LOCUS       CP057082                4678 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB38-C24 plasmid pRHB38-C24_8, complete
            sequence.
ACCESSION   CP057082
VERSION     CP057082.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148394
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4678)
  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 4678)
  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                     :: RH04 T3-C24
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140.926036525725x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 05:31:07
            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)                     :: 5,830
            CDSs (total)                      :: 5,691
            Genes (coding)                    :: 5,293
            CDSs (with protein)               :: 5,293
            Genes (RNA)                       :: 139
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 398
            CDSs (without protein)            :: 398
            Pseudo Genes (ambiguous residues) :: 0 of 398
            Pseudo Genes (frameshifted)       :: 138 of 398
            Pseudo Genes (incomplete)         :: 233 of 398
            Pseudo Genes (internal stop)      :: 59 of 398
            Pseudo Genes (multiple problems)  :: 32 of 398
            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..4678
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB38-C24"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB38-C24_8"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4257..4678,1..877))
                     /locus_tag="HVZ77_29110"
     CDS             complement(join(4257..4678,1..877))
                     /locus_tag="HVZ77_29110"
                     /inference="COORDINATES: protein motif:HMM:NF024700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="QMC48076.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESGITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFLSGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            2636..2830
                     /locus_tag="HVZ77_29115"
     CDS             2636..2830
                     /locus_tag="HVZ77_29115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="QMC48073.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3467..3580
                     /locus_tag="HVZ77_29120"
     CDS             3467..3580
                     /locus_tag="HVZ77_29120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMC48074.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(3815..4252)
                     /locus_tag="HVZ77_29125"
     CDS             complement(3815..4252)
                     /locus_tag="HVZ77_29125"
                     /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="QMC48075.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     Typing          complement(2121..2390)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.706"
                     /coverage="93.0"
                     /evalue="9.77e-93"
     Typing          complement(2502..2600)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2904..2988)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          2999..3536
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.993"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ccgaaatctc cccattagca gtttttttca cgactctaag agaaaatact ttttgatttt
       61 ttgcaaaatt ctgaatcgag ctgaataaat tttttaaatt atcatcatct gtttttatgt
      121 tgccaaacgg aaattcaggc gcaacttcat caagataaat atcattaatc tgaaaggctg
      181 gtaatatttt ttttagccaa gctttaaaat cttcagattc atttataagc ttcatggtaa
      241 ttccagtaaa cattccttcg ttagaaccag aaagaaatac cacattacta aaccaattca
      301 caacacgctt tgagtgctcc ccattaaatc cagcaacaac agaaacaaag ggaacatctt
      361 ctcttgtctt ctgaatgacc ccatccttta taaaaagatt tgactcgcta aatgctgctt
      421 tatttatttc aataagttga ccatctcgct caaagagaat agtctccctt gtttttggcg
      481 tgtagtacaa ccactcttct tttatcttcc cttgaaataa agataatccg tatctgtatt
      541 taatcccatc cgcaataaaa gtcatttcca tttcagatgg tttagtaggc cccgcctcat
      601 caagtaaaaa agggactaca ttcttcgtaa tgccactttc gatagcttgc acagaatgca
      661 ggacaatatc tttcattaaa gatattgtct tcatgagatt agattttccg ctagcgttag
      721 ctccgaaaat caaagcagac ttcagtatcc gctcatccct tactgacact acattagcca
      781 agtttatatc gtctttcgat gacgacaccg ccaacatgct catattttga gcttccatga
      841 aggaaaatgc gtttgaaaga ctaaagttaa ccatcataag aacaccccta acaacaccct
      901 taaactcaaa aattgcacaa tattgacaaa attctagatt aagaatagca taaccccgta
      961 ctaaaacaac aaaagggtcc aatagacagc acattatgag tagataagtt aacgaccagc
