LOCUS       NZ_CP059951             5631 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 268.2 plasmid p4, complete sequence.
ACCESSION   NZ_CP059951
VERSION     NZ_CP059951.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13613889
            Assembly: GCF_014170975.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Moffat,J., Chalmers,G., Reid-Smith,R., Mulvey,M., Aguno,A.,
            Calvert,J., Cormier,A., Ricker,N. and Boerlin,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-DEC-2019) Pathobiology, University of Guelph, 50 Stone
            Road E, Guelph, Ontario N1G 2W1, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 22.7x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:25:31
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,957
            CDSs (total)                      :: 4,841
            Genes (coding)                    :: 4,618
            CDSs (with protein)               :: 4,618
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 223
            CDSs (without protein)            :: 223
            Pseudo Genes (ambiguous residues) :: 0 of 223
            Pseudo Genes (frameshifted)       :: 82 of 223
            Pseudo Genes (incomplete)         :: 139 of 223
            Pseudo Genes (internal stop)      :: 54 of 223
            Pseudo Genes (multiple problems)  :: 49 of 223
            Pseudo Genes (short protein)      :: 2 of 223
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059951.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="268.2"
                     /host="Turkey"
                     /db_xref="taxon:562"
                     /plasmid="p4"
                     /geo_loc_name="Canada"
                     /collection_date="2016/2017"
     gene            join(5387..5631,1..79)
                     /locus_tag="H5C70_RS24455"
                     /old_locus_tag="H5C70_24455"
     CDS             join(5387..5631,1..79)
                     /locus_tag="H5C70_RS24455"
                     /old_locus_tag="H5C70_24455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            288..>719
                     /locus_tag="H5C70_RS24960"
                     /pseudo=""
     CDS             288..>719
                     /locus_tag="H5C70_RS24960"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            757..1287
                     /locus_tag="H5C70_RS24465"
                     /old_locus_tag="H5C70_24465"
     CDS             757..1287
                     /locus_tag="H5C70_RS24465"
                     /old_locus_tag="H5C70_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1294..1527
                     /locus_tag="H5C70_RS24470"
                     /old_locus_tag="H5C70_24470"
     CDS             1294..1527
                     /locus_tag="H5C70_RS24470"
                     /old_locus_tag="H5C70_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2008..3060
                     /locus_tag="H5C70_RS24475"
                     /old_locus_tag="H5C70_24475"
     CDS             2008..3060
                     /locus_tag="H5C70_RS24475"
                     /old_locus_tag="H5C70_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            3062..3928
                     /locus_tag="H5C70_RS24480"
                     /old_locus_tag="H5C70_24480"
     CDS             3062..3928
                     /locus_tag="H5C70_RS24480"
                     /old_locus_tag="H5C70_24480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(5131..5322)
                     /locus_tag="H5C70_RS24485"
                     /old_locus_tag="H5C70_24485"
     CDS             complement(5131..5322)
                     /locus_tag="H5C70_RS24485"
