LOCUS       CP057308                6507 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C09 plasmid pRHB30-C09_7, complete
            sequence.
ACCESSION   CP057308
VERSION     CP057308.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148293
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6507)
  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 6507)
  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-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132.647008810688x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:59:30
            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)                     :: 5,680
            CDSs (total)                      :: 5,553
            Genes (coding)                    :: 5,179
            CDSs (with protein)               :: 5,179
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 374
            CDSs (without protein)            :: 374
            Pseudo Genes (ambiguous residues) :: 0 of 374
            Pseudo Genes (frameshifted)       :: 134 of 374
            Pseudo Genes (incomplete)         :: 213 of 374
            Pseudo Genes (internal stop)      :: 59 of 374
            Pseudo Genes (multiple problems)  :: 31 of 374
            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..6507
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB30-C09"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C09_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            185..298
                     /locus_tag="HVY76_28290"
     CDS             185..298
                     /locus_tag="HVY76_28290"
                     /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="replication initiation protein"
                     /protein_id="QMF75889.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(533..970)
                     /locus_tag="HVY76_28295"
     CDS             complement(533..970)
                     /locus_tag="HVY76_28295"
                     /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="QMF75890.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     gene            complement(975..2273)
                     /locus_tag="HVY76_28300"
     CDS             complement(975..2273)
                     /locus_tag="HVY76_28300"
                     /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="QMF75891.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESGITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFLSGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            3185..3550
                     /locus_tag="HVY76_28305"
     CDS             3185..3550
                     /locus_tag="HVY76_28305"
                     /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="QMF75892.1"
                     /translation="MARSAKPRKRKPAPQRSKLPRYVVKLHPDDFFDEEDAEVLRFDNF
                     DDAVECCADLGIPFFLDAGNKKLVFWFVRVDDEGYPEIARCTEREFATILAGISAGGMY
                     CPECGTVHWPDGVTPPV"
                     /name="hypothetical protein"
     gene            3550..4737
                     /locus_tag="HVY76_28310"
     CDS             3550..4737
                     /locus_tag="HVY76_28310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013747467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="QMF75894.1"
