LOCUS       NZ_CP056966             1553 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB41-C20 plasmid pRHB41-C20_6,
            complete sequence.
ACCESSION   NZ_CP056966
VERSION     NZ_CP056966.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148429
            Assembly: GCF_013801425.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1553)
  AUTHORS   AbuOun,M., Jones,H., Stubberfield,E., Gilson,D., Shaw,L.P.,
            Hubbard,A.T.M., Chau,K.K., Sebra,R., Peto,T.E.A., Crook,D.W.,
            Read,D.S., Gweon,H.S., Walker,A.S., Stoesser,N., Smith,R.P.,
            Anjum,M.F. and On Behalf Of The Rehab,Consortium.
  TITLE     A genomic epidemiological study shows that prevalence of
            antimicrobial resistance in Enterobacterales is associated with the
            livestock host, as well as antimicrobial usage
  JOURNAL   Microb Genom 7 (10) (2021)
   PUBMED   34609275
REFERENCE   2  (bases 1 to 1553)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JUN-2020) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: RH01 T3-C20
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132.253115999787x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013801425.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:40:09
            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)                     :: 4,826
            CDSs (total)                      :: 4,703
            Genes (coding)                    :: 4,568
            CDSs (with protein)               :: 4,568
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 135
            CDSs (without protein)            :: 135
            Pseudo Genes (ambiguous residues) :: 0 of 135
            Pseudo Genes (frameshifted)       :: 54 of 135
            Pseudo Genes (incomplete)         :: 74 of 135
            Pseudo Genes (internal stop)      :: 23 of 135
            Pseudo Genes (multiple problems)  :: 17 of 135
            Pseudo Genes (short protein)      :: 2 of 135
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056966.1.
            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..1553
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C20"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB41-C20_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            1..477
                     /locus_tag="HV012_RS23955"
                     /old_locus_tag="HV012_23960"
     CDS             1..477
                     /locus_tag="HV012_RS23955"
                     /old_locus_tag="HV012_23960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1084..1164
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="87.0"
                     /evalue="2.0600000000000002e-29"
     Typing          complement(1367..1475)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.091"
                     /coverage="100.0"
                     /evalue="9.09e-49"
     Typing          complement(709..969)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagct
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccttt gcgtgttttt gctccccgtt ctccagaaaa
      601 aaccgagccg ccacggttcc ggcagcgcct tgagcgctac cggaaaccgt ctggggagaa
      661 ccccagaccc ccatcgctgc aacaccgacg gtctacgacc acctaccaac cgcatggctg
      721 cctgttccgt gcaaatgggc tttgcagggg gctggcgcgg ttcctggcga cctgaaagcc
      781 cctggttagg ggtatcggcg cgcttgacct cctgagagcc tctgtaagcg tttttcgcgc
      841 cttccatgcc ctggcgggca tctaaaaccc gtttcgtgcg tctgagagct tttgagcgcg
      901 tttgaggggc tatctggcga ctcatcccca aaagaacaac accgggatca ccgacaacat
      961 gcgagaggtg gcaccgctcg ccgcagcccc agcgaccgaa cgttagtgag cgagtgggcg
     1021 aggaagcgga agagaaccgg aaaccacatt gagcacgtac gcactgatgc ggggtgtcgg
     1081 ggcgaagccc tgaccagatg gcaaacggaa tatcgtcgcg ggtgacggta ttacatttgc
     1141 acatcctgtc ccgatttctg aggcgtttta gcggtgaacg gacggcaaaa ccatgatgga
     1201 gctgttgaac gttgagagcg tgaaatctgg caaaaatcac agctggtaag gcttgcagag
     1261 gagtaagcca gtatacactc cgctatcgct acgtgactgg gtcagggctt cgccccgaca
     1321 cccccaaagg gcgttgcgtt gcacgcaaca cccttgccta gaatagatct tttacgccga
     1381 tttgtaagtg gttgtttttt tagtgtgttt tttatttacc tgtcgcatcc aggatgacac
     1441 aacgttgtcg catcctggat gcgacaacac gcaacaaggt gttgcacaga tgtgtcatga
     1501 tggcttagat ttgaaccaac gttagtgcat gggattttca gagggaaaaa atc
//
