LOCUS       CP057599                4671 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB21-C12 plasmid pRHB21-C12_3, complete
            sequence.
ACCESSION   CP057599
VERSION     CP057599.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148195
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4671)
  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 4671)
  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-C12
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 119.987251593702x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 10:24:23
            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)                     :: 4,812
            CDSs (total)                      :: 4,694
            Genes (coding)                    :: 4,583
            CDSs (with protein)               :: 4,583
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 111
            CDSs (without protein)            :: 111
            Pseudo Genes (ambiguous residues) :: 0 of 111
            Pseudo Genes (frameshifted)       :: 49 of 111
            Pseudo Genes (incomplete)         :: 52 of 111
            Pseudo Genes (internal stop)      :: 31 of 111
            Pseudo Genes (multiple problems)  :: 18 of 111
            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..4671
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB21-C12"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB21-C12_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4511..4671,1..598))
                     /locus_tag="HVX78_24035"
     CDS             complement(join(4511..4671,1..598))
                     /locus_tag="HVX78_24035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001555316.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMK25520.1"
                     /translation="MSGIENSNQGPGWHDHNTPYGTIHSYDGDSHSGYGAHSGGNGGNR
                     HEGISDKTHISIPSTRNYNGYYMSMCVNNLKAHEGFKNTMYKDSEGNITVGIGHLLSTP
                     DMAASLPFTRTHTWHGHGDDMEKEVAASKKEITDAFNNFKKDSRQVPMNLHLSNDAVIG
                     LCISDVQTTEKGLRSLYSGYDGFSNSRKTALVDMGFNLGIPKLSRNFPNFNAAVNRGDW
                     ESAARESHRNLHQRGDQRNKDTADQLRDKH"
                     /name="hypothetical protein"
     gene            852..1289
                     /locus_tag="HVX78_24040"
     CDS             852..1289
                     /locus_tag="HVX78_24040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="QMK25515.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTAGQAEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAEREQLQNEIAQLRQALEQERKRGFWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            1370..1798
                     /gene="exc2"
                     /locus_tag="HVX78_24045"
     CDS             1370..1798
                     /gene="exc2"
                     /locus_tag="HVX78_24045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000830439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="QMK25516.1"
                     /translation="MKRSGGTRYMYLSALITVSAALTACTPKTSLEQHTRHYVYASDDG
                     FDPNFYTKKADTTRMMIPFFQQFREMGVKDKAAGVSAETAQQRIKEFHSEEFLQSLRTT
                     TTFAGRKYTNSDMPSPEKMKLLADTISAIYLDGYEGRQ"
                     /name="exc2"
     gene            2629..2820
                     /locus_tag="HVX78_24050"
     CDS             2629..2820
                     /locus_tag="HVX78_24050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="QMK25517.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGETL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3806..3937)
