LOCUS       CP058018                3081 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB04-C08 plasmid pRHB04-C08_5, complete
            sequence.
ACCESSION   CP058018
VERSION     CP058018.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147987
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3081)
  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 3081)
  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                     :: RH13 T1-C08
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 85.4803193605213x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:14:43
            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)                     :: 4,884
            CDSs (total)                      :: 4,765
            Genes (coding)                    :: 4,668
            CDSs (with protein)               :: 4,668
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 47 of 97
            Pseudo Genes (incomplete)         :: 48 of 97
            Pseudo Genes (internal stop)      :: 30 of 97
            Pseudo Genes (multiple problems)  :: 24 of 97
            CRISPR Arrays                     :: 4
            ##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..3081
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB04-C08"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB04-C08_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            283..582
                     /locus_tag="HVV70_24405"
     CDS             283..582
                     /locus_tag="HVV70_24405"
                     /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="QMQ34453.1"
                     /translation="MANITNFDMWLDDVDGDHEEVMALYDAVQNVSDMGVYKCVEGNGR
                     DTWVVSSNHHHEDLFLESVVDKGDFLKLIKKRLCGGENVESWYGFQRNMSNDHS"
                     /name="hypothetical protein"
     gene            654..1376
                     /locus_tag="HVV70_24410"
     CDS             654..1376
                     /locus_tag="HVV70_24410"
                     /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="QMQ34454.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTDSYIDLI
                     CRDKESRDIVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     KTSILAVSKLNLHWIFVEPDGSVTIKKPDSSMMKNGNGNGREVSLVNGVFKRFIPGDFM
                     PTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPNIADIKAEAESRSGKWTLSNVKIEY
                     QFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(2226..2420)
                     /locus_tag="HVV70_24415"
                     /pseudo=""
     CDS             complement(2226..2420)
                     /locus_tag="HVV70_24415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2705..3028
                     /locus_tag="HVV70_24420"
     CDS             2705..3028
                     /locus_tag="HVV70_24420"
                     /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="QMQ34455.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          2456..2694
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.083"
                     /coverage="99.0"
                     /evalue="1.3000000000000001e-110"
     Typing          complement(1659..2183)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.774"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          2706..3025
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.18e-62"
ORIGIN
        1 aaccgatcgc cattcacttt catgcatagc tatgcagtga gctgaaagcg atcctgacgc
       61 atttttccgg tttaccccgg ggaaaacatc tctttttgcg gtgtttgcgg cagaatcgcg
      121 ttcagcgcgt tttagcggtg cgcgtaatgc gacgttatgg taaataccta ccttgctcac
