LOCUS       NZ_CP038795             4091 bp    DNA     circular CON 19-JUN-2024
DEFINITION  Escherichia coli strain PF9285 plasmid pDW54_4, complete sequence.
ACCESSION   NZ_CP038795
VERSION     NZ_CP038795.1
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 4091)
  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  JOURNAL   Unpublished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 4091)
  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
            CP038795.1.
            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..4091
                     /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_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /genotype="ST10"
     gene            complement(194..895)
                     /locus_tag="E5M00_RS27420"
                     /old_locus_tag="E5M00_27420"
     CDS             complement(194..895)
                     /locus_tag="E5M00_RS27420"
                     /old_locus_tag="E5M00_27420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /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_011666799.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1428..1718)
                     /locus_tag="E5M00_RS27430"
                     /old_locus_tag="E5M00_27430"
     CDS             complement(1428..1718)
                     /locus_tag="E5M00_RS27430"
                     /old_locus_tag="E5M00_27430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001514113.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     GETQLRAWLLHLLKTEVTRQADVSRIQPLIDELNALPKPVPKEVSENDQQA"
                     /name="hypothetical protein"
     gene            1889..4036
                     /gene="mobQ"
                     /locus_tag="E5M00_RS27435"
                     /old_locus_tag="E5M00_27435"
     CDS             1889..4036
                     /gene="mobQ"
                     /locus_tag="E5M00_RS27435"
                     /old_locus_tag="E5M00_27435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_024236174.1"
                     /translation="MAIYHLSMKILSRSKGYSAVASAAYRAGEKILDERTGVIHDYTRK
                     NGVASAVILTPANAPAWCANRAELWNAVEKAERRKNSQLAREFELAIPRELAQDAARET
                     VLNFVRENFVSRGMIADVAFHNLGGSNPHAHIMLSMRAITPDGFGEKVREWNDWTHAET
                     WRGSWADHANRALANAGYQEEIDHRSYERQGVEKTPGIHLGKSACAMEKWGIETERGEQ
                     NRLINRLNLEIQVSRDELRNSELTEPARRMADLLNIELPDNATSYILHDIIEALPTDSN
                     AAWKLTSKAMSMMADMQATRRRWEDLNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWV
                     APEYGREQEKIQSLSQRMEKLRQHHWKVEKQDIPASQKAFETQWQQWGASGLADLREQL
                     RKREEELRRKEQEETERRRAEQLRRNDNAVMDSGVLKAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRARIFESVDLMRDRSGYICERSEIGQRPPLQHVYSSATFEQ
                     LLTQVCQTWPQHTRDLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSMGGVVRLNGTLYPAFAVPTADNSQLVINALTDKGLRFA
                     GYGEAVNHDADSPARPAPELMQFHLKTWSEPLFAIVNTPEKQPDHLFRSLGFERTWDEW
                     QRDEYARTHATERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(1723..1873)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.81"
                     /coverage="85.0"
                     /evalue="3.53e-55"
     Typing          complement(1890..2244)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(196..895)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.301"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1848..4033
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.726"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gacagggatg aatgcaagaa gcacacacat aacacaaatc aactttatag ttttcccgcc
       61 cccgaaaaat tgggggttct tttttcactg tgccagagcg tttatgacgc aattttttac
      121 ttcaccagta ccttcgcatg ccaaacacaa aaaaaacgcg tcagagagcg ttttagaggc
      181 cttaaaatcg attctagatc gtcatcttga tctgtttgtc ttccttgaag cgaaaatgca
      241 gggctacaac cgtgcgcccc ttcttgatcg tctcaagcgt tacagccaag tcgctttttt
      301 gattcagttc gtcaacgcaa ggtcttaata attgctggtt cagagactta tatgtttgat
      361 atttatgctc tatatcaagc attgagcgaa aatcatcgag ggcgataata cgttcccctg
      421 tgctgcggaa ttgctggaga agttcgtata ttcttatgct gtaacttctt gataaattgg
      481 agatgttctt aattacaact ctagtaaatt gccccttcaa ctgtgtcaga taaggcatga
      541 ccgcatctga aaaagtgatt tgggctttgc cctcaccttt agcgtactgt gcccgatact
      601 ggatccagcg gaactcctcg cgcttctcat cgtccttaag gatgatcgac ctgtcccaca
