LOCUS       NZ_CP073992             3402 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB10 plasmid pYLMB10d, complete sequence.
ACCESSION   NZ_CP073992
VERSION     NZ_CP073992.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877303
            Assembly: GCF_024585705.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3402)
  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  JOURNAL   Unpublished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 3402)
  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 06:55:18
            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)                     :: 4,648
            CDSs (total)                      :: 4,530
            Genes (coding)                    :: 4,307
            CDSs (with protein)               :: 4,307
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 223
            CDSs (without protein)            :: 223
            Pseudo Genes (ambiguous residues) :: 0 of 223
            Pseudo Genes (frameshifted)       :: 72 of 223
            Pseudo Genes (incomplete)         :: 145 of 223
            Pseudo Genes (internal stop)      :: 43 of 223
            Pseudo Genes (multiple problems)  :: 38 of 223
            Pseudo Genes (short protein)      :: 3 of 223
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073992.1.
            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..3402
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB10"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB10d"
                     /geo_loc_name="Cuba: Santa Cruz del Norte"
                     /collection_date="2015"
                     /genotype="ST1716"
                     /note="Broiler"
     gene            join(3345..3402,1..677)
                     /locus_tag="KFU65_RS23080"
                     /old_locus_tag="KFU65_22865"
     CDS             join(3345..3402,1..677)
                     /locus_tag="KFU65_RS23080"
                     /old_locus_tag="KFU65_22865"
                     /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_257204749.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNGNGNGNGREVSLVNGGFKRFIP
                     GDFMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKEEAKSRGGKWTLSNV
                     KIEYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(<951..1031)
                     /locus_tag="KFU65_RS23085"
                     /pseudo=""
     CDS             complement(<951..1031)
                     /locus_tag="KFU65_RS23085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     gene            1467..1658
                     /locus_tag="KFU65_RS23090"
                     /old_locus_tag="KFU65_22870"
     CDS             1467..1658
                     /locus_tag="KFU65_RS23090"
                     /old_locus_tag="KFU65_22870"
                     /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_021314601.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNDLDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2550..2762
                     /locus_tag="KFU65_RS23095"
                     /old_locus_tag="KFU65_22875"
     CDS             2550..2762
                     /locus_tag="KFU65_RS23095"
                     /old_locus_tag="KFU65_22875"
                     /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_089634954.1"
                     /translation="MSNIKPDSLIRITKRKNENGDETTDLEWKPGSKEAIATGAAAGAA
                     LGSAVPVIGTAVGAVIGGTLALIFG"
                     /name="hypothetical protein"
     gene            2975..3274
                     /locus_tag="KFU65_RS23100"
                     /old_locus_tag="KFU65_22880"
     CDS             2975..3274
                     /locus_tag="KFU65_RS23100"
                     /old_locus_tag="KFU65_22880"
                     /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_023281092.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHPEALFLASAVARDTFLKLIRERLCGGEDVDSWYGFQRNISNDHS"
                     /name="hypothetical protein"
     Typing          complement(905..1290)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="89.0"
                     /evalue="3.81e-158"
ORIGIN
        1 ttgttcaagc ttctttagaa aaatattttt ttcgacaagg gttcgatata gatacgggat
