LOCUS       NZ_CP073993             2579 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB10 plasmid pYLMB10e, complete sequence.
ACCESSION   NZ_CP073993
VERSION     NZ_CP073993.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877303
            Assembly: GCF_024585705.1
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  JOURNAL   Unpublished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 06:55:18
            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)                     :: 4,648
            CDSs (total)                      :: 4,530
            Genes (coding)                    :: 4,307
            CDSs (with protein)               :: 4,307
            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)              :: 223
            CDSs (without protein)            :: 223
            Pseudo Genes (ambiguous residues) :: 0 of 223
            Pseudo Genes (frameshifted)       :: 72 of 223
            Pseudo Genes (incomplete)         :: 145 of 223
            Pseudo Genes (internal stop)      :: 43 of 223
            Pseudo Genes (multiple problems)  :: 38 of 223
            Pseudo Genes (short protein)      :: 3 of 223
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073993.1.
            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="MB10"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB10e"
                     /geo_loc_name="Cuba: Santa Cruz del Norte"
                     /collection_date="2015"
                     /genotype="ST1716"
                     /note="Broiler"
     gene            <838..993
                     /locus_tag="KFU65_RS23105"
                     /old_locus_tag="KFU65_22885"
                     /pseudo=""
     CDS             <838..993
                     /locus_tag="KFU65_RS23105"
                     /old_locus_tag="KFU65_22885"
                     /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"
     gene            1087..1731
                     /locus_tag="KFU65_RS23110"
                     /old_locus_tag="KFU65_22890"
     CDS             1087..1731
                     /locus_tag="KFU65_RS23110"
                     /old_locus_tag="KFU65_22890"
                     /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(2113..2349)
                     /locus_tag="KFU65_RS23115"
                     /old_locus_tag="KFU65_22895"
     CDS             complement(2113..2349)
                     /locus_tag="KFU65_RS23115"
                     /old_locus_tag="KFU65_22895"
                     /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"
     ARG             1088..1728
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2..109)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.25e-49"
     Typing          88..579
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ggcacggatg tggaaatcag tgaagtgctt catgtagcag gagaaaaaag gcggcaccag
       61 cgcgtcagca ggatatgtag tacaggatat attccgcttc ctcgctcact gactcgctgc
      121 gctcggtcgt tcggctgcgg cgagcggtgc cggcttacag gcggggcgga aatttcctgg
      181 gagataccag gaaggagctt aacagggaag agataaggcc gcggcgaagc cgtttttcca
      241 taggctccgc ccccctgaca aacatcatga aatctgacgc tcaaatcagt ggtggcgaaa
      301 cccgatgcgg cttaaagata ccaggcgttt ccccctggtg gctccctcgt gctcccccgc
      361 attcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt atctcattcc
      421 acgcctgaca ctcagttccg cgaaggcagt tcgctcctgg atggactgta tgcacgaacc
      481 ccccgttcag tccgactgct gcgccttatc cggtaactat catcttgagt ccaacccgga
      541 aagacacgac ttatcgccac tggcagcagc cactggtaac tgatttagag gagttagtct
      601 tgaagttatg cgcctgttaa ggctaaactg aaagaacaga tttggttact gcgctcctcg
      661 taagccagtt accacggttc aaagagttgc tgctctgaga accttcgaaa aaccgccttg
      721 cagggcggtt ttttcgttta cagagcaaga gattacgacg ccacagaaag gatctcaaga
      781 agatccttca ccgtaatgga aatctatcca atccgagcac ataggataca catcgttata
      841 acgctggatc tgcgtgaatt ccagcagcag caagagaaag actttctaca aaccagctta
      901 cagcaggcta aatttaacca gaaaaaagcc gctgaattac tgggtctgac ttatcatcag
      961 ctacgtgcct tgctgaagaa acaccagatc taatacgcat ttgcaggtgt catactggcg
     1021 ggtttgacgc ataacgtcat aaggtttacc atggcgtcat tactgtataa aaacacaggc
     1081 atagatatga ctctggcatt agttggcgaa aaaattgaca gaaatcgctt caccggtgag
     1141 aaagttgaaa atagtacatt ttttaactgc gatttttcag gtgccgacct gagcggcact
     1201 gaatttatcg gctgccagtt ctatgatcgc gaaagtcaga aagggtgcaa ttttagtcgc
     1261 gcaatgctga aagatgccat tttcaaaagc tgtgatttat caatggcaga tttccgcaac
     1321 gtcagtgcct tgggcattga aattcgccac tgccgcgcac aaggcgcaga tttccgcggt
     1381 gcaagcttta tgaatatgat caccacgcgc acctggtttt gcagcgcata tatcactaat
     1441 actaatctaa gctacgccaa tttttcgaaa gtcgtgttgg aaaagtgtga gctgtgggaa
     1501 aaccgctgga tggggactca ggtactgggt gcgacgttca gtggttcaga tctctccggc
     1561 ggcgagtttt cgactttcga ctggcgagca gcaaacttca cacattgcga tctgaccaat
     1621 tcggagttag gtgacttaga tattcggggt gttgatttac aaggcgttaa gttagacagc
     1681 taccaggcat cgttgctcat ggagcggctt ggcatcgctg tgattggtta gttcagcgtt
     1741 tacaccggga gatgcgtttg acgatttact tttacccgcg atcatcgcgt ttattgagtt
     1801 tattatttat ctatgcgatt ccgatgaaaa attcgcacga aaatatggct aactcatagc
     1861 aaaaaaaaag ccccctaagg gctttttttt gtacctgacg gtcagaccga ttaaacataa
     1921 catcccttgc ccgcaccccc gcaggcgccc tcagcgcaat cctgctgcat cagggccgtt
     1981 tccagcacct ttcctcacca gtatcccgga aaaacgcccc tgatgatttc tgcgcgactg
     2041 catggctatg cacgcaggtg aatggcaggt gatttcgcag cgtcagcacc actaaaccgc
     2101 caaaagccaa aatcagcggc gcggcgcgcg cggacgtgac caggcaaaat cggactgctg
     2161 ccgctcatcc tcacgtaatg cacgctggcg gtcggcgtaa cgctgcaact caatttgcgc
     2221 acgcgctctg ttcaggacga tgtgccggtt aggctgattt agctttttac ctgacgctct
     2281 ttcagctgcg gcaacagcat catcaagaaa ttttttctct gcaggcgtca agtttgtcag
     2341 tctggccata acgttctcca gtcagaataa atcagcacag tctgccagac acagtagaaa
     2401 cgatgaagcg ccagcgacgg tgaaaggcag tcagaaacgg tgaacgggag cggattttaa
     2461 tccggtgccg tgaggcgttg gacaagccgc aggcgcgtca ttagctttta gccggtttcg
     2521 gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg tatactggct gactatgtt
//
