LOCUS       CP057737                3971 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB16-C13 plasmid pRHB16-C13_7, complete
            sequence.
ACCESSION   CP057737
VERSION     CP057737.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148137
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3971)
  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 3971)
  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                     :: RH02 T2-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 102.558880900888x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 12:35:52
            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)                     :: 5,948
            CDSs (total)                      :: 5,829
            Genes (coding)                    :: 5,602
            CDSs (with protein)               :: 5,602
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 227
            CDSs (without protein)            :: 227
            Pseudo Genes (ambiguous residues) :: 0 of 227
            Pseudo Genes (frameshifted)       :: 70 of 227
            Pseudo Genes (incomplete)         :: 134 of 227
            Pseudo Genes (internal stop)      :: 42 of 227
            Pseudo Genes (multiple problems)  :: 15 of 227
            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..3971
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB16-C13"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB16-C13_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3959..3971,1..182)
                     /locus_tag="HVX20_29720"
     CDS             join(3959..3971,1..182)
                     /locus_tag="HVX20_29720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="QMM14556.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1248..1430
                     /locus_tag="HVX20_29725"
     CDS             1248..1430
                     /locus_tag="HVX20_29725"
                     /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="QMM14555.1"
                     /translation="MGFWDKAFDVAKTVGKAAWEETKAANEPRQPGGCKLKTAPVRPVV
                     AARPAEYVCSEDLFY"
                     /name="hypothetical protein"
     gene            1445..1633
                     /locus_tag="HVX20_29730"
     CDS             1445..1633
                     /locus_tag="HVX20_29730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957857.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMM14557.1"
                     /translation="MLTRKSIDTVLLSVGAEKLSQREWDWMKMLKPMDPPPAMVTTSIL
                     KRRGDTAALTLLQDTGV"
                     /name="hypothetical protein"
     gene            1643..2842
                     /locus_tag="HVX20_29735"
     CDS             1643..2842
                     /locus_tag="HVX20_29735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558175.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="QMM14558.1"
                     /translation="MLSGFTPRPLKRLFTANQCWTSFLDAGGLRDIEVEAVTKMLACGT
                     RILGVKEFGCDNPDCQHVKYLTNSCGSRACPSCGKKATDLWTATQLNRLPDCDWVHLVF
                     TLPDTLWPVFESNRWLLNDVCRLAVENLLYAARKRGLEPGIFCAIHTYGRRLNWHPHVH
                     VSVTCGGLNKHGQWKKLSFLKDAMRSRWMWNMRQLLLKAWSEGMAMPESLSHITTESQW
                     RSLVLKSGGKYWHVYMSKKTAGGRNTARYLGRYLKKPPIAASRLAHYNGGASLSFRYLD
                     HKTGETATETLTQRELVARMKQHIPEKFFKMVRYFGFLANRVCGEKLPQVYRALGMDKP
                     EPVAKVCYAQMVKQFLSRDPFECVLCGCRMVYRRAIAGLNVSGLKKNARDISLLRYMPA
                     "
                     /name="IS91 family transposase"
     gene            3044..3184
                     /locus_tag="HVX20_29740"
     CDS             3044..3184
                     /locus_tag="HVX20_29740"
                     /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="QMM14559.1"
                     /translation="MSLSDRELARIIATERHSTPLRAGAAMAELKRRGYANAEEIKALL
                     K"
                     /name="hypothetical protein"
     Typing          complement(256..338)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          complement(3451..3695)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.683"
                     /coverage="88.0"
                     /evalue="1.55e-95"
     Typing          complement(3825..3923)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
ORIGIN
        1 aacaaactgc gctgaatatg gcgcgattta tcaaaagcca gagcctgaca ctgcttgaaa
       61 aactggatgc tctggatgcc gacgaacagg cggccatgtg cgaacgactg cacgaactcg
      121 cggaagaact ccagaacagc atccaggttc gctttgagac cgaaagtgaa acaggaacat
      181 aacgaagctg acggaggcgc tcacggcttg tccgcgagcg ttttcggcag cagacaagcc
      241 cgccagggcg cgtcagcggg tgtcggggcg aagccctgac ccagtcacgt agcgatagcg
