LOCUS       CP057679                6760 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB18-C09 plasmid pRHB18-C09_3, complete
            sequence.
ACCESSION   CP057679
VERSION     CP057679.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148154
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6760)
  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 6760)
  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                     :: RH13 T2-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 72.4714844609595x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 10:07:55
            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)                     :: 4,799
            CDSs (total)                      :: 4,682
            Genes (coding)                    :: 4,596
            CDSs (with protein)               :: 4,596
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 86
            CDSs (without protein)            :: 86
            Pseudo Genes (ambiguous residues) :: 0 of 86
            Pseudo Genes (frameshifted)       :: 46 of 86
            Pseudo Genes (incomplete)         :: 39 of 86
            Pseudo Genes (internal stop)      :: 20 of 86
            Pseudo Genes (multiple problems)  :: 18 of 86
            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..6760
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB18-C09"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB18-C09_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(6560..6760,1..2436)
                     /locus_tag="HVX37_23980"
     CDS             join(6560..6760,1..2436)
                     /locus_tag="HVX37_23980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="QML45752.1"
                     /translation="MAKKPKSAGREKLLFNKLKQFDEPGLFHDNYQTPDYIQANLKDIL
                     RPYQHSALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKEFGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSHELEIDGEKITIAPVDIFPSVPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILDLRPDNRLFEFTATIDLANKDIGQKYRDKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESIRRHLANKKLQLSSDTSIWHKVIQRYADSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTVEHARLKEDFKKSAVYQAGKLYFNEVEEIERSSRNWETYSLETRFEIQYQI
                     ACEESLDNLTGTKGGIIKPEPLVLDERFYRKAMQRISFYALDNLKRFFPKLTGIREFIR
                     SDAYLGKLKITVSVPQSLDFTTVPAKDKLHLLENVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVAINQKITAAPTIGKKWYVYDNAILNQLEHRLIKMLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(3616..3810)
                     /locus_tag="HVX37_23985"
     CDS             complement(3616..3810)
                     /locus_tag="HVX37_23985"
                     /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="QML45753.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4690..6555
                     /locus_tag="HVX37_23990"
     CDS             4690..6555
                     /locus_tag="HVX37_23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006816428.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="QML45754.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGVDIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCILEGGMTKENQGKDEIYYNEIIAMDEVDSLLSPKAFTNAKRYTKEGVK
