LOCUS       CP057292                3126 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C16 plasmid pRHB30-C16_6, complete
            sequence.
ACCESSION   CP057292
VERSION     CP057292.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148295
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3126)
  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 3126)
  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 T3-C16
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 133.162200925436x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:08:53
            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)                     :: 5,197
            CDSs (total)                      :: 5,073
            Genes (coding)                    :: 4,833
            CDSs (with protein)               :: 4,833
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 71 of 240
            Pseudo Genes (incomplete)         :: 154 of 240
            Pseudo Genes (internal stop)      :: 35 of 240
            Pseudo Genes (multiple problems)  :: 19 of 240
            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..3126
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB30-C16"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C16_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(2610..3126,1..236))
                     /locus_tag="HVY78_25970"
     CDS             complement(join(2610..3126,1..236))
                     /locus_tag="HVY78_25970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMF65535.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVAG"
                     /name="hypothetical protein"
     gene            complement(695..1018)
                     /locus_tag="HVY78_25975"
     CDS             complement(695..1018)
                     /locus_tag="HVY78_25975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QMF65536.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            1303..1497
                     /locus_tag="HVY78_25980"
     CDS             1303..1497
                     /locus_tag="HVY78_25980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="QMF65537.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQRRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2442..2585
                     /locus_tag="HVY78_25985"
     CDS             2442..2585
                     /locus_tag="HVY78_25985"
                     /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="QMF65538.1"
                     /translation="MNTKVLFVKKALKSITCATLSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     Typing          complement(1028..1266)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.417"
                     /coverage="99.0"
                     /evalue="6.069999999999999e-104"
     Typing          1533..2036
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.528"
                     /coverage="95.0"
                     /evalue="8.27e-156"
     Typing          complement(699..1018)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.93e-62"
ORIGIN
        1 tttgtttgag gtatagagtc gtaccaagca ggcccatgat tagctttgat tgtattgttt
       61 atcgcattac gcagagcaac ctcaatcatc tggacaagac aaaaaaaatc gccagacaga
      121 tcttggtagg caacgtatgc cccaaccttt tcttgatcag tagcgcaccc aagaaatgtt
      181 tcatagaaag ataatcttgg tacagaaatt gagctaatta aacttgttgt atccatgaaa
      241 actcacttat ctctttacta tgaatatttt tcagactacc attacaacat tcgaggagca
      301 ggcgaactac cgtttttctg tgtacctcta gagcgtaaaa tataacaaaa aagcccacta
      361 cagagtgggc ttttttgtta tatttatcta tatgaaacaa ccagttatag ttattgtttc
      421 ataataagga ttgaatactc ttcacaatcc ataacatcag aaaatacttt gctgccaatt
      481 taccataact ccccttacgc gcaccgctaa aacgcgctga acgcgattct gccgcaaaca
      541 ccgcaaaaag agatgtttta cccagtgaaa actggaaaaa tgcgtcagga tcgttttcag
      601 ctcactgcat agctatgcat gaaagtgaat ggcgatcggt ttgggggctt acggcgttca
      661 taccgtctgt tttcgacagt ttctctccgg gaagctaatc tgccataagc ctggataaca
      721 gggcccggtg atactccgta atagcgatca gcacctccgc atactctctg tccccgacac
      781 gcttgccgtc gataaagagt tttttctgta acgcccccag tctcataact tctttcagta
      841 cccgatcatc agtcagtgag ttaactttct taccgagagc tgccgcccgt aaaaaaccgg
      901 aaacggtctt gccgcattca gcagcccttt ttctgatttc ctggtcttct tctgccgtca
      961 gacgaacagg gcgactgata gcccgcctgc gcgtattact tccacttcgt tttgtcataa
     1021 aacatggctc cgtatctgac atggggtgtc ggggcaaagc cctgaccagg gtaattgtaa
     1081 tagcgtgcat gcatgcgcgg tataacaatt gcacatcctg tcctgtcagc aagttcgaat
     1141 taccgacaaa ggcacggcag ttttttggca gtgacagtgt tgcctgacag aaatacccgt
     1201 taaagcgtca gacggcagaa taccggcggc aaaactgccg aaaagtggta cgcgatataa
     1261 tcacacgacg cagatgacag acagaacgga gaaaacagaa agatgaacaa gcagcagcaa
     1321 accgtactta acatggcagg attcataaaa agccagagcc tgacgctgct cgaaaaactg
     1381 gacgcacttg atgctgacga acaggccgcc atgtgtgaga agctgcacga actcgcggaa
     1441 gaacttcaga acagcataca gagacgcttt gaagcggaaa atcgcaccgg gatataacgc
     1501 atccggacag gatgcagaac ggcatagagg agcgtaagga gaaaatgtca cataaggcgc
     1561 tcttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcgactgcg gcgagcggtg
     1621 tcagctcact caaaggcggt aatgcggtta tccacagaat caggggataa agccggaaag
     1681 aacatgtgag caaaagacaa agacccagaa gaagagcacg caggaggcgt ttttccatag
     1741 gctccgcccc cctgacgagc atcacaaaaa ccgacgctca agtcagaggt ggcgaaaccc
     1801 gacaggactt aaagatacca ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt
     1861 cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttgtc tcattccacg
     1921 cctgacactc agttccgggt aggcagttcg ctccaagctg gactgtatgc acgaaccccc
     1981 cgttcagtcc gactactgcg ccttatccgg taactatcgt cttgagtcca acccggaaag
     2041 gcacgactta tcgccattgg cagcagccac tggtaactga tttagaggag ttagtcttga
     2101 agttacgtgc cagttaaggc taaactggaa taacaagttt tggtgactgc gctcctctta
     2161 agccagttac cgcggttcag aaacttgccg gttgctgaac cttcgaaaaa ccaccttgcc
     2221 gggtggtttt ttcgttttta agattacgat gggcgcgata tgaactcaag gaaatccgta
     2281 attaaattat aaaacttcgt gaattaatgg aaaaactgat gtgaatcagc tatttatcct
     2341 taagatttga tgttagatat ggtataatta accattcaaa tagatggaat aaaaagtcaa
     2401 cgctgccatt agaacggcat aagaaataga ggattatgaa aatgaatact aaagttcttt
     2461 ttgtgaaaaa agctttgaaa tcaattactt gcgcaactct ttcgctctta ccggctttaa
     2521 gtcgcgcagt aacagagtta cgtagccttt cggctgcgcg acttaaagcc ggtaagagct
     2581 tttgattgta tcacattttc ccttaaaagt caaccggcta ccttaagctc cctgcactta
     2641 atcctcccta taatccccat aacatactct atcgtgcagc gttcataaaa gcgcctatcg
     2701 tgcccaataa actcaataag ttcctttttc tcgttagaga cgatactcaa ggcattcatt
     2761 aaaaaattga actctttcaa catattattt atggcttgac tatgcgactt gcagtggtgt
     2821 tttttccaaa taggctcatg gtgaaaaagt cgattcctaa acaaaagaac tttatgaaac
     2881 tcgtcaaaca gcgctttaac cttcatatcc cccccaccca aaggattctt cgcatgagga
     2941 aatgtttttg ccttgttctc tggagtccag atgtagcacg gcctttgcgt atccctatat
     3001 ggggcatcta acatataaac ccaaaagcca aaggttagac ggcaaataac atcatcatcc
     3061 gtatacctta cgccacactc atctagtgct ttttgtttcg catttaaaac aagatcctga
     3121 gatttc
//
