LOCUS       CP056924                5264 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB42-C22 plasmid pRHB42-C22_4, complete
            sequence.
ACCESSION   CP056924
VERSION     CP056924.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148440
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5264)
  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 5264)
  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                     :: RH12 T3-C22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 144.484403346878x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 04:59:14
            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)                     :: 4,864
            CDSs (total)                      :: 4,750
            Genes (coding)                    :: 4,646
            CDSs (with protein)               :: 4,646
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 45 of 104
            Pseudo Genes (incomplete)         :: 58 of 104
            Pseudo Genes (internal stop)      :: 21 of 104
            Pseudo Genes (multiple problems)  :: 17 of 104
            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..5264
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB42-C22"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB42-C22_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            249..1817
                     /gene="cea"
                     /locus_tag="HV023_24260"
     CDS             249..1817
                     /gene="cea"
                     /locus_tag="HV023_24260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /protein_id="QMA67993.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            complement(1814..2155)
                     /locus_tag="HV023_24265"
     CDS             complement(1814..2155)
                     /locus_tag="HV023_24265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058758.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="QMA67994.1"
                     /translation="MSLRYYIKNILFGLYCTLIYIYLITKNSEGYYFLVSDKMLYAIVI
                     STILCPYSKYAIEYIAFNFIKKDFFERRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            2203..2340
                     /locus_tag="HV023_24270"
     CDS             2203..2340
                     /locus_tag="HV023_24270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /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="QMA67995.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(3352..3546)
                     /locus_tag="HV023_24275"
     CDS             complement(3352..3546)
                     /locus_tag="HV023_24275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="QMA67996.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EEIQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4316..4735)
                     /gene="exc2"
                     /locus_tag="HV023_24280"
     CDS             complement(4316..4735)
                     /gene="exc2"
                     /locus_tag="HV023_24280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="QMA67997.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="exc2"
     gene            complement(4816..5253)
                     /locus_tag="HV023_24285"
     CDS             complement(4816..5253)
                     /locus_tag="HV023_24285"
                     /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="QMA67998.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="entry exclusion protein 1"
