LOCUS       CP057182                2519 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB34-C04 plasmid pRHB34-C04_5, complete
            sequence.
ACCESSION   CP057182
VERSION     CP057182.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148337
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2519)
  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 2519)
  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                     :: RH03 T3-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 165.58193898008x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:49:39
            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)                     :: 4,916
            CDSs (total)                      :: 4,798
            Genes (coding)                    :: 4,549
            CDSs (with protein)               :: 4,549
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 249
            CDSs (without protein)            :: 249
            Pseudo Genes (ambiguous residues) :: 0 of 249
            Pseudo Genes (frameshifted)       :: 95 of 249
            Pseudo Genes (incomplete)         :: 154 of 249
            Pseudo Genes (internal stop)      :: 40 of 249
            Pseudo Genes (multiple problems)  :: 37 of 249
            ##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..2519
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB34-C04"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB34-C04_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2260..2519,1..727)
                     /locus_tag="HVZ20_24560"
     CDS             join(2260..2519,1..727)
                     /locus_tag="HVZ20_24560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QME18870.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSASDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGETLSRMNMAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPSMFTRDYVKHARWVELWRECLRVDYDPSVDVRAVKPRKPKDGE
                     SLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLKL
                     DQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     gene            11..727
                     /locus_tag="HVZ20_24565"
     CDS             11..727
                     /locus_tag="HVZ20_24565"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QME18869.1"
                     /translation="MWQARFYQSLPRIVADYPDARWMFLTLTVRNCAIGELGETLSRMN
                     MAFQRLKDRKEFRPVQGWIRTTEVTRGSDGSAHPHFHTLMMVPPSMFTRDYVKHARWVE
                     LWRECLRVDYDPSVDVRAVKPRKPKDGESLACATAELVRGAVAETLKYSTKPADMVADP
                     EWFLELTRQTHKRRFVATGGALKDVLKLDQETDADMVIGDDISEGDDDGSRIAFEWKTE
                     VRKYRRSPTKDKTESG"
                     /name="protein rep"
     gene            77..727
                     /locus_tag="HVZ20_24570"
     CDS             77..727
                     /locus_tag="HVZ20_24570"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QME18868.1"
                     /translation="MFLTLTVRNCAIGELGETLSRMNMAFQRLKDRKEFRPVQGWIRTT
                     EVTRGSDGSAHPHFHTLMMVPPSMFTRDYVKHARWVELWRECLRVDYDPSVDVRAVKPR
                     KPKDGESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGAL
                     KDVLKLDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     Typing          730..814
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="93.0"
                     /evalue="7.3e-29"
     Typing          940..1195
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.798"
                     /coverage="89.0"
