LOCUS       NZ_CP073942             3180 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB53 plasmid pYLMB53c, complete sequence.
ACCESSION   NZ_CP073942
VERSION     NZ_CP073942.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877315
            Assembly: GCF_024585465.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3180)
  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  JOURNAL   Unpublished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 3180)
  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 06:49:49
            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)                     :: 4,622
            CDSs (total)                      :: 4,505
            Genes (coding)                    :: 4,296
            CDSs (with protein)               :: 4,296
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 59 of 209
            Pseudo Genes (incomplete)         :: 133 of 209
            Pseudo Genes (internal stop)      :: 38 of 209
            Pseudo Genes (multiple problems)  :: 22 of 209
            Pseudo Genes (short protein)      :: 4 of 209
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073942.1.
            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..3180
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB53"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB53c"
                     /geo_loc_name="Cuba: Nueva Paz"
                     /collection_date="2014"
                     /genotype="ST5728"
                     /note="Laying hens"
     gene            complement(938..1582)
                     /locus_tag="KFU83_RS23000"
                     /old_locus_tag="KFU83_22835"
     CDS             complement(938..1582)
                     /locus_tag="KFU83_RS23000"
                     /old_locus_tag="KFU83_22835"
                     /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(1676..>1831)
                     /locus_tag="KFU83_RS23005"
                     /old_locus_tag="KFU83_22840"
                     /pseudo=""
     CDS             complement(1676..>1831)
                     /locus_tag="KFU83_RS23005"
                     /old_locus_tag="KFU83_22840"
                     /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(942..1582)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2561..2734
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(2091..2582)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ctgtatcgtt catgcctgca tgaacgggtt attcttcctg actacagaat tacatcgctc
       61 cttcagttca tacatcactt tcacaacact tttacaacac tccttcggcc tgtacatcac
      121 ttttacaaca cttttacatc atttatacat cacttttaca tcattccttc agctcatacg
      181 tcactttcat cctctgtgcc atttgtacat cacccccttc ctgaacgtgc tgacagcggg
      241 ttttccggct gcgccggcaa cgcttcacgg ccacgcaata aattgcgtcc ccgttcaccg
      301 ttttcggatg ggaagaacgc cggaaacagg acttcccctg gctgaatggt gtgaatttcc
      361 gcgctatgca cttgcgcgca tactcatgca tgccgtaaaa acagagcctg cgcgtttctg
      421 gcgggttttc ggggggtttg ttgcctgttt taccggtttc ccgtcagaaa cgccctcaga
      481 gcctctcagg cggtgcacgc aagggatgtt atgtttaatc ggtctgaccg tcaggtacaa
      541 aaaaaagccc ttagggggct ttttttttgc tatgagttag ccatattttc gtgcgaattt
      601 ttcatcggaa tcgcatagat aaataataaa ctcaataaac gcgatgatcg cggggtattt
      661 gtattgagga tgtcagtaaa cgggatgaca tggctgaagt tgagattata aataagacat
      721 ggcttcatga ttcgggagtg gttattcgtt gttctcgcga aaatgaattg gttagatatt
      781 catcaaattc ctgtccagaa tgcagcatta gatggcatgt cgttgatgcg gtaggtcagg
      841 atattcgtcc actggagaaa acgtttcaca atgcttgcca ggagtcgtac tggttaaaag
      901 taaatcgtca aacgcatctc ccggtgtaaa cgctgaacta accaatcaca gcgatgccaa
      961 gccgctccat gagcaacgat gcctggtagc tgtctaactt aacgccttgt aaatcaacac
     1021 cccgaatatc taagtcacct aactccgaat tggtcagatc gcaatgtgtg aagtttgctg
     1081 ctcgccagtc gaaagtcgaa aactcgccgc cggagagatc tgaaccactg aacgtcgcac
     1141 ccagtacctg agtccccatc cagcggtttt cccacagctc acacttttcc aacacgactt
     1201 tcgaaaaatt ggcgtagctt agattagtat tagtgatata tgcgctgcaa aaccaggtgc
     1261 gcgtggtgat catattcata aagcttgcac cgcggaaatc tgcgccttgt gcgcggcagt
     1321 ggcgaatttc aatgcccaag gcactgacgt tgcggaaatc tgccattgat aaatcacagc
     1381 ttttgaaaat ggcatctttc agcattgcgc gactaaaatt gcaccctttc tgactttcgc
     1441 gatcatagaa ctggcagccg ataaattcag tgccgctcag gtcggcacct gaaaaatcgc
     1501 agttaaaaaa tgtactattt tcaactttct caccggtgaa gcgatttctg tcaatttttt
     1561 cgccaactaa tgccagagtc atatctatgc ctgtgttttt atacagtaat gacgccatgg
     1621 taaaccttat gacgttatgc gtcaaacccg ccagtatgac acctgcaaat gcgtattaga
     1681 tctggtgttt cttcagcaag gcacgtagct gatgataagt cagacccagt aattcagcgg
     1741 cttttttctg gttaaattta gcctgctgta agctggtttg tagaaagtct ttctcttgct
     1801 gctgctggaa ttcacgcaga tccagcgtta taacgatgtg tatcctatgt gctcggattg
     1861 gatagatttc cattacggtg aaggatcttc ttgagatcct ttctgtggcg tcgtaatctc
     1921 ttgctctgta aacgaaaaaa ccgccctgca aggcggtttt tcgaaggttc tcagagcagc
     1981 aactctttga accgtggtaa ctggcttacg aggagcgcag taaccaaatc tgttctttca
     2041 gtttagcctt aacaggcgca taacttcaag actaactcct ctaaatcagt taccagtggc
     2101 tgctgccagt ggcgataagt cgtgtctttc cgggttggac tcaagatgat agttaccgga
     2161 taaggcgcag cagtcggact gaacgggggg ttcgtgcata cagtccatcc aggagcgaac
     2221 tgccttcgcg gaactgagtg tcaggcgtgg aatgagataa acgcggccat aacagcggaa
     2281 tgacaccggt aaaccgaaag gcaggaatgc gggggagcac gagggagcca ccagggggaa
     2341 acgcctggta tctttaagcc gcatcgggtt tcgccaccac tgatttgagc gtcagatttc
     2401 atgatgtttg tcaggggggc ggagcctatg gaaaaacggc ttcgccgcgg ccttatctct
     2461 tccctgttaa gctccttcct ggtatctccc aggaaatttc cgccccgcct gtaagccggc
     2521 accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaatat
     2581 atcctgtact acatatcctg ctgacgcgct ggtgccgcct tttttctcct gctacatgaa
     2641 gcacttcact gatttccaca tccgtgccaa catagtcagc cagtatacac tccgctagcg
     2701 ctacgtgact ggttcagggc tgcgccccga aacccgctaa caacctctct gctactggat
     2761 atcaccccat gccatctgaa tatgatgaac aacggggttc gactgatacg cagcttcccg
     2821 gcgaatatga cctttttgat ttaatggcga aggttactga agagatcctg catgcccctg
     2881 tggattctgg gccgcctgtc ggccgggaag cgttatagct ttttcgcttg cccgcgtacg
     2941 tggtaatacg ccggtattac cttttatttc tttattttca tgtaattaca gtgggttttt
     3001 aatacctggg tattactcgt gaaaacgaaa cattactttt ttttctttta attcatgcag
     3061 ttgcgatgaa aatcgcggct gcgttaggtg tatgaccatt ttgaggttga aaaataatca
     3121 accatggcgg gtgatttacg caggttaagg ggagatcgtg acaaaaaaaa gcgttcctca
//
