LOCUS       CP057383                4664 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB28-C11 plasmid pRHB28-C11_4, complete
            sequence.
ACCESSION   CP057383
VERSION     CP057383.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148268
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  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 4664)
  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                     :: RH01 T2-C11
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 155.059959151347x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 08:23:03
            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)                     :: 4,675
            CDSs (total)                      :: 4,550
            Genes (coding)                    :: 4,414
            CDSs (with protein)               :: 4,414
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 64 of 136
            Pseudo Genes (incomplete)         :: 64 of 136
            Pseudo Genes (internal stop)      :: 26 of 136
            Pseudo Genes (multiple problems)  :: 18 of 136
            CRISPR Arrays                     :: 3
            ##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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB28-C11"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB28-C11_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4343..4664,1..1250)
                     /locus_tag="HVY51_23355"
     CDS             join(4343..4664,1..1250)
                     /locus_tag="HVY51_23355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013199864.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GGDEF domain-containing protein"
                     /protein_id="QMG74442.1"
                     /translation="MECIFMRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIE
                     KDLLYANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMF
                     NSVLVVSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLS
                     HPIYDKGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAV
                     DRPMVMSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILI
                     AYAKSVLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYA
                     EADRLKKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVI
                     DVDFFKEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAK
                     CVAERIRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKV
                     IVYSAI"
                     /name="GGDEF domain-containing protein"
     gene            2307..2630
                     /locus_tag="HVY51_23360"
     CDS             2307..2630
                     /locus_tag="HVY51_23360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="QMG74445.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2569..3333
                     /locus_tag="HVY51_23365"
                     /pseudo=""
     CDS             2569..3333
                     /locus_tag="HVY51_23365"
                     /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            3308..3793
                     /locus_tag="HVY51_23370"
     CDS             3308..3793
                     /locus_tag="HVY51_23370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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="QMG74443.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3797..4012
                     /gene="mbeD"
                     /locus_tag="HVY51_23375"
     CDS             3797..4012
                     /gene="mbeD"
                     /locus_tag="HVY51_23375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="QMG74444.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="mbeD"
     Typing          2022..2194
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(1546..2097)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          2308..2624
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
     Typing          2621..4116
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgttgttag taatgatgct gttgttctgg cgacttcgcc agaatctctt gatttagttg
       61 gtacccgctt gaattcaagt gccagcaaat tggcggttga ggaaaagaaa ccattcatat
      121 cttcaccgtt aaaatcagtt gctgggaatt tgattatttt gttgtcacat cctatttatg
      181 ataagggtgg caattacata gggtatgtcg gtgggtctat atatctaaaa aaacatagtt
      241 tatttggcga tgttttgagc aggcattttt tcaagaacaa cactgaaatt agcattgtta
      301 gtgatgatgg gaatgtgatc tttaataacg ataaaagtgc tgttgatcgg cctatggtta
      361 tgtctgatga tttgaaatca aagttaactg cgtctgatag aggtgagggg gcattttttt
      421 cttcggggca tagatatctt cttggttatg ctagtatgaa aaataccgct tggaatgtgt
      481 tggtttatag tcgtgctgac agtgtgacta ctattcttat tgcttatgct aaaagtgtac
      541 ttgttctgct aattataata attattgtgt tttcacttat ttcatatttc attgcctcca
      601 gtatttcact tcctttagaa aagcttgcta tatctaccaa tgctaaagat atcggagctt
      661 cgctagttta tattaaagct atcaatgctt ggtatgccga agctgatagg cttaaaaagg
