LOCUS       CP057074                4145 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB39-C03 plasmid pRHB39-C03_3, complete
            sequence.
ACCESSION   CP057074
VERSION     CP057074.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148396
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4145)
  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 4145)
  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                     :: RH09 T3-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 153.536239466272x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 05:04:26
            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)                     :: 4,718
            CDSs (total)                      :: 4,594
            Genes (coding)                    :: 4,363
            CDSs (with protein)               :: 4,363
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 89 of 231
            Pseudo Genes (incomplete)         :: 135 of 231
            Pseudo Genes (internal stop)      :: 36 of 231
            Pseudo Genes (multiple problems)  :: 24 of 231
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB39-C03"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB39-C03_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3053..4145,1..50))
                     /gene="fepE"
                     /locus_tag="HVZ79_23570"
     CDS             complement(join(3053..4145,1..50))
                     /gene="fepE"
                     /locus_tag="HVZ79_23570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator"
                     /protein_id="QMC42732.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="fepE"
     gene            209..707
                     /locus_tag="HVZ79_23575"
                     /pseudo=""
     CDS             209..707
                     /locus_tag="HVZ79_23575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS5 family transposase"
                     /name="IS5 family transposase"
     gene            complement(1295..1408)
                     /locus_tag="HVZ79_23580"
     CDS             complement(1295..1408)
                     /locus_tag="HVZ79_23580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMC42733.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2594..2776)
                     /locus_tag="HVZ79_23585"
                     /pseudo=""
     CDS             complement(2594..2776)
                     /locus_tag="HVZ79_23585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            2773..3015
                     /locus_tag="HVZ79_23590"
                     /pseudo=""
     CDS             2773..3015
                     /locus_tag="HVZ79_23590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     Typing          complement(1292..1677)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 taacggggaa aatcgaggtc cgtgtttttc ttgaaatcca tcgctgacat aaccgttctt
       61 ctttttggag cgcagtaaat ttctgcctga ttggttgcag tggtcggatg atacaagaaa
      121 gtaagaataa tctgaacgcc agattgatct atctgtagac cgactatcag atttagggaa
      181 ggtgcgaaca agtccctgat ataagatcat gtttgtcatc tggagccatg gaacagggtt
      241 catcatgagt catcaactta ccttcgccga cagtgaattc agcagtaagc gccgtcagac
      301 cagaaaagag attttcttgt cccgcatgga gcagattctg ccatggcaaa acatggtgga
      361 agtcatcgag ccgttttacc ccaaggctgg taatggccgg cgaccttatc cgctggaaac
      421 catgctacgc attcactgca tgcagcattg gtacaacctg agcgatggcg cgatcgaaga
      481 tgctctgtac gaaatcgcct ccatgcgtct gtttgcccgg ttacatgaaa gccagcatcc
      541 gggccaaggt ggagcaccca tttcgcatca tcaagcgaca gttcggcttc gtgaaagcca
      601 gatacaaggg gttgctgaaa aacgataacc aactggcgat gttattcacg ctggccaacc
      661 tgtttcgggc ggaccaaatg atacgtcagt gggagagatc tcactaaaaa ctgggaataa
      721 cgccttaaat ggcgaagaaa cggtctaaat aggctgattc aaggcattta cgggagaaaa
      781 aaatcggctc aaacatgaag aaatgaaatg actgagtcaa ccgagaagaa tttccccgct
      841 tattcgcacc ttccctaata gcgcggctgc gattctactt ttttcacctg aacctgaaga
      901 ggcgtttgtg gctccgcagt gtgggcatga ctttgctgtt tcgtgtattt ccttgccgca
