LOCUS       NZ_CP073966             4772 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB31 plasmid pYLMB31d, complete sequence.
ACCESSION   NZ_CP073966
VERSION     NZ_CP073966.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877309
            Assembly: GCF_024585585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4772)
  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  JOURNAL   Unpublished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 4772)
  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 06:37:15
            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)                     :: 4,983
            CDSs (total)                      :: 4,858
            Genes (coding)                    :: 4,586
            CDSs (with protein)               :: 4,586
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 272
            CDSs (without protein)            :: 272
            Pseudo Genes (ambiguous residues) :: 0 of 272
            Pseudo Genes (frameshifted)       :: 90 of 272
            Pseudo Genes (incomplete)         :: 179 of 272
            Pseudo Genes (internal stop)      :: 68 of 272
            Pseudo Genes (multiple problems)  :: 61 of 272
            Pseudo Genes (short protein)      :: 4 of 272
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073966.1.
            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..4772
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB31"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB31d"
                     /geo_loc_name="Cuba: Santa Cruz del Norte"
                     /collection_date="2015"
                     /genotype="ST167"
                     /note="Broiler"
     gene            173..256
                     /locus_tag="KFU79_RS24935"
     CDS             173..256
                     /locus_tag="KFU79_RS24935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_058652899.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPDRHD"
                     /name="hypothetical protein"
     gene            complement(850..1317)
                     /locus_tag="KFU79_RS24725"
                     /old_locus_tag="KFU79_24500"
     CDS             complement(850..1317)
                     /locus_tag="KFU79_RS24725"
                     /old_locus_tag="KFU79_24500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011899450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_153266272.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYATVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     gene            1852..2403
                     /locus_tag="KFU79_RS24730"
                     /old_locus_tag="KFU79_24505"
     CDS             1852..2403
                     /locus_tag="KFU79_RS24730"
                     /old_locus_tag="KFU79_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            complement(2602..2817)
                     /locus_tag="KFU79_RS24735"
                     /old_locus_tag="KFU79_24510"
     CDS             complement(2602..2817)
                     /locus_tag="KFU79_RS24735"
                     /old_locus_tag="KFU79_24510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137420.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2821..3306)
                     /locus_tag="KFU79_RS24740"
                     /old_locus_tag="KFU79_24515"
     CDS             complement(2821..3306)
                     /locus_tag="KFU79_RS24740"
                     /old_locus_tag="KFU79_24515"
                     /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_089624851.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3341..4045)
                     /locus_tag="KFU79_RS24940"