      181 ttttagagca tgaggcaaaa aaggtaaaaa cttatttgct taacagcccc tatcactgtg
      241 taaattaact tctgaaaact aaaaaaatgg gggggggata gtatggcgaa tattactaat
      301 tttgatatgt ggttagatga tgttgatggc gatcatgagg aggttatggc tctttatgat
      361 gctgttcaga atgtaagtga tatgggagtc tataagtgcg ttgaaggtaa tgggagggat
      421 acttgggtcg tgagctcgaa tcatcatcac gaagatcttt ttctagaatc agttgtggat
      481 aagggggatt tcctcaagtt gattaaaaaa agactatgtg gcggagaaaa tgttgaatca
      541 tggtatggat ttcaacgaaa tatgtcgaat gatcactcgt aatcgtacag agagttctcc
      601 ttgtgggaac tcttaaaata tgacgttata gtaaatagga tgcgtagggg tttgtggctc
      661 ttatggtgac gagaaggtac ttactaggtg gtgaatatcc ctccgaggaa tttgttcaag
      721 cttctttaga aaaatatttt tttcgtcaag ggtttgatat agatacggat tcttatattg
      781 accttatttg ccgtgataaa gaatctaggg atattgtgtg gcatattgaa gtaaaaggga
      841 aaacatcaca accagggttg gattttcgaa cttgtcttgg acaattagtg cagagaatga
      901 caaaagataa tattaattat gctattgctg ttccaagaat aaaacagtat gaaagattaa
      961 tagaaaaaac gagcattctt gctgttagta aattgaattt acactggata tttgttgagc
     1021 ctgatggcag tgtgacaatt aagaagcctg atagctctat gatgaaaaat gggaatggta
     1081 atggaagaga agtttctctt gtgaatgggg tgtttaaaag atttattccg ggtgatttta
     1141 tgccaacttg ctcatatgga aaagctcctg ttgtatttaa atcatctcgg cgagaaatgt
     1201 gggattggct ggacgatttt gttatttcaa atggggtgat cccaaatatt gctgatatta
     1261 aagcagaggc tgaatcgcgg agtgggaaat ggacgctttc taatgttaaa atagagtatc
     1321 agttttggaa aatatatcac ttatataagg ggcatttttt ctatcaatct gagtagctga
     1381 ctcctttgtt catcacatgc catgatcttc ttgagattca ttcgctcaaa gcgtaatctc
     1441 tttctcggaa aacgaaaaaa ccacctgggg aggtggtttt tcgaaggttc agtaagttgg
     1501 ggaacttctg aaccgtggta acagtcttgt gcgagacatg tcaccaaatc tgtcctttca
     1561 gtgtagccgc agtcaggcca ccacttcaag aactctcgat acatctctcg cacatcctgt
     1621 ctaccagtgg ccgttgtcaa tggcgattag tcgtgtctta ccgggttgga ctcaagacga
     1681 tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc
     1741 ttggagcgaa cgacctacac tgaactgaga taccaacagc gtgagctatg agaaagcgcc
     1801 acgcttcccg aagggagaaa ggcggacagg tatccggtaa gcggcagggt cggaacagga
     1861 gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt
     1921 cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg
     1981 aaaaacgcca ctggcgcggc cttttccggg ttattgttct ttgctcacat gtttcttttg
     2041 gcgttatccc ctgattctgt ggatcaccgc attaccgtct ttgagtgggc tgataccgct
     2101 cgccgcagcc gaacggccga gcgcagcgag tcagtgagcg aggaagcgga aaagtgcctg
     2161 atgtagcatt ttctccttac gcacaggtat accattctgc atcctgtctg gtgccggata
     2221 tactgttata ccccggtgcc attttccgct tcaaagcgtg tctgtatgct gttctggagt
     2281 tcttccgcga gttcgtgcag cttctcacac atggcggcct attcgtcggc atcgagtgcg
     2341 tccagctttt cgagcagtgt caggctctgg ctttttatga atcctgccat gttgagtacg
     2401 gcttgctgct gcttgttcat cttttcgttt tctccgttct gtctgtcatc tgcgttgtgt
     2461 gattatatcg cgtaccactt ttcgactgtt ttaccgccgg tattctgccg tctgactctt
     2521 tgacgggcat ttctgcctga caatactgtc actgctaaaa aactgccgtg cctttatcgg
     2581 taattcgaac ttgctgacag gacaggatgt gtaattgtta taccgcgcat acatgcgcgc
     2641 tattacaatt accctggtca gggcttcgcc ccgacacccc atgtcagata cggaaccatg
     2701 ttttatgaca aaacgaagtg gaagtaatac gcgcaggcgg gctatcagtc gccctgttcg
     2761 tctgacggca gaagaagacc aggaaatcag aaaaagggct gctgaatgcg gcaagaccgt
     2821 ttccggtttt ttacgggcgg cagctctcgg taagaaagtt aactcactga ctgatgaccg
     2881 ggtgctgaaa gaagttatgc gactgggggc gttgcagaaa aaactcttta tcgacggcaa
     2941 gcgtgtcggg gacagggagt atgcggaggt gctgatcgct attacggagt atcaccgggc
     3001 cctgttatcc aggcttatgg cagattagct tcccggagag aaactgtcga aaacagacgg
     3061 tatgaacgcc gtaagccccc a
//