                     ENITKFNDDENLIIKGNNLIALHSIKKLYAGKVKLIYIDPPYNTGSDSFKYNDRFNRST
                     WLTFMKNRLEVAKEMLSDDGFIFIQCDDNESAYLKVLCDSIFGEENYRNSIYWHRTYAG
                     KTVKSKLPWNTDTILFYSKKESSLLEPYTAELSAADIKSYNKDDFDGRGKYNTVSLQKT
                     SSPGPQTTYDYIDNTGKKWSCPEKGWRMTKEKLKALENDNRLYITDKTIREKYYLKERK
                     EIGKQIDNFWHDIGNLNRVSDVAFIDGQKTEKLMQRIISLASKENDIVLDFHLGSGTSA
                     AAAHKMGRRYIGIEQMDYINEITVPRLQKVIEGEQGGISKDVNWQGSGSFVYVELVELN
                     AYFIHEIQKAQSTEELEKLFAVMKTEAYLNYQVALENVLSAEYEVDGILHKVAFSELEL
                     HEQKQLLIEILDKNQLYVNVSDMEDSDLNISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     Typing          3451..3536
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          3847..3945
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          4070..4325
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.248"
                     /coverage="89.0"
                     /evalue="2.69e-98"
     Typing          complement(2880..3433)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.075"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctgcattacc gtcacctgct gtttcacatg gcaaccggtg cagggaaaac gatggttatg
       61 gcaggaacga tactctatct atttaaagag ttcgggtatc agaacttcat ctttttcgta
      121 cataccgacg cgattatcca gaaaacgcga gagaacctac ttaacccgca atcgccgaag
      181 tacctgttca gtcatgagct ggaaatcgac ggggaaaaaa tcaccatcgc accggtagat
      241 atattcccgt ccgtaccgga acgcaacacg atttacctca agctctcgac tatccataag
      301 atgcacgatg agctgaacag ctatcgagag aacagcatta cctacgagga tttaaaagaa
      361 atcccgcttg tgctactcgg tgacgaggcg catcacttca acgccggcac caaagctaga
      421 ggcaagtcga aaacctcacc ggagaacgag gagcagactt gggagcgtac gattgagaac
      481 atcctcgacc tgcgaccgga taaccgcctg ttcgagttca ccgctaccat tgaccttgca
      541 aacaaagata tcggacagaa ataccgtgac aaggtggtat atcagtatga tctgaagcag
      601 ttcatgtcag acggttactc gaaaaaggtc atgctgttgg aagcaaacca gaacgacagc
      661 gacaagatgc tcgatgcggt actgttaagc cagtaccgta aactgacggc agcagatcac
      721 ggcatcaccg gctttaaacc ggtcattctg ttcaagtcga ataagattgc gatatcaaag
      781 gcgaagcagg aggagttttc gcaactgatt gccgccatga cacctgagag catcagacgt
      841 catctggcta acaaaaaact ccagctcagc tctgacacca gtatctggca taaagtgatt
      901 cagcgttacg ctgacagtga tttagtgacg gtgactggac aaattcagga ggactttaac
      961 gactttaacc tgctgaacgt caacaagtca gacctgctgg aggaaaaccc cgtcctgctg
     1021 aatacactgg aagaagtcga taatccagtg agagccgtct ttgctgtcgc gaaggtgaat
     1081 gaaggctggg acgtacttaa cctctacgat attgttcgca taagcgagca ggcgagcagc
     1141 agcaaaacca gcacggacag cgaagcgcag cttattgggc gaggtgcgcg ttactacccg
     1201 ttcatttatg acggtcaacg tagcttcacc cgccgttttg ataacagtac gaaggatttg
     1261 agcgtactgg agcaactgca ctatcacacc atcaatgaac cggcgtacat caaaacactg
     1321 cacgcctctc tggagcaggc ggacattgac gtgcatcagg atggcggagg tacggttgaa
     1381 cacgccagat tgaaagaaga ctttaaaaag tccgccgtgt atcaggcggg taagctgtac
     1441 tttaacgaag tggaagagat tgagagaagc agccgaaact gggaaaccta ctcgctggaa
     1501 acacgctttg aaatacagta tcagatcgct tgcgaggagt cgctggacaa cctgacaggc
     1561 acaaaggggg ggatcataaa accggaacca ctggtactgg acgagcgttt ttaccgcaag
     1621 gcgatgcaaa gaatcagctt ttacgcgcta gataacctga aacgcttctt cccgaaactg
