LOCUS       NZ_CP074039             4066 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI7 plasmid pYLPI7f, complete sequence.
ACCESSION   NZ_CP074039
VERSION     NZ_CP074039.1
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 4066)
  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  JOURNAL   Unpublished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 4066)
  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
            CP074039.1.
            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..4066
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI7"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI7f"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST162"
                     /note="Post-weaning piglet"
     gene            join(3720..4066,1..361)
                     /locus_tag="KFU70_RS25505"
                     /old_locus_tag="KFU70_25290"
     CDS             join(3720..4066,1..361)
                     /locus_tag="KFU70_RS25505"
                     /old_locus_tag="KFU70_25290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(603..2756)
                     /gene="mobQ"
                     /locus_tag="KFU70_RS25510"
                     /old_locus_tag="KFU70_25295"
     CDS             complement(603..2756)
                     /gene="mobQ"
                     /locus_tag="KFU70_RS25510"
                     /old_locus_tag="KFU70_25295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029350.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPEDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            2935..3189
                     /gene="mobC"
                     /locus_tag="KFU70_RS25515"
                     /old_locus_tag="KFU70_25300"
     CDS             2935..3189
                     /gene="mobC"
                     /locus_tag="KFU70_RS25515"
                     /old_locus_tag="KFU70_25300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091749.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2399..2757)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          2758..2928
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="97.0"
                     /evalue="2.6299999999999998e-81"
     Typing          3..360
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.359"
                     /coverage="98.0"
                     /evalue="1.49e-99"
     Typing          3721..4066
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(613..2843)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.46"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttttctgac gcggtaatgc cttatctgac acagttgaag gggcaattca ccagagtcgt
       61 cattaaaaat atttctaatt tatcaagaag ttacagcata agaatatacg aaattctcca
      121 gcaattccgc agtactgggg aacgtattat cgccctcgat gattttaaat catcactgat
      181 gcttgatggt aaatataaag atttcaaaac gttaaacagg gatctaataa aaccctgtgt
      241 tgacgaactg aacaaaaaaa gcgacttggc tgtaacggtt gagacgatca aaaaggggcg
      301 cacggttgta gccctgcatt ttcgcttcaa ggaagacaaa cagatcaaga tgacgatcta
      361 gaatcgattt taaggcacct aaaacgctca ctgtcgcgtt tttcttgtgt caggaatgcg
      421 aaggtactat tgaagtgaaa agttgcgtca aaaacgctct gatgcagcaa aaaaagaacc
      481 cccaattttt gggggcggaa aaacaaaact atgtttgcgc tatgtgagtg tgcttcttgc
      541 attcatccct gtcgatgaac atcgacgaac ataacacgat gttaaacaaa acaaaatatt
      601 gttcacattc cctgtgacca accgcgatca ggtctcctct cggtggcgtg tgttcgtgca
      661 tcttcctcgc gccgccattc gtcccaggta cgattgaaac ccagcgagcg gaacagatga
      721 tccggctgtt tttctggtgt gttgacgaca gcaaaaagcg gtgcctcacg ggttttcaga
      781 tgaaactcca taagttccgg cgcaggtgat atgtggctgt ctgcatcgtg atttacggca
      841 acaccatacc ctgcataccg taacccctta tcggtcagtg cactgatgac cagctggctg
      901 ttatcggctg agggaacggc aaacgcggga tacagcgtac cattaagccg gacaacaccg
      961 cccagagagt catccacgcc catgaccagc aaaagctgaa gctggcgggt ttcccggtcg
