LOCUS       CP057355                5428 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB29-C05 plasmid pRHB29-C05_2, complete
            sequence.
ACCESSION   CP057355
VERSION     CP057355.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148276
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5428)
  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 5428)
  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 T3-C05
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140.066054248392x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 08:21:47
            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)                     :: 4,675
            CDSs (total)                      :: 4,561
            Genes (coding)                    :: 4,459
            CDSs (with protein)               :: 4,459
            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)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 46 of 102
            Pseudo Genes (incomplete)         :: 60 of 102
            Pseudo Genes (internal stop)      :: 16 of 102
            Pseudo Genes (multiple problems)  :: 16 of 102
            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..5428
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB29-C05"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB29-C05_2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5111..5428,1..207))
                     /gene="cni"
                     /locus_tag="HVY59_23335"
     CDS             complement(join(5111..5428,1..207))
                     /gene="cni"
                     /locus_tag="HVY59_23335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_061352107.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin N immunity protein"
                     /protein_id="QMG47814.1"
                     /translation="MDIKDRNKISKKISFSLLLLLSPFALIFFSYNNAPIPLLEKIIAY
                     LSLPGFHSLNNPPLSEAFNLYVHTAPLAAISLFIFTHKELELKPKSSPLRALKILTPFT
                     ILYISMIYCFLLTDTELTLSSKTFVLMSKNDLFLSFFYITLYIGIYIFTYLYFWFLIGT
                     YKLFTRGGILP"
                     /name="cni"
     gene            235..372
                     /locus_tag="HVY59_23340"
     CDS             235..372
                     /locus_tag="HVY59_23340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001329514.1"
                     /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="QMG47815.1"
                     /translation="MCGKILLILFFIMTLSACQVNHIRDVKGGTVAPSSSSRLTGVEIK
                     "
                     /name="colicin release lysis protein"
     gene            complement(1377..1571)
                     /locus_tag="HVY59_23345"
     CDS             complement(1377..1571)
                     /locus_tag="HVY59_23345"
                     /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="QMG47816.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2379..2549)
                     /locus_tag="HVY59_23350"
     CDS             complement(2379..2549)
                     /locus_tag="HVY59_23350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005074609.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMG47817.1"
                     /translation="MSKAPIGTTASTGQKCPESGVWKVVGTPSTTAPIAKGNVMPPYNG
                     KAVTWKLTQYA"
                     /name="hypothetical protein"
     gene            complement(2743..3162)
                     /gene="exc2"
                     /locus_tag="HVY59_23355"
     CDS             complement(2743..3162)
                     /gene="exc2"
                     /locus_tag="HVY59_23355"
                     /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="QMG47818.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQHFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="exc2"
     gene            complement(3243..3680)
                     /locus_tag="HVY59_23360"
     CDS             complement(3243..3680)
                     /locus_tag="HVY59_23360"
                     /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="QMG47819.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGFVSYRTSQDGRR
