LOCUS       NZ_CP062912             4073 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli O112ab:H8 strain Res13-Lact-EA06-22 plasmid
            unnamed32, complete sequence.
ACCESSION   NZ_CP062912
VERSION     NZ_CP062912.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304114
            Assembly: GCF_015571915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O112ab:H8
  ORGANISM  Escherichia coli O112ab:H8
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  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  JOURNAL   Unpublished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 4073)
  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                     :: 16-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: PC-31
            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 16:08:20
            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)                     :: 5,268
            CDSs (total)                      :: 5,143
            Genes (coding)                    :: 4,932
            CDSs (with protein)               :: 4,932
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 81 of 211
            Pseudo Genes (incomplete)         :: 129 of 211
            Pseudo Genes (internal stop)      :: 50 of 211
            Pseudo Genes (multiple problems)  :: 46 of 211
            Pseudo Genes (short protein)      :: 3 of 211
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062912.1.
            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..4073
                     /organism="Escherichia coli O112ab:H8"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-EA06-22"
                     /serotype="O112ab:H8"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:2778653"
                     /plasmid="unnamed32"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-04-10"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            95..208
                     /locus_tag="IMP05_RS26455"
     CDS             95..208
                     /locus_tag="IMP05_RS26455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071531573.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="replication initiation protein"
     gene            419..1348
                     /locus_tag="IMP05_RS23960"
                     /old_locus_tag="IMP05_23960"
     CDS             419..1348
                     /locus_tag="IMP05_RS23960"
                     /old_locus_tag="IMP05_23960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000571803.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_251123027.1"
                     /translation="MIEMDMPNTIHYPHVIPFISQGKINAIKSTFGNNLSDRECYGIYI
                     WSQKASSAIYPLLQQLEVTLRNSIDKEATKLIGQKWWDNVYTDTSKSKHGDFIHNINKA
                     IIRYENEFKKKNPSMANTKIIAPHDDIIAHTDFYTWQAVLSDAFHTQSRSEASRALWPR
                     LTYRVLKGLDRSKDEGTARIDFLNELNEIRNYRNRLSHNDCIWIKIHSKNLQSAVETIR
                     EKINKIEGLIKTINPQVHLSLTKWGSFYHAKRICSQKEAELHLGKGIINSTTDEMNTIL
                     DQLYALTADGKLTGVVKRNTNNIAFHKF"
                     /name="Abi family protein"
     gene            1942..2535
                     /locus_tag="IMP05_RS23965"
                     /old_locus_tag="IMP05_23965"
     CDS             1942..2535
                     /locus_tag="IMP05_RS23965"
                     /old_locus_tag="IMP05_23965"
                     /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="hypothetical protein"