                     /old_locus_tag="KFU79_24520"
                     /pseudo=""
     CDS             complement(<3341..4045)
                     /locus_tag="KFU79_RS24940"
                     /old_locus_tag="KFU79_24520"
                     /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(3984..4307)
                     /locus_tag="KFU79_RS24750"
                     /old_locus_tag="KFU79_24525"
     CDS             complement(3984..4307)
                     /locus_tag="KFU79_RS24750"
                     /old_locus_tag="KFU79_24525"
                     /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_000957080.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4409..4596)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.864"
                     /coverage="87.0"
                     /evalue="5.83e-49"
     Typing          2..473
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.263"
                     /coverage="92.0"
                     /evalue="6.24e-142"
     Typing          4542..4772
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.086"
                     /coverage="99.0"
                     /evalue="1.44e-78"
     Typing          complement(2499..3994)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.585"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaacccgaca ggacttaaag ataccaggcg tttccccctg gtggctccct cgtgcgctct
       61 cctgttcctg cctttcggtt taccggtgtc attccgctgt tatggccgcg tttatctcat
      121 tccacgcctg acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga
      181 accccccgtt cagtccgacc gctgcgcctt gtccggtaac tatcgtcttg agtccaaccc
      241 ggatagacac gactaatcgc cattggcaac ggccactggt aagcaggatg tgcgagagat
      301 gtaacgagag ttcttgaagt ggcggcctaa ctgaggctac actgaaagga cagtatttgg
      361 tgacatgtct cgcacaagac tgttaccacg gttagagaat ctgccaggat taactaacct
      421 tcgaaaaaac cacctgccag ggtggttttt tcgtttctga gcaagagact acgacgagcc
      481 actgatgatc tcaagtgttc atttctgata ttcacagcag aataactgtt aggatatagg
      541 gtatctatag ccaggagctt caagaaatcc agacacagca atggattcca gggttatcga
      601 aaaaaattag tatataggtt gcaaccaaaa tgttggttgc aaatctacat cacgatgttt
      661 atgattattg tactgcaaga gcattcgcag ggggcatcaa ccagtaatag gccttctgtg
      721 ccgggcagtc agatggctgg tcatctgccg ggtagttacg acaagcgtcg gtttctgaac
      781 cctatgtgct aaggaaatgc tgcgactacc aacgaattca taaagggcgc tttttagcgc
      841 cctatttttt tattcaatat gaccaaccaa agtaccgtgc gccgtccttc gtgtgtacgc
      901 agtcacaacg acatagatcc aacctgactc agtttcaggc gcttctctgg gctcaagaat
      961 tacgatgcct accgacgact ttagcactgc aggccgatgt ttaccgcttg tactgttgaa
     1021 ctcgcaatat attggtacgc cacgacgaat aatatcccgg acaaaacgag ccacatcatt
     1081 aacggtcgca tatcccagct taaccagttc ctgctcgtgc tcagcccaga tatggcgaac
     1141 accaaagccc cggttagggc cagtatgcct accaacacgc aagaagatgt cgccagcagg
     1201 aataacatca cctttagaat taatttcagg gacacggcca tagcaatcaa gcccatcagg
     1261 gtgagctata gcgctgttag gtgaaccagc tacaccgtaa ttgtttggag caggcacaaa
     1321 acgatcctta ttgagtagag tccgcatatg gtaccagaga ggaaacaagc ggaaggagcc
     1381 caagaaaaaa gcagagacga taaaaagaat ccttatggat tatttttttg tcctttcatc
     1441 cttggcgcat aaggatatca cacctgaaaa tgtgacgtgc gaatcgccct agcagctaga
     1501 tttaccataa catcccttgc ccgcaccgct ccggacgggt tcagcgtgaa agcggcgtta
     1561 gcccggtaaa accggcagta aactccccgc taaaccgcgc attctgcgcc tgataaattt
     1621 cacgcggctg catagccatg cagccacgtg aatggctcat gctttcaatg tatatcctcg
     1681 tccaagcccc tgttttaacc ggtttatcaa aaaaacaaac aggaagcctt atcactaaca
     1741 ataaaagagg taggggctgc attttatcgc ataaaaaaca tttacaacac aaattctatc
     1801 gtatagattt cataaaaaaa tgaaattgac tcacctatta agggtttcta tatgaaagat
