LOCUS       NZ_CP073941             4509 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB53 plasmid pYLMB53b, complete sequence.
ACCESSION   NZ_CP073941
VERSION     NZ_CP073941.1
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 4509)
  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  JOURNAL   Unpublished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 4509)
  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
            CP073941.1.
            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..4509
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB53"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB53b"
                     /geo_loc_name="Cuba: Nueva Paz"
                     /collection_date="2014"
                     /genotype="ST5728"
                     /note="Laying hens"
     gene            283..429
                     /locus_tag="KFU83_RS23125"
     CDS             283..429
                     /locus_tag="KFU83_RS23125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_077890892.1"
                     /translation="MHEPPVQSDCCASSGNFQLDSNPERHDKAPLAAATGKRVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            855..1517
                     /locus_tag="KFU83_RS22975"
                     /old_locus_tag="KFU83_22810"
     CDS             855..1517
                     /locus_tag="KFU83_RS22975"
                     /old_locus_tag="KFU83_22810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000430080.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNVR domain-containing protein"
                     /protein_id="WP_257188417.1"
                     /translation="MEKNSSDIDVIELFLFLKNKIMSIILFVVFSLILSSIFLLINKNK
                     ISVKYELNMITNSPGMIINCGDDFYCKANMIQSIIKSKSNSITSNIDEKGKKINLSWAG
                     DDRYKPSVAAEVNAIHQAIDDWYIQDYKTYKNIVNNQGGNYINGTETYAKIALLTKTNI
                     SGEKNFISINNETVNKKYQPALIMTLTLIIAIIFSSSYHIIKRSIFEYKNKLNRSFY"
                     /name="GNVR domain-containing protein"
     gene            complement(2424..2639)
                     /locus_tag="KFU83_RS22980"
                     /old_locus_tag="KFU83_22815"
     CDS             complement(2424..2639)
                     /locus_tag="KFU83_RS22980"
                     /old_locus_tag="KFU83_22815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_102882745.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWQSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2646..3137)
                     /locus_tag="KFU83_RS22985"
                     /old_locus_tag="KFU83_22820"
     CDS             complement(2646..3137)
                     /locus_tag="KFU83_RS22985"
                     /old_locus_tag="KFU83_22820"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_139246509.1"
                     /translation="MSSLLTLAKDLEQQSKAQKQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILIVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            complement(<3172..3876)
                     /locus_tag="KFU83_RS23130"
                     /old_locus_tag="KFU83_22825"
                     /pseudo=""
     CDS             complement(<3172..3876)
                     /locus_tag="KFU83_RS23130"
                     /old_locus_tag="KFU83_22825"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3815..4138)