      301 gagtgtatac tggcttaact atgcggcatc agtgcagatt ataagaaaga gcaccatatg
      361 cggtgtgaaa taccgcacag atgcgtaagg agaaaatgcc gcatcaggcg cacttccgct
      421 tcctcgctca ctgactcgct acgctcggtc gttcggctgc ggcgagcggt gaaaacgatc
      481 tgacatgatc aaaatgatct tcatgcgcta aatgtacaaa agccccgtga cagaatcaca
      541 gggcttcggt actctaattc tttgcagata cctgccagga tcagacgtag caatctaaat
      601 cctagcaggg ctggctagta ttgtcactac cagcttaata ccattcaacg acattaaacc
      661 catatctgca ccttagatgc tcaggtctac gccccggact ccggcaggat aaacaggcaa
      721 ctggtggaaa cgtaacttaa ccgcgaaaga gttaagctct gccccgtctc gctgtacgat
      781 aactagcacc tgataaaatg agcaactaag gagctgtaag aggtaaagtg tgattgcaaa
      841 cgtctggcac ttcacccaca aaatcaagcc gttgcaaggt aagaaaaaca aagaaacgat
      901 ctagacgaag gtcgctacgc tccccgtgat ttatacatta cccaccacgg gggcattagg
      961 cttttattgc ttttttttga tagttatcat gttcttagta acactaagag caacctgata
     1021 gccgtcctcc agcacatcgt tgacaccaat taaacggatt atgtagagtg cactatacaa
     1081 ttctttgttt aacagaggtg gaagatggca ccaacaatat atagagctaa gtgcttggat
     1141 tgtaagcatg aatggactag cagagcaggt tatgggacac cagactactg cccaaaatgc
     1201 cgtagccgca gaatatcaac atctccgatt ggataaagga gaccactatg ggattctggg
     1261 ataaagcttt tgatgtagct aaaaccgtag gaaaagctgc atgggaagaa acaaaagctg
     1321 caaatgaacc acggcagcct ggcggctgca aattgaaaac cgccccggtt cgtcctgttg
     1381 ttgccgcacg ccccgcagaa tatgtatgct ctgaggacct gttttattaa ggactcatcc
     1441 ccttatgttg acccgcaaaa gtatcgatac agttctgctc tctgttggtg ctgagaagct
     1501 ctcacaacga gaatgggact ggatgaaaat gctcaaaccc atggacccac cacctgcgat
     1561 ggtgacgacc tccatcctga agcgccgtgg cgatacagca gcccttaccc tgctacagga
     1621 taccggggtt taatccatcc tcatgttgtc cggttttact ccccgccctc tgaaacgtct
     1681 gttcacagcc aaccagtgct ggacgtcctt cctggatgcg ggcggtctgc gcgatatcga
     1741 ggttgaagcc gtcaccaaaa tgctggcctg cggcacacgg atactgggtg taaaagagtt
     1801 cgggtgtgat aacccggact gtcagcacgt aaagtacctg accaactcat gcggcagccg
     1861 tgcctgcccg tcctgcggaa agaaggccac agacctgtgg acagcaacac agctgaatcg
     1921 tcttcctgac tgcgactggg tacatctggt cttcaccctg ccggacacgc tgtggccggt
     1981 gttcgaaagc aaccgctggc tgctgaatga cgtgtgccgt ctggcggtgg agaatctgct
     2041 gtatgccgcc cgaaaacggg ggctggaacc cggtatcttc tgcgccatcc acacgtatgg
     2101 ccgtcgtctc aactggcatc cgcatgtaca tgtgtctgta acctgtggag gtctgaataa
     2161 gcatggtcag tggaaaaagc tgagcttcct gaaagacgcg atgcgttcac ggtggatgtg
     2221 gaatatgcgg cagctgcttc tgaaagcgtg gtcagagggg atggcaatgc cggagtcgtt
     2281 gtcacatatc acgacggaat cacagtggag aagcctggtg ctgaaatccg gcggaaaata
     2341 ctggcatgtg tacatgtcga agaagacagc cggagggcgg aatacggcac gctacctggg
     2401 tcgttatctg aagaagccac caatagcggc ttcccgactg gctcattaca acggaggggc
     2461 aagcctgagc ttccgttacc tggaccacaa aacgggagaa acggcgacgg aaacgctgac
     2521 acagcgtgag ctggtcgcga ggatgaaaca gcacatcccg gagaagtttt ttaagatggt
     2581 gaggtacttc gggttccttg ccaaccgtgt gtgtggagag aagctgccgc aggtgtaccg
     2641 tgcactgggg atggataaac cggaaccagt ggcgaaagtg tgctatgcac aaatggtgaa
     2701 acagttcctg agtcgtgacc cgttcgaatg cgtgctgtgt ggctgccgga tggtataccg
     2761 ccgggccatt gcggggctga atgtatcagg gctgaagaaa aacgcgcggg atatcagtct
     2821 actgaggtat atgccggcct gacacaggct aagtgtgccc gggaatcggt gaaagtataa
     2881 aaaacagcct gttacggtat aaaaatcgac catacagaga gggaaaccac cggagtggtg
     2941 ggaaaagcag aaaggctcac gtggcataag gcgtggacaa tggtatcgac tggtttttca
     3001 atttcctata cgtgaacgag ccaagcagta cagagaagag gtagtgtcac tcagcgatcg
     3061 cgaactagca agaatcattg caacagaacg ccacagcaca ccattaagag ctggcgctgc
     3121 aatggctgag ttaaaaagaa gaggctatgc taatgccgaa gaaataaaag ccctcctaaa
     3181 ataaccatag actccattta ccataacgtc gcattgtacg caccgctaaa acgcgctgaa
     3241 cgcgattctg ccgcaaacac cgcaaaaaga gatgttttcc ccggggtaaa ccggaaaaat
     3301 gcgtcaggat cgctttcagc tcactgcata gctatgcatg aaagtgaatg acgatcggtt
     3361 tgggcgcata cagtgcccat gagacacatt ttcggacatt ttcagttcgt gaatccctga
     3421 ctcattgcta tatatctgaa tagacacccc tagcagcgcc cccaggggca tcctgtaaaa
     3481 aaacacaccg cgccgctagc agcaccccta atataaaacg atgtttttta tgaaaatagt
     3541 cagtaccacc cctacaaagc ggtgtcggcg cggtgttgta gctgcgttaa cgacgctgtt
     3601 ttaaataaat cagatttaaa caatataaat ccacaaacat aactcaatga tattaaagaa
     3661 aaatcagcaa aaagttagtt ttgcgtgggg tgtggcattt caggcatgag aacagactcg
     3721 cgtttttccg gagtatcagc ggaattattg attaagaaac actcgacgca gagcgaaatt
     3781 ttatgcaaca gcggctgcac tgcacaggga ttatttatca gttgatatgc tgtgccatga
     3841 tacgtcctaa aaaaacagga caggatgtgc aattgtaata ccgtcgcccg caacgtctta
     3901 caattaccac ctggtcaggg tccacccgac acccggtact gacggagaac aacggaaggt
     3961 gaacaaacag c
//