                     /translation="MLPRFADIFQQGNRWLNWLEKQPEGSVRPVVTESVTKIMACGTTL
                     MGYTQWCCSSPDCCHTKKVCFRCKSRSCPHCGVKAGAQWIQYLLSLVPDCPWQHIVFTL
                     PCQYWSLVFHNRWLLAEMSRIAADVILEICHQTDVEPGIFTVIHTWGRDQQWHPHIHLS
                     TTAGGVTSGHTWKNLHFYARKVMSMWRYRITRLLSRKYPELVIPDELAVEGNSKRDWNR
                     FLDTHYRRGWNVNISRVMDNATHVAVYFGSYLKKPPVPMSRLEHYAGQDEIGLRYNSHR
                     TKREEYLLMSGDEFMERFSWHVADKGFRMVRYYGFLSPVKRRLLEEVVYVITETVRKTA
                     MQIRWRGMYQRLLKVDPLKCILCGSQMRFTGLKRGYRLAELVLMHERLARQQVCG"
                     /name="IS91 family transposase"
     gene            5861..6055
                     /locus_tag="HVY76_28315"
     CDS             5861..6055
                     /locus_tag="HVY76_28315"
                     /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="QMF75893.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(5346..5615)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.706"
                     /coverage="93.0"
                     /evalue="9.77e-93"
     Typing          complement(5727..5825)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(6129..6213)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          7..502
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.28"
                     /coverage="99.0"
                     /evalue="1.36e-133"
ORIGIN
        1 tcagaggtgg cgaaacccga caggacttaa agataccagg cgtttccccc tggtgactcc
       61 ctcgtgcgct ctcctgttcc tgccattcgg tttaccggtg tcactccgct gttatggccg
      121 cgtttgtctc attccacgcc tgacactcag ttccgggtag gcagttcgct ccaagctgga
      181 ctgtatgcac gaaccccccg ttcagtccga ccgctgcgcc ttttccggta actatcaact
      241 tgagtccaac ccggaaagac acgacaaaac gccaatggca gcagccactg gtaactgatt
      301 tagaggagtt agtcttgaag ttatgcgcct gttaaggcta aactgaaaga acagatttgg
      361 ttactgcgct cctcataagc cagttacctt ggttcacaga gcgccaactc ttagaaccgt
      421 cgaaaaaccg cccgccaagg cggttttttc gtttacagag caagagatta cgacgagagc
      481 atcacaatct caagaagatc ttttcttaac atacaataca actgtatctc atctattttt
      541 gactcttcca gaagcgatga tctctatcaa aaaacacgat atagaacaca ttatctctca
      601 gaaatccggc gactcttctt ttctgcccgc caatgttttt tataaccccc caatcctcat
      661 cagaggatat ctcatctggg catctaaaat cgtttacagc tgactcagga aatcgagtgt
      721 agttagtaaa cacaccgtca gaaatcactt tagtgattcc attcgccgtt agataaacca
      781 atttttcaat gagatcaggt aggctaccat catctttcca tgtatttatg gactgcccaa
      841 catcatcgac gttatgaaaa tgcttaaaac taatagatat aaatctatca gtcgttttcg
      901 ctgtgctctt tgaaggtttt gtttcctcat tcctcgaaga gcttcgaatg cttttgcctc
      961 tctttggcat ataatcatcc ctcaggcatt agcttttcaa attcattaag attatcaaat
     1021 aacgggattg catcaaaagc acctgataaa taatcattcc catatgatgg cttcaatgat
     1081 ctttgtttct ctttgtactc aaccaaagaa taaagatggc tactccctga ctttacatcc
     1141 ttgtcaacaa accaaatttg gtctcgtcta aagcaatcag tattcattaa attaacatcc
     1201 tgaactgcag cgattacttg gctaaaccct tcactttgcg catgaaatat cctaaataaa
     1261 aacttagata aaagggtatg gaactttgaa tcgaactcat caaccaataa taagttattg
     1321 ttaatcatgg cgttataaat aggcccaagg agatagacta tctttttggt cccctctgat
