LOCUS       NZ_CP081718             3249 bp    DNA     circular CON 02-NOV-2023
DEFINITION  Escherichia coli strain CX04 plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP081718
VERSION     NZ_CP081718.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18446038
            Assembly: GCF_019971015.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3249)
  AUTHORS   Yang,X., Tran,F. and Zhang,P.
  TITLE     Genetic characterization of Escherichia coli recovered from beef
            production environments, which harbor the locus of heat resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3249)
  AUTHORS   Yang,X., Tran,F. and Zhang,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-AUG-2021) Food Safety, Agriculture & Agri-Food Canada,
            6000 C & E Trail, Lacombe, Alberta T4L 1W1, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 26-JAN-2021
            Assembly Method                   :: flye v. 2.8.2
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 88x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/02/2023 04:25:52
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,225
            CDSs (total)                      :: 5,110
            Genes (coding)                    :: 4,820
            CDSs (with protein)               :: 4,820
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 290
            CDSs (without protein)            :: 290
            Pseudo Genes (ambiguous residues) :: 0 of 290
            Pseudo Genes (frameshifted)       :: 107 of 290
            Pseudo Genes (incomplete)         :: 174 of 290
            Pseudo Genes (internal stop)      :: 56 of 290
            Pseudo Genes (multiple problems)  :: 44 of 290
            Pseudo Genes (short protein)      :: 3 of 290
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP081718.1.
            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..3249
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CX04"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Canada: Alberta"
                     /collection_date="2014/2015"
     gene            451..675
                     /locus_tag="J6O07_RS25940"
                     /old_locus_tag="J6O07_25845"
     CDS             451..675
                     /locus_tag="J6O07_RS25940"
                     /old_locus_tag="J6O07_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000879771.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6290 family protein"
                     /protein_id="WP_000879771.1"
                     /translation="MLAIRLSDEIESRLDSLAKQTGRTKTFYAREAILAHLEDLEDYYL
                     SAETAARVRRGDEAVHSSEDVRKSLGLDD"
                     /name="DUF6290 family protein"
     gene            659..925
                     /locus_tag="J6O07_RS25945"
                     /old_locus_tag="J6O07_25850"
     CDS             659..925
                     /locus_tag="J6O07_RS25945"
                     /old_locus_tag="J6O07_25850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000262326.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000262326.1"
                     /translation="MVWTINYSDRALKSLRKMDKQNARRIVDFMDLRIAVAADPRQSGK
                     PLKGELGEFWRYRVGDYRILCEIRDDELVILAATIGHRREVYD"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1035..1247
                     /locus_tag="J6O07_RS25950"
                     /old_locus_tag="J6O07_25855"
     CDS             1035..1247
                     /locus_tag="J6O07_RS25950"
                     /old_locus_tag="J6O07_25855"
                     /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_039509481.1"
                     /translation="MGDFERTYGAGADFDRIIDENNSEYFRDERQKAKNSKKEFSSFQD
                     ALVWAKANPGKTIVRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(1668..1802)
                     /locus_tag="J6O07_RS26220"
                     /old_locus_tag="J6O07_25860"
     CDS             complement(1668..1802)
                     /locus_tag="J6O07_RS26220"
                     /old_locus_tag="J6O07_25860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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_072035952.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHDKAPLAAATGNRFRGGES"
                     /name="replication initiation protein"
     gene            2656..2883
                     /locus_tag="J6O07_RS25955"
                     /old_locus_tag="J6O07_25865"
     CDS             2656..2883
                     /locus_tag="J6O07_RS25955"
                     /old_locus_tag="J6O07_25865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_206659768.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(2931..3116)
