LOCUS       CP057309                5962 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C09 plasmid pRHB30-C09_8, complete
            sequence.
ACCESSION   CP057309
VERSION     CP057309.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148293
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5962)
  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 5962)
  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..5962
                     /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_8"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(70..336)
                     /locus_tag="HVY76_28320"
     CDS             complement(70..336)
                     /locus_tag="HVY76_28320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008944190.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /protein_id="QMF75900.1"
                     /translation="MTPEICKASRALVNLTQKELALMAGIATPTIADFERGARKPHGNN
                     LRSIIIAFENNGLDFVEEDGEIIGIFIRRKNVRTEESIDLSGH"
                     /name="helix-turn-helix transcriptional regulator"
     gene            427..1554
                     /locus_tag="HVY76_28325"
     CDS             427..1554
                     /locus_tag="HVY76_28325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283633.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="QMF75895.1"
                     /translation="MPHRNTSNKLTCIESFCGAGGMSLGLKQAGFDVRLAFDINENAVE
                     TYNKNIGNHCEKLDASIVSGKFLLEKAGIKTRLDLFSGGPPCQGFSKQKRGAHLLDDDR
                     NKLVLEYSRLVNELKPRAFLFENVEIFGQKRGKDLINEIKNKLIDYNIYTYFICSSDFG
                     VAQKRGRFLMIGIDKSEGKVVPKLLKSDKTLTIRDVIGQLPPPPEDYKEHPDIPNHIKC
                     KIKKINEERFSYVPPGGGWKDIPFNLRLKCHQKVDTASGGWPDVYGRLEWDKQCPTITA
                     GFDSFTRGRYGHPSQNRAITLREGAMLQGFPVNYRFYGNRDAIRLQIGNAVPPPVSYAA
                     GTAIINCLNTMQDKNHFNFQNPMELDKDGQFSLAI"
                     /name="DNA cytosine methyltransferase"
     gene            complement(1538..2347)
                     /locus_tag="HVY76_28330"
     CDS             complement(1538..2347)
                     /locus_tag="HVY76_28330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000479291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II site-specific deoxyribonuclease"
                     /protein_id="QMF75901.1"
                     /translation="MFLLKNKAGYGYFGSFNGVNTQEYHSFTFDGEYSRPVRDDLFITD
                     YDFFVSGFREFNESLKNIGSRWTSFDSRRANKIIYTSVMSVACCFDLWKSGSRKTPGTF
                     FEIFMAAVLKLMIPDELFSKHIPLIDQLESDDESIDPSSVSTDIVIKSKCKNASVVIPL
                     KITTRERIVQPFAQQRILDSYFGNGVYFSFLACISETQQDKKKKKVNHICVPGTIKLYQ
                     KYLSSLSGMYYCDIPERYLERDLTDIIPVKSMGDFLFDIYSFFRLQD"
                     /name="type II site-specific deoxyribonuclease"
     gene            complement(3072..3305)
                     /gene="mbeD"
                     /locus_tag="HVY76_28335"
     CDS             complement(3072..3305)
                     /gene="mbeD"
                     /locus_tag="HVY76_28335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QMF75896.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(3312..3830)
                     /locus_tag="HVY76_28340"
     CDS             complement(3312..3830)
                     /locus_tag="HVY76_28340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="QMF75897.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(3808..4518)
                     /locus_tag="HVY76_28345"
                     /pseudo=""
     CDS             complement(3808..4518)
                     /locus_tag="HVY76_28345"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4508..4831)
                     /locus_tag="HVY76_28350"
     CDS             complement(4508..4831)
                     /locus_tag="HVY76_28350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QMF75898.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQRVQ
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4896..5087
                     /locus_tag="HVY76_28355"