                     /locus_tag="KFU83_RS22995"
                     /old_locus_tag="KFU83_22830"
     CDS             complement(3815..4138)
                     /locus_tag="KFU83_RS22995"
                     /old_locus_tag="KFU83_22830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_171765792.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4254..4430)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.382"
                     /coverage="100.0"
                     /evalue="3.3800000000000004e-70"
     Typing          2..452
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.584"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2333..3825)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.4"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aggaagagac ttaacagtga agcgataagg ccacggcgga gccgtttttc cataggctcc
       61 gcccccctga caagcatcac gaaatctgac gctcaaatca gtggtggcga aacccgacag
      121 gactataaag ataccaggcg tttccccctg gcggctccct cgtgcgctct cctgttcctg
      181 cctttcggtt taccggtgtc attccgctgt tatggccgcg tttatctcat tccacgcctg
      241 acactcagtt ccgggaaggc agttcgctcc aagctggact gtatgcacga accccccgtt
      301 cagtccgact gctgcgcctc ctccggtaac tttcaacttg attccaaccc ggaaaggcac
      361 gacaaagcgc cactggcagc agccactggt aagagggtgt acaagagatt actgatacag
      421 agttcttgaa gtcagagcca aactacggct aaactggaag gacgaatttg gtggcagcgg
      481 tcttgtacac cctgttacca cggttcagaa gttccccaac ttactgaacc ttcgaaaaac
      541 cacctcccca ggtggttttt tcgttttcag agcaagagat tacggctgta acgcaaggat
      601 ctcaagaaga tcttaaaata tgttgaaagg atacaggctg acaacaactc cctccataga
      661 catgatcgaa caaaaaagaa acaaaaaaat gattttagga gttttctcac acctaaatag
      721 taggtaaaat gtttttttat tcgattggct tttaaaatga aatacactaa atccgcaaaa
      781 atattcatca cagccatttt aattttattt atttatttaa cccatacttt aataaatatt
      841 atcggtatat aaaaatggaa aaaaattcat ctgatattga tgtcatcgag ttatttctct
      901 ttctcaaaaa caaaataatg agtattattt tgtttgttgt tttttcattg attttatcat
      961 ctattttttt gttaataaac aaaaacaaaa taagtgtaaa gtacgaatta aatatgatca
     1021 ctaattcgcc gggtatgatt attaactgtg gggatgactt ttattgcaaa gcgaatatga
     1081 tacaatcaat aataaaaagc aaaagcaatt ctataacatc aaatatcgat gaaaaaggaa
     1141 aaaaaataaa cctatcatgg gctggtgatg accgttacaa accctctgtt gccgctgaag
     1201 taaacgctat ccatcaagct attgatgact ggtacatcca agattataaa acttataaaa
     1261 acatagttaa caaccagggc ggcaactata taaatggcac tgaaacatat gcaaaaattg
     1321 cattattaac taaaacaaac atttccggag aaaaaaactt tatttcaatc aataatgaaa
     1381 cagtgaataa aaagtatcaa ccagctttaa ttatgactct aacattaatt atagctatta
     1441 ttttttcctc ctcgtatcat ataatcaaaa gatctatttt tgaatataaa aataagttaa
     1501 acaggtcttt ttattagcct gtgacggtta atagcagtat tctaataata tccgttacac
     1561 gccagatgca gaaaagcccg ctaatagcgg gcctcccgat aaaacctcaa gtgactaagg
     1621 gcagtcagat ctagttctca cccttccatt gcctgactga tttcccgtgg tactgggcca
     1681 gttacagcag tttttatgcc catgaagcat ccgactggcc acctcgagat ctccattttt
     1741 aagatacaca cataatttca ttagaccatc tacagctgac tgataccgca actcaccttt
     1801 agcatgaaga ttcagaaccg tggatatata agtctgcatt tcagtttcat caggcccgtt
     1861 ttttttgctg aatccattta ccaatatcca gtccatatgt tactaaaaaa taatatatgc
