LOCUS       CP055674                3126 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C19 plasmid pRHB30-C19_6, complete
            sequence.
ACCESSION   CP055674
VERSION     CP055674.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148297
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3126)
  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 3126)
  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                     :: RH02 T3-C19
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 168.684881854874x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/18/2020 16:37:18
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,187
            CDSs (total)                      :: 5,063
            Genes (coding)                    :: 4,824
            CDSs (with protein)               :: 4,824
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 71 of 239
            Pseudo Genes (incomplete)         :: 153 of 239
            Pseudo Genes (internal stop)      :: 35 of 239
            Pseudo Genes (multiple problems)  :: 19 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..3126
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB30-C19"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C19_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(316..639)
                     /locus_tag="HVY80_25920"
     CDS             complement(316..639)
                     /locus_tag="HVY80_25920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QLN07921.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            924..1118
                     /locus_tag="HVY80_25925"
     CDS             924..1118
                     /locus_tag="HVY80_25925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="QLN07922.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQRRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2063..2206
                     /locus_tag="HVY80_25930"
     CDS             2063..2206
                     /locus_tag="HVY80_25930"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QLN07923.1"
                     /translation="MNTKVLFVKKALKSITCATLSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     gene            complement(2231..2983)
                     /locus_tag="HVY80_25935"
     CDS             complement(2231..2983)
                     /locus_tag="HVY80_25935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QLN07924.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVAG"
                     /name="hypothetical protein"
     Typing          complement(649..887)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.417"
                     /coverage="99.0"
                     /evalue="6.069999999999999e-104"
     Typing          1154..1657
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.528"
                     /coverage="95.0"
                     /evalue="8.27e-156"
     Typing          complement(320..639)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.93e-62"
ORIGIN
        1 atatttatct atatgaaaca accagttata gttattgttt cataataagg attgaatact
       61 cttcacaatc cataacatca gaaaatactt tgctgccaat ttaccataac tccccttacg
      121 cgcaccgcta aaacgcgctg aacgcgattc tgccgcaaac accgcaaaaa gagatgtttt
      181 acccagtgaa aactggaaaa atgcgtcagg atcgttttca gctcactgca tagctatgca
      241 tgaaagtgaa tggcgatcgg tttgggggct tacggcgttc ataccgtctg ttttcgacag
      301 tttctctccg ggaagctaat ctgccataag cctggataac agggcccggt gatactccgt
      361 aatagcgatc agcacctccg catactctct gtccccgaca cgcttgccgt cgataaagag
      421 ttttttctgt aacgccccca gtctcataac ttctttcagt acccgatcat cagtcagtga
      481 gttaactttc ttaccgagag ctgccgcccg taaaaaaccg gaaacggtct tgccgcattc
      541 agcagccctt tttctgattt cctggtcttc ttctgccgtc agacgaacag ggcgactgat
      601 agcccgcctg cgcgtattac ttccacttcg ttttgtcata aaacatggct ccgtatctga
      661 catggggtgt cggggcaaag ccctgaccag ggtaattgta atagcgtgca tgcatgcgcg
      721 gtataacaat tgcacatcct gtcctgtcag caagttcgaa ttaccgacaa aggcacggca
      781 gttttttggc agtgacagtg ttgcctgaca gaaatacccg ttaaagcgtc agacggcaga
      841 ataccggcgg caaaactgcc gaaaagtggt acgcgatata atcacacgac gcagatgaca
      901 gacagaacgg agaaaacaga aagatgaaca agcagcagca aaccgtactt aacatggcag
      961 gattcataaa aagccagagc ctgacgctgc tcgaaaaact ggacgcactt gatgctgacg
     1021 aacaggccgc catgtgtgag aagctgcacg aactcgcgga agaacttcag aacagcatac
     1081 agagacgctt tgaagcggaa aatcgcaccg ggatataacg catccggaca ggatgcagaa
     1141 cggcatagag gagcgtaagg agaaaatgtc acataaggcg ctcttccgct tcctcgctca
     1201 ctgactcgct acgctcggtc gttcgactgc ggcgagcggt gtcagctcac tcaaaggcgg
     1261 taatgcggtt atccacagaa tcaggggata aagccggaaa gaacatgtga gcaaaagaca
     1321 aagacccaga agaagagcac gcaggaggcg tttttccata ggctccgccc ccctgacgag
     1381 catcacaaaa accgacgctc aagtcagagg tggcgaaacc cgacaggact taaagatacc
     1441 aggcgtttcc ccctggtggc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg
     1501 gtgtcattcc gctgttatgg ccgcgtttgt ctcattccac gcctgacact cagttccggg
     1561 taggcagttc gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgactactgc
     1621 gccttatccg gtaactatcg tcttgagtcc aacccggaaa ggcacgactt atcgccattg
     1681 gcagcagcca ctggtaactg atttagagga gttagtcttg aagttacgtg ccagttaagg
     1741 ctaaactgga ataacaagtt ttggtgactg cgctcctctt aagccagtta ccgcggttca
     1801 gaaacttgcc ggttgctgaa ccttcgaaaa accaccttgc cgggtggttt tttcgttttt
     1861 aagattacga tgggcgcgat atgaactcaa ggaaatccgt aattaaatta taaaacttcg
     1921 tgaattaatg gaaaaactga tgtgaatcag ctatttatcc ttaagatttg atgttagata
     1981 tggtataatt aaccattcaa atagatggaa taaaaagtca acgctgccat tagaacggca
     2041 taagaaatag aggattatga aaatgaatac taaagttctt tttgtgaaaa aagctttgaa
     2101 atcaattact tgcgcaactc tttcgctctt accggcttta agtcgcgcag taacagagtt
     2161 acgtagcctt tcggctgcgc gacttaaagc cggtaagagc ttttgattgt atcacatttt
     2221 cccttaaaag tcaaccggct accttaagct ccctgcactt aatcctccct ataatcccca
     2281 taacatactc tatcgtgcag cgttcataaa agcgcctatc gtgcccaata aactcaataa
     2341 gttccttttt ctcgttagag acgatactca aggcattcat taaaaaattg aactctttca
     2401 acatattatt tatggcttga ctatgcgact tgcagtggtg ttttttccaa ataggctcat
     2461 ggtgaaaaag tcgattccta aacaaaagaa ctttatgaaa ctcgtcaaac agcgctttaa
     2521 ccttcatatc ccccccaccc aaaggattct tcgcatgagg aaatgttttt gccttgttct
     2581 ctggagtcca gatgtagcac ggcctttgcg tatccctata tggggcatct aacatataaa
     2641 cccaaaagcc aaaggttaga cggcaaataa catcatcatc cgtatacctt acgccacact
     2701 catctagtgc tttttgtttc gcatttaaaa caagatcctg agatttcttt gtttgaggta
     2761 tagagtcgta ccaagcaggc ccatgattag ctttgattgt attgtttatc gcattacgca
     2821 gagcaacctc aatcatctgg acaagacaaa aaaaatcgcc agacagatct tggtaggcaa
     2881 cgtatgcccc aaccttttct tgatcagtag cgcacccaag aaatgtttca tagaaagata
     2941 atcttggtac agaaattgag ctaattaaac ttgttgtatc catgaaaact cacttatctc
     3001 tttactatga atatttttca gactaccatt acaacattcg aggagcaggc gaactaccgt
     3061 ttttctgtgt acctctagag cgtaaaatat aacaaaaaag cccactacag agtgggcttt
     3121 tttgtt
//
