LOCUS       CP057181                2974 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB34-C04 plasmid pRHB34-C04_4, complete
            sequence.
ACCESSION   CP057181
VERSION     CP057181.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148337
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2974)
  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 2974)
  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                     :: RH03 T3-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 165.58193898008x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:49:39
            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)                     :: 4,916
            CDSs (total)                      :: 4,798
            Genes (coding)                    :: 4,549
            CDSs (with protein)               :: 4,549
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 249
            CDSs (without protein)            :: 249
            Pseudo Genes (ambiguous residues) :: 0 of 249
            Pseudo Genes (frameshifted)       :: 95 of 249
            Pseudo Genes (incomplete)         :: 154 of 249
            Pseudo Genes (internal stop)      :: 40 of 249
            Pseudo Genes (multiple problems)  :: 37 of 249
            ##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..2974
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB34-C04"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB34-C04_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2595..2974,1..55)
                     /locus_tag="HVZ20_24540"
     CDS             join(2595..2974,1..55)
                     /locus_tag="HVZ20_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000739145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QME18867.1"
                     /translation="MKKNDDMLCLVIKLLLSVFIAFIFAFKYKQELLSALSEQVYYQLL
                     VVVTIISGFLANPIGYFIYNIHVYLRRKISKEYNAEYLSEQVKLLSKTDLKNISEKHKE
                     MIESWGGRDPLSEFKIELVSAELERLRKSKNDQATQPTTE"
                     /name="hypothetical protein"
     gene            complement(480..803)
                     /locus_tag="HVZ20_24545"
     CDS             complement(480..803)
                     /locus_tag="HVZ20_24545"
                     /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="QME18864.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            1075..1269
                     /locus_tag="HVZ20_24550"
     CDS             1075..1269
                     /locus_tag="HVZ20_24550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001399823.1"
                     /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="QME18865.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENSTGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2087..2611
                     /locus_tag="HVZ20_24555"
     CDS             2087..2611
                     /locus_tag="HVZ20_24555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001067571.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QME18866.1"
                     /translation="MNPDLLVIFERALEGITSVSVQKKTNDTYTLKSDHLNTYMLLTII
                     SGNNEDDKLKLKLSFVLSLPIDGVNKDILDGIIKAGFSLQENSPCKLIGITETDNELKV
                     ELVIFYTDYASVFSEADREDKYKESDFKLIVLSMLSELYSCSMGINNFISKTLLSALEN
                     IKKGTKDEEKR"
                     /name="hypothetical protein"
     Typing          complement(813..1038)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.75"
                     /coverage="99.0"
                     /evalue="2.28e-73"
     Typing          1313..1832
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.476"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(484..803)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="8.759999999999999e-61"
