LOCUS       NZ_CP074045             4663 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI6 plasmid pYLPI6c, complete sequence.
ACCESSION   NZ_CP074045
VERSION     NZ_CP074045.1
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 4663)
  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  JOURNAL   Unpublished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 4663)
  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
            CP074045.1.
            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..4663
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI6"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI6c"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST641"
                     /note="Newborn piglet"
     gene            complement(join(3549..4663,1..28))
                     /gene="wzz(fepE)"
                     /locus_tag="KFU63_RS23110"
                     /old_locus_tag="KFU63_22905"
     CDS             complement(join(3549..4663,1..28))
                     /gene="wzz(fepE)"
                     /locus_tag="KFU63_RS23110"
                     /old_locus_tag="KFU63_22905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            223..1204
                     /locus_tag="KFU63_RS23115"
                     /old_locus_tag="KFU63_22910"
     CDS             join(223..1014,1016..1204)
                     /locus_tag="KFU63_RS23115"
                     /old_locus_tag="KFU63_22910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_048909999.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element IS5 family transposase"
                     /protein_id="WP_225899375.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAHQHEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="IS5-like element IS5 family transposase"
     gene            complement(<1353..1484)
                     /locus_tag="KFU63_RS23120"
                     /pseudo=""
     CDS             complement(<1353..1484)
                     /locus_tag="KFU63_RS23120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(1792..1905)
                     /locus_tag="KFU63_RS23125"
                     /old_locus_tag="KFU63_22915"
     CDS             complement(1792..1905)
                     /locus_tag="KFU63_RS23125"
                     /old_locus_tag="KFU63_22915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(3090..>3272)
                     /locus_tag="KFU63_RS23130"
                     /old_locus_tag="KFU63_22920"
                     /pseudo=""
     CDS             complement(3090..>3272)
                     /locus_tag="KFU63_RS23130"
                     /old_locus_tag="KFU63_22920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            <3269..3511
                     /locus_tag="KFU63_RS23135"
                     /old_locus_tag="KFU63_22925"
                     /pseudo=""
     CDS             <3269..3511
                     /locus_tag="KFU63_RS23135"
                     /old_locus_tag="KFU63_22925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     Typing          complement(1789..2174)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 tgtttttctt gaaatccatc gctgacataa ccgttcttct ttttggagcg cagtaaattt
       61 ctgcctgatt ggttgcagtg gtcggatgat acaagaaagt aagaataatc tgaacgccag
      121 attgatctat ctgtagaccg actatcagat ttagggaagg tgcgaacaag tccctgatat
      181 gagatcatgt ttgtcatctg gagccatgga acagggttca tcatgagtca tcaacttacc
      241 ttcgccgaca gtgaattcag cagtaagcgc cgtcagacca gaaaagagat tttcttgtcc
      301 cgcatggagc agattctgcc atggcaaaac atggtggaag tcatcgagcc gttttacccc
      361 aaggctggta atggccggcg accttatccg ctggaaacca tgctacgcat tcactgcatg
      421 cagcattggt acaacctgag cgatggcgcg atcgaagatg ctctgtacga aatcgcctcc
      481 atgcgtctgt ttgcccggtt atccctggat agcgccttgc cggaccgcac caccatcatg
      541 aatttccgcc acctgctgga gcagcatcaa ctggcccgcc aattgttcaa gaccatcaat
      601 cgctggctgg ccgaagcagg cgtcatgatg actcaaggca ccttggtcga tgccaccatc
      661 attgaggcac ccagctcgac caagaacaaa gagcagcaac gcgatccgga gatgcatcag
      721 actaagaaag gcaatcagtg gcactttggc atgaaggccc acattggtgt cgatgccaag
      781 agtggcctga cccacagcct agtcaccacc gcggccaacg agcatgacct caatcagctg
      841 ggtaatctgc tgcatggaga ggagcaattt gtctcagccg atgccggcta ccaaggggcg
      901 ccacagcgcg aggagctggc cgaggtggat gtggactggc tgatcgccga gcgccccggc
      961 aaggtaagaa ccttgaaaca gcatccacgc aagaacaaaa cggcccatca acatcgaata
     1021 catgaaagcc agcatccggg ccaaggtgga gcacccattt cgcatcatca agcgacagtt
