LOCUS       NZ_CP074040             3372 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI7 plasmid pYLPI7g, complete sequence.
ACCESSION   NZ_CP074040
VERSION     NZ_CP074040.1
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 3372)
  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  JOURNAL   Unpublished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 3372)
  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
            CP074040.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI7"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI7g"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST162"
                     /note="Post-weaning piglet"
     gene            join(3012..3372,1..200)
                     /locus_tag="KFU70_RS25520"
     CDS             join(3012..3372,1..200)
                     /locus_tag="KFU70_RS25520"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            207..440
                     /locus_tag="KFU70_RS25525"
                     /old_locus_tag="KFU70_25305"
     CDS             207..440
                     /locus_tag="KFU70_RS25525"
                     /old_locus_tag="KFU70_25305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1756..1947)
                     /locus_tag="KFU70_RS25530"
                     /old_locus_tag="KFU70_25310"
     CDS             complement(1756..1947)
                     /locus_tag="KFU70_RS25530"
                     /old_locus_tag="KFU70_25310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1996..2334
                     /locus_tag="KFU70_RS25535"
                     /old_locus_tag="KFU70_25315"
     CDS             1996..2334
                     /locus_tag="KFU70_RS25535"
                     /old_locus_tag="KFU70_25315"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_251302571.1"
                     /translation="MKREKMLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTG
                     KLPTLSPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVR
                     EQGVRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          1592..1675
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          3..523
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="84.916"
                     /coverage="99.0"
                     /evalue="8.25e-73"
     Typing          2325..3367
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.126"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggcaggaaag caagattgcg aaaaatatcc tgactatcag agagcaggaa aacacgctgg
       61 cgaaactcga ggcaaaaacc tggggggtga cgttcgtcaa tggcgagaac gggaaatttc
      121 tggtgttgcc ggacggggtg aaaggggaaa acacctggac ggtgggcgac aagaacgccg
      181 tgaggctggt cagggagtaa acgagtatga cggaactgga agggcatttg ctgaacgcct
      241 tagagcattt gcaacaggac tatatgcggc ggctgaacga gtgggagagc gccttcgcgg
      301 aattgcagaa gatgcacgag gttacgcaac ggaacaacgc gatactgaac gagcgcgtcg
      361 tgatattgag tcagcaggtg cagagattag ccgggcaagt ggatcgcttg agtcggttat
      421 ttatcgcgaa caacagctaa gggatgaaca ggagcgtgcc cggtacagac atgaggtaca
      481 ggaacgcgcg gcacgggttc ggagtgggcc atcaatggag atgtgaccgg ggaagtgacg
      541 aaatcttgcc attttgacca gttcgacggc tggggcgagc gaaacaaatc gtgtgccgta
      601 tttgtgcata gctatgcaac atcctgaaaa cgcatttcac gcgtttttgg ggattcagcc
      661 aggggaaaac atggtttttt tactttttga gcgtaaagac gtgaaaaatc tcgttattgc