     Typing          3195..3279
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="100.0"
                     /evalue="6.62e-29"
     Typing          3583..3681
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3806..4061
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(2626..3184)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcatagttt cagtaaaaca taatgaggtc tgagaacggt aatgtttgtg ctggtttttg
       61 tggcatcggg cgagaatagc gcgtggtgtg aaagactgtt tttttgatcg ttttcacaaa
      121 aatggaagtc cacagtcttg acagggaaaa tgcagcggcg tagcttttat gctgtatata
      181 aagccagtgg ttatatgtac agtatttatt tttaacttat tgttttaaaa gtcaaagagg
      241 attttataat ggaaaccgcg gtagcgtact ataaagatgg tgttccttat gatgataagg
      301 gacaggtaat tattactctt ttgaatggta ctcctgacgg gagtggctct ggcggcggag
      361 gtggaaaagg aggcagtaaa agtgaaagtt ctgcagctat tcatgcaact gctaaatggt
      421 ctactgctca attaaagaaa acacaggcag agcaggctgc ccgggcaaaa gctgcagcgg
      481 aagcacaggc gaaagcaaag gcaaacaggg atgcgctgac tcagcgcctg aaggatatcg
      541 tgaatgaggc tcttcgtcac aatgcctcac gtacgccttc agcaacagag cttgctcatg
      601 ctaataatgc agctatgcag gcggaagcag agcgtttgcg ccttgcgaaa gcagaagaaa
      661 aagcccgtaa agaagcggaa gcagcagaaa aggcttttca ggaagcagaa caacgacgta
      721 aagagattga acgggagaag gctgaaacag aacgccagtt gaaactggct gaagctgaag
      781 agaaacgact ggctgcattg agtgaagaag ctaaagctgt tgagatcgcc caaaaaaaac
      841 tttctgctgc acaatctgaa gtggtgaaaa tggatggaga gattaagact ctcaattctc
      901 gtttaagctc cagtatccat gcccgtgatg cagaaatgaa aacgctcgct ggaaaacgaa
      961 atgaactggc tcaggcatcc gctaaatata aagaactgga tgagctggtc aaaaaactat
     1021 caccaagagc caatgatccg cttcagaacc gtcctttttt tgaagcaacc agacgacggg
     1081 ttggggccgg taagattaga gaagaaaaac aaaaacaggt aacagcatca gaaacacgta
     1141 ttaaccggat aaatgctgat ataactcaga tccagaaggc tatttctcag gtcagtaata
     1201 atcgtaatgc cggtatcgct cgtgttcatg aagctgaaga aaatttgaaa aaagcacaga
     1261 ataatctcct taattcacag attaaggatg ctgttgatgc aacagttagc ttttatcaaa
     1321 cgctgactga aaaatatggt gaaaaatatt cgaaaatggc acaggaactt gctgataagt
     1381 ctaaaggtaa gaaaatcggc aatgtgaatg aagctctcgc tgcttttgaa aaatacaagg
     1441 atgttttaaa taagaaattc agcaaagccg atcgtgatgc tatttttaat gcgttggcat
     1501 cggtgaagta tgatgactgg gctaaacatt tagatcagtt tgccaagtac ttgaagatta
     1561 cggggcatgt ttcttttgga tatgatgtgg tatctgatat cctaaaaatt aaggatacag
     1621 gtgactggaa gccactattt cttacattag agaagaaagc tgcagatgca ggggtgagtt
     1681 atgttgttgc tttacttttt agcttgcttg ctggaactac attaggtatt tggggtattg
     1741 ctattgttac aggaattcta tgctcctata ttgataagaa taaacttaat actataaatg
     1801 aggtgttagg gatttaatta ttctttattg atataaaaag tcctagcaat ccaaatggga
     1861 ttgctaggac caaacaaagt agattatata gcataaatag gtttaatttt gctacggggg
     1921 cgttatttag gttttttctt ctttcgaaaa aatctttctt tatgaagtta aaagctatgt
     1981 attcaatagc atattttgaa tatggacata gaatagtgct tatcactatt gcatatagca
     2041 tcttatctga cacaaggaaa taataccctt cgctgttttt tgttataagg tatatatata
     2101 taagtgtgca gtacaggcca aataaaatat tttttatgta gtatcttaag ctcataaatt
     2161 aaacctcgcc atatattctt ttcattttat aaggatcgag ttatgaggaa aagatttttt
     2221 gtgggaatat tcgcgataaa cctccttgtt ggatgtcagg ctaactatat acgtgatgtt
     2281 cagggaggga ccatcgcacc atcctcctct tctaaactga cggggatcgc ggttcagtag
     2341 aaaagatcaa aggatcttct tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa
     2401 caaaaaaacc accgctacca acggtggttt gtttgccgga tcaagagcta ccaactcttt
     2461 ttccgaaggt aactggcttc agcagagcgc agataccaaa tactgtcctt ctagtgtagc