      961 tcctcggcag taaaccattg aactcatttt ttatcctcga gcttattttt agttgggatg
     1021 cataatatcc gatgttttat aacgatatgc atcctatatg ctcgggtggg atagatttcc
     1081 attatggtga aggatcttct tgagatcctt tctgtagcgt cgtaatctct tgctcagtaa
     1141 acgaaaaaac cgcccagcaa ggcggttttt cgaaggttct cagagctgca actctttgaa
     1201 ccgtggtaac tggcttatga ggagcgcagt aaccaaatct gttctttcag tttagcctta
     1261 acaggcgcat aacttcaaga ctaactcctc taaatcagtt accagtggct gctgccagtg
     1321 gcgctttgtc gtgtctttcc ggcttggact caagtcgata gttaccggag aagacgcagc
     1381 ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg
     1441 aactgagtgt caggcgtgga atgagataaa cgcggccata acagcggaat gacaccggta
     1501 aaccgaaagg caggaacagg agagcgcacg agggagccac cagggggaaa cgcctggtat
     1561 ctttaagtcc tgtcgggttt cgccaccact gatttgagcg tcagattctg tgatgcttgt
     1621 caggggggcg gagcctatgg aaaaccggca acgccgcggc cttttctttt gcctctcgat
     1681 cctctctcat tgcctgtgcc ttaatgtctc cgttccctcc gctcgccgca gccgaacgac
     1741 cgagcgtagc gagtcagtga gcgaggaagc ggaatatccc cggacttatc ttcggcaccg
     1801 tacgcgccag tgctgcattt tttaatacga tgcaggatag ggctaacgcc gcaaagtgac
     1861 gtcacctgac gttcctggat tacaaaggtt aaagcagcgg acaggaaatt ttttgtgccc
     1921 acagctatgc tggcttattc acaaaacagc gggacaagat gtgtttttgg agtaccgccg
     1981 gcccgctaaa gactcctggt tagctcccgc atgtttgcta tctttttgct accattttgc
     2041 tacttttttg ctatctccag agtcttctgg tctttcggtt gctatccttt tgctactttt
     2101 ttgctatcaa aatgctacct ctcccttctt gcaataaatg accaaggcac gttagcgatg
     2161 tatacatcgc cgcgccgcaa gggtgcccct tccgaatccc gttcatcact gcgtgctgat
     2221 tcatccacgt taaatccgac ccccttagca ataaatccag ccatgcctga cggcctggcc
     2281 aacgcctcac ggccgcacag taaactgcac acccgtgagg cgttattcgt gaggttcagt
     2341 ggtgcttttg ggcgtccagc cggattttag ccgctaaaat cccggccatg catgtgtgtg
     2401 catagccatg cagacgcgcc agaatcatca ggcgcgtttt ttcacgatat aggcacaggg
     2461 aagtgtcgga aacaggcagg aagacccaga aacgccctga gagcctctca ggcggtgcac
     2521 gcaacggatg ttatggtaaa tctgcctcac agactggtac aaaaaaagcc ccgcagggct
     2581 tttttgctat gagttagcca tattttcttg cgaatttttc atcggaatcg catagataaa
     2641 taataaactc aataaacgcg atgatcgcgg gtatgaatgt ccagcaaaaa attagataca
     2701 ggaatccctg tcctatttta cctaagtaaa atttatgtac gccaaatcca ccaaggaaga
     2761 atgctaagaa agatgatggc ggtggaggtc aattttgagc agggtgcgat tggcccgatg
     2821 cacaatcacc cgcatgaaca gcttacctat gtgctctccg gggagttcga gtttacgata
     2881 ggtgaagaaa agcagatcgt gacggcgggc gatacgctct ataaagcgcc gcacgtgatg
     2941 cacggctgca tttgcctgaa gcccggcacc cttctggata cctttacgcc ggtgcgcgac
     3001 gatttcctga aataaaaaaa ggcgctgaat cagcgccttt ttaatatcgt cgttactctg
     3061 ttgctggcgt tacggccgtt atcggctctg gcaacggatt acgcgagagc attgcctcac
     3121 gcagcagcac gctgccgcag gcaaacaggc cgcccagaat ccctgccagc agcacaatca
     3181 gggctttgcc cggaccgtct tttttcaccg gcagtgacgg tgaaagctga tacctgaagg
     3241 gttcaagctt cacgtcttcc acggacagtt tttgcaactg agtcagatag tattcacggt
     3301 tctggaaatc cgcattcagc tcggccacgt ccttcagatt cttttcaatc tgcagctttt
     3361 gcgcaatacc gtcagcaccc agcgccacgg agtagtcagg atcgtctttt accgcctgtc
     3421 cgttgctgta aaccggcttc ttaatgcctg ccgcgttcgc cacttccagc gaatagttga
     3481 ggcgctgcag gttggtgttg tggatattgg tcagacgcac gcgatccagc tccagctgct
     3541 gctgaacgac tttcgttttc agcgtgatct ggttacggat attttccatc gtctcctgct
     3601 caacaatgcg ggagatatag ttgatgtaac cttccagaac cgtctgcgcg tctcccgccg
     3661 tcggggcggt aaagctcagc gtccatgagg tatacggcgc tttgtctgcg tctttaacct
     3721 gcgtgttatc tgtcgctttc attttctcag caatattcac caccgcgcga tgcagctcca
     3781 gcgggtctac ctcggtgcct tccagctgag acatcacgta cggggaggtt ttcatgtact
     3841 cttcgagcag cgactgcgac tgaaactttt tgatgaacag gttaaacacg tctccacggc
     3901 tcaccttcgc gtcgacgtcc agcacctgca gcgtcaccat catctggcgc agcgtgttcc
     3961 actgcgtctg ctcggccggc gtgatcacgg ctttactggt ccatttttgc gggattaaaa
     4021 acgcaatggc caaccctact acggcgaacg ccaggacgat cgtcacaata cgttttttgg
     4081 ctgccagaag tacgtctaac aaccccagga gatctatctc tttggtgctt accgccggag
     4141 tggca
//
