LOCUS       NZ_CP059911             3245 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 181.1 plasmid p4, complete sequence.
ACCESSION   NZ_CP059911
VERSION     NZ_CP059911.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13613900
            Assembly: GCF_014170615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3245)
  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                   :: 17.8x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:45:49
            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)                     :: 5,554
            CDSs (total)                      :: 5,429
            Genes (coding)                    :: 5,160
            CDSs (with protein)               :: 5,160
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 1 of 269
            Pseudo Genes (frameshifted)       :: 114 of 269
            Pseudo Genes (incomplete)         :: 181 of 269
            Pseudo Genes (internal stop)      :: 51 of 269
            Pseudo Genes (multiple problems)  :: 64 of 269
            Pseudo Genes (short protein)      :: 4 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059911.1.
            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..3245
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="181.1"
                     /host="Turkey"
                     /db_xref="taxon:562"
                     /plasmid="p4"
                     /geo_loc_name="Canada"
                     /collection_date="2016/2017"
     gene            <2..931
                     /locus_tag="H5C80_RS28040"
                     /pseudo=""
     CDS             <2..931
                     /locus_tag="H5C80_RS28040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001001722.1"
                     /GO_function="GO:0016757 - glycosyltransferase activity
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="glycosyltransferase"
                     /name="glycosyltransferase"
     gene            941..1633
                     /gene="rfaY"
                     /locus_tag="H5C80_RS27400"
                     /old_locus_tag="H5C80_27400"
     CDS             941..1633
                     /gene="rfaY"
                     /locus_tag="H5C80_RS27400"
                     /old_locus_tag="H5C80_27400"
                     /EC_number="2.7.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000633080.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="lipopolysaccharide core heptose(II) kinase RfaY"
                     /protein_id="WP_000633081.1"
                     /translation="MITSIRYRGFSFYYKDNDNKYKEIFDEILAYNFKTVKVLRNIDDT
                     KVSLIDTKYGRYVFKVFAPKTKRNERFFKSFVKGDYYQNLIVETDRVRSAGLTFPNDFY
                     FLAERKIFNYASVFIMLIEYVEGVELNDMPIIPENVKAEIKASMEKLHALNMLSGDPHR
                     GNFIVSKDGVRIIDLSGKSCTAERKARDRLAMERHLGIANEIKDYGYYSVIYRTKLRKF
                     IKKLKGKA"
                     /name="rfaY"
     gene            1659..2687
                     /locus_tag="H5C80_RS27405"
                     /old_locus_tag="H5C80_27405"
     CDS             1659..2687
                     /locus_tag="H5C80_RS27405"
                     /old_locus_tag="H5C80_27405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001626264.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="UDP-galactose--(galactosyl) LPS
                     alpha1,2-galactosyltransferase"
                     /protein_id="WP_001696312.1"
                     /translation="MDLLAESITEVAVSGEIANTDRVLNIAYGIDRNFLFGAAVSMQSV
                     VMHNPYLAVKFHLFTDYIDEDYLQRVNAFTNKNANVEVRIYKVSNAFIDIFPSLKQWSY
                     ATFFRLVAFQYLSETIENLLYIDADVICKGSLAGLLDINFDGDKFAAVIKDVPFMQEKP
                     AKRLAIEGLPGNYFNAGVVYLQLEAWAKNDFMNKAIAMLASDPQHTKYKCLDQDILNIL
                     FFGHCIFISGDYDCFYGIDYELKNKSDEDYKKTITDDTKLIHYVGVTKPWNDWTNYPCQ
                     KYFNEAYQASCWNDVAFIPATNEKQYQVKSRHLKRNGKIASSFYYFMLYYSKKIARKHF
                     SK"
                     /name="UDP-galactose--(galactosyl) LPS
                     alpha1,2-galactosyltransferase"
     gene            2719..>3183
                     /locus_tag="H5C80_RS28045"
                     /old_locus_tag="H5C80_27395"
                     /pseudo=""
     CDS             2719..>3183
                     /locus_tag="H5C80_RS28045"
                     /old_locus_tag="H5C80_27395"
