LOCUS       CP057367                4664 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB28-C20 plasmid pRHB28-C20_4, complete
            sequence.
ACCESSION   CP057367
VERSION     CP057367.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148273
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-C20
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 169.962581629708x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 08:37:48
            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)                     :: 4,493
            CDSs (total)                      :: 4,374
            Genes (coding)                    :: 4,177
            CDSs (with protein)               :: 4,177
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 197
            CDSs (without protein)            :: 197
            Pseudo Genes (ambiguous residues) :: 0 of 197
            Pseudo Genes (frameshifted)       :: 82 of 197
            Pseudo Genes (incomplete)         :: 107 of 197
            Pseudo Genes (internal stop)      :: 28 of 197
            Pseudo Genes (multiple problems)  :: 19 of 197
            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-C20"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB28-C20_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(86..1657)
                     /locus_tag="HVY56_22445"
     CDS             complement(86..1657)
                     /locus_tag="HVY56_22445"
                     /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="QMG56617.1"
                     /translation="MECIFMRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIE
                     KDLLYANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMF
                     NSVLVVSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLS
                     HPIYDKGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAV
                     DRPMVMSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILI
                     AYAKSVLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYA
                     EADRLKKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVI
                     DVDFFKEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAK
                     CVAERIRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKV
                     IVYSAI"
                     /name="GGDEF domain-containing protein"
     gene            complement(1988..2203)
                     /gene="mbeD"
                     /locus_tag="HVY56_22450"
     CDS             complement(1988..2203)
                     /gene="mbeD"
                     /locus_tag="HVY56_22450"
                     /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="QMG56618.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="mbeD"
     gene            complement(2207..2692)
                     /locus_tag="HVY56_22455"
     CDS             complement(2207..2692)
                     /locus_tag="HVY56_22455"
                     /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="QMG56619.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(2667..3431)
                     /locus_tag="HVY56_22460"
                     /pseudo=""
     CDS             complement(2667..3431)
                     /locus_tag="HVY56_22460"
                     /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(3370..3693)
                     /locus_tag="HVY56_22465"
     CDS             complement(3370..3693)
                     /locus_tag="HVY56_22465"
                     /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="QMG56620.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3807..3979)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          3904..4455
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(1885..3380)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3377..3693)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
ORIGIN
        1 aagggataac aagaggatcc gcttcttgcc cactcttcgc cacaaaaaaa acgacacact
       61 agcgcgtaaa gcatcatcaa aaaactcaaa tagcgctata tacaatcact ttattacgcc
      121 cctccctttt ggcttgataa agagcatcgt cagcattttt cagcaaaaaa tcgatcctac
      181 caagaggatc atcttgtgtt gccacaccag cagatatggt gacccgcaag ttattaggga
      241 agacagtact ttcaataaca ctcctaatac gctccgcaac acacttagct gttaccacag
      301 atgtattcgg caggaaaaca acaaactctt cgccaccaaa ccgacaaaca acatcttcac
      361 tacggcaaca ggaattaata atatgagcca aagaaacaag cacctcatct ccgaccccat
      421 gcccgaaact gtcatttatc tctttaaaaa aatcaacatc aattacaata actgaacacc
      481 ctgaatcccg cttatgattc tgtattttac ttaaaaaccc caatctatta ttcacgccgg
      541 taaggggatc tttaagcgcc acctcattta gagaatcaac tctttccatc attaccttaa
      601 tatacgtaaa aagcgccttt ttaagcctat cagcttcggc ataccaagca ttgatagctt
      661 taatataaac tagcgaagct ccgatatctt tagcattggt agatatagca agcttttcta
      721 aaggaagtga aatactggag gcaatgaaat atgaaataag tgaaaacaca ataattatta
