LOCUS       CP057415                5964 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB27-C20 plasmid pRHB27-C20_8, complete
            sequence.
ACCESSION   CP057415
VERSION     CP057415.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148263
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5964)
  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 5964)
  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 T2-C20
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 146.358368757903x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 08:24:32
            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)                     :: 5,633
            CDSs (total)                      :: 5,500
            Genes (coding)                    :: 5,127
            CDSs (with protein)               :: 5,127
            Genes (RNA)                       :: 133
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 373
            CDSs (without protein)            :: 373
            Pseudo Genes (ambiguous residues) :: 0 of 373
            Pseudo Genes (frameshifted)       :: 136 of 373
            Pseudo Genes (incomplete)         :: 211 of 373
            Pseudo Genes (internal stop)      :: 61 of 373
            Pseudo Genes (multiple problems)  :: 34 of 373
            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..5964
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB27-C20"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB27-C20_8"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(689..922)
                     /gene="mbeD"
                     /locus_tag="HVY46_28120"
     CDS             complement(689..922)
                     /gene="mbeD"
                     /locus_tag="HVY46_28120"
                     /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="QMG97784.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(929..1447)
                     /locus_tag="HVY46_28125"
     CDS             complement(929..1447)
                     /locus_tag="HVY46_28125"
                     /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="QMG97785.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(1425..2147)
                     /locus_tag="HVY46_28130"
                     /pseudo=""
     CDS             complement(1425..2147)
                     /locus_tag="HVY46_28130"
                     /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(2125..2448)
                     /locus_tag="HVY46_28135"
     CDS             complement(2125..2448)
                     /locus_tag="HVY46_28135"
                     /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="QMG97786.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2513..2704
                     /locus_tag="HVY46_28140"
     CDS             2513..2704
                     /locus_tag="HVY46_28140"
                     /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="QMG97787.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3662..3928)
                     /locus_tag="HVY46_28145"
     CDS             complement(3662..3928)
                     /locus_tag="HVY46_28145"
                     /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="QMG97788.1"
