LOCUS       NZ_CP073980             5128 bp    DNA     circular CON 02-DEC-2023
DEFINITION  Escherichia coli strain MB20 plasmid pYLMB20d, complete sequence.
ACCESSION   NZ_CP073980
VERSION     NZ_CP073980.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877306
            Assembly: GCF_024585645.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  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  JOURNAL   Unpublished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 5128)
  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                   :: 12/02/2023 11:02:18
            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)                     :: 4,950
            CDSs (total)                      :: 4,832
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 194
            CDSs (without protein)            :: 194
            Pseudo Genes (ambiguous residues) :: 0 of 194
            Pseudo Genes (frameshifted)       :: 53 of 194
            Pseudo Genes (incomplete)         :: 138 of 194
            Pseudo Genes (internal stop)      :: 38 of 194
            Pseudo Genes (multiple problems)  :: 34 of 194
            Pseudo Genes (short protein)      :: 4 of 194
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073980.1.
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB20"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB20d"
                     /geo_loc_name="Cuba: Santa Cruz del Norte"
                     /collection_date="2015"
                     /genotype="ST10"
                     /note="Broiler"
     gene            complement(join(4756..5128,1..302))
                     /locus_tag="KFU64_RS24635"
                     /old_locus_tag="KFU64_24410"
     CDS             complement(join(4756..5128,1..302))
                     /locus_tag="KFU64_RS24635"
                     /old_locus_tag="KFU64_24410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_072644308.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRSRESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDNLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISSLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     gene            650..1066
                     /locus_tag="KFU64_RS24640"
                     /old_locus_tag="KFU64_24415"
     CDS             650..1066
                     /locus_tag="KFU64_RS24640"
                     /old_locus_tag="KFU64_24415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /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_057103209.1"
                     /translation="MSDQKNNLDLQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            1231..1494
                     /locus_tag="KFU64_RS24645"
                     /old_locus_tag="KFU64_24420"
     CDS             1231..1494
                     /locus_tag="KFU64_RS24645"
                     /old_locus_tag="KFU64_24420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072644307.1"
                     /translation="MAVYTSETKKFLDSVSHDKTWWTSRYNPADDVPVSGIYRCTVCGK
                     EITSNKDDPFPPQNHHQHSQSQAIKWQLIVRTDTQGNGCGSK"
                     /name="protein L"
     gene            complement(1653..2345)
                     /locus_tag="KFU64_RS24650"
                     /old_locus_tag="KFU64_24425"
     CDS             complement(1653..2345)
                     /locus_tag="KFU64_RS24650"
                     /old_locus_tag="KFU64_24425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000550475.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3800 domain-containing protein"
                     /protein_id="WP_072644306.1"
                     /translation="MHLLYVDESGTPSDPTLNHFVLSGISVFEKQTHWIEQEMNAIAAR
                     FNADDPYERELHGSPMRGGRDGWKNFSFNDRKQAIKDCLALLTQKHRDIRIFACVVPKG
                     ALDGKDVITESFYQISSRFDMYLSRLHHQGATSRGVAIFDKSSTEKSIQSLARTFKDTG