                     EFETSELIRAYGELKQNETPERHSAGQAENPHDQPTERILRELNELKQCLTLMLEDKQA
                     QDMDRKRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            3939..5102
                     /gene="cna"
                     /locus_tag="HVY59_23365"
     CDS             3939..5102
                     /gene="cna"
                     /locus_tag="HVY59_23365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032488335.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin colicin N"
                     /protein_id="QMG47820.1"
                     /translation="MGSNGADNAHNNAFGGGKNPGIGNTSGAGSNGSASSNRGNSNGWS
                     WSNKPHKNDGFHSDGSYHITFHGDNNSKPKPGGNSGNRGNNGDGASAKVGEITITPDNS
                     KPGRYISSNPEYSLLAKLIDAESIKGTEVYTFHTRKGQYVKVTVPDSNIDKMRVDYVNW
                     KGPKYNNKLVKRFVSQFLLFRKEEKEKNEKEALLKASELVSGMGDKLGEYLGVKYKNVA
                     KEVANDIKNFHGRNIRSYNEAMASLNKVLANPKMKVNKSDKDAIVNAWKQVNAKDMANK
                     IGNLGKAFKVADLAIKVEKIREKSIEGYNTGNWGPLLLEVESWIIGGVVAGVAISLFGA
                     VLSFLPISGLAVTALGVIGIMTISYLSSFIDANRVSNINNIISSVIR"
                     /name="cna"
     Typing          1220..1304
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          1608..1706
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1831..2086
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(651..1196)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.526"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgtatgaaca tagagattga atgcttcgct taggggcggg ttgtttaatg aatgaaatcc
       61 tggtagggat aggtatgcga tgattttttc gaggagtggt attggtgcat tattataact
      121 gaaaaatatt aatgcgaatg gggaaagtaa gagcagaaga ctgaatgata ttttttttga
      181 tatcttattt ctgtctttta tatccatgtt gctttctttg gatggttgaa aattatgtgt
      241 gggaaaattt tattaatctt gttttttatc atgacactta gtgcatgtca ggtcaatcac
      301 atccgtgatg tgaaaggagg gactgttgct ccatcatcat catccagact aacaggggtt
      361 gaaattaagt aaaagatcaa aggatcctct tgagatcctt tttttctacg cgtaatctgc
      421 tgcctgtaaa cgaaaaaacc gcctggggag gcggtttagt cgaaggttaa gtcagttggg
      481 gactgcttaa ccgaggtaac tggcttcagc agagcgcaga taccaaatac tgtcctttca
      541 gtgtagccgc agttgggcca tcacttcaag aactctgtaa gcatctggat aaatctcgct
      601 ctgctaatcc ggttaccagt ggctgctgcc agtggcgtta aggcgtgtct taccgggttg
      661 gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc
      721 acacagccca gcttggagcg aacgacctac accaagccga gataccaaca gcgtgagcta
      781 tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg
      841 gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt
      901 cctgtcgggt ttcgccacct ctgacttgag tgtcggtttt tgtgatgctc gtcagggggg
      961 cggagcctat ggaaaaacgc catcggcgcg gcctttttcc ggttcctggt tttttgctca
     1021 catgttcttt ccggccttat cccctgattc tgtggataac cgtattaccg tctttgagtg
     1081 agctgatacc gctcgccgca gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc
     1141 ggaagagcgc ctgatgcggt atgttctcct tacgcatctg tgcggcattt cacacccggc
     1201 atggcgtgct tttcatacaa tccgcactga tgccgcatag ttaagccagt atacactccg
     1261 ctatcgctac gtgactgggt cagggcttcg ccccgacacc cgctgacgcg ccctggcggg
     1321 cttgtctgct gccgaaaacg ctcgcggaca agccgtgagc gcctccgtca gcttcgttat
     1381 gttcctgttt cactttcggt ctcaaagcga acctggatgc tgttctggag ttcttccgcg
     1441 agttcgtgca gtcgttcgca catggccgcc tgttcgtcgg catccagagc atccagtttt
     1501 tcaagcagtg tcaggctctg gcttttgata aatcgcgcca tattcagcgc agtttgttgc
     1561 tgtttgttca ccttccgttg ttctccgtca gtaccgggtg tcgggtggac cctgaccagg
     1621 tggtaattgt aagacgttgc gggcgacggt attacaattg cacatcctgt cctgtttttt
     1681 taggacgtat catggcacag catatcaact gataaataat ccctgtgcag tgcagccgct
     1741 gttgcataaa atttcgctct gcgtcgagtg tttcttaatc aataattccg ctgatactcc
     1801 ggaaaaacgc gagtctgttc tcatgcctga aatgcccaca ccccacgcaa aaacaatttt
     1861 ttgctgattt ttctttataa atagagagtt atgacaaatt agttcttctt gctctctttg
     1921 tgatatttaa aaaagcggtg tcggcgcggt gttgtagctg cgccaacacc gctttttagg
     1981 ggtggtactg actattttca taaaaaacat cattttatat taggggtgct gctagcggcg
     2041 cggtgtgttt ttttacagga cgcccctggg ggcgctgcta ggggtgtctg ttcagatatg
     2101 tagcaatgag tcagggattc acgaactgaa aatgtccgaa aatgtgtctc atgggcaccg
