LOCUS       NZ_CP074041             1454 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI7 plasmid pYLPI7h, complete sequence.
ACCESSION   NZ_CP074041
VERSION     NZ_CP074041.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877292
            Assembly: GCF_024585925.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1454)
  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  JOURNAL   Unpublished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 1454)
  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 07:00:44
            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)                     :: 5,135
            CDSs (total)                      :: 5,008
            Genes (coding)                    :: 4,808
            CDSs (with protein)               :: 4,808
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 64 of 200
            Pseudo Genes (incomplete)         :: 130 of 200
            Pseudo Genes (internal stop)      :: 42 of 200
            Pseudo Genes (multiple problems)  :: 35 of 200
            Pseudo Genes (short protein)      :: 3 of 200
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074041.1.
            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..1454
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI7"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI7h"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST162"
                     /note="Post-weaning piglet"
     gene            1..441
                     /locus_tag="KFU70_RS25540"
                     /old_locus_tag="KFU70_25325"
     CDS             1..441
                     /locus_tag="KFU70_RS25540"
                     /old_locus_tag="KFU70_25325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000031238.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000031238.1"
                     /translation="MSKDVERITQINDQGEIIGGFVAVIRPKQKSAFQRHFTMNQDALR
                     ILAKELTGEQFKVLMLMLADLDYENFIQIAQADIAETLGMQKTNVSRAVRALLDVGVIF
                     EGPKVGRSKTYRLNEQFGWKGTVTNHKKALKNGFSVIQGGRI"
                     /name="hypothetical protein"
     Typing          1034..1119
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="95.0"
                     /evalue="4.33e-36"
     Typing          complement(673..933)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.13"
                     /coverage="100.0"
                     /evalue="1.84e-104"
ORIGIN
        1 atgagtaagg atgtcgagag aatcactcag ataaatgacc agggtgagat tatcggcggc
       61 ttcgttgccg ttatccgccc taaacaaaaa tcagcatttc agaggcattt caccatgaat
      121 caagacgcat tacggatctt ggctaaggaa ttaaccgggg agcaattcaa ggtcttaatg
      181 ctgatgcttg cagatctgga ttacgaaaac ttcattcaga tcgcccaagc agatattgct
      241 gaaactttag ggatgcagaa aacgaatgtt agtcgcgccg ttcgcgcgct actggatgtt
      301 ggggtgatct ttgagggacc taaagtcggc agatcaaaaa cataccggct gaatgaacaa
      361 tttggttgga aaggcaccgt aaccaaccac aaaaaggcac tcaaaaacgg ctttagtgtc
      421 attcagggcg gccggattta aagagccagc ggcaggcgga caatccacag aacattgcat
      481 gcaatttcta gtggattgtc tatcctgcat tgctcttttg ccgcctcaaa tcccttgcgt
      541 gtttttgctc cccgatctcc agaacgaccg agccgccacg gttccggcag cgccttgagc
      601 gcaaccggaa accgtctggg gagaccccca ggcccccatc gctgtaacac cgacggtcta
      661 cgacacctac caaccgagtg gctgcctgta ccgtgcaaat gggctttgca gggggctggc
      721 gcggttcctg gcgacctgaa agcccctagt taggggtatc ggcgcgcctg acctcctgag
      781 agcctctgta agcgtttttc gcgccttcca tgccctgacg ggcatttaaa acccttttcg
      841 tgcgcctgag aacttctgag cgcgtttgaa gggctatctg acgactaatc cccgaaagaa
      901 caacaacggg atcaccgaca acatgcgaga ggtgataccg ctcgccgcaa gtcgatgacc
      961 gagcgtagcg agcgaatcga cgaggaagcg gaagagaacc ggaagccaca ttgagcactt
     1021 acgcactgat gtggggtgtc ggggcgaagc cctgaccaga tggcaattgt aatagcgtcg
     1081 cgtgtgacgg tattacaatt gcacatcctg tcccgatttc tgaggcgttt taacggtgaa
     1141 cggacggcaa aaacatgatg gagctgttga acgtggagag cgcgaaatcg gacaaaaatc
     1201 acggttgacg aggcttgcag aggagtaagc cagtatacac tccgctatcg ctacgtgact
     1261 gggtcagggc ttcgccccga caccccaaag agcagctagg ataaatatct aatggaatca
     1321 atgcgttaga cgcctaatat aaagatacag aaaggagaat aaaaacatta ataaaatcta
     1381 agggttacag ttgacatagt tatcaataat gataacactg ttatcattat tgataactca
     1441 aatagggttc aaag
//
