LOCUS       NZ_CP074026             3608 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PK5 plasmid pYLPK5b, complete sequence.
ACCESSION   NZ_CP074026
VERSION     NZ_CP074026.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877295
            Assembly: GCF_024585865.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3608)
  AUTHORS   Lopez-Dorta,Y., Brilhante,M., Hernandez-Fillor,R.E., Baez,M.,
            Espinosa,I. and Perreten,V.
  TITLE     Molecular epidemiology of Extended-Spectrum Beta-Lactamase-producing
            Escherichia coli from food-producing animals in Cuba using
            whole-genome sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3608)
  AUTHORS   Lopez-Dorta,Y., Brilhante,M. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-APR-2021) Institute of Veterinary Bacteriology,
            University of Bern, Langgassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/24/2023 06:25:43
            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)                     :: 4,557
            CDSs (total)                      :: 4,439
            Genes (coding)                    :: 4,223
            CDSs (with protein)               :: 4,223
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 67 of 216
            Pseudo Genes (incomplete)         :: 118 of 216
            Pseudo Genes (internal stop)      :: 55 of 216
            Pseudo Genes (multiple problems)  :: 26 of 216
            Pseudo Genes (short protein)      :: 5 of 216
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074026.1.
            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..3608
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK5"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPK5b"
                     /geo_loc_name="Cuba: Matanzas"
                     /collection_date="2016-07"
                     /genotype="ST1397"
                     /note="Newborn piglet"
     gene            join(3416..3608,1..569)
                     /locus_tag="KFU66_RS22650"
                     /old_locus_tag="KFU66_22480"
     CDS             join(3416..3608,1..569)
                     /locus_tag="KFU66_RS22650"
                     /old_locus_tag="KFU66_22480"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA methyltransferase"
                     /protein_id="WP_080223457.1"
                     /translation="MVVLADIKIDDVESENTEIKKKKRVQGGEATSNVTMSAHLSGNAE
                     VFPQILDLHVPEGAVIADVTFGGGVFWKKVNLDKYKLLATDIANGVDCRDLPYEETSLD
                     ALVLDPPYMEGLLRNNASHKAGDGTHSTFRKYYSNGDEKSVAGAPKWHAAVTDLYYKAS
                     DEAFRVLKDNGVFIVKCQDEVSANKQWLTHVEIINYCESLGFYTKDLFVVVRSNKAGVS
                     RMKKQVHARKNHSYFLVFIKLPEKKRKKKTL"
                     /name="DNA methyltransferase"
     gene            complement(564..1238)
                     /locus_tag="KFU66_RS22655"
                     /old_locus_tag="KFU66_22485"
     CDS             complement(564..1238)
                     /locus_tag="KFU66_RS22655"
                     /old_locus_tag="KFU66_22485"
                     /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_080223456.1"
                     /translation="MREPSILEKWEISEEKLTELVDKNPSLRGMILGYVAEDKFHELFL
                     EDERVKEVSKDDDHDRKKKGDRTFIYKGKKFTVEVKSLQTAMCKKNEDGTYSGKAQVDG
                     SDRRIVKFPDDSELNTTLLLKGEFDLLAVNCFAFGDGWKFVFAKNSDLPTSTFKKYTEE
                     QRKQLIASLIPVTWPPKPPFSDDPFHLLDEMIAAPEEEPVIEESSELKEVKEDIDVVRV
                     KS"
                     /name="hypothetical protein"
     gene            complement(1235..1462)
                     /locus_tag="KFU66_RS22660"
                     /old_locus_tag="KFU66_22490"
     CDS             complement(1235..1462)
                     /locus_tag="KFU66_RS22660"
                     /old_locus_tag="KFU66_22490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011383102.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_080223455.1"
                     /translation="MKRDERYEKLQKLLIFHRKRLGFTQKMLSEALGKPQSYISKYETG
                     ERRIDAIELIDICNELGVPFYNLIMEVTKK"
                     /name="helix-turn-helix transcriptional regulator"
     gene            2317..2508
                     /locus_tag="KFU66_RS22665"
                     /old_locus_tag="KFU66_22495"
     CDS             2317..2508
                     /locus_tag="KFU66_RS22665"
                     /old_locus_tag="KFU66_22495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1818..2442)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.489"
                     /coverage="99.0"
                     /evalue="7.24e-157"
