LOCUS       NZ_CP038794             4715 bp    DNA     circular CON 19-JUN-2024
DEFINITION  Escherichia coli strain PF9285 plasmid pDW54_3, complete sequence.
ACCESSION   NZ_CP038794
VERSION     NZ_CP038794.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333172
            Assembly: GCF_004771235.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4715)
  AUTHORS   Wuthrich,D., Brilhante,M.Q., Hausherr,A., Becker,J., Meylan,M. and
            Perreten,V.
  TITLE     A novel trimethoprim resistance gene dfrA36 characterized from
            Escherichia coli from calves
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4715)
  AUTHORS   Wuthrich,D., Brilhante,M. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-APR-2019) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern CH-3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-MAR-2019
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; MinION Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004771235.1-RS_2024_06_19
            Annotation Date                   :: 06/19/2024 16:06:03
            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)                     :: 5,402
            CDSs (total)                      :: 5,278
            Genes (coding)                    :: 5,018
            CDSs (with protein)               :: 5,018
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 91 of 260
            Pseudo Genes (incomplete)         :: 189 of 260
            Pseudo Genes (internal stop)      :: 42 of 260
            Pseudo Genes (multiple problems)  :: 55 of 260
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP038794.1.
            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..4715
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PF9285"
                     /isolation_source="Rectal swab from healthy swiss fattening
                     veal calves"
                     /host="bovine"
                     /db_xref="taxon:562"
                     /plasmid="pDW54_3"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /genotype="ST10"
     gene            complement(271..465)
                     /locus_tag="E5M00_RS27390"
                     /old_locus_tag="E5M00_27390"
     CDS             complement(271..465)
                     /locus_tag="E5M00_RS27390"
                     /old_locus_tag="E5M00_27390"
                     /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_135798832.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSILVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1541..2497
                     /locus_tag="E5M00_RS27400"
                     /old_locus_tag="E5M00_27400"
     CDS             1541..2497
                     /locus_tag="E5M00_RS27400"
                     /old_locus_tag="E5M00_27400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000280763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000280763.1"
                     /translation="MYLIEEALTSWLLNEYKKPVITKEEISLQIYLFYLKKEYNGERIY
                     QIRKNKAGPNEFEKNILKLLKSGVLSRVESNDKHHAYPHLIGGFYEVFFVKGNDGSPEN
                     DIVCSTYPYGYLSYLSAMDWHNITDKIPKIIHFTTCRSEQWKNKFYHDFQKDNPDIDEA
                     KQFMPRFPRNSEVNGIKIIVTQETNYVEPMKARNSPVRVSSIGKTFMDMTRRPDYCGGE
                     EHVLESFIEHGKKYAPLIIKEVDKLGRHIDKVRVGFILDRIIGVNNKKISEWKQEAGKY
                     RGSSKVLSPKSPFSPYFDEEWFISINVDMVKSYGKRN"
                     /name="hypothetical protein"
     gene            2481..3347
                     /locus_tag="E5M00_RS27405"
                     /old_locus_tag="E5M00_27405"
     CDS             2481..3347
                     /locus_tag="E5M00_RS27405"
                     /old_locus_tag="E5M00_27405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000409995.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="WP_000409995.1"
                     /translation="MEKEINNWIEESGGKYRLMRQAVHIILKSISIEESLNEMMVMKGG
                     TLLGVKHGSDRYTKDIDFSTEKKLSEIDLGDFFNRFNDSMDVAEAELGYGIKCKVQSHK
                     IQPNAQGTFPTVQINIAFCDRSNASAMKRLESNQSPSVINIDFSFNEKTYDFDFLSLDG
