LOCUS       NZ_CP062897             3319 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-ER02-39 plasmid unnamed14,
            complete sequence.
ACCESSION   NZ_CP062897
VERSION     NZ_CP062897.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304147
            Assembly: GCF_015571875.1
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  JOURNAL   Unpublished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                     :: 13-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-17
            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 14:40:58
            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)                     :: 5,033
            CDSs (total)                      :: 4,914
            Genes (coding)                    :: 4,610
            CDSs (with protein)               :: 4,610
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 304
            CDSs (without protein)            :: 304
            Pseudo Genes (ambiguous residues) :: 0 of 304
            Pseudo Genes (frameshifted)       :: 94 of 304
            Pseudo Genes (incomplete)         :: 226 of 304
            Pseudo Genes (internal stop)      :: 46 of 304
            Pseudo Genes (multiple problems)  :: 53 of 304
            Pseudo Genes (short protein)      :: 3 of 304
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062897.1.
            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-ER02-39"
                     /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            18..341
                     /gene="mobA"
                     /locus_tag="IMP38_RS23385"
                     /old_locus_tag="IMP38_23405"
     CDS             18..341
                     /gene="mobA"
                     /locus_tag="IMP38_RS23385"
                     /old_locus_tag="IMP38_23405"
                     /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(576..956)
                     /gene="lsoB"
                     /locus_tag="IMP38_RS23390"
                     /old_locus_tag="IMP38_23410"
     CDS             complement(576..956)
                     /gene="lsoB"
                     /locus_tag="IMP38_RS23390"
                     /old_locus_tag="IMP38_23410"
                     /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(953..1993)
                     /gene="lsoA"
                     /locus_tag="IMP38_RS23395"
                     /old_locus_tag="IMP38_23415"
     CDS             complement(953..1993)
                     /gene="lsoA"
                     /locus_tag="IMP38_RS23395"
                     /old_locus_tag="IMP38_23415"
                     /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(2859..3053)
                     /locus_tag="IMP38_RS23400"
                     /old_locus_tag="IMP38_23420"
     CDS             complement(2859..3053)
                     /locus_tag="IMP38_RS23400"
                     /old_locus_tag="IMP38_23420"
                     /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          3089..3319
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="96.0"
                     /evalue="7.66e-118"
     Typing          complement(2300..2824)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          19..338
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.94e-62"
ORIGIN
        1 atacggagcc atgttttatg acaaaacgaa gtggaagtaa tacgcgcagg cgggctatca
       61 gtcgccctgt tcgtctgacg gcagaagaag accaggaaat cagaaaaagg gctgctgaat
      121 gcggcaagac cgtttctggt tttttacggg cggcagctct cggtaagaaa gttaattcac
      181 tgactgatga ccgggtgctg aaagaagtca tgcgactggg ggcgttgcag aaaaaactct
      241 ttatcgacgg caagcgtgtc ggggacagag agtatgcgga ggtgctgata gctattacgg
      301 agtatcaccg ggccctgtta tccaggctta tggcagatta gcttcccgga gggaaactgt