                     YEYGKLRNFSEVPLFLDSKASRLIQLADLVSYSIFRKFEFNDDEFYKIIENRFDYHNGK
                     VHGLYVAH"
                     /name="DUF3800 domain-containing protein"
     gene            3572..3766
                     /locus_tag="KFU64_RS24655"
                     /old_locus_tag="KFU64_24430"
     CDS             3572..3766
                     /locus_tag="KFU64_RS24655"
                     /old_locus_tag="KFU64_24430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_072644309.1"
                     /translation="MNKQQQIALNMARFIKSQSLTLLEKLDALDADEQATMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3467..3551
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.393"
                     /coverage="87.0"
                     /evalue="5.15e-16"
     Typing          complement(3843..3924)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="98.0"
                     /evalue="1.43e-25"
     Typing          4225..4748
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.604"
                     /coverage="99.0"
                     /evalue="7.85e-161"
ORIGIN
        1 gtcattgcac attcctgacg ctctgagtaa taacctttga ttatctgtag gttatcgcca
       61 tagatctgta ctaatgctcg atggtaggct tgctgagcct ggtgcgccaa ttcaccccga
      121 gaagcaaact ttgctttgat ctcagcagta aagaacttca cctgaatcaa ctgtgactct
      181 cttgatctta tcggaagtag ttgttcttca aagagtttat agagatctaa ccacttatat
      241 cccgaacgct taaccaatcc gtgataaaaa ttaaacccat ctacgtaaac tattgttctc
      301 attttatttc gcgcataaaa aaaccgcctc taaaggcggt tttaacaaca aaaactaacg
      361 ttagcaaaca gtttaagttg tagttcctca gggttaaaac taaccgagag ggcggtttca
      421 agctcctgaa ggaagacgcg taacttaatc gctgcccacc taaagggagg tttagagcct
      481 caagggagct gcgtaactta atcgcgctac caagaggtga gtgtagatta agtatagtta
      541 aatataatga tattataagc gcgatggtgt cgtactaatt atatgaatta atttaccaac
      601 ctgctaagct gaagtcttct atgaagactt cagcttagca ggttggtata tgtcagatca
      661 aaaaaataat ttagaccttc aaaaacagac acttgaatct aaatggggga aggaggcgtt
      721 aagcatggga tggtcagcca ttcctacatc ccttttcttc ctgcagggcg cactcaatat
      781 gacccccaca acattcaatg tgctacttca tctaatcatc cactggtgga aaccctatga
      841 ttggccacat ccatctcaag agagcatcgc ggttagaatg ggagtttcat caagaacagt
      901 tcaacgctca ctccaagaac ttgaaaatta cggattgctt acaaaaattc gtacaagcaa
      961 ggacaaccct aagtacaaag ggcgaaacat ttacgatatg tctcttttag ttaagtcact
     1021 aaacattctt acgccagacc ttaatgccaa actgaacgaa aagtaaccat aaaataattt
     1081 taaaaatcag accattacag cttatattta ccatagcatc tctattttag cgtttttcaa
     1141 tcatcgccag atgattgaaa aacgctaaaa aaaaccaaac ttataaaaag gatccccctc
     1201 cgccctatac attttggaaa ggaaaggcaa atggctgtat acacctctga gactaaaaaa
     1261 tttttagaca gtgtttctca cgataaaact tggtggacat cacgatataa cccagctgac
     1321 gatgtaccgg tatcagggat ctatcgttgt actgtttgcg gaaaagagat aactagcaat
     1381 aaagatgacc cgtttccgcc gcaaaaccat catcaacaca gccaaagtca ggcaatcaag
     1441 tggcaattaa ttgtcagaac agatacgcaa ggaaatggtt gtggttctaa ataactcaaa
     1501 agcccttagg ggcttttttg tacctagcgg tcagacggat taaacataac atccgttgta
     1561 cgctacgcat gaaaaagccc gcgtagcggg cttcgcgtcg atggtcacaa ggaactctta
     1621 cttatagata gtgcgtattc acaactattc cattagtggg ctacgtaaag cccgtgaact
     1681 ttaccattat ggtagtcaaa gcgattctct atgattttgt agaactcatc atcattgaac
     1741 tcaaacttcc tgaaaattga gtacgacaca agatcagcaa gctgaatcag ccttgacgct
     1801 ttggaatcca aaaataaagg tacttcagag aagttgcgaa gttttccata ctcatatcca
     1861 gtatctttaa acgtacgggc aagagattga atactttttt ctgtcgacga tttatcaaaa
     1921 atggccaccc ctcgagacgt tgctccttgg tgatgtaagc gacttaaata catgtcgaaa
     1981 cgagacgata tttgataaaa agactctgtt attacatcct tcccatctaa ggctcccttg
     2041 ggtacaacac atgcaaatat gcgaatatcc cgatgctttt gagtaaggag tgctaagcaa
