LOCUS       CP058106                6230 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB01-C04 plasmid pRHB01-C04_3, complete
            sequence.
ACCESSION   CP058106
VERSION     CP058106.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147948
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6230)
  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 6230)
  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                     :: RH11 T1-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 115.102049370518x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:38:15
            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)                     :: 4,859
            CDSs (total)                      :: 4,740
            Genes (coding)                    :: 4,643
            CDSs (with protein)               :: 4,643
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 47 of 97
            Pseudo Genes (incomplete)         :: 42 of 97
            Pseudo Genes (internal stop)      :: 23 of 97
            Pseudo Genes (multiple problems)  :: 15 of 97
            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..6230
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB01-C04"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB01-C04_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5176..6230,1..673)
                     /locus_tag="HVV31_24180"
     CDS             join(5176..6230,1..673)
                     /locus_tag="HVV31_24180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012961.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin"
                     /protein_id="QMR37913.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPIYVSV
                     TDVLTPAQVKQRQDEENRLQQEWNDTHPVEVAERNYEQARAELDQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKDKSDADAALGAALERRKQKENKEKDSKGKLDKESKRNKPGKATGKGKP
                     VGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFKDSNK
                     TNIQKGKAPFARKKDQVGGRERFELHHDKPISQDGGVYDMDNIRVTTPKRHIDIHRGK"
                     /name="colicin"
     gene            676..936
                     /locus_tag="HVV31_24185"
     CDS             676..936
                     /locus_tag="HVV31_24185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000412701.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="QMR37914.1"
                     /translation="MELKHSISDYTEAEFLEFVKKICRAEGATEEDDNKLVREFERLTE
                     HPDGSDLIYYPRDDREDSPEGIVKEIKEWRAANGKPGFKQG"
                     /name="bacteriocin immunity protein"
     gene            998..1141
                     /locus_tag="HVV31_24190"
     CDS             998..1141
                     /locus_tag="HVV31_24190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_072020761.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="QMR37915.1"
                     /translation="MKKITGIILLLLAVIILAACQANYIRDVQGGTVSPSSTAEVTGLA
                     TQ"
                     /name="colicin release lysis protein"
     gene            1638..2657
                     /locus_tag="HVV31_24195"
     CDS             1638..2657
                     /locus_tag="HVV31_24195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMR37916.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(2918..3316)
                     /locus_tag="HVV31_24200"
     CDS             complement(2918..3316)
                     /locus_tag="HVV31_24200"
                     /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="QMR37917.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQENERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            3493..4419
                     /locus_tag="HVV31_24205"
     CDS             3493..4419
                     /locus_tag="HVV31_24205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="QMR37918.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFETAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREYGFD
                     MRDGVSRQERTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4422..4955
                     /locus_tag="HVV31_24210"
     CDS             4422..4955
