LOCUS       CP056990                2255 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C11 plasmid pRHB41-C11_6, complete
            sequence.
ACCESSION   CP056990
VERSION     CP056990.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148424
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2255)
  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 2255)
  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 T3-C11
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 134.704823216905x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 04:10:52
            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)                     :: 5,228
            CDSs (total)                      :: 5,103
            Genes (coding)                    :: 4,846
            CDSs (with protein)               :: 4,846
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 95 of 257
            Pseudo Genes (incomplete)         :: 143 of 257
            Pseudo Genes (internal stop)      :: 48 of 257
            Pseudo Genes (multiple problems)  :: 24 of 257
            CRISPR Arrays                     :: 1
            ##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..2255
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C11"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C11_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2063..2255,1..311)
                     /locus_tag="HV007_26130"
     CDS             join(2063..2255,1..311)
                     /locus_tag="HV007_26130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000809479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMB22606.1"
                     /translation="MKQIKFRLTDEEYNVAHINAISNGVNSVNAFAKRKVLDISATPSK
                     VIVSNEPSVPVKTCLYPHELELIKRNAALHGMSVSREIAIRLRKSVLKSEVCLYPEEVQ
                     VLRKLSTTINRIGRNIHFIISGDRFCTVNDPDFRNEIRELTALCETVDKTIEQLVFSVN
                     NRFG"
                     /name="hypothetical protein"
     gene            1086..1601
                     /locus_tag="HV007_26135"
     CDS             1086..1601
                     /locus_tag="HV007_26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="QMB22607.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1676..1960
                     /locus_tag="HV007_26140"
     CDS             1676..1960
                     /locus_tag="HV007_26140"
                     /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="DNA-binding response regulator"
                     /protein_id="QMB22608.1"
                     /translation="MTKHDAIRISQLHQIFYDDEGLIDSEKNVTILYSIGFTIDEIAYF
                     GNTTPGTVQGQLFNARAKLSCASASSLRPMILLRLLSLIIFEQDRLNRL"
                     /name="DNA-binding response regulator"
     Typing          complement(557..817)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="3.95e-106"
ORIGIN
        1 tggagttaat aaagcgtaat gctgcattac acgggatgag cgttagccga gaaatagcaa
       61 tacgcttacg taaatcagtg ttgaaaagcg aagtttgtct ttatcccgaa gaagtgcagg
      121 tgctcagaaa gctttcaaca actattaata gaattggtcg aaatattcat tttataatta
      181 gtggcgatcg tttttgcaca gttaacgatc ctgatttcag aaatgagata agggaactta
      241 cagcattatg cgaaacagtc gataaaacaa tagagcaatt agtttttagt gttaataatc
      301 gttttgggta aaaacgtatt atcaagaacc gactgtaggt catgggcaaa cgttgcagaa
      361 ttgcgtcaga gacgtcattt tgcggcgttt gccctatcct gcatcggggt taaaccacga
      421 agatttttat tccccgttct tcggaacgac cgaagccgcc acggttccga ttgcgccttg
      481 agcgcaaccg gaaaccgact ggggagaacc ccagaccccc atcgcggcaa caccgacggt
      541 ctacgaccac ctaccaaccg cgtggctgcc tgttccgtgc aaatgggctt tgcagggggc
      601 tgacgcggtt cctggcgacc tgaaagcccc tggttagggg tatcggcgcg cctgacctcc
      661 tgaaaccctc tgtaagcgtt tttcgcgcct tccatgccct gacgggcatt taaaccccgt
      721 ctcgtgtgtc tgagagcttc tgagcgcgtt tcaggggcta tctgacgact catccccgaa
      781 agaataacaa cgggatcacc gacaacatgc gagaggtgac accgctcgcc gcagccccag
      841 cgaccgaacg tagtgagcga gtgggcgagg aagcggaaga gaaccagaag ccatattgag
      901 cacttacgct cgtagttaag aactaagaag ggaatttctt gaaacccgca tgaatcctag
      961 aaagtggtga tcaggatctg taccttgtaa gctcagatcc ggtaccttgc aggctcaaaa
     1021 aataattgat tttgagctta tgaggattta ttgtgaatct ccaaagctca aaaaaggatg
     1081 caataatgag ctcactaagc ttgcagagat acgaaacgaa cccattttta gagcttatga
     1141 caatcccgat gaaggggaaa cggatacaag tatctcgtct tggacgtgat gacaacgttt
     1201 tggttaatca aaacacggga gaaaagtttg ggacgcatgt aaccactttt aagcgtgtgg
     1261 atagtgagca atttgttaaa ttgtttactg cgaatattgg gctaacattt gatttatcat
     1321 cggcaggaat taaagctttt aatgtcctgt tatgggctgt tcaaaaacag gcttttgcaa
     1381 aagatcaggt tcttttagat tccagagctc ttgatgactt tttgaaaagc tatgatagct
     1441 taaaactaag ttacgctacg ttaaagcgag ggatcaacga gttagaaaaa gctcagatta
     1501 tagcaaagac aatgcgaaaa ggattttatt tcataaatcc taactttgta tttaatggcg
     1561 atagaatagc gtttacaact ctgatcgaga gggattgtta atataatcgt cgcagtcgaa
     1621 caaaactcca cttttgttcg actgctaatc acaacaacct attagggagg ttattatgac
     1681 taagcatgat gctatacgca tttctcaact tcatcaaatc ttttacgatg acgagggatt
     1741 aattgattca gaaaagaacg tgaccatttt atacagcata ggatttacta ttgatgaaat
     1801 agcttatttt gggaatacaa caccgggaac agttcaggga cagttattta atgcaagagc
     1861 taaattaagt tgtgcttcag cttcatcttt aagaccgatg attttgttga gattgctttc
     1921 actcataatc tttgagcaag accgcttaaa taggctgtaa tcaatgcagg atagacaatc
     1981 atggtcaaat gggtaccatt ttccatgatt gtccaaaaac ggggtttttg cctgtgcctg
     2041 ccgcaggctc ttaggaggtt ctatgaagca aattaaattc agattgaccg acgaggaata
     2101 caacgttgct catattaatg ctatttcaaa tggcgttaat agtgtaaatg cttttgcaaa
     2161 gaggaaggtt ttagatatta gcgcaacacc ttcaaaggtt atcgtatcga atgaaccatc
     2221 tgtaccagta aaaacatgtt tatacccaca tgaac
//