ORIGIN
        1 cttttggtgg cggcgtattt tggaaaaaag ttaatcttga taagtacaag ctgttggcaa
       61 cagatattgc taacggagtc gattgtcgag atctccctta tgaggaaaca agccttgatg
      121 ccttagtact tgatcctcca tatatggagg gattacttcg caacaatgct tcgcataaag
      181 caggggatgg aacacattct acgttcagaa aatattactc taacggcgac gaaaaaagtg
      241 tagcaggggc tccaaaatgg catgcagctg ttaccgatct ttattataag gctagtgatg
      301 aagcatttag ggttttaaaa gataatggtg tttttattgt aaaatgccaa gatgaggttt
      361 cggctaacaa acaatggttg actcatgttg aaataataaa ctattgcgaa tctcttggct
      421 tctatactaa agatcttttt gtcgttgttc gtagtaacaa ggctggggtt tctcgaatga
      481 agaaacaggt tcatgcaagg aagaatcaca gttacttcct tgtttttata aagcttccgg
      541 aaaagaaaag aaagaagaaa acgttatgat tttactctaa ctacatctat atcttctttt
      601 acttctttta attcactact ttcttctatc actggttcct cttctggcgc tgcaatcatc
      661 tcgtccagaa ggtggaatgg gtcatcactg aatggtggtt ttggtggcca agtcacagga
      721 atcagtgagg caataagttg tttcctttgt tcttctgtgt attttttgaa tgttgaggtg
      781 ggaaggtcag aattttttgc aaaaacaaat ttccatccat caccaaaagc aaagcaatta
      841 acggctaata ggtcaaactc tcctttcaag agtaacgtcg tatttagttc tgaatcgtct
      901 gggaatttta ctattcttcg atcactgccg tctacttggg cttttcctga ataagttccg
      961 tcttcatttt tcttgcacat tgcggtttgc aagcttttaa cttcaactgt aaatttttta
     1021 cctttataaa taaaggttct atctcctttt ttctttctgt catgatcgtc gtctttagaa
     1081 acctccttta ctctttcatc ttcaaggaat agctcgtgaa atttatcctc agcaacataa
     1141 cctaaaatca ttcctctaag agatgggttt ttatcaacca attcagttaa tttttcttcg
     1201 cttatttccc atttttctag aatcgagggt tctctcattt ttttgttact tccataatta
     1261 agttatagaa cggcacgcct aattcattac aaatatctat taattcaatt gcatctattc
     1321 tcctctctcc agtttcatat tttgagatat aagattgagg ctttcctaac gcttcagata
     1381 gcattttttg ggtaaatccc agccttttcc tatgaaaaat caatagcttt tgtagctttt
     1441 cgtatcgttc gtctcttttc atttaatgat tttgtatccc aatatcgaat aacccaaatt
     1501 gggataattg cgagggaggg ggggggggga gtagggctgt tctgctaaag gaatgcagcg
     1561 tttttagaga ggatcttctt gagatcattt ctctccgagc gtactctttg tccttaaaac
     1621 gaaaaaacca cctggggagg tggtttttcg aaggttcagt aagttgggga acttctgaac
     1681 cgtggtaaca gtcttgtgcg agacgtgtca ccaaattcgt ccttccagtg tagcctcagt
     1741 tagggcacca cttcaagaac tctcgataca tctctcgcac attctgtcta ccaatggcta
     1801 ccgccactgg cgatttgtcg tgtctttccg ggttggactc aagttgatag ttaccggaac
     1861 gggcgtggta gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaactg
     1921 cctacccgga actgagtgtc aggcgtggaa tgagataaac gcggccataa cagcggaatg
     1981 acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagcgacc agggggaaac
     2041 gcctgggatc tttatagtcc tgtcgggttt cgccaccact gatttgagcg tcagattttc
     2101 gtgatgcttg tcaggggggc ggagcctatg gaaaaacgcc ccggcggggc gtggcctttt
     2161 cgcccttgtc cttagctttc gttatgctta ccgttacgtt atctgcttat cttccctccg
     2221 ctcgccgcag actcatgacc gaacggagtg agcgaatgag cgaggaagcg gaaaaccatc
     2281 cgaacgtaca gtaagcactt tcgcgccggg gccttcatga acaaacaaca aaagactgcc
     2341 gttaacatgg ctaaattcat ccaggatcag tccctgcttc ttctggacag gcttaatgag
     2401 ctggatctgg atcatgaggc tgatttctgc gagaaactcc atgaggatgc ggaacgcctt
     2461 taccgaagcc tgtcagcgcg cctgaatgag cagcaggacg gtgcgtaatg gctccgttct
     2521 gggtattacc ggagtaatac cggcatcgcc ttaattttca ttgtgttagc gcttaacatt
     2581 attaccccgg taatacccag aatccctgtg ttttttcttt tttatttatt tttcatgaag
     2641 ttgcgatgaa aatcgcagct gcgttaggtg tatgtcattt tttagtatat aaaacgacca
     2701 ctcccgagtg ctggcgccgc aggttaagga tgattctggc taaaaagcgt ccttttccgg
     2761 gaaagggtca tgctcgtatg accctatggg ttcagcgact acacataaac tacaaaattg
     2821 catctgcttt taccccagaa cgcgggtgta caacagaatt acatcaaaag tacatcaaaa
     2881 ttacatcact tttacgtcag atcgcgggtg tacaacagaa ttacatcaaa agtacatcac
     2941 ttttacgtca cttttacatc atttttacgt cagatccgtt ccctgaacca ttcgtacatc
     3001 cgccccctct tcctgggcct cctgcacgtg ctgaaaatgg tttttccggc tgtgccggca
     3061 acgcctcacg gccacgcaat aaattgcgtc cccgttcacc gttttcggat aagaagaaca
     3121 tcggaaacag gacttccact ggctgcacgg cgtgaatttc cgcgctatgc acttgcgcgc
     3181 atactcatgc atgccgtaaa aacagagcct gcgcgtttct ggcgggtttt cgggtggttt
     3241 gttgcctgtt ttgccggttt cccgtcagaa acgccctgag agcctctcag gcggtgcacg
     3301 caacggatgt tatggtaaat ccttttttcg gagcgaatgt ttagacagat actcttgata
     3361 agagtggaga tgactggcat tcttgagtaa ttgaatattc caaaatgggt tttttatggt
     3421 ggttttagca gatattaaaa tagacgatgt agaatcggaa aacactgaaa ttaaaaagaa
     3481 aaagagggtt caaggcggtg aggctacgag taatgtaacg atgtcagcgc acctgagcgg
     3541 caacgccgaa gttttcccgc aaatcctaga cttgcatgtt cctgaagggg ctgtgattgc
     3601 ggatgtca
//
