LOCUS       NZ_CP074046             2393 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI6 plasmid pYLPI6d, complete sequence.
ACCESSION   NZ_CP074046
VERSION     NZ_CP074046.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877291
            Assembly: GCF_024585945.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2393)
  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  JOURNAL   Unpublished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 2393)
  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 06:31:00
            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)                     :: 4,647
            CDSs (total)                      :: 4,529
            Genes (coding)                    :: 4,315
            CDSs (with protein)               :: 4,315
            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)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 51 of 214
            Pseudo Genes (incomplete)         :: 155 of 214
            Pseudo Genes (internal stop)      :: 31 of 214
            Pseudo Genes (multiple problems)  :: 26 of 214
            Pseudo Genes (short protein)      :: 3 of 214
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074046.1.
            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..2393
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI6"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI6d"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST641"
                     /note="Newborn piglet"
     gene            88..633
                     /locus_tag="KFU63_RS23140"
                     /old_locus_tag="KFU63_22930"
     CDS             88..633
                     /locus_tag="KFU63_RS23140"
                     /old_locus_tag="KFU63_22930"
                     /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="SHOCT domain-containing protein"
                     /protein_id="WP_257182284.1"
                     /translation="MRERYLNKISNFDMARIVLFIAIQIISCVFMFWGAIPALIVFFSY
                     LAMRKECNLKPIEKSKVYISVYMLLTAALVLFLFVYKAGMFRGGGDYFPLVFVFILLYV
                     YHLAFHKLWLRTIDENSSIIIENGIFNFNRKNAPVGFSRKDVNNIDTLLKLNEARKEGI
                     ISEDEFNKLKKRLNILND"
                     /name="SHOCT domain-containing protein"
     gene            complement(869..1003)
                     /locus_tag="KFU63_RS23270"
     CDS             complement(869..1003)
                     /locus_tag="KFU63_RS23270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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_071996625.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGNRFRGGES"
                     /name="replication initiation protein"
     Typing          complement(894..1371)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.364"
                     /coverage="92.0"
                     /evalue="1.32e-143"
ORIGIN
        1 agttactgct tttctatttt ttgaaataat attaatatca ggcgattgat tttaaattaa
       61 ttaactatga ttgaatggtg gtgatttatg cgcgaacggt atttaaataa aatatctaat
      121 tttgatatgg caagaatagt gttgtttata gccattcaaa ttatctcttg tgtttttatg
      181 ttctgggggg ctattcctgc cttgattgtt tttttctcat atttagccat gaggaaggaa
      241 tgtaatttaa agccgataga gaagtctaag gtttacatat ccgtttacat gcttcttaca
      301 gccgctttgg tactgtttct tttcgtgtat aaagctggca tgtttagagg gggcggtgat
      361 tatttccctc tcgtttttgt ttttattttg ctttatgttt accatctcgc ttttcataaa
      421 ttatggttgc gaacgataga tgaaaactca tcaataataa ttgaaaacgg gatttttaat
      481 tttaatcgta aaaatgcacc tgtaggattt agtcggaaag atgtaaataa cattgatact
      541 cttcttaaat taaacgaggc tagaaaagaa ggtattataa gtgaagatga gtttaataaa
      601 ttaaaaaaaa gactaaatat tcttaacgac tgattttttg ctaactaaag gtaaagaaag
      661 cttatgaatc tttgataaga ttgaatatct tcttgtcatt gattttttat cgtcgtaatc
      721 ttcttccctg caaacgaaaa aaccacccgg caaggtggtt tttcgaaggt tcgcaagagt
      781 tgacgctctt ttgaaccgcg gtaactggct tggaggagca cagtcaccaa aactgtcctt
      841 tcagtgtagc cttatcgcac ccgaaatttc aagactctcc tcctctaaac ctgttaccag
      901 tggctgctgc cagaggcgct tttgcatgtc tttccgggtt ggactcaaga cgatagttac
      961 cggacaaggc gcagcagtcg gactgaacgg ggggttcgtg catacagtcc atcctggagc
     1021 gaactgccta cccggaactg agtgtcaggc gtggaatgag acaaacgcgg ccataacagc
     1081 ggaatgacac cggtaaaccg aagggcagga atgcggggga gcacgaggga gccatcaggg
     1141 ggaaacgcct ggtatctcta agccgcatcg ggtttcgcca ccactgattt gagcgtctga
     1201 ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cggcaacgcc gcttcctttt
     1261 ctcttccttt cccaatttga ttgctactag cctactcctt tacttctgag ccggtaacgc
     1321 ccgccgcagt ctcacgtccg gagcgtagcg accgagtgag cgaggaggcg taatttcatc
     1381 gactcctgca tttttcactt acgccctaca gctacatttt tcacctgcca ggggtcagtt
     1441 tggatataga gaattattgt acggtaagcc tgttttttga acagacttac ctatagcaat
     1501 agggtgtact cccgcgctat acggcatttt cagaggtttg accttaatcg gataacctaa
     1561 atgggatact gcaagagcga caacttaaaa gcgatagcca ctgacgcaaa atcaacccct
     1621 tacgaaccaa gattggttaa ataatgcgct taacgtacaa aaaattccga tctccaaact
     1681 gaccccttct tcgcctctta tgtttctcga atgaatcgat ggggacagga aatgttttgt
     1741 ggccaccgcc gcttcgccgg caccacaaaa ctgtcggaca agatgtgttt ttggagtacc
     1801 gccggcacca aaaacatttc atcaggcgcc gcccgatacg ctgagtttcg tgcgtacgaa
     1861 atttctctgc tgttgagatc tagggcagga ttcgcaaagt gctggcgttt gtacccaccg
     1921 gaagctgccg cgcctggcgg cttggccaac gcctcacggc cgcacagtca actgtgcacc
     1981 cgttcaccgt taccagatcc cctgattccg gccgggcctg cctgcactgg ccaaagcctt
     2041 aaaactgcgc aatcagcagc gcgggggcag ttgataacca ctttttactg tcatacttat
     2101 ttgccggctc tctgatcggt accggctgac tgtttgtgca aattttgtcg gacatcctga
     2161 ccctcgatgt ccgttttttt tgttcaaaat tcgcctttag tgccagcatt cgtccgaaac
     2221 cggccgccat tcacttccgt gcatagccat gcaggcgcgc agaaatcatc aggcgcgttt
     2281 tttcacgata tggacaggga aaggtgccgg aaacgcagag gacgcggcag aaacgcgctg
     2341 agggcctctc agggggtgcg ggcaaggggt gttatggtaa atgccccata ttc
//