     CDS             4896..5087
                     /locus_tag="HVY76_28355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="QMF75899.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(5166..5250)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          5270..5815
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.727"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2969..4518)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgccggttac tgaacctttg agaaaaccgc cctgcaaggc ggttttttct tttcgataag
       61 atgatgccct caatgacctg acagatcaat agattcctcg gttctgacat tctttcttct
      121 gataaagatt ccgattatct caccatcctc ctcaacaaaa tccaatccat tgttttcaaa
      181 agcaataatg atagatctca agttgtttcc atgaggtttt cttgcgccgc gctcaaaatc
      241 agcaatggtt ggtgtcgcta ttcccgccat aagagctagc tctttctgag tcaagttaac
      301 taaggcccta gaggccttac aaatttcagg agtcatattt ttaatatgat tttgtatcaa
      361 aacattgacc tctaggtata attaacgcta tcatacatgt aaacggcccc ttgtaagtga
      421 gacatcatgc cacatagaaa cacatctaat aaactaacgt gcatcgaaag tttttgtggt
      481 gccgggggta tgtccctcgg attaaaacaa gcaggttttg atgttaggtt ggcatttgat
      541 attaatgaaa atgctgtaga aacctacaac aaaaacattg gtaatcattg cgaaaaatta
      601 gatgcttcta ttgttagcgg gaagtttctt ttggaaaaag caggcataaa aacgagacta
      661 gatcttttta gtggtggacc gccttgtcaa ggattttcaa aacaaaaaag aggcgcccat
      721 cttcttgatg acgatagaaa caagttagtt cttgaatatt ctaggctagt taatgaatta
      781 aaacctagag cttttttatt tgaaaatgtg gaaatttttg gtcaaaaaag aggcaaagat
      841 ctaattaatg agattaagaa caagttgatt gattacaata tatacacata tttcatctgc
      901 tcatctgatt ttggagttgc gcaaaaaaga ggccgtttcc taatgattgg aatagacaag
      961 tcagaaggta aagtcgtccc caaactatta aaatcagata aaacccttac aataagagat
     1021 gtaattggtc agttaccgcc tccaccagag gattataaag agcatccaga cataccaaat
     1081 catataaaat gtaaaataaa aaagattaat gaagaaaggt tttcatacgt tcctcctggt
     1141 ggaggatgga aagatatacc attcaactta aggttaaaat gccaccaaaa ggttgataca
     1201 gcatcgggag gatggcctga cgtttatggg aggcttgaat gggacaaaca atgcccaacc
     1261 ataacggcag gcttcgatag tttcactagg ggtaggtatg gacacccatc acaaaataga
     1321 gcaataacat taagggaggg cgcaatgcta caaggattcc ctgtaaacta tagattctat
     1381 ggtaaccgtg atgctattag gctacaaatt ggaaatgctg ttccaccgcc agtatcctac
     1441 gcagcaggaa cagcaataat taattgttta aacacaatgc aagataaaaa tcactttaac
     1501 ttccaaaacc caatggagtt ggataaggat ggacaattta gtcttgcaat ctaaagaaag
     1561 agtaaatatc aaataagaaa tcacccatag atttgaccgg tattatgtcg gtcaaatctc
     1621 tttccaagta acgctctgga atatcacagt aatacatacc agagagacta gagagatatt
     1681 tttgatataa ttttattgtt cccggaacac atatatgatt aacctttttt ttcttcttgt
     1741 cttgttgcgt ctcgctaata cacgctaaga aagaaaaata aacaccattt ccaaagtatg
     1801 agtccaatat tctctgctga gcaaatggtt gaacaattct ctctcttgta gttatcttta
     1861 atggtataac tacactagcg tttttgcatt tagattttat aacaatatca gtagacacgc
     1921 ttgatggatc aattgactca tcatctgatt caagctgatc tattagtggt atgtgctttg
     1981 agaaaagctc atcaggaatc atcaacttta atactgctgc catgaaaatt tcaaaaaatg
     2041 ttcccggagt ctttctgcta ccacttttcc aaagatcaaa acagcatgca acagacatta
     2101 cagatgtata aattatttta ttagctctcc tagaatcaaa tgatgtccat ctactaccaa
     2161 tattcttcaa actttcattg aactctctaa accctgatac aaagaaatca taatcagtaa
     2221 taaagagatc atctcttact ggcctggaat attcaccatc aaatgtaaat gaatgatatt
     2281 cctgtgtatt caccccatta aatgaaccaa agtaaccata ccctgctttg ttttttaata
     2341 aaaacattgc atattctatt acctgcaatg tttctgatat atggttcacg tttaaattat
     2401 aaagccgtga agcaacgtca attttttctt tcaagatatc catatttttc tcataccttt
     2461 tctatgttaa ttttgtttat tagtgaatat tttttcatat aaatagagcg atttttattt
     2521 accataacgt ctcattgtac gcaccgctga aacgcgttcg gcgcgatcac ggcagcagac
     2581 aggtaaaaat ggcaacaaac cacccgaaaa actgccgcga tcgcacccgg taaattttaa
     2641 ccacatgcat agctatgcag ccatgtgaat cacgcaggaa ttgccagcca gagacagctg
     2701 aaacggattt ttttcatgct ttcggaagcg aagaagacgg ggaccggagc gggaaaacag
     2761 aagttcaggg gaatgagcgc gatctggcaa tagaggcaaa acacagcaac aaaagacaca