                     /locus_tag="J6O07_RS25960"
                     /old_locus_tag="J6O07_25870"
     CDS             complement(2931..3116)
                     /locus_tag="J6O07_RS25960"
                     /old_locus_tag="J6O07_25870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_054626234.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLEKLDVLDLDDEAADCERMHEQAE
                     ALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1694..2183)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.13"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 gtttctgagc ggttttcagg gggtaagatg tgttcttttg caggtgaggt cgtagaaacg
       61 ccctgagagc ctctcaggcg gtgcacgcaa cagatgttat gttcaatcag actgatctgc
      121 gggtacaaaa aaagccccgg agggctttta actactgact tatttttttg aggatttgct
      181 gggtttcaat ttgtcagtat tccccggcgt ttttttattg tcacgctggc gtttatcagg
      241 ttcccctgtt gaatcggcaa ttcgtttcgg acccggctta agacccataa tcgttatcct
      301 ttcaatagtt aagaggaaag ccctcaagct ggatatattg acagcgttac ggattatcaa
      361 gaggggccag caagattatt ttttgttctt ttaggttgat tgcgatacta ttgctataca
      421 tgtatatcaa atggtgttca ggaggtttat atgcttgcta tccggttatc tgatgagatt
      481 gagtcccgtc tggactcgct ggcgaagcaa accggcagaa caaagacgtt ctatgcgcgg
      541 gaagcaatac tggcgcatct ggaagacctg gaagattatt atctttcagc agaaactgcc
      601 gcacgcgttc gccgtggtga tgaagccgtg cattcgtctg aagacgtgag gaagtcactt
      661 ggtctggacg attaactatt ccgaccgggc gctcaaatcg ttacgcaaga tggacaaaca
      721 gaacgcacga cggattgtgg attttatgga tttacgcatt gcagttgctg ccgatcctcg
      781 ccagtcaggg aagccgctca aaggtgagct gggcgagttc tggcgctatc gggtgggaga
      841 ttatcgcatt ctgtgtgaga tccgggatga cgagctggtt atccttgccg ccaccattgg
      901 ccatcgccgc gaagtttacg actgaagccc gctatgcggg ctttttttga tgctgacaac
      961 ggatgttatg gtaaataaga gtgtctgttg gatattttaa atctgttttt ttattaaatt
     1021 tatgggggta ggaaatgggg gattttgagc gtacctacgg agctggtgct gattttgatc
     1081 ggataattga tgagaataac agcgaatatt ttcgagatga gcgccaaaaa gctaaaaatt
     1141 cgaaaaaaga attctcttct tttcaagatg ctttggtttg ggcgaaagct aatcctggta
     1201 aaacgatagt aagatctcca gacggtgtgg gatttattga aaaatgaaag agtggattca
     1261 ctgtaaaacg gcagtcattt tttggacaac actggctata tacgtactca tatgtttcac
     1321 agtgtcgtat gttggagtct atgttacgta cattgcaggg cctattttgt tagttacagg
     1381 aattcttgca tggcttacga aacctagtag taattcaaat aaatctaata tgtgactggg
     1441 taagacgaac ttcatccaac cataaaaccc gcttttttaa acggatcttc ttgagatcat
     1501 ttagggagaa tcgtaatctc ttagctctgt aaacgaaaaa accacccggc aaggtggctt
     1561 tttcgaaggt tcgcaagagt tgacgctctt ttgaaccgcg gtaactggct tggaggagca
     1621 cagtcacaaa atagtccttt cagtgtagcc ttatcgcacc cgaaatttca agactctcct
     1681 cctctaaacc tgttaccagt ggctgctgcc agtggcgctt tgtcgtgtct ttccgggttg
     1741 gactcaagac gatagttacc ggataaggcg cagcagtcgg actgaacggg gggttcgtgc
     1801 atacagtcca gcttggagcg aactgcctac ccggaactga gtgtcaggcg tggaatgaga
     1861 taaacgcggc cataacagcg gaatgacacc ggtaaaccga aaggcaggaa caggagagcg
     1921 cacgagggag ccaccagggg gaaacgcctg gtatctttaa gtcctgtcgg gtttcgccac
     1981 cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct atggaaaaac
     2041 ggcttcgccg tggccttctt gcttccctgt taagcttctt cctggaagat gccaggaaat
     2101 ttccgccccg ccagtaagcc ggtaccgctc gccgcagccg aacgaccgag cggagcgagt
     2161 cagtgagcga ggaagcggaa tatctccggg cttatctttg gcaccgtacg cgccatagct
     2221 gcatttttta atacgatgca ggatagggca aacgccgcaa aatgacgtca tccgacatca
     2281 ttcctccgcg ttcgtccagt gacctacagt cggctctggg gtgtcggggc tgtgccctga
     2341 ccaggcgttt tggagtatcg ccaccgtggt ggcggtgcta caacacatat cctgtccctt
     2401 ccttggcatc tctgaagttt agccagtata cactccgcta gcgctacgtg actggttcag
     2461 ggctgcgccc cgacacccgc taaaagcact gacgcgcctg cggcttgccc aaccccgcgc
     2521 cgtccgggaa agaatttccc gatcgacccg acgtttctgt ttacctgtga tgttaacgtt
     2581 tggatctttt tcccgggttt acctattttc ttctaatgaa gcgttcacag ctgacgttaa
     2641 tagatgggtg ctttcatgtt tggtttttca ccaggagaac ttatgaacct ttgccccgat
     2701 gaacgtctgc tctttgtgcg gatgatttcc gctatgcttc gccgttcggg cggtgatgcg
     2761 ggtgctgtta tgtttgaggc gtatcgccat attgtgtccg ataccaatca agctcgtcgt
     2821 tcctgcatgc tcgacctgct cgaaagcgtc aggcatgact atgtacacgg tggatataca
     2881 tagttgccct ggatacgctt ttcgtctaag tgagcgttct tttcgtctct ttattcgccg
     2941 tcctgtatac cgaagcgtgc gctcagcttc tgataaagcg cttctgcctg ttcgtgcatt
     3001 cgctcacagt cggctgcctc gtcatcaaga tcgagcacgt cgagtttttc gagcagcagc
     3061 gactgcgccc ggataaattt tgccatgttc agtgcggctg attcctgttt tgtcatacgg
     3121 ctttttcccg gttttatggt gatcgcagac tgaaatctta cttcattcac ttgagtgcat
     3181 agccatgcag gtacgcagaa atcatcagcg cgtttctgag cggttttcag ggggtaagat
     3241 gtgttcttt
//
