LOCUS       NZ_CP062840             3319 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PER02-33 plasmid unnamed14,
            complete sequence.
ACCESSION   NZ_CP062840
VERSION     NZ_CP062840.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304229
            Assembly: GCF_015571655.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3319)
  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  JOURNAL   Unpublished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 3319)
  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                     :: 27-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-19
            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 15:52:52
            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)                     :: 5,045
            CDSs (total)                      :: 4,923
            Genes (coding)                    :: 4,618
            CDSs (with protein)               :: 4,618
            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)         :: 227 of 305
            Pseudo Genes (internal stop)      :: 46 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
            CP062840.1.
            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..3319
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-PER02-33"
                     /serotype="O-untypeable:H4"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamed14"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-03-20"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            complement(117..311)
                     /locus_tag="IMQ20_RS23435"
                     /old_locus_tag="IMQ20_23455"
     CDS             complement(117..311)
                     /locus_tag="IMQ20_RS23435"
                     /old_locus_tag="IMQ20_23455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            595..918
                     /gene="mobA"
                     /locus_tag="IMQ20_RS23440"
                     /old_locus_tag="IMQ20_23460"
     CDS             595..918
                     /gene="mobA"
                     /locus_tag="IMQ20_RS23440"
                     /old_locus_tag="IMQ20_23460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1153..1533)
                     /gene="lsoB"
                     /locus_tag="IMQ20_RS23445"
                     /old_locus_tag="IMQ20_23465"
     CDS             complement(1153..1533)
                     /gene="lsoB"
                     /locus_tag="IMQ20_RS23445"
                     /old_locus_tag="IMQ20_23465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /protein_id="WP_000710826.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(1530..2570)
                     /gene="lsoA"
                     /locus_tag="IMQ20_RS23450"
                     /old_locus_tag="IMQ20_23470"
     CDS             complement(1530..2570)
                     /gene="lsoA"
                     /locus_tag="IMQ20_RS23450"
                     /old_locus_tag="IMQ20_23470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /protein_id="WP_000068433.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     Typing          347..586
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(2877..3319)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.526"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          596..915
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.54e-62"
ORIGIN
        1 cgccgcagtc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agagcgtctg
       61 acgtggcatt ttctccttac gctccgctat gccgttctgc atcctgtccg ggtgcgttat
      121 atcccggtgc gattttccgc ttcaaagcgt gtctgtatgc tgttctgaag ttcttccgcg
      181 agttcgtgca gcttctcaca catggcggcc tgttcgtcag catcgagtgc gtccagtttt
      241 tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtac ggtttgctgc
