LOCUS       CP057375                5886 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB28-C15 plasmid pRHB28-C15_5, complete
            sequence.
ACCESSION   CP057375
VERSION     CP057375.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148271
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5886)
  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 5886)
  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                     :: RH01 T2-C15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 165.998511090652x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 08:18:12
            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)                     :: 4,909
            CDSs (total)                      :: 4,793
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 155
            CDSs (without protein)            :: 155
            Pseudo Genes (ambiguous residues) :: 0 of 155
            Pseudo Genes (frameshifted)       :: 59 of 155
            Pseudo Genes (incomplete)         :: 84 of 155
            Pseudo Genes (internal stop)      :: 29 of 155
            Pseudo Genes (multiple problems)  :: 15 of 155
            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..5886
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB28-C15"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB28-C15_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(47..307)
                     /locus_tag="HVY54_24485"
     CDS             complement(47..307)
                     /locus_tag="HVY54_24485"
                     /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="QMG65713.1"
                     /translation="MELKHSISDYTEAEFLEFVKKICRAEGATEEDDNKLVREFERLTE
                     HPDGSDLIYYPRDDREDSPEGIVKEIKEWRAANGKPGFKQG"
                     /name="bacteriocin immunity protein"
     gene            complement(310..1693)
                     /locus_tag="HVY54_24490"
                     /pseudo=""
     CDS             complement(310..1693)
                     /locus_tag="HVY54_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012961.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="colicin"
                     /name="colicin"
     gene            complement(1914..2447)
                     /locus_tag="HVY54_24495"
     CDS             complement(1914..2447)
                     /locus_tag="HVY54_24495"
                     /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="QMG65714.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(2450..3376)
                     /locus_tag="HVY54_24500"
     CDS             complement(2450..3376)
                     /locus_tag="HVY54_24500"
                     /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="QMG65715.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFETAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREYGFD
                     MRDGVSRQERTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            3553..3951
                     /locus_tag="HVY54_24505"
     CDS             3553..3951
                     /locus_tag="HVY54_24505"
                     /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="QMG65716.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQENERKQAVQNRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQELKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(4212..5231)
                     /locus_tag="HVY54_24510"
     CDS             complement(4212..5231)
                     /locus_tag="HVY54_24510"
                     /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="QMG65717.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(5728..5871)
                     /locus_tag="HVY54_24515"
     CDS             complement(5728..5871)
                     /locus_tag="HVY54_24515"
                     /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="QMG65718.1"
                     /translation="MKKITGIILLLLAVIILAACQANYIRDVQGGTVSPSSTAEVTGLA
