LOCUS       NZ_CP073952             3348 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB50 plasmid pYLMB50c, complete sequence.
ACCESSION   NZ_CP073952
VERSION     NZ_CP073952.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877312
            Assembly: GCF_024585525.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3348)
  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  JOURNAL   Unpublished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 3348)
  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 06:56:29
            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)                     :: 4,724
            CDSs (total)                      :: 4,607
            Genes (coding)                    :: 4,385
            CDSs (with protein)               :: 4,385
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 69 of 222
            Pseudo Genes (incomplete)         :: 143 of 222
            Pseudo Genes (internal stop)      :: 46 of 222
            Pseudo Genes (multiple problems)  :: 37 of 222
            Pseudo Genes (short protein)      :: 4 of 222
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073952.1.
            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..3348
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB50"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB50c"
                     /geo_loc_name="Cuba: Guines"
                     /collection_date="2013"
                     /genotype="ST716"
                     /note="Laying hens"
     gene            join(3214..3348,1..36)
                     /locus_tag="KFU75_RS23455"
                     /old_locus_tag="KFU75_23260"
     CDS             join(3214..3348,1..36)
                     /locus_tag="KFU75_RS23455"
                     /old_locus_tag="KFU75_23260"
                     /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="hypothetical protein"
                     /protein_id="WP_152924371.1"
                     /translation="MSYVSERKSELVKAQQRKMDPSSPDSAPINQGLMDFILLAMKVDD
                     GFVQRGRIHGA"
                     /name="hypothetical protein"
     gene            complement(40..648)
                     /locus_tag="KFU75_RS23460"
                     /old_locus_tag="KFU75_23265"
     CDS             complement(40..648)
                     /locus_tag="KFU75_RS23460"
                     /old_locus_tag="KFU75_23265"
                     /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="hypothetical protein"
                     /protein_id="WP_063859057.1"
                     /translation="MAKCLLVKVRRETSVAVFRQCEIREKYLAIYKESFDEVITYLEKA
                     GALEPGVLRLTTIDDNAIRAWKSQWKGRSRKHAHGAWDWQNLVSKRARSCKRFDVAVWG
                     EDVLCGLSVGKLTRGKKTVRMDYLEACPTAHPLEKRITMIVVAVALSVAKKVGAQHVAI
                     FNPIKDKEEKVLKHYQSYGFTQRMLYGRFLKNVLYKEVV"
                     /name="hypothetical protein"
     gene            888..1352
                     /locus_tag="KFU75_RS23465"
                     /old_locus_tag="KFU75_23270"
     CDS             888..1352
                     /locus_tag="KFU75_RS23465"
                     /old_locus_tag="KFU75_23270"
                     /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="hypothetical protein"
                     /protein_id="WP_072796159.1"
                     /translation="MENKNNLSSEVKNHVSKWGKTNISAGWTIIPNALLENQSRLGLSC
                     IDTMVLINLIMHWWEKDNPPRPSKKRLANMLGVSLKTVQRSFIHLEQCGAIKRIPRYKE
                     GKDNARTTNHYDLNGLVDLLEGFSKELIEEREANRKSEVNRPKKRGNPKS"
                     /name="hypothetical protein"
     gene            complement(2053..2253)
                     /locus_tag="KFU75_RS23470"
                     /old_locus_tag="KFU75_23275"
     CDS             complement(2053..2253)
                     /locus_tag="KFU75_RS23470"
                     /old_locus_tag="KFU75_23275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_061585996.1"
                     /translation="MTDDRTLQLRLTGFRKAEASLRLEGMDPSGTPLYESVKTRILSGD
                     ITFDEGRTEIRAHYQKRANSN"
                     /name="antitoxin VbhA family protein"
     gene            2797..2941
                     /locus_tag="KFU75_RS23475"
                     /pseudo=""
     CDS             2797..2941
                     /locus_tag="KFU75_RS23475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          2305..2905