     1921 ggaatgagtc atcatgcggt taatttacca taacatctgt tgcccgcacc gccccggaca
     1981 gcttcgccgc gaacggggcg gcagtcagcc aaaaccaaca acaacccacc cggtaaacca
     2041 ccccgatcgc gacagataaa ttttacccga ctgcataacc atgcagccag atgcatggcg
     2101 tgtaaagtca cactaaaatc agcgctaacg ccttaaaaac aggtaaatgc ttctccagcc
     2161 agtcccacag cccggccgcc agatacaggc agttaagtac agcttcaatg acgttaagca
     2221 atttcataat tccccccagg tataggccgt gatctttttg atcacgaacc tatttagcgg
     2281 gagaagtaag agcccctctt cgtgcgggtt gtcagctgcc tggatggttt aaagtgtcgg
     2341 cccgcggtag gttttctgcg gctggcgctc cagctccagt gttttctgat actcattctc
     2401 cctctgccgg aactcggtgg cattcagctc ccggacaagc ggcgcagctg ctcgcttaaa
     2461 ctcagcacct gcgtgctcaa gtccgacacg cgctcgttca gcaccgcgtt ctcccgttgc
     2521 ataagcccac acatgctctg ccattccgcg aaggcgctct cccattcgtc cagcctttgc
     2581 gagtagtcct gctgtagctg ctctaatgcg ctcagcaact gcttttccag ctctgtcatc
     2641 ttccgctact cctgtttcag gcggatccat gtcgtcccgt cgtaagggat ggcttcggtt
     2701 tgcatccccg gcggcaggat aagaaacctc cggccgtcgc tgctctcctg atagcgcact
     2761 ccccacgtcc gggcggtcat tttcgccagg gtatcttcct gctgacgaag atgcgtgtaa
     2821 ttgtcggtta tctgctgccc ctgccaccac agtatgctcc cgctcgtgcc gatcagcagc
     2881 gctgacacaa tcaggatggt gagccatgtc cgcccggcag tccgcagtac gctccgccgg
     2941 tttttctcca tcgcctcgct catactctgc tcgtgggcga ggatggcgtc gctgattctc
     3001 ctcgcgcttg cgctcagttc cgctctgaca gactgctcgt gctcgctgaa tgcggctttc
     3061 agcatctcgc cggtactctg cttctgcgct ttcgattgct gctctaagtc cttcgccagc
     3121 gttaaaagac tgctcataga tggctccctt cagtcggatg tttcgccccc cgtccgggtc
     3181 ggcaatgctg atactgcttt tcgtggtgcg caccacctca aaacctgacc gttccagcgc
     3241 ctcagtgatg tcctgacggg ttttcagctc cccggacgaa gcaaggttca acagtccgcg
     3301 cgtgatggat tctgcggcct cctgcttcgt tttcggcagt ccggacggcg tgaccagcgc
     3361 ccggcggttt tccggtgcgt tcgggtcgtg cagccccagt ctgccgttca cgatggtctg
     3421 ccaggcatcg atacgcggcc ggtcggcgcg gtcgtagtac ggctggagcc gcctgccagt
     3481 cagcagctcg gtattgggga tcagaaagtt cagctccaga cgccccttgt cctcgtgctc
     3541 cacccacaga atgctgtact gatctttatc aagtccgggc atcagaaccc gctcgaagct
     3601 ggccatcagt ttttcccgct ggccgggagg cagatcggcc tccgcaaacg acaggacgcc
     3661 ggaggtgtat ttcttcacgt aaggcgacgc gtcaatcagc tcccggactt cttccggctt
     3721 cccctgcagg acgctggcgc cttcacgctg ccggtcttta cccagcagat agtccaccgg
     3781 cccggcgcca ccgccgcggc cacgtggatg aaatttaacg atcatcgtcc gttcctttct
     3841 caagaacggc gtgccgcagc cgctcaaggc cggcatcgat ggccatcagc gccgccacaa
     3901 tctgtaccct gtcatggccg gtgccgccgc cggcgttaac acggcgggct atctggttca
     3961 ggttattgcc catgccggcg agctgccgca gcagcgccgg cgatattgac ggaagtctgc
     4021 cggcacgtgc cggcttctca tcgaggcagg tctgacgcat ccacgccgcc agctgcctgc
     4081 cgtcgcagcg ctcaagcaat cgcctgtgct catcctccgt cacccacatg gtgagcatct
     4141 tgttccgttt ctctgacaaa ccagtctcct gataacaccg ggacggaagg gaaaaccttt
     4201 cccggtcggc gcggggttgg acaagccgca ggcgcgtcag tggcttttag cgggtttcgg
     4261 ggcgcagccc tgaaccagtc acgcagcgct agcggagtgt atactggctt actatgttgg
     4321 cacggatgcg gcggatgtca gtgaagtact tcatgtggaa ggagaaaaaa ggcggcacgg
     4381 gggcgtcagc agaatatgcg atacaggata tattccgctt cctcgctcac tgactcgctg
     4441 cgctcggtcg ttcggctgcg gcgagcggta ccggcttact ggcggggcgg aaatttcctg
     4501 ggagatgcc
//