      781 taattagcag aacaagtaca cttttagcat aagcaataag aatagtagtc acactgtcag
      841 cacgactata aaccaacaca ttccaagcgg tatttttcat actagcataa ccaagaagat
      901 atctatgccc cgaagaaaaa aatgccccct cacctctatc agacgcagtt aactttgatt
      961 tcaaatcatc agacataacc ataggccgat caacagcact tttatcgtta ttaaagatca
     1021 cattcccatc atcactaaca atgctaattt cagtgttgtt cttgaaaaaa tgcctgctca
     1081 aaacatcgcc aaataaacta tgttttttta gatatataga cccaccgaca taccctatgt
     1141 aattgccacc cttatcataa ataggatgtg acaacaaaat aatcaaattc ccagcaactg
     1201 attttaacgg tgaagatatg aatggtttct tttcctcaac cgccaatttg ctggcacttg
     1261 aattcaagcg ggtaccaact aaatcaagag attctggcga agtcgccaga acaacagcat
     1321 cattactaac aacaagaact gaattaaaca taccagactg caatcttaac ctatccgcct
     1381 catctttaag tgagtcaata tcattagttg attttatttt ttttgctcca tatgctaatt
     1441 caccttgagc catttcaata taaccactca ttacatctga cattttcata gcgtacgatg
     1501 aattagcata aagcaaatct ttttctatat tttcgcgctg aaaaaccata ataacggcaa
     1561 tcagaaaaat agaagttaac aaaatcccac caacggacaa ggttatgact atcggacgaa
     1621 ggtgaggctt tttaattctc ataaaaatac actccatata ataaaaaatg ccgcatttac
     1681 cataacatcc cttatcagca ccgccccgga cgggttcgga acaaatgcgg cgtcagcccg
     1741 gtaaaaccgg cagcaaactc tccgctaaac cgcgcattct gcgccagata aatttcaccc
     1801 ggctgcatgg ctatgcagtc gggtgaatgg ctccggcttt cagcgcagat gtccgccgaa
     1861 agccccgttt tatcaggtta tcacagtgaa gggctgttat acgtccgctg tcgctgagat
     1921 cgctccagct ccagcgcttt ctgatgctgc accacgcgct cctgctcccg gtgcagctcg
     1981 acggcattca gtcgctcgac aaccggcgca gctgctcgct caaactctgc acctgcctgc
     2041 tcaagcccgt gacgcgctcg ctcagcgctg cgttctcccg ttgcataaga ccagacatcg
     2101 tccgccattc cgcgaaggcg ctctcccact cgtccagcct tttcgagtag tcctgctgta
     2161 gctgctctaa tgcgctcagc aactgttttt ccagctccgt catgtgctat ttccccgcca
     2221 gtatcatcca gctcgaatcc tctccgaacc gtcccgcttc cgggttcacc ttcacgcagc
     2281 ggcgtctctg ctcgccgcag gtcgagagct gcacgccgct gttcctctct gacagcatgg
     2341 cctgcgtgct cttctgctcc cggatggtcg tgtagttgtc gagtatctgc tgcccctgcc
     2401 accacagaat gcccgcgctc gaggcgatca gcagcgcgga gaccaggacg atggtcagcc
     2461 acgtctggct gaccatgcgc accatgcctt tcgtgcgctg gctcatggct gaggacagtt
     2521 tccggtcgtg gtcgaggatg gcggcgctga ttctcttcgc gctttcgttc agttccgctt
     2581 ttacagattt ctcgtgctcg ctgaatgcgg ctttcagcat ctcgccggta ttctgctgct
     2641 gcgctttcga tttctgctct aagtccttcg ccagcgttaa aagactgttc ataaatggct
     2701 cccttcagtc ggatgtttcg ccccccgtcc gggtcggcaa tgctgatact gctttttgtg
     2761 gtgcggacca cctcaaaacc tgcgctttcc agcgcctcag tgacatcctg acgggttttc
     2821 agctccccgg atgaggcaag agcaagcaga ccgcgtgtaa tcgcttctgc agcctcctgc
     2881 ttcgctttag gcagtgcaga cggtgtgacc agtgcccgcc ggttctccgg tgcgttcggg
     2941 tcgtgcagcc ccagtctgcc gttcacgatg gtctgccagg catcgatgcg tggacggtcg
     3001 gcgcgatcgt aatacggctg gagccgtctg ccggtcagca gctccgtgtt cgggatcaga
     3061 aaattcagct caagccgccc cttgtcacga tgctccaccc acaggatgct gtactggtct
     3121 ttatcaagtc cgggcatcag aacccgctca aagcttgcca tcagcttttc ccgctggccg
     3181 gaaggtaaat ccgcttccgc aaacgacagt accccggagg tgtatttctt aacgtaaggc
     3241 gacgcgtcaa tcagctcccg gacttcttcc ggcttcccct gcaggacggt ggcgccttca
     3301 cgctgccggt ctttacccag cagatagtcc accggcccgg cgccaccgcc gcgaccgcgt
     3361 ggatgaaatt taacgatcat cgtccgttcc tttctcaaga acggcgtgcc gcagccgctc
     3421 aagtccggca tcgatggcca tcagcgccgc aacaatctgc accctgtcat ggccggtacc
     3481 gccgccggcg ttaacacggc gggctatctg gttcaggtta ttgcccatgc cggcaagctg
     3541 gcgcagcagc gccggcgaga ttgagggaag ctttccggaa cgtgccggct tttcgtccag
     3601 gcaggtctgc cgcatccacg ccgccagctg cctgccgtca cagcgctcaa gcagccgccg
     3661 gtgctcgccc tccgtcaccc acatggtgag catcttgttc cgtttctctg acaaaccggc
     3721 ctcctgataa cgccgggacg ggcgggaaag gctttcccgg tcggcgcggg gttggacaag
     3781 ccgcaggcgc gtcaggcttt tggcgggttt cggggcgcag ccctgaacca gtcacgtagc
     3841 gctagcggag tgtatactgg cttactatgt tggcacggat gcgagtgtca gtgaagtgct
     3901 tcatgtggca ggagaaaaat gcagcagcgg agcgtcagca gaatatgtga tacaggatat
     3961 attccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtac
     4021 cgacttacag gcggggcgga aatttcctgg gagatgccag gaagaagctt aacagggaag
     4081 cgataaggcc acggcgaagc cgtttttcca taggctccgc ccccctgaca agcatcacga
     4141 aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga cttaaagata ccaggcgttt
     4201 ccccctggtg gctccctcgt gcgctctcct gttcctgcct ttcggtttac cgatgtcaat
     4261 ccgctgttat ggccgcgttt atctcattcc acgcctgaca ctcggttccg ggaaggcagt
     4321 tcgctccaag ctggactgta tgcacgaacc ccccgttcag cccgactacc acgttgtccc
     4381 ggtaactatc atcttgagtc caacccggaa cagacacgaa aaatcgccag tggcggtagc
     4441 cattagtaag aggattcacg gagcggagta gtagagtgtt ctacagagtt cttgaagtgg
     4501 tggcctgact gcggctacac tggaaggaca gttttggtac ctgcgctccg tgaaagccag
     4561 ttaccttcgg aagaaagagt tggtagctct gaattccggc aaacgaacca ccgttggtag
     4621 cggtggtttt tttgtttaca gggtatgaga ttacgacgac atcg
//
