LOCUS       CP057159                3525 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB35-C09 plasmid pRHB35-C09_6, complete
            sequence.
ACCESSION   CP057159
VERSION     CP057159.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148350
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3525)
  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 3525)
  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 T3-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 130.632759251172x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 06:06:10
            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)                     :: 5,293
            CDSs (total)                      :: 5,165
            Genes (coding)                    :: 4,923
            CDSs (with protein)               :: 4,923
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 119 of 242
            Pseudo Genes (incomplete)         :: 123 of 242
            Pseudo Genes (internal stop)      :: 53 of 242
            Pseudo Genes (multiple problems)  :: 47 of 242
            CRISPR Arrays                     :: 3
            ##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..3525
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB35-C09"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB35-C09_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3251..3525,1..340)
                     /locus_tag="HVZ33_26450"
     CDS             join(3251..3525,1..340)
                     /locus_tag="HVZ33_26450"
                     /inference="COORDINATES: protein motif:HMM:NF025107.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="QMD75016.1"
                     /translation="MSTKNAQKEQKKESLITTHWGDDATIHGWTAIPNSLLMLQGDLGI
                     GSTEMCILLNILMHQWPESGESISFPSIGTIASRIGVSKRTIQRGVSNLEALGILTRYQ
                     STRNDPLTNGANIFDSTPLKEYLNKKAKGITISNSNKKKERKKTGITPNIKLPRICPKC
                     SKTKATSHEEVVKFFGVRKTMAGEIINSYCKECRASEKDLF"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(627..950)
                     /locus_tag="HVZ33_26455"
     CDS             complement(627..950)
                     /locus_tag="HVZ33_26455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QMD75013.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MED"
                     /name="nikA protein"
     gene            1222..1431
                     /locus_tag="HVZ33_26460"
     CDS             1222..1431
                     /locus_tag="HVZ33_26460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001399823.1"
                     /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="QMD75014.1"
                     /translation="MNKQQQTALNIAKFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTRAGCRTA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2205..2930)
                     /locus_tag="HVZ33_26465"
     CDS             complement(2205..2930)
                     /locus_tag="HVZ33_26465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001427890.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="QMD75015.1"
                     /translation="MASMETEQQPQQTTEQIEVKTKRVQCFIDGYNLYHAIEETGNKAL
                     HWVDLKSLCKRYLPKNASIDNVFWFSAKPSHLSRAINENYQNYTNALTECGVDVIGGRF
                     KKKNVTCEADNGCGGVFHKHEEKESDVNLAISLVSGACNDEYDIAIIITADSDLCPPIK
                     YVRERFPNKELWLVAPPGRIRRATDLCSLSSRSMEIKNGALRACCMRDEFYKDGVLVAR
                     RPQEWRAVANTRQRRARSR"
                     /name="NYN domain-containing protein"
     Typing          complement(960..1185)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.583"
                     /coverage="99.0"
                     /evalue="1.05e-76"
     Typing          1437..1956
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.264"
                     /coverage="93.0"
                     /evalue="0.0"
     Typing          complement(631..950)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="4.29e-63"
ORIGIN
        1 taacctagag gcattgggga tattaactag ataccaatca acaaggaatg accctctaac
       61 caatggcgct aatatattcg actcaactcc tctaaaagaa tatttaaaca aaaaagctaa
      121 aggcataaca attagcaaca gcaacaaaaa gaaagaaaga aagaaaaccg gaattacacc