                     /translation="MTPEICKASRALVNLTQKELALMAGIATPTIADFERGARKPHGNN
                     LRSIIIAFENNGLDFVEEDGEIIGIFIRRKNVRTEESIDLSGH"
                     /name="helix-turn-helix transcriptional regulator"
     gene            4019..5146
                     /locus_tag="HVY46_28150"
     CDS             4019..5146
                     /locus_tag="HVY46_28150"
                     /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="QMG97789.1"
                     /translation="MPHRNTSNKLTCIESFCGAGGMSLGLKQAGFDVRLAFDINENAVE
                     TYNKNIGNHCEKLDASIVSGKFLLEKAGIKTRLDLFSGGPPCQGFSKQKRGAHLLDDDR
                     NKLVLEYSRLVNELKPRAFLFENVEIFGQKRGKDLINEIKNKLIDYNIYTYFICSSDFG
                     VAQKRGRFLMIGIDKSEGKVVPKLLKSDKTLTIRDVIGQLPPPPEDYKEHPDIPNHIKC
                     KIKKINEERFSYVPPGGGWKDIPFNLRLKCHQKVDTASGGWPDVYGRLEWDKQCPTITA
                     GFDSFTRGRYGHPSQNRAITLREGAMLQGFPVNYRFYGNRDAIRLQIGNAVPPPVSYAA
                     GTAIINCLNTMQDKNHFNFQNPMELDKDGQFSLAI"
                     /name="DNA cytosine methyltransferase"
     gene            complement(5130..5939)
                     /locus_tag="HVY46_28155"
     CDS             complement(5130..5939)
                     /locus_tag="HVY46_28155"
                     /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="QMG97790.1"
                     /translation="MFLLKNKAGYGYFGSFNGVNTQEYHSFTFDGEYSRPVRDDLFITD
                     YDFFVSGFREFNESLKNIGSRWTSFDSRRANKIIYTSVMSVACCFDLWKSGSRKTPGTF
                     FEIFMAAVLKLMIPDELFSKHIPLIDQLESDDESIDPSSVSTDIVIKSKCKNASVVIPL
                     KITTRERIVQPFAQQRILDSYFGNGVYFSFLACISETQQDKKKKKVNHICVPGTIKLYQ
                     KYLSSLSGMYYCDIPERYLERDLTDIIPVKSMGDFLFDIYSFFRLQD"
                     /name="type II site-specific deoxyribonuclease"
     Typing          complement(2799..2880)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          2900..3445
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.727"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(601..2135)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.715"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tctgatatat ggttcacgtt taaattataa agccgtgaag caacgtcaat tttttctttc
       61 aagatatcca tatttttctc ataccttttc tatgttaatt ttgtttatta gtgaatattt
      121 tttcatataa atagagcgat ttttatttac cataacgtct cattgcccgc accgcagaaa
      181 cgcgttcggt gcgatcacgg cagcagacag gtaaaaatgg caacaaacca cccgaaaaac
      241 tgccgcgatc gcacccggta aattttaacc acatgcatag ctatgcagcc atgtgaatca
      301 cgcaggaatt gccagccaga gacagctgaa acggattttt ttcatgcttt cggaagcgaa
      361 gaagacgggg accggagcgg gaaaacagaa gttcagggga atgagcgcga tctggcaata
      421 gaggcaaaac acagcaacaa aagacacacc agaatcgcgc ccgtatgcgt tttaacgcgt
      481 tcctgtgttt tcagcaaggt ctgactgaag cgcgttcccg gtgcccccga accaaccatt
      541 atcccaaaaa atgcaccgga aacgcgctga caacatttta gcctgtctct gattaccatg
      601 ccatccagtg tccgttcctg tatttccagc tggcgctcac gctccaggga taactcatgt
      661 tcgcgctcct gtatcagccg ttcgtccctt atctcctgtt ctcgctgtat aactggctca
      721 agcgttctgt ccgctcgctc aagtgctgca cctgctgact caactgcatg acctgctcgt
      781 tcagcatcgc gttgtcccgt tgcgtaagcg aaaacatttt ctgcaattcc acgaaggcgc