     1021 acagaactca tgaccggcat cagcgtcggt ggcagacgtc cctgcgtaaa atccaccttc
     1081 cttgctgcca gtgatggcat ggctggctgg cggtcttctc caagacagaa agactccggc
     1141 catgtcttcg gttggcggag attgcgggta tgttgcggcc atgtctggca aacctgcgtc
     1201 agaagttgct caaaggtcgc agaggaataa acacgttgca gtggtggatg ttgaccgatt
     1261 tcgcttcggt cacagatata accactcctg tcacgcatta aatcaacact ctcaaagatc
     1321 ctggtgcggt atttctccag ctcgttcccc cagagcgtat attctccgtt ccggttgtga
     1381 agcagaaggt aacaggtcat ttccccgtta ccaggcatgg gagcctcgcc ataccccgta
     1441 acgactgctc tcagcacccc tgaatccata acggcattgt cattttttct gagctgctcc
     1501 gcgcgactac gttctgtatc ctccagctcc ttccggcgca attcctcttc acgtttaagc
     1561 aactgggatc tgagagctgc aaggccggat tccccccact gctgccactg tttttcaaat
     1621 gccgtctgac tcgcgggaat gtcctgtttc tccaccttcc ggtaatgctg tcgcaatttt
     1681 tccatttgct ggctcagaga ctggattttt ccctgctcac tacggtattc cggtgcagcc
     1741 cattgcatca ggggaatacg ggaaaaaccg gacgaaaacg gcgatgattt tttcaggctg
     1801 gcagcatggc tcatcgcttc ctttcgttcg gtgttcagct cttcccagcg tctgcgcgtc
     1861 gcctgcatat ctgccatcat cgacatggcg ttactggtga gtttccatgc cgcgttactg
     1921 tcctccggca acgcttcgat gatgtcacgt agtgtgtacg aagttgcgtt gtcaggaagc
     1981 ccgatattca gaaggtcagc cacacggcgg gcaggctctg tcagcccgct gttcctgagt
     2041 tcggtgcggg aaatctgtat ttccaggtta agcctgttaa tcagacgatt ctgttcgccg
     2101 cgttctgttt cgataccgcg tgtttccatc gcacaggcag actttccgag gtgaatacca
     2161 ggcgttttct caagcccctg tcgctcgtat gaacgatggt ctatctcttc ctgataaccg
     2221 gcgttcgcca gtgccctgtt tgcatggtca gcccatgatg cacgccacgt ctcggcatgt
     2281 gtccggtcgt tccagtccct gacctttccg ccgaacccag caggtccgac agccctcgtg
     2341 gtcagcatga tgtgcgcatg gggatttgtt ttatccatgt gatggaacgc cacatcagca
     2401 atcatgccct gactgacaaa gttttctctg acaaaggcga gaacggtttc ccgtgcggca
     2461 tcctgcggca gttcacgggg gatagcgagt tcaatttccc gcgcaagttg tgagttcttc
     2521 cggcgttcgg ccttctcaac ggcattccag agttcggcac ggttcgtaca ccaggcaggg
     2581 gctgtcgcgg gggtcagaat cacagcctca gccacaccgc ttttgcgggt gtagtcgtga
     2641 gtcagtccgg tacgctcatc aagcattagt gaaccagaac gataggcagc agaagcaacg
     2701 gcgctgtagc cgttgcttct ggagatgatt ttcatactga gatgataaat cgccatttct
     2761 gccgtaatgc ctttttgcag ttttctttca gccccgcagg gcgcacacaa tcgaaacgga
     2821 gtggagattg tataagtgcg cacttcgtga tttgccgtgc attatgccag ctcagttttt
     2881 aaactaccag tgacgcgcta aaatgcgatt tttcaccgcg cacggagtca cgaaatgagc
     2941 agaacactcg aacagaagat tgccgaagct gaggccagat tacagcgcct gaaggcgaag
     3001 agccggagcc tggacacagc gcagaaggtc attgtgggtg cagcattgct ggcaaaggtc
     3061 agaaagccgg aggaagtgca gttgcgagct tggttactcc agttcctgaa ggcagaggtg
     3121 acacggcagg ctgatgtgac gcgaatactg ccgctgatta acgagctgga ggcgctgcca
     3181 gagcagtgat tgtatcgtcc gctcgccgca gcccagcgac cgaacgttag cgagcgagtg
     3241 ggcgaggaag cggaagtgaa tcagtcgcca ggttgagcac atacgcacgg tttttcgaca
     3301 ggtgatatgc gctgaacccg catgaatact ggatttccac agggttggag ggggtgtatt
     3361 cggaattttc aatcctgatt ttttgcaata cattgttttt atttgatttt tattttcagc
     3421 accccaagtt atccacaggc tcgccgttaa gtttttagat cttgttttta agatcttgtt
     3481 tttaatactt gttttagggt cgaaattcct gattaaaaac aatgcgttac acgtgcatag
     3541 gtgggggaat ttaaggtaaa ggtgatataa tttaaggtgc ttgggtgagg taatttaagg
     3601 taaaggtgag gagatttaag gtaatattca caggaaaatg gggggtgaaa atataattgc
     3661 tcaccaatgc taaaggtgat aggtttttat ttcacctcat ttttggcctg gtggttaaaa
     3721 tgacatcaaa ccctctgata gcctataagt ccaatgcgct ggttgaggcc agttacaagc
     3781 taactttaca agaacagcgt ttcttattgc tctgcataag ccgacttaac tccggtactg
     3841 acgtagcttc acctgaattg caaaagacaa tgaccattac agctgcggaa tattttgatt
     3901 cattccctga tatggggcgg aaaaatgccg aggttcagct acaggaagcg atcgatcgtt
     3961 tgtgggacag gtcgatcatt ctcaaggacg acgagaagcg cgaggagttc cgctggattc
     4021 agtatcgggc acagtacgcg aggggagagg ggaaagcaca aatcac
//