                     /locus_tag="HVX78_24055"
     CDS             complement(3806..3937)
                     /locus_tag="HVX78_24055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001368419.1"
                     /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="QMK25518.1"
                     /translation="MRGLVFCALILILPGCQANYIRDVQGGTVAPSSSSAATGIEIR"
                     /name="colicin release lysis protein"
     gene            complement(3949..4428)
                     /locus_tag="HVX78_24060"
     CDS             complement(3949..4428)
                     /locus_tag="HVX78_24060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001485345.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMK25519.1"
                     /translation="MIKRLLFLYVALLFLSEGAYASVTVFIAPSWERNTDSVNEIYKYI
                     DDINSNNHVIDQAYVEPIRKELGVYRDYIQKKLINFNGKGVCKLSITTGSTGVKDIEPP
                     DVVLLNSLAENSSLDCKKLYREIQSIVDNDPSLLFPEKIKSNGLLSIDMIIVMGR"
                     /name="hypothetical protein"
     Typing          2987..3534
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.374"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taaatcccat atccactaag gcagtttttc tagagttaga aaaaccatca taaccagaat
       61 ataaagaacg caagcctttc tctgtagtct gaacatcgga aatacataat ccaataacag
      121 catcatttga taaatgcaag ttcattggta cttgtctaga gtctttttta aagttattaa
      181 aagcatcggt tatttctttt tttgatgctg caacttcttt ttccatatca tcaccatgac
      241 catgccatgt atgagttctt gtaaaaggga gagatgccgc catatctggc gtagatagca
      301 aatgaccaat accaacagta atattacctt cgctatcctt atacatggtg tttttgaacc
      361 cctcatgggc ttttaaatta ttaacacaca tgctcatata gtagccatta tagtttctgg
      421 tagatggtat actaatatgt gtcttatcag aaataccttc atggcgattt cccccattac
      481 caccagaatg agcaccataa ccgctatggc tgtccccatc ataactatga attgttccat
      541 agggagtatt gtgatcatgc caccccggac cttgattaga attttcaata ccactcatct
      601 taatttcctc tttgacattt aaaacaacga tcaatacaac tgtatatata accactagtt
      661 ttatatacag tttaaaatta cgccgctgcg ttttccctgt caaccctgtg gattttcatt
      721 tttgtgaaaa cggtcaaaaa aacagccact cacaccatgt gccatccccg ccagatgcca
      781 caaaaaccag cacaaacatt accgttctcc ggcctcagta tgttttactg agaccatgag
      841 atgagacacc tatgggacac tgtcacttta tggcatggca cacactccgg gacgcactga
      901 aaatgacggg cagatcgcgt tcacagtttt accgtgatat gcgcgcaggc cttgtcagtt
      961 accgtacaag ccaggacgga cgacgggagt ttgaaactag tgaactgatc cgggcatacg
     1021 gcgaattaaa gcggaatgag acaccagaaa ggcacacagc gggacaggca gaaaaacctc
     1081 atgatcagca gacagaacgc attctccggg agctgaacga gctgaaacaa tgcctgacgc
     1141 tgatgcttga ggataaacaa gcccaggata cggagcgccg gcgccaggaa gcagaacggg
     1201 aacaactaca gaatgagata gcccagctca ggcaggcgct ggagcaggaa aggaaacggg
     1261 gattctggtc ccggttgttt ggtcgctgaa cgctgtcaga gactgatgat aagatagtct
     1321 tctgataata actcaccgaa aataaataca ttaaggtaag gagactcgca tgaaacgttc
     1381 tggcggcaca cgctatatgt atcttagcgc cctgataact gtgtcagcag ccctcacagc
     1441 ctgtacccca aaaaccagcc tggaacaaca tacccggcat tatgtttatg cttcagatga
     1501 tgggttcgat cctaacttct acaccaagaa agctgacacc acacggatga tgattccgtt
     1561 ctttcagcag ttcagggaga tgggggtgaa agacaaagca gccggagtat cagcagaaac
     1621 ggcacagcaa cgcataaaag aattccactc tgaagaattc cttcagtcac tgagaaccac
     1681 aaccaccttt gcgggcagaa aatacacgaa cagtgatatg ccatcaccgg aaaaaatgaa
     1741 gctgctggct gacacgattt ctgcgattta tctcgatggc tacgagggaa gacagtaagt
     1801 ggatttacca taatccctta attgtacgca ccattaaaac gcgttgagcg cgattctgac
