LOCUS       NZ_CP056938             2064 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB42-C13 plasmid pRHB42-C13_3,
            complete sequence.
ACCESSION   NZ_CP056938
VERSION     NZ_CP056938.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148437
            Assembly: GCF_013799825.1
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-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 167.125291100868x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013799825.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:19:57
            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)                     :: 4,500
            CDSs (total)                      :: 4,383
            Genes (coding)                    :: 4,258
            CDSs (with protein)               :: 4,258
            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)              :: 125
            CDSs (without protein)            :: 125
            Pseudo Genes (ambiguous residues) :: 0 of 125
            Pseudo Genes (frameshifted)       :: 41 of 125
            Pseudo Genes (incomplete)         :: 73 of 125
            Pseudo Genes (internal stop)      :: 19 of 125
            Pseudo Genes (multiple problems)  :: 10 of 125
            Pseudo Genes (short protein)      :: 2 of 125
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056938.1.
            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-C13"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB42-C13_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(1913..2064,1..568)
                     /locus_tag="HV020_RS22360"
                     /old_locus_tag="HV020_22365"
     CDS             join(1913..2064,1..568)
                     /locus_tag="HV020_RS22360"
                     /old_locus_tag="HV020_22365"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_249417917.1"
                     /translation="MWQARFYQSLSRIVADYPDARWMFLTLTVRNCAIGELGEMLNRMN
                     AAFQRMKVRKEFLPVQGWIRTTEVTRGSDGSAHPHFHTLMMAPPGMLNGKSYVRHERWV
                     ELWRECLRVDYDPNVDVRAVKPRKPKDGESLACATAELVRGAVAETLKYSTKPADMVAD
                     PEWFLELTRQTHKRRFVATGGALKDVLKLDQETDADMVIGDDISEGDDDGSRIAFEWKT
                     EVRKYRRSPTKDKTESD"
                     /name="protein rep"
     Typing          572..658
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.182"
                     /coverage="96.0"
                     /evalue="9.44e-28"
     Typing          complement(990..1071)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="96.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(295..486)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.446"
                     /coverage="100.0"
                     /evalue="2.86e-91"
ORIGIN
        1 gaaggttcgc aaggagttcc tgcctgttca gggctggatc cgcacaacgg aagttacccg
       61 cggcagcgac ggcagcgcac acccgcactt ccataccttg atgatggctc ctcctggcat
      121 gctaaatggg aaaagttacg tcaggcatga acgctgggtt gagctatggc gggagtgcct
      181 gcgggttgat tatgacccga atgttgatgt ccgggcagtg aaaccccgca agccgaagga
      241 tggcgagtcc ttagcctgcg cgaccgctga actggtgcgc ggcgcagtgg ccgaaaccct
      301 gaaatattcc acgaagccgg ctgacatggt ggccgatcct gaatggttcc tcgaactgac
      361 tcgccagacg cacaagcgcc gctttgtggc gaccggcggc gcactcaaag atgtgctgaa
      421 actcgatcag gaaaccgacg ccgacatggt gatcggagat gatatttccg agggcgacga
      481 tgacggttca cgcatcgcgt tcgaatggaa aaccgaggtc agaaagtacc gccgctcacc
      541 gacgaaagat aaaactgaat cagactagca gggtgtcggg gcgcagccct gaccaggtgg
      601 taattgtgat agcgtcgcgt gtgacggtat tacaattaca catcctgtcc cgattttttc
      661 gccagaacgc tggcagagca tcggcagttc tgcgccgtta acccctccgc aggagcgcac
      721 agtttcccga cgaaggagag aaactactaa gtgcgcatcc acacttaacg cgcggatgat
      781 ttttggcacc gcagccacca cagctacgca aaaatttcgg cgaacggaca gcaaatcatt
      841 ttgccgtttt tgtgccgcag ccgttccgcg cgatcgacaa actggcagtc ggggaatctc
      901 acgaagtgcg cacttataca aacttcactt cgtttcgttt gtcgtgcggt ctgcgacgct
      961 caaaaaaccg agaaacggcg ggaattttcg ggacaggatg tgtaattgta ataccgtcac
     1021 acgcgacgct atcacaatta ccacctggtc agggctgcgc cccgacaccc cgccaacgcc
     1081 tcacggcccg cgaaaaaatt ccgcgtaccg ctcaccgttc ccgaactcgt caaacagaaa
     1141 atcgcggggc cccgcgcctc tggcgtgggt tccgattttg tgattgacga cggcacgggg
     1201 aaaacactgg ggatggtggt tggtgtcacg gagtgaggcc aaccacctgc aagacggttt
     1261 tttgttgttc acaaaatcgg ggtgaaagtc tgtggatgag atgggtgtaa gtgggtgggg
     1321 ttgggaggtt tttggttact gaaaatccag ctcaaaattc aagcaaatct cgcgcgtgat
     1381 ccttgtattt atacttaagg gataactcta ggattcaaat tcgcctccag cccttgtgcc
     1441 gcaaggcctg aggggggatt tgtcggaaaa tggttttgga gttattctgt cgggagtggt
     1501 tgcgttaaaa gtgacccccg caacgacggg catcgttcgg gggtgtgacc acctgcagaa
     1561 actggattca tgatgagagc aacaggtgat atggcaatga taacacgtca atcgagccat
     1621 cgcccagtat ggggcggtgt gcatgcaaaa ccctaaactc cagtacctca ctgattattc
     1681 cccctctgat gcgccctggg acgcacacag aagcgtttct gacgacgtgg gagggattta
     1741 cctgcttgcg gccgaatatg agcactacgg ggctcgtatg gcttcctgtg gcggtttact
     1801 gcgtttcggg tggtctaccc tcaaggaaac cggagaaacg cgtctgaggc tgcgtgaggc
     1861 acatttctgc cgtgtccggc actgtcctgt ctgccagtgg aggcgctccc tgatgtggca
     1921 agcccgtttc taccagtccc tgtcgcgtat cgtggcggat tatcccgatg cccgctggat
     1981 gttcctgacc ctgaccgtgc gcaactgtgc gattggggaa ctgggcgaga tgctgaaccg
     2041 gatgaatgca gcttttcagc gtat
//