                     TQ"
                     /name="colicin release lysis protein"
     BGC             1..5886
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          complement(4457..5231)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(2454..3376)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.403"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgaaagaatg ccagccattc atccataaac aaccggcatt catattttag ccctgtttaa
       61 atcctggctt accgttagca gctcgccatt ctttaatttc tttaacaatc ccttcaggac
      121 tatcttccct gtcatcgcga ggataataaa tcagatctga accatctggg tgctcagtta
      181 atcgctcaaa ctctctcact aatttattgt catcctcttc agtagcacct tcagctctac
      241 atattttttt tacaaactcc agaaattcag cctcggtata atcactaata ctatgtttca
      301 gttccatttt tacttacctc tatgaatatc aatatgtcgc ttaggtgtgg tcactctgat
      361 attatccata tcatagacac caccatcctg actgattggt ttatcatgat gtaattcaaa
      421 gcgttcccta ccacctactt ggtctttctt ccttgcaaaa ggtgcttttc ccttttgaat
      481 gttcgtctta ttactgtctt taaattgctt actaagctcg ggatcttttg acacttcttc
      541 ccagaatttc ttccggaaat cgtcaaaact tttaaattct ttatcacgca acttatcagc
      601 aatgcgatca ggaattggcg ctcctgaatc tttacccgca tcatcaagcc atttatcacc
      661 aactggtttt cctttacccg tcgccttccc tggcttattc cgtttactct ccttatctaa
      721 tttatcctta gagtcctttt ctttattttc cttctgctta cggcgttcca gcgcagcacc
      781 taacgcagca tcagcatcag acttatcttt tgcagcagca tcaaatgcag ccttcttatt
      841 atttacatcc gtctgtgccc gctgggcctt aagccctgcc atttgccaca ttcggtgacc
      901 agcagccatt ggttctcggg caaatcgctc gaattgtttt atttcagcct ttgcatcagc
      961 aagagtttta ttcgcagcat caagttcact tttacgagaa ttataaacct gaacagcttt
     1021 agcctgtcgt tcctggtttc tggcaacatc tttattagcc tgatccagtt ctgcgcgggc
     1081 ctgttcataa ttgcgttcag ccacttctac aggatgtgtg tcattccatt cctgctggag
     1141 gcgattttcc tcatcctgac gttgttttac ctgtgcaggg gtaagaacat ctgtcactga
     1201 tacataaatc ggcttctgcc cactttcttt cggaaaacgg atcaccgctt catgtgaacc
     1261 accaccaaag gtaaatcctg caggaacggc agtccggcct ttatcctccg taataccacg
     1321 gggaagggtt gttgacaccg gaaggccttt gacagtgctg actgtcagag aagggacacc
     1381 aggaaatgat gcgtgaaata cccagcgttc cggcaccagg agttgccaaa gcaggaaaac
     1441 caaatgccac tgctgctacg gatgaattgc tgccaccacc ggaattacca ttccccccgc
     1501 cattaccatt gccggagcca cctccccagt gaacaccact accggaaccg ccaccccatg
     1561 gattattttc cgaactccat cctgaaccgt cagaagcccc accatttcca ccaagccccg
     1621 tagggccgcc attaatgtta ccacctgtgt tatgtgcgcc actgttgtgg tcgcgtccat
     1681 ctccaccgct cataaaaatt ccctctttta agcgttaaaa caattgatta catagttaat
     1741 actgtacata aaaccactgg ttttatgtac agatcaaaaa gtactcgcca ttattttttc
     1801 tgtcaagtca gggggggata ttttttggca gttcggagga atcactcatg aaaacggtga
     1861 acggaacgcg aaatcctttc gcgggtcgtg aggcgttgga caagcgaagc gcgtcagttt
     1921 ttccggctct tacccgtgac aggtttctcc accagtttat cttccagtgt cacaactttc
     1981 tgatacaccg ccgctgtggc gttgtagttc ctgtcgagta ttgttttcat tccccatccg
     2041 agcacacaga acataaccag aaaagccact gacaccccac ccagccattt ccagctatac
     2101 cctttaaggg tgttgtattc ctgcacgata ttgctgtgaa ttgtcgcaat atccctgttc
     2161 agggcatccg cgtttgcctt catgtttgcg actgactctt ccagccgctg aaaatcctgg
     2221 ctgatgcgct cacctatcag tcctgccacg tccagcttct gcacctcatt tctgacttca
     2281 tccctgacct gttttgccac accgtcagaa atatcccgat atccgcgaag tgtttccctt
     2341 gccacagcca gagaatcagc aacagctttc tgttgctcca ttgcggtatg ttgcagatgc
     2401 tccaccgata acaggagcgt gagtaatttt tcttctgtgc tggccatgtt cagaatccca
     2461 tagaaaatcc acgtgacggt gatttaaccc gttcaggttc agttcgctcc tgtctgctca
     2521 ctccgtctct catgtcaaag ccatactccc gcgcaacatc atgttgcagc cttctgacca
     2581 gttcatgttg cttaaccgga gtgtccagcc attccctgat gtcatgcccg accgttcgcg
     2641 cctgttcaag atggcgggaa tagtccggtt cagaccgttt ttgcatgatg tcatgacgct
     2701 gggcatcatc aagccgtccg gcagtttcaa aacccagatg cacttcagga cgtcgttcaa
