LOCUS       NZ_CP062834             3319 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Lact-PER04-33 plasmid unnamed14,
            complete sequence.
ACCESSION   NZ_CP062834
VERSION     NZ_CP062834.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304231
            Assembly: GCF_015571635.1
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  JOURNAL   Unpublished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                     :: 30-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-22-B
            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 15:44:03
            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)                     :: 5,036
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            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)              :: 312
            CDSs (without protein)            :: 312
            Pseudo Genes (ambiguous residues) :: 0 of 312
            Pseudo Genes (frameshifted)       :: 98 of 312
            Pseudo Genes (incomplete)         :: 228 of 312
            Pseudo Genes (internal stop)      :: 49 of 312
            Pseudo Genes (multiple problems)  :: 54 of 312
            Pseudo Genes (short protein)      :: 3 of 312
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062834.1.
            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-PER04-33"
                     /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(join(2562..3319,1..283))
                     /gene="lsoA"
                     /locus_tag="IMQ22_RS23360"
                     /old_locus_tag="IMQ22_23380"
     CDS             complement(join(2562..3319,1..283))
                     /gene="lsoA"
                     /locus_tag="IMQ22_RS23360"
                     /old_locus_tag="IMQ22_23380"
                     /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(1149..1343)
                     /locus_tag="IMQ22_RS23365"
                     /old_locus_tag="IMQ22_23385"
     CDS             complement(1149..1343)
                     /locus_tag="IMQ22_RS23365"
                     /old_locus_tag="IMQ22_23385"
                     /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            1627..1950
                     /gene="mobA"
                     /locus_tag="IMQ22_RS23370"
                     /old_locus_tag="IMQ22_23390"
     CDS             1627..1950
                     /gene="mobA"
                     /locus_tag="IMQ22_RS23370"
                     /old_locus_tag="IMQ22_23390"
                     /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(2185..2565)
                     /gene="lsoB"
                     /locus_tag="IMQ22_RS23375"
                     /old_locus_tag="IMQ22_23395"
     CDS             complement(2185..2565)
                     /gene="lsoB"
                     /locus_tag="IMQ22_RS23375"
                     /old_locus_tag="IMQ22_23395"
                     /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"
     Typing          1379..1618
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(590..1114)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          1628..1947
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.54e-62"
ORIGIN
        1 tgtattcaaa gttctttgtg tctgaataca aacagttttc ttttataatc aaggcgattt
       61 catcaaagta agtgttattt tgcccagacg ctcttccgat agtggtattt ccgcctgatg
      121 gcattagttt tattaagaag tctattcctt tatatgtgcc agatatgtga gtttctcttt
      181 cgttttttac attagaggaa tagtttgtga cgccattctg cgtcagagca gactcaatct
      241 tgtcaatatt gatatttagt gctttaaacg ggttctgtgc cattgggtca atccgttgtt
      301 ttttttgaat atgtacagat cttgtttttt tgtcaacgga atagctgttc gttgacttga