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.05"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 ggctttgttc aacgtggtcg tattcacggc gcatagctat caaacaactt ctttgtacag
       61 cacgtttttc aaaaagcgtc catacaacat tctttgtgta aacccgtaag actggtagtg
      121 ttttaacact ttttcttctt tgtcttttat cggattgaat atggctacgt gctgtgcccc
      181 tactttttta gctactgaca gagccacagc aaccacaatc attgtgattc gtttctccaa
      241 cggatgagct gttggacaag cctctagata atccattcta actgtctttt taccacgggt
      301 tagctttcca actgaaagcc cacaaagcac atcctctccc caaacagcca catcaaatct
      361 tttacaagaa cgagctctct ttgatacaag gttctgccaa tcccaagcac catgagcgtg
      421 cttacgagac ctgcctttcc attggctctt ccatgcacga atagcattgt catcgattgt
      481 agtgagcctt aaaacgccgg gctctaaagc acctgccttc tcaagataag ttataacttc
      541 atcgaatgac tctttgtaaa tcgcgagata tttttctcta atttcgcatt gtctaaaaac
      601 cgccacgctc gtctccctcc tgaccttgac cagtaaacat tttgccataa aaaaaccact
      661 ttaaatcatt tgctaacatt ttggttagtg gtcaacaaag accatatcct atggtacatt
      721 taaaccccac cctgtggact ttaaaaacca tagggtatgg tctgatttga ccacacagaa
      781 aaagatatag tgggacaata cgttaagaca atgacgcaag gtgaacggta aaacgttcaa
      841 tatataaaat gccctctagc ctcagatgac cacaggatgc atgttttatg gaaaacaaaa
      901 ataacctgtc gagcgaagta aagaaccacg taagcaagtg ggggaagaca aacatttctg
      961 caggatggac gattatccca aatgccttac tggaaaatca gtccaggttg ggtcttagct
     1021 gtattgatac gatggttctc ataaacctca taatgcattg gtgggaaaaa gataaccccc
     1081 caagaccttc gaaaaagaga ctggcgaaca tgctgggcgt ttcactaaaa accgttcaaa
     1141 gaagttttat tcatttggaa cagtgtggtg ccatcaagcg gatacctcga tacaaagaag
     1201 ggaaagacaa tgccagaaca acaaaccatt acgatctgaa cggactggta gacctgctgg
     1261 aaggtttttc gaaagagctt atcgaagaaa gagaggcgaa tcgaaaaagt gaagttaata
     1321 gacctaagaa gcgcggtaat ccgaaaagtt aataggctga caaacacact ctcctgtaga
     1381 gagtccaatt taccataaca tctcttgcgt gcaccgccgc agaggccctc agcgcgtttc
     1441 tgccgcgtgc gggccgtttc cggcaccttt ccctgtccat atcgtgaaaa aacgcgcctg
     1501 atgatttctg cgcgcctgca tggctatgca cggaagtgaa tggcggctgg tttcggacga
     1561 atgctggcac taaaggcgaa ttttgaacaa aaaaaacgga catcgagggt caggatgtcc
     1621 gacaaaattt gcacaaacag tcagccggta ccgatcagag agccggcaaa taagtatgac
     1681 agtaaaaagt ggttatcaac tgcccccgcg ctgctgattg cgcagtttta gggctttggc
     1741 cagtgcaggc aggcccggcc ggaatcaggg gatctggtaa cggtgaacgg gtgcacagtt
     1801 gactgtgcgg ccgtgaggcg ttggccaagc cgccaggcgc ggcagcttcc ggtgggtaca
     1861 aacgccagca ctttgcgaat cctgccctag atctcaacag cagagaaatt tcgtacgcac
     1921 gaaactcagc gtatcgggcg gcgcctgatg aaacattctg gagtgtcggc ggtactccaa
     1981 aaacacatct tgtcccgctg atgttgtcac tggcgcaaag cggcggtaat gacaagacat
     2041 ttcctgtccg cgtcagttac tgttcgcccg cttctggtaa tgagcccgta tctcagtgcg
     2101 gccttcatcg aaggtgatgt caccggaaag aatccttgtc tttaccgatt cataaagcgg
     2161 ggttcctgat ggatccatcc cttcaagcct gagagaggcc tccgctttac ggaaccctgt
     2221 caggcgcagt tgcagtgtcc gatcatcagt catggttttt cctttgagca gtcatgcgaa
     2281 taaggcaggc gtaaagttag ctaactttac atgtcctgcc cggatgttgc cgttgtatag
     2341 ctgtgcaggg aaaagtggaa aacgacagga aactgttgca gccgggtgtg taatcaggga
     2401 ggaaacgtgt gtaccgagcg acacgatccc tgttcagcat tacagacatt acgcttcctc
     2461 ggtcattcgc tcacttcgtt cggtcatgac actgcggcga gcgttacctg ctcaggcaga
     2521 aggccataag gaggttctgg ggattgccgg ttttccatag gcttcgccct cctgacaagc
     2581 ttcacagaaa tcaggtgatt tccggcgctc aaatcagaag tggcgaaacc tgacaggact
     2641 taaagatccc caccgtttcc gatgggtcgc tccctcgtgc gctctcctgt tcccaccctg
     2701 aggtttaccc gttgcagtcc gccgtaaggt ggcgttttct cattcctacc cgtgcaactg
     2761 ggttccttgt aggtggttcg ctccaagctg ggctgtatgc acgaactccc cgttcagccc
     2821 gactaccacg tctttatcag gtaactgtac tcttgaatcc aaccctgaaa gacacgacaa
     2881 agcgccactg gcggtagcca ttggtagcag tgagtgcgag aggtgtatcg agagttcttg
     2941 aagttaaagc ctgactacag ctacactgga aggacagatt tggtgacacg tctcgcacaa
     3001 gactgttacc taggttcaaa gagccgcaaa ctcaatgaac tggaaaaaaa ccgccccgca
     3061 aaggcggttt ttttcttttg aaagaaaaga gtacgctttg cagaagaggc gagtcaacaa
     3121 cagtcatctc tttttgaaaa tatagagatc tcgttatttt tttatccact tgttatagtg
     3181 tctacatccc catacaagac agagagtcac aagatgagtt atgtatctga gcgcaaaagt
     3241 gagctggtaa aggcacagca acgcaaaatg gatccatcct ctcctgattc agctccaatc
     3301 aatcagggtc ttatggactt catcctgctt gctatgaaag tagatgac
//
