LOCUS       NZ_CP062828             3319 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PER12-33-A plasmid unnamed14,
            complete sequence.
ACCESSION   NZ_CP062828
VERSION     NZ_CP062828.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304239
            Assembly: GCF_015571615.1
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  JOURNAL   Unpublished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                     :: 19-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-26-F
            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 15:10:08
            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)                     :: 5,039
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,614
            CDSs (with protein)               :: 4,614
            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)              :: 303
            CDSs (without protein)            :: 303
            Pseudo Genes (ambiguous residues) :: 0 of 303
            Pseudo Genes (frameshifted)       :: 93 of 303
            Pseudo Genes (incomplete)         :: 226 of 303
            Pseudo Genes (internal stop)      :: 46 of 303
            Pseudo Genes (multiple problems)  :: 53 of 303
            Pseudo Genes (short protein)      :: 3 of 303
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062828.1.
            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-PER12-33-A"
                     /serotype="O-untypeable:H4"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamed14"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-03-27"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            join(2545..3319,1..266)
                     /gene="lsoA"
                     /locus_tag="IMQ30_RS23400"
                     /old_locus_tag="IMQ30_23420"
     CDS             join(2545..3319,1..266)
                     /gene="lsoA"
                     /locus_tag="IMQ30_RS23400"
                     /old_locus_tag="IMQ30_23420"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /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"
     gene            263..643
                     /gene="lsoB"
                     /locus_tag="IMQ30_RS23405"
                     /old_locus_tag="IMQ30_23425"
     CDS             263..643
                     /gene="lsoB"
                     /locus_tag="IMQ30_RS23405"
                     /old_locus_tag="IMQ30_23425"
                     /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(878..1201)
                     /gene="mobA"
                     /locus_tag="IMQ30_RS23410"
                     /old_locus_tag="IMQ30_23430"
     CDS             complement(878..1201)
                     /gene="mobA"
                     /locus_tag="IMQ30_RS23410"
                     /old_locus_tag="IMQ30_23430"
                     /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            1485..1679
                     /locus_tag="IMQ30_RS23415"
                     /old_locus_tag="IMQ30_23435"
     CDS             1485..1679
                     /locus_tag="IMQ30_RS23415"
                     /old_locus_tag="IMQ30_23435"
                     /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"
     Typing          complement(1211..1450)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          1715..2236
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.437"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(882..1201)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.54e-62"
ORIGIN
        1 catcatcatc aaagaacctt ggcgaatact tcactgaaaa caaacccaaa tatataatca
       61 gagaaataca ccaagaaact ataaatggtg aaatagcgga agttttgtgt gaatgctaca
      121 cttactggca tgagaacagg catggtttgt ttcatatgaa accaggaata gctgacacga
      181 agacaattaa caaattagaa tcaatcgcaa tcatcgatac cgtttgccaa ttaatagatg
      241 gtggcgtagc taggttgaaa ttatgaaaaa agataaaaaa tatcaaatag aagcaataaa
