LOCUS       CP058034                4664 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB03-C12 plasmid pRHB03-C12_4, complete
            sequence.
ACCESSION   CP058034
VERSION     CP058034.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147979
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-C12
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 105.800720179989x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 13:53:24
            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)                     :: 4,561
            CDSs (total)                      :: 4,439
            Genes (coding)                    :: 4,329
            CDSs (with protein)               :: 4,329
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 46 of 110
            Pseudo Genes (incomplete)         :: 48 of 110
            Pseudo Genes (internal stop)      :: 31 of 110
            Pseudo Genes (multiple problems)  :: 13 of 110
            CRISPR Arrays                     :: 1
            ##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-C12"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB03-C12_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            212..1783
                     /locus_tag="HVV62_22775"
     CDS             212..1783
                     /locus_tag="HVV62_22775"
                     /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="QMQ52507.1"
                     /translation="MECIFMRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIE
                     KDLLYANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMF
                     NSVLVVSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIVLLS
                     HPIYDKGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAV
                     DRPMVMSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILI
                     AYAKSVLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYA
                     EADRLKKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVI
                     DVDFFKEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAK
                     CVAERIRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKV
                     IVYSAI"
                     /name="GGDEF domain-containing protein"
     gene            2840..3163
                     /locus_tag="HVV62_22780"
     CDS             2840..3163
                     /locus_tag="HVV62_22780"
                     /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="QMQ52510.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3102..3866
                     /locus_tag="HVV62_22785"
                     /pseudo=""
     CDS             3102..3866
                     /locus_tag="HVV62_22785"
                     /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            3841..4326
                     /locus_tag="HVV62_22790"
     CDS             3841..4326
                     /locus_tag="HVV62_22790"
                     /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="QMQ52508.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            4330..4545
                     /gene="mbeD"
                     /locus_tag="HVV62_22795"
     CDS             4330..4545
                     /gene="mbeD"
                     /locus_tag="HVV62_22795"
                     /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="QMQ52509.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="mbeD"
     Typing          2555..2727
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(2079..2630)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          3154..4649
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.982"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acggggcttt cggcggacat ctgcgctgaa agccggagcc attcacccga ctgcatagcc
       61 atgcagccgg gtgaaattta tctggcgcag aatgcgcggt ttagcggaga gtttgctgcc
      121 ggttttaccg ggctgacgcc gcatttgttc cgaacccgtc cggggcggtg ctgataaggg
      181 atgttatggt aaatgcggca ttttttatta tatggagtgt atttttatga gaattaaaaa
      241 gcctcacctt cgtccgatag tcataacctt gtccgttggt gggattttgt taacttctat
      301 ttttctgatt gccgttatta tggtttttca gcgcgaaaat atagaaaaag atttgcttta
      361 tgctaattca tcgtacgcta tgaaaatgtc agatgtaatg agtggttata ttgaaatggc
      421 tcaaggtgaa ttagcatatg gagcaaaaaa aataaaatca actaatgata ttgactcact
      481 taaagatgag gcggataggt taagattgca gtctggtatg tttaattcag ttcttgttgt
      541 tagtaatgat gctgttgttc tggcgacttc gccagaatct cttgatttag ttggtacccg
      601 cttgaattca agtgccagca aattggcggt tgaggaaaag aaaccattca tatcttcacc
      661 gttaaaatca gttgctggga atttgattgt tttgttgtca catcctattt atgataaggg
      721 tggcaattac atagggtatg tcggtgggtc tatatatcta aaaaaacata gtttatttgg
      781 cgatgttttg agcaggcatt ttttcaagaa caacactgaa attagcattg ttagtgatga
      841 tgggaatgtg atctttaata acgataaaag tgctgttgat cggcctatgg ttatgtctga