       61 cttatattga ccttatttgt cgtgataaag aatctaggga tgttgtgtgg catattgaag
      121 taaaagggaa aacatcacag ccagggttgg attttcgaac ttgtcttgga caattagtgc
      181 agagaatgac aaaagataat attaattatg ctattgctgt tccaagaata aaacagtatg
      241 aaagattaat agaagaaacg agcattcttg ctgttagtaa attgaattta cactggatat
      301 ttgttgggcc tgatggcagt gtgacaatta aggaacctga tagctctacg atgaaaaatg
      361 gtaatggtaa tggtaatggt aatggaagag aagtttctct tgtgaatgga gggtttaaaa
      421 gatttattcc gggggatttt atgccaactt gctcatatgg gaaagctcct gttgtattta
      481 aatcatctcg gcgagaaatg tgggattggt tggacgattt tgttatttca aatggggtga
      541 tcccaagtat tgctgatatt aaagaagagg ctaaatcgcg gggtgggaaa tggacgcttt
      601 ctaatgttaa aatagagtat cagttttgga aaatatatca cttgtataag gggcattttt
      661 tctatcaatc tgagtagctg actcatttgt tcatcaaatg ccatgatctt cttgagattc
      721 attcgctcaa agcgtaatct ctttctcgga aaacgaaaaa accacctggg gaggtggttt
      781 ttcgaaggtt cagtaagttg gggaacttct gaaccgtggt aacagtcttg tgcgagacat
      841 gtcaccaaat ctgtcctttc agtgtagccg cagtcaggcc accacttcaa gaactctcga
      901 tacatctctc gcacatcctg tctaccagtg gccgttgtca atggcgatta gtcgtgtctt
      961 accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg
     1021 ggttcgtgca cacagcccag cttggagcga acgacctaca ccgaactgag ataccaacag
     1081 cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatctggta
     1141 agcggcaggg tcggaacagg agagcgcacg agggagcgac cagggggaaa cgcctggtat
     1201 ctttatagtc ctgtcgggtt tcgccaccac tgatttgagc gtcagattct gtgatgcttg
     1261 tcaggggggc ggagcctatg gaaaaacgcc ccgccggggc gtggcctttt cgcccttgtc
     1321 cttagctttc gttatgctta ccgttacgtt atctgcttat cctccctccg ctcgccgcag
     1381 actcatgacc gaacggagtg agcgaatgag cgaggaagcg gaaaaccatc agaacgtaca
     1441 gtaagcactt tcgcgccggg gctttcatga acaaacaaca aaagactgcc gttaacatgg
     1501 ctaaattcat ccaggatcag tccctgcttc ttctggacag gcttaatgac ctggatctgg
     1561 atcatgaggc tgatttctgc gagaaactcc atgaggatgc ggaacgcctt taccgaagcc
     1621 tgtcagcgcg cctgaatgag cagcaggacg gtgcgtaatg gctccgttct gggtattacc
     1681 ggggtaatac cggcatcgcc ttaattttca ttgtgttagc gcttaacatt attaccccgg
     1741 taatacccag aatccctgta ttttttattt tttatttatt tttcatgaag ttgcgatgaa
     1801 aatcgcagct gcgttaggtg tatgtcattt tttagtatat aaaacgacca ctcccgagtg
     1861 ctggcgccgc aggttaagga tgattctggc taaaaagcgt ccttttccgg gaaagggtca
     1921 tgctcgtatg accctatggg ttcagcgact acacataaac tacaaaattg catctgcttt
     1981 taccccagaa cgcgggtgta caacagaatt acatcaaaag tacatcaaaa ttacatcact
     2041 tttacgtcag atcgcgggtg tacaacagaa ttacatcaaa agtacatcac ttttacatca
     2101 tttttacgtc agatctgacc tctgagctat tcgtacatcc gccccctctt cctgggcctc
     2161 ctgcacgtgc tgaaaatggt ttttccggct gtgccggcaa cgcctcacgg ccacgcaata
     2221 aattgcgtcc ccgttcaccg ttttcgggta agaagaacat cggaaacagg acttaccccg
     2281 gctgaatggc gtgaatttcc gcgctatgca cttgtgcgca tactcatgca tgccgtaaaa
     2341 acagagcctg cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt taccggtttc
     2401 ccgtcagaaa cgcgctcagg ccgtctgagc ggtgcgcgta atgaggcgtt atggtaaatg
     2461 cagggttttt aatatatgta gttgaaatgt agcctaggtg gagggagagt gtttttggtg
     2521 tatacgtttc aatcttacgt gaggtgcgaa tgagcaatat taaacctgat agtctgatcc
     2581 ggattacaaa aagaaagaat gaaaatggcg atgaaacaac agatttagaa tggaagcctg
     2641 gttcaaaaga ggcaattgcc acaggcgcgg ctgctggagc agcactaggt tctgctgttc
     2701 ctgtaatagg aactgcagtc ggggctgtga tcggtgggac tttagcttta atttttggat
     2761 aaccaagttt agagcgaaac acccgtcaag aatggcggaa ggtagcctgc taaaagcggg
     2821 cttttttacg ctcatgcgag caatgaggcg ttatggtaaa tgcctgtctt gctcactttt
     2881 agagcatgag gcaaaaaagg taaaaactta tttgcttaac agcccctatc actatgtaaa
     2941 ttaactcctg aaaactaaaa aatggaggat tggcatggcg actgctacta attttgatgc
     3001 gtggttagat gatgttgatg gcgattatga ggaggttatg gctctttatg attccgttca
     3061 gaatgtaagt gatatggggt tgtatcagtg tgttgagggt ggtcggggtg atgcttgggt
     3121 cgtgagctct aatcatcatc cagaagctct ttttctagca tcagctgtgg ctagggatac
     3181 tttcctcaaa ttgattagag aaaggctatg tggcggcgaa gatgttgatt catggtatgg
     3241 atttcaacga aatatatcga atgatcactc gtaatcgtac agagagttcc ctttgtagga
     3301 actcttaaaa tatgacgtta tagtaaatag gatgcgtagg ggttgtggct cttatggtga
     3361 cgagaaggta cttactaggt ggtgaatatc cttccgagga at
//