     2161 tatgcgccca aaccgatcgc cattcacttt catgcatagc tatgcagtga gctgaaagcg
     2221 atcctgacgc atttttccgg ttttcgcttg gtaaaacatc tctttttgcg gtgttcgcgg
     2281 cagaatcgcg ttcagcgcgt tttagcggtg cgtacaatta agggattatg gtaaatccaa
     2341 gaataacgaa aaagcccccg gtgggggctt ttgagatatc aagcgtattg ggttaatttc
     2401 caagttacgg cttttccgtt atacggaggc attacattgc ctttggcaat tggtgctgta
     2461 gttgaaggcg ttcctaccac tttccaaaca ccgctttcag ggcatttttg tccggttgaa
     2521 gctgttgtac caattggggc tttagacata ttgattcctc ttgtatgttt tatccgtatg
     2581 cttgtgtagc aatacttatt tctggtttag aaatcagctt tcaagcgggc ttaaaggtcg
     2641 ttttttcaca gatgtgattg tggtcatatt tttaacaaag ttgtatatga ttttggcgtt
     2701 gtaagttttg gttttgttat aaaggactta tggaaaatca acttactgcc tgccctcgta
     2761 gccatcgaga taaacagccg aaatggtgtc agccagcagc ctggattttt tcggggtgag
     2821 gtctttgctg cggtaatcgg tacccgcaaa ttgtgttgtg cctcggagtg agtttaaaaa
     2881 ttcctgactg tgaaagtgct gaatgcgttg ctgcacatca ctccgtgatt ttcctgtcgc
     2941 tttatcttta gctcccatat cccagaactg ccgaaaaaaa ggcaccatca ttcgtgttgt
     3001 gtcggccttc tgggtggaaa agttaggatc aaaaccgtca tcagaagcat atacgtaatg
     3061 ccgggtatgt tgttccacgc tgccctttgg ggtacaggct gtgagagcta ctgttgctgt
     3121 tatcatggcg ataagacaca gtttgtttcc ggtacgtctc atgagtgtct ccctaccttc
     3181 aagtgtttat tctcggtgag ttattatccg aagactattt tatcatcagt ctctgacagc
     3241 gttcagcgac cgaacagcct ggaccagaat ccccgtttct tttccagttc cagtgcctgc
     3301 ctgagctggg ctatctcatt ctgcagctgt tcccgttctg cttcctggcg tttgcgatcc
     3361 atatcctgtg cctgtttgtc ctcaagcatc agcgtcaggc attgtttcag ctcattcagc
     3421 tcccggagaa tgcgttctgt cggctgatca tgtggatttt ctgcctgtcc cgcactgtgc
     3481 ctttctggtg tctcattctg ctttaattcg ccgtatgccc ggatcagttc actggtttca
     3541 aactcccgtc gtccgtcttg actggtacgg taactgacaa agcctgcgcg catatcacgg
     3601 taaaactgtg agcgcgatct gcctgtcatt ttcagtgcgt cacggagtgt gtgccatgcc
     3661 ataaagtgac agtgtcccat aggtgtctca tctcatggtt tcagtaaaac ataatgaggt
     3721 ctgagaacgg taatgtttgt gctggttttt gtggtatccg gcgggaatag cacgtggtgt
     3781 gggtggctgt ttttttgatc gttttcacaa aaacgaaaat tcccagggtt gacaggaaaa
     3841 acgcagcggc gtaattttaa actgtatata aaaccagtgg ttatgtgtac agtatttatt
     3901 tttaacggtt tgttttaaaa gtcaaagagg gatttattat gggtagtaat ggcgcagata
     3961 atgcacataa caatgctttt ggtggaggga aaaatccggg cattggtaat accagtggcg
     4021 caggaagtaa tggtagtgca tcaagtaacc gaggaaattc caatggatgg tcatggagta
     4081 ataagcctca taaaaatgat ggcttccaca gtgatggttc ttaccatatt acatttcatg
     4141 gggacaataa ttcaaagcct aaacctggag ggaatagtgg aaatcgaggt aataacggtg
     4201 atggagcgag tgctaaggtt ggagagataa caatcacacc tgacaactcg aaaccaggtc
     4261 gttatatttc gtcaaatcct gaatattcat tgttggcaaa attaattgat gcggaatcaa
     4321 ttaaaggtac agaggtatat acttttcaca ccagaaaagg tcagtatgtt aaggttactg
     4381 ttccagatag taatattgat aaaatgagag ttgattatgt gaactggaag ggaccgaaat
     4441 ataacaataa acttgtgaag aggtttgtga gccagttttt attatttagg aaggaagaaa
     4501 aagaaaaaaa tgaaaaagaa gccttgctaa aggctagtga acttgtgtct ggtatggggg
     4561 ataagcttgg cgagtatctt ggagtaaaat ataaaaatgt agctaaggaa gttgccaatg
     4621 atattaaaaa cttccatggt cgtaatattc gtagctataa tgaagcaatg gcttcactta
     4681 ataaagtgtt agcaaatcca aagatgaaag taaacaaatc tgataaggat gccattgtga
     4741 atgcctggaa acaggttaat gctaaggaca tggctaataa gattggtaat cttggcaagg
     4801 catttaaggt tgctgattta gctataaagg ttgagaaaat tagggaaaaa agcattgagg
     4861 gatacaatac tggcaactgg ggacctctcc tgttggaggt tgaatcatgg atcattggtg
     4921 gcgttgttgc tggagttgct attagtttat tcggggctgt gttgagtttt ctcccaatct
     4981 ctggacttgc agttactgcg ttgggggtaa taggaataat gacgattagt tacttgtcat
     5041 ctttcataga tgcaaatcga gtttcgaata taaataacat tatatctagt gttattcgat
     5101 gatattagtg tcaggggagt attcctcccc tggtaaatag cttatatgtt cctataagga
     5161 accaaaagta caaatatgtg aatatatata tcccaatata tagtgttata tagaaaaaag
     5221 acaaaaacag atcgtttttt gacattaata caaatgtttt tgatgacaag gttagttctg
     5281 tgtcagttag caagaaacag tatatcatgg atatataaag aatagtgaaa ggagttaata
     5341 tctttagtgc ccgcagaggt gacgactttg gttttaactc taattctttg tgtgtgaata
     5401 tgaataagct gattgcagct aaaggggc
//
