LOCUS       NZ_CP056953             2064 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB42-C01 plasmid pRHB42-C01_3,
            complete sequence.
ACCESSION   NZ_CP056953
VERSION     NZ_CP056953.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148432
            Assembly: GCF_013800985.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2064)
  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 2064)
  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                     :: RH12 T3-C01
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 158.536495436243x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013800985.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:31:04
            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)                     :: 4,559
            CDSs (total)                      :: 4,442
            Genes (coding)                    :: 4,302
            CDSs (with protein)               :: 4,302
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 47 of 140
            Pseudo Genes (incomplete)         :: 82 of 140
            Pseudo Genes (internal stop)      :: 20 of 140
            Pseudo Genes (multiple problems)  :: 11 of 140
            Pseudo Genes (short protein)      :: 2 of 140
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056953.1.
            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..2064
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB42-C01"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB42-C01_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(894..1883)
                     /locus_tag="HV015_RS22650"
                     /old_locus_tag="HV015_22660"
     CDS             complement(894..1883)
                     /locus_tag="HV015_RS22650"
                     /old_locus_tag="HV015_22660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_181576157.1"
                     /translation="MQNPKLQYLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYEHYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLSRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRMKVRKEFLPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMAPPGMLNGKSYVRHERWVELWRECLRVDYDPNVDVRAVKPRKPKDG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESD"
                     /name="protein rep"
     Typing          392..473
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="96.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(805..891)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.182"
                     /coverage="96.0"
                     /evalue="9.44e-28"
     Typing          977..1168
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.446"
                     /coverage="100.0"
                     /evalue="2.86e-91"
ORIGIN
        1 aaatcccccc tcaggccttg cggcacaagg gctggaggcg aatttgaatc ctagagttat
       61 cccttaagta taaatacaag gatcacgcgc gagatttgct tgaattttga gctggatttt
      121 cagtaaccaa aaacctccca accccaccca cttacaccca tctcatccac agactttcac
      181 cccgattttg tgaacaacaa aaaaccgtct tgcaggtggt tggcctcact ccgtgacacc
      241 aaccaccatc cccagtgttt tccccgtgcc gtcgtcaatc acaaaatcgg aacccacgcc
      301 agaggcgcgg ggccccgcga ttttctgttt gacgagttcg ggaacggtga gcggtacgcg
      361 gaattttttc gcgggccgtg aggcgttggc ggggtgtcgg ggcgcagccc tgaccaggtg
      421 gtaattgtga tagcgtcgcg tgtgacggta ttacaattac acatcctgtc ccgaaaattc
      481 ccgccgtttc tcggtttttt gagcgtcgca gaccgcacga caaacgaaac gaagtgaagt
      541 ttgtataagt gcgcacttcg tgagattccc cgactgccag tttgtcgatc gcgcggaacg
      601 gctgcggcac aaaaacggca aaatgatttg ctgtccgttc gccgaaattt ttgcgtagct
      661 gtggtggctg cggtgccaaa aatcatccgc gcgttaagtg tggatgcgca cttagtagtt
      721 tctctccttc gtcgggaaac tgtgcgctcc tgcggagggg ttaacggcgc agaactgccg
      781 atgctctgcc agcgttctgg cgaaaaaatc gggacaggat gtgtaattgt aataccgtca
      841 cacgcgacgc tatcacaatt accacctggt cagggctgcg ccccgacacc ctgctagtct
      901 gattcagttt tatctttcgt cggtgagcgg cggtactttc tgacctcggt tttccattcg
      961 aacgcgatgc gtgaaccgtc atcgtcgccc tcggaaatat catctccgat caccatgtcg
     1021 gcgtcggttt cctgatcgag tttcagcaca tctttgagtg cgccgccggt cgccacaaag
     1081 cggcgcttgt gcgtctggcg agtcagttcg aggaaccatt caggatcggc caccatgtca
     1141 gccggcttcg tggaatattt cagggtttcg gccactgcgc cgcgcaccag ttcagcggtc
     1201 gcgcaggcta aggactcgcc atccttcggc ttgcggggtt tcactgcccg gacatcaaca
     1261 ttcgggtcat aatcaacccg caggcactcc cgccatagct caacccagcg ttcatgcctg
     1321 acgtaacttt tcccatttag catgccagga ggagccatca tcaaggtatg gaagtgcggg
     1381 tgtgcgctgc cgtcgctgcc gcgggtaact tccgttgtgc ggatccagcc ctgaacaggc
     1441 aggaactcct tgcgaacctt catacgctga aaagctgcat tcatccggtt cagcatctcg
     1501 cccagttccc caatcgcaca gttgcgcacg gtcagggtca ggaacatcca gcgggcatcg
     1561 ggataatccg ccacgatacg cgacagggac tggtagaaac gggcttgcca catcagggag
     1621 cgcctccact ggcagacagg acagtgccgg acacggcaga aatgtgcctc acgcagcctc
     1681 agacgcgttt ctccggtttc cttgagggta gaccacccga aacgcagtaa accgccacag
     1741 gaagccatac gagccccgta gtgctcatat tcggccgcaa gcaggtaaat ccctcccacg
     1801 tcgtcagaaa cgcttctgtg tgcgtcccag ggcgcatcag agggggaata atcagtgagg
     1861 tactggagtt tagggttttg catgcacacc gccccatact gggcgatggc tcgattgacg
     1921 tgttatcatt gccatatcac ctgttgctct catcatgaat ccagtttctg caggtggtca
     1981 cacccccgaa cgatgcccgt cgttgcgggg gtcactttta acgcaaccac tcccgacaga
     2041 ataactccaa aaccattttc cgac
//