      721 acttgcgatc tttcgtcggc gggcgtagaa cgaaaacagc tcgccaggaa ggcgagctgt
      781 ttcgggttca ttgaggtctc tgacctcctc aatgttcctg tggaaactgt tgagatccac
      841 aacagaaacc agttcattca gtttgcatga gccttctgta ttcttcaaga atttttcaac
      901 agcacagtct cccaggaacc ccgaaaaaaa cctgtttttg cagatacttg cgtatttgcg
      961 agaatcgttt gcggttgggg gagctgtgac gacggcgacc gcacgcgtga gagttccgct
     1021 accggcgcag agagtttcat cgacagcgga cacctgatga gttgccacaa aaaccgtatg
     1081 tagcgcggct agattggttg agttagacct tggcggcagt tcccggtatg tggtggcgtg
     1141 acgggtgaga tggtgcggcg aagacgcata cgtcacgcag gcgcgggttc ttccactgac
     1201 gcgccccgtg atcgatggcc ttggctccgt ccggcatatc gagagcggca aactacccgt
     1261 cccttcactg ggaggggtga gttgttgccg ttccctccaa cctttcacca tccggcatat
     1321 cgcacgatcc catgtgcacc gcaactcctg ataactccag tgcaaaaaaa aaaacggatc
     1381 tgcatcacaa cgagagtgat cccaccgctc gccgcagccc cagcgaccga acgtagtgag
     1441 cgagtgggcg aggaagcgga agagtcacag atgcaagcat tgtgcactta cgcgcctgtg
     1501 ccagtgtccg cgtgtgtgct gtttatcggg tgcgctgttt ttacatctgt gcggcttttt
     1561 actcctgaca tggtgcactt cccatccatg tctgcaccga tgcaaaatga gataagccag
     1621 tatacacatc gctatcgctc tgtgaactgg gtcagggctg cgccccgaca cccgcactga
     1681 cgcgccctgg cgggcttgtc tgctcccggc atccgctcac aggcaagctg tgaacgtctc
     1741 cgggagctgc atgtttcagt tgctttcacc gtcatcgccg aagcgtgcga ggcaactgcg
     1801 gtagagttcg tcggcgtggt cgtgaagtga ttcgcagatg tctgcctgtt cgtccgcgtc
     1861 cagatcgttg agtttttcca gcagggttag cgtctggctt ctgataaagc gagccatgtt
     1921 aagggctgtt ttttcctgtt tggtcatggt cttaaggctc cttgtatggg ggatttgtta
     1981 gggggaatga taccgatgaa acgcgagaag atgctcacga tacgggttac cgatgaggag
     2041 cacgcccggt tactggaacg ctgcgagggt aaacgactgg cggaatggat gcggcgggtc
     2101 tgtctggggg agccggttgc acgcacagga aaactgccga cactatcgcc gccattgctg
     2161 cggcatctgg ctgccatcgg gaacaacctg aaccagacag cccggaaggt gaacagcggc
     2221 cagtggtctt cgattgaccg ggttcatgtg gtggccgcac tgatggccat cgagggtgaa
     2281 ttgcgccagt tgcggcaggc tgtcagggaa cagggggtac gggatgatag ttaaatttca
     2341 tgccaggggg aaaggcggtg gaagtggccc ggtcgattac ctgctgggtc gggagcgtaa
     2401 ccgcgaaggc gcaacggtgc tccggggtaa cccggaagaa gtgcgggaac tcattgattc
     2461 cacgccattc tcgaagaaat acacttcagg cgttctgtcg ttcgcggaga aggagttacc
     2521 gccgggtgaa cgcgaaagag tgatgacgag ctttgagcgt gttcttatgc ccggtctcga
     2581 aaaagaccag tacagcattc tctgggtgga acaccaggat aaggggcggc tcgaactgaa
     2641 ttttgtcatc ccgaacatgg agctacagag cggtaagcgc ctccagccgt actacgaccg
     2701 cgcggacagg ccgaggataa atgcctggca gacgctggtt aatcatcatt acgggctgcg
     2761 tgacccgaac gcaccggaga acagacggac gcttgtcacg ccaaataatc tgccaaaagc
     2821 gaaacaggag gccgcagaag cgattacacg gggtcttgag gctctttacc atgccggagc
     2881 aataaaaacg cgtcaggatg tcacagaggc gcttacagcg gcaggttttg aggtggtgag
     2941 gacaaccaaa agcagcatca gtattgccga cccggagggg gggcggaatc tcaggctaaa
     3001 gggggcgctg tatgagcaat cttttacaaa tgggaacaga cttcgagaag aaactgaaag
     3061 agcgagccgc ttctaccgag aacatgctga acagcgagtt caggaagctc gaagagtctg
     3121 tagacaaggc attgagctta aacaggcaga aaatcagaga cgctatcagc gaacatacaa
     3181 catccgtgaa aaagcaactg gatacgctga gcaccaccgt gagcatgcag ttcagcacca
     3241 cagaggccga actgtcccgg cagcagaaaa aactgctctg gcgggtgatc aaagggcgga
     3301 tactgtttcc ggcgctgacc gcgctcagcg tcacgggcgg cattttcctg gggtgctggg
     3361 ggctgatgga gt
//