      301 aaataaagat aaaactttat ttattgtcta tgctactgat atttatagcc cgagcgaatt
      361 tttctcaaaa atcgaatccg acttgaagaa aaagaaaagc aagggtgatg ttttttttga
      421 tttaataatt cctaacggtg gaaaaaaaga tcgttacgtc tatacgtcat ttaatggcga
      481 gaagttttca agttacacat taaacaaagt tacgaaaact gatgaatata atgatttatc
      541 tgagctctcg gcttcgttct ttaaaaagaa ctttgataag atcaacgtaa accttctatc
      601 caaagccaca tcatttgctt tgaaaaaagg cattccaata taatatcaag ccagaagaca
      661 tttaccataa cgtctcatta cgcgcaccgc taaaacgcgc tgaacgcgat tctgacgcag
      721 acaccgcaaa aagagatgtt ttaccccgga aaaacaggaa ggatgcgtca ggatcgtttt
      781 cagctcactg catagctatg catgaaagtg aatggcgatc ggtttgggga cttacggcgt
      841 tcataccgtc tgttttcgac agtttccctc cgggaagcta atctgccata agcctggata
      901 acagggcccg gtgatactcc gtaatagcta tcagcacctc cgcatactct ctgtccccga
      961 cacgcttgcc gtcgataaag agttttttct gcaacgcccc cagtcgcatg acttctttca
     1021 gcacccggtc atcagtcagt gaattaactt tcttaccgag agctgccgcc cgtaaaaaac
     1081 cagaaacggt cttgccgcat tcagcagccc tttttctgat ttcctggtct tcttctgccg
     1141 tcagacgaac agggcgactg atagcccgcc tgcgcgtatt acttccactt cgttttgtca
     1201 taaaacatgg ctccgtatct gacatgggtg tcggggcaaa gccctgacca gggtaattgt
     1261 aatagcgtgc atgtatgcgc ggtataacaa ttgcacatcc tgtcctgtca gcaagctcga
     1321 attaccgaca aaagcacggc agttttttgg cagtgacagt gttgtctgac agaaatgccc
     1381 gtcaaagagt cagacagcag aataccggcg gtaaaacagt cgaaaagtgg tactcgatat
     1441 aatcacacaa cgcagatgac agaaagaacg gagaaaacag aaagatgaac aagcagcagc
     1501 aaaccgtact caacatggcg ggattcataa aaagccagag cctgacgctg ctcgaaaaac
     1561 tggacgcact cgatgctgac gaacaggccg ccatgtgtga gaagctgcac gaactcgcgg
     1621 aagaacttca gaacagcata cagacacgct ttgaagcgga aaatcgcacc gggatataac
     1681 gcacccggac aggatgcaga acggcatagc ggagcgtaag gagaaaatgc cacgtcagac
     1741 gctcttccgc ttcctcgctc actgactcgc tacgctcggt cgttcgactg cggcgagcgg
     1801 tgtcagctca ctcaaaggcg gtaatacggt tatccacaga atcaggggat aacgccggaa
     1861 agaacatgtg agcaaaaagc aaagcaccgg aacaagccag cgccgatgcc gtttttccat
     1921 aggctccgcc cccctgacga gcatcacaaa aatcgacgct caagtcagag gtggcgaaac
     1981 ccgacaggac tataaagata ccaggcgttt ccccctggaa gctccctcgt gcgctctcct
     2041 gttccgaccc tgccgcttac cggatacctg tccgcctttc tcccttcggg aagcgtggcg
     2101 ctttctcata gctcacgctg ttggtatctc agttcggtgt aggtcgttcg ctccaagctg
     2161 ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg ccttatccgg taactatcgt
     2221 cttgagtcca acccggaaag acacgactta acgccactgg cagcagccat tggtaactga
     2281 tttagaggag tttgtcttga agttatgcac ctgttaaggc taaactgaaa gaacagattt
     2341 tggtgactgc gctcctccaa gccagttacc ttggttcaaa gagttggtag ctcagcgaac
     2401 cttgagaaaa ccaccgttgg tagcggtggt ttttctttat ttatgagatg atgaatcaat
     2461 cggtctatca agtcaacgaa cagctattcc gttgacaaaa aaacaagatc tgtacatatt
     2521 caaaaaaaac aacggattga cccaatggca cagaacccgt ttaaagcact aaatatcaat
     2581 attgacaaga ttgagtctgc tctgacgcag aatggcgtca caaactattc ctctaatgta
     2641 aaaaacgaaa gagaaactca catatctggc acatataaag gaatagactt cttaataaaa
     2701 ctaatgccat caggcggaaa taccactatc ggaagagcgt ctgggcaaaa taacacttac
     2761 tttgatgaaa tcgccttgat tataaaagaa aactgtttgt attcagacac aaagaacttt
     2821 gaatacacca ttccaaaatt cagtgatgat gacagggcaa atctatttga atttctttct
     2881 gaagagggga taacaataac agaagataat aataacgatc ctaattgtaa acaccaatat
     2941 attatgacca ccagcaatgg tgacagggtc agggcaaaaa tttacaagcg cggctctatt
     3001 caattccaag gaaaatacct tcaaatcgcg agtttgatta acgatttcat gtgctcaata
     3061 ctaaacatga aagagattgt cgaacaaaaa aataaagaat ttaatgttga cataaaaaaa
     3121 gaaactattg agtccgagtt gcatagcaaa ctaccaaaaa gcatcgataa aatccatgaa
     3181 gatatcaaaa aacagctatc atgctcgcta ataatgaaaa aaatagatgt cgaaatggaa
     3241 gattactcaa catactgctt ctctgcatta agagctatag aaggctttat atatcaaata
     3301 cttaatgatg tttgcaatc
//