      841 tctcccattc gctcagccgc tgcatatagt cctgttgcag ttgctctaag gcgttcagca
      901 aatgtctttc cagctccgtc actctgtgtc actccgtcag ttgtacccag tccttctcct
      961 gatagggaat caccgttgcc gatttcccgt acggaaggac cagaaatttc cttctcccgt
     1021 cctgcacaaa ctccacgccc catgtcttcg cgttcagttt ctgcaatgtt tcttcctgta
     1081 tcctgatttc ttccaggttc gcctgtatcc gcccgccaag ataccagagc gtcccgccac
     1141 tcacggtaaa caggaaaagg accatcccca gtaacatcat gcccgtattc cctgccagct
     1201 ttaacacgtc cttcctgtgc tgcatcatcg cctctttcac cccttcccgg tgttttttca
     1261 gtgattcctc tgtcgaagct gtgaacaggg ctatagcgtc tttgattttc gtctcgtttg
     1321 atgtcacagc cttgcttaca gatttttcga gcttgctgaa ctcgtcgttc agcattgtct
     1381 ctgtagattc ggctctctct ttcagctttt tctcgaactc cgcgcccgtc tgtaaaagat
     1441 tgctcataga atgctccttt cagtctgata ttcttcccgc cgttcgggtc tgcaatgctg
     1501 atactgcttc gcgtcaccct gaccacttca agccctgcct ctgtgagcgc ctgaatcaca
     1561 tcctgacggc cttttatctc cccgacatga taaagagcgt ctatcccgcg tgtgacgctc
     1621 tctgcaagcg cctgtttcgt ttccggcagg ttatcaggga gagtcagtat ccggcggttc
     1681 tccggggcgt tggggtcatg cagcccgtaa tggtgattaa ccagcgtctg ccaggcatca
     1741 attctcggcc tgtctgcccg gtcgtagtac ggctggaggc gttttccgct ctgtagctcc
     1801 atgttcggaa tgacaaaatt cagctcaagc cgtcccttgt cctggtgctc cacccacagg
     1861 atgctgtact gatttttttc gagaccgggc atcagtacac gctcaaagct cgccatcacc
     1921 ttttcacgtc ctcccggcgg cagctccttc tccgcgaacg acagaacacc tgacgtgtat
     1981 ttcttcgcaa atggcgtggc atcgatgagt tcccggactt cttccggatt accctgaagc
     2041 accgttgccc cttcccggtt acgctccctt cccagcaggt aatcaaccgg accactgcca
     2101 ccgccttttc ccctggcatg aaacttaact atcatcccgc gctccatgtt ccctgacgac
     2161 ctgccgtaag ctgcgcaact ctctctcgat ggccatcagt gcggccacca cctgaacccg
     2221 gtcaccggaa gaccactgcc cgctgttcac cttcctcgcc gtctgattca gattattccc
     2281 gatggcagcc agctggcgca gtaacggcgg tgccagtgtc ggcagcttcc cggaacgggc
     2341 aaccggctca cccagacaga cccgccgcat ccataccgcc agctgtttac cctcacagcg
     2401 ttccagtaac cgtgcatgtt catcatcagt aacccgtatc gtgagcatcc tctcgcgttt
     2461 catcggtatc attaccccat gaacagaaat ccccccttac acggaggcat cagtgactaa
     2521 acaggaaaaa accgccctta acatggcccg ctttatcaga agccagacat taacgctgct
     2581 ggaaaagctc aacgaactgg acgcggatga acaggcagac atctgtgaat cgcttcacga
     2641 ccacgccgat gagctttacc gcagctgcct cgcacgcttc ggggatgacg gtgaaaacct
     2701 ctgacacata cagctcccgg agacggtcac agcttgtctg tgagcggatg ccgggagcag
     2761 acaagcccgt cagggcgcgt caggccgttg accttgcggg tgtcggggcg cagccatgac
     2821 ccagtcacgt agcgatagcg gagtgtatac tggcttaact atgtggaatc agtgcggatt
     2881 ataagaaaag agcaccatat acggtgtgaa ataccgcaca gatgcgtaag gagaaaatgc
     2941 cgcatcaggc gctcttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg
     3001 cggcgagcgg tatcagcgca ctcaaaggcg taatacggtt atccacagaa tcaggggata
     3061 aggccggaaa gaacatgtga gcaaaaaggc aaaggccaac aaaaggccgc gccgttggcg
     3121 tttttccata ggctccgccc ccctgacgag catcacagaa atcgacgctc aagtcagagg
     3181 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggtgg ctccctcgtg
     3241 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     3301 agcgtggcgc tttctcatag ctcacgctgt aggtatctcg gttcagtgta ggtcgttcgc
