LOCUS       NZ_CP062885             3319 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PEA06-10 plasmid unnamed14,
            complete sequence.
ACCESSION   NZ_CP062885
VERSION     NZ_CP062885.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304175
            Assembly: GCF_015571775.1
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  JOURNAL   Unpublished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                     :: 21-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-32
            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 13:28:07
            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)                     :: 5,044
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,617
            CDSs (with protein)               :: 4,617
            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)         :: 226 of 305
            Pseudo Genes (internal stop)      :: 47 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
            CP062885.1.
            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-PEA06-10"
                     /serotype="O-untypeable:H4"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="unnamed14"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-04-11"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            complement(99..479)
                     /gene="lsoB"
                     /locus_tag="IMP66_RS23425"
                     /old_locus_tag="IMP66_23445"
     CDS             complement(99..479)
                     /gene="lsoB"
                     /locus_tag="IMP66_RS23425"
                     /old_locus_tag="IMP66_23445"
                     /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(476..1516)
                     /gene="lsoA"
                     /locus_tag="IMP66_RS23430"
                     /old_locus_tag="IMP66_23450"
     CDS             complement(476..1516)
                     /gene="lsoA"
                     /locus_tag="IMP66_RS23430"
                     /old_locus_tag="IMP66_23450"
                     /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"
     gene            complement(2382..2576)
                     /locus_tag="IMP66_RS23435"
                     /old_locus_tag="IMP66_23455"
     CDS             complement(2382..2576)
                     /locus_tag="IMP66_RS23435"
                     /old_locus_tag="IMP66_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            2860..3183
                     /gene="mobA"
                     /locus_tag="IMP66_RS23440"
                     /old_locus_tag="IMP66_23460"
     CDS             2860..3183
                     /gene="mobA"
                     /locus_tag="IMP66_RS23440"
                     /old_locus_tag="IMP66_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"
     Typing          2612..2851
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(1823..2347)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          2861..3180
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.54e-62"
ORIGIN
        1 aaacatctct ttttgcggtg tctgcgtcag aatcgcgttc agcgcgtttt agcggtgcgc
       61 gtaatgagac gttatggtaa atgtcttctg gcttgatatt atattggaat gccttttttc
      121 aaagcaaatg atgtggcttt ggatagaagg tttacgttga tcttatcaaa gttcttttta
      181 aagaacgaag ccgagagctc agataaatca ttatattcat cagttttcgt aactttgttt
      241 aatgtgtaac ttgaaaactt ctcgccatta aatgacgtat agacgtaacg atcttttttt
      301 ccaccgttag gaattattaa atcaaaaaaa acatcaccct tgcttttctt tttcttcaag
      361 tcggattcga tttttgagaa aaattcgctc gggctataaa tatcagtagc atagacaata