     1081 cggcttcgtg aaagccagat acaaggggtt gctgaaaaac gataaccaac tggcgatgtt
     1141 attcacgctg gccaacctgt ttcgggcgga ccaaatgata cgtcagtggg agagatctca
     1201 ctaaaaactg ggaataacgc cttaaatggc gaagaaacgg tctaaatagg ctgattcaag
     1261 gcatttacgg gagaaaaaaa tcggctcaaa catgaagaaa tgaaatgact gagtcaaccg
     1321 agaagaattt ccccgcttat tcgcaccttc cctaatagcg cggctgcgat tctacttttt
     1381 tcacctgaac ctgaagaggc gtttgtggct ccgcagtgtg ggcatgactt tgctgtttcg
     1441 tgtatttcct tgccgcatcc tcggcagtaa accattgaac tcatttttta tcctcgagct
     1501 tatttttagt tgggatgcat aatatccgat gttttataac gatatgcatc ctatatgctc
     1561 gggtgggata gatttccatt atggtgaagg atcttcttga gatcctttct gtagcgtcgt
     1621 aatctcttgc tcagtaaacg aaaaaaccgc ccagcaaggc ggtttttcga aggttctcag
     1681 agctgcaact ctttgaaccg tggtaactgg cttatgagga gcgcagtaac caaatctgtt
     1741 ctttcagttt agccttaaca ggcgcataac ttcaagacta actcctctaa atcagttacc
     1801 agtggctgct gccagtggcg ctttgtcgtg tctttccggc ttggactcaa gtcgatagtt
     1861 accggagaag acgcagcggt cggactgaac ggggggttcg tgcatacagt ccagcttgga
     1921 gcgaactgcc tacccggaac tgagtgtcag gcgtggaatg agataaacgc ggccataaca
     1981 gcggaatgac accggtaaac cgaaaggcag gaacaggaga gcgcacgagg gagccaccag
     2041 ggggaaacgc ctggtatctt taagtcctgt cgggtttcgc caccactgat ttgagcgtca
     2101 gattctgtga tgcttgtcag gggggcggag cctatggaaa accggcaacg ccgcggcctt
     2161 ttcttttgcc tctcgatcct ctctcattgc ctgtgcctta atgtctccgt tccctccgct
     2221 cgccgcagcc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga atatccccgg
     2281 acttatcttc ggcaccgtac gcgccagtgc tgcatttttt aatacgatgc aggatagggc
     2341 taacgccgca aagtgacgtc acctgacgtt cctggattac aaaggttaaa gcagcggaca
     2401 ggaaatgttt tgtgcccaca gctatgctgg cttattcaca aaacagcggg acaagatgtg
     2461 tttttggagt accgccggcc cgctaaagac tcctggttag ctcccgcatg tttgctatct
     2521 ttttgctacc attttgctac ttttttgcta tctccagagt cttctggtct ttcggttgct
     2581 atccttttgc tacttttttg ctatcaaaat gctacctctc ccttcttgca ataaatgacc
     2641 aaggcacgtt agcgatgtat acatcgccgc gccgcaaggg tgccccttcc gaatcccgtt
     2701 catcactgcg tgctgattca tccacgttaa atccgacccc cttagcaata aatccagcca
     2761 tgcctgacgg cctggccaac gcctcacggc cgcacagtaa actgcacacc cgtgaggcgt
     2821 tattcgtgag gttcagtggt gcttttgggc gtccagccgg attttagccg ctaaaatccc
     2881 ggccatgcat gtgtgtgcat agccatgcag acgcgccaga atcatcaggc gcgttttttc
     2941 acgatatagg tacagggaag tgtcggaaac aggcaggaag acccagaaac gccctgagag
     3001 cctctcaggc ggtgcacgca acggatgtta tggtaaatct gcctcacaga ctggtacaaa
     3061 aaaagcccga agggcttttt tgctatgagt tagccatatt ttcttgcgaa tttttcatcg
     3121 gaatcgcata gataaataat aaactcaata aacgcgatga tcgcgggtat gaatgtccag
     3181 caaaaaatta gatacaggaa tccctgtcct attttaccta agtaaaattt atgtacgcca
     3241 aatccaccaa ggaagaatgc taagaaagat gatggcggtg gaggtcaatt ttgagcaggg
     3301 tgcgattggc ccgatgcaca atcacccgca tgaacagctt acctatgtgc tctccgggga
     3361 gttcgagttt acgataggtg aagaaaagca gatcgtgacg gcgggcgata cgctctataa
     3421 agcgccgcac gtgatgcacg gctgcatttg cctgaagccc ggcacccttc tggatacctt
     3481 tacgccggtg cgcgacgatt tcctgaaata aaaaaaggcg ctgaatcagc gcctttttaa
     3541 tatcgtcgtt actctgttgc tggcgttacg gccgttatcg gctctggcaa cggattacgc
     3601 gagagcattg cctcacgcag cagcacgctg ccgcaggcaa acaggccgcc cagaatccct
     3661 gccagcagca caatcagggc tttgcccgga ccgtcttttt tcaccggcag tgacggtgaa
     3721 agctgatacc tgaagggttc aagcttcacg tcttccacgg acagtttttg caactgagtc
     3781 agatagtatt cacggttctg gaaatccgca ttcagctcgg ccacgtcctt cagattcttt
     3841 tcaatctgca gcttttgcgc aataccgtca gcacccagcg ccacggagta gtcaggatcg
     3901 tcttttaccg cctgtccgtt gctgtaaacc ggcttcttaa tgcctgccgc gttcgccact
     3961 tccagcgaat agttgaggcg ctgcaggttg gtgttgtgga tattggtcag acgcacgcga
     4021 tccagctcca gctgctgctg aacgactttc gttttcagcg tgatctggtt acggatattt
     4081 tccatcgtct cctgctcaac aatgcgggag atatagttga tgtaaccttc cagaaccgtc
     4141 tgcgcgtctc ccgccgtcgg ggcggtaaag ctcagcgtcc atgaggtata cggcgctttg
     4201 tctgcgtctt taacctgcgt gttatctgtc gctttcattt tctcagcaat attcaccacc
     4261 gcgcgatgca gctccagcgg gtctacctcg gtgccttcca gctgagacat cacgtacggg
     4321 gaggttttca tgtactcttc gagcagcgac tgcgactgaa actttttgat gaacaggtta
     4381 aacacgtctc cacggctcac cttcgcgtcg acgtccagca cctgcagcgt caccatcatc
     4441 tggcgcagcg tgttccactg cgtctgctcg gccggcgtga tcacggcttt actggtccat
     4501 ttttgcggga ttaaaaacgc aatggccaac cctactacgg cgaacgccag gacgatcgtc
     4561 acaatacgtt ttttggctgc cagaagtacg tctaacaacc ccaggagatc tatctctttg
     4621 gtgcttaccg ccggagtggc ataacgggga aaatcgaggt ccg
//