     1861 atgaaagctg ttgtggtttt taccgggaag gatttgaaca taatgagaac tgaggggggg
     1921 tcaggctact ggcatgccag aacagacagg ctcaacgatg ccgattacct catagcagta
     1981 agaaacagaa gggaaacgtg ggcagtaaaa gacctggaac acggcacagc attcctgatc
     2041 gccaaaatta ccgggtgttt taaaagccct gattacgacg acaggaacgt cataaccttt
     2101 gatgaatacg cagaaattca cactccaaaa gcatggaaaa tgctaaccga tggtcagcgc
     2161 tatccggttg cttacctgag cgcacaggaa gcttttttac gtattggggt aacaccggaa
     2221 caactggaat ggaagaaatt ccatccttca tccccatcgg ttcctaatac agtgattcct
     2281 ggtctggctg aagagaaaac agaaaaactc tcccttaacg aggcaattga aagagccaaa
     2341 aaggatatta gcaacgcaac agggattgat agctcagcca taacaataag catcaagatc
     2401 tgatgaagcg tgaacaacaa gatagcagcc tcatgttcta gaactgaacc tgtgcgccag
     2461 aaacagcaag cccatgcttt tccggcgcac agattcaaag tgacggaccg ttgtacgttc
     2521 gctgtcgctg agatcgttcc agctccagcg ctttctgatg ctgcgccgcc cgttcctgct
     2581 cacgatgtgc ctctatcacg ttcagccttg tgacaaccgg cgcagctgct cgctcaaact
     2641 ctgcacctgc ctgctcaagc ccgtgacgcg ctcgctcagc gccgcgttct cccgttgcat
     2701 aagaccaaac atcgtccgcc attccgcgaa ggcgttctcc cactcgtcca gccttttcga
     2761 gtagtcctgc tgtagctgct ctaatgcgct cagcaactgt ttttccagct ccgtcatgtg
     2821 ctatttcccc gccagtatca tccagctcga atcctctccg aaccgtcccg cttccgggtt
     2881 caccctcacg cagcggcgtc tctgctctcc gcaggtcgag agctgcacgc cgctgttcct
     2941 ctcggacagc atggcctgcg tgctcttctg ctcccggatg atcgtgtaat tgtcgagtat
     3001 ctgctgcccc tgccaccata gaatgcttgc gcccgatgct gtcagcagtg tagacaccag
     3061 gacgatggtc agccacgtct ggctgaccat acgcaccatg cctttcgtgc gctggctcat
     3121 ggctgaggac agcttccggt cgtggtcgag gatggcggcg ctgattctct tctcgctttc
     3181 gctcagttcc gctctgacag acttctcgtg ctcgctgaat gcgactttca gcatctcgcc
     3241 ggtactctgc tgctgcgctt tcgatttctg ctctaagtcc ttcgccagcg ttaaaagact
     3301 gttcatagat ggctcccttc agtcggatgt ttcgcccccc gtccgggtcg gcaatgctga
     3361 tgctgctttt tgtggtgcgc accacctcaa aacctgcgct ttctagcgcc tcagtgacgt
     3421 cttggcgggt tttcagctcc ccggacgagg ctaaggccag taaaccccgt gtaattgcct
     3481 gagcggcttc ctgcttcgtt ttcggcagcg cggacggcgt gaccagcgcc cgccggtttt
     3541 caggcgcgtt cgggtcatgc agccccagcc tgccgttcac gatggtctgc caggcatcaa
     3601 tgcgcggacg gtcggcgcgg tcgtaatacg gctggagacg cctgcctgtc agcagctcca
     3661 tgttcgggat caggaagttc agctccagcc gccccttatc ctggtgctca acccacagca
     3721 cgctgtactg gtctttatcg agtccgggca tcagaacccg ttcaaagctc gccatcagct
     3781 tttcgcgctg cccgggcggt aaatcctttt cggcaaagga caggacgccg gatgtgtact
     3841 tttttgcgta gggcgaggcg tcgataagct ccctgacttc ttccggcttc ccctgcagaa
     3901 cggtggcgcc gtcgcgctgt cggtctttcc ccagcagata atccaccgga ccggcgccac
     3961 cgccgcgccc tcgcgggtga aacttaacga tcatcgtctg cacccttttc cagcacggca
     4021 tgccgcagcc gctcgagtcc ggcatctatg gccatcagcg cggcgacaac ctgcacgcgg
     4081 tcgtgcccgc tgccgccacc ggcgttaacc tgccgggcaa tctggttgag gttattcccc
     4141 atgccggcaa gctgacgaag cagcgccggc gagatcgagg gaagcttgcc ggcgcgggcg
     4201 ggtttctcgg ccaggcacgt ctggcgcatc caggctgcaa gctgtttacc gtcgcagcgt
     4261 tccagcagac ggcggtgctc atcttcggtc acccacatgg tgagcatctt gttccgtttc
     4321 tctgacaaac cgatctcctg ataacgccgg gacgggcggg aaatcttttc ccggtcggcg
     4381 cggtgttgga caagccgcag gcgcgtcagt ggttttagca ggtttcgggg cgcagccctg
     4441 aaccagtcac gtagcgctag cggagtgtat actggctcaa tatgttacgg cggagtaaca
     4501 cgtaatgaaa gtgcttcatg tggcagggga aaaatgcagc tgcagggcgt acaggagaaa
     4561 atggaggtta cggtgatatg acgcctcctc gctcactcgg tcgcttccgc tcctgacgtt
     4621 aggctgcggc gggcgttacc tgcaaacgga taagagcaaa ggcatacggc atggcaagca
     4681 ggacaggaaa aggatgcggc gctgccgttt ttccataggc tccgcccccc tgacaagcat
     4741 cacgaaatct gacgctcaaa tcagtggtgg cg
//
