LOCUS       NZ_CP062906             4067 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-EB12-05 plasmid unnamed471,
            complete sequence.
ACCESSION   NZ_CP062906
VERSION     NZ_CP062906.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304132
            Assembly: GCF_015571955.1
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  JOURNAL   Unpublished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-7
            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 14:44:38
            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)                     :: 4,902
            CDSs (total)                      :: 4,782
            Genes (coding)                    :: 4,552
            CDSs (with protein)               :: 4,552
            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)              :: 230
            CDSs (without protein)            :: 230
            Pseudo Genes (ambiguous residues) :: 0 of 230
            Pseudo Genes (frameshifted)       :: 63 of 230
            Pseudo Genes (incomplete)         :: 152 of 230
            Pseudo Genes (internal stop)      :: 47 of 230
            Pseudo Genes (multiple problems)  :: 33 of 230
            Pseudo Genes (short protein)      :: 4 of 230
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062906.1.
            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-EB12-05"
                     /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            join(3556..4067,1..1642)
                     /gene="mobQ"
                     /locus_tag="IMP23_RS00540"
                     /old_locus_tag="IMP23_00540"
     CDS             join(3556..4067,1..1642)
                     /gene="mobQ"
                     /locus_tag="IMP23_RS00540"
                     /old_locus_tag="IMP23_00540"
                     /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"
     gene            complement(1885..2592)
                     /locus_tag="IMP23_RS00545"
                     /old_locus_tag="IMP23_00545"
     CDS             complement(1885..2592)
                     /locus_tag="IMP23_RS00545"
                     /old_locus_tag="IMP23_00545"
                     /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(3126..3377)
                     /gene="mobC"
                     /locus_tag="IMP23_RS00550"
                     /old_locus_tag="IMP23_00550"
     CDS             complement(3126..3377)
                     /gene="mobC"
                     /locus_tag="IMP23_RS00550"
                     /old_locus_tag="IMP23_00550"
                     /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"
     Typing          complement(3382..3555)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="98.0"
                     /evalue="2.6299999999999998e-81"
     Typing          3556..3914
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          complement(1886..2592)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1633
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.263"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3470..4065
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.99"
                     /coverage="99.0"
                     /evalue="4.08e-124"
ORIGIN
        1 tgcaaacagg gcactggcga acgccggtta tcaggaagag atagaccatc gttcatacga
       61 gcgacagggg cttgagaaaa cgcctggtat tcacctcgga aagtctgcct gtgcgatgga
      121 aacacgcggt atcgaaacag aacgcggcga acagaatcgt ctgattaaca ggcttaacct
      181 ggaaatacag atttcccgca ccgaactcag gaacagcggg ctgacagagc ctgcccgccg
      241 tgtggctgac cttctgaata tcgggcttcc tgacaacgca acttcgtaca cactacgtga
      301 catcatcgaa gcgttgccgg aggacagtaa cgcggcatgg aaactcacca gtaacgccat
      361 gtcgatgatg gcagatatgc aggcgacgcg cagacgctgg gaagagctga acaccgaacg
      421 aaaggaagcg atgagccatg ctgccagcct gaaaaaatca tcgccgtttt cgtccggttt
      481 ttcccgtatt cccctgatgc aatgggctgc accggaatac cgtagtgagc agggaaaaat
      541 ccagtctctg agccagcaaa tggaaaaatt gcgacagcat taccggaagg tggagaaaca
      601 ggacattccc gcgagtcaga cggcatttga aaaacagtgg cagcagtggg gggaatccgg
      661 ccttgcagct ctcagatccc agttgcttaa acgtgaagag gaattgcgcc ggaaggagct
      721 ggaggataca gaacgtagtc gcgcggagca gctcagaaaa aatgacaatg ccgttatgga