                     DDDNDSVKTYSLTDLMAEKYRSVLQQKVRERNREQDIYDINYLLGKYEFSRQDKYKILE
                     SLLKKSEGKQLDNLLNVKGIRDVEIIERSSQRYQDLSSTVKSLPLFEDAYEKVACFYES
                     LPWDIFK"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            3344..3997
                     /locus_tag="E5M00_RS27410"
                     /old_locus_tag="E5M00_27410"
     CDS             3344..3997
                     /locus_tag="E5M00_RS27410"
                     /old_locus_tag="E5M00_27410"
                     /EC_number="3.1.3.16"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016249761.1"
                     /GO_function="GO:0004722 - protein serine/threonine
                     phosphatase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PP2C family serine/threonine-protein phosphatase"
                     /protein_id="WP_000560060.1"
                     /translation="MIAFSFSDIGNRCENLDLLSTINCQNDVFGMVIMDGYSCSEWNMK
                     ILSGRLDKCVFSGDLNKDIIEPCKSVPVKAAVCFLFKNNTHLHIYNAGDCRVYNKSGVL
                     LTEDNSVAWKRLKENGIDNKKIPHLVCYCPDRNYLTSFVDFCSDEIIFNHSVFDLNDEN
                     KEVILCTDGFWEHFNDGTVIDLMKDNPESNLAKFTKNIPGNAENHTVCYVRFPS"
                     /name="PP2C family serine/threonine-protein phosphatase"
     gene            complement(4219..4332)
                     /locus_tag="E5M00_RS28450"
     CDS             complement(4219..4332)
                     /locus_tag="E5M00_RS28450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427893.1"
                     /translation="MHEPPVQPDCCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="hypothetical protein"
     Typing          116..198
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          502..600
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          725..980
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.124"
                     /coverage="89.0"
                     /evalue="5.65e-115"
     Typing          complement(4261..4715)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.53"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgaccgagcg tagcgagtca gtgagcgagg aagcggaaaa gcgcctggac gcgcattttc
       61 tccttacgca tctgtgcgga atttcacacc cggcatgggg cacttttcat acaatctgca
      121 ctgatgccgc atagttaagc cagtatacac tccgctatcg ctacgtgact gggtcagggc
      181 ttcgccccga cacccgctga cgcgccttgg cgggcttgtc tgctgccgaa aacgctcgcg
      241 gacaagccgt gagcgcctcc gtcagcttcg ttatgttcct gtttcacttt cggtctcaaa
      301 gcgaaccagg atgctgttct ggagttcttc cgcgagttcg tgcagtcgtt cgcacatggc
      361 cgcctgttcg tcggcatcca gagcatccag tttttcaagc agtgtcaggc tctggctttt
      421 gataaatcgc gccatattca gcgcagtttg ttgctgtttg ttcaccttcc gttgttctcc
      481 gtcagtaccg ggtgtcgggt ggaccctgac caggtggtaa ttgtaagacg ttgcgggcga
      541 cggtattaca attgcacatc ctgtcctgtt tttttaggac gtatcatggc acagcatatc
      601 aactgataaa taatccctgt gcagtgcagc cgctgttgca taaaatttcg ctctgcgtcg
      661 agtgtttctt aatcaataat tccgctgata ctccggaaaa acgcgagtct gttctcatgc
      721 ctgaaatgcc cacaccccac gcaaaaacaa ttttttgctg atttttcttt ataaatagag
      781 agttatgaca aattagttct tcttgctctc tttgtgatat ttaaaaaagc ggtgtcggcg
      841 cggtgttgta gctgcgccaa caccgctttt taggggtggt actgactatt ttcataaaaa
      901 acatcacttt atattagggg tgctgctagc ggcgcggtgt gtttttttac aggacgcccc
      961 tgggggcgct gctaggggtg tctgttcaga tatgtagcaa tgagtcaggg attcacgaac
     1021 tgaaaatgtc cgaaaatgtg tctcatgggc accgtatgcg cccaaaccga tcgccattca
     1081 ctttcatgca tagctatgca gtgagctgaa agcgatcctg ccgcattttt ccggtttacc
     1141 ccggggaaaa catctctttt tgcggtgttt gcggcagaat cgcgttcagc gcgttttagc
     1201 ggtgcgcgta atgcgacgtt atggtaaatg acgctgaaaa atgatctttt acgctcatcg
     1261 tttatgagca acagatgtcc taatcatgga tttgaactat aaccgccgct gaattgatcg
     1321 catgaggtgt tatgaaaacg gtgatataag taaacttttt cttgacttcc tacttattat
     1381 cctataaaat aaatccttag gatttatttt ataggatatc aaaaatataa aaatggcaaa
     1441 tgcttgtttg ttattatttt tttcttgaca atcaatctct aatagaatat acgtccttag
     1501 gacgtatatt ctattagaga ctaaaccgaa aaggttgaat atgtatctta tcgaagaagc
