LOCUS       NZ_CP073928             1546 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB98 plasmid pYLMB98b, complete sequence.
ACCESSION   NZ_CP073928
VERSION     NZ_CP073928.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877319
            Assembly: GCF_024585385.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1546)
  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  JOURNAL   Unpublished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 1546)
  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 06:36:18
            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)                     :: 4,858
            CDSs (total)                      :: 4,738
            Genes (coding)                    :: 4,474
            CDSs (with protein)               :: 4,474
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 264
            CDSs (without protein)            :: 264
            Pseudo Genes (ambiguous residues) :: 0 of 264
            Pseudo Genes (frameshifted)       :: 94 of 264
            Pseudo Genes (incomplete)         :: 169 of 264
            Pseudo Genes (internal stop)      :: 52 of 264
            Pseudo Genes (multiple problems)  :: 45 of 264
            Pseudo Genes (short protein)      :: 4 of 264
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073928.1.
            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..1546
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB98"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB98b"
                     /geo_loc_name="Cuba: San Nicolas"
                     /collection_date="2013"
                     /genotype="ST410"
                     /note="Laying hens"
     gene            1..477
                     /locus_tag="KFU77_RS24180"
                     /old_locus_tag="KFU77_23985"
     CDS             1..477
                     /locus_tag="KFU77_RS24180"
                     /old_locus_tag="KFU77_23985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /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 domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1082..1163
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(1360..1468)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(710..967)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="99.0"
                     /evalue="3.93e-111"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgtttt gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcgtgttttt gctccccgat cccaagaacg
      601 accgcgtcgc cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca ccaaccagcc gaatagctgc
      721 ctgtaccgtg caaataggct ttgcagggag ctgacgcggt tcctagcgac ctgaaagccc
      781 ctggttaggg gtatcggcgc gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tggcgggcat ttaaacccgt ttcgtgcgtc tgagagcttc tgagcgtgtt
      901 tgaagggcta tctgacgact catccccgaa agaacaacaa cgggatcacc gacaacatgc
      961 gagaggtgat cccgctcgcc gcaagtcgat gaccgagcgt agcgagcgaa tcgacgagga
     1021 agcggaagag aaccggaagt tacattgagc acttacgcac ggatgcaggg tgtcggggtg
     1081 aagccctgac caggtgggga atgtctgagt gcgcgtgcgc ggtccgacat tcccacatcc
     1141 tgtcccgatt tctgaggcgt tttaacggtg aacggacggc aaaaacatga tcgagctgtt
     1201 gaacgtggag agcgcgaaat cgggcaaaat catggctgac gaggcttgca gaggagtaag
     1261 ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg acaccccaaa
     1321 agggcgttgc gttgcgcgca acacccttgc ctagaataga tcttttacgc cgatttgtaa
     1381 gttgttgttt ttttagtgtg ttttttgttt acctgtcgca tccagggtga cacaacgttg
     1441 tcgcatcctg gatgcgacaa cacgcaacaa ggtgttgcac agatgtgtca tgatggctta
     1501 gatttgaacc aacgttagtg catgggattt tcagagggaa aaaatc
//
