LOCUS       NZ_CP074016             3145 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PI24 plasmid pYLPI24d, complete sequence.
ACCESSION   NZ_CP074016
VERSION     NZ_CP074016.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877297
            Assembly: GCF_024585825.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3145)
  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  JOURNAL   Unpublished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 3145)
  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 06:36:49
            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)                     :: 4,780
            CDSs (total)                      :: 4,663
            Genes (coding)                    :: 4,389
            CDSs (with protein)               :: 4,389
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 274
            CDSs (without protein)            :: 274
            Pseudo Genes (ambiguous residues) :: 0 of 274
            Pseudo Genes (frameshifted)       :: 73 of 274
            Pseudo Genes (incomplete)         :: 195 of 274
            Pseudo Genes (internal stop)      :: 43 of 274
            Pseudo Genes (multiple problems)  :: 36 of 274
            Pseudo Genes (short protein)      :: 3 of 274
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074016.1.
            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..3145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PI24"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPI24d"
                     /geo_loc_name="Cuba: San Jose de Las Lajas"
                     /collection_date="2018-05"
                     /genotype="ST710"
                     /note="Post-weaning piglet"
     gene            complement(join(2962..3145,1..740))
                     /locus_tag="KFU81_RS23710"
                     /old_locus_tag="KFU81_23565"
     CDS             complement(join(2962..3145,1..740))
                     /locus_tag="KFU81_RS23710"
                     /old_locus_tag="KFU81_23565"
                     /EC_number="2.3.-.-"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0016747 - acyltransferase activity,
                     transferring groups other than amino-acyl groups [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="acyltransferase"
                     /protein_id="WP_257171037.1"
                     /translation="MVVILHITLKSHINNGSSYIHFGHAGVDIFFAISGFIMCYISEKK
                     DTDTILFLKNRVIRIYPIYIITLIPFIIIFLLMPQIVNTHGQPPSILKSITLIPFFNGG
                     YLNLVAWTLSYEIYFYLIFSISLLLRKNAIFASITTILTLILIGKSFNIEFISSLISVE
                     FIFGMMIYKLIFKKTELNKYTSLVIILIGAGVIYTTPSDIALKNDLYRVLYYGIPSAMI
                     LTGVLSPSISKFNSKTLTVLGDSSYSIYLTHILTINIVYVAFSYFGMQQKMYFIMVATA
                     VLMSTIIGVTVHLKIEKPVIKKIRSI"
                     /name="acyltransferase"
     gene            complement(1077..1235)
                     /locus_tag="KFU81_RS23715"
     CDS             complement(1077..1235)
                     /locus_tag="KFU81_RS23715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_244471812.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWDSRAMIM
                     RLILQNP"
                     /name="replication initiation protein"
     gene            complement(1722..1916)
                     /locus_tag="KFU81_RS23720"
                     /old_locus_tag="KFU81_23570"
     CDS             complement(1722..1916)
                     /locus_tag="KFU81_RS23720"
                     /old_locus_tag="KFU81_23570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2201..2524
                     /gene="mobA"
                     /locus_tag="KFU81_RS23725"
                     /old_locus_tag="KFU81_23575"
     CDS             2201..2524
                     /gene="mobA"
                     /locus_tag="KFU81_RS23725"
                     /old_locus_tag="KFU81_23575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_024222953.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKKAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYVEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          1952..2192
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.521"
                     /coverage="100.0"