                     /locus_tag="HVV31_24210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMR37919.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     BGC             176..6230
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          1639..2413
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          3494..4416
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.403"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgatgctgcg aataaaactc ttgctgatgc aaaggctgaa ataaaacaat tcgagcgatt
       61 tgcccgagaa ccaatggctg ctggtcaccg aatgtggcaa atggcagggc ttaaggccca
      121 gcgggcacag acggatgtaa ataataagaa ggctgcattt gatgctgctg caaaagataa
      181 gtctgatgct gatgctgcgt taggtgctgc gctggaacgc cgtaagcaga aggaaaataa
      241 agaaaaggac tctaagggta aattagataa ggagagtaaa cggaataagc cagggaaggc
      301 gacgggtaaa ggaaaaccag ttggtgataa atggcttgat gatgcgggta aagattcagg
      361 agcgccaatt cctgatcgca ttgctgataa gttgcgtgat aaagaattta aaagttttga
      421 cgatttccgg aagaaattct gggaagaagt gtcaaaagat cccgagctta gtaagcaatt
      481 taaagacagt aataagacga acattcaaaa gggaaaagca ccttttgcaa ggaagaaaga
      541 ccaagtaggt ggtagggaac gctttgaatt acatcatgat aaaccaatca gtcaggatgg
      601 tggtgtctat gatatggata atatcagagt gaccacacct aagcgacata ttgatattca
      661 tagaggtaag taaaaatgga actgaaacat agtattagtg attataccga ggctgaattt
      721 ctggagtttg taaaaaaaat atgtagagct gaaggtgcta ctgaagagga tgacaataaa
      781 ttagtgagag agtttgagcg attaactgag cacccagatg gttcagatct gatttattat
      841 cctcgcgatg acagggaaga tagtcctgaa gggattgtta aagaaattaa agaatggcga
      901 gctgctaacg gtaagccagg atttaaacag ggctaaaata tgaatgccgg ttgtttatgg
      961 atgaatggct ggcattcttt cacaacaagg agtcgttatg aaaaaaataa cagggattat
     1021 tttattgctt cttgcagtca ttattctggc tgcatgtcag gcaaactata tccgggatgt
     1081 tcagggcggg actgtatccc cgtcatcaac agctgaagtg accggattag caacgcagta
     1141 acccgaaatc ctctttgaca aaaacaaagc gtgtcaggct gattctgatg cgcttttttt
     1201 tgaaatgtca caaaaattcc atgcgggaga tgagagctaa aatccccgtg cagaactttc
     1261 caccccgggc gagaaaactt gtcattttga cctgttcgcc cttcggaaca gtcgaaatcg
     1321 atcgcgcatc gctttcgtgc atagttatgc agccctctaa aaacgattct ggcgcgtttt
     1381 tctggtttgg cttggtgttt tcttgtcttt ttgcgttttt tgcgtcagaa agcgactgag
     1441 ggcgttttaa ggggtgcgta caacgggagt tatggtaaat ggatcggttt tgcgggaagg
     1501 atcgacagga tttgccgttg ggtgtagtgt aagcgactga aaaacaaacg cccctgaaat
     1561 catgtccaga tccggcaaga ttcaacatga aatacagagg gcgtgtaggt cgcataaccc
     1621 ggagagaatc gtaacacatg agcgccgcgc ttcaatactt cgacgaaaat ttaccccatc
     1681 gtccctatca cacggatgat ctcgctttcg gccttcgcat ctccggcaaa gggcgtgcgc
     1741 ttcttgcgcg gtacatccag cagaaccagc ctcatgcgca gttctggctg gtttttgacg
     1801 ttgaccgcga gggggctgcg attgactgga gcgaccggaa cgcccccgcg ccgaacatca
     1861 ccgttaaaaa tcctgtgaac ggacacgctc acctgctcta cgcactcaac atcgccgtga
     1921 gaaccgcgcc tgatgcctcg gttaaggcgc tgaaatatgc cgcagcggtt gaacgttcgc
     1981 tgtgtgagaa actttgtgct gatgtgaact acagcggcct gatttgcaaa aatccgttcc
     2041 acctggaatg gcaggtgatg gagtggcgcg aggacgccta taccctcgat gaactggcag
     2101 attatctcga tttgagcgcc tcagagcgtc gtagcatcga taaacattac gggatggggc
     2161 gaaactgcca cctgttcgaa atgacgcgca aatgggctta cagggcgatt cgtcagggct
     2221 ggccagcgtt ctcacagtgg cttgaagcgg tgatccagcg tgtcgaaatg tacaatgcat
     2281 cgcttcccgt tccgctttca ctggctgaat gtcgggctat tggcaagagc attgcgaaat
     2341 acacgcacag gaacttcacg ccggaaactt tcgcacagta tgtggctgat acgcacacgc
     2401 cagaaattca ggcagcacgc ggtcgcaagg gcgggaaggc caattcgtca gaaaatcagt
     2461 cggacaaagg gaaaaaaagc gccgctgttc ggtggactgc taacgacgac aaacgtcgta
     2521 gggcgcttga tatgtatatc ttgggagcgt caacggaaga tattgcagtg gcggttggtg
     2581 ttagcagccg gactattcga cgctggatgg ataattctgg agaatggcta accaagaaac
     2641 aaataattaa atgttagtta acaaagaagc aacactaccc cccgtttttt gttaatggga
     2701 tgttaaattc gcggacatga acaagcctat atcagataac agcgcctttc ggcgtctttt
     2761 tgagcagcgg gctttccggc ggttttctcc tctcagccca gcaatggtgc ggcttaccgc
     2821 atgattgagg tggtcgtgct cgccgcagtc tcatgaccga gcgtagcgag cgaatgagcg
     2881 aggaagcacc agggaaccgg aacacggatg gaggcactta cgcgtctggg tttggggatg