                     /old_locus_tag="H5C70_24485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4956..5037
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          4312..4499
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          70..1631
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcactgatg gccatcgggg atgagctgcg ccggctgcgt ctggcggtca gggaacaggg
       61 ggcgcgggat gatagttaag tttcatgcca ggggaaaagg tggtggcagt ggtccggttg
      121 attacctgct gggaagggag cgtaaccggg aaggggcaac ggtgcttcag gggaatccgg
      181 aagaggtccg ggaactcatc gatgccacgc catttgcgaa gaaatacacg tcaggtgttc
      241 tgtcgttcgc ggagaaggag ctgccgcctg gagggcgtga aaaagtgatg gcgagctttg
      301 agcgtgtact gatgcccggt ctcgagaaaa atcagtacag catcctgtgg gtggagcacc
      361 aggacaaggg acggcttgag ctgaattttg tcattccgaa catggagcta cagaccggaa
      421 aacgcctcca gccgtactac gaccgggcag acaggccgag aattgatgcc tggcagacgc
      481 tggtgaatca ccattacggt ctgcatgacc ccaacgcccc ggagaaccgc cggacgctga
      541 cccttcctga taacctgccg gaaacgaaac aggcgcttgc tgagggcgtc acacgcggga
      601 tagacgcgct ttaccatgcc ggagagataa aaggccgtca ggatgtgatt caggcgctca
      661 cagaggcggg gcttgaagtg gtcagggtga cgcgaagcag tatcagcatt gcagacccga
      721 acggcgggag gaatatcaga ctgaaaggag cgttttatga gcaatctttt acagacgggc
      781 gcggagttcg agaaaaagct gaaagagaga gccgaatcta cagagaaaat gctgaacgac
      841 gagttcagga agctcgaaga atctgtaaac agggaactga cctcaaacga atctttaatc
      901 aggaacgcta tcaacgacca tacaacagcc ctgaaagaac tgctggagag gtatcagaaa
      961 acgaccgtcg atacgatgga cgcgcactgg aaaaccgtac tgaaaatgag cgtgaaacgc
     1021 tggctgtggc tgattatcgt ctcagtactg atgtttgcca cgaccgggag tctgctgtgg
     1081 taccagggca tgaagataaa cgcgaatatg aatattctcc gcgagcagaa agagagtctg
     1141 gagaagctga acgcgaagac atggggcgtg cgttatcacg aggacagcaa cggacgtttt
     1201 ctggtgttgc cgaaggggat gaaagccgaa acgaactgga cgaaggacaa cggcaaactg
     1261 aacgcagtga gactggtgca ggagtgacag agcatgacgg agctggaaag acatttgctg
     1321 aacgcattag agcaactgca acaggactat atgcagcggc tgaacgaatg ggagaacgcc
     1381 ttcgtggaat tgcagaaaat gttttcgctt acgcaacggg acaacgcgat gctgaacggg
     1441 cgagtcatgc agttgagtca gcaggtgcag cacttgagcg agcggacaga acgcttgagc
     1501 cagttataca gcgagaacag gagataaggg atgaacggct gatgcaggaa cgcgaacatg
     1561 agttatctct ggagcgggag cgtcagccgg aaatccagga gcggacactg gatggccctt
     1621 cgctgggatg gtgaaaccat gaaaaatgac gtgttcagtg gattaaggcg ggctaatgtg
     1681 gcctgtagca tctggttgca taggtattca tgcggttaaa atttatcagg tgcgatcgcg
     1741 gcagtttttc gggtggtttg ttgccatttt tacctgtctg ctgccgtgat cgcaccgaac
     1801 gcgttttggc ggtgcgtaca atgcgacgtt atggtaaatg gagcggattt tcaggaagga
     1861 gtgatactaa caactcgaac actgtgcaaa taatgatttt tttaaaatat cggtaacgat
     1921 aataaattat ttcgttttac gccggtaata aatataatgt agtttcagta tataaaaaaa
     1981 tatatgaggt gtcttgtggg agctttcatg aatcttcaac aacgtataaa taaactacca
     2041 caattatcat ccagtttttc atttggaaaa gatattgata atattcattc atttatcttt
     2101 aacgaaactt ctaaagataa aattgaagat ttactaagaa aatgggtgtc aggcaatcag
     2161 ccctgtgtat ttggtaaatt ggcaagcaag aaaattaaag ggcttgattt ccatttatct
     2221 attgtaaata gcccccaact atataatgat gatggtcatt tgtttgattt tttgcgtaat
     2281 gaaagagttc gttttaaaga acgcgcaaga agaggagagg tcagtgcgca tctcatttat
     2341 tttattcatc cacaacttgc ctttgctcgt ccatcagaag agttagtgga catacaaaaa
     2401 tatatttgtt cgctgcatat gccagagtgc tatccaataa aagaggatgt tatttatact
     2461 gaaagcgtac catttcagga taaagatggg ctaaaaatat ataaggctgg tgttaatgtt
     2521 ttttactctt ctgctcatag aacaagaaat catgatagaa gaataccagg gggaatactt
     2581 atttctgtaa atgccccggg gcattttatg aggctggcga tagaaaaagg tttctataaa
     2641 gatcaagaac aagcgttagc ggatattcgt aacatgacta ttcagtctgt tggtaagggt