                     /protein_id="WP_012537770.1"
                     /translation="MSGRKFGRLPNWWARSSWLVNNVRSNEIGGGIASMKCLLALSVLI
                     DFHSRTASVSFTGMERLTGLSRPMIVKGVAKLEKDGLIKIDREMFVNSYELTVQPNDDR
                     WAKVPVDTIRKKLNTISNRGMAPFVALKLYLTIISLRYQSNNTVKVTHETLRSYTGVQP
                     NQIRFGLDVLYCSRLIHLQPKEDRESNIYEIIGL"
                     /name="hypothetical protein"
     gene            complement(2546..2737)
                     /locus_tag="IMP05_RS26460"
     CDS             complement(2546..2737)
                     /locus_tag="IMP05_RS26460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001479926.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_225879636.1"
                     /translation="MCLMGTVCAQTVRHSFSCIAMQWAENDPDAFFRFSLGKTSLFAVS
                     ASESRSVRFSGARNATLW"
                     /name="hypothetical protein"
     gene            3308..3502
                     /locus_tag="IMP05_RS23970"
                     /old_locus_tag="IMP05_23970"
     CDS             3308..3502
                     /locus_tag="IMP05_RS23970"
                     /old_locus_tag="IMP05_23970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2794..3049)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="89.0"
                     /evalue="1.24e-101"
     Typing          complement(3174..3272)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(3584..3670)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2..204
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.059"
                     /coverage="93.0"
                     /evalue="1.83e-91"
     Typing          3869..4070
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.61"
                     /coverage="94.0"
                     /evalue="7.05e-86"
ORIGIN
        1 cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgtt ggtatctcag
       61 ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga
      121 ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaaggc acgccttaac
      181 gccactggca gcagccactg gtaactgatt tagaggagtt tgtcttgaag ttatgcacct
      241 gttaaggcta aactgaaaga acagattttg gtgactgcgc tcctccaagc cagttacctt
      301 ggttcacaga gcgccaactc tttgaacctt cgaaaaaccg cccgccaagg cggttttttc
      361 gtttaacact ctacaactat ccatacgtgt atggcaacat ccaatcacca ctaagtgtat
      421 gatagagatg gatatgccaa atacaattca ttaccctcat gtaataccat ttatatccca
      481 aggaaaaata aatgctataa aaagcacgtt tggtaataac ctgtctgata gggagtgcta
      541 cgggatatat atatggagcc agaaagcctc atctgccata tatccattac tgcaacaact
      601 cgaagttact ttgagaaact cgattgataa agaagcgaca aaactaatag gccaaaaatg
      661 gtgggataat gtatacaccg acacatcaaa aagcaaacac ggtgacttca tacataatat
      721 aaacaaagca ataataagat atgagaatga attcaagaaa aaaaacccat caatggcaaa
      781 taccaaaata attgcacctc atgatgacat cattgcacac acagattttt acacatggca
      841 agcggttttg agcgatgctt ttcatacaca atcaagatct gaagcatcaa gagccttatg
      901 gcccaggctc acctacagag tactgaaggg attagataga agcaaagatg aaggcacagc
      961 cagaattgat ttcttaaacg agctgaatga gatcagaaac tacagaaata ggttatcgca
     1021 taatgattgc atatggataa aaatacactc taaaaatttg caatctgcag tagaaacaat
     1081 aagagaaaaa ataaacaaaa tagaaggact gataaaaacg ataaacccac aggtacacct
     1141 atcattaacg aagtggggtt ccttttatca cgccaaaaga atatgttctc aaaaagaggc
     1201 cgaattgcat ctaggcaaag gaataatcaa tagcacaaca gatgagatga acacaattct
     1261 agatcaacta tacgcactaa ctgctgacgg aaagctaacg ggtgttgtaa aacgaaatac