     1021 ttaaaaagag gtgtatatga agttttttct ataccaaatg gtcccatttg cctcagtgat
     1081 tagctcagca gtgctggctt ttcactcggt atctgggtgg ggatggttcc tttttgtcgc
     1141 gtttatgctc agtggcgctg acactgtaaa aaaatacgta gggagtgaaa catgaatgag
     1201 gagaagcaaa aattgttgaa gtaagtgggt tagcctgtac caccagaact aacccgtaac
     1261 aaaccatacg caaatgcggc gcttgagtac cacctcaagt gctttgataa agccagccac
     1321 aagatctgtt ggttgctaca gtacaatttt gatagcaaaa atcaacattc atgtggcgaa
     1381 aataggaaat gcaacatgca gacggacgag cctcaggcat acatttttcg cccttacata
     1441 acggtaaagg gcaaacggat aacccgtcct aacgggggaa tgtttaagat cccaattaat
     1501 cgggaaaaga aaaaacaata accaccgaag catgcaagct tcggtcccta acttagttta
     1561 tgtaaggaaa gcaacatggc cttttatgta gatagcacag cgaaattttt aacaaaaaca
     1621 accgagcctg aagggagtgt atggcggtat tactataagc cgggaaatac ttgtccggct
     1681 tccggcattt accgctgcac gaactgtggt gatgaagtga cgtgcaataa agatgatcct
     1741 ttgccaccgc aaaatcatag gcagcataat gtcccaggtg acatccgatg ggaattggta
     1801 gtgatgacaa agacgaagta acttactagg ccgtctacgg acggcttttt tatacctgcc
     1861 aatcagctgg atttaccata acatccgatt gcgcgcaccg ctaaaacgcg ctgaacgcga
     1921 ttctgccgca aacaccgcaa aaagagatgt tttccccggg gtaaaccgga aaaatgcgtc
     1981 aggctcgctt tcagctcact gcatagctat gcatgaaagt gaatgacgat cggtttgggc
     2041 gcatacagtg cccatgagac acattttcgg acattttcag ttcgtgaatc cctgactcat
     2101 tgctacatat ctgaacagac acccctggca gcgcccccag gggcgtcctg taaaaaaaca
     2161 caccgcgcag ctagcagccc cccctaatat aagatgatgt tttttatgaa aatagtcagt
     2221 accaccccta aaaagcggtg tcggcgcggt gttgtagctg cgccaacacc gcttttttaa
     2281 atatcacaaa gagagcaaga agaactaatt tgtcataact ctctatttat aaagaaaaat
     2341 cagcaaaaaa ttgtttttgc gtggggtgtg ggcatttcgg gcatgagaac agactcgcgt
     2401 ttttccggag tatcagcgga attattgatt aagaaacact cgacgcagag cgaaatttta
     2461 tgcaacagcg gctgcactgc acagggatta tttatcagtt gatatgctgt gccatgatac
     2521 gtcctaaaga aacaggacag gatgtgcaat tgtaataccg tcgcccgcaa cgtcttacaa
     2581 ttaccacctg ctcagggtcc ccccgacacc cggaactgac ggagaacaac ggaaggtgaa
     2641 caaacaacaa caaactgcgc tgaatatggc gcgatttatc aaaagccaga gcctgacact
     2701 gcttgaaaaa ctggatgctc tggatgccga cgaacaggcg gccatgtgcg aacgactgca
     2761 cgaactcgca gaagaactcc agaacagcat ccagattcgc tttgaggccg aaagtgaaac
     2821 aggaacataa cgaagctgac ggaggcggtc acggctttcc cgtgggcgtt ttcgtcagca
     2881 gacaagcccg tcagggcgcg tcagggggtt tcggggcgaa gccctgaacc agtcacgtag
     2941 cgatagcgga gtgtatactg gcttaaccat gcggcatcag tgcggattgt atgaaaagta
     3001 cgccatgccg ggtgtgaaat gccgcacaga tgcgtaagga gaaaatgcat gtccaggcgc
     3061 ttttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcgactgcg gcgagcggta
     3121 ctgactcaca caaaaacggt aacacagtta tccacagaat caggggataa ggccggaaag
     3181 aacatgtgag caaaagacca ggaacaggag gaaggccgcg ccgctggcgt ttttccatag
     3241 gctccgcccc cctgacgagc atcacaaaaa ccgacgctca agtcagaggt ggcgaaaccc
     3301 gacaggactt aaagatacca ggcgtttccc cctggtgact ccctcgtgcg ctctcctgtt
     3361 cctgccattc ggtttaccgg tgtcactccg ctgttatggc cgcgtttgtc tcattccacg
     3421 cctgacactc agttccgggt aggcagttcg ctccaagctg gactgtatgc acgaaccccc
     3481 cgttcagtcc gaccgctgcg ccttttccgg taactatcaa cttgagtcca acccggaaag
     3541 acacgacaaa acgccaatgg cagcagccac tggtaactga tttagaggag ttagtcttga
     3601 agttatgcgc ctgttaaggc taaactgaaa gaacagattt ggttactgcg ctcctcataa
     3661 gccagttacc ttggttcaca gagcgccaac tcttagaacc gtcgaaaaac cgcccgccaa
     3721 ggcggttttt tcgtttacag agcaagagat tacgacgaga gcatcacaat ctcaagaaga
     3781 tcttttctta acatacaata caactgtatc tcatctattt ttgactcttc cagaagcgat
     3841 gatctctatc aaaaaacacg atatagaaca cattatctct cagaaatccg gcgactcttc
     3901 ttttctgccc gccaatgttt tttataaccc cccaatcctc atcagaggat atctcatctg
     3961 ggcatctaaa atcgtttaca gctgactcag gaaatcgagt gtagttagta aacacaccgt
     4021 cagaaatcac tttagtgatt ccattcgccg ttagataaac caatttttca atgagatcag
     4081 gtaggctacc atcatctttc catgtattta tggactgccc aacatcatcg acgttatgaa
     4141 aatgcttaaa actaatagat ataaatctat cagtcgtttt cgctgtgctc tttgaaggtt
     4201 ttgtttcctc attcctcgaa gagcttcgaa tgcttttgcc tctctttggc atataatcat
     4261 ccctcaggca ttagcttttc aaattcatta agattatcaa ataacgggat tgcatcaaaa
     4321 gcacctgata aataatcatt cccatatgat ggcttcaatg atctttgttt ctctttgtac
     4381 tcaaccaaag aataaagatg gctactccct gactttacat ccttgtcaac aaaccaaatt
     4441 tggtctcgtc taaagcaatc agtattcatt aaattaacat cctgaactgc agcgattact
     4501 tggctaaacc cttcactttg cgcatgaaat atcctaaata aaaacttaga taaaagggta
     4561 tggaactttg aatcgaactc atcaaccaat aataagttat tgttaatcat ggcgttataa
     4621 ataggcccaa ggagatagac tatctttttg gtcccctctg attcaaaatc aatgggaa
//
