LOCUS       NZ_CP073972             2955 bp    DNA     circular CON 02-DEC-2023
DEFINITION  Escherichia coli strain MB30 plasmid pYLMB30d, complete sequence.
ACCESSION   NZ_CP073972
VERSION     NZ_CP073972.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877308
            Assembly: GCF_024585605.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2955)
  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  JOURNAL   Unpublished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 2955)
  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                   :: 12/02/2023 11:31:50
            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)                     :: 5,253
            CDSs (total)                      :: 5,125
            Genes (coding)                    :: 4,874
            CDSs (with protein)               :: 4,874
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 0 of 251
            Pseudo Genes (frameshifted)       :: 66 of 251
            Pseudo Genes (incomplete)         :: 185 of 251
            Pseudo Genes (internal stop)      :: 44 of 251
            Pseudo Genes (multiple problems)  :: 44 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073972.1.
            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..2955
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB30"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB30d"
                     /geo_loc_name="Cuba: Santa Cruz del Norte"
                     /collection_date="2015"
                     /genotype="ST1638"
                     /note="Broiler"
     gene            261..452
                     /locus_tag="KFU82_RS26025"
                     /old_locus_tag="KFU82_25820"
     CDS             261..452
                     /locus_tag="KFU82_RS26025"
                     /old_locus_tag="KFU82_25820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            648..1163
                     /locus_tag="KFU82_RS26030"
                     /old_locus_tag="KFU82_25825"
     CDS             648..1163
                     /locus_tag="KFU82_RS26030"
                     /old_locus_tag="KFU82_25825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012311399.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_257190224.1"
                     /translation="MAGDLRRLRGDRDKKSVPHCIVHACMNGLFFLTTELYRSFSSYIT
                     FTTLLHHFYIICTSLLHHSFSSYVTFTSVPSSVPFVHPTPFLNVLKTVFPAVPATPHGH
                     AINCVPVHRFRIRRTSETGLTPAEWREFPRYALARILMHAVKTEPARFWRVFGWFVACF
                     TGFPSETP"
                     /name="hypothetical protein"
     gene            1731..1979
                     /locus_tag="KFU82_RS26035"
                     /old_locus_tag="KFU82_25830"
     CDS             1731..1979
                     /locus_tag="KFU82_RS26035"
                     /old_locus_tag="KFU82_25830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017096688.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_029793011.1"
                     /translation="MKNVRMQFDLPEDRLDELDSLMKKCGISTKKELFNYALTMLEWAV
                     DESESGHEIAAIDRDSKQFYALRMPILKRVNRTSTAN"
                     /name="hypothetical protein"
     gene            2052..2423
                     /locus_tag="KFU82_RS26040"
                     /old_locus_tag="KFU82_25835"
     CDS             2052..2423
                     /locus_tag="KFU82_RS26040"
                     /old_locus_tag="KFU82_25835"
                     /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_024242345.1"
                     /translation="MSDSLDGFTEGDTSKEKQAVKQPKKFFSDVDDSADRRHLRWTKSG
                     VTLAMTILVAVMNWMVISMLYHVVDEELSLIRSGFMQADARTVTTSVYLALIAGTVAEV
                     SALFLIIVKSVFKNNNNDI"
                     /name="hypothetical protein"
     Typing          complement(2493..2918)
