LOCUS       CP057286                3126 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C17 plasmid pRHB30-C17_6, complete
            sequence.
ACCESSION   CP057286
VERSION     CP057286.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148296
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-C17
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 142.37324793805x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:16:45
            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)                     :: 5,196
            CDSs (total)                      :: 5,072
            Genes (coding)                    :: 4,832
            CDSs (with protein)               :: 4,832
            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)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 71 of 240
            Pseudo Genes (incomplete)         :: 154 of 240
            Pseudo Genes (internal stop)      :: 35 of 240
            Pseudo Genes (multiple problems)  :: 19 of 240
            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-C17"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C17_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            396..1148
                     /locus_tag="HVY79_25965"
     CDS             396..1148
                     /locus_tag="HVY79_25965"
                     /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="QMF60702.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVAG"
                     /name="hypothetical protein"
     gene            complement(1173..1316)
                     /locus_tag="HVY79_25970"
     CDS             complement(1173..1316)
                     /locus_tag="HVY79_25970"
                     /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="QMF60703.1"
                     /translation="MNTKVLFVKKALKSITCATLSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     gene            complement(2261..2455)
                     /locus_tag="HVY79_25975"
     CDS             complement(2261..2455)
                     /locus_tag="HVY79_25975"
                     /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="QMF60704.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQRRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2740..3063
                     /locus_tag="HVY79_25980"
     CDS             2740..3063
                     /locus_tag="HVY79_25980"
                     /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="QMF60705.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          2493..2731
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.417"
                     /coverage="99.0"
                     /evalue="6.069999999999999e-104"
     Typing          complement(1720..2226)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.415"
                     /coverage="95.0"
                     /evalue="8.27e-156"
     Typing          2741..3060
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.93e-62"
ORIGIN
        1 cattcacttt catgcatagc tatgcagtga gctgaaaacg atcctgacgc atttttccag
       61 ttttcactgg gtaaaacatc tctttttgcg gtgtttgcgg cagaatcgcg ttcagcgcgt
      121 tttagcggtg cgcgtaaggg gagttatggt aaattggcag caaagtattt tctgatgtta
      181 tggattgtga agagtattca atccttatta tgaaacaata actataactg gttgtttcat
      241 atagataaat ataacaaaaa agcccactct gtagtgggct tttttgttat attttacgct
      301 ctagaggtac acagaaaaac ggtagttcgc ctgctcctcg aatgttgtaa tggtagtctg
      361 aaaaatattc atagtaaaga gataagtgag ttttcatgga tacaacaagt ttaattagct
      421 caatttctgt accaagatta tctttctatg aaacatttct tgggtgcgct actgatcaag
      481 aaaaggttgg ggcatacgtt gcctaccaag atctgtctgg cgattttttt tgtcttgtcc
      541 agatgattga ggttgctctg cgtaatgcga taaacaatac aatcaaagct aatcatgggc
      601 ctgcttggta cgactctata cctcaaacaa agaaatctca ggatcttgtt ttaaatgcga
      661 aacaaaaagc actagatgag tgtggcgtaa ggtatacgga tgatgatgtt atttgccgtc
      721 taacctttgg cttttgggtt tatatgttag atgccccata tagggatacg caaaggccgt
      781 gctacatctg gactccagag aacaaggcaa aaacatttcc tcatgcgaag aatcctttgg
      841 gtggggggga tatgaaggtt aaagcgctgt ttgacgagtt tcataaagtt cttttgttta
      901 ggaatcgact ttttcaccat gagcctattt ggaaaaaaca ccactgcaag tcgcatagtc
      961 aagccataaa taatatgttg aaagagttca attttttaat gaatgccttg agtatcgtct
     1021 ctaacgagaa aaaggaactt attgagttta ttgggcacga taggcgcttt tatgaacgct
     1081 gcacgataga gtatgttatg gggattatag ggaggattaa gtgcagggag cttaaggtag
     1141 ccggttgact tttaagggaa aatgtgatac aatcaaaagc tcttaccggc tttaagtcgc
     1201 gcagccgaaa ggctacgtaa ctctgttact gcgcgactta aagccggtaa gagcgaaaga
     1261 gttgcgcaag taattgattt caaagctttt ttcacaaaaa gaactttagt attcattttc
     1321 ataatcctct atttcttatg ccgttctaat ggcagcgttg actttttatt ccatctattt
     1381 gaatggttaa ttataccata tctaacatca aatcttaagg ataaatagct gattcacatc
     1441 agtttttcca ttaattcacg aagttttata atttaattac ggatttcctt gagttcatat
     1501 cgcgcccatc gtaatcttaa aaacgaaaaa accacccggc aaggtggttt ttcgaaggtt
     1561 cagcaaccgg caagtttctg aaccgcggta actggcttaa gaggagcgca gtcaccaaaa
     1621 cttgttattc cagtttagcc ttaactggca cgtaacttca agactaactc ctctaaatca
     1681 gttaccagtg gctgctgcca atggcgataa gtcgtgcctt tccgggttgg actcaagacg
     1741 atagttaccg gataaggcgc agtagtcgga ctgaacgggg ggttcgtgca tacagtccag
     1801 cttggagcga actgcctacc cggaactgag tgtcaggcgt ggaatgagac aaacgcggcc
     1861 ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc
     1921 caccaggggg aaacgcctgg tatctttaag tcctgtcggg tttcgccacc tctgacttga
     1981 gcgtcggttt ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg cctcctgcgt
     2041 gctcttcttc tgggtctttg tcttttgctc acatgttctt tccggcttta tcccctgatt
     2101 ctgtggataa ccgcattacc gcctttgagt gagctgacac cgctcgccgc agtcgaacga
     2161 ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg ccttatgtga cattttctcc
     2221 ttacgctcct ctatgccgtt ctgcatcctg tccggatgcg ttatatcccg gtgcgatttt
     2281 ccgcttcaaa gcgtctctgt atgctgttct gaagttcttc cgcgagttcg tgcagcttct
     2341 cacacatggc ggcctgttcg tcagcatcaa gtgcgtccag tttttcgagc agcgtcaggc
     2401 tctggctttt tatgaatcct gccatgttaa gtacggtttg ctgctgcttg ttcatctttc
     2461 tgttttctcc gttctgtctg tcatctgcgt cgtgtgatta tatcgcgtac cacttttcgg
     2521 cagttttgcc gccggtattc tgccgtctga cgctttaacg ggtatttctg tcaggcaaca
     2581 ctgtcactgc caaaaaactg ccgtgccttt gtcggtaatt cgaacttgct gacaggacag
     2641 gatgtgcaat tgttataccg cgcatgcatg cacgctatta caattaccct ggtcagggct
     2701 ttgccccgac accccatgtc agatacggag ccatgtttta tgacaaaacg aagtggaagt
     2761 aatacgcgca ggcgggctat cagtcgccct gttcgtctga cggcagaaga agaccaggaa
     2821 atcagaaaaa gggctgctga atgcggcaag accgtttccg gttttttacg ggcggcagct
     2881 ctcggtaaga aagttaactc actgactgat gatcgggtac tgaaagaagt tatgagactg
     2941 ggggcgttac agaaaaaact ctttatcgac ggcaagcgtg tcggggacag agagtatgcg
     3001 gaggtgctga tcgctattac ggagtatcac cgggccctgt tatccaggct tatggcagat
     3061 tagcttcccg gagagaaact gtcgaaaaca gacggtatga acgccgtaag cccccaaacc
     3121 gatcgc
//