     2101 tctttgatcg cttgttttct gtcattgaaa gaaaaatttt tccagccatc tcgtccacct
     2161 ctcatcggtg aaccatgcaa ttctctttca tacgggtcat cagcattaaa tcgagccgca
     2221 attgcattca tctcttgctc tatccagtga gtttgctttt caaatactga tataccagaa
     2281 aggacaaaat gattaagagt agggtctgat ggtgtaccag actcatcaac gtacaagaga
     2341 tgcatctaag actccttaaa cgaaaaaggc cgcgcaaatg cgcggccttt ttatgaatta
     2401 ggcaagccag tgcgataaac atcgcataca ccgctatggg cagcgaactg actcaatatc
     2461 aatgataaca ggcaagtgca tatttaccca aataatttat acacacacca tagccatgag
     2521 caatcaaata acataaattc aatcagatag tttcttcacc gtcattctga tttaccataa
     2581 catctgttgc gtgcaccatc tcagacgccc tcagggcatt tctgcgccct ccagcctatt
     2641 tccggcatct ttccctgtcc atatcgtgaa aaaacgcgcc tgatgatttc tgcgcatctg
     2701 catggctatg cacgaacatg cctggccgga attttagcgg ctaaaatcct gcgaactgct
     2761 caaaaggctc gctgaacccc atcgataacg gtgaacgggt gcacagttta ctgtgcggtc
     2821 gtgaggcgtt gagcaacgag ctttgcgagg cggtaggggt tctgagagcc agctgcaggc
     2881 tcaggagaaa acattctgtt ttcggggcag ataccgcaaa tgacgtcatt ttgcggcgtc
     2941 tgccctatcc tgcatcgcaa cgtctaaagg atgtgagtac aaacgccagc actttgcgaa
     3001 tcctgccctc gatctgaaca aaagcaaaat ttcgtacgta cgaaattcag ggtatcaggc
     3061 tgcgcctgat gaaatgtttt tggtgccggc ggtactccaa aaacacatct tgtccgacag
     3121 ttttgtggtg ccggcgaagc ggcggtggcc acaaaacatt tcctgtcccc atcgattcat
     3181 tcgagaaaca taagaggcga agaaggggtc agtttggaga tcggaaattt ttgtacgtta
     3241 agcgcattat ttaaccaatc ttggttcgta aggggttgat tttgcgtcag tggctatcgc
     3301 ttttaagttg tcgctcttgc agtatcgcat ttaggttatc cgattaaggt caaacctctg
     3361 aaaatgccgt atagcgcggg agtacaccct attgctatag gtaagtctgt tcaaaaaaca
     3421 ggcttaccgt acaataattc tctatatcca aactgacccc taaagaaaca ggacaggatg
     3481 tgcaattgta ataccgtcgc ccgcaacgtc ttacaattac cacctggtca gggtccaccc
     3541 gacacccggt actgacggag aacaacggaa ggtgaacaaa cagcaacaaa ttgcgctgaa
     3601 tatggcgcga tttatcaaaa gccagagcct gacactactt gaaaaactgg atgctctgga
     3661 tgccgacgaa caggcgacca tgtgcgaacg actgcacgaa ctcgcggaag agctccagaa
     3721 cagcatccag gttcgctttg agaccgaaag tgaaacaggg acataacgaa gctgacggag
     3781 gcgctcacgg cttgtccgcg agcgttttcg gcagcagaca agcccgtcag ggcgcgtcag
     3841 tggggttcgg ggcgaagccc tgaaccagtc acgtagagat agcggagtgt atacgggctt
     3901 aatcatgcag catcagtgcg gattgtatga aaagtttgcc atatccggag tgaaatgccg
     3961 cacagatgcg taaggagaat atgcctgttc aggcgctctt ccgcttcctc gctcactgac
     4021 tcgctacgct cggtcgttcg gctgcggcga gcggtgtctg ctcactcaaa gatggtaata
     4081 cagttatcca cagaatccga ggataacgcc ggaaagaaca tgtgagcaac aagacgaaac
     4141 ccggaaaaag gcagcgccgg tggcgttttt ccataggctt cgcccccctg acgagcatca
     4201 caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggacttaaag ataccaggcg
     4261 tttccccctg gtggctccct cgtgcgctct cctgttcctg ccattcggtt taccggtgtc
     4321 actccgctgt tatggccgcg tttgtctcat tccacgcctg acactcagtt ccgggtaggc
     4381 agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgact gctgcgcctt
     4441 ttccggtaac tatcgtcttg agtccaatcc ggaaagacac gacttatcgc cactggcagc
     4501 agccattggt aacaggattc acggagcaga gtagtagaag tgcttctaca gagttcttga
     4561 agtgatggcc tgactgcggc tacactggaa ggacagtttt ggtatctgcg ctccgtgaaa
     4621 gccagttacc ttcggaaaaa agagttggta gctcttgatt ccggcaaaca aaccaccgtt
     4681 ggtagcggtg gtttttttgt ttgcaggaca tgagattacg acgagagtaa aaggatcaca
     4741 agaagatccg gctgtttacc agtgatttgg cttcagtatt ggctttcgcc tagtggggac
     4801 tttatctggc aataaagcta atcttaaggc ttcataggat acatatggca agctccaatc
     4861 ccctaaacta gccagactac taatcactcg actagtatct tgttcccttg gcactacaat
     4921 tcctattttt aactcaggtc gatcggcttt tatcatttct attggcggta tcatatctga
     4981 gtcgttagta cagagaacca attgttctgc ctcaccacgg atcgcatcgc gatacatttc
     5041 taaagccatt ctaacgtcgg tctgcttttc ttctaacttc cagaccgttg ttctatccgt
     5101 ttttgatggc ggatgcccct cattaaag
//