     1561 gctaacgtct tggttgttga atgaatataa aaaaccagtc ataaccaaag aagaaatctc
     1621 tttgcagatt tacctttttt atttaaaaaa agaatataat ggtgagagga tatatcaaat
     1681 tagaaagaac aaagcaggac ctaatgaatt tgaaaaaaat atattaaaat tattaaagtc
     1741 aggggtttta tcaagagttg aaagtaacga taagcatcat gcttaccccc atttaattgg
     1801 cggtttctat gaggtctttt ttgttaaagg taacgatggt tctccggaaa atgatatagt
     1861 gtgctctacg tatccatatg gatacttatc ctatttatcc gctatggatt ggcataacat
     1921 cacagataaa atacccaaga taatccactt tacgacatgt cgttccgaac agtggaagaa
     1981 taagttctat catgattttc aaaaggataa tcctgatata gacgaagcca aacaattcat
     2041 gcctagattt ccaagaaatt ctgaggtcaa tggaataaaa attatcgtta cacaagaaac
     2101 aaattatgtt gagccaatga aggctcgtaa ttcccctgtc agggtatcat ctatcggtaa
     2161 gacctttatg gatatgacca ggcggcctga ttactgtggt ggtgaggagc atgtattgga
     2221 atcatttatt gagcacggta aaaaatatgc acctctgatt ataaaggaag tcgataagct
     2281 tggccgtcat attgacaagg taagggttgg attcattttg gatagaatta ttggggttaa
     2341 taataaaaaa ataagcgaat ggaaacaaga ggcgggtaaa tacagaggta gttcgaaagt
     2401 gctatctcca aagagtccat tctcacctta ctttgatgaa gaatggttta tttctattaa
     2461 tgttgatatg gttaagtctt atggaaaaag aaattaataa ttggatcgaa gagtctggtg
     2521 ggaagtacag gttgatgcgg caggctgtac atataatact taaatctatt tctatagagg
     2581 agagtttgaa tgaaatgatg gttatgaagg gagggactct tcttggtgtt aagcatggta
     2641 gtgatagata cacaaaggat attgattttt ctaccgaaaa aaaactttct gaaattgact
     2701 tgggggattt tttcaatagg tttaatgact caatggatgt tgctgaggct gaattgggat
     2761 atggtattaa atgtaaagtt caatctcata aaattcaacc taatgcacaa ggaacatttc
     2821 caactgtaca gataaatata gccttttgcg atcgttctaa tgcgtctgca atgaaaaggc
     2881 ttgaatctaa tcaatcacct tcagtgataa atatcgattt tagctttaac gaaaaaacgt
     2941 atgattttga ctttttatca ttagatggtg atgatgacaa tgatagcgta aagacctaca
     3001 gcttaactga tttgatggct gaaaaatatc gatccgtttt gcaacaaaaa gttagagaga
     3061 gaaatcgaga gcaagatata tatgatatca attatctttt aggtaaatat gagttttctc
     3121 ggcaagataa gtataaaata ctggagtctc ttttaaaaaa gagtgaaggt aaacaattgg
     3181 ataatctctt aaacgttaaa ggtataaggg atgtagaaat tatcgagcgt tccagtcagc
     3241 gatatcagga tttatcatcc accgttaaat cattacctct ttttgaagat gcttatgaaa
     3301 aagttgcctg tttctatgaa agtcttccgt gggatatatt caaatgatag cgttcagttt
     3361 tagtgatatt ggtaacagat gtgaaaactt agacttatta tctacgataa attgtcaaaa
     3421 tgatgtgttt ggaatggtta ttatggatgg gtattcctgc tctgagtgga atatgaaaat
     3481 tctctctggt aggttagata agtgcgtgtt ttctggtgat ctgaataaag atattattga
     3541 accatgcaag tcagttcctg ttaaggctgc agtatgtttc ctttttaaaa ataatacgca
     3601 cctccatata tataacgcag gagattgccg tgtatataac aaaagtggag tccttctaac
     3661 agaggataac tcggttgcct ggaaaagatt aaaggaaaat ggaatcgata ataaaaaaat
     3721 acctcacctc gtttgttatt gcccagacag aaattatcta acatcatttg ttgatttctg
     3781 ctctgatgag ataattttca atcattcagt ttttgattta aatgatgaaa acaaagaggt
     3841 tattttatgt actgatgggt tttgggagca ttttaatgat ggtactgtta ttgacctcat
     3901 gaaagataac ccagaatcta acttggctaa atttactaaa aatatcccgg gtaacgcaga
     3961 gaatcatacg gtttgctacg ttagattccc ttcttgattt cgtgtttttt gaagaagcta
     4021 ttgagatctt cgtgtcatat agataatctc ttttctgtaa aagaaaaaaa ccgcctttgc
     4081 ggggcggttt tctcttaggt tcaaagagtt tgcggctcga agaaccaagg taactggctt
     4141 ggaggagcgc agtcaccaaa acctgttctt tcagtttagc cttaactggc gcatgacttc
     4201 aagactaact cctctaaatc agttaccagt ggctgctgcc agtggcgtta aggcgtgtct
     4261 taccgggttg gactcaagac gatagttacc ggataaggcg cagcagtcgg gctgaacggg
     4321 gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga gataccaaca
     4381 gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt
     4441 aagcggcagg gtcggaacag gagagcgcac gagggagcca ccagggggaa acgtctggta
     4501 tctttaagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgatttct gtgatgctcg
     4561 tcaggggggc ggagcctatg gaaaaacgcc tgcggcgcgg ccttcttcct gttcttggtc
     4621 ttttgctcac atgttctttc cggccttatc ccctgattct gtggataacc gtgctgccgt
     4681 ttttgtgtaa gtcagtaccg ctcgccgcag ccgaa
//