      361 tagaccgatt gattcatcat ctcataaata aagaaaaacc accgctacca acggtggttt
      421 tctcaaggtt cgctgagcta ccaactcttt gaaccaaggt aactggcttg gaggagcgca
      481 gtcaccaaaa tctgttcttt cagtttagcc ttaacaggtg cataacttca agacaaactc
      541 ctctaaatca gttaccaatg gctgctgcca gtggcgttaa gtcgtgtctt tccgggttgg
      601 actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca
      661 cacagcccag cttggagcga acgacctaca ccgaactgag ataccaacag cgtgagctat
      721 gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg
      781 tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc
      841 ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc
      901 ggagcctatg gaaaaacggc atcggcgctg gcttgttccg gtgctttgct ttttgctcac
      961 atgttctttc cggcgttatc ccctgattct gtggataacc gtattaccgc ctttgagtga
     1021 gctgacaccg ctcgccgcag tcgaacgacc gagcgtagcg agtcagtgag cgaggaagcg
     1081 gaagagcgtc tgacgtggca ttttctcctt acgctccgct atgccgttct gcatcctgtc
     1141 cgggtgcgtt atatcccggt gcgattttcc gcttcaaagc gtgtctgtat gctgttctga
     1201 agttcttccg cgagttcgtg cagcttctca cacatggcgg cctgttcgtc agcatcgagt
     1261 gcgtccagtt tttcgagcag cgtcaggctc tggcttttta tgaatcccgc catgttgagt
     1321 acggtttgct gctgcttgtt catctttctg ttttctccgt tctttctgtc atctgcgttg
     1381 tgtgattata tcgagtacca cttttcgact gttttaccgc cggtattctg ctgtctgact
     1441 ctttgacggg catttctgtc agacaacact gtcactgcca aaaaactgcc gtgcttttgt
     1501 cggtaattcg agcttgctga caggacagga tgtgcaattg ttataccgcg catacatgca
     1561 cgctattaca attaccctgg tcagggcttt gccccgacac ccatgtcaga tacggagcca
     1621 tgttttatga caaaacgaag tggaagtaat acgcgcaggc gggctatcag tcgccctgtt
     1681 cgtctgacgg cagaagaaga ccaggaaatc agaaaaaggg ctgctgaatg cggcaagacc
     1741 gtttctggtt ttttacgggc ggcagctctc ggtaagaaag ttaattcact gactgatgac
     1801 cgggtgctga aagaagtcat gcgactgggg gcgttgcaga aaaaactctt tatcgacggc
     1861 aagcgtgtcg gggacagaga gtatgcggag gtgctgatag ctattacgga gtatcaccgg
     1921 gccctgttat ccaggcttat ggcagattag cttcccggag ggaaactgtc gaaaacagac
     1981 ggtatgaacg ccgtaagtcc ccaaaccgat cgccattcac tttcatgcat agctatgcag
     2041 tgagctgaaa acgatcctga cgcatccttc ctgtttttcc ggggtaaaac atctcttttt
     2101 gcggtgtctg cgtcagaatc gcgttcagcg cgttttagcg gtgcgcgtaa tgagacgtta
     2161 tggtaaatgt cttctggctt gatattatat tggaatgcct tttttcaaag caaatgatgt
     2221 ggctttggat agaaggttta cgttgatctt atcaaagttc tttttaaaga acgaagccga
     2281 gagctcagat aaatcattat attcatcagt tttcgtaact ttgtttaatg tgtaacttga
     2341 aaacttctcg ccattaaatg acgtatagac gtaacgatct ttttttccac cgttaggaat
     2401 tattaaatca aaaaaaacat cacccttgct tttctttttc ttcaagtcgg attcgatttt
     2461 tgagaaaaat tcgctcgggc tataaatatc agtagcatag acaataaata aagttttatc
     2521 tttatttttt attgcttcta tttgatattt tttatctttt ttcataattt caacctagct
     2581 acgccaccat ctattaattg gcaaacggta tcgatgattg cgattgattc taatttgtta
     2641 attgtcttcg tgtcagctat tcctggtttc atatgaaaca aaccatgcct gttctcatgc
     2701 cagtaagtgt agcattcaca caaaacttcc gctatttcac catttatagt ttcttggtgt
     2761 atttctctga ttatatattt gggtttgttt tcagtgaagt attcgccaag gttctttgat
     2821 gatgatggat tgcaaacatc attaagtatt tgatatataa agccttctat agctcttaat
     2881 gcagagaagc agtatgttga gtaatcttcc atttcgacat ctattttttt cattattagc
     2941 gagcatgata gctgtttttt gatatcttca tggattttat cgatgctttt tggtagtttg
     3001 ctatgcaact cggactcaat agtttctttt tttatgtcaa cattaaattc tttatttttt
     3061 tgttcgacaa tctctttcat gtttagtatt gagcacatga aatcgttaat caaactcgcg
     3121 atttgaaggt attttccttg gaattgaata gagccgcgct tgtaaatttt tgccctgacc
     3181 ctgtcaccat tgctggtggt cataatatat tggtgtttac aattaggatc gttattatta
     3241 tcttctgtta ttgttatccc ctcttcagaa agaaattcaa atagatttgc cctgtcatca
     3301 tcactgaatt ttggaatgg
//