     1681 acaggtattc gggagttcat acgcagtgac gcctatcttg gtaagctgaa aatcaccgtc
     1741 agcgtaccgc agtcactgga tttcaccacc gtaccggcaa aagataagct gcacctactg
     1801 gaaaacgttt tgctgcgtat ctcagagaat gtgcgtcgca atgaccagaa ggtaaaaggc
     1861 acgtaccgat ttatcagcca gccggtgaaa gaggtgatta aagattacag tttgcatatt
     1921 gacccgtcgg tagccattaa ccagaaaatc accgccgctc ccaccattgg taaaaaatgg
     1981 tacgtgtacg ataatgcgat actaaatcag cttgagcatc gtctgataaa aatgctggaa
     2041 gcattcatgc cgaagctaaa agcgcgttat gacgatattt acgtactgcg taacgacgag
     2101 cagtcaacgc gctttaagct cacggagttc ggcggcgtgc gtgggtttat gccagatttc
     2161 atcatgatac tgacgcgcca ttcagacaac acttactggc aggtgttcct tgaaccgaag
     2221 ggggatgacc gtctgctgga tgacgcatgg aaagaacgga tgctcgaaac actgaatgac
     2281 agggagcgca ttgtaattga tgaaaatgag cacgtcagac tggttgggat taaattcttt
     2341 gccaatagcc agatggacgt ttttgtcagc gacatgcaga acaagctgaa tgatggagaa
     2401 tcgctcgaaa cctcctcgct ctccctacca ctgtaagtca cgacaataaa ataacggagc
     2461 attacgctcc gttattttat tgttatctcg aactacctcc cagggaggtg atgattgctc
     2521 ctgtaatggt tgcattgttt gttcttgctg ttgcgaatca ttagttttga atggtggtta
     2581 aaaaccgttc gctatgttta tgcctggggg ggggatgagg gggaaaagat tcaaggatcc
     2641 tcttgtgatc ctttttttct gcgcgtaatc tgcagcctgt aaacgaaaaa accaccctgg
     2701 caggtggttt ttcgaaggtt agctaatcct ggcagattat ctaaccgggt aactggcttg
     2761 gaggagcgca gtcaccaaaa tctgttcttt cagtttagcc ttaacaggtg cataacttca
     2821 agacaaactc ctctaaatca gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt
     2881 accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg
     2941 ggttcgtgca cacagcccag cttggagcga acgacctaca ccgaaccgag ataccaacag
     3001 cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta
     3061 agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat
     3121 ctttatagtc ctgtcgggtt tcgccgactc tgacttgagc gtcgattttt gtgatgctcg
     3181 tcaggggggc ggagcctatg gaaaaacgcc agcggcgcgg cctttttccg gttcctgctc
     3241 ttttgctcac atgttctttc cggccttatc ccctgattcg gtggataatc taattactgt
     3301 ctttgcgtga gttgataccg ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag
     3361 cgaggaagcg gaagagcgtc ggaagttgca ttttctcctt acgcatctgt gcggcatttc
     3421 acatcggtta tggtgtactt ttcatacaat ctgcactgat gccgcatagt taagccagta
     3481 tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc gctaaaaccc
     3541 cctgacgcgc cctgacgggc ttgtctgctg acgaaaacgc ccacgggaaa gccgtgaccg
     3601 cctccgtcag cttcgttatg ttcctgtttc actttcggcc tcaaagcgaa tctggatgct
     3661 gttctggagt tcttctgcga gttcgtgcag tcgttcgcac atggccgcct gttcgtcggc
     3721 atccagagca tccagttttt caagcagtgt caggctctgg cttttgataa atcgcgccat
     3781 attcagcgca gtttgttgtt gtttgttcac cttccgttgt tctccgtcag ttccgggtgt
     3841 cggggggacc ctgagcaggt ggtaattgta agacgttgcg ggcgacggta ttacaattgc
     3901 acatcctgtc ctgtttcttt aggacgtatc atggcacagc atatcaactg ataaataatc
     3961 cctgtgcagt gcagccgctg ttgcataaaa tttcgctctg cgtcgagtgt ttcttaatca
     4021 ataattccgc tgatactccg gaaaaacgcg agtctgttct catgcctgaa atgcccacac
     4081 cccacgcaaa aacaagtttt tgctgatttt tctttataaa tagagagtta tgacaaatta
     4141 gttcttcttg ctctctttgt gatatttaaa aaagcggtgt tggcgcagct acaacaccgc