     1381 tcaaaatcaa tgggaaccga aatctcccca ttagcagttt ttttcacgac tctaagagaa
     1441 aatacttttt gattttttgc aaaattctga atcgagctga ataaattttt taaattatca
     1501 tcatctgttt ttatgttgcc aaacggaaat tcaggcgcaa cttcatcaag ataaatatca
     1561 ttaatctgaa aggctggtaa tatttttttt agccaagctt taaaatcttc agattcattt
     1621 ataagcttca tggtaattcc agtaaacatt ccttcgttag aaccagaaag aaataccaca
     1681 ttactaaacc aattcacaac acgctttgag tgctccccat taaatccagc aacaacagaa
     1741 acaaagggaa catcttctct tgtcttctga atgaccccat cctttataaa aagatttgac
     1801 tcgctaaatg ctgctttatt tatttcaata agttgaccat ctcgctcaaa gagaatagtc
     1861 tcccttgttt ttggcgtgta gtacaaccac tcttctttta tcttcccttg aaataaagat
     1921 aatccgtatc tgtatttaat cccatccgca ataaaagtca tttccatttc agatggttta
     1981 gtaggccccg cctcatcaag taaaaaaggg actacattct tcgtaatgcc actttcgata
     2041 gcttgcacag aatgcaggac aatatctttc attaaagata ttgtcttcat gagattagat
     2101 tttccgctag cgttagctcc gaaaatcaaa gcagacttca gtatccgctc atcccttact
     2161 gacactacat tagccaagtt tatatcgtct ttcgatgacg acaccgccaa catgctcata
     2221 ttttgagctt ccatgaagga aaatgcgttt gaaagactaa agttaaccat cataagaaca
     2281 cccctaacaa cacccttaaa ctcaaaaatt gcacaatatt gacaaaattc tagattaaga
     2341 atagcataac cccgtactaa aacaacaaaa gggtccaata gacagcacat tatgagtaga
     2401 taagttaacg accagcttaa aaagaggtgt atatgaagtt ttttctatac caaatggtcc
     2461 catttgcctc agtgattagc tcagcagtgc tggcttttca ctcggtatct gggtggggat
     2521 ggttcctttt tgtcgcgttt atgctcagtg gcgctgacac tgtaaaaaaa tacgtaggga
     2581 gtgaaacatg aatgaggaga agcaaaaatt gttgaagtaa gtgggttagc ctgtaccacc
     2641 agaactaacc cgtaacaaac catacgcaaa tgcggcgctt gagtaccacc tcaagtgctt
     2701 tgataaagcc agccacaaga tctgttggtt gctacagtac aattttgata gcaaaaatca
     2761 acattcatgt ggcgaaaata ggaaatgcaa catgcagacg gacgagcctc aggcatacat
     2821 ttttcgccct tacataacgg taaagggcaa acggataacc cgtcctaacg ggggaatgtt
     2881 taagatccca attaatcggg aaaagaaaaa acaataacca ccgaagcatg caagcttcgg
     2941 tccctaactt agtttatgta aggaaagcaa catggccttt tatgtagata gcacagcgaa
     3001 atttttaaca aaaacaaccg agcctgaagg gagtgtatgg cggtattact ataagccggg
     3061 aaatacttgt ccggcttccg gcatttaccg ctgcaccgag taggcagcct ggcggctgcg
     3121 gcttgtcatg gtctggaatt accgttataa aaaaagataa tgtcattgtc tttcaggtag
     3181 ttatatggcc cgttcagcta aaccccgtaa acgcaaaccc gcaccacaaa gaagcaaact
     3241 tccccgctat gttgtgaaac ttcatccgga tgattttttt gacgaagaag acgctgaagt
     3301 tctgcgcttt gataattttg acgatgccgt tgagtgctgc gctgacctgg gtattccgtt
     3361 ctttctggat gcaggaaaca aaaagctggt cttctggttt gttcgtgtcg atgacgaagg
     3421 gtatccggaa atagcccgct gtacggagcg ggagtttgcg accattcttg ccggtatcag
     3481 tgccggtggt atgtactgcc cggaatgcgg cacagttcac tggccggatg gcgttacccc
     3541 acccgtctga tgcttccccg ttttgccgat atttttcagc agggtaaccg ctggcttaac
     3601 tggctggaga aacagccgga aggttcagtg cgtccggtgg tgactgagtc agtgacaaaa
     3661 atcatggcat gcgggaccac gctgatgggc tacacgcaat ggtgctgttc gtcaccggac
     3721 tgttgccaca ccaaaaaggt ctgcttccgg tgtaaaagcc gctcctgtcc gcactgcggg
     3781 gtgaaggctg gcgcacagtg gatacagtat ctgctgagcc tggtccccga ctgcccgtgg
     3841 cagcatattg tgttcacact tccctgccag tactggtccc tggtgttcca caaccggtgg
     3901 ttactggcag agatgagccg cattgcagcg gatgtgatac tggaaatctg ccatcagaca