                     /inference="COORDINATES: protein motif:HMM:NF013882.2"
                     /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="glycosyltransferase family 25 protein"
                     /name="glycosyltransferase family 25 protein"
ORIGIN
        1 gctaaatgtt tcctacggta tcgataagaa ttttttgtat ggtgctggcg tttcaatttc
       61 ttccgttttg attaataatt cagatattaa ttttgtcttt catgttttca ctgattatgt
      121 agatgacgat tatttaaagt catttaatga aacggcaaaa caatttaata cctcaattat
      181 tgtatattta attgacccca aatactttgc tgatctgccg acgtcacagt tttggtcgta
      241 cgcaacatac ttcagggtat tgtcttttga atatctgagt gaaagtattt ctacactgct
      301 gtatctggat gccgatgttg tttgtaaagg aagcctgaaa cctctcacag aaattatatt
      361 taaagatgag tttgctgcgg tcattcctga caatgatagt actcaggcgg catgtgcaaa
      421 acgcctcaac attcccgaaa tgaatggacg ttatttcaat gcaggcgtta tctatgtcaa
      481 tcttaaaaaa tggcatgaag caaatttgac accgtattta ctcacgcttt tacgagggga
      541 aactaaatat ggctctctta aatatttaga tcaggatgcg ttgaatatcg catttaatat
      601 gaataatatc tacctcgcga aggattttga tactatttat accctgaaaa acgaacttca
      661 tgatcgtagt catcgaaagt atcagcaaac cattaccgat aaaacagtat tgattcacta
      721 tacagggata actaaaccat ggcatagctg ggctggatat ccatctgcat catactttaa
      781 tatcgcgcgt gaacaatctc cctggaagaa atatcctctt aaagaggcgc ggactgttgc
      841 agaaatgcag aaacaatata agcatctgtt tgcccatggt gagtatatta aaggtataac
      901 ttcattaatt aagtacaagc ttaagaaata aattactctt atgattacaa gtatacgcta
      961 tcgcggcttc tcattttatt acaaagataa cgataataaa tataaagaaa tctttgatga
     1021 aatactggcc tataatttta aaacagtaaa agtattacgt aatattgatg ataccaaagt
     1081 atcgttgatt gatacgaaat atggtcgcta tgtttttaaa gtctttgctc ccaaaacgaa
     1141 aaggaatgaa cgttttttta aatcttttgt aaaaggtgac tactatcaga atttgatcgt
     1201 tgaaaccgat cgtgtcagaa gtgcaggtct tacttttcct aatgattttt attttctggc
     1261 tgagcgtaaa attttcaact atgccagtgt ttttatcatg cttatcgagt atgtcgaggg
     1321 cgtagaactc aatgatatgc cgattattcc agaaaatgtt aaagcagaaa ttaaggcttc
     1381 aatggaaaaa ttgcatgcct taaatatgct atcgggcgac cctcaccggg gtaactttat
     1441 cgttagtaaa gatggtgtca ggataattga cctatccggt aaaagctgta cggcagagcg
     1501 taaagctcgt gatcgtctgg ccatggaacg tcacctgggt attgccaacg aaataaaaga
     1561 ttatggctac tattcagtaa tctacagaac caaactacgc aaatttatta aaaaattaaa
     1621 aggcaaagcg taaaccacac agtcaaaacg gaaccaacat ggatttatta gctgagagta
     1681 ttactgaagt cgctgtctct ggggaaattg ctaacaccga tcgtgtgtta aatatcgctt
     1741 acggtattga ccgcaacttt ttatttggtg cggcagtatc tatgcaatca gttgttatgc
     1801 ataacccgta ccttgcggtt aagtttcatc tctttactga ctacattgat gaagattatc
     1861 tacaacgtgt taatgctttt accaacaaaa atgctaacgt tgaagtaaga atttataaag
     1921 tctccaatgc ctttattgat atcttcccca gcctgaaaca gtggtcttat gcaacattct
     1981 tccgtttagt tgcgttccag tatttgagtg aaactattga aaatctgtta tatatcgatg
     2041 ctgatgtcat ctgtaaaggc tcattagctg gattgcttga tattaatttt gatggcgata
     2101 agttcgcggc tgttattaaa gatgtgcctt ttatgcagga aaaaccagcg aagcgtctgg
     2161 ctatagaggg acttccaggg aattatttca acgccggtgt agtatatctg cagcttgaag
     2221 catgggcgaa aaatgatttt atgaataaag ccattgctat gctggcaagt gacccgcagc
     2281 acacgaaata taaatgcctt gatcaggata ttttaaatat tctgttcttt ggtcattgta
     2341 tttttattag cggcgattat gattgctttt atggcattga ctatgagtta aaaaataaaa
     2401 gcgatgaaga ttataaaaag accattaccg atgatactaa gctgattcat tatgttggcg
     2461 taacgaagcc ctggaacgac tggacgaatt atccctgcca gaagtatttt aatgaggctt
     2521 atcaggcttc ttgctggaat gatgtggcgt ttattccagc cacgaatgaa aagcagtatc
     2581 aagtgaaatc cagacatttg aaaagaaatg gtaaaattgc atcttcattt tactatttca
     2641 tgctctatta tagtaagaaa atagcgcgta agcatttttc caaataatta ttaagattaa
     2701 tcatccagag attttttaat gaacttgccc atttatattg tctcacttaa aagagatatt
     2761 gagcgaagaa ataaaataaa tgatgttttt tatcgattaa atattaattt tgattttttt
     2821 gatgccatag atgctaaaga ccctcaaaat aaagaaatta ttgataaaat gagattaagt
     2881 ggtgtcggcg cagaaatgac tgatggagaa attgcttgta cattaagtca tcagcttata
     2941 tatcaggata tgatagataa aaatatagaa tgggcagtca ttctcgagga tgatgttatc
     3001 gtcaatgaga aatttaaaaa atttctgcaa tattttaatc tttctgaaaa agacaagtta
     3061 aaacataata atttgtattt gcttggagga cagaaaggat tacatgatta tccggtattg
     3121 gggcaaagcc tttttagtaa agttaaggta agtacttgta cttttcggcg tgttaatttc
     3181 aataaaaata aaattcggcg tacatgttca tatttgatga ataaagatat ggcacaaaat
     3241 ttgct
//