     4201 gccgacaccg ctttttaggg gtggtactga ctattttcat aaaaaacatc atcttatatt
     4261 aggggtgctg ctagcggcgc ggtgtgtttt tttacaggac gcccctgggg gcgctgctag
     4321 gggtgtctgt tcagatatgt agcaatgagt cagggattca cgaactgaaa atgtccgaaa
     4381 atgtgtctca tgggtactgt atgcgcccaa accgatcgtc attcactttc atgcatagct
     4441 atgcagtgag ctgaaagtga tcctgacgca tttttccggt ttaccccggg gaaaacatct
     4501 ctttttgcgg tgtttgcggc agaatcgcgt tcagcgcgtt ttagcggtgc gcgcaagagc
     4561 gtttatgtta aatactactc gttctggtgc attttcccgc aactgaatcc aactcatcgc
     4621 tgttgggttc cagcgccgaa cgctatacct tacaatcatt ccaatattta acagtcataa
     4681 ggccatgaca tgcagaccga attaataaaa gaacttaaca aggttttaaa agcgttcccg
     4741 caattctgga atggagagga attacaacgt tcaatggtga gtgacgctat cagtcaaaag
     4801 cagccagatc ttatcaaggc attagtcgat aatgaaaaag tccgctctgt ttatggtgtg
     4861 gatattgatg gcatttttat ctttgatttt gacaaattat gtggtcttct aaaatacaaa
     4921 gaatattggg ctaatagctt tactaaatac cggaacaaag tgggattaac tagcgaaggt
     4981 aaataccttg attacagttc tgatgtggtg ctggattttc ctttcaagga ttgtattctt
     5041 gaaggtggaa tgaccaaaga aaatcaggga aaagatgaga tttattataa tgaaatcata
     5101 gcaatggatg aagttgactc tttgctttct cccaaggcgt tcactaatgc taagcgatat
     5161 accaaagagg gggtaaaaga aaatatcact aaatttaacg atgatgaaaa tttaataatt
     5221 aagggaaaca atctcattgc actacattca ataaaaaaac tttacgcagg aaaagtaaag
     5281 ttaatttata tagacccgcc ttacaataca gggagtgata gctttaagta taatgatcga
     5341 ttcaatcgct caacatggtt gacattcatg aaaaataggc ttgaggtggc taaagaaatg
     5401 ctttccgatg atggctttat ttttattcaa tgcgatgata atgaatcagc atatcttaaa
     5461 gttttatgtg attcaatttt tggagaagag aattatagaa actcaatcta ttggcataga
     5521 acctacgcag ggaaaactgt aaaaagtaag ttgccatgga atacagatac aatattgttt
     5581 tattctaaaa aagaaagttc attattagag ccatatacag cagaacttag tgctgctgac
     5641 attaaatcct ataacaagga tgattttgat ggaaggggta aatacaacac tgttagcttg
     5701 caaaaaacaa gctctccagg gccgcaaaca acttatgatt atatagataa tacaggtaag
     5761 aaatggagtt gccctgaaaa agggtggaga atgacaaagg aaaagttaaa ggctttggaa
     5821 aacgacaata ggctatatat cactgacaaa acaatacgag aaaaatatta tcttaaagaa
     5881 agaaaagaga tcgggaaaca aatagataat ttttggcatg acattgggaa tttaaatagg
     5941 gtttccgatg ttgcttttat tgatggacaa aaaactgaaa aattaatgca acggataatt
     6001 agccttgctt ccaaagaaaa tgatatcgtc ttggactttc atctcggcag cggaactagc
     6061 gcagcagcag cccataaaat gggacgtcgc tatatcggta ttgagcagat ggattacatc
     6121 aatgagatca ccgtgccacg tttgcaaaaa gtcattgagg gtgagcaggg aggtatctca
     6181 aaagacgtca actggcaggg gagcggcagc tttgtctacg ttgaactagt ggaactgaac
     6241 gcttacttca tacatgaaat ccagaaagcg cagtccacgg aagaactcga aaaactcttt
     6301 gccgtgatga agacagaggc atatctcaac tatcaggtgg ctctggaaaa tgtgctgtcc
     6361 gctgagtacg aagtggatgg gatcctccat aaggtagcat tcagtgaact ggaactgcat
     6421 gagcagaagc agcttttgat tgaaatccta gataagaacc agctctacgt gaatgtctct
     6481 gatatggagg acagcgacct gaacatttca gagagtgata aagcctttac ccgcagcttc
     6541 tacggaatgg agtgacggca tggcgaagaa accgaagtca gcaggtagag agaagctgct
     6601 gtttaacaag ctgaagcagt tcgatgaacc aggactgttc cacgataact atcagacgcc
     6661 ggactatatt caggcaaacc tgaaagatat cctgcgtccc tatcagcaca gcgcactgcg
     6721 ttacctgcat tacacgcaac gtaaacgtga tgacgcgctt
//