     3961 gatgtggagc cggggatatt cacggtgatc cacacatggg ggcgtgacca gcagtggcat
     4021 ccgcatatcc atttatcgac aactgccggt ggtgtgacgt cgggccacac ctggaaaaat
     4081 cttcattttt acgcgcgtaa ggtgatgagc atgtggcgtt accggataac gcggctactg
     4141 tcccggaaat acccggagct ggtaataccg gatgaactgg cagtggaagg aaacagcaaa
     4201 cgggactgga atcgcttcct ggacacgcat taccgccgcg gctggaatgt caacatatcc
     4261 agggtgatgg ataacgccac acatgtggcg gtgtacttcg gctcttacct gaaaaagcca
     4321 ccggtgccga tgagtcggct ggagcattat gccggtcagg atgaaatcgg tctgcgttac
     4381 aacagtcacc gtacaaaacg ggaagaatac ctgttgatga gtggagatga gttcatggaa
     4441 aggttctcct ggcatgtagc agataagggg ttccgtatgg tgaggtacta cggtttcctg
     4501 agtccggtga agcgccgctt actggaagaa gttgtgtacg tcataacgga gacggtgaga
     4561 aaaacggcga tgcaaatcag gtggagaggg atgtatcaga ggttactgaa ggttgacccg
     4621 ctgaagtgca ttctgtgcgg aagtcagatg cgttttacgg ggctgaagcg gggttaccga
     4681 ctggcagagc tggtcctgat gcatgagcga ctggcacgac agcaggtgtg cggctgagag
     4741 ccgcagaggg gaagttgcgt ccattttacc ggaaacggag caaaaaaccg ccattcatac
     4801 cctgtatcaa tcagtgtcat cctgtttaat agtcgtttcc gctcatatgg tgcacaaggg
     4861 gtgttgaaga aacatccgtt ttgtggtgct tttttagtct tttggggatt taaattccta
     4921 tcgatgaact gtggtgatga agtgacgtgc aataaagatg atcctttgcc accgcaaaat
     4981 cataggcagc ataatgtccc aggtgacatc cgatgggaat tggtagtgat gacaaagacg
     5041 aagtaactta ctaggccgtc tacggacggc ttttttatac ctgccaatca gctggattta
     5101 ccataacatc cgattgcgcg caccgctaaa acgcgctgaa cgcgattctg ccgcaaacac
     5161 cgcaaaaaga gatgttttcc ccggggtaaa ccggaaaaat gcgtcaggct cgctttcagc
     5221 tcactgcata gctatgcatg aaagtgaatg acgatcggtt tgggcgcata cagtgcccat
     5281 gagacacatt ttcggacatt ttcagttcgt gaatccctga ctcattgcta catatctgaa
     5341 cagacacccc tggcagcgcc cccaggggcg tcctgtaaaa aaacacaccg cgcagctagc
     5401 agccccccct aatataagat gatgtttttt atgaaaatag tcagtaccac ccctaaaaag
     5461 cggtgtcggc gcggtgttgt agctgcgcca acaccgcttt tttaaatatc acaaagagag
     5521 caagaagaac taatttgtca taactctcta tttataaaga aaaatcagca aaaaattgtt
     5581 tttgcgtggg gtgtgggcat ttcgggcatg agaacagact cgcgtttttc cggagtatca
     5641 gcggaattat tgattaagaa acactcgacg cagagcgaaa ttttatgcaa cagcggctgc
     5701 actgcacagg gattatttat cagttgatat gctgtgccat gatacgtcct aaagaaacag
     5761 gacaggatgt gcaattgtaa taccgtcgcc cgcaacgtct tacaattacc acctgctcag
     5821 ggtccccccg acacccggaa ctgacggaga acaacggaag gtgaacaaac aacaacaaac
     5881 tgcgctgaat atggcgcgat ttatcaaaag ccagagcctg acactgcttg aaaaactgga
     5941 tgctctggat gccgacgaac aggcggccat gtgcgaacga ctgcacgaac tcgcagaaga
     6001 actccagaac agcatccaga ttcgctttga ggccgaaagt gaaacaggaa cataacgaag
     6061 ctgacggagg cggtcacggc tttcccgtgg gcgttttcgt cagcagacaa gcccgtcagg
     6121 gcgcgtcagg gggtttcggg gcgaagccct gaaccagtca cgtagcgata gcggagtgta
     6181 tactggctta accatgcggc atcagtgcgg attgtatgaa aagtacgcca tgccgggtgt
     6241 gaaatgccgc acagatgcgt aaggagaaaa tgcatgtcca ggcgcttttc cgcttcctcg
     6301 ctcactgact cgctacgctc ggtcgttcga ctgcggcgag cggtactgac tcacacaaaa
     6361 acggtaacac agttatccac agaatcaggg gataaggccg gaaagaacat gtgagcaaaa
     6421 gaccaggaac aggaggaagg ccgcgccgct ggcgtttttc cataggctcc gcccccctga
     6481 cgagcatcac aaaaaccgac gctcaag
//