      181 caacataaaa ttaccacgca tttgcccaaa atgttcgaaa actaaagcaa ccagccacga
      241 agaagttgtt aaattttttg gtgtgcgaaa aacaatggct ggggaaataa taaattcata
      301 ttgcaaagaa tgccgagctt ctgaaaaaga tctattttaa acagttgacc attttttata
      361 tggccaactg cccccactca agtaaatggg actgtttcta acgctcccat ttaccataac
      421 gtcacattac gcgcaccgct aaaacgcgct gaacgcgatt ctgccgcaaa taccgcaaaa
      481 agagatgttt tccccggggt aaaccggaaa aatgcgtcag gatcgctttc agctcactgc
      541 atagctatgc atgaaagtga atggcgatcg gtttgggagc ttacggcgtt cataccgtct
      601 gttttcgaca gtttctctcc gggaagctaa tcttccataa gcctggataa cagggcccgg
      661 tgatactccg taatagctat cagcacctcc gcatactctc tgtccccgac acgcttaccg
      721 tcgataaaga gttttttctg caacgccccc agtcgcatga cttctttcag cacccggtca
      781 tcagtcagtg aattaacttt cttaccgaga gctgccgccc gtaaaaaacc agaaacggtc
      841 ttgccgcatt cagcagccct ttttctgatt tcctggtctt cttctgccgt cagacgaaca
      901 gggcgactga tagcccgcct gcgcgtatta cttccacttc gttttgtcat aaaacatggc
      961 tccgtatctg acatggggtg tcggggcgaa gccctgacca gggtaattgt aatagcgtgc
     1021 atgtatgcgc ggtataacaa ttgcacatcc tgtcctgtct gcaagttcga attaccaaca
     1081 aagcactgct gttttttggc agtgacagtg ttgtctgact gaaatgtccg tcggcagaat
     1141 accggcggta agacggtcga aaagtggtgc gcgatataat cacacgacgc agatgacaga
     1201 cagaacggag aaaacagaaa gatgaacaag cagcagcaaa ccgcactcaa catagcaaaa
     1261 ttcataaaaa gccagagcct gacgctgctc gaaaaactgg acgcactcga tgctgacgaa
     1321 caggccgcca tgtgtgagaa actgcacgaa ctcgcagaag aactccagaa cagcatacag
     1381 acacgctttg aagcggaaaa tcgcacacgg gcaggatgca gaacggcata gcggagcgta
     1441 aggagaaaat gccacgtcag acgctcttcc gcttcctcgc tcactgactc gctacgctcg
     1501 gtcgttcgac tgcggcgagc ggtgtcagct cactcaaaga cggtaatgag gttatccaca
     1561 gaatcagggg ataaagccaa aagaaacatg tgagcaaaaa acaagaaccc gaaaaaggcc
     1621 gcgccggtgg cgtttttcca taggctccgc ccccctgacg agcatcacaa aaatcgacgc
     1681 tcaagtcaga ggtggcgaaa cccgacagga cttaaagata ccaggcgttt ccccctggaa
     1741 gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc
     1801 tcccttcggg aagcgtggcg ctttctcata gctcacgctg ttggtatctc agttcggtgt
     1861 aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg
     1921 ccttatccgg taactatcgt cttgagtcca acccggaaag acacgactta acgccactgg
     1981 cagcagtcat tggtaactga tttagaggag ttgagtcttg aagttatgca cctgataagg
     2041 ctaaactgaa agaacaagtt ttggcgactg tgctcctcca agccagttac ctcggttcaa
     2101 agagcgccaa ctctatgaac cttcgaaaaa ccgcccgcca aggcggtttt ttcgttttca
     2161 acctagttag attaatctcc ttgcgctagc tgcgtcaaca aagcctaacg acttctagcc
     2221 cttctttgcc tggtattggc aacagctcgc cattcctgag gccttctggc tacaagtact
     2281 ccatctttgt agaactcatc acgcatacag caggctctca aagcaccatt cttgatctcc
     2341 atacttctcg atgacagaga gcagagatct gtcgctcgcc tgattctccc cggaggagct
     2401 acaagccaaa gctctttatt agggaatcgc tctcttacgt atttaatagg ggggcataag
     2461 tcagaatccg cagtgataat aatggctata tcatactcat cattacacgc accagacact
     2521 agacttatag ccaaattaac atcggactct ttttcttcat gcttatggaa aactccacca
     2581 catccattat cagcttcgca cgttacattc ttttttttaa aacgtccacc gataacatca
     2641 acaccacatt cggttaaagc gttggtgtaa ttttgataat tttcatttat ggctcttgat
     2701 aaatgtgatg gcttagcgga aaaccaaaaa acattatcaa tagatgcatt tttaggaagg
     2761 tatctcttgc ataaagattt aagatcaacc caatgaagag ctttattacc agtctcttca
     2821 attgcatgat ataaattata cccatcaata aagcactgca ctcgctttgt ttttacttcg
     2881 atttgctcag tagtttgttg tggttgctgc tctgtttcca tacttgccat ttttgacctc
     2941 tagatagcaa aaaggcctgc atatgcaggc ctttttgcgt ctcttaaccg cagttaacag
     3001 accactgtat ggacgcatcc aatacaggaa gaattttgta caatgcgctt ccaagcctcg
     3061 acttggatag ccactaagag cataactctt aggtagtgga ctcaacttaa gttctatata
     3121 aaaaaagagc aaatggatga catttatgtc atcctaaaag atacatgtta ctacctaact
     3181 actcttaata taagagtagt taggtagtaa ctattcacat tttgattttt ttttcgcgag
     3241 aaaagcatct atgagcacaa aaaacgcaca gaaagaacaa aaaaaagagt cattaatcac
     3301 tactcactgg ggagatgatg caaccataca tgggtggacg gctataccaa atagcctcct
     3361 tatgctgcaa ggtgatcttg gtattgggag tactgagatg tgtattctgc tgaatatatt
     3421 gatgcatcaa tggcctgagt caggggagtc aatatctttt ccgtcaattg gtaccattgc
     3481 atcaagaata ggtgtatcta aaagaacaat tcaacgcggg gttag
//
