LOCUS       CP057619                3005 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB21-C02 plasmid pRHB21-C02_3, complete
            sequence.
ACCESSION   CP057619
VERSION     CP057619.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148186
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3005)
  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 3005)
  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                     :: RH06 T2-C02
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 130.374798636072x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 10:28:39
            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)                     :: 5,063
            CDSs (total)                      :: 4,947
            Genes (coding)                    :: 4,837
            CDSs (with protein)               :: 4,837
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 49 of 110
            Pseudo Genes (incomplete)         :: 50 of 110
            Pseudo Genes (internal stop)      :: 32 of 110
            Pseudo Genes (multiple problems)  :: 16 of 110
            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..3005
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB21-C02"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB21-C02_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(2792..3005,1..170))
                     /locus_tag="HVX69_25295"
     CDS             complement(join(2792..3005,1..170))
                     /locus_tag="HVX69_25295"
                     /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="QMK62565.1"
                     /translation="MKFFKPKTDAIEYIRVEPSFSKTSSNINNAKSGSDTNSQPGFILR
                     SQIEEMIKNHRPKTEKEIKAESEGLIRLCSMAFIFLIVLSIFMLIVYFGIKDRELPDFA
                     NNLMALMTTLVGAIGGFIYGTKK"
                     /name="hypothetical protein"
     gene            complement(167..844)
                     /locus_tag="HVX69_25300"
     CDS             complement(167..844)
                     /locus_tag="HVX69_25300"
                     /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="QMK62562.1"
                     /translation="MENKAVTISTQLAIFIDSTIARPDLLFNSLNSEIGEVIDAMPQTL
                     PLPADAPADIPRVIGTSSFGKFNLNISLNRIDFVENYTPTEEIEKSVTEFKLKCNTLIA
                     TIFQKYGVVRIGLVGNYYIPHKNPSQLIADLYLNENKRNLDEITIRINNRDTFKNIQIN
                     NVINLSQGQVTAQNYNGNAVIVQLDYNSTDNNTPLDEGLTLALFKEKSIAYNSKHVEDV
                     SGL"
                     /name="hypothetical protein"
     gene            1410..1643
                     /locus_tag="HVX69_25305"
     CDS             1410..1643
                     /locus_tag="HVX69_25305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015675076.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMK62566.1"
                     /translation="MSVDFCDARQGGGAYGKTPAVLASSGALLFAHMFFPALSPDSVDN
                     RITAFECADTARRSRTTERSESVSEEAEERLM"
                     /name="hypothetical protein"
     gene            complement(1693..1887)
                     /locus_tag="HVX69_25310"
     CDS             complement(1693..1887)
                     /locus_tag="HVX69_25310"
                     /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="QMK62563.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2160..2483
                     /locus_tag="HVX69_25315"
     CDS             2160..2483
                     /locus_tag="HVX69_25315"
                     /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="QMK62564.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          1925..2151
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.25"
                     /coverage="99.0"
                     /evalue="2.24e-83"
     Typing          complement(1135..1664)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.6"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2161..2480