                     /name="rep_cluster_2374"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.766"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtcctgtcg ggtttcgcca ccactgattt gagcgtccga ttctgtgatg cttgtcaggg
       61 gggcggagcc tatggaaaaa cgccccggcg gggcgttgcc ttttagccct tgtccttagc
      121 tttcgttatg cttaccgtta cgttatctgc ttatcttccc tccgctcgcc gcagactcat
      181 gaccgaacgg agtgagcgaa tgagcgagga agcggaaaac catcagaacg tacagtaagc
      241 actttcgcgc cggggctttc atgaacaaac aacaaaagac tgccgttaac atggctaaat
      301 tcatccagga tcagtccctg cttcttctgg acaggcttaa tgagctggat ctggatcatg
      361 aggctgattt ctgcgagaaa ctccatgagg atgcggaacg cctttaccga agcctgtcag
      421 cgcgcctgaa tgagcagcag gacggtgcgt aatggctccg ttctgggtat taccggagta
      481 ataccggcat cgccttaatt ttcattgtct tagcgcttaa cattattacc ccggtaatac
      541 ccagaatccc tgtatttttt cttttttatt tatttttcat gcagttgcga tgaaagtcgc
      601 ggctgcgtta ggtgtatgac cattttgagg ttgaaaaata atcaaccatg gcgggtgatt
      661 tacgcaggtt aaggggagat cgtgacaaaa aaagcgttcc tcactgtatc gttcatgcct
      721 gcatgaacgg gttattcttc ctgactacag aattatatcg ctccttcagt tcatacatca
      781 cttttacaac acttttgcat cacttttaca tcatttgtac atcactttta catcattcct
      841 tcagctcata cgtcactttt acgtcagttc catcctctgt gccatttgta catccgaccc
      901 ccttcctgaa cgtgctgaaa acggtttttc cggctgtgcc ggcaacgcct cacggccacg
      961 caataaattg cgtccccgtt caccgttttc ggataagaag aacatcggaa acaggactta
     1021 ccccggctga atggcgtgaa tttccgcgct atgcacttgc gcgcatactc atgcatgccg
     1081 taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc tgttttaccg
     1141 gttttccgtc agaaacgccc tgaggccgtt ttagcggtgc gtacaatact tgagttatgt
     1201 taaatgcacc taagatttgg atgattgttt catctcgtta caactactgt tgtcttttta
     1261 acctatatcg ttttatactc gtaatatgct ccaattacac tcgacaatgg agatgtttga
     1321 gtgtaagata caatctggag cccattacga ggtgtggtgg gtaaactgga gatttcacct
     1381 gtgagcgagt taactcaaaa ctgctcctcg acctccagga acagtgagga ctgcaccgac
     1441 ttcgaagaac tgcctcctaa agagctttct ttgaaggatt ggttctcagt ctttactgag
     1501 gtcgatgagt aataaccacc atggaggagt tttcacaacc tcctccatgg tggggataac
     1561 ctgcttgcgg agaagagata aggctaagcc ttatccaaat taggagtatc ataagtatat
     1621 gaaacttaat ttatttatag gtagagatat ataaatacca acggtcctaa tggtgaagaa
     1681 tgtgcagcat agagtacaag gatgacatgc tggcccctcg gagattagtt atgaaaaatg
     1741 tacgtatgca attcgatcta cctgaagata ggttggatga actcgattct ttaatgaaga
     1801 agtgcggcat aagtactaaa aaagagttgt tcaactacgc gttaacaatg cttgagtggg
     1861 ctgtggacga gtccgaaagt ggtcacgaaa tcgcagctat cgatagagac agtaagcaat
     1921 tttatgctct acgaatgcct attcttaagc gagtgaaccg tacatctact gcaaattaac
     1981 ttatcacttg atgtgttaag gagaaggcca gcttaaactg gccttctttt tttattcaag
     2041 agggtttgat tgtgtccgat agcctagatg gatttactga aggcgatacc tcaaaagaaa
     2101 aacaagcggt aaaacaaccc aagaagttct ttagtgacgt cgacgattca gcagatagac
     2161 ggcatctgag atggacaaaa agtggcgtta ctctggctat gacaattttg gttgctgtaa
     2221 tgaactggat ggtcataagc atgctatatc acgtagttga tgaagagctt tctctgatac
     2281 gaagtggctt tatgcaagca gacgcaagga ctgtaactac tagtgtttat ttggctttga
     2341 ttgctggaac agttgctgag gtatctgctt tatttttgat aattgtaaag tcagttttta
     2401 agaacaataa caatgatata tgaagttgat tccagtcgtt agatgtagtg tcacacatgg
     2461 ttttgttctg tctgtcttga gatcactcta atcaaaatgt aatctcttgg gactgaaacg
     2521 aaaaaaccac ccggcaaggt ggttttttcg aaggttcatt aaccggcaag tttctgaacc
     2581 gtggtaactg gctttcgcag agcacagaaa ccgaattcgt tttaacagtg tagccgtagt
     2641 ctgccttaca cttcaacacc tcaacgcttc tttgttctgc gaatctgtta cctgtggctg
     2701 ctgccattgg cgttttaacg cgttttttcc gggttggact caaggtgata gttactggaa
     2761 aaaacgcagc agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact
     2821 gccttcccgg atctgagtgt caggcgtgga gtgagaaaac gcggccataa cagcggaatg
     2881 acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagccacc agggggaaac
     2941 gcctggtatc tttat
//
