LOCUS       NZ_CP074027             2579 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PK5 plasmid pYLPK5c, complete sequence.
ACCESSION   NZ_CP074027
VERSION     NZ_CP074027.1
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 2579)
  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  JOURNAL   Unpublished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 2579)
  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
            CP074027.1.
            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..2579
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK5"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPK5c"
                     /geo_loc_name="Cuba: Matanzas"
                     /collection_date="2016-07"
                     /genotype="ST1397"
                     /note="Newborn piglet"
     gene            complement(join(2469..2579,1..3))
                     /locus_tag="KFU66_RS22670"
                     /old_locus_tag="KFU66_22500"
     CDS             complement(join(2469..2579,1..3))
                     /locus_tag="KFU66_RS22670"
                     /old_locus_tag="KFU66_22500"
                     /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="hypothetical protein"
                     /protein_id="WP_032667588.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHDLSPLAAATGN"
                     /name="hypothetical protein"
     gene            703..939
                     /locus_tag="KFU66_RS22675"
                     /old_locus_tag="KFU66_22505"
     CDS             703..939
                     /locus_tag="KFU66_RS22675"
                     /old_locus_tag="KFU66_22505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012772745.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            complement(1321..1965)
                     /locus_tag="KFU66_RS22680"
                     /old_locus_tag="KFU66_22510"
     CDS             complement(1321..1965)
                     /locus_tag="KFU66_RS22680"
                     /old_locus_tag="KFU66_22510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(2059..>2214)
                     /locus_tag="KFU66_RS22685"
                     /old_locus_tag="KFU66_22515"
                     /pseudo=""
     CDS             complement(2059..>2214)
                     /locus_tag="KFU66_RS22685"
                     /old_locus_tag="KFU66_22515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     ARG             complement(1325..1965)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          365..538
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(2..386)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.99"
                     /coverage="81.0"
                     /evalue="2.56e-151"
     Typing          complement(2268..2579)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.588"
                     /coverage="99.0"
                     /evalue="1.17e-59"
ORIGIN
        1 catacagtcc atccaggagc gaactgcctt cgcggaactg agtgtcaggc gtggaatgag
       61 ataaacgcgg ccataacagc ggaatgacac cggtaaaccg aaaggcagga atgcggggga
      121 gcacgaggga gccaccaggg ggaaacgcct ggtatcttta agccgcatcg ggtttcgcca
      181 ccactgattt gagcgtcaga tttcatgatg tttgtcaggg gggcggagcc tatggaaaaa
      241 cggcttcgcc gcggccttat ctcttccctg ttaagctcct tcctggtatc tcccaggaaa
      301 tttccgcccc gcctgtaagc cggcaccgct cgccgcagcc gaacgaccga gcgcagcgag
      361 tcagtgagcg aggaagcgga atatatcctg tactacatat cctgctgacg cgctggtgcc
      421 gccttttttc tcctgctaca tgaagcactt cactgatttc cacatccgtg ccaacatagt
      481 cagccagtat acactccgct agcgctacgt gactggttca gggctgcgcc ccgaaaccgg
      541 ctaaaagcta atgacgcgcc tgcggcttgt ccaacgcctc acggcaccgg attaaaatcc
      601 gctcccgttc accgtttctg actgcctttc accgtcgctg gcgcttcatc gtttctactg
      661 tgtctggcag actgtgctga tttattctga ctggagaacg ttatggccag actgacaaac
      721 ttgacgcctg cagagaaaaa atttcttgat gatgctgttg ccgcagctga aagagcgtca
      781 ggtaaaaagc taaatcagcc taaccggcac atcgtcctga acagagcgcg tgcgcaaatt
      841 gagttgcagc gttacgccga ccgccagcgt gcattacgtg aggatgagcg gcagcagtcc
      901 gattttgcct ggtcacgtcc gcgcgcgccg cgccgctgat tttggctttt ggcggtttag
      961 tggtgctgac gctgcgaaat cacctgccat tcacctgcgt gcatagccat gcagtcgcgc
     1021 agaaatcatc aggggcgttt ttccgggata ctggtgagga aaggtgctgg aaacggccct
     1081 gatgcagcag gattgcgctg agggcgcctg cgggggtgcg ggcaagggat gttatgttta
     1141 atcggtctga ccgtcaggta caaaaaaaag cccttagggg gctttttttt tgctatgagt
     1201 tagccatatt ttcgtgcgaa tttttcatcg gaatcgcata gataaataat aaactcaata
     1261 aacgcgatga tcgcgggtaa aagtaaatcg tcaaacgcat ctcccggtgt aaacgctgaa
     1321 ctaaccaatc acagcgatgc caagccgctc catgagcaac gatgcctggt agctgtctaa
     1381 cttaacgcct tgtaaatcaa caccccgaat atctaagtca cctaactccg aattggtcag
     1441 atcgcaatgt gtgaagtttg ctgctcgcca gtcgaaagtc gaaaactcgc cgccggagag
     1501 atctgaacca ctgaacgtcg cacccagtac ctgagtcccc atccagcggt tttcccacag
     1561 ctcacacttt tccaacacga ctttcgaaaa attggcgtag cttagattag tattagtgat
     1621 atatgcgctg caaaaccagg tgcgcgtggt gatcatattc ataaagcttg caccgcggaa
     1681 atctgcgcct tgtgcgcggc agtggcgaat ttcaatgccc aaggcactga cgttgcggaa
     1741 atctgccatt gataaatcac agcttttgaa aatggcatct ttcagcattg cgcgactaaa
     1801 attgcaccct ttctgacttt cgcgatcata gaactggcag ccgataaatt cagtgccgct
     1861 caggtcggca cctgaaaaat cgcagttaaa aaatgtacta ttttcaactt tctcaccggt
     1921 gaagcgattt ctgtcaattt tttcgccaac taatgccaga gtcatatcta tgcctgtgtt
     1981 tttatacagt aatgacgcca tggtaaacct tatgacgtta tgcgtcaaac ccgccagtat
     2041 gacacctgca aatgcgtatt agatctggtg tttcttcagc aaggcacgta gctgatgata
     2101 agtcagaccc agtaattcag cggctttttt ctggttaaat ttagcctgct gtaagctggt
     2161 ttgtagaaag tctttctctt gctgctgctg gaattcacgc agatccagcg ttataacgat
     2221 gtgtatccta tgtgctcgga ttggatagat ttccattacg gtgaaggatc ttcttgagat
     2281 cctttctgtg gcgtcgtaat ctcttgctct gtaaacgaaa aaaccgccct gcaaggcggt
     2341 ttttcgaagg ttctcagagc agcaactctt tgaaccgtgg taactggctt acgaggagcg
     2401 cagtaaccaa atctgttctt tcagtttagc cttaacaggc gcataacttc aagactaact
     2461 cctctaaatc agttaccagt ggctgctgcc agtggcgata agtcgtgtct ttccgggttg
     2521 gactcaagat gatagttacc ggataaggcg cagcagtcgg actgaacggg gggttcgtg
//
