LOCUS       CP057080                5973 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB38-C24 plasmid pRHB38-C24_6, complete
            sequence.
ACCESSION   CP057080
VERSION     CP057080.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148394
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5973)
  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 5973)
  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..5973
                     /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_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5394..5973,1..230)
                     /locus_tag="HVZ77_29025"
     CDS             join(5394..5973,1..230)
                     /locus_tag="HVZ77_29025"
                     /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="QMC48058.1"
                     /translation="MFLLKNKAGYGYFGSFNGVNTQEYHSFTFDGEYSRPVRDDLFITD
                     YDFFVSGFREFNESLKNIGSRWTSFDSRRANKIIYTSVMSVACCFDLWKSGSRKTPGTF
                     FEIFMAAVLKLMIPDELFSKHIPLIDQLESDDESIDPSSVSTDIVIKSKCKNASVVIPL
                     KITTRERIVQPFAQQRILDSYFGNGVYFSFLACISETQQDKKKKKVNHICVPGTIKLYQ
                     KYLSSLSGMYYCDIPERYLERDLTDIIPVKSMGDFLFDIYSFFRLQD"
                     /name="type II site-specific deoxyribonuclease"
     gene            complement(214..1341)
                     /locus_tag="HVZ77_29030"
     CDS             complement(214..1341)
                     /locus_tag="HVZ77_29030"
                     /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="QMC48059.1"
                     /translation="MPHRNTSNKLTCIESFCGAGGMSLGLKQAGFDVRLAFDINENAVE
                     TYNKNIGNHCEKLDASIVSGKFLLEKAGIKTRLDLFSGGPPCQGFSKQKRGAHLLDDDR
                     NKLVLEYSRLVNELKPRAFLFENVEIFGQKRGKDLINEIKNKLIDYNIYTYFICSSDFG
                     VAQKRGRFLMIGIDKSEGKVVPKLLKSDKTLTIRDVIGQLPPPPEDYKEHPDIPNHIKC
                     KIKKINEERFSYVPPGGGWKDIPFNLRLKCHQKVDTASGGWPDVYGRLEWDKQCPTITA
                     GFDSFTRGRYGHPSQNRAITLREGAMLQGFPVNYRFYGNRDAIRLQIGNAVPPPVSYAA
                     GTAIINCLNTMQDKNHFNFQNPMELDKDGQFSLAI"
                     /name="DNA cytosine methyltransferase"
     gene            1432..1698
                     /locus_tag="HVZ77_29035"
     CDS             1432..1698
                     /locus_tag="HVZ77_29035"
                     /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="QMC48064.1"
                     /translation="MTPEICKASRALVNLTQKELALMAGIATPTIADFERGARKPHGNN
                     LRSIIIAFENNGLDFVEEDGEIIGIFIRRKNVRTEESIDLSGH"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(2643..2834)
                     /locus_tag="HVZ77_29040"
     CDS             complement(2643..2834)
                     /locus_tag="HVZ77_29040"
                     /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="QMC48060.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2899..3222
                     /locus_tag="HVZ77_29045"
     CDS             2899..3222
                     /locus_tag="HVZ77_29045"
                     /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="QMC48061.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQRVQ
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3212..3922
                     /locus_tag="HVZ77_29050"
                     /pseudo=""
     CDS             3212..3922
                     /locus_tag="HVZ77_29050"
                     /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            3900..4430
                     /locus_tag="HVZ77_29055"
     CDS             3900..4430
                     /locus_tag="HVZ77_29055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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="QMC48062.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTAALKELLERYQKTTVSTMDTHWQIVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINENMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4437..4670
                     /gene="mbeD"
                     /locus_tag="HVZ77_29060"
     CDS             4437..4670
                     /gene="mbeD"