      721 cgctttttac gtatattaag gtaatgatgg aaagagttga ttctctaaat gaggtggcgc
      781 ttaaagatcc ccttaccggc gtgaataata gattggggtt tttaagtaaa atacagaatc
      841 ataagcggga ttcagggtgt tcagttattg taattgatgt tgattttttt aaagagataa
      901 atgacagttt cgggcatggg gtcggagatg aggtgcttgt ttctttggct catattatta
      961 attcctgttg ccgtagtgaa gatgttgttt gtcggtttgg tggcgaagag tttgttgttt
     1021 tcctgccgaa tacatctgtg gtaacagcta agtgtgttgc ggagcgtatt aggagtgtta
     1081 ttgaaagtac tgtcttccct aataacttgc gggtcaccat atctgctggt gtggcaacac
     1141 aagatgatcc tcttggtagg atcgattttt tgctgaaaaa tgctgacgat gctctttatc
     1201 aagccaaaag ggaggggcgt aataaagtga ttgtatatag cgctatttga gttttttgat
     1261 gatgctttac gcgctagtgt gtcgtttttt ttgtggcgaa gagtgggcaa gaagcggatc
     1321 ctcttgttat cccttcgatg tcgtcgtaat ctcataccct gtaaacaaaa aaaccaccgc
     1381 taccaacggt ggttcgtttg ccggaattca gagctaccaa ctctttcttc cgaaggtaac
     1441 tggctttcac ggagcgcagg taccaaaact gtccttccag tgtagccgca gtcaggccac
     1501 cacttcaaga actctgtaga acactctact actccgctcc gtgaatcctc ttactaatgg
     1561 ctaccgccac tggcgatttt tcgtgtctgt tccgggttgg actcaagatg atagttaccg
     1621 ggacaacgtg gtagtcgggc tgaacggggg gttcgtgcat acagtccagc ttggagcgaa
     1681 ctgccttccc ggaaccgagt gtcaggcgtg gaatgagata aacgcggcca taacagcgga
     1741 ttgacatcgg taaaccgaaa ggcaggaaca ggagagcgca cgagggagcc accaggggga
     1801 aacgcctggt atctttaagt cctgtcgggt ttcgccacca ctgatttgag cgtcagattt
     1861 cgtgatgctt gtcagggggg cggagcctat ggaaaaacgg cttcgccgtg gccttatcgc
     1921 ttccctgtta agcttcttcc tggcatctcc caggaaattt ccgccccgcc tgtaagtcgg
     1981 taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaata
     2041 tatcctgtat cacatattct gctgacgctc cgctgctgca tttttctcct gccacatgaa
     2101 gcacttcact gacactcgca tccgtgccaa catagtaagc cagtatacac tccgctagcg
     2161 ctacgtgact ggttcagggc tgcgccccga aacccgccaa aagcctgacg cgcctgcggc
     2221 ttgtccaacc ccgcgccgac cgggaaagcc tttcccgccc gtcccggcgt tatcaggagg
     2281 ccggtttgtc agagaaacgg aacaagatgc tcaccatgtg ggtgacggag ggcgagcacc
     2341 ggcggctgct tgagcgctgt gacggcaggc agctggcggc gtggatgcgg cagacctgcc
     2401 tggacgaaaa gccggcacgt tccggaaagc ttccctcaat ctcgccggcg ctgctgcgcc
     2461 agcttgccgg catgggcaat aacctgaacc agatagcccg ccgtgttaac gccggcggcg
     2521 gtaccggcca tgacagggtg cagattgttg cggcgctgat ggccatcgat gccggacttg
     2581 agcggctgcg gcacgccgtt cttgagaaag gaacggacga tgatcgttaa atttcatcca
     2641 cgcggtcgcg gcggtggcgc cgggccggtg gactatctgc tgggtaaaga ccggcagcgt
     2701 gaaggcgcca ccgtcctgca ggggaagccg gaagaagtcc gggagctgat tgacgcgtcg
     2761 ccttacgtta agaaatacac ctccggggta ctgtcgtttg cggaagcgga tttaccttcc
     2821 ggccagcggg aaaagctgat ggcaagcttt gagcgggttc tgatgcccgg acttgataaa
     2881 gaccagtaca gcatcctgtg ggtggagcat cgtgacaagg ggcggcttga gctgaatttt
     2941 ctgatcccga acacggagct gctgaccggc agacggctcc agccgtatta cgatcgcgcc
     3001 gaccgtccac gcatcgatgc ctggcagacc atcgtgaacg gcagactggg gctgcacgac
     3061 ccgaacgcac cggagaaccg gcgggcactg gtcacaccgt ctgcactgcc taaagcgaag
     3121 caggaggctg cagaagcgat tacacgcggt ctgcttgctc ttgcctcatc cggggagctg
     3181 aaaacccgtc aggatgtcac tgaggcgctg gaaagcgcag gttttgaggt ggtccgcacc
     3241 acaaaaagca gtatcagcat tgccgacccg gacggggggc gaaacatccg actgaaggga
     3301 gccatttatg aacagtcttt taacgctggc gaaggactta gagcagaaat cgaaagcgca
     3361 gcagcagaat accggcgaga tgctgaaagc cgcattcagc gagcacgaga aatctgtaaa
     3421 agcggaactg aacgaaagcg cgaagagaat cagcgccgcc atcctcgacc acgaccggaa
     3481 actgtcctca gccatgagcc agcgcacgaa aggcatggtg cgcatggtca gccagacgtg
     3541 gctgaccatc gtcctggtct ccgcgctgct gatcgcctcg agcgcgggca ttctgtggtg
     3601 gcaggggcag cagatactcg acaactacac gaccatccgg gagcagaaga gcacgcaggc
     3661 catgctgtca gagaggaaca gcggcgtgca gctctcgacc tgcggcgagc agagacgccg
     3721 ctgcgtgaag gtgaacccgg aagcgggacg gttcggagag gattcgagct ggatgatact
     3781 ggcggggaaa tagcacatga cggagctgga aaaacagttg ctgagcgcat tagagcagct
     3841 acagcaggac tactcgaaaa ggctggacga gtgggagagc gccttcgcgg aatggcggac
     3901 gatgtctggt cttatgcaac gggagaacgc agcgctgagc gagcgcgtca cgggcttgag
     3961 caggcaggtg cagagtttga gcgagcagct gcgccggttg tcgagcgact gaatgccgtc
     4021 gagctgcacc gggagcagga gcgcgtggtg cagcatcaga aagcgctgga gctggagcga
     4081 tctcagcgac agcggacgta taacagccct tcactgtgat aacctgataa aacggggctt
     4141 tcggcggaca tctgcgctga aagccggagc cattcacccg actgcatagc catgcagccg
     4201 ggtgaaattt atctggcgca gaatgcgcgg tttagcggag agtttgctgc cggttttacc
     4261 gggctgacgc cgcatttgtt ccgaacccgt ccggggcggt gctgataagg gatgttatgg
     4321 taaatgcggc attttttatt atatggagtg tatttttatg agaattaaaa agcctcacct
     4381 tcgtccgata gtcataacct tgtccgttgg tgggattttg ttaacttcta tttttctgat
     4441 tgccgttatt atggtttttc agcgcgaaaa tatagaaaaa gatttgcttt atgctaattc
     4501 atcgtacgct atgaaaatgt cagatgtaat gagtggttat attgaaatgg ctcaaggtga
     4561 attagcatat ggagcaaaaa aaataaaatc aactaatgat attgactcac ttaaagatga
     4621 ggcggatagg ttaagattgc agtctggtat gtttaattca gttc
//