     1321 caacaatatc gcatttcaca agttttagat cacaaaatag aaaaggcccg acagtttcct
     1381 gtcgagcctc atccaaatct cttgccatta tcacctttcg gtggagcgtg gccttaatgt
     1441 cattgtgaat ctataaaaat ttcacaatgc attaaagcga aagctcaagg cttcactgcc
     1501 atacatgata catcatcatc aggaaaaaga gcaaactatt tcccatgatc acgccaaagc
     1561 ttaccatcca ccatttacca atagatcaaa aaacacacaa caaaaataac taaaaacgcc
     1621 gattaaacca gcattatcaa atttacattt accagttaaa aaacgataaa aacaagataa
     1681 catcatgttt tatatgggaa aacaagcaac cacaaaatat tgctttatct agatttattc
     1741 taataagcgt atataaagtt aaaacacaac aacttagtat gcgactggag gaccaattgg
     1801 aaaccctcaa caatttgctg gtaacgctaa cttccgcaaa gccggaggtt ttggtttctg
     1861 ttgtatcttt aggtgcaatg gttttcatgt atatgataat aaagctattt atatctctcc
     1921 ttgaccgaaa atggggtaaa aatgagcggt agaaaatttg gcaggcttcc aaactggtgg
     1981 gcccgaagct catggcttgt aaacaatgtt cgttcaaatg agataggggg cggcattgca
     2041 tcaatgaaat gcttgttagc tctatccgtc ttgattgatt tccattcaag aacagcctca
     2101 gtatcattta ccggaatgga aagactgact ggactaagcc gccccatgat agtgaaagga
     2161 gtagccaaac ttgagaaaga tggtcttata aagatagata gagagatgtt tgttaactcc
     2221 tatgaattaa cagtacagcc aaatgatgat aggtgggcaa aagtaccagt agatactatc
     2281 aggaaaaaac taaacaccat atcgaacagg gggatggccc catttgtggc attaaaacta
     2341 tatttaacaa ttataagcct tcgttatcag tcaaataata ctgttaaggt gacacatgaa
     2401 acactgagaa gctatacagg tgtccagcca aaccagatta ggttcggctt agatgtactg
     2461 tactgtagtc gcctgataca tctgcaacca aaagaagata gagagtcaaa catctatgaa
     2521 ataatcggcc tatgaggaaa tgcatttacc ataacgtcgc attacgcgca ccgctaaaac
     2581 gcactgaacg cgattctgac gcagataccg caaaaagaga tgttttaccc agtgaaaacc
     2641 gaaaaaatgc gtcaggatcg ttttcagccc actgcatagc tatgcatgaa aatgaatgac
     2701 gaacggtttg ggcgcatacg gtgcccatga gacacatttt cggacatttt cagttcgtga
     2761 atccctgact cattgctaca tatctgaaca gacacccctg gcagcgcccc caggggcgtc
     2821 ctgtaaaaaa acacaccgcg ccgctagcag cacccctgat ataaaatgat gttttttata
     2881 aaaatagtca gtaccccccc tacaaagcgg tgtcggcgcg gtgttgtagc tgcgccggca
     2941 ccgctttttt aaatatcgca aagagagcaa gagaaactaa tttttcataa ctctctattt
     3001 ataaagaaaa atcagcaaaa acttgttttt gcgtggggtg tgggcatttc aggaatgaga
     3061 acagactcgc gtttttccgg agtatcagcg gaattattga ttaagaaaca ctcgacgcag
     3121 agcgaaattt tatgcaacag cggctgcact gcacagggat tatttatcag ttgatatgct
     3181 gtgccatgat acgtcctaaa aaaacaggac aggatgtgca attgtaatac cgtcgcccgc
     3241 aacgtcttac aattaccagc tgctcagggt ccccccgaca cccggaactg acggagaaca
     3301 acggaaggtg aacaaacaac aacaaactgc gctgaatatg gcgcgattta tcaaaagcca
     3361 gagcctgaca ctgcttgaaa aactggatgc tctggatgcc gacgaacagg cagccatgtg
     3421 cgaacgactg cacgaactcg cggaagaact ccagaacagc atccaggttc gctttgagac
     3481 cgaaagtgaa acaggaacat aacgaagctg acggaggcgc tcacggcttg tccgcgagcg
     3541 ttttcggcag cagacaagcc cgtcagggcg cgtcaggggg ttttagcggg tgtcggggcg
     3601 cagccatgac ccagtcacgt agcgatagcg gagtgtatac tggcttaacc atgcggcatc
     3661 agtgcggatt gtatgaaaag tgccccatgc cgggtgtgaa atgccgcaca gatgcgtaag
     3721 gagaaaatgc acgtccaggc gcttttccgc ttcctcgctc actgactcgc tacgctcggt
     3781 cgttcggctg cggcgagcgg tactgactca cacaaaaacg gtaacacagt tatccacaga
     3841 atcaggggat aagaccggaa agaacatgtg agcaacaagg caaagccagg acaaaaggcc
     3901 gcgccgctgg cgtttttcca taggctccgc ccccctgacg agcatcacaa aaaccgacgc
     3961 tcaagtcaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctgga
     4021 agctccctcg tgcgctctcc tgttccgacc ctgccgctta ccggatacct gtc
//