      421 aataaagttt tatctttatt ttttattgct tctatttgat attttttatc ttttttcata
      481 atttcaacct agctacgcca ccatctatta attggcaaac ggtatcgatg attgcgattg
      541 attctaattt gttaattgtc ttcgtgtcag ctattcctgg tttcatatga aacaaaccat
      601 gcctgttctc atgccagtaa gtgtagcatt cacacaaaac ttccgctatt tcaccattta
      661 tagtttcttg gtgtatttct ctgattatat atttgggttt gttttcagtg aagtattcgc
      721 caaggttctt tgatgatgat ggattgcaaa catcattaag tatttgatat ataaagcctt
      781 ctatagctct taatgcagag aagcagtatg ttgagtaatc ttccatttcg acatctattt
      841 ttttcattat tagcgagcat gatagctgtt ttttgatatc ttcatggatt ttatcgatgc
      901 tttttggtag tttgctatgc aactcggact caatagtttc tttttttatg tcaacattaa
      961 attctttatt tttttgttcg acaatctctt tcatgtttag tattgagcac atgaaatcgt
     1021 taatcaaact cgcgatttga aggtattttc cttggaattg aatagagccg cgcttgtaaa
     1081 tttttgccct gaccctgtca ccattgctgg tggtcataat atattggtgt ttacaattag
     1141 gatcgttatt attatcttct gttattgtta tcccctcttc agaaagaaat tcaaatagat
     1201 ttgccctgtc atcatcactg aattttggaa tggtgtattc aaagttcttt gtgtctgaat
     1261 acaaacagtt ttcttttata atcaaggcga tttcatcaaa gtaagtgtta ttttgcccag
     1321 acgctcttcc gatagtggta tttccgcctg atggcattag ttttattaag aagtctattc
     1381 ctttatatgt gccagatatg tgagtttctc tttcgttttt tacattagag gaatagtttg
     1441 tgacgccatt ctgcgtcaga gcagactcaa tcttgtcaat attgatattt agtgctttaa
     1501 acgggttctg tgccattggg tcaatccgtt gttttttttg aatatgtaca gatcttgttt
     1561 ttttgtcaac ggaatagctg ttcgttgact tgatagaccg attgattcat catctcataa
     1621 ataaagaaaa accaccgcta ccaacggtgg ttttctcaag gttcgctgag ctaccaactc
     1681 tttgaaccaa ggtaactggc ttggaggagc gcagtcacca aaatctgttc tttcagttta
     1741 gccttaacag gtgcataact tcaagacaaa ctcctctaaa tcagttacca atggctgctg
     1801 ccagtggcgt taagtcgtgt ctttccgggt tggactcaag acgatagtta ccggataagg
     1861 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     1921 acaccgaact gagataccaa cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
     1981 gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc
     2041 ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg
     2101 agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac ggcatcggcg
     2161 ctggcttgtt ccggtgcttt gctttttgct cacatgttct ttccggcgtt atcccctgat
     2221 tctgtggata accgtattac cgcctttgag tgagctgaca ccgctcgccg cagtcgaacg
     2281 accgagcgta gcgagtcagt gagcgaggaa gcggaagagc gtctgacgtg gcattttctc
     2341 cttacgctcc gctatgccgt tctgcatcct gtccgggtgc gttatatccc ggtgcgattt
     2401 tccgcttcaa agcgtgtctg tatgctgttc tgaagttctt ccgcgagttc gtgcagcttc
     2461 tcacacatgg cggcctgttc gtcagcatcg agtgcgtcca gtttttcgag cagcgtcagg
     2521 ctctggcttt ttatgaatcc cgccatgttg agtacggttt gctgctgctt gttcatcttt
     2581 ctgttttctc cgttctttct gtcatctgcg ttgtgtgatt atatcgagta ccacttttcg
     2641 actgttttac cgccggtatt ctgctgtctg actctttgac gggcatttct gtcagacaac
     2701 actgtcactg ccaaaaaact gccgtgcttt tgtcggtaat tcgagcttgc tgacaggaca
     2761 ggatgtgcaa ttgttatacc gcgcatacat gcacgctatt acaattaccc tggtcagggc
     2821 tttgccccga cacccatgtc agatacggag ccatgtttta tgacaaaacg aagtggaagt
     2881 aatacgcgca ggcgggctat cagtcgccct gttcgtctga cggcagaaga agaccaggaa
     2941 atcagaaaaa gggctgctga atgcggcaag accgtttctg gttttttacg ggcggcagct
     3001 ctcggtaaga aagttaattc actgactgat gaccgggtgc tgaaagaagt catgcgactg
     3061 ggggcgttgc agaaaaaact ctttatcgac ggcaagcgtg tcggggacag agagtatgcg
     3121 gaggtgctga tagctattac ggagtatcac cgggccctgt tatccaggct tatggcagat
     3181 tagcttcccg gagggaaact gtcgaaaaca gacggtatga acgccgtaag tccccaaacc
     3241 gatcgccatt cactttcatg catagctatg cagtgagctg aaaacgatcc tgacgcatcc
     3301 ttcctgtttt tccggggta
//
