LOCUS       NZ_CP062817             3319 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain Res13-Sevr-PER06-05-b-A plasmid unnamed14,
            complete sequence.
ACCESSION   NZ_CP062817
VERSION     NZ_CP062817.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304267
            Assembly: GCF_015571555.1
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  JOURNAL   Unpublished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                     :: 29-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-28-H
            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 15:40:21
            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)                     :: 5,038
            CDSs (total)                      :: 4,916
            Genes (coding)                    :: 4,613
            CDSs (with protein)               :: 4,613
            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)       :: 94 of 303
            Pseudo Genes (incomplete)         :: 225 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
            CP062817.1.
            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-Sevr-PER06-05-b-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="2017-04-11"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            join(2543..3319,1..264)
                     /gene="lsoA"
                     /locus_tag="IMQ58_RS23415"
                     /old_locus_tag="IMQ58_23435"
     CDS             join(2543..3319,1..264)
                     /gene="lsoA"
                     /locus_tag="IMQ58_RS23415"
                     /old_locus_tag="IMQ58_23435"
                     /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            261..641
                     /gene="lsoB"
                     /locus_tag="IMQ58_RS23420"
                     /old_locus_tag="IMQ58_23440"
     CDS             261..641
                     /gene="lsoB"
                     /locus_tag="IMQ58_RS23420"
                     /old_locus_tag="IMQ58_23440"
                     /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(876..1199)
                     /gene="mobA"
                     /locus_tag="IMQ58_RS23425"
                     /old_locus_tag="IMQ58_23445"
     CDS             complement(876..1199)
                     /gene="mobA"
                     /locus_tag="IMQ58_RS23425"
                     /old_locus_tag="IMQ58_23445"
                     /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            1483..1677
                     /locus_tag="IMQ58_RS23430"
                     /old_locus_tag="IMQ58_23450"
     CDS             1483..1677
                     /locus_tag="IMQ58_RS23430"
                     /old_locus_tag="IMQ58_23450"
                     /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(1209..1448)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          1713..2234
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.437"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(880..1199)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.54e-62"
ORIGIN
        1 tcatcatcaa agaaccttgg cgaatacttc actgaaaaca aacccaaata tataatcaga
       61 gaaatacacc aagaaactat aaatggtgaa atagcggaag ttttgtgtga atgctacact
      121 tactggcatg agaacaggca tggtttgttt catatgaaac caggaatagc tgacacgaag
      181 acaattaaca aattagaatc aatcgcaatc atcgataccg tttgccaatt aatagatggt
      241 ggcgtagcta ggttgaaatt atgaaaaaag ataaaaaata tcaaatagaa gcaataaaaa
      301 ataaagataa aactttattt attgtctatg ctactgatat ttatagcccg agcgaatttt
      361 tctcaaaaat cgaatccgac ttgaagaaaa agaaaagcaa gggtgatgtt ttttttgatt
