LOCUS       NZ_CP051612             1907 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli O25b:H4-ST131 strain 2019_APHA plasmid
            pAPHA_2019_3, complete sequence.
ACCESSION   NZ_CP051612
VERSION     NZ_CP051612.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14594835
            Assembly: GCF_014217135.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O25b:H4-ST131
  ORGANISM  Escherichia coli O25b:H4-ST131
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1907)
  AUTHORS   Duggett,N.A., Randall,L., Lemma,F., Teale,C. and Anjum,M.F.
  TITLE     First detection of the pandemic Escherichia coli ST131 blaCTX-M-27
            fimH30(R) human clone in pigs from United Kingdom
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1907)
  AUTHORS   Duggett,N.A., Randall,L., Lemma,F., Teale,C. and Anjum,M.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-APR-2020) Bacteriology, Animal and Plant Health
            Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, United
            Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50x
            Sequencing Technology             :: Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:46:59
            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)                     :: 5,088
            CDSs (total)                      :: 4,976
            Genes (coding)                    :: 4,749
            CDSs (with protein)               :: 4,749
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 227
            CDSs (without protein)            :: 227
            Pseudo Genes (ambiguous residues) :: 0 of 227
            Pseudo Genes (frameshifted)       :: 80 of 227
            Pseudo Genes (incomplete)         :: 169 of 227
            Pseudo Genes (internal stop)      :: 39 of 227
            Pseudo Genes (multiple problems)  :: 52 of 227
            Pseudo Genes (short protein)      :: 3 of 227
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051612.1.
            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..1907
                     /organism="Escherichia coli O25b:H4-ST131"
                     /mol_type="genomic DNA"
                     /strain="2019_APHA"
                     /isolation_source="cecal sample"
                     /host="Pig"
                     /db_xref="taxon:941322"
                     /plasmid="pAPHA_2019_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2019"
                     /genotype="ST131"
     gene            complement(join(832..1907,1..>1))
                     /gene="waaL"
                     /locus_tag="HHM37_RS25120"
                     /old_locus_tag="HHM37_25135"
                     /gene_synonym="rfaL"
                     /pseudo=""
     CDS             complement(join(832..1907,1..>1))
                     /gene="waaL"
                     /locus_tag="HHM37_RS25120"
                     /old_locus_tag="HHM37_25135"
                     /gene_synonym="rfaL"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000958045.1"
                     /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="O-antigen ligase"
                     /name="waaL"
     gene            42..806
                     /locus_tag="HHM37_RS25125"
                     /old_locus_tag="HHM37_25140"
     CDS             42..806
                     /locus_tag="HHM37_RS25125"
                     /old_locus_tag="HHM37_25140"
                     /inference="COORDINATES: protein motif:HMM:NF013257.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glycosyltransferase family 9 protein"
                     /protein_id="WP_250998167.1"
                     /translation="MLTLCKHLRDLQFDIVLDPFETMPSFKHSLILSSLKDSYILGFDQ
                     WYKRYYSFYHPHDECLKEHMSTRATEILKHIYGEGEFSTDYDLHLPVDVEDKIKEFIGD
                     TRIVIINPLGAKKICRLTFEQIKVIYQEMKLHFENYRVIFTGLPQDLLTIPIPEIETLP
                     FNEFIYTVALTKYSDFVISVDTALVHIAAAYHKPTLAFYPNSRTPEYPSHLIWSPNNHK
                     SIQIVSPTFTVKDIDTETLTDSVKRLSCIDKK"
                     /name="glycosyltransferase family 9 protein"
ORIGIN
        1 tatttgagtt ctgtattaaa gaatcaaccg gtttccttaa aatgcttact ctatgtaagc
       61 atctgcggga tttgcagttc gatattgtat tagacccctt tgaaaccatg ccctcattta
      121 agcatagttt aatattatca agtttaaaag attcttacat tctgggtttt gatcaatggt
      181 ataaacgtta ctattcattt taccatcccc acgatgaatg tttaaaagaa catatgagta
      241 cacgagcaac agaaatactg aagcatattt atggtgaggg tgaattctcc accgactacg
      301 acttgcattt accagtagat gttgaagata aaataaaaga atttattgga gatacaagaa
      361 tagtcattat taacccatta ggtgcaaaaa aaatatgccg acttacgttt gagcaaataa
      421 aagttatata tcaagaaatg aaactacact ttgaaaatta tcgggtgata tttaccgggt
      481 taccgcaaga tttattgaca ataccaatac ctgaaatcga aacactacca tttaatgagt
      541 ttatttatac cgttgcgttg accaagtata gtgattttgt catttctgtt gatacagctc
      601 ttgttcatat cgctgcggct tatcataaac caacgcttgc attttatcct aattcacgta
      661 ctccggaata tccctcacat ttaatttggt ccccaaataa tcataaatca atacaaatag
      721 tatccccaac atttacggtg aaagatatcg atactgaaac tttaactgat tcagtaaaga
      781 gattaagttg tatagataag aagtgagttt taactcactt cttaaacttg tttattcttg
      841 attaatagta ttgttacgat tattaataac gagtaagagg actatagcgg atataacgat
      901 aattggaatg ctgcgtgccc atatgatcac atcactgagt ccaatcccca caatgccaag
      961 cgttaatatc aacaaaccca aagctcgtct tttatatgct gtataaaaca gtgaaaaata
     1021 gaggaaaagg atggaaataa ttcccatcag acctttcagt gaccctgctt caattatctc
     1081 attatgtaga tgtacgttag aaaactccaa tgcccctctt agcctgttgt gttctgcaac
     1141 taacaaattc atattttcag cgcgtgactc tgctgatcta aatgaaaaag gtgactttat
     1201 gaatatattt aaaccaattt cgtacattgc cagtcttgca cctagggaag tcacgctatt
     1261 agcattggta taactgttta aatcatttaa tgcttcatta tagcgattct gtattggttt
     1321 attaaatata attactatgc tagctaatat agcaattagt agaacaatag aggaagtgaa
     1381 tttcttgggt gatttattat aataagctat taatgcagca acacaaatta tagggaacag
     1441 gagtagggtt gctctggttt gtgttagcgc cagaacataa agtaccgcgc aactatttaa
     1501 taaaaataaa aaaggatggt ttttcttagt ataaagaatc gcaacgccac taactatccc
     1561 tattagcata gttgaatatg ctgctcctgt tgccgttcct acaccaaaag aaatgcggtc
     1621 attttcatga atgctattaa tatacattgc atatccagca attagaaatg acagagaata
     1681 taaagtgtat aatacactct ctttttttga ttttagctgg ctagttagtg tcaagaaaac
     1741 aataaaagaa ccaaatataa aaattttggc agtatttaaa taactatggt aagtagcacg
     1801 aaatggcgaa ttatctattt taaacgcaga ataccaaatt aaatcaagta agcctattaa
     1861 aaatatagaa aggggaagaa taaggttttt tatattataa ttttctt
//
