LOCUS       CP058039                2460 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB03-C08 plasmid pRHB03-C08_4, complete
            sequence.
ACCESSION   CP058039
VERSION     CP058039.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147977
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2460)
  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 2460)
  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-C08
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 102.885002925307x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 13:14:04
            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)                     :: 4,392
            CDSs (total)                      :: 4,274
            Genes (coding)                    :: 4,026
            CDSs (with protein)               :: 4,026
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 248
            CDSs (without protein)            :: 248
            Pseudo Genes (ambiguous residues) :: 0 of 248
            Pseudo Genes (frameshifted)       :: 115 of 248
            Pseudo Genes (incomplete)         :: 111 of 248
            Pseudo Genes (internal stop)      :: 45 of 248
            Pseudo Genes (multiple problems)  :: 21 of 248
            CRISPR Arrays                     :: 2
            ##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..2460
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB03-C08"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB03-C08_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2183..2460,1..226)
                     /locus_tag="HVV60_21950"
     CDS             join(2183..2460,1..226)
                     /locus_tag="HVV60_21950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001565850.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMQ56536.1"
                     /translation="MAKRGAGVNTKKISRLERHTYMDENGEVKQDSKIETFSIPAEPPY
                     VKLYIADIAMIHGLSKSQNDVLLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKN
                     IIAALVDKQIFFRAGRGELEANPFLFARGDWPSIYERRKKIELKISYDTNGRTVQTKVM
                     DDEC"
                     /name="hypothetical protein"
     gene            213..443
                     /locus_tag="HVV60_21955"
     CDS             213..443
                     /locus_tag="HVV60_21955"
                     /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="hypothetical protein"
                     /protein_id="QMQ56537.1"
                     /translation="MMNAEDKLFKNVDRLMLHDSLKKNEVLTVWERTFLSSVYSIYRRT
                     SGNKYSTKGLSPKQKNAAFSILKKYNYHLMD"
                     /name="hypothetical protein"
     gene            complement(542..1558)
                     /locus_tag="HVV60_21960"
     CDS             complement(542..1558)
                     /locus_tag="HVV60_21960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001707479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="QMQ56538.1"
                     /translation="MRSPDWLDVRQNEGVSMANYAIMRCKKLTGMGSVASALQHCYRER
                     ETPNADAERTPENYCSVSQSADEAMGKLRELLPEKRRKDAVLAVEYVMTASPEWWNEAT
                     PRQQAEFFARSEQWLEKKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGG
                     RSKMREDQSTYAESVKKLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPR
                     VLRKGIFTKDVEDQAAIAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKR
                     LQSVTEPFKGLSREQMTEILMMAQRFKQKNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="plasmid recombination protein"
     Typing          complement(546..1558)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.041"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagggttcat attgaatatc agacctttaa aaacataatt gcggctcttg tagataaaca
       61 aatattcttc cgggcagggc gtggggaact tgaagctaac ccctttcttt ttgcacgggg
      121 agactggcca tcaatttacg aaagaagaaa gaaaattgag ttaaagatca gttatgacac
      181 caatggaaga acggtgcaga cgaaggtaat ggatgatgaa tgctgaagat aaacttttta
      241 aaaatgtaga caggctaatg ctgcatgatt cactaaaaaa gaatgaggtt ctgactgttt
      301 gggagcgtac ttttttaagc agtgtttaca gcatatatcg tagaactagc ggtaataaat
      361 actcaactaa gggtttgtca ccaaagcaga aaaacgcagc tttttctatt ttgaaaaaat
      421 acaattacca tctgatggat tagctggcct cagcgttata cagggcggca gaacctgatc
      481 tctggaatgc cgcaaatgac gtcactttgc ggcgttagcc ctatcctgca tcgcatcaaa
      541 actaacgctc cataccaccc atgccacgcg atcgcgtctg tcgctgtttt tcacgttcaa
      601 tacgctgctg tttttccttt tcctggtttt tctgcttaaa ccgctgagcc atcatcagga
      661 tttcggtcat ctgctctctg gaaagcccct taaaaggctc tgtaacgctc tgtaggcgtt
      721 tctgctgcgc atccatagtc ttctgtagct cacgcgctct ttttgcgttc tgggcgctct
      781 gagaggccat agcgatggtt cctgcaaagc catcgttcac tgcgtggctt agacgtttgg
      841 ctatggctgc ctgatcttcc acgtctttgg tgaaaatgcc cttccgcaat acacgcggct
      901 ccagcgcctc cggcgagatc gatacctggc tacgggtgcc acggtttatc gattcgtagt
      961 agtgctgaac tgtctgatgc gtggcgcggc ttccctcgat gccgcgctca agacccagtt
     1021 tttttactga ttcagcgtag gtgctctgat cttcacgcat ctttgaccgc ccgccaataa
     1081 actctttcgc ggacagccgt ccatcctgcg tcaatggcac cacgaacgca gacaggtgcg
     1141 gggtggcctc gtcccggtga accaccgccg ccacaacacg atccttcccg tatttcttct
     1201 ccagccattg ctcagagcgg gcgaaaaact ccgcctgctg ccgcggtgtg gcctcgttcc
     1261 accactcagg gcttgccgtc ataacgtatt caacagccag taccgcatct ttacggcgtt
     1321 tttccggcaa cagctcccgc agctttccca tcgcctcatc tgccgactga gacacagagc
     1381 agtagttttc tggtgtccgt tcagcgtcag cattcggcgt ctcacgctcc ctgtagcagt
     1441 gctgcaaagc gctggccaca ctgcccattc ccgtcagctt tttgcagcgc attatcgcgt
     1501 aattcgccat gcttaccccc tcgttctggc gtacatccag ccagtcgggg gatcgcattg
     1561 cgatgcctcc ggcgggccac tatcaggatg atagtgtact cactagactt tgctacgcaa
     1621 aatcgttcgg gcagcaagct gccagaaggt caaaatcaac ggcagtctgg caggtggaag
     1681 gcgtcgctcc gcgccacccc ccaccactgc caagcctgtt ttatccggtg agtcgtcaag
     1741 ggtaaatggc actcgcttcg ctcgcccctg acgaaatcag gcaatgaata tcgtttttga
     1801 aagagcagga accgctcgcc gcaagaacgg attagggagc ggcatcgccg cgagtctgtc
     1861 cgttcgagga agcggaattt ccactccccg gacatagaaa tccgtacgct ccagactcaa
     1921 aaaagctcgt ttttcgatgt ttaaaaatgg cgtttttcag cctttatttt ccctcttaat
     1981 atatagatat agatatggga acccgcttgt accaagggct agagcgaaga atcgtactca
     2041 cctcaaggac taatcgtact cacctcaagt actaatcgta ctcacctcaa ggactaatcg
     2101 tactcacctc aagtactaat cgtacttgat gcaaaggact tgactgtatg tctctttagt
     2161 acttaaatgc gagtactaaa tcatggcgaa acgtggggct ggagtgaata cgaaaaagat
     2221 ttctaggctt gaacggcata catacatgga tgaaaacggt gaggtaaaac aagactctaa
     2281 gatcgagacc ttttccatcc cagccgaacc tccctacgtc aagctataca ttgcagacat
     2341 tgcgatgatt catggtttat caaaatctca aaatgatgtg cttttacaat tggcaatgct
     2401 gattggatgg gatgggtttg tgtctgtatc aaaaactaga tttgaaaaaa ccatacagcc
//
