LOCUS       NZ_CP074018             2164 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI24 plasmid pYLPI24f, complete sequence.
ACCESSION   NZ_CP074018
VERSION     NZ_CP074018.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877297
            Assembly: GCF_024585825.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2164)
  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  JOURNAL   Unpublished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 2164)
  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                   :: 08/24/2023 06:36:49
            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)                     :: 4,780
            CDSs (total)                      :: 4,663
            Genes (coding)                    :: 4,389
            CDSs (with protein)               :: 4,389
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 274
            CDSs (without protein)            :: 274
            Pseudo Genes (ambiguous residues) :: 0 of 274
            Pseudo Genes (frameshifted)       :: 73 of 274
            Pseudo Genes (incomplete)         :: 195 of 274
            Pseudo Genes (internal stop)      :: 43 of 274
            Pseudo Genes (multiple problems)  :: 36 of 274
            Pseudo Genes (short protein)      :: 3 of 274
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074018.1.
            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..2164
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI24"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI24f"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST710"
                     /note="Post-weaning piglet"
     gene            54..167
                     /locus_tag="KFU81_RS23915"
                     /old_locus_tag="KFU81_23595"
     CDS             54..167
                     /locus_tag="KFU81_RS23915"
                     /old_locus_tag="KFU81_23595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071789001.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            401..829
                     /locus_tag="KFU81_RS23745"
                     /old_locus_tag="KFU81_23600"
     CDS             401..829
                     /locus_tag="KFU81_RS23745"
                     /old_locus_tag="KFU81_23600"
                     /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_130559423.1"
                     /translation="MSLNMTFSITEVREGRIGSLVITKELYDKLEKYSRSNGLITSTYD
                     HGHGVVRYYTVKYCLQMNYHGQNHPQKYLIKRGGRYPSKYAMVKKTVEELEYSTPTFDA
                     ICRNIAIKYPHMVKFANYISETPLKGFAATFNNSVGND"
                     /name="hypothetical protein"
     gene            complement(1608..1799)
                     /locus_tag="KFU81_RS23750"
                     /old_locus_tag="KFU81_23605"
     CDS             complement(1608..1799)
                     /locus_tag="KFU81_RS23750"
                     /old_locus_tag="KFU81_23605"
                     /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"
     Typing          2..167
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.802"
                     /coverage="100.0"
                     /evalue="2.18e-78"
     Typing          1675..2113
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.5"
                     /coverage="90.0"
                     /evalue="3.44e-140"
ORIGIN
        1 ttccacgcct gacactcagt tccgggaagg cagttcgctc caagctggac tgtatgcacg
       61 aaccccccgt tcagtccgac tgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
      121 cggtaagaca tgcaaaagcg ccactggcag cagccactgg taactgattt agaggagatg
      181 gacttgaagt catgtgccgg ttaaggctaa actgaaagga caagttttgg tgactgcgct
      241 cctccaagcc agttacctcg gttcaaagag ttggtagctc tgagaacctt cgaaaaaccg
      301 ccttgcaggg cggttttttc gtttctggat aagagactac gacgacagac ggataatctc
      361 aagaaaatcc tctctaacag gttatattca gagtaaaaaa gtgagcttaa atatgacttt
      421 ttcaataaca gaagtgcgtg aggggcgtat cggctcttta gttattacaa aagagcttta
      481 cgataaatta gaaaaatact ctcgctcaaa tggattaata acatccacat acgaccatgg
      541 tcatggcgtt gttagatact acaccgtgaa atattgcctc cagatgaact atcacggaca
      601 aaatcatcct caaaaatatc ttattaaaag aggggggaga tatcccagca agtatgcaat
      661 ggtcaaaaaa accgttgaag agttagagta ttcaacaccg acatttgacg caatatgcag
      721 gaacatagca ataaaatacc cacacatggt caagtttgct aattacatat cagaaacccc
      781 attaaaaggc ttcgccgcaa cctttaataa ctccgttggt aatgattaag tgttatttac
      841 cataacatcc cttgcccgca ccgcctcagg cgccctcaga gcgtttctga cgggaaaccg
      901 gcaaaacagg caacaaacca cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg
      961 gcatgcatga gtatgcgcac aagtgcatag cgcggaaatt cacgccattc agccggggta
     1021 agtcctgttt ccgatgttct tcttacccga aaacggtgaa cggggacgca atttattgcg
     1081 tggccgtgag gcgttgccgg cgcagccgga aaacccgttt tcagcacgtt caggaagggg
     1141 gtcgatgtac gaatggttca gggaacggat ctgaggtaat ccggtagtta ctttgtagtt
     1201 tatctgtagt tttcttgtag tctattagta gtctgccacg ttttttgtag ttttcttgta
     1261 gtttttttgt agtctgccat cactaatgca aaacgttttt tgtagtttat ctgtagtttt
     1321 tggttgctca gatggtcatg caagcatgac catcaaagaa taggacgctt tatagccaaa
     1381 taacccttaa cctacggaga gcgccctacc aaaaatgatg attttttaac ccttaaatgg
     1441 tcatacacct aacgcagccg cgattttcat cgcaacttca tgaaaaataa ataaaaaaga
     1501 aaaaatacag ggattctggg tattaccggg gtaataatgt taagcgccaa gacaatgaaa
     1561 attaaggcga tgccggtatt actccggtaa tacccagaac ggagccatta cgcaccgtcc
     1621 tgctgctcat tcaggcgcgc tgacaggctt cggtaaaggc gttccgcatc ctcatggagt
     1681 ttctcgcaga aatcagcctc atgatccaga tccagctcat taagcctgtc cagaagaagc
     1741 agggactgat cctggatgaa tttagccatg ttaacggcag tcttttgttg tttgttcatg
     1801 aaggccccgg cgcgaaagtg cttactgtac gttctgatgg ttttccgctt cctcgctcat
     1861 tcgctcactc cgttcggtca tgagtctgcg gcgagcggag ggaagataag cagataacat
     1921 aacggtaagc ataacgaaag ctaaggacaa gggcgaaaag gccacgcccc gccggggcgt
     1981 ttttccatag gctccgcccc cctgacaagc atcacgaaat ctgacgctca aatcagtggt
     2041 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggtggc tccctcgtgc
     2101 gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg ccgcgtttgt
     2161 ctca
//