                     /locus_tag="HVZ77_29060"
                     /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="QMC48063.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQQDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     Typing          2481..2565
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          complement(1913..2458)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.727"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3213..4774
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.737"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tagcgtgtat tagcgagacg caacaagaca agaagaaaaa aaaggttaat catatatgtg
       61 ttccgggaac aataaaatta tatcaaaaat atctctctag tctctctggt atgtattact
      121 gtgatattcc agagcgttac ttggaaagag atttgaccga cataataccg gtcaaatcta
      181 tgggtgattt cttatttgat atttactctt tctttagatt gcaagactaa attgtccatc
      241 cttatccaac tccattgggt tttggaagtt aaagtgattt ttatcttgca ttgtgtttaa
      301 acaattaatt attgctgttc ctgctgcgta ggatactggc ggtggaacag catttccaat
      361 ttgtagccta atagcatcac ggttaccata gaatctatag tttacaggga atccttgtag
      421 cattgcgccc tcccttaatg ttattgctct attttgtgat gggtgtccat acctacccct
      481 agtgaaacta tcgaagcctg ccgttatggt tgggcattgt ttgtcccatt caagcctccc
      541 ataaacgtca ggccatcctc ccgatgctgt atcaaccttt tggtggcatt ttaaccttaa
      601 gttgaatggt atatctttcc atcctccacc aggaggaacg tatgaaaacc tttcttcatt
      661 aatctttttt attttacatt ttatatgatt tggtatgtct ggatgctctt tataatcctc
      721 tggtggaggc ggtaactgac caattacatc tcttattgta agggttttat ctgattttaa
      781 tagtttgggg acgactttac cttctgactt gtctattcca atcattagga aacggcctct
      841 tttttgcgca actccaaaat cagatgagca gatgaaatat gtgtatatat tgtaatcaat
      901 caacttgttc ttaatctcat taattagatc tttgcctctt ttttgaccaa aaatttccac
      961 attttcaaat aaaaaagctc taggttttaa ttcattaact agcctagaat attcaagaac
     1021 taacttgttt ctatcgtcat caagaagatg ggcgcctctt ttttgttttg aaaatccttg
     1081 acaaggcggt ccaccactaa aaagatctag tctcgttttt atgcctgctt tttccaaaag
     1141 aaacttcccg ctaacaatag aagcatctaa tttttcgcaa tgattaccaa tgtttttgtt
     1201 gtaggtttct acagcatttt cattaatatc aaatgccaac ctaacatcaa aacctgcttg
     1261 ttttaatccg agggacatac ccccggcacc acaaaaactt tcgatgcacg ttagtttatt
     1321 agatgtgttt ctatgtggca tgatgtctca cttacaaggg gccgtttaca tgtatgatag
     1381 cgttaattat acctagaggt caatgttttg atacaaaatc atattaaaaa tatgactcct
     1441 gaaatttgta aggcctctag ggccttagtt aacttgactc agaaagagct agctcttatg
     1501 gcgggaatag cgacaccaac cattgctgat tttgagcgcg gcgcaagaaa acctcatgga
     1561 aacaacttga gatctatcat tattgctttt gaaaacaatg gattggattt tgttgaggag
     1621 gatggtgaga taatcggaat ctttatcaga agaaagaatg tcagaaccga ggaatctatt
     1681 gatctgtcag gtcattgagg gcatcatctt atcgaaaaga aaaaaccgcc ttgcagggcg
     1741 gttttctcaa aggttcagta accggcaagt ttctgaacca gggtaactgg cttggaggag
     1801 cgcagtcacc aaaacttgtt ctttcagttt agccttaact ggcgcataac ttcaagacta
     1861 actcctctaa atcagttacc agtggctgct gccaatggtg ttttgcatgt ctttccgggt
     1921 tggactcaag atgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt
     1981 gcacacagcc cagcttggag cgaacgacct acactgaacc gagataccta cagcgtgagc
     2041 tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca
     2101 gggtcggaac aggagagcgc acgagggagc caccaggggg aaacgcctgg tatctttata
     2161 gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tctgtgatgc tcgtcagggg
     2221 ggcggagcct atggaaaaac gccaacggcg cggccttttg ttggcctttg cctttttgct
     2281 cacatgttct ttccggcctt atcccctgat tctgtggata accgtattac gcctttgagt
     2341 gcgctgatac cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag
     2401 cggaagagcg cctgatgcgg cattttctcc ttacgcatct gtgcggtatt tcacaccgta
     2461 tatggtgctc ttttcttata atccgcactg attccacata gttaagccag tatacactcc
     2521 gctatcgcta cgtgactggt tcagggcttc gccccgaaac cccctgacgc gccctgacgg
     2581 gcttgtctgc tcccggcatc cgctcacaga caagctgtga cagtctccgg gagctgtatg
     2641 tgtcagaggt tttcaccgtc atccccgaag cgtgcgaggc agctgcggta aagctcgtcg
     2701 gcgtggtcgt gaagtgattc acaaatatcg gcctgttcat ctgcgtccag ttcgttgagc