      301 tgcttgttca tctttctgtt ttctccgttc tttctgtcat ctgcgttgtg tgattatatc
      361 gagtaccact tttcgactgt tttaccgccg gtattctgct gtctgactct ttgacgggca
      421 tttctgtcag acaacactgt cactgccaaa aaactgccgt gcttttgtcg gtaattcgag
      481 cttgctgaca ggacaggatg tgcaattgtt ataccgcgca tacatgcacg ctattacaat
      541 taccctggtc agggctttgc cccgacaccc atgtcagata cggagccatg ttttatgaca
      601 aaacgaagtg gaagtaatac gcgcaggcgg gctatcagtc gccctgttcg tctgacggca
      661 gaagaagacc aggaaatcag aaaaagggct gctgaatgcg gcaagaccgt ttctggtttt
      721 ttacgggcgg cagctctcgg taagaaagtt aattcactga ctgatgaccg ggtgctgaaa
      781 gaagtcatgc gactgggggc gttgcagaaa aaactcttta tcgacggcaa gcgtgtcggg
      841 gacagagagt atgcggaggt gctgatagct attacggagt atcaccgggc cctgttatcc
      901 aggcttatgg cagattagct tcccggaggg aaactgtcga aaacagacgg tatgaacgcc
      961 gtaagtcccc aaaccgatcg ccattcactt tcatgcatag ctatgcagtg agctgaaaac
     1021 gatcctgacg catccttcct gtttttccgg ggtaaaacat ctctttttgc ggtgtctgcg
     1081 tcagaatcgc gttcagcgcg ttttagcggt gcgcgtaatg agacgttatg gtaaatgtct
     1141 tctggcttga tattatattg gaatgccttt tttcaaagca aatgatgtgg ctttggatag
     1201 aaggtttacg ttgatcttat caaagttctt tttaaagaac gaagccgaga gctcagataa
     1261 atcattatat tcatcagttt tcgtaacttt gtttaatgtg taacttgaaa acttctcgcc
     1321 attaaatgac gtatagacgt aacgatcttt ttttccaccg ttaggaatta ttaaatcaaa
     1381 aaaaacatca cccttgcttt tctttttctt caagtcggat tcgatttttg agaaaaattc
     1441 gctcgggcta taaatatcag tagcatagac aataaataaa gttttatctt tattttttat
     1501 tgcttctatt tgatattttt tatctttttt cataatttca acctagctac gccaccatct
     1561 attaattggc aaacggtatc gatgattgcg attgattcta atttgttaat tgtcttcgtg
     1621 tcagctattc ctggtttcat atgaaacaaa ccatgcctgt tctcatgcca gtaagtgtag
     1681 cattcacaca aaacttccgc tatttcacca tttatagttt cttggtgtat ttctctgatt
     1741 atatatttgg gtttgttttc agtgaagtat tcgccaaggt tctttgatga tgatggattg
     1801 caaacatcat taagtatttg atatataaag ccttctatag ctcttaatgc agagaagcag
     1861 tatgttgagt aatcttccat ttcgacatct atttttttca ttattagcga gcatgatagc
     1921 tgttttttga tatcttcatg gattttatcg atgctttttg gtagtttgct atgcaactcg
     1981 gactcaatag tttctttttt tatgtcaaca ttaaattctt tatttttttg ttcgacaatc
     2041 tctttcatgt ttagtattga gcacatgaaa tcgttaatca aactcgcgat ttgaaggtat
     2101 tttccttgga attgaataga gccgcgcttg taaatttttg ccctgaccct gtcaccattg
     2161 ctggtggtca taatatattg gtgtttacaa ttaggatcgt tattattatc ttctgttatt
     2221 gttatcccct cttcagaaag aaattcaaat agatttgccc tgtcatcatc actgaatttt
     2281 ggaatggtgt attcaaagtt ctttgtgtct gaatacaaac agttttcttt tataatcaag
     2341 gcgatttcat caaagtaagt gttattttgc ccagacgctc ttccgatagt ggtatttccg
     2401 cctgatggca ttagttttat taagaagtct attcctttat atgtgccaga tatgtgagtt
     2461 tctctttcgt tttttacatt agaggaatag tttgtgacgc cattctgcgt cagagcagac
     2521 tcaatcttgt caatattgat atttagtgct ttaaacgggt tctgtgccat tgggtcaatc
     2581 cgttgttttt tttgaatatg tacagatctt gtttttttgt caacggaata gctgttcgtt
     2641 gacttgatag accgattgat tcatcatctc ataaataaag aaaaaccacc gctaccaacg
     2701 gtggttttct caaggttcgc tgagctacca actctttgaa ccaaggtaac tggcttggag
     2761 gagcgcagtc accaaaatct gttctttcag tttagcctta acaggtgcat aacttcaaga
     2821 caaactcctc taaatcagtt accaatggct gctgccagtg gcgttaagtc gtgtctttcc
     2881 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     2941 tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata ccaacagcgt
     3001 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc
     3061 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
     3121 tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg atgctcgtca
     3181 ggggggcgga gcctatggaa aaacggcatc ggcgctggct tgttccggtg ctttgctttt
     3241 tgctcacatg ttctttccgg cgttatcccc tgattctgtg gataaccgta ttaccgcctt
     3301 tgagtgagct gacaccgct
//
