LOCUS       NZ_CP074017             2579 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI24 plasmid pYLPI24e, complete sequence.
ACCESSION   NZ_CP074017
VERSION     NZ_CP074017.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877297
            Assembly: GCF_024585825.1
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  JOURNAL   Unpublished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; Canu v. 2.1.1
            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 06:36:49
            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)                     :: 4,780
            CDSs (total)                      :: 4,663
            Genes (coding)                    :: 4,389
            CDSs (with protein)               :: 4,389
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 274
            CDSs (without protein)            :: 274
            Pseudo Genes (ambiguous residues) :: 0 of 274
            Pseudo Genes (frameshifted)       :: 73 of 274
            Pseudo Genes (incomplete)         :: 195 of 274
            Pseudo Genes (internal stop)      :: 43 of 274
            Pseudo Genes (multiple problems)  :: 36 of 274
            Pseudo Genes (short protein)      :: 3 of 274
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074017.1.
            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="PI24"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI24e"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST710"
                     /note="Post-weaning piglet"
     gene            join(2097..2579,1..198)
                     /locus_tag="KFU81_RS23730"
                     /old_locus_tag="KFU81_23580"
     CDS             join(2097..2579,1..198)
                     /locus_tag="KFU81_RS23730"
                     /old_locus_tag="KFU81_23580"
                     /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="QnrB family quinolone resistance pentapeptide
                     repeat protein"
                     /protein_id="WP_012772744.1"
                     /translation="MASLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGA
                     DLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQ
                     GADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATF
                     SGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGI
                     AVIG"
                     /name="QnrB family quinolone resistance pentapeptide repeat
                     protein"
     gene            complement(580..816)
                     /locus_tag="KFU81_RS23735"
                     /old_locus_tag="KFU81_23585"
     CDS             complement(580..816)
                     /locus_tag="KFU81_RS23735"
                     /old_locus_tag="KFU81_23585"
                     /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            <1884..2039
                     /locus_tag="KFU81_RS23740"
                     /old_locus_tag="KFU81_23590"
                     /pseudo=""
     CDS             <1884..2039
                     /locus_tag="KFU81_RS23740"
                     /old_locus_tag="KFU81_23590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707212.3"
                     /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             2098..2579
                     /name="QnrB10"
                     /gene="QnrB10"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.38"
                     /coverage="71.24"
     ARG             2..198
                     /name="QnrB19"
                     /gene="QnrB19"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="30.37"
     Typing          complement(982..1155)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1134..1625
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 acgttcagtg gttcagatct ctccggcggc gagttttcga ctttcgactg gcgagcagca
       61 aacttcacac attgcgatct gaccaattcg gagttaggtg acttagatat tcggggtgtt
      121 gatttacaag gcgttaagtt agacagctac caggcatcgt tgctcatgga gcggcttggc
      181 atcgctgtga ttggttagtt cagcgtttac accgggagat gcgtttgacg atttactttt
      241 acccgcgatc atcgcgttta ttgagtttat tatttatcta tgcgattccg atgaaaaatt
      301 cgcacgaaaa tatggctaac tcatagcaaa aaaaaagccc cctaagggct tttttttgta
      361 cctgacggtc agaccgatta aacataacat cccttgcccg cacccccgca ggcgccctca
      421 gcgcaatcct gctgcatcag ggccgtttcc agcacctttc ctcaccagta tcccggaaaa
      481 acgcccctga tgatttctgc gcgactgcat ggctatgcac gcaggtgaat ggcaggtgat
      541 ttcgcagcgt cagcaccact aaaccgccaa aagccaaaat cagcggcgcg gcgcgcgcgg
      601 acgtgaccag gcaaaatcgg actgctgccg ctcatcctca cgtaatgcac gctggcggtc
      661 ggcgtaacgc tgcaactcaa tttgcgcacg cgctctgttc aggacgatgt gccggttagg
      721 ctgatttagc tttttacctg acgctctttc agctgcggca acagcatcat caagaaattt
      781 tttctctgca ggcgtcaagt ttgtcagtct ggccataacg ttctccagtc agaataaatc
      841 agcacagtct gccagacaca gtagaaacga tgaagcgcca gcgacggtga aaggcagtca
      901 gaaacggtga acgggagcgg attttaatcc ggtgccgtga ggcgttggac aagccgcagg
      961 cgcgtcatta gcttttagcc ggtttcgggg cgcagccctg aaccagtcac gtagcgctag
     1021 cggagtgtat actggctgac tatgttggca cggatgtgga aatcagtgaa gtgcttcatg
     1081 tagcaggaga aaaaaggcgg caccagcgcg tcagcaggat atgtagtaca ggatatattc
     1141 cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag cggtgccggc
     1201 ttacaggcgg ggcggaaatt tcctgggaga taccaggaag gagcttaaca gggaagagat
     1261 aaggccgcgg cgaagccgtt tttccatagg ctccgccccc ctgacaaaca tcatgaaatc
     1321 tgacgctcaa atcagtggtg gcgaaacccg atgcggctta aagataccag gcgtttcccc
     1381 ctggtggctc cctcgtgctc ccccgcattc ctgcctttcg gtttaccggt gtcattccgc
     1441 tgttatggcc gcgtttatct cattccacgc ctgacactca gttccgcgaa ggcagttcgc
     1501 tcctggatgg actgtatgca cgaacccccc gttcagtccg actgctgcgc cttatccggt
     1561 aactatcatc ttgagtccaa cccggaaaga cacgacttat cgccactggc agcagccact
     1621 ggtaactgat ttagaggagt tagtcttgaa gttatgcgcc tgttaaggct aaactgaaag
     1681 aacagatttg gttactgcgc tcctcgtaag ccagttacca cggttcaaag agttgctgct
     1741 ctgagaacct tcgaaaaacc gccttgcagg gcggtttttt cgtttacaga gcaagagatt
     1801 acgacgccac agaaaggatc tcaagaagat ccttcaccgt aatggaaatc tatccaatcc
     1861 gagcacatag gatacacatc gttataacgc tggatctgcg tgaattccag cagcagcaag
     1921 agaaagactt tctacaaacc agcttacagc aggctaaatt taaccagaaa aaagccgctg
     1981 aattactggg tctgacttat catcagctac gtgccttgct gaagaaacac cagatctaat
     2041 acgcatttgc aggtgtcata ctggcgggtt tgacgcataa cgtcataagg tttaccatgg
     2101 cgtcattact gtataaaaac acaggcatag atatgactct ggcattagtt ggcgaaaaaa
     2161 ttgacagaaa tcgcttcacc ggtgagaaag ttgaaaatag tacatttttt aactgcgatt
     2221 tttcaggtgc cgacctgagc ggcactgaat ttatcggctg ccagttctat gatcgcgaaa
     2281 gtcagaaagg gtgcaatttt agtcgcgcaa tgctgaaaga tgccattttc aaaagctgtg
     2341 atttatcaat ggcagatttc cgcaacgtca gtgccttggg cattgaaatt cgccactgcc
     2401 gcgcacaagg cgcagatttc cgcggtgcaa gctttatgaa tatgatcacc acgcgcacct
     2461 ggttttgcag cgcatatatc actaatacta atctaagcta cgccaatttt tcgaaagtcg
     2521 tgttggaaaa gtgtgagctg tgggaaaacc gctggatggg gactcaggta ctgggtgcg
//