     3361 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     3421 aactatcatc ttgagtccaa cccggaaaga catgcaaaac accattggca gcagccactg
     3481 gtaactgatt tagaggagtt agtcttgaag ttatgcgcca gttaaggcta aactgaaaga
     3541 acaagttttg gtgactgcgc tcctccaagc cagttaccct ggttcagaaa cttgccggtt
     3601 actgaacctt tgagaaaacc gccctgcaag gcggtttttt cttttcgata agatgatgcc
     3661 ctcaatgacc tgacagatca atagattcct cggttctgac attctttctt ctgataaaga
     3721 ttccgattat ctcaccatcc tcctcaacaa aatccaatcc attgttttca aaagcaataa
     3781 tgatagatct caagttgttt ccatgaggtt ttcttgcgcc gcgctcaaaa tcagcaatgg
     3841 ttggtgtcgc tattcccgcc ataagagcta gctctttctg agtcaagtta actaaggccc
     3901 tagaggcctt acaaatttca ggagtcatat ttttaatatg attttgtatc aaaacattga
     3961 cctctaggta taattaacgc tatcatacat gtaaacggcc ccttgtaagt gagacatcat
     4021 gccacataga aacacatcta ataaactaac gtgcatcgaa agtttttgtg gtgccggggg
     4081 tatgtccctc ggattaaaac aagcaggttt tgatgttagg ttggcatttg atattaatga
     4141 aaatgctgta gaaacctaca acaaaaacat tggtaatcat tgcgaaaaat tagatgcttc
     4201 tattgttagc gggaagtttc ttttggaaaa agcaggcata aaaacgagac tagatctttt
     4261 tagtggtgga ccgccttgtc aaggattttc aaaacaaaaa agaggcgccc atcttcttga
     4321 tgacgataga aacaagttag ttcttgaata ttctaggcta gttaatgaat taaaacctag
     4381 agctttttta tttgaaaatg tggaaatttt tggtcaaaaa agaggcaaag atctaattaa
     4441 tgagattaag aacaagttga ttgattacaa tatatacaca tatttcatct gctcatctga
     4501 ttttggagtt gcgcaaaaaa gaggccgttt cctaatgatt ggaatagaca agtcagaagg
     4561 taaagtcgtc cccaaactat taaaatcaga taaaaccctt acaataagag atgtaattgg
     4621 tcagttaccg cctccaccag aggattataa agagcatcca gacataccaa atcatataaa
     4681 atgtaaaata aaaaagatta atgaagaaag gttttcatac gttcctcctg gtggaggatg
     4741 gaaagatata ccattcaact taaggttaaa atgccaccaa aaggttgata cagcatcggg
     4801 aggatggcct gacgtttatg ggaggcttga atgggacaaa caatgcccaa ccataacggc
     4861 aggcttcgat agtttcacta ggggtaggta tggacaccca tcacaaaata gagcaataac
     4921 attaagggag ggcgcaatgc tacaaggatt ccctgtaaac tatagattct atggtaaccg
     4981 tgatgctatt aggctacaaa ttggaaatgc tgttccaccg ccagtatcct acgcagcagg
     5041 aacagcaata attaattgtt taaacacaat gcaagataaa aatcacttta acttccaaaa
     5101 cccaatggag ttggataagg atggacaatt tagtcttgca atctaaagaa agagtaaata
     5161 tcaaataaga aatcacccat agatttgacc ggtattatgt cggtcaaatc tctttccaag
     5221 taacgctctg gaatatcaca gtaatacata ccagagagac tagagagata tttttgatat
     5281 aattttattg ttcccggaac acatatatga ttaacctttt ttttcttctt gtcttgttgc
     5341 gtctcgctaa tacacgctaa gaaagaaaaa taaacaccat ttccaaagta tgagtccaat
     5401 attctctgct gagcaaatgg ttgaacaatt ctctctcttg tagttatctt taatggtata
     5461 actacactag cgtttttgca tttagatttt ataacaatat cagtagacac gcttgatgga
     5521 tcaattgact catcatctga ttcaagctga tctattagtg gtatgtgctt tgagaaaagc
     5581 tcatcaggaa tcatcaactt taatactgct gccatgaaaa tttcaaaaaa tgttcccgga
     5641 gtctttctgc taccactttt ccaaagatca aaacagcatg caacagacat tacagatgta
     5701 taaattattt tattagctct cctagaatca aatgatgtcc atctactacc aatattcttc
     5761 aaactttcat tgaactctct aaaccctgat acaaagaaat cataatcagt aataaagaga
     5821 tcatctctta ctggcctgga atattcacca tcaaatgtaa atgaatgata ttcctgtgta
     5881 ttcaccccat taaatgaacc aaagtaacca taccctgctt tgttttttaa taaaaacatt
     5941 gcatattcta ttacctgcaa tgtt
//