                     /evalue="5.73e-105"
     Typing          complement(1675..1756)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="93.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(454..645)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.964"
                     /coverage="100.0"
                     /evalue="6.14e-93"
ORIGIN
        1 gcgctccctg atgtggcaag cccgttttta tcagtctttg ccgcgtattg tggctgacta
       61 tccagacgca cgatggatgt ttctgaccct gaccgtgcgc aactgtgcga taggggagct
      121 gggcgagaca ctgagccgaa tgaacatggc cttccagcga ctgaaggatc gcaaagagtt
      181 tcgacctgtt cagggctgga tccgcacgac ggaggttact cgaggcagcg acggtagcgc
      241 acacccgcac ttccataccc tgatgatggt gccgccctcg atgttcacgc gtgactatgt
      301 caaacatgcg cgctgggttg aattgtggcg ggagtgtctg cgggtggatt acgacccgag
      361 tgttgatgtc cgggcagtga aaccccgcaa gccgaaggac ggcgaatcgc tggcctgcgc
      421 gaccgccgaa ctggtgcgcg gtgcggtggc cgaaaccctg aaatattcca cgaagccggc
      481 tgacatggtg gccgatcctg aatggttcct cgaactgact cgccagacgc acaaacgccg
      541 ctttgtggcg accggcggcg cactcaaaga cgtgctgaaa ctcgatcagg aaaccgacgc
      601 cgacatggtg atcggggatg atatttccga gggcgacgat gacggttcac gcatcgcgtt
      661 cgagtggaaa accgaggtca gaaagtaccg tcgctcaccg acgaaagata aaactgaatc
      721 aggctagcgg ggtgtcgggg tgcacccctg accagatggc aattgtgata gcgtcgcgtg
      781 tgacggtatt acaattgcac atcctgtcct gtttcaactg ataaataatc cctgtgcagt
      841 acagccgctg ttgcataaaa tttcgctctg cgtcgagtgt ttcttaatca agaattccgc
      901 tgatactccg gaaaaacgcg agtctgttct catgcctgaa atgcccacac cccacgcaaa
      961 aacaattttt tgctgattct tctttataaa tagagagtta tgacaaatta gtttctcttg
     1021 ctctctttgt gatatttaaa aaagcggtgt cggcgcggtg ttgtagctgc gccgacaccg
     1081 ctttgtaggg gtggtactga ctattttcat aaaaaacata atcttatatt aggggtgctg
     1141 ctagcggcgc ggtgtgtttt tttacaggac gcccctgggg gcgctgctag gggtgtctgt
     1201 tcagatatgt agcaatgagt cagggattca cgaattgaaa atgtccgaaa atatgtctca
     1261 tgggcactgt atgcgcccaa accgatcgcc attcagtttc atgcatagtc atgcaacgcg
     1321 ctgaaaacgt tcctgacgca tttttccggt ttaccatggg gaaaacatcc ctttttgcgg
     1381 tgttcgcggc agaatcgcgt tcagcgcgtt ttagcggtgc gcgtaacaag tccttacacc
     1441 acgcgcccca ccccgcggtc gttcccgttc cgtacagcta tcgccaccga cgcgccaaat
     1501 tctggcgacc ggacagcaaa tcattttgcc gtttttgtgc cgcagccgtt ccgcgtgatc
     1561 gacaaactgg cagtcaggga atctcacgaa gtgcgcactt atacaaactt cacttcgttt
     1621 cgtttgtcgt gcggtctgcg acgctcaaaa aaccgagaaa cggcgggaat tttcgggaca
     1681 ggatgtgtaa ttgtaatacc gtcacacgcg acgctatcac aattaccacc tggtcagggc
     1741 tgcgccccga caccccgcca acgcctcacg gcccgcgaaa aaattccgcg taccgctcac
     1801 cgttcccgaa ctcgtcaaac agaaaatcgc ggggccccgc gcctctggcg tgggttccga
     1861 ttttgtgatt gacgacggca cggggaaaac actggggatg gtggttggtg tcacggagtg
     1921 aggccaacca cctgcaagac ggttttttgt tgctgaaaat ccagctcaaa attcaagcaa
     1981 atctcgcgcg cgatccttgt atttatactt aagggataac tctggggata aaaaatagct
     2041 acaggccttg tgtggcaagg ctttgcggct tatttgcgtt gtagaaggtt ttagaagtat
     2101 tctgtcgaaa gtggttgcat taaaagcgac ccccgcaact gcgctaacag ttcgggggtg
     2161 tgaccacctg taggaattcg aattggtgac acgacaacac aggtgatatg gcaatgataa
     2221 cacgtcagat gagccatcgc ccacaatcgg gtggtgtgca tgaaaaatcc tgaactccag
     2281 aacctcacgg actattcccc ctcagatgcg ccatgggacg ctcacagaag cgcttctgac
     2341 gacgtgggag ggatttacct gcttgcagct gaatatgagc gttacggggc gcgtatggcc
     2401 tcctgtggcg gtttactgcg ttttgggtgg tctaccctca aggaaaccgg agaaacgcga
     2461 ctgaggctgc gtgaggcgca tttctgccgt gtccggcact gtcctgtctg ccagtggag
//
