LOCUS       CP058029                4664 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB03-C16 plasmid pRHB03-C16_3, complete
            sequence.
ACCESSION   CP058029
VERSION     CP058029.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147980
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 T1-C16
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 90.0087138364517x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:08:09
            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)                     :: 4,455
            CDSs (total)                      :: 4,334
            Genes (coding)                    :: 4,168
            CDSs (with protein)               :: 4,168
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 87 of 166
            Pseudo Genes (incomplete)         :: 71 of 166
            Pseudo Genes (internal stop)      :: 32 of 166
            Pseudo Genes (multiple problems)  :: 21 of 166
            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="RHB03-C16"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB03-C16_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3789..4664,1..696)
                     /locus_tag="HVV63_22240"
     CDS             join(3789..4664,1..696)
                     /locus_tag="HVV63_22240"
                     /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="QMQ48177.1"
                     /translation="MECIFMRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIE
                     KDLLYANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMF
                     NSVLVVSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLS
                     HPIYDKGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAV
                     DRPMVMSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILI
                     AYAKSVLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYA
                     EADRLKKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVI
                     DVDFFKEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAK
                     CVAERIRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKV
                     IVYSAI"
                     /name="GGDEF domain-containing protein"
     gene            1753..2076
                     /locus_tag="HVV63_22245"
     CDS             1753..2076
                     /locus_tag="HVV63_22245"
                     /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="QMQ48180.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2015..2779
                     /locus_tag="HVV63_22250"
                     /pseudo=""
     CDS             2015..2779
                     /locus_tag="HVV63_22250"
                     /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            2754..3239
                     /locus_tag="HVV63_22255"
     CDS             2754..3239
                     /locus_tag="HVV63_22255"
                     /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="QMQ48178.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3243..3458
                     /gene="mbeD"
                     /locus_tag="HVV63_22260"
     CDS             3243..3458
                     /gene="mbeD"
                     /locus_tag="HVV63_22260"
                     /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="QMQ48179.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="mbeD"
     Typing          1468..1640
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(992..1543)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          1754..2070
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
     Typing          2067..3562
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.982"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataataatta ttgtgttttc acttatttca tatttcattg cctccagtat ttcacttcct
       61 ttagaaaagc ttgctatatc taccaatgct aaagatatcg gagcttcgct agtttatatt
      121 aaagctatca atgcttggta tgccgaagct gataggctta aaaaggcgct ttttacgtat
      181 attaaggtaa tgatggaaag agttgattct ctaaatgagg tggcgcttaa agatcccctt
      241 accggcgtga ataatagatt ggggttttta agtaaaatac agaatcataa gcgggattca
      301 gggtgttcag ttattgtaat tgatgttgat ttttttaaag agataaatga cagtttcggg
      361 catggggtcg gagatgaggt gcttgtttct ttggctcata ttattaattc ctgttgccgt
      421 agtgaagatg ttgtttgtcg gtttggtggc gaagagtttg ttgttttcct gccgaataca
      481 tctgtggtaa cagctaagtg tgttgcggag cgtattagga gtgttattga aagtactgtc
      541 ttccctaata acttgcgggt caccatatct gctggtgtgg caacacaaga tgatcctctt
      601 ggtaggatcg attttttgct gaaaaatgct gacgatgctc tttatcaagc caaaagggag
      661 gggcgtaata aagtgattgt atatagcgct atttgagttt tttgatgatg ctttacgcgc
      721 tagtgtgtcg ttttttttgt ggcgaagagt gggcaagaag cggatcctct tgttatccct
      781 tcgatgtcgt cgtaatctca taccctgtaa acaaaaaaac caccgctacc aacggtggtt
