LOCUS       NZ_CP042592             2724 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain PK6 plasmid pRHEcCUB-4, complete sequence.
ACCESSION   NZ_CP042592
VERSION     NZ_CP042592.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12512712
            Assembly: GCF_008823185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2724)
  AUTHORS   Hernandez-Fillor,R.E., Brilhante,M., Baez-Arias,M., Espinosa,I. and
            Perreten,V.
  TITLE     First genome of multidrug-resistant E. coli from Cuba carrying
            blaCTX-M-32 on an IncX1 plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2724)
  AUTHORS   Hernandez-Fillor,R.E., Brilhante,M. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-AUG-2019) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 14-MAY-2019
            Assembly Method                   :: Unicycler v. 0.4.4
            Assembly Name                     :: CENSAIVB_Ecoli_PK6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_008823185.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 04:08:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,705
            CDSs (total)                      :: 4,583
            Genes (coding)                    :: 4,379
            CDSs (with protein)               :: 4,379
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 58 of 204
            Pseudo Genes (incomplete)         :: 142 of 204
            Pseudo Genes (internal stop)      :: 32 of 204
            Pseudo Genes (multiple problems)  :: 26 of 204
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042592.1.
            Bacteria and source DNA available from Laboratory of Animal
            Bacteriology. National Centre for Animal and Plant Health (CENSA).
            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..2724
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK6"
                     /serotype="O162:O89:H10"
                     /isolation_source="healthy pig from farm"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pRHEcCUB-4"
                     /geo_loc_name="Cuba: Matanzas"
                     /collection_date="2016-07"
                     /collected_by="Carelia Martha Marrero Moreno"
                     /identified_by="Rosa Elena Hernandez Fillor"
                     /genotype="ST1695"
     gene            complement(404..598)
                     /locus_tag="FTO72_RS23505"
                     /old_locus_tag="FTO72_23505"
     CDS             complement(404..598)
                     /locus_tag="FTO72_RS23505"
                     /old_locus_tag="FTO72_23505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1390..2154
                     /locus_tag="FTO72_RS23510"
                     /old_locus_tag="FTO72_23510"
     CDS             1390..2154
                     /locus_tag="FTO72_RS23510"
                     /old_locus_tag="FTO72_23510"
                     /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_063081626.1"
                     /translation="MLGKIWCSLITVTFTLLIGCVPQPKPVDKFDINKLLNVTDSETTT
                     DLAIPSPAQQDPIWQTSLLTGRQLKEGIDAGKIKRGDVFRAKIDLKYTIVNKSQLPPAL
                     DVFRSVLIGDPSAWNDLIAIDISDSKHTKTGKYVAQNAFGARVKVDEVKSERYLLALDA
                     ANTLSTTAIKMGVEGCAVTEDSLNSFVLEYVAELDESTYQQEKGIIPAEYSSPTDIRIN
                     NYYFKGEVRAARLIDSTTGKPYPCKLSFIIRY"
                     /name="hypothetical protein"
     Typing          144..327
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.185"
                     /coverage="86.0"
                     /evalue="1.26e-45"
     Typing          635..733
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          858..1113
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(2..194)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.268"