      421 taataattcc taacggtgga aaaaaagatc gttacgtcta tacgtcattt aatggcgaga
      481 agttttcaag ttacacatta aacaaagtta cgaaaactga tgaatataat gatttatctg
      541 agctctcggc ttcgttcttt aaaaagaact ttgataagat caacgtaaac cttctatcca
      601 aagccacatc atttgctttg aaaaaaggca ttccaatata atatcaagcc agaagacatt
      661 taccataacg tctcattacg cgcaccgcta aaacgcgctg aacgcgattc tgacgcagac
      721 accgcaaaaa gagatgtttt accccggaaa aacaggaagg atgcgtcagg atcgttttca
      781 gctcactgca tagctatgca tgaaagtgaa tggcgatcgg tttggggact tacggcgttc
      841 ataccgtctg ttttcgacag tttccctccg ggaagctaat ctgccataag cctggataac
      901 agggcccggt gatactccgt aatagctatc agcacctccg catactctct gtccccgaca
      961 cgcttgccgt cgataaagag ttttttctgc aacgccccca gtcgcatgac ttctttcagc
     1021 acccggtcat cagtcagtga attaactttc ttaccgagag ctgccgcccg taaaaaacca
     1081 gaaacggtct tgccgcattc agcagccctt tttctgattt cctggtcttc ttctgccgtc
     1141 agacgaacag ggcgactgat agcccgcctg cgcgtattac ttccacttcg ttttgtcata
     1201 aaacatggct ccgtatctga catgggtgtc ggggcaaagc cctgaccagg gtaattgtaa
     1261 tagcgtgcat gtatgcgcgg tataacaatt gcacatcctg tcctgtcagc aagctcgaat
     1321 taccgacaaa agcacggcag ttttttggca gtgacagtgt tgtctgacag aaatgcccgt
     1381 caaagagtca gacagcagaa taccggcggt aaaacagtcg aaaagtggta ctcgatataa
     1441 tcacacaacg cagatgacag aaagaacgga gaaaacagaa agatgaacaa gcagcagcaa
     1501 accgtactca acatggcggg attcataaaa agccagagcc tgacgctgct cgaaaaactg
     1561 gacgcactcg atgctgacga acaggccgcc atgtgtgaga agctgcacga actcgcggaa
     1621 gaacttcaga acagcataca gacacgcttt gaagcggaaa atcgcaccgg gatataacgc
     1681 acccggacag gatgcagaac ggcatagcgg agcgtaagga gaaaatgcca cgtcagacgc
     1741 tcttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcgactgcg gcgagcggtg
     1801 tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa cgccggaaag
     1861 aacatgtgag caaaaagcaa agcaccggaa caagccagcg ccgatgccgt ttttccatag
     1921 gctccgcccc cctgacgagc atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc
     1981 gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt
     2041 tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct
     2101 ttctcatagc tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg
     2161 ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct
     2221 tgagtccaac ccggaaagac acgacttaac gccactggca gcagccattg gtaactgatt
     2281 tagaggagtt tgtcttgaag ttatgcacct gttaaggcta aactgaaaga acagattttg
     2341 gtgactgcgc tcctccaagc cagttacctt ggttcaaaga gttggtagct cagcgaacct
     2401 tgagaaaacc accgttggta gcggtggttt ttctttattt atgagatgat gaatcaatcg
     2461 gtctatcaag tcaacgaaca gctattccgt tgacaaaaaa acaagatctg tacatattca
     2521 aaaaaaacaa cggattgacc caatggcaca gaacccgttt aaagcactaa atatcaatat
     2581 tgacaagatt gagtctgctc tgacgcagaa tggcgtcaca aactattcct ctaatgtaaa
     2641 aaacgaaaga gaaactcaca tatctggcac atataaagga atagacttct taataaaact
     2701 aatgccatca ggcggaaata ccactatcgg aagagcgtct gggcaaaata acacttactt
     2761 tgatgaaatc gccttgatta taaaagaaaa ctgtttgtat tcagacacaa agaactttga
     2821 atacaccatt ccaaaattca gtgatgatga cagggcaaat ctatttgaat ttctttctga
     2881 agaggggata acaataacag aagataataa taacgatcct aattgtaaac accaatatat
     2941 tatgaccacc agcaatggtg acagggtcag ggcaaaaatt tacaagcgcg gctctattca
     3001 attccaagga aaataccttc aaatcgcgag tttgattaac gatttcatgt gctcaatact
     3061 aaacatgaaa gagattgtcg aacaaaaaaa taaagaattt aatgttgaca taaaaaaaga
     3121 aactattgag tccgagttgc atagcaaact accaaaaagc atcgataaaa tccatgaaga
     3181 tatcaaaaaa cagctatcat gctcgctaat aatgaaaaaa atagatgtcg aaatggaaga
     3241 ttactcaaca tactgcttct ctgcattaag agctatagaa ggctttatat atcaaatact
     3301 taatgatgtt tgcaatcca
//
