LOCUS       NZ_CP074000             4088 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain PM7 plasmid pYLPM7d, complete sequence.
ACCESSION   NZ_CP074000
VERSION     NZ_CP074000.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877301
            Assembly: GCF_024585745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4088)
  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  JOURNAL   Unpublished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 4088)
  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
            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 06:53:12
            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)                     :: 4,738
            CDSs (total)                      :: 4,611
            Genes (coding)                    :: 4,432
            CDSs (with protein)               :: 4,432
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 52 of 179
            Pseudo Genes (incomplete)         :: 120 of 179
            Pseudo Genes (internal stop)      :: 32 of 179
            Pseudo Genes (multiple problems)  :: 25 of 179
            Pseudo Genes (short protein)      :: 2 of 179
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074000.1.
            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..4088
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PM7"
                     /isolation_source="Rectal Swab"
                     /host="Pig"
                     /db_xref="taxon:562"
                     /plasmid="pYLPM7d"
                     /geo_loc_name="Cuba: La Lisa"
                     /collection_date="2018-05"
                     /genotype="ST9362"
                     /note="Fattening pigs"
     gene            complement(join(4016..4088,1..77))
                     /locus_tag="KFU86_RS23575"
                     /old_locus_tag="KFU86_23400"
     CDS             complement(join(4016..4088,1..77))
                     /locus_tag="KFU86_RS23575"
                     /old_locus_tag="KFU86_23400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001442891.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            1197..1646
                     /locus_tag="KFU86_RS23580"
                     /old_locus_tag="KFU86_23405"
     CDS             1197..1646
                     /locus_tag="KFU86_RS23580"
                     /old_locus_tag="KFU86_23405"
                     /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="tRNA modification GTPase"
                     /protein_id="WP_280136091.1"
                     /translation="MIDGLDSASGKMTDTIRKSVATALNQVEQELKQTGLAQQKPAEDA
                     LGNMVFTAQDAVLAMRREMSRYTWKSAIYLVMSIFFVLASCAAALTWFIDDGYERVAEM
                     QRMEAVWQKKAPLADISRCDGKPCVKVDTRQSFGDKKDTWMIIKK"
                     /name="tRNA modification GTPase"
     gene            complement(1687..3219)
                     /locus_tag="KFU86_RS23585"
                     /old_locus_tag="KFU86_23410"
     CDS             complement(1687..3219)
                     /locus_tag="KFU86_RS23585"
                     /old_locus_tag="KFU86_23410"
                     /inference="COORDINATES: protein motif:HMM:NF013080.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phosphoethanolamine transferase"