     2761 ttctccagca gcgttaatgt ctggcttctt ataaagcggg ccatgttaag ggcggttttt
     2821 tcctgtttgg tcactgatgc ctccgtgtaa gggggatttc tgttcatggg ggtaatgata
     2881 ccgatgaaac gcgagaggat gctcacaata cgggttactg atgatgaaca tgcccggtta
     2941 cttgaacgct gtgagggtaa acagctggcg gtatggatgc ggcgggtctg tctgggtgag
     3001 ccggttgccc gctccgggag gctgccgaca ctggcaccgc cgttactgcg tcagctggcc
     3061 gccatcggga ataacctgaa tcagactgcg aggaaggtga acagcgggca gtggtcttcc
     3121 ggtgaccggg ttcaggtggt ggccgcactg atggccatcg agagagagtt gcgcagctta
     3181 cggcaggtgg tcagggaaca gagagtgcag gatgatagtt aagtttcatg ccaggggaaa
     3241 aggtggtggc agtggtccgg ttgattacct gctgggaagg gagcgaaacc gggaaggggc
     3301 aacggtgctt cagggtaatc cggaagaagt ccgggaactc atcgatgcca cgccatttgc
     3361 gaagaaatac acgtcaggtg ttctgtcgtt cgcggagaag gagctgccgc cgggaggacg
     3421 tgaaaaggtg atggcgagct ttgagcgtgt actgatgccc ggtctcgaaa agaatcagta
     3481 cagcatcctg tgggtggagc accaggacaa gggacggctt gagctgaatt ttgtcattcc
     3541 gaacatggag ctacagaccg gaaaacgcct ccagccgtac tacgaccggg cagacaggcc
     3601 gagaattgat gcctggcaga cgctggtgaa tcaccattac gggctgcatg accccaacgc
     3661 cccggagaac cgccggatac tgactctctc tgataacctg ccggaaacga aacaggcgct
     3721 tgctgagagc gtcacacgcg ggatagacgc tctttatcat gtcggggaga taaaaggccg
     3781 tcaggatgtg attcaggcgc tcacagaggc agggcttgaa gtggtcaggg tgacgcgaag
     3841 cagtatcagc attgcagacc cgaacggtgg gaagaatatc aggctgaaag gagcatttta
     3901 tgagcaatct tttacagacg ggcgcggagt tcgagaaaaa gctgaaagag agagccgaat
     3961 ctacagagac aatgctgaac gacgagttca ggaagctcga agaatctgta aacagggaac
     4021 tgacctcaaa cgaatcttta atcaggaacg ctatcaacga ccatacagca gccctgaaag
     4081 aacttctgga gaggtatcag aaaacgaccg tcagcacgat ggacacacac tggcaaatcg
     4141 tgctgaaaat gagcgtgaaa cgctggctgt ggctgattat cgtctcagta ctgatgtttg
     4201 ccacgaccgg gagtctgctg tggtaccagg gcatgaagat aaacgagaat atgaatattc
     4261 tccgcgagca gaaagagagt ctggagaagc tgaacgcgaa gacatggggc gtgcgttatc
     4321 acgaggacag caacggacgt tttctggtgt tgccgaaggg gatgaaagcc gaaacgaact
     4381 ggacgaagga caacggcaaa ctgaacgcag tgagactggt gcaggagtga cagagcatga
     4441 cggagctgga aagacatttg ctgaacgcct tagagcaact gcaacaggac tatatgcagc
     4501 ggctgaacga atgggagagc gccttcgtgg aattgcagaa aatgttttcg cttacgcaac
     4561 aggacaacgc gatgctgaac gagcaggtca tgcagttgag tcagcaggtg cagcacttga
     4621 gcgagcggac agaacgcttg agccagttat acagcgagaa caggagataa gggacgaacg
     4681 gctgatacag gagcgcgaac atgagttatc cctggagcgt gagcgccagc cggaaataca
     4741 ggaacgcaca ctggatggcc cttcgctggg atggtaatca gagacaggct aaaatgttgt
     4801 cagcgcgttt ccggtgcatt ttttgggata atggttggtt cgggggcacc gggaacgcgc
     4861 ttcagtcaga ccttgctgaa aacacaggaa cgcgttaaaa cgcatacggg cgcgattctg
     4921 gtgtgtcttt tgttgctgtg ttttgccgtt attgccagat cgcgctcatt cccctgaatt
     4981 tctgtttttc cgctccggtt ccgtcttctg cctttccgaa agtatgaaaa aaatccgttt
     5041 cagcagtctc tggctggaaa ttcctgcgtg attcacatgg ctgcatagct atgcatgtgg
     5101 ttaaaattta ccgggtgcga tcgcggcagt ttttcgggtg gtttgttgcc atttttacct
     5161 gtctgctgcc gtgatcgcac cgaacgcgtt ttagtggtgc gtacaatgag acgttatggt
     5221 aaataaaaat cgctctattt atatgaaaaa atattcacta ataaacaaaa ttaacataga
     5281 aaaggtatga gaaaaatatg gatatcttga aagaaaaaat tgacgttgct tcacggcttt
     5341 ataatttaaa cgtgaaccat atatcagaaa cattgcaggt aatagaatat gcaatgtttt
     5401 tattaaaaaa caaagcaggg tatggttact ttggttcatt taatggggtg aatacacagg
     5461 aatatcattc atttacattt gatggtgaat attccaggcc agtaagagat gatctcttta
     5521 ttactgatta tgatttcttt gtatcagggt ttagagagtt caatgaaagt ttgaagaata
     5581 ttggtagtag atggacatca tttgattcta ggagagctaa taaaataatt tatacatctg
     5641 taatgtctgt tgcatgctgt tttgatcttt ggaaaagtgg tagcagaaag actccgggaa
     5701 cattttttga aattttcatg gcagcagtat taaagttgat gattcctgat gagcttttct
     5761 caaagcacat accactaata gatcagcttg aatcagatga tgagtcaatt gatccatcaa
     5821 gcgtgtctac tgatattgtt ataaaatcta aatgcaaaaa cgctagtgta gttataccat
     5881 taaagataac tacaagagag agaattgttc aaccatttgc tcagcagaga atattggact
     5941 catactttgg aaatggtgtt tatttttctt tct
//