     2701 gggtattcac atccggaagg gatttctaca acatggcatt cagaatctaa tttggatcgt
     2761 tttggatgcc cagtgcacac cggtaatagt tcttattaca gcggttttta tcatactgat
     2821 gtattaattc caggagaatt aactaaggat gaaagattgc tccatgaaat agaaaatagt
     2881 gatccaatga tcttcaactg gaatgtattg ttttatgttt cattagaaga gtttcctata
     2941 gatgatcctt attatggaga gtttattggt attcctgtag atgatgcatc tatgtttttt
     3001 aactcctttc aaccaaggaa atttgaaaac aaaccccttt atgagaaaga ggatgattaa
     3061 tatgattaaa ggaatgcttt ttgctttttt agcagcgttc tcatgggggg cagctatcgt
     3121 aatgagcaaa aaaggagttg aagaactaga tgccggaggg gtgtttttct ggcagatttg
     3181 tagtgcagta atactatctt ggatagttct ttttataaaa agaaaaaaac tcccattaaa
     3241 ctcaaaagcg atacttgctt atgcgacagg cgtttttgaa ccattcttag cgtatacttt
     3301 tacactctac ggactttatt ttatttcagc aggaagcgca tcaattattt tttcacttga
     3361 atcagtgttt atattggtgt tgtctgttct tatttgctca gttaaaatta attccccgca
     3421 atattttata ttgttcctta taggtgcaat tgttggcagt attttggtag ccttgccaga
     3481 catcagtaat ggatcgaata atattgttgg atattgtctt gttgttgccg gtgtgttatc
     3541 ggcagcattt tatgttgtta tatcgtctcg ccttattaaa tcgtttgagc ctatcacatt
     3601 attgagcgga cagttgacat tctcccttat actgtcatcg ctctttattt ttatatctaa
     3661 atcatcaatt tatcttccgt tggaatccgt gattattgtt ttttcatctg gaatattaca
     3721 atatttttta gctttttgtt tttacttgaa ctccttgcgt tggctcccag ttcatttggc
     3781 agggataatg ttgtacttta ttccgctagt tgcattattt ttgtcatggt tgtttttgga
     3841 tgaacaattc acattcttac agggggtagg atttattgta actgtgctaa gtgtatattt
     3901 tcttaacaga aaatactcag aggagtaaca ttctgttcag gattgccccc cggcctccat
     3961 cgataccgtg ccaaatgcac gtaaaaaacg ggagcgtttc tggtgtcgga atgtaaccaa
     4021 gggggtcaga ggcgcgctaa aacgctctca ggggagtcaa atagagacgt ttgtaacaaa
     4081 aagatcaaag gatcctcttg agatcctttt tttctgcgcg taatctgctg cctgtaaacg
     4141 aaaaaaccgc cttgcagggc ggtttgatcg aaggttaagt cagcttgcag actgcttaac
     4201 caggtaactg tcttatgcga gacgagtcac caaaattgtt cttctagtgt agccgcactc
     4261 cggcagccac ttcaagtact ctctaaatat ctcgcacatg acttttacca atggctgctg
     4321 ccagtggcgc tttgtggtgt cttttccggg ttggacccaa gagaacagtt accggagaag
     4381 gcgcagcagt cgggctgaac ggggggttcc tgcatacagc ccagcccgga gcgaactgcc
     4441 taagtcgccc cgagatacca gaagacgtga gctatgagaa agcgccacgt gtcccgtaag
     4501 ggagaaaggc ggaaaaggta tccggtaatc gatatggcgg gaacgtgggg gcgcaggagg
     4561 gagcgattca ccggaaacgg tgatgatctt taagccacgt cgggtttcgc caccgctggc
     4621 ggatttcatg gttgagccgc aaggctccca cagatgcacc gaaaaagtgt ctgttttgtg
     4681 aagtccgtca ggggggcgga gcctatggaa aaagcgcctc cggcgcggcc tttcccgggg
     4741 tttcgttttt tgcgcacatg ttctttcctg gtttatcccc gggttctgtg gataacaggg
     4801 ttagcgtttt tgagaaagga gagtccgctc gccgcagccg aacgaccgag cgtagcgagt
     4861 cagtgagcga ggaagcggaa gagcgcctga actggcattt tctccttacg catctgtgcg
     4921 gcatttcaca ccggacatgg cgcacttttc atacaatccg cactgatgcc gaatggttaa
     4981 gccagtatac actccgctat cgctacgtga ctgggtcagg gcttcgcccc gacaccccaa
     5041 aggtcaacgg cctgacgcgc cctggcgggc ttgtctgctc ccggcatccg ctcacagaca
     5101 agctgtgacc gtctccggga gctgcatgtg tcagcggttt tcaccgtcat ccccgaagcg
     5161 tgcgaggcaa ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac agatgtctgc
     5221 ctgttcatcc gcgtccagtt cgttgagctt ctccagcagc gttaatgtct ggcctctgat
     5281 gaagcgggcc atgttaaggg cggttttttc ctgtttggtc actgatgcct ccgtgtaagg
     5341 gggggttctg ttcatggggg taatgatacc gatgaaacgc gagaggatgc tcacgatacg
     5401 ggttactgat gatgaacatg cccggttact ggaacgctgt gagggtaaac aactggcggt
     5461 atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaagc tgccgacact
     5521 ggcaccgccg ttactgcgtc agctggccgc catcgggaat aaccttaacc agacagcgag
     5581 gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg c
//