ORIGIN
        1 agagagactg agaaaatcaa agaacgacca agcgacacaa ccaacaacag aataggcgaa
       61 aaaaatagca cttatgcggc gccacatata aaaatctaca cccaagtaac ttcaagatgc
      121 atgattaaag cccccccccc tcaacaactt ccaccatgcc gtactttggg caccgattcc
      181 tgcaacttga agttaccatc ggtatagtga aaaacataaa actcgatctc tacaattcac
      241 acagcgctac taatgaccca catttaccat aacgtctcat tacgcgcacc gctaaaacgc
      301 gctgaacgcg attctgccgc aaacaccgca aaaagagatg ttttccccgg ggtaaatcgg
      361 aaaaatgcgg caggatcgct ttcagctcac tgcatagcta tgcatgaaag tgaatggcga
      421 tcggtttggt gacttacggc gttcataccg tctgttttcg acagtttccc tccgggaagc
      481 taatctgcca taagcctgga taacagggcc cggtgatact ccgtaatagc tatcagcacc
      541 tccgcatact ctctgtcccc gacacgcttg ccgtcgataa agagtttttt ctgcaacgcc
      601 cccagtcgca tgacttcttt cagcacccgg tcatcagtca gtgaattaac tttcttaccg
      661 agagctgccg cccgtaaaaa accagaaacg gtcttgccac attcagcagc cctttttctg
      721 atttcctggt cttcttctgc cgtcagacga acagggcgac tgatagcccg cctgcgcgta
      781 ttacttccac ttcgttttgt cataaaacat ggctccgtat ctgacatagg gtgtcggggc
      841 gaagccctga ccagggtaat tgtaatagcg tgcatgtatg cgcggtataa caattgcaca
      901 tcctgtcctg tctgcaagtt cgaattacca acaaagcact gctgtttttt ggcagtgaca
      961 gtgttgtctg actgaaatat ccgtaggcag aatgccggcg gtaagacggt cgaaaagtgg
     1021 tgcgcgatat aatcacacga cgcaaatgac agacagaacg gagaaaacag aaagatgaac
     1081 aagcagcagc aaactgtact caacatggcg ggattcataa aaagccagag cctgacactg
     1141 ctcgaaaagc tggacgcact cgatgccgac gaacaggccg ccatgtgtga gaagctgcac
     1201 gaactcgcgg aagaactcca gaacagcata cagacacgct ttgaagcgga aaatagcacc
     1261 ggggcataac ggtgtatccg gcatcagaca ggatgcagaa cggtatacct gtgcgtaagg
     1321 agaaaatgat acataaggcg ctcttccgct tcctcgctca ctgactcgct acgctcggcc
     1381 gttcggctgc ggcgagcggt atcagctcac tcaaaaacgg taatgtggtg atccacagaa
     1441 tcaggggata aagccaaaag gagcatgtga gcaaaaaaca agaaccagga aaaggccgcg
     1501 ccgatggcgt ttttccatag gctccgcccc cctgacaagc atcacaaaaa tcgacgctca
     1561 agtcagaggt ggcgaatccc gacaggacta taaagatacc aggcgtttcc ccctggaagc
     1621 tccctcgtgc gctctcctgt tccgaccatg ccgtttaccg gatacctgtc cgcctttctc
     1681 ccttcaggaa gcgtggcgct ttctcatagc tcacgctgtt ggtatctcgg cccggtgtag
     1741 atcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ctaccacgtt
     1801 gttccggtaa ctatcacctt gattccaacc cgaaacagac acgaaaatcg ccagtggcgg
     1861 tagccattgg taaacaggat gtgcgagaga tgtatcgaga gttcttgaag tggttacctt
     1921 actccggcta cactgaaagg acagatttgg tgacatgtct cgcacaagac tgttacctcg
     1981 gttcaggaac ttgccggttt actgaacctt agaaaaacca ccttgccggg tggttttttc
     2041 ttttccgtag gttaaggcgg caaaacagca acgtcaaggt aaacaaatga atccagacct
     2101 attagtgatt tttgagcgag ctttagaagg cataacatca gtctcggtac aaaaaaaaac
     2161 aaatgacaca tatactttaa aatccgacca tctcaacaca tacatgttgc taacaataat
     2221 aagtggaaat aacgaagatg ataagctgaa attaaagcta tcttttgttt tatccttacc
     2281 aatagatggg gtgaacaaag acatattaga cggcataata aaggctggct tttctttaca
     2341 agaaaactct ccttgcaaac taataggcat aacagaaact gataatgaat tgaaggtaga
     2401 gcttgttata ttttacactg attacgcatc tgtatttagc gaggctgaca gagaagataa
     2461 atataaagaa tcagatttca aactaatagt gttatcaatg ctttcagagc tgtattcttg
     2521 ctcaatggga ataaacaact tcatttcaaa aaccttgctc agcgctcttg agaacatcaa
     2581 aaaaggtaca aaagatgaag aaaaacgatg atatgctatg ccttgtaatt aagctgctct
     2641 taagtgtttt tattgctttc atttttgcat tcaaatacaa acaggagctc ctgtcagctt
     2701 tatctgagca ggtatactat cagttactgg tcgttgtaac cataatttca ggctttttag
     2761 ccaatccaat tggatatttt atttacaata tccatgtata tttgcgcaga aaaatatcca
     2821 aggaatacaa tgctgagtac ttatctgagc aagtaaaatt attgtcaaaa accgacttaa
     2881 aaaacataag cgaaaagcac aaagaaatga ttgagtcttg gggagggcga gatccgctaa
     2941 gcgaattcaa aatagaatta gtgagcgcag aact
//