                     /coverage="99.0"
                     /evalue="8.76e-71"
     Typing          complement(2202..2699)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.066"
                     /coverage="99.0"
                     /evalue="8.08e-141"
ORIGIN
        1 gcttgtcagg ggggcggagc ctatggaaaa acggcagcgg cgtatccttt ttttgccctg
       61 cttgtcatgc cgtatgcctt tgctcttatc cgtatgcagg taacgcccgc cgcagccgaa
      121 cggcaggagc ggcagcgacc gagtgagcga ggaggcgtca tatcaccgta actcccattt
      181 tctcccttac gccctgtagc tgcattttcc cctgtcacat gaagcacttt tattaagtgt
      241 taccccgccg taacatattt agccagtata cactccgcta tcgctacgtg actgggtcat
      301 ggctgcgccc cgacacccgc taaaaccccc tgacgcgccc tgacgggctt gtctgctgac
      361 gaaaacgccc acgggaaagc cgtgaccgcc tccgtcagct tcgttatgtt cctgtttcac
      421 tttcggcctc aaagcgaatc tggatgctgt tctggagttc ttctgcgagt tcgtgcagtc
      481 gttcgcacat ggccgcctgt tcgtcggcat ccagagcatc cagtttttca agcagtgtca
      541 ggctctggct tttgataaat cgcgccatat tcagcgcagt ttgttgttgt ttgttcacct
      601 tccgttgttc tccgtcagtt ccgggtgtcg gggggaccct gagcaggtgg taattgtaag
      661 acgttgcggg cgacggtatt acaattgcac atcctgtcct gtttctttag gacgtatcat
      721 ggcacagcat atcaactgat aaataatccc tgtgcagtgc agccgctgtt gcataaaatt
      781 tcgctctgcg tcgagtgttt cttaatcaat aattccgctg atactccgga aaaacgcgag
      841 tctgttctca tgcctgaaat gcccacaccc cacgcaaaaa caagtttttg ctgatttttc
      901 tttataaata gagagttatg acaaattagt tcttcttgct ctctttgtga tatttaaaaa
      961 agcggtgtcg gcgcggtgtt gtagctgcgc caacaccgct ttttaggggt ggtactgact
     1021 attttcataa aaaacatcat cttatattag gggtgctgct agcggcgcgg tgtgtttttt
     1081 tacaggacac ccctgggggc gctgctaggg gtgtctgttc agatatgtag caatgagtca
     1141 gggattcacg aactgaaaat gtccgaaaat gtgtctcatg ggcactgtat gcgcccaaac
     1201 cgatcgtcat ttactttcat gcatagctat gcagtgagct gaaagcgatc ctgacgcatt
     1261 tttccggttt accccgggga gaacatctct ttttgcggtg ttcgcggcag aatcgcgttc
     1321 agcgcgtttt agcggtgcgc gcaacggatg ttatgttgaa ttcctttttt atggagctat
     1381 ggagctagca tgttgggaaa aatatggtgt tcactgatta cagttacttt cacattattg
     1441 attggatgtg ttccacaacc gaaaccggtt gataaatttg atataaacaa acttcttaac
     1501 gtcacagata gtgaaacaac tacagatctt gcgatcccat cacccgctca acaagaccct
     1561 atttggcaga cttccttgtt gacagggcgg caattgaagg aagggattga cgcaggaaaa
     1621 ataaagcgtg gtgatgtgtt tcgggcaaaa atcgacctga agtatacgat agtcaataag
     1681 tctcaactac cacctgcact tgacgttttc cgaagtgtgt taatagggga cccatcagcg
     1741 tggaatgatc tcattgctat tgatatatct gactccaagc ataccaaaac ggggaaatat
     1801 gtagcccaga atgcttttgg cgcaagagtt aaggtagatg aggttaaatc agaacgttac
     1861 ttattggcgc ttgatgcggc gaatacacta tcgactacag cgatcaaaat gggagttgag
     1921 ggatgtgcgg taacagagga ctctcttaat tcctttgtgc tcgagtacgt tgctgaatta
     1981 gatgaaagca cataccagca ggagaaagga attattcctg ctgaatacag tagccctaca
     2041 gatattcgta ttaacaatta ctatttcaaa ggggaagtta gagctgctcg attgattgac
     2101 tcgacaaccg ggaaaccata cccatgtaag ttaagtttta tcataaggta ttaaagatac
     2161 actatgccga gattgatatg ttgactcagt tttataaaag gatcttcttg agatcctttt
     2221 tatctacgcg taatctcttg ctctgtaaac gaaaaaaccg ccctgcaagg cggtttttcg
     2281 aaggttctct gagctaccaa ctctttgaac cgcggtaact ggcttagagg agcgcagtca
     2341 ccaaaacttg tcctttcagt ttagccttaa ctggcgcata acttcaagac tctcctcctc
     2401 taaatcagtt accaatggct accgccaatg gcgatttgtc gtgccttttc gggttggact
     2461 caagacgata gttaccgaaa agagcgtggt agtcggactg aacggggggt tcgtgcatac
     2521 agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagataaa
     2581 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
     2641 agggagccac cagggggaaa cgcctggtat ctttaagtcc tgtcgggttt cgccaccact
     2701 gatttgagcg tcagatttcg tgat
//
