagcac actcacatag cgcaaacata gttttgtttt
     3961 tccgccccca aaaattgggg gttctttttt ttgctgcatc agagcgtttt tgacgcaact
     4021 tttcacttca atagtacctt cgcattcctg acacaagaaa aacgcga
//