      781 ttcaggggtg ctgagagcag tcgttacggg gtatggcgag gctcccatgc ctggtaacgg
      841 ggaaatgacc tgttaccttc tgcttcacaa ccggaacgga gaatatacgc tctgggggaa
      901 cgagctggag aaataccgca ccaggatctt tgagagtgtt gatttaatgc gtgacaggag
      961 tggttatatc tgtgaccgaa gcgaaatcgg tcaacatcca ccactgcaac gtgtttattc
     1021 ctctgcgacc tttgagcaac ttctgacgca ggtttgccag acatggccgc aacatacccg
     1081 caatctccgc caaccgaaga catggccgga gtctttctgt cttggagaag accgccagcc
     1141 agccatgcca tcactggcag caaggaaggt ggattttacg cagggacgtc tgccaccgac
     1201 gctgatgccg gtcatgagtt ctgtcgaccg ggaaacccgc cagcttcagc ttttgctggt
     1261 catgggcgtg gatgactctc tgggcggtgt tgtccggctt aatggtacgc tgtatcccgc
     1321 gtttgccgtt ccctcagccg ataacagcca gctggtcatc agtgcactga ccgataaggg
     1381 gttacggtat gcagggtatg gtgttgccgt aaatcacgat gcagacagcc acatatcacc
     1441 tgcgccggaa cttatggagt ttcatctgaa aacccgtgag gcaccgcttt ttgctgtcgt
     1501 caacacacca gaaaaacagc cggatcatct gttccgctcg ctgggtttca atcgtacctg
     1561 ggacgaatgg cggcgcgagg aagatgcacg aacacacgcc accgagagga gacctgatcg
     1621 cggttggtca cagggaatgt gaacaatatt ttgttttgtt taacatcgtg ttatgttcgt
     1681 cgatgttcat cgacagggat gaatgcaaga agcacactca catagcgcaa acatagtttt
     1741 gtttttccgc ccccaaaaat tgggggttct tttttttgct gcatcagagc gtttttgacg
     1801 caacttttca cttcaatagt accttcgcat tcctgacaca agaaaaacgc gacagtgagc
     1861 gttttaggtg ccttaaaatc gattctagat cgtcatcttg atctgtttgt cttccttgaa
     1921 gcgaaaatgc agggctacaa ccgtgcgccc ctttttgatc gtctcaaccg ttacagccag
     1981 gtcgcttttt ttgttcagtt cgtcaacaca gggttttatt agatccctgt ttaacgtttt
     2041 gaaatcttta tatttaccat caagcatcag tgatgattta aaatcatcga gggcgataat
     2101 acgttcccca gtactgcgga attgctggag aatttcgtat attcttatgc tgtaacttct
     2161 tgataaatta gaaatatttt taatgacgac tctggtgaat tgccccttca actgtgtcag
     2221 ataaggcatt accgcgtcag aaaaagtgat ttgtgctttc ccctctcccc tcgcgtactg
     2281 tgcccgatac tgaatccagc ggaactcctc gcgcttctcg tcgtccttga gaatgatcga
     2341 cctgtcccac aaacgatcga tcgcttcctg tagctgaacc tcggcatttt tccgccccat
     2401 atcagggaat gaatcaaaat attccgcagc tgtaatggtc attgtctttt gcaattcagg
     2461 tgaagctacg tcagtaccgg agttaagtcg gcttatgcag agcaataaga aacgctgttc
     2521 ttgtaaagtt agcttgtaac tggcctcaac cagcgcattg gacttatagg ctatcagagg
     2581 gtttgatgtc attttaacca ccaggccaaa aatgaggtga aataaaaacc tatcaccttt
     2641 agcattggtg agcaattata ttttcacccc ccattttcct gtgaatatta ccttaaatct
     2701 cctcaccttt accttaaatt acctcaccca agcaccttaa attatatcac ctttacctta
     2761 aattccccca cctatgcacg tgtaacgcat tgtttttaat caggaatttc gaccctaaaa
     2821 caagtattaa aaacaagatc ttaaaaacaa gatctaaaaa cttaacggcg agcctgtgga
     2881 taacttgggg tgctgaaaat aaaaatcaaa taaaaacaat gtattgcaaa aaatcaggat
     2941 tgaaaattcc gaatacaccc cctccaaccc tgtggaaatc cagtattcat gcgggttcag
     3001 cgcatatcac ctgtcgaaaa accgtgcgta tgtgctcaac ctggcgactg attcacttcc
     3061 gcttcctcgc ccactcgctc gctaacgttc ggtcgctggg ctgcggcgag cggacgatac
     3121 aatcactact ctggcagcgc ctccagctcg ttaatcagcg gcagtattcg cgtcacatca
     3181 gcctgccgtg tcacctctgc cttcaggaac tggagtaacc aagctcgcaa ctgcacttcc
     3241 tccggctttc tgacctttgc cagcaatgct gcacccacaa tgaccttctg cgctgtgtcc
     3301 aggctccggc tcttcgcctt caggcgctgt aatctggcct cagcttcggc aatcttctgt
     3361 tcgagtgttc tgctcatttc gtgactccgt gcgcggtgaa aaatcgcatt ttagcgcgtc
     3421 actggtagtt taaaaactga gctggcataa tgcacggcaa atcacgaagt gcgcacttat
     3481 acaatctcca ctccgtttcg attgtgtgcg ccctgcgggg ctgaaagaaa actgcaaaaa
     3541 ggcattacgg cagaaatggc gatttatcat ctcagtatga aaatcatctc cagaagcaac
     3601 ggctacagcg ccgttgcttc tgctgcctat cgttctggtt cactaatgct tgatgagcgt
     3661 accggactga ctcacgacta cacccgcaaa agcggtgtgg ctgaggctgt gattctgacc
     3721 cccgcgacag cccctgcctg gtgtacgaac cgtgccgaac tctggaatgc cgttgagaag
     3781 gccgaacgcc ggaagaactc acaacttgcg cgggaaattg aactcgctat cccccgtgaa
     3841 ctgccgcagg atgccgcacg ggaaaccgtt ctcgcctttg tcagagaaaa ctttgtcagt
     3901 cagggcatga ttgctgatgt ggcgttccat cacatggata aaacaaatcc ccatgcgcac
     3961 atcatgctga ccacgagggc tgtcggacct gctgggttcg gcggaaaggt cagggactgg
     4021 aacgaccgga cacatgccga gacgtggcgt gcatcatggg ctgacca
//