     1861 gcaggcacag caaaaagaaa tgtttacccc caggaaaacc ggaaaaatgc gtcaggatcg
     1921 ttttcagggc gttgcatgac tatgcacgaa actgaatagc gatctgtttg ggcgcatacg
     1981 gtgcccatga ggcacatttt cggacatttt cagttcgtga atccctggct cattgctaca
     2041 tatccgggca gacacccctg gcagcgcccc caggggtgtt atgtaaaaaa aggcgacgcg
     2101 cccctagggg cgcccctaca ttaattaact gttttttcta cagatagtca gtactgaccc
     2161 taagcagggt cgtcatagcg tcgccatagg gtcgtcgacg acgtgctttt gtataaatct
     2221 gaataagaaa atacattttt aaaaccataa caacatgatt taaaaagaaa atcagcaaaa
     2281 agttggtttt gcgtggggtg tggacatttc agacatgaga acagactcgc gtttttccgg
     2341 agtatcagcg gaatatctga ttaaaaaaca ctcgccgcag agcgcgattt tatgcaacag
     2401 cggctgtact gcacagggat tatttatcag ttgatatgct gtgccatgat attgctattg
     2461 ccgaaaggga cgtcgtttta cggcgttttc cctatcctgc atcgcactgg ccgcgttcga
     2521 atgtttgcgc ccctgactaa ccgctcactc agctttatca ctctcgcctg cgtcacagtt
     2581 atcatgctcc catgaacaga aattccctta cacggagaca tcagaccagt gaccaaacag
     2641 gaaaaaaccg ccctgaacat ggcccgcttc atcagaagcc agacattaac cctgctggag
     2701 aagctcaacg aactggacgc ggatgaacag gcagacatct gtgaatcgct tcacgaccac
     2761 gccgatgagc tttaccgcag ttgcctcgca cgtttcgggg atgacggtga aaccctctga
     2821 catatgcagc tcccggagac ggtcacagct tgtctgtgag cgaatgccgg gagcagacaa
     2881 gcccgtcagg gcgcgtcagc gggttttagc gggtgtcggg gcgcagccat gacccagtca
     2941 cgtagcgata gcggagtgta tactggctta atcatgcggc atgtccggtg tgaaatgccg
     3001 cacagatgcg taaggagaaa atgccagtat aggcgctctt ccgcttcctc gctcactgac
     3061 tcgctacgct cggtcgttcg gctgcggcga gcggtgtcta ctcactcaaa agctgtaata
     3121 cagttatcca cagaatcagg ggataatgcc ggaaagaaca tgtgagcaaa aaggcaaaac
     3181 cagggcaaaa ggccgcgccg ctggcgtttt tccataggct ccgcccccct gacgagcatc
     3241 acaaaaattg acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg
     3301 cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgcca cttaccggat
     3361 acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgttggt
     3421 atctcggctt ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa ccccccgttc
     3481 agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg
     3541 acttaacgcc actggcagca gccactggta gaggatgtac aagaaattgc tgatacgtag
     3601 ttcttgaagt gaaggaccga ctgcggctac actgaaagga cagatttggt ggcagcggtc
     3661 ttgtacaccc tgttacctcg ggttagaaag cctgagaaac ttctaacctt cgaaagaacc
     3721 cacgcctgag aacgtgggtt ttttcgttta caggcagcag attacgcgta gaaaaaaagg
     3781 atctcaagaa gatcctttaa tctttttacc taatttcgat tccagtagct gctgagctag
     3841 aagatggcgc aacagtccct ccttgaacat ccctgatata atttgcctga cagccgggca
     3901 atattaaaat tagcgcacaa aaaaccaaac cacgcataga attgtatttt atctccccat
     3961 aacaatgatc atatcaattg ataacaaacc atttgacttt attttctcag gaaataaaag
     4021 tgacggatcg ttatcaacaa tactttgtat ttctctatac agttttttac agtctaatga
     4081 tgagttttcc gccaatgagt ttaacaaaac aacatctgga ggctcaatat ctttaacacc
     4141 tgtacttcct gttgttatcg ataatttaca aactcccttc ccattaaagt taattagttt
     4201 tttctggata taatctcgat atacccctaa ctccttccta ataggttcta catatgcttg
     4261 atcgatgaca tggttattac tatttatatc atcaatatat ttatatatct cattaactga
     4321 atctgtattc ctttcccaac ttggagcaat gaatactgtt acagatgcat aagcaccttc
     4381 tgataagaac aataaagcaa catataagaa taataaccgc ttgatcatat aatccattcc
     4441 cattataggt tgatgtattt catctttaat ataagatgaa atacatctca tatctatatg
     4501 ttatggtcta ttaatgttta tcccgcaact gatctgctgt atccttgttt ctctgatcgc
     4561 ctcgttgatg aagatttcga tggctttcac gtgctgcaga ctcccaatcc ccacggttca
     4621 cagcagcatt aaagttcgga aagtttctcg atagcttagg aattcctaag t
//