     2761 tgccctgttc tttcagcgtc cggcagtcaa tgaagcccct ttcaaagcca tgctttctca
     2821 tatgttcgtt gtgcttcacc tcccagcgtt ttcgcaattc ccgcaactgc tctttttgct
     2881 gagtgggagt caggcttcct gaatcctttt tcgcacctcc ccgctcggga tacctggcgt
     2941 tatagcgccg gaaatactgt tccggtgtac gttcaatgcc atcattcaca cgctgactca
     3001 tcatgatatg cgcatgaggc tgttcccctc cctcaatgct cgctttcgga ttgtgaatgg
     3061 caaaactcca tgcatgccgt tcgccagctt cctgacgtac aaaatcctgc accagttcaa
     3121 ggcgctgttc cggtgtcagt tcacggggca gcgctatctc cagttcccga taagtcgaac
     3181 cgtttgcacg ttcaaactgg tcagccgcct gccagaaatg tgagggatta tctcgcgccc
     3241 attccggcat gtttccgtgt gcggaatatt ccaaatcctg acggtcgcgg tatttctctt
     3301 tgcgctcgat gtaatcggcg tggtttgcag cctgcccctt gccaccaaat ttaacgctga
     3361 ggtgataggt tgccacggtt tcagccctcc gcaggagcgc actgtttctc gacgaaggag
     3421 agaaacatat aagtgcgctt ccttctaatt ttacgaatta gcacggaaga taccccctgc
     3481 acccgccgac cgcaagcgat atactgcacg accacaacac accgcaaaaa aacaccaggg
     3541 agcaccacga acatgcgcat cagcaacatc gaatggctga agaaacggat cggattcatc
     3601 aggaagctcg gagaacagac cgcacgacag agacagatta ttgacctgct cgacaacgaa
     3661 gcaggactca cagaacagga acgcaaactc ctccacgtac tggcaacagc ggaaaaaaac
     3721 gacttacagg cacaggagaa cgaacgaaaa caggcggtcc aaaatcgaat cgagggaaaa
     3781 aaacaacgac gagaacgcaa tcaccgactc tttctcgcgg ctgggctact gatcgaagca
     3841 ggactggtag acacaaaaac aggcgagcta tgctataaaa aagacaggat attacaggaa
     3901 cttaaggaaa ttaagtacga tctggagaca tccccaaacc cagacgcgta agtgcctcca
     3961 tccgtgttcc ggttccctgg tgcttcctcg ctcattcgct cgctacgctc ggtcatgaga
     4021 ctgcggcgag cacgaccacc tcaatcatgc ggtaagccgc accattgctg ggctgagagg
     4081 agaaaaccgc cggaaagccc gctgctcaaa aagacgccga aaggcgctgt tatctgatat
     4141 aggcttgttc atgtccgcga atttaacatc ccattaacaa aaaacggggg gtagtgttgc
     4201 ttctttgtta actaacattt aattatttgt ttcttggtta gccattctcc agaattatcc
     4261 atccagcgtc gaatagtccg gctgctaaca ccaaccgcca ctgcaatatc ttccgttgac
     4321 gctcccaaga tatacatatc aagcgcccta cgacgtttgt cgtcgttagc agtccaccga
     4381 acagcggcgc tttttttccc tttgtccgac tgattttctg acgaattggc cttcccgccc
     4441 ttgcgaccgc gtgctgcctg aatttctggc gtgtgcgtat cagccacata ctgtgcgaaa
     4501 gtttccggcg tgaagttcct gtgcgtgtat ttcgcaatgc tcttgccaat agcccgacat
     4561 tcagccagtg aaagcggaac gggaagcgat gcattgtaca tttcgacacg ctggatcacc
     4621 gcttcaagcc actgtgagaa cgctggccag ccctgacgaa tcgccctgta agcccatttg
     4681 cgcgtcattt cgaacaggtg gcagtttcgc cccatcccgt aatgtttatc gatgctacga
     4741 cgctctgagg cgctcaaatc gagataatct gccagttcat cgagggtata ggcgtcctcg
     4801 cgccactcca tcacctgcca ttccaggtgg aacggatttt tgcaaatcag gccgctgtag
     4861 ttcacatcag cacaaagttt ctcacacagc gaacgttcaa ccgctgcggc atatttcagc
     4921 gccttaaccg aggcatcagg cgcggttctc acggcgatgt tgagtgcgta gagcaggtga
     4981 gcgtgtccgt tcacaggatt tttaacggtg atgttcggcg cgggggcgtt ccggtcgctc
     5041 cagtcaatcg cagccccctc gcggtcaacg tcaaaaacca gccagaactg cgcatgaggc
     5101 tggttctgct ggatgtaccg cgcaagaagc gcacgccctt tgccggagat gcgaaggccg
     5161 aaagcgagat catccgtgtg atagggacga tggggtaaat tttcgtcgaa gtattgaagc
     5221 gcggcgctca tgtgttacga ttctctccgg gttatgcgac ctacacgccc tctgtatttc
     5281 atgttgaatc ttgccggatc tggacatgat ttcaggggcg tttgtttttc agccgcttac
     5341 actacaccca acggcaaatc ctgtcgatcc ttcccgaaaa accgatccat ttaccataac
     5401 tcccgttgta cgcacccctt aaaacgccct cagtcgcttt ctgacgcaaa aaacgcaaaa
     5461 agacaagaaa acaccaggcc aaaccagaaa aacgcgccag aatcgttttt agagggctgc
     5521 ataactatgc acgaaagcga tgcgcgatcg atttcgactg ttccgaaggg cgaacaggtc
     5581 aaaatgacaa gttttctcgc cctgggtgga aagttctgca cggggatttt agctctcatc
     5641 tcccgcatgg aatttttgtg acatttcaaa aaaaagcgca tcagaatcag cctgacacgc
     5701 tttgtttttg tcaaagagga tttcgggtta ctgcgttgct aatccggtca cttcagctgt
     5761 tgatgacggg gatacagtcc cgccctgaac atcccggata tagtttgcct gacatgcagc
     5821 cagaataatg actgcaagaa gcaataaaat aatccctgtt atttttttca taacgactcc
     5881 ttgttg
//