                     /evalue="7.71e-113"
     Typing          complement(1164..1693)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.843"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2202..2521
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="1.5699999999999998e-61"
ORIGIN
        1 taagaagagt caccaagtac tgttagtgtt tttgagttaa attttgaaat ggaaggtgac
       61 aaaacaccag tgagaatcat tgcggaaggt attccgtaat acagaacgcg atataggtcg
      121 ttcttaaggg ctatatctga tggggtcgtg tatatgacac ctgcgccaat tagtattata
      181 acaagagatg tatatttgtt tagttctgtc tttttaaata ttagcttgta tatcatcatt
      241 ccgaagataa actcaactga aattagggat gaaatgaatt cgatattaaa tgatttccct
      301 attagtataa gggttaatat ggttgtaatg gatgcaaaga tagcgttttt gcgtaaaagc
      361 agagatattg aaaatattaa gtaaaagtat atttcgtaac taagtgtcca agctactaag
      421 tttaagtagc caccgttgaa aaatggtatc aatgtaattg attttaatat tgatgggggt
      481 tgtccatgtg tgtttacaat ttgaggcatc aataaaaaga taattataaa tgggataagc
      541 gtgatgatgt atattgggta tattcttata accctgtttt ttaaaaacaa aatggtgtct
      601 gtgtcttttt tttctgatat gtaacacatg ataaagcctg aaatggcaaa aaagatatcc
      661 acacctgcgt ggccaaaatg tatatacgag ctgccattat ttatatgtga ttttagtgtt
      721 atgtgaagaa tcacaaccat taggcaagca aagaaacgga gatattgaat tgacaggatc
      781 attgggggcc tttagttttt ttttgcgata tactacgttt tgggttaaaa aatgctctca
      841 aggttgttgg ttgagagtgt ggtgtgatgg ggggcagagt gtgatttttc ttaacaagat
      901 cttgagattc tccctgtctc gtcgtagtct tcttgcgaat aaaacgaaaa accgcccaaa
      961 gggcggtttt cgaaggttct tggagctacc aactccttga accgaggtaa ctggcttcag
     1021 cagagcacag ctaccaaata ctgttctttt agtgtagccg tagttgggtg gtcacttcaa
     1081 gggttctgta atataagcct cattatcatt gctctgctat cccagttacc aatggctgct
     1141 gccagtggcg ttaagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag
     1201 gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc
     1261 tacaccgggc cgagatacca acagcgtgag ctatgagaaa gcgccatgct tcccgaaggg
     1321 agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag
     1381 cttccggggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctggctt
     1441 gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgcctgcggc
     1501 gctggcttct tccggtgctt tgctttttgc tcacatgttc tttccggctt tatcccctga
     1561 ttctgtggat aaccgtatta ccgcctttga gtgagctgac accgctcgcc gcagtcgaac
     1621 gaccgagcgt agcgagtcag tgagcgagga agcggaaaag cgccttatgt gacattttct
     1681 ccttacgctc tgttgtgccg ttcggcatcc tgtcctgagc gttatctctc tgtgctattt
     1741 tctacttcaa agcgtgtctg tatgctgttc tggagttctt ctgcgagttc gtgcagcttc
     1801 tcacacatgg tggcctgctc gtcagcatcg agtgcgtcca gtttttcgag cagcgtcagg
     1861 ctctggcttt ttatgaatcc cgccatgttg agtacggctt gctgctgctt gttcatcttt
     1921 tcgttttctc cgttctgtct gtcatctgcg ttgtgtgatt atatcgcgta ccacttttcg
     1981 actgttttgc tgccgctatt ctgccgcctg gctttttgac gggcatttct gtcagacaac
     2041 actggcactg ccaaaaaact gccgtgcctt tgtcggtaat tcgagcctgc tgacaggaca
     2101 ggatgtgcaa ttgttatacc gcgcatgcat gcacgctatt acaattaccc tggtcagggc
     2161 tttgccccga caccccatat cagatacgga gccatgtttt atgacaaaac gtagtggaag
     2221 taatacgcgc aggcgggcta tcagtcgccc tgttcgtctg acggcagaag aagaccagga
     2281 aatcagaaaa aaggctgctg aatgcggcaa gaccgtttcc ggttttttac gggcggcagc
     2341 tctcggtaag aaagttaact cactgactga tgaccgggtg ctgaaagaag ttatgcgact
     2401 gggtgcgttg cagaaaaaac tctttatcga cggcaagcgt gtcggggaca gggagtatgt
     2461 ggaggtgctg atagctatta cggagtatca ccgggccctg ttatccaggc ttatggctga
     2521 ttagcttccc ggagagaaaa ctgtcgaaaa cagacggtat gaacaccgta agctcccaaa
     2581 gtgatcacca ttcgctttca tgcataacta tgcagcgagc tgaaaacgat cctgacgcat
     2641 ccttcctgtt tttccggggt aaaacatctc tttttgcggt gtctgcgtca gaatcgcgtt
     2701 cagcgcgttt cagtggtgcg tacaattcga cgttatgtta aattttgttt attgcctatc
     2761 ttgctgatag gagctttatt atataagtat gtttattaat gcattaataa tgttgatatt
     2821 aaatttttct ggtgatacga gagctggctc cctgatgttg taatctttat ggttaattct
     2881 ctatttggaa ggggaggggg agtttcagac gatagggtaa atgagccatt agtgttttta
     2941 atggctcggt gcttttattg tttaaatgga tcttattttt tttattactg gcttctctat
     3001 ttttaaatgc accgttacgc caataattgt tgacattaga acggcggtag caaccattat
     3061 aaaatacatc ttttgttgca ttccaaaata cgaaaatgca acataaacga tgtttatagt
     3121 aagtatgtgt gtaagataaa ttgaa
//