                     /protein_id="WP_064753817.1"
                     /translation="MHTKLFKSFLFLSFSAVIISLSRFTLRAVGDSNPLFFNVLMVSFF
                     ISLLLGSKRRYYLLMLPISIIVAAYAPIGFTYGFPSYQYVASLFATDIQESVEFLSLIP
                     YKSYIYAISIPFLFAAIYILSLRLNFRPLKNRAYVITGVVFLTISSDAIMFIKKTEDAV
                     TKVRLEMNELSKYAKRNDWQGIHQTEKTKYDYYVLVIGESARRDYFHAYGYPVKNTEFI
                     DSTKGIIVNGLDSAGVYTIGSLRLMLTQGDKLKWQPNYNMNIMGMANKAGFETYWLSNQ
                     GQFGKWDSPISSIAKMADESYFTKSQDYNEKNTPDSLLIKKLKQIIAKNTNKKRFIVLH
                     TMGSHPSACDRVSGMRNQIKVKSDINKYIACYVSSIKQTDEFLKSVYETMSQSENVKKF
                     SIIYFSDHGMVHREMNGRIYLNNNYISKYHHDIPLIKISSDDIDRKEVSSKKSGLMFVN
                     GLANWMGVEGKSINPYNLFDGIPSSQDYGLSKQGYKVDDPAIDITSDLEPSD"
                     /name="phosphoethanolamine transferase"
     Typing          complement(71..286)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.33"
                     /coverage="100.0"
                     /evalue="3.27e-96"
     Typing          498..961
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.832"
                     /coverage="91.0"
                     /evalue="2.2599999999999998e-136"
ORIGIN
        1 attaaatcaa aaaggtcata ttcgccggga agctgcgtat cagtcgaatc cagttgttca
       61 tcatattcag atggcatggg gtgatatcca gtagcggaga ggttgttagc gggtttcggg
      121 gcgcagccct gaaccagtca cgtagcgcta gcagagtgta tactggctaa atatgttacg
      181 gcggagtagt aatttatgaa agtgcttcat gtggcaaggg aaaaatgagg ctaccgggcg
      241 taagtgcatc atgcaggtaa ggatgaagtg acgcctcctc gctcactcgg tcgctacgct
      301 cctgccgtga gactgcggcg ggcgttacct gctcaaagat aaaagcataa gcaagcggcg
      361 cttaaatcag gaagggccag gaaaaggatg cggcgttgcc gttttttcat aggctccgcc
      421 cccctggcgg aattcataaa cagacacttt ttcggtgcat ctgtgggagc ctcagctcaa
      481 ccatgaatcc gacagcggtg acgaaacccg acaggactta aagatcccca ccgtttccga
      541 taggtcgctc cctcgtgcgc tctcctgttc ctgcccttcg gtttaccggt gtcactccgc
      601 tgttatggcc gcggtttctc attccacgcc tgacactcag ttccgggtag gcagttcgct
      661 ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccactgcgcc ttatccggta
      721 actatcgtct tgagtccaac ccggaaagac acgacttatc gccattggca gtagccactg
      781 gtaaacagga tgtgcgagag atgtatcgag agttcttgaa gtggtggcct gactacggct
      841 acactggaag gacggatttg gtgacatgtc tcgcacaaga ctgttaccac ggttagataa
      901 tctgccagga ttaactaacc ttcgaaaaac cacctgccag ggtggttttt tcgttttcag
      961 agactacatc tcgtcacatg taactgtcaa cgcaacgatt tcatctacac ccacacaacc
     1021 aaaccttttg cagggtaaga cacataagaa acgagcttaa cgaaggtcgc tacgctccct
     1081 cttggttttt atatatcggg catcagcagg cgcaggagaa gcgcgtctcc gctctgatag
     1141 acgcattcca gaaagagtcc accctgctca gccagcagac ggcgctgctt gctcaggtga
     1201 ttgacgggct ggacagcgcg tccgggaaaa tgacggatac catcaggaaa agtgttgcca
     1261 ctgcgttaaa tcaggttgag caggaattaa aacagaccgg actggcgcag caaaagcccg
     1321 ccgaggatgc gctgggtaac atggttttta ctgctcagga tgctgtactc gccatgcggc
     1381 gtgagatgtc acggtatacg tggaagtctg cgatttatct cgtgatgtcg atattcttcg
     1441 tcctggcttc ctgcgcggca gccctgacct ggtttatcga cgacggctac gagcgggttg
     1501 cggaaatgca aaggatggag gccgtctggc agaaaaaagc gccgctggct gatatatcgc