     2521 cgtagtcggg ccactacttc aagaactctg tagcaccgtt tgtgccatca tcgctctgct
     2581 aatccggtta ccagtggctg ctgccagtgg cgttaaggcg tgccttaccg ggttggactc
     2641 aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca
     2701 gcccagcttg gagcgaacga cctacaccga actgagatac caacagcgtg agctatgaga
     2761 aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg
     2821 aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt
     2881 cgggtttcgc cacctctgac ttgagcgtct atttttgtga tgctcgtcag gggggcggag
     2941 cctatggaaa aacgcctgct acgtggcctt cttcctgttc ctggtctttt gctcacatgt
     3001 tctttccggc cttatcccct gattctgtgg ataactgtgt taccgttttt gtgtgagtca
     3061 gtaccgctcg ccgcagtcga acgaccgagc gtagcgagtc agtgagcgag gaagcggaaa
     3121 agcgcctgga cgcgcatttt ctccttacgc atctgtgcgg catttcacac ccggcatggg
     3181 gcacttttca tacaatctgc actgatgccg catagttaag ccagtataca catcgctatc
     3241 gctctgtgac tggttcaggg ctttgccccg aaaccccctg acgcgccctg gcgggcttgt
     3301 ctgctgccga aaacgctcgc ggacaagccg tgagcgcctc cgtcagcctc gttatgtccc
     3361 tgtttcactt tcggtctcaa agcgaacctg gatgctgttc tggatctctt ccgcgagttc
     3421 gtgcagtcgt tcgcacatgg ccgcctgttc gtcggcatcc agagcatcca gtttttcaag
     3481 tagtgtcagg ctctggcttt tgataaatcg cgccatattc agcgcagttt gttgctgttt
     3541 gttcaccttc cgttgttctc cgtcagtacc gggtgtcggg tggaccctga ccaggtggta
     3601 attgtaagac gttgcgggcg acggtattac aattacacat cctgtcctgt ttctttagga
     3661 cgtatcatgg cacagcatat caactgataa ataatccctg tgcagtgcag ccgctgttgc
     3721 ataaaatttc gctctgcgtc gagtgtttct taatcaataa ttccgctgat actccggaaa
     3781 aacgcgagtc tgttctcatg cctgaaatgc ccacacccca cgcaaaaaca agtttttgct
     3841 gatttttctt tataaataga gagttatgac aaattagttc ttcttgctct ctttgtgata
     3901 tttaaaaaag cggtgtcggc gcggtgttgt agctgcgcca acaccgcttt ttaggggtgg
     3961 tactgactat tttcataaaa aacatcatct tatattaggg gtgctgctag cggcgcggtg
     4021 tgttttttta caggatgccc ctgggggcgc tgctaggggt gtctattcag atatatagca
     4081 atgagtcagg gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg cactgtatgc
     4141 gcccaaaccg atcgtcattc actttcatgc atagctatgc agtgagctga aagcgatcct
     4201 gacgcatttt tccggtttac cccggggaaa acatctcttt ttgcggtgtt tgcggcagaa
     4261 tcgcgttcag cgcgttttag cggtgcgtac aattaaggga ttatggtaaa tccacttact
     4321 gtctgccctc gtagccatcg agataaaccg cagaaatcgt gtcagccagc agcctggatt
     4381 ttttcggggt aaggtctttg ctgcggtaat cagtacccgc aaattgagtt gtgccccgga
     4441 gtgagtttaa aaattcctgg ctgtgaaact gctgaatgcg ttgttgcaca tcactccgtg
     4501 attttcctgt cgctttatct ttagctccca tatcccagaa ctgccgaaaa aaaggcacca
     4561 tcattcgtgt tgtgtcggct ttttgggtgg aaaagttggg atcaaaaccg tcatcagaag
     4621 catatacgta atgccgggta tgttgttcca cgctgccctt tggggtacag gctgtgagag
     4681 ctactgttgc tgttatcatg gcgataagac aaagtttgtt tccggtacgt ctcatgagtg
     4741 tctccctacc ttaaagtatt tattctcggt gagttattat ccgaagacta ttttatcatc
     4801 agtctctgac agcgttcagc gaccgaacaa cctggaccag aatccccgtt tcttttccag
     4861 ttccagtgcc tgcctgagct gggctatctc attttgtagc tgttcccgtt ctgcttcctg
     4921 gcgtctgcga tccatatcct gtgcctgttt atcctcaagc atcagcgtca ggcattgttt
     4981 cagctcattc agctcccgga gaatgcgttc tgtctgctga tcatgtggat tttctgcatg
     5041 tccctcactg tgcctttctg gtgtctcatt ctgctttaat tcgccgtatg cccggatcag
     5101 ttcactggtt tcaaactccc gtcgtccgtc cctgccggta cggtaactga caaggcctgc
     5161 gcgcatatca cggtaaaact gtgaacgcga tctgcctgtc atttttagtg cgtcccggag
     5221 tgtgtgccat gccataaagt gacagtgtcc catagatgtc tcat
//