     2941 tctccagatc gtacttaatt tccttaagtg cctgtaatat cctgtctttt ttatagcata
     3001 gctcgcctgt ttttgtgtct accagtcctg cttcgatcag tagcccagcc gcgagaaaga
     3061 gtcggtgatt gcgttctcgt cgttgttttt ttccctcgat tcgtttttgg accgcctgtt
     3121 ttcgttcgtt ctcctgtgcc tgtaagtcgt ttttttccgc tgttgccagt acgtggagga
     3181 gtttgcgttc ctgttctgtg agtcctgctt cgttgtcgag caggtcaata atctgtctct
     3241 gtcgtgcggt ctgttctccg agcttcctga tgaatccgat ccgtttcttc agccattcga
     3301 tgttgctgat gcgcatgttc gtggtgctcc ctggtgtttt tttgcggtgt gttgtggtcg
     3361 tgcagtatat cgcttgcggt cggcgggtgc agggggtatc ttccgtgcta attcgtaaaa
     3421 ttagaaggaa gcgcacttat atgtttctct ccttcgtcga gaaacagtgc gctcctgcgg
     3481 agggctgaaa ccgtggcaac ctatcacctc agcgttaaat ttggtggcaa ggggcaggct
     3541 gcaaaccacg ccgattacat cgagcgcaaa gagaaatacc gcgaccgtca ggatttggaa
     3601 tattccgcac acggaaacat gccggaatgg gcgcgagata atccctcaca tttctggcag
     3661 gcggctgacc agtttgaacg tgcaaacggt tcgacttatc gggaactgga gatagcgctg
     3721 ccccgtgaac tgacaccgga acagcgcctt gaactggtgc aggattttgt acgtcaggaa
     3781 gctggcgaac ggcatgcatg gagttttgcc attcacaatc cgaaagcgag cattgaggga
     3841 ggcgaacagc ctcatgcgca tatcatgatg agtcagcgtg tgaatgatgg cattgaacgt
     3901 acaccggaac agtatttccg gcgctataac gccaggtatc ccgagcgggg aggtgcgaaa
     3961 aaggattcag gaagcctgac tcccactcag caaaaagagc agttgcggga attgcgaaaa
     4021 cgctgggagg tgaagcacaa cgaacatatg agaaagcatg gctttgaaag gggcttcatt
     4081 gactgccgga cgctgaaaga acagggcatt gaacgacgtc ctgaagtgca tctgggtttt
     4141 gaaactgccg gacggcttga tgatgcccag cgtcatgaca tcatgcaaaa acggtctgaa
     4201 ccggactatt cccgccatct tgaacaggcg cgaacggtcg ggcatgacat cagggaatgg
     4261 ctggacactc cggttaagca acatgaactg gtcagaaggc tgcaacatga tgttgcgcgg
     4321 gagtatggct ttgacatgag agacggagtg agcagacagg agcgaactga acctgaacgg
     4381 gttaaatcac cgtcacgtgg attttctatg ggattctgaa catggccagc acagaagaaa
     4441 aattactcac gctcctgtta tcggtggagc atctgcaaca taccgcaatg gagcaacaga
     4501 aagctgttgc tgattctctg gctgtggcaa gggaaacact tcgcggatat cgggatattt
     4561 ctgacggtgt ggcaaaacag gtcagggatg aagtcagaaa tgaggtgcag aagctggacg
     4621 tggcaggact gataggtgag cgcatcagcc aggattttca gcggctggaa gagtcagtcg
     4681 caaacatgaa ggcaaacgcg gatgccctga acagggatat tgcgacaatt cacagcaata
     4741 tcgtgcagga atacaacacc cttaaagggt atagctggaa atggctgggt ggggtgtcag
     4801 tggcttttct ggttatgttc tgtgtgctcg gatggggaat gaaaacaata ctcgacagga
     4861 actacaacgc cacagcggcg gtgtatcaga aagttgtgac actggaagat aaactggtgg
     4921 agaaacctgt cacgggtaag agccggaaaa actgacgcgc ttcgcttgtc caacgcctca
     4981 cgacccgcga aaggatttcg cgttccgttc accgttttca tgagtgattc ctccgaactg
     5041 ccaaaaaata tccccccctg acttgacaga aaaaataatg gcgagtactt tttgatctgt
     5101 acataaaacc agtggtttta tgtacagtat taactatgta atcaattgtt ttaacgctta
     5161 aaagagggaa tttttatgag cggtggagat ggacgcgacc acaacagtgg cgcacataac
     5221 acaggtggta acattaatgg cggccctacg gggcttggtg gaaatggtgg ggcttctgac
     5281 ggttcaggat ggagttcgga aaataatcca tggggtggcg gttccggtag tggtgttcac
     5341 tggggaggtg gctccggcaa tggtaatggc ggggggaatg gtaattccgg tggtggcagc
     5401 aattcatccg tagcagcagt ggcatttggt tttcctgctt tggcaactcc tggtgccgga
     5461 acgctgggta tcgccgtctc tggtgaggct ttatctgcgg caatagctga tatctttgca
     5521 gccctgaaag gtccgtttaa attcagcgca tggggtattg cgctttacgg cattctgcca
     5581 tctgaaatag caaaagatga cccgaatatg atgtcaaaga ttgtgacgtc attaccggca
     5641 gaaacagtga cgaatgttca ggtcagtaca cttccgctgg accaggcaac tgtcagcgtg
     5701 acgaaacgtg tgacagatgt tgtgaaggac acacgacagc atattgccgt agttgcaggt
     5761 gtgcctatga gtgtgcctgt tgtgaatgcc aaaccaacac gtactccagg tgtatttcac
     5821 gcatcatttc ctggtgtccc ttctctgaca gtcagcactg tcaaaggcct tccggtgtca
     5881 acaacccttc cccgtggtat tacggaggat aaaggccgga ctgccgttcc tgcaggattt
     5941 acctttggtg gtggttcaca tgaagcggtg atccgtttcc cgaaagaaag tgggcagaag
     6001 ccgatttatg tatcagtgac agatgttctt acccctgcac aggtaaaaca acgtcaggat
     6061 gaggaaaatc gcctccagca ggaatggaat gacacacatc ctgtagaagt ggctgaacgc
     6121 aattatgaac aggcccgcgc agaactggat caggctaata aagatgttgc cagaaaccag
     6181 gaacgacagg ctaaagctgt tcaggtttat aattctcgta aaagtgaact
//