      841 cgtttgccgg aattcagagc taccaactct ttcttccgaa ggtaactggc tttcacggag
      901 cgcaggtacc aaaactgtcc ttccagtgta gccgcagtca ggccaccact tcaagaactc
      961 tgtagaacac tctactactc cgctccgtga atcctcttac taatggctac cgccactggc
     1021 gatttttcgt gtctgttccg ggttggactc aagatgatag ttaccgggac aacgtggtag
     1081 tcgggctgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc cttcccggaa
     1141 ccgagtgtca ggcgtggaat gagataaacg cggccataac agcggattga catcggtaaa
     1201 ccgaaaggca ggaacaggag agcgcacgag ggagccacca gggggaaacg cctggtatct
     1261 ttaagtcctg tcgggtttcg ccaccactga tttgagcgtc agatttcgtg atgcttgtca
     1321 ggggggcgga gcctatggaa aaacggcttc gccgtggcct tatcgcttcc ctgttaagct
     1381 tcttcctggc atctcccagg aaatttccgc cccgcctgta agtcggtacc gctcgccgca
     1441 gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc ggaatatatc ctgtatcaca
     1501 tattctgctg acgctccgct gctgcatttt tctcctgcca catgaagcac ttcactgaca
     1561 ctcgcatccg tgccaacata gtaagccagt atacactccg ctagcgctac gtgactggtt
     1621 cagggctgcg ccccgaaacc cgccaaaagc ctgacgcgcc tgcggcttgt ccaaccccgc
     1681 gccgaccggg aaagcctttc ccgcccgtcc cggcgttatc aggaggccgg tttgtcagag
     1741 aaacggaaca agatgctcac catgtgggtg acggagggcg agcaccggcg gctgcttgag
     1801 cgctgtgacg gcaggcagct ggcggcgtgg atgcggcaga cctgcctgga cgaaaagccg
     1861 gcacgttccg gaaagcttcc ctcaatctcg ccggcgctgc tgcgccagct tgccggcatg
     1921 ggcaataacc tgaaccagat agcccgccgt gttaacgccg gcggcggtac cggccatgac
     1981 agggtgcaga ttgttgcggc gctgatggcc atcgatgccg gacttgagcg gctgcggcac
     2041 gccgttcttg agaaaggaac ggacgatgat cgttaaattt catccacgcg gtcgcggcgg
     2101 tggcgccggg ccggtggact atctgctggg taaagaccgg cagcgtgaag gcgccaccgt
     2161 cctgcagggg aagccggaag aagtccggga gctgattgac gcgtcgcctt acgttaagaa
     2221 atacacctcc ggggtactgt cgtttgcgga agcggattta ccttccggcc agcgggaaaa
     2281 gctgatggca agctttgagc gggttctgat gcccggactt gataaagacc agtacagcat
     2341 cctgtgggtg gagcatcgtg acaaggggcg gcttgagctg aattttctga tcccgaacac
     2401 ggagctgctg accggcagac ggctccagcc gtattacgat cgcgccgacc gtccacgcat
     2461 cgatgcctgg cagaccatcg tgaacggcag actggggctg cacgacccga acgcaccgga
     2521 gaaccggcgg gcactggtca caccgtctgc actgcctaaa gcgaagcagg aggctgcaga
     2581 agcgattaca cgcggtctgc ttgctcttgc ctcatccggg gagctgaaaa cccgtcagga
     2641 tgtcactgag gcgctggaaa gcgcaggttt tgaggtggtc cgcaccacaa aaagcagtat
     2701 cagcattgcc gacccggacg gggggcgaaa catccgactg aagggagcca tttatgaaca
     2761 gtcttttaac gctggcgaag gacttagagc agaaatcgaa agcgcagcag cagaataccg
     2821 gcgagatgct gaaagccgca ttcagcgagc acgagaaatc tgtaaaagcg gaactgaacg
     2881 aaagcgcgaa gagaatcagc gccgccatcc tcgaccacga ccggaaactg tcctcagcca
     2941 tgagccagcg cacgaaaggc atggtgcgca tggtcagcca gacgtggctg accatcgtcc
     3001 tggtctccgc gctgctgatc gcctcgagcg cgggcattct gtggtggcag gggcagcaga
     3061 tactcgacaa ctacacgacc atccgggagc agaagagcac gcaggccatg ctgtcagaga
     3121 ggaacagcgg cgtgcagctc tcgacctgcg gcgagcagag acgccgctgc gtgaaggtga
     3181 acccggaagc gggacggttc ggagaggatt cgagctggat gatactggcg gggaaatagc
     3241 acatgacgga gctggaaaaa cagttgctga gcgcattaga gcagctacag caggactact
     3301 cgaaaaggct ggacgagtgg gagagtgcct tcgcggaatg gcggacgatg tctggtctta
     3361 tgcaacggga gaacgcagcg ctgagcgagc gcgtcacggg cttgagcagg caggtgcaga
     3421 gtttgagcga gcagctgcgc cggttgtcga gcgactgaat gccgtcgagc tgcaccggga
     3481 gcaggagcgc gtggtgcagc atcagaaagc gctggagctg gagcgatctc agcgacagcg
     3541 gacgtataac agcccttcac tgtgataacc tgataaaacg gggctttcgg cggacatctg
     3601 cgctgaaagc cggagccatt cacccgactg catatccatg cagccgggtg aaatttatct
     3661 ggcgcagaat gcgcggttta gcggagagtt tgctgccggt tttaccgggc tgacgccgca
     3721 tttgttccga acccgtccgg ggcggtgctg ataagggatg ttatggtaaa tgcggcattt
     3781 tttattatat ggagtgtatt tttatgagaa ttaaaaagcc tcaccttcgt ccgatagtca
     3841 taaccttgtc cgttggtggg attttgttaa cttctatttt tctgattgcc gttattatgg
     3901 tttttcagcg cgaaaatata gaaaaagatt tgctttatgc taattcatcg tacgctatga
     3961 aaatgtcaga tgtaatgagt ggttatattg aaatggctca aggtgaatta gcatatggag
     4021 caaaaaaaat aaaatcaact aatgatattg actcacttaa agatgaggcg gataggttaa
     4081 gattgcagtc tggtatgttt aattcagttc ttgttgttag taatgatgct gttgttctgg
     4141 cgacttcgcc agaatctctt gatttagttg gtacccgctt gaattcaagt gccagcaaat
     4201 tggcggttga ggaaaagaaa ccattcatat cttcaccgtt aaaatcagtt gctgggaatt
     4261 tgattatttt gttgtcacat cctatttatg ataagggtgg caattacata gggtatgtcg
     4321 gtgggtctat atatctaaaa aaacatagtt tatttggcga tgttttgagc aggcattttt
     4381 tcaagaacaa cactgaaatt agcattgtta gtgatgatgg gaatgtgatc tttaataacg
     4441 ataaaagtgc tgttgatcgg cctatggtta tgtctgatga tttgaaatca aagttaactg
     4501 cgtctgatag aggtgagggg gcattttttt cttcggggca tagatatctt cttggttatg
     4561 ctagtatgaa aaataccgct tggaatgtgt tggtttatag tcgtgctgac agtgtgacta
     4621 ctattcttat tgcttatgct aaaagtgtac ttgttctgct aatt
//