      661 aacgatcaat tgcttcctgt agctgaacct cggcattttt ccgccccata tcagggaatg
      721 agtcgaaata ctcttcggcg gtaacagtca tggtcttttg caattcagtg gattctgcat
      781 cagaacccga cttcaatcga ccaatgcaaa gtaacaagaa tcgctgttcc tgaagagtca
      841 atttatagct ggcctcaacc agtgcattgg atttgtaggc aatcagatcc gacattgtaa
      901 atccctcaac ctaaggtaat gagtaaaata taaacattcc tttaggtaaa ggcaatgtga
      961 tttaatttta atatcccttt tcctgtgaat attaccttaa atcatattgc ctttacctta
     1021 aatcatattg ccaatccacc ttaaatcata ttgcctttac cttaaattat attacctata
     1081 gtcttctaaa ctcttgaatt tcataagaaa attcgaccct aaaacaagta ttaaaaacaa
     1141 gatcttaaaa acaagatcta aaaacttaac ggcgagcctg tggaaaactt ggggtgttca
     1201 aaacaaaaaa tcatgaaaaa caacaggtta caaaaaagca ggttcgcaag ctttagcaaa
     1261 accccgctca accctgtgga aatccagtat tcatgcgggt tcagcgcata tcacctgtcg
     1321 aaaaaccgtg cgtatgtgct caatctggcg acggattcac ttccgcttcc tcgcccactc
     1381 gctcgctaac gctcggtcgc tggggctgcg gcgagcggac ggtgcattca cgcctgttgg
     1441 tcgttttctg acacttcttt ggggactggt tttggtaacg cgttcagttc gtcaatcaac
     1501 ggctgtatcc tgctcacatc agcctgccgt gttacctctg tcttcaggag atgaagcaac
     1561 caggctcgta gttgtgtttc cccaggcttc ctgacctttg ccagcaatgc cgctcccaca
     1621 atgaccttct gcgctgtgtc caggctcctg ctcttcgcct tcagacgctg caatctggcc
     1681 tcagcatcgg caatcttctg ttcgagtgtt ctactcattc cgtaactccg tgcgcggtga
     1741 aaaatcgcat tttagcgcgt cactggtagt ttaaaaactg aactggcata atgcacagca
     1801 aatcacgaag tgcgcactta tacaaactct ccttcgtcga gtttgtgtgc gccctgcggg
     1861 gctaaaagaa aacggcaaca acgacacgat ggcaatttat catctcagca tgaagattct
     1921 ttccagaagc aagggctaca gcgccgttgc ttctgctgcc tatcgtgccg gagaaaaaat
     1981 actggatgag cgcaccggag tgattcacga ctacacccgc aaaaacggtg tagccagcgc
     2041 agtgattctg acgccagcaa acgccccagc atggtgtgcg aaccgcgccg aactctggaa
     2101 tgctgttgaa aaagccgagc ggcggaaaaa ctcacaactt gcgcgggagt tcgaactcgc
     2161 catcccccgt gaactggcgc aggatgccgc acgggaaaca gttctcaact tcgtaaggga
     2221 aaactttgtc agtcgcggca tgatcgccga cgtggccttt cacaatctgg gcgggtcaaa
     2281 cccacacgcg cacatcatgc tatccatgag ggcaatcacg cctgacggct tcggggagaa
     2341 agtccgtgag tggaatgact ggactcacgc cgaaacatgg cggggatcat gggcagacca
     2401 tgcgaacagg gcgctggcga acgccggtta tcaggaagag atagaccatc gttcatacga
     2461 gcgacagggg gttgagaaaa cgcctggcat tcacctcgga aagtcggcct gtgcgatgga
     2521 aaagtggggc atcgaaacag aacgcggcga acagaatcgc ctgattaaca ggcttaacct
     2581 ggaaatacag gtttcccgcg acgaactcag gaacagtgag ctgacagagc ccgcacgccg
     2641 tatggctgac cttctgaata ttgagcttcc tgacaacgca acttcgtaca tactgcatga
     2701 catcatcgaa gcgttgccga cggacagtaa cgcagcatgg aaactcacca gtaaagccat
     2761 gtcgatgatg gcagatatgc aggcgacgcg cagacgctgg gaagatctga acaccgaacg
     2821 aaaggaagcg atgagccatg ctgccagcct gaaaaaatca tcgccgtttt cgtccggttt
     2881 ttcccgtatt cccctgatgc aatgggttgc accggaatac ggccgcgaac aggaaaaaat
     2941 ccagtcgttg agccagcgca tggaaaaatt gcggcagcat cactggaagg ttgagaaaca
     3001 ggacattccc gcgagtcaaa aagcatttga aacacagtgg cagcagtggg gtgcatctgg
     3061 ccttgcagat ctccgagaac agttgcgtaa acgtgaagag gaattgcgcc ggaaggagca
     3121 ggaggaaaca gaacgtcgtc gggcggagca actcaggaga aatgacaatg ccgttatgga
     3181 ttcaggggta ctgaaagcag tcgttacggg gtatggcgag gcccccatgc caggtaacgg
     3241 ggaaatgacc tgttaccttc tgcttcacaa ccggaacgga gaatatacgc tctgggggaa
     3301 cgaactggag aaataccgcg ccagaatttt tgagagtgtt gatttaatgc gtgacaggag
     3361 tggttatatc tgtgagcgaa gcgaaatcgg tcaacgtcca ccactgcaac atgtttattc
     3421 ctctgcgacc tttgagcaac tgctgacgca ggtttgccag acatggccgc aacatacccg
     3481 cgatctccgc cagccgaaga catggccgga gtctttctgt cttggagaag accgccagcc
     3541 agccatgcca tcactggcgg caaggaaggt ggattttacg cagggacgtc tgccaccgac
     3601 tctgatgccg gtaatgagtt ctgtcgaccg tgaaacccgc cagcttcagc ttttgctggt
     3661 catgggtgtg gatgactcta tgggcggtgt tgtccggctt aatggtacgc tgtatcccgc
     3721 gtttgccgtc cccacagccg acaacagcca gctggtaatc aatgcactga ccgacaaagg
     3781 tttacgcttt gcaggctatg gtgaagcggt aaaccacgat gctgacagtc cggcacgtcc
     3841 tgcgccggaa cttatgcagt ttcatctgaa aacctggagc gaaccgcttt ttgctatcgt
     3901 caacacgcca gaaaaacagc cggatcatct gttccgctcg ctgggctttg agcgcacctg
     3961 ggatgaatgg caacgtgatg aatatgcccg aacacacgcc accgagagga gacatgatcg
     4021 cggttggtca cagtgaatgt gaccaatatt ttgttttgtt taacatcgtg ttatgttcgt
     4081 cgatgttcat c
//
