LOCUS       CP057009                3071 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C01 plasmid pRHB41-C01_3, complete
            sequence.
ACCESSION   CP057009
VERSION     CP057009.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148420
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3071)
  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 3071)
  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                     :: RH01 T3-C01
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 179.118669934113x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 04:23:46
            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)                     :: 4,669
            CDSs (total)                      :: 4,547
            Genes (coding)                    :: 4,373
            CDSs (with protein)               :: 4,373
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 174
            CDSs (without protein)            :: 174
            Pseudo Genes (ambiguous residues) :: 0 of 174
            Pseudo Genes (frameshifted)       :: 73 of 174
            Pseudo Genes (incomplete)         :: 87 of 174
            Pseudo Genes (internal stop)      :: 33 of 174
            Pseudo Genes (multiple problems)  :: 18 of 174
            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..3071
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C01"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C01_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2582..3071,1..155)
                     /locus_tag="HV003_23340"
     CDS             join(2582..3071,1..155)
                     /locus_tag="HV003_23340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="QMB39167.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            2333..2488
                     /gene="pspF"
                     /locus_tag="HV003_23345"
                     /pseudo=""
     CDS             2333..2488
                     /gene="pspF"
                     /locus_tag="HV003_23345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /note="transcriptional activator for pspABCE which are
                     induced in response to phage proteins, membrane altering
                     stresses, and impaired proton expor; incomplete; partial on
                     complete genome; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="phage shock protein operon transcriptional
                     activator"
                     /name="pspF"
     ARG             2547..3070
                     /name="QnrB10"
                     /gene="QnrB10"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.43"
                     /coverage="77.43"
     ARG             4..155
                     /name="QnrB19"
                     /gene="QnrB19"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="23.36"
     Typing          complement(1431..1604)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1583..2074
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 tcgactggcg agcagcaaac ttcacacatt gcgatctgac caattcggag ttaggtgact
       61 tagatattcg gggtgttgat ttacaaggcg ttaagttaga cagctaccag gcatcgttgc
      121 tcatggagcg gcttggcatc gctgtgattg gttagttcag cgtttacacc gggagatgcg
      181 tttgacgatt tacttttaac cagtacgact cctggcaagc attgtgaaac gttttctcca
      241 gtggacgaat atcctgacct accgcatcaa cgacatgcca tctaatgctg cattctggac
      301 aggaatttga tgaatatcta accaattcat tttcgcgaga acaacgaata accactcccg
      361 aatcatgaag ccatgtctta acgaaaatat ggctaactca tagcaaaaaa aaagccccct
      421 aagggctttt ttttgtacct gacggtcaga ccgattaaac ataacatccc ttgcgtgcac
      481 cgcctgagag gctctgaggg cgtttctgac gggaaaccgg taaaacaggc aacaaaccac
      541 ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg catgcatgag tatgcgcgca
      601 agtgcatagc gcggaaattc acaccattca gccaggggaa gtcctgtttc cggcgttctt
      661 cccatccgaa aacggtgaac ggggacgcaa tttattgcgt ggccgtgaag cgttgccggc
      721 gcagccggaa aacccgctgt cagcacgttc aggaaggggg tgatgtacaa atggcacaga
      781 ggatgaaagt gacgtatgag ctgaaggaat gatgtaaaag tgatgtataa atgatgtaaa
      841 agtgatgcaa aagcgttgta aaagtgatgt acaggccgaa ggagtgttgt aaaagtgttg
      901 taaaagtgat gtatgaactg aaggagcgat gtaattctgt agtcaggaag aataacccgt
      961 tcatgcaggc atgaacgata cagtgaggaa cgcttttttt tgtcacgatc tccccttaac
     1021 ctgcgtaaat cacccgccat ggttgattat ttttcaacct caaaatggtc atacacctaa
     1081 cgcagccgcg attttcatcg caactgcatg aattaaaaga aaaaaaagta atgtttcgtt
     1141 ttcacgagta atacccaggt attaaaaacc cactgtaatt acatgaaaat aaagaaataa
     1201 aaggtaatac cggcgtatta ccacgtacgc gggcaagcga aaaagctata acgcttcccg
     1261 gccgacaggc ggcccagaat ccacaggggc atgcaggatc tcttcagtaa ccttcgccat
     1321 taaatcaaaa aggtcatatt cgccgggaag ctgcgtatca gtcgaacccc gttgttcatc
     1381 atattcagat ggcatggggt gatatccagt agcagagagg ttgttagcgg gtttcggggc
     1441 gcagccctga accagtcacg tagcgctagc ggagtgtata ctggctgact atgttggcac
     1501 ggatgtggaa atcagtgaag tgcttcatgt agcaggagaa aaaaggcggc accagcgcgt
     1561 cagcaggata tgtagtacag gatatattcc gcttcctcgc tcactgactc gctgcgctcg
     1621 gtcgttcggc tgcggcgagc ggtgccggct tacaggcggg gcggaaattt cctgggagat
     1681 accaggaagg agcttaacag ggaagagata aggccgcggc gaagccgttt ttccataggc
     1741 tccgcccccc tgacaaacat catgaaatct gacgctcaaa tcagtggtgg cgaaacccga
     1801 tgcggcttaa agataccagg cgtttccccc tggtggctcc ctcgtgctcc cccgcattcc
     1861 tgcctttcgg tttaccggtg tcattccgct gttatggccg cgtttatctc attccacgcc
     1921 tgacactcag ttccgcgaag gcagttcgct cctggatgga ctgtatgcac gaaccccccg
     1981 ttcagtccga ctgctgcgcc ttatccggta actatcatct tgagtccaac ccggaaagac
     2041 acgacttatc gccactggca gcagccactg gtaactgatt tagaggagtt agtcttgaag
     2101 ttatgcgcct gttaaggcta aactgaaaga acagatttgg ttactgcgct cctcgtaagc
     2161 cagttaccac ggttcaaaga gttgctgctc tgagaacctt cgaaaaaccg ccttgcaggg
     2221 cggttttttc gtttacagag caagagatta cgacgccaca gaaaggatct caagaagatc
     2281 cttcaccgta atggaaatct atccaatccg agcacatagg atacacatcg ttataacgct
     2341 ggatctgcgt gaattccagc agcagcaaga gaaagacttt ctacaaacca gcttacagca
     2401 ggctaaattt aaccagaaaa aagccgctga attactgggt ctgacttatc atcagctacg
     2461 tgccttgctg aagaaacacc agatctaata cgcatttgca ggtgtcatac tggcgggttt
     2521 gacgcataac gtcataaggt ttaccatggc gtcattactg tataaaaaca caggcataga
     2581 tatgactctg gcattagttg gcgaaaaaat tgacagaaat cgcttcaccg gtgagaaagt
     2641 tgaaaatagt acatttttta actgcgattt ttcaggtgcc gacctgagcg gcactgaatt
     2701 tatcggctgc cagttctatg atcgcgaaag tcagaaaggg tgcaatttta gtcgcgcaat
     2761 gctgaaagat gccattttca aaagctgtga tttatcaatg gcagatttcc gcaacgtcag
     2821 tgccttgggc attgaaattc gccactgccg cgcacaaggc gcagatttcc gcggtgcaag
     2881 ctttatgaat atgatcacca cgcgcacctg gttttgcagc gcatatatca ctaatactaa
     2941 tctaagctac gccaattttt cgaaagtcgt gttggaaaag tgtgagctgt gggaaaaccg
     3001 ctggatgggg actcaggtac tgggtgcgac gttcagtggt tcagatctct ccggcggcga
     3061 gttttcgact t
//