     2821 ccagaatcgc gcccgtatgc gttttaacgc gttcctgtgt tttcagcaag gtctgactga
     2881 agcgcgttcc cggtgccccc gaaccaacca ttatcccaaa aaatgcaccg gaaacgcgct
     2941 gacaacattt tagcctgtct ctgattacca tccaagcgaa gggccatcct gtgtccattc
     3001 ctgtatttcc ggctggcgct cacgctccag ggataacgca tgttcgcgct cctgtatcag
     3061 ccgttcgtcc cttatctcct gttctcgctg tataactggc tcaagcgttc tgtccgctcg
     3121 ctcaagtgct gcacctgctg actcaactgc atgacctgct cgttcagcat cgcgttgtcc
     3181 cgttgcgtaa gcgaaaacat tttctgcaat tccacgaagg cgctctccca ttcgctcagc
     3241 cgctgcatat agtcctgttg cagttgctct aaggcgttca gcaaatgtct ttccagctcc
     3301 gtcactctgt gtcactccgt cagttgtacc cagtccttct cctgataggg aatcaccgtt
     3361 gccgatttcc cgtacggaag gaccagaaat ttccttctcc cgtcctgcac aaactccacg
     3421 ccccatgtct tcgcgttcag tttctgcaat gtttcttcct gtatcctgat ttcttccagg
     3481 ttcgcctgta tccgcccgcc aagataccag agcgtcccgc cactcacggt aaacaggaaa
     3541 aggaccatcc ccagtaacat catgcccgta ttccctgcca gctttaacac gtccttcctg
     3601 tgctgcatca tcgcctcttt caccccttcc cggtgttttt tcagtgattc ctctgtcgaa
     3661 gctgtgaaca gggctatagc gtctttgatt ttcgtctcgt ttgatgtcac agccttgctt
     3721 acagattttt cgagcttgct gaactcgtcg ttcagcattg tctctgtaga ttcggctctc
     3781 tctttcagct ttttctcgaa ctccgcgccc gtctgtaaaa gattgctcat agaatgctcc
     3841 tttcagtctg atattcttcc cgccgttcgg gtctgcaatg ctgatactgc ttcgcgtcac
     3901 cctgaccact tcaagccctg cctctgtgag cgcctgaatc acatcctgac ggccttttat
     3961 ctccccgaca tgataaagag cgtctatccc gcgtgtgacg ctctctgcaa gcgcctgttt
     4021 cgtttccggc aggttatcag ggagagtcag tatccggcgg ttctccgggg cgttggggtc
     4081 atgcagcccg taatggtgat taaccagcgt ctgccaggca tcaattctcg gcctgtctgc
     4141 ccggtcgtag tacggctgga ggcgttttcc gctctgtagc tccatgttcg gaatgacaaa
     4201 attcagctca agccgtccct tgtcctggtg ctccacccac aggatgctgt actgattttt
     4261 ttcgagaccg ggcatcagta cacgctcaaa gctcgccatc accttttcac gtcctcccgg
     4321 cggcagctcc ttctccgcga acgacagaac acctgacgtg tatttcttcg caaatggcgt
     4381 ggcatcgatg agttcccgga cttcttccgg attaccctga agcaccgttg ccccttcccg
     4441 gttacgctcc cttcccagca ggtaatcaac cggaccactg ccaccgcctt ttcccctggc
     4501 atgaaactta actatcatcc tgcactctct gttccctgac cacctgccgt aagctgcgca
     4561 actctctctc gatggccatc agtgcggcca ccacctgaac ccggtcaccg gaagaccact
     4621 gcccgctgtt caccttcctc gcagtctgat tcaggttatt cccgatggcg gccagctgac
     4681 gcagtaacgg cggtgccagt gtcggcagcc tcccggagcg ggcaaccggc tcacccagac
     4741 agacccgccg catccatacc gccagctgtt taccctcaca gcgttcaagt aaccgggcat
     4801 gttcatcatc agtaacccgt attgtgagca tcctctcgcg tttcatcggt atcattaccc
     4861 ccatgaacag aaatccccct tacacggagg catcagtgac caaacaggaa aaaaccgccc
     4921 ttaacatggc ccgctttata agaagccaga cattaacgct gctggagaag ctcaacgaac
     4981 tggacgcaga tgaacaggcc gatatttgtg aatcacttca cgaccacgcc gacgagcttt
     5041 accgcagctg cctcgcacgc ttcggggatg acggtgaaaa cctctgacac atacagctcc
     5101 cggagactgt cacagcttgt ctgtgagcgg atgccgggag cagacaagcc cgtcagggcg
     5161 cgtcaggggg tttcggggcg aagccctgaa ccagtcacgt agcgatagcg gagtgtatac
     5221 tggcttaact atgtggaatc agtgcggatt ataagaaaag agcaccatat acggtgtgaa
     5281 ataccgcaca gatgcgtaag gagaaaatgc cgcatcaggc gctcttccgc ttcctcgctc
     5341 actgactcgc tacgctcggt cgttcggctg cggcgagcgg tatcagcgca ctcaaaggcg
     5401 taatacggtt atccacagaa tcaggggata aggccggaaa gaacatgtga gcaaaaaggc
     5461 aaaggccaac aaaaggccgc gccgttggcg tttttccata ggctccgccc ccctgacgag
     5521 catcacagaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac
     5581 caggcgtttc cccctggtgg ctccctcgtg cgctctcctg ttccgaccct gccgcttacc
     5641 ggatacctgt ccgcctttct cccttcggga agcgtggcgc tttctcatag ctcacgctgt
     5701 aggtatctcg gttcagtgta ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc
     5761 gttcagcccg accgctgcgc cttatccggt aactatcatc ttgagtccaa cccggaaaga
     5821 catgcaaaac accattggca gcagccactg gtaactgatt tagaggagtt agtcttgaag
     5881 ttatgcgcca gttaaggcta aactgaaaga acaagttttg gtgactgcgc tcctccaagc
     5941 cagttaccct ggttcagaaa ct
//
