LOCUS       CP057006                2460 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C03 plasmid pRHB41-C03_5, complete
            sequence.
ACCESSION   CP057006
VERSION     CP057006.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148421
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 T3-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 170.662648303445x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 03:11:22
            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)                     :: 4,437
            CDSs (total)                      :: 4,318
            Genes (coding)                    :: 4,056
            CDSs (with protein)               :: 4,056
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 262
            CDSs (without protein)            :: 262
            Pseudo Genes (ambiguous residues) :: 0 of 262
            Pseudo Genes (frameshifted)       :: 119 of 262
            Pseudo Genes (incomplete)         :: 121 of 262
            Pseudo Genes (internal stop)      :: 46 of 262
            Pseudo Genes (multiple problems)  :: 22 of 262
            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="RHB41-C03"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C03_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(1904..2460,1..460)
                     /locus_tag="HV004_22175"
     CDS             join(1904..2460,1..460)
                     /locus_tag="HV004_22175"
                     /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="QMB34792.1"
                     /translation="MRSPDWLDVRQNEGVSMANYAIMRCKKLTGMGSVASALQHCYRER
                     ETPNADAERTPENYCSVSQSADEAMGKLRELLPEKRRKDAVLAVEYVMTASPEWWNEAT
                     PRQQAEFFARSEQWLEKKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGG
                     RSKMREDQSTYAESVKKLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPR
                     VLRKGIFTKDVEDQAAIAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKR
                     LQSVTEPFKGLSREQMTEILMMAQRFKQKNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="plasmid recombination protein"
     gene            complement(559..789)
                     /locus_tag="HV004_22180"
     CDS             complement(559..789)
                     /locus_tag="HV004_22180"
                     /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="QMB34793.1"
                     /translation="MMNAEDKLFKNVDRLMLHDSLKKNEVLTVWERTFLSSVYSIYRRT
                     SGNKYSTKGLSPKQKNAAFSILKKYNYHLMD"
                     /name="hypothetical protein"
     gene            complement(776..1279)
                     /locus_tag="HV004_22185"
     CDS             complement(776..1279)
                     /locus_tag="HV004_22185"
                     /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="QMB34794.1"
                     /translation="MAKRGAGVNTKKISRLERHTYMDENGEVKQDSKIETFSIPAEPPY
                     VKLYIADIAMIHGLSKSQNDVLLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKN
                     IIAALVDKQIFFRAGRGELEANPFLFARGDWPSIYERRKKIELKISYDTNGRTVQTKVM
                     DDEC"
                     /name="hypothetical protein"
     Typing          3..457
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.395"
                     /coverage="99.0"
                     /evalue="6.62e-74"
     Typing          1905..2458
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.378"
                     /coverage="99.0"
                     /evalue="1.06e-125"
ORIGIN
        1 catcgaggga agccgcgcca cgcatcagac agttcagcac tactacgaat cgataaaccg
       61 tggcacccgt agccaggtat cgatctcgcc ggaggcgctg gagccgcgtg tattgcggaa
      121 gggcattttc accaaagacg tggaagatca ggcagccata gccaaacgtc taagccacgc
      181 agtgaacgat ggctttgcag gaaccatcgc tatggcctct cagagcgccc agaacgcaaa
      241 aagagcgcgt gagctacaga agactatgga tgcgcagcag aaacgcctac agagcgttac
      301 agagcctttt aaggggcttt ccagagagca gatgaccgaa atcctgatga tggctcagcg
      361 gtttaagcag aaaaaccagg aaaaggaaaa acagcagcgt attgaacgtg aaaaacagcg
      421 acagacgcga tcgcgtggca tgggtggtat ggagcgttag ttttgatgcg atgcaggata
      481 gggctaacgc cgcaaagtga cgtcatttgc ggcattccag agatcaggtt ctgccgccct
      541 gtataacgct gaggccagct aatccatcag atggtaattg tattttttca aaatagaaaa
      601 agctgcgttt ttctgctttg gtgacaaacc cttagttgag tatttattac cgctagttct
      661 acgatatatg ctgtaaacac tgcttaaaaa agtacgctcc caaacagtca gaacctcatt
      721 cttttttagt gaatcatgca gcattagcct gtctacattt ttaaaaagtt tatcttcagc
      781 attcatcatc cattaccttc gtctgcaccg ttcttccatt ggtgtcataa ctgatcttta
      841 actcaatttt ctttcttctt tcgtaaattg atggccagtc tccccgtgca aaaagaaagg
      901 ggttagcttc aagttcccca cgccctgccc ggaagaatat ttgtttatct acaagagccg
      961 caattatgtt tttaaaggtc tgatattcaa tatgaaccct gggctgtatg gttttttcaa
     1021 atctagtttt tgatacagac acaaacccat cccatccaat cagcattgcc aattgtaaaa
     1081 gcacatcatt ttgagatttt gataaaccat gaatcatcgc aatgtctgca atgtatagct
     1141 tgacgtaggg aggttcggct gggatggaaa aggtctcgat cttagagtct tgttttacct
     1201 caccgttttc atccatgtat gtatgccgtt caagcctaga aatctttttc gtattcactc
     1261 cagccccacg tttcgccatg atttagtact cgcatttaag tactaaagag acatacagtc
     1321 aagtcctttg catcaagtac gattagtact tgaggtgagt acgattagtc cttgaggtga
     1381 gtacgattag tacttgaggt gagtacgatt agtccttgag gtgagtacga ttcttcgctc
     1441 tagcccttgg tacaagcggg ttcccatatc tatatctata tattaagagg gaaaataaag
     1501 gctgaaaaac gccattttta aacatcgaaa aacgagcttt tttgagtctg gagcgtacgg
     1561 atttctatgt ccggggagtg gaaattccgc ttcctcgaac ggacagactc gcggcgatgc
     1621 cgctccctaa tccgttcttg cggcgagcgg ttcctgctct ttcaaaaacg atattcattg
     1681 cctgatttcg tcaggggcga gcgaagcgag tgccatttac ccttgacgac tcaccggata
     1741 aaacaggctt ggcagtggtg gggggtggcg cggagcgacg ccttccacct gccagactgc
     1801 cgttgatttt gaccttctgg cagcttgctg cccgaacgat tttgcgtagc aaagtctagt
     1861 gagtacacta tcatcctgat agtggcccgc cggaggcatc gcaatgcgat cccccgactg
     1921 gctggatgta cgccagaacg agggggtaag catggcgaat tacgcgataa tgcgctgcaa
     1981 aaagctgacg ggaatgggca gtgtggccag cgctttgcag cactgctaca gggagcgtga
     2041 gacgccgaat gctgacgctg aacggacacc agaaaactac tgctctgtgt ctcagtcggc
     2101 agatgaggcg atgggaaagc tgcgggagct gttgccggaa aaacgccgta aagatgcggt
     2161 actggctgtt gaatacgtta tgacggcaag ccctgagtgg tggaacgagg ccacaccgcg
     2221 gcagcaggcg gagtttttcg cccgctctga gcaatggctg gagaagaaat acgggaagga
     2281 tcgtgttgtg gcggcggtgg ttcaccggga cgaggccacc ccgcacctgt ctgcgttcgt
     2341 ggtgccattg acgcaggatg gacggctgtc cgcgaaagag tttattggcg ggcggtcaaa
     2401 gatgcgtgaa gatcagagca cctacgctga atcagtaaaa aaactgggtc ttgagcgcgg
//