      901 tgatttgaaa tcaaagttaa ctgcgtctga tagaggtgag ggggcatttt tttcttcggg
      961 gcatagatat cttcttggtt atgctagtat gaaaaatacc gcttggaatg tgttggttta
     1021 tagtcgtgct gacagtgtga ctactattct tattgcttat gctaaaagtg tacttgttct
     1081 gctaattata ataattattg tgttttcact tatttcatat ttcattgcct ccagtatttc
     1141 acttccttta gaaaagcttg ctatatctac caatgctaaa gatatcggag cttcgctagt
     1201 ttatattaaa gctatcaatg cttggtatgc cgaagctgat aggcttaaaa aggcgctttt
     1261 tacgtatatt aaggtaatga tggaaagagt tgattctcta aatgaggtgg cgcttaaaga
     1321 tccccttacc ggcgtgaata atagattggg gtttttaagt aaaatacaga atcataagcg
     1381 ggattcaggg tgttcagtta ttgtaattga tgttgatttt tttaaagaga taaatgacag
     1441 tttcgggcat ggggtcggag atgaggtgct tgtttctttg gctcatatta ttaattcctg
     1501 ttgccgtagt gaagatgttg tttgtcggtt tggtggcgaa gagtttgttg ttttcctgcc
     1561 gaatacatct gtggtaacag ctaagtgtgt tgcggagcgt attaggagtg ttattgaaag
     1621 tactgtcttc cctaataact tgcgggtcac catatctgct ggtgtggcaa cacaagatga
     1681 tcctcttggt aggatcgatt ttttgctgaa aaatgctgac gatgctcttt atcaagccaa
     1741 aagggagggg cgtaataaag tgattgtata tagcgctatt tgagtttttt gatgatgctt
     1801 tacgcgctag tgtgtcgttt tttttgtggc gaagagtggg caagaagcgg atcctcttgt
     1861 tatcccttcg atgtcgtcgt aatctcatac cctgtaaaca aaaaaaccac cgctaccaac
     1921 ggtggttcgt ttgccggaat tcagagctac caactctttc ttccgaaggt aactggcttt
     1981 cacggagcgc aggtaccaaa actgtccttc cagtgtagcc gcagtcaggc caccacttca
     2041 agaactctgt agaacactct actactccgc tccgtgaatc ctcttactaa tggctaccgc
     2101 cactggcgat ttttcgtgtc tgttccgggt tggactcaag atgatagtta ccgggacaac
     2161 gtggtagtcg ggctgaacgg ggggttcgtg catacagtcc agcttggagc gaactgcctt
     2221 cccggaaccg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc ggattgacat
     2281 cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccaccaggg ggaaacgcct
     2341 ggtatcttta agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga tttcgtgatg
     2401 cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc gtggccttat cgcttccctg
     2461 ttaagcttct tcctggcatc tcccaggaaa tttccgcccc gcctgtaagt cggtaccgct
     2521 cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga atatatcctg
     2581 tatcacatat tctgctgacg ctccgctgct gcatttttct cctgccacat gaagcacttc
     2641 actgacactc gcatccgtgc caacatagta agccagtata cactccgcta gcgctacgtg
     2701 actggttcag ggctgcgccc cgaaacccgc caaaagcctg acgcgcctgc ggcttgtcca
     2761 accccgcgcc gaccgggaaa gcctttcccg cccgtcccgg cgttatcagg aggccggttt
     2821 gtcagagaaa cggaacaaga tgctcaccat gtgggtgacg gagggcgagc accggcggct
     2881 gcttgagcgc tgtgacggca ggcagctggc ggcgtggatg cggcagacct gcctggacga
     2941 aaagccggca cgttccggaa agcttccctc aatctcgccg gcgctgctgc gccagcttgc
     3001 cggcatgggc aataacctga accagatagc ccgccgtgtt aacgccggcg gcggtaccgg
     3061 ccatgacagg gtgcagattg ttgcggcgct gatggccatc gatgccggac ttgagcggct
     3121 gcggcacgcc gttcttgaga aaggaacgga cgatgatcgt taaatttcat ccacgcggtc
     3181 gcggcggtgg cgccgggccg gtggactatc tgctgggtaa agaccggcag cgtgaaggcg
     3241 ccaccgtcct gcaggggaag ccggaagaag tccgggagct gattgacgcg tcgccttacg
     3301 ttaagaaata cacctccggg gtactgtcgt ttgcggaagc ggatttacct tccggccagc
     3361 gggaaaagct gatggcaagc tttgagcggg ttctgattcc cggacttgat aaagaccagt
     3421 acagcatcct gtgggtggag catcgtgaca aggggcggct tgagctgaat tttctgatcc
     3481 cgaacacgga gctgctgacc ggcagacggc tccagccgta ttacgatcgc gccgaccgtc
     3541 cacgcatcga tgcctggcag accatcgtga acggcagact ggggctgcac gacccgaacg
     3601 caccggagaa ccggcgggca ctggtcacac cgtctgcact gcctaaagcg aagcaggagg
     3661 ctgcagaagc gattacacgc ggtctgcttg ctcttgcctc atccggggag ctgaaaaccc
     3721 gtcaggatgt cactgaggcg ctggaaagcg caggttttga ggtggtccgc accacaaaaa
     3781 gcagtatcag cattgccgac ccggacgggg ggcgaaacat ccgactgaag ggagccattt
     3841 atgaacagtc ttttaacgct ggcgaaggac ttagagcaga aatcgaaagc gcagcagcag
     3901 aataccggcg agatgctgaa agccgcattc agcgagcacg agaaatctgt aaaagcggaa
     3961 ctgaacgaaa gcgcgaagag aatcagcgcc gccatcctcg accacgaccg gaaactgtcc
     4021 tcagccatga gccagcgcac gaaaggcatg gtgcgcatgg tcagccagac gtggctgacc
     4081 atcgtcctgg tctccgcgct gctgatcgcc tcgagcgcgg gcattctgtg gtggcagggg
     4141 cagcagatac tcgacaacta cacgaccatc cgggagcaga agagcacgca ggccatgctg
     4201 tcagagagga acagcggcgt gcagctctcg acctgcggcg agcagagacg ccgctgcgtg
     4261 aaggtgaacc cggaagcggg acggttcgga gaggattcga gctggatgat actggcgggg
     4321 aaatagcaca tgacggagct ggaaaaacag ttgctgagcg cattagagca gctacagcag
     4381 gactactcga aaaggctgga cgagtgggag agcgccttcg cggaatggcg gacgatgtct
     4441 ggtcttatgc aacgggagaa cgcagcgctg agcgagcgcg tcacgggctt gagcaggcag
     4501 gtgcagagtt tgagcgagca gctgcgccgg ttgtcgagcg actgaatgcc gtcgagctgc
     4561 accgggagca ggagcgcgtg gtgcagcatc agaaagcgct ggagctggag cgatctcagc
     4621 gacagcggac gtataacagc ccttcactgt gataacctga taaa
//