      361 cgaaaacaga cggtatgaac gccgtaagtc cccaaaccga tcgccattca ctttcatgca
      421 tagctatgca gtgagctgaa aacgatcctg acgcatcctt cctgtttttc cggggtaaaa
      481 catctctttt tgcggtgtct gcgtcagaat cgcgttcagc gcgttttagc ggtgcgcgta
      541 atgagacgtt atggtaaatg tcttctggct tgatattata ttggaatgcc ttttttcaaa
      601 gcaaatgatg tggctttgga tagaaggttt acgttgatct tatcaaagtt ctttttaaag
      661 aacgaagccg agagctcaga taaatcatta tattcatcag ttttcgtaac tttgtttaat
      721 gtgtaacttg aaaacttctc gccattaaat gacgtataga cgtaacgatc tttttttcca
      781 ccgttaggaa ttattaaatc aaaaaaaaca tcacccttgc ttttcttttt cttcaagtcg
      841 gattcgattt ttgagaaaaa ttcgctcggg ctataaatat cagtagcata gacaataaat
      901 aaagttttat ctttattttt tattgcttct atttgatatt ttttatcttt tttcataatt
      961 tcaacctagc tacgccacca tctattaatt ggcaaacggt atcgatgatt gcgattgatt
     1021 ctaatttgtt aattgtcttc gtgtcagcta ttcctggttt catatgaaac aaaccatgcc
     1081 tgttctcatg ccagtaagtg tagcattcac acaaaacttc cgctatttca ccatttatag
     1141 tttcttggtg tatttctctg attatatatt tgggtttgtt ttcagtgaag tattcgccaa
     1201 ggttctttga tgatgatgga ttgcaaacat cattaagtat ttgatatata aagccttcta
     1261 tagctcttaa tgcagagaag cagtatgttg agtaatcttc catttcgaca tctatttttt
     1321 tcattattag cgagcatgat agctgttttt tgatatcttc atggatttta tcgatgcttt
     1381 ttggtagttt gctatgcaac tcggactcaa tagtttcttt ttttatgtca acattaaatt
     1441 ctttattttt ttgttcgaca atctctttca tgtttagtat tgagcacatg aaatcgttaa
     1501 tcaaactcgc gatttgaagg tattttcctt ggaattgaat agagccgcgc ttgtaaattt
     1561 ttgccctgac cctgtcacca ttgctggtgg tcataatata ttggtgttta caattaggat
     1621 cgttattatt atcttctgtt attgttatcc cctcttcaga aagaaattca aatagatttg
     1681 ccctgtcatc atcactgaat tttggaatgg tgtattcaaa gttctttgtg tctgaataca
     1741 aacagttttc ttttataatc aaggcgattt catcaaagta agtgttattt tgcccagacg
     1801 ctcttccgat agtggtattt ccgcctgatg gcattagttt tattaagaag tctattcctt
     1861 tatatgtgcc agatatgtga gtttctcttt cgttttttac attagaggaa tagtttgtga
     1921 cgccattctg cgtcagagca gactcaatct tgtcaatatt gatatttagt gctttaaacg
     1981 ggttctgtgc cattgggtca atccgttgtt ttttttgaat atgtacagat cttgtttttt
     2041 tgtcaacgga atagctgttc gttgacttga tagaccgatt gattcatcat ctcataaata
     2101 aagaaaaacc accgctacca acggtggttt tctcaaggtt cgctgagcta ccaactcttt
     2161 gaaccaaggt aactggcttg gaggagcgca gtcaccaaaa tctgttcttt cagtttagcc
     2221 ttaacaggtg cataacttca agacaaactc ctctaaatca gttaccaatg gctgctgcca
     2281 gtggcgttaa gtcgtgtctt tccgggttgg actcaagacg atagttaccg gataaggcgc
     2341 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     2401 ccgaactgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     2461 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc
     2521 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc
     2581 gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacggc atcggcgctg
     2641 gcttgttccg gtgctttgct ttttgctcac atgttctttc cggcgttatc ccctgattct
     2701 gtggataacc gtattaccgc ctttgagtga gctgacaccg ctcgccgcag tcgaacgacc
     2761 gagcgtagcg agtcagtgag cgaggaagcg gaagagcgtc tgacgtggca ttttctcctt
     2821 acgctccgct atgccgttct gcatcctgtc cgggtgcgtt atatcccggt gcgattttcc
     2881 gcttcaaagc gtgtctgtat gctgttctga agttcttccg cgagttcgtg cagcttctca
     2941 cacatggcgg cctgttcgtc agcatcgagt gcgtccagtt tttcgagcag cgtcaggctc
     3001 tggcttttta tgaatcccgc catgttgagt acggtttgct gctgcttgtt catctttctg
     3061 ttttctccgt tctttctgtc atctgcgttg tgtgattata tcgagtacca cttttcgact
     3121 gttttaccgc cggtattctg ctgtctgact ctttgacggg catttctgtc agacaacact
     3181 gtcactgcca aaaaactgcc gtgcttttgt cggtaattcg agcttgctga caggacagga
     3241 tgtgcaattg ttataccgcg catacatgca cgctattaca attaccctgg tcagggcttt
     3301 gccccgacac ccatgtcag
//