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.96e-62"
ORIGIN
        1 ggtctgtggt tttttatcat ttcctctatt tgagatctta aaatgaatcc aggctgtgag
       61 tttgtgtcac ttcctgattt cgcattattt atattgctac ttgtttttga gaatgatggt
      121 tctacacgaa tgtattcaat cgcatctgtt tttggtttga aaaatttcat aatccactca
      181 catcctcaac atgcttggag ttataagcaa tggatttttc tttaaatagg gctaaggtta
      241 acccttcgtc aagtggtgtg ttattatcgg ttgagttgta gtcaagttga actatcaccg
      301 catttccatt gtagttctgt gcggttactt gtccttggct taaattgatg acattgttta
      361 tttgtatatt tttgaatgta tcgcggttat ttattcttat tgttatttca tctaaatttc
      421 ttttgttttc gtttaaatac agatcagcta ttagttgaga tggattttta tgtgggatgt
      481 aatagttacc aactaggccg attcttacga ctccatattt ttggaatatt gttgctatta
      541 gcgtattgca ctttaatttg aattccgtta ctgatttttc gatctcctca gtaggggtgt
      601 agttttctac aaaatctatt ctgtttagtg atatgtttaa gttgaacttg ccaaaggacg
      661 atgtgccaat aacgcgaggg atatctgcag gtgcatctgc aggcagggga agcgtctgtg
      721 gcattgcgtc tataacttcg ccaatttctg agtttaggct attaaagaga agatctggtc
      781 tagctatggt gctgtcaata aatattgcta gctgtgttga tattgtgacg gccttgtttt
      841 ccattttttc tttcctattt tgcattggta ttaattgaag tattgcgaaa ttaacgtgtt
      901 gtgagtatct taaacgaaaa aaccaccctg gcaggtggtt tttcgaaggt tagctaatcc
      961 tggcagattg tctaaccggg taactggctt cagcagagcg cagataccaa atactgtcct
     1021 tctagtgtag ccgtagtcag gccatcactt caagaactct gtaagcatct ggacaaatct
     1081 cgctctgcta actcggttac caatggctgc tgccagtggt gcttttgcat gtcttaccgg
     1141 gttggactca agacgatagt taccggataa ggcgcagtgg tcgggctgaa cggggggttc
     1201 gtgcacacag cccagcttgg agcgaacgac ctacaccggg ccgagatacc tacagcgtga
     1261 gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc cggtaagcgg
     1321 cagggtcgga acaggagagc gcacgaggga gcttccaggg ggaaacgcct ggtatcttta
     1381 tagtcctgtc gggtttcgcc acctctgact tgagcgtcga tttttgtgat gctcgtcagg
     1441 ggggcggagc ctatggaaaa acgcctgcgg tgctggcttc ttccggtgct ttgctttttg
     1501 ctcacatgtt ctttccggct ttatcccctg attctgtgga taaccgtatt accgcctttg
     1561 agtgcgctga caccgctcgc cgcagtcgaa cgaccgagcg tagcgagtca gtgagcgagg
     1621 aagcggaaga gcgccttatg tgacattttc tccttacgct ctgttgtgcc gttcggcatc
     1681 ctgccctgag cgttatatct ctgtgctatt ttctacttca aagcgtgtct gtatgctgtt
     1741 ctggagttct tctgcgagtt cgtgcagctt ctcacacatg gtggcctgct cgtcagcatc
     1801 gagtgcgtcc agtttttcga gcagcgtcag gctctggctt tttatgaatc ccgccatgtt
     1861 gagtacagtt tgctgctgct tgttcatctt tctgttttct ccgttctgtc tgtcatctgc
     1921 gtcgtgtgat tatatcgcgc accacttttg gaccgtctta ccgccggtat tctgccgacg
     1981 gacatttcag tcagacaaca ctgtcactgc caaaaaactg ccgtgccttt gtcggtaatt
     2041 cgagcttgct gacaggacag gatgtgtaat tgttataccg cgcatacatg cacgctatta
     2101 caattaccct ggtcagggct ttgccccgac accccatgtc agatacggag ccatgtttta
     2161 tgacaaaacg aagtggaagt aatacgcgca ggcgggctat cagtcgccct gttcgtctga
     2221 cggcagaaga agaccaggaa atcagaaaaa gggctgctga atgcggcaag accgtttccg
     2281 gttttttacg ggcggcagct ctcggtaaga aagttaactc actgactgat gatcgggtac
     2341 tgaaagaagt tatgagactg ggggcgttac agaaaaaact ctttatcgac ggcaagcgtg
     2401 tcggggatag ggaatatgcg gaggtgctga tcgctattac ggagtatcac cgtgccctgt
     2461 tatccaggct tatggcagat tagcttcccg gggagaaaac tgtcgaaaac agacggtatg
     2521 aacaccgtaa gcccccaaac cgatcgccat tcactttcat gcatagctat gcagtgagct
     2581 gaaagcaatc ctgacgcatt tttccggttt accccgggga aaacatctct ttttgcggtg
     2641 tctgcgtcag aatcgcgttc agcgcgtttt ggcggtgcgc gtaatgagat gttatggtaa
     2701 atggtgtcag gtaacggttg taaaagcccc gaagtatggg gctggtgtgc ttgtgtgtta
     2761 tttgtttttt ttatttgtgt ttttgtctgt gttatttttt tgttccatat ataaaaccac
     2821 ctatcgctcc aactaatgtt gtcattagtg ccatcaggtt atttgcaaaa tctggtagtt
     2881 ctctatcttt tattccgaaa taaacgatta acataaaaat tgataaaact attaaaaata
     2941 taaaggccat ggagcaaagc cttataagac cttcgctttc agcctttatt tctttttctg
     3001 ttttc
//