     1561 gttgtgacgg taaaccctgc gtgaaagtag ataccagaca gtcatttggc gataaaaaag
     1621 acacctggat gattatcaaa aaataaaaaa acggagcgga atgctccgtt taacgtgtta
     1681 cttaattcag tcggatggtt ctaaatcact ggtgatatca attgcaggat catcgacttt
     1741 atagccctgc ttacttaagc cgtagtcctg tgaactaggt ataccatcaa agaggttata
     1801 tgggttgatt gattttccct ccacccccat ccagttagcc aatccattaa caaacatcaa
     1861 tcctgatttt ttagaactaa cttctttcct gtctatatca tcagatgata tttttattaa
     1921 tgggatgtcg tggtggtatt tactaatata gttattattt agatagattc gaccattcat
     1981 ttcacgatga accatcccat gatctgaaaa ataaataatt gagaatttct ttacattttc
     2041 agactgagac atggtttcat acacagactt caagaattca tcggtctgct taatacttga
     2101 tacataacaa gcgatgtatt tatttatatc acttttgacc ttgatttgat tccgcatacc
     2161 gctaaccctg tcacaggctg atgggtgcga tcccattgta tgcaatacga taaacctttt
     2221 tttatttgta ttttttgcta tgatttgttt taacttttta attaaaagtg aatctggtgt
     2281 gttcttttca ttatagtctt gtgattttgt gaaatatgat tcatcagcca tttttgcaat
     2341 tgatgaaata ggagagtccc atttcccgaa ctgcccttgg tttgacagcc agtacgtttc
     2401 aaatccagcc ttattagcca tgcccataat attcatgttg tagttaggtt gccatttcaa
     2461 cttatcacct tgcgtcaaca tcagtcgtaa tgagcctata gtataaactc cagcagaatc
     2521 caatccgttt acaataatcc cttttgttga gtcaataaat tctgtgtttt taacagggta
     2581 cccgtaagca tgaaaataat ctcttcgtgc gctttcaccg atgactagta cataataatc
     2641 atattttgtt ttttctgttt gatgaatacc ctgccaatca tttctttttg catattttga
     2701 tagttcattc atttccaatc ttaccttggt gacagcatcc tcggtttttt taataaacat
     2761 aatagcatct gatgaaatgg ttagaaatac aaccccagta attacataag ctctattttt
     2821 taatggtctg aaatttaacc tcaaagatag aatgtatatt gctgcaaata aaaaagggat
     2881 ggatatagca tatatataag atttgtatgg aattaaagat aagaactcta ctgattcttg
     2941 aatgtcagtt gcaaataatg atgccacata ttgataagat gggaatccat atgtgaaccc
     3001 tattggtgcg taagcagcta caataattga aatgggcaac atcaataaat agtatcggcg
     3061 cttagaacct aataataaac taatgaaaaa tgaaaccatt aatacattga aaaacaaagg
     3121 gttggaatca cctacagccc ttaatgtaaa tctagataat gatataatca cagccgaaaa
     3181 agacaaaaac aaaaaggatt taaaaagttt tgtatgcatg gaaatagtca ataaaattaa
     3241 attggtaata caatatacta cattaatagg gggcgtaact aggtgatgga tttaccataa
     3301 catctcttgc gtgcaccgcc tgagaggccc tcagggcgtt tctgacggga aaccggtaaa
     3361 acaggcaaca aaccacccga aaacccgcca gaaacgcgca ggctctgttt ttacggcatg
     3421 catgagtatg cgcgcaagtg catagcgcag aatttcacac cattcagcca ggggaagtcc
     3481 tgtttccggc gttcttctta cccgaaaacg gtgaacgggg acgcaattta ttgcgtgacc
     3541 gtgaagcgtt ggcaagagca tcaagcatga agagaagggg gtcggatgta cgaatggttc
     3601 agagaactgt tatgacgtaa ttcagtagta aatcagtagt agataagtag tcatcctcct
     3661 ccgatttgta gtaaatcagt agtaaatcag tagtgacgct gtagtttatt agtagtcagg
     3721 aggaataagc tgttcataca agtatgaacg agctagttat ggacgctttt tttcacagat
     3781 ctcctcagaa taggcaaagc tcagcccggt aaggagatga ttctttatcc cttaaatggc
     3841 catacaccat acgcaaccgc gattttcatc gcaattgcat gaattaaaag gtaaaaactg
     3901 aagttcccgt ttatttatgt aatacgcaac gtattacaac cacctgtaat cacatgaaaa
     3961 taaagaaata agatgtaata ccggcgtatt acacgtacgc gggtaagcga aaaagctata
     4021 acgcttcccg gccgacaggc ggcccaaaat ccaccggggc gtgcaggttc tcttcagtaa
     4081 cctgcgcc
//
