LOCUS       CP055732                3142 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB13-C14 plasmid pRHB13-C14_9, complete
            sequence.
ACCESSION   CP055732
VERSION     CP055732.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148098
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3142)
  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 3142)
  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                     :: RH03 T1-C14
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.3972219793898x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/18/2020 17:04:29
            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)                     :: 5,159
            CDSs (total)                      :: 5,038
            Genes (coding)                    :: 4,830
            CDSs (with protein)               :: 4,830
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 85 of 208
            Pseudo Genes (incomplete)         :: 110 of 208
            Pseudo Genes (internal stop)      :: 38 of 208
            Pseudo Genes (multiple problems)  :: 24 of 208
            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..3142
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB13-C14"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB13-C14_9"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3114..3142,1..502)
                     /locus_tag="HVW81_25745"
     CDS             join(3114..3142,1..502)
                     /locus_tag="HVW81_25745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007848.1"
                     /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="QLM74971.1"
                     /translation="MINSRYKTNPFLEGMIVPVKGKQVRLSRLGRDENILVNQNTGEVQ
                     GTHVTTYKRVDGEQFVKLFTANIALTFDLSAQGIKAFNVLMWAMQKQSVSKDEVFLDTH
                     IREEFLAVYNDKDKPIKLSQPTFARGLAELTKAQIIAKTIRQGVYWINPNFAFNGDRIA
                     FTTLIERQSNNEK"
                     /name="replication/maintenance protein RepL"
     gene            516..1292
                     /locus_tag="HVW81_25750"
     CDS             516..1292
                     /locus_tag="HVW81_25750"
                     /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="hypothetical protein"
                     /protein_id="QLM74972.1"
                     /translation="MRKKNMFPPGSLSIKLNNPLTKYEIIEILSEYLSMLEITFGIKEF
                     RLFSYLECVLNGEKQAIYHKGNNAIVSGFSLDSMEDINNRKINKIMLSCDDFDAMQKID
                     NMLNMKAEPNPYEHFKSFLSLVPANLAYDLIRKTDELVELERMEKIKEKNELREKKREK
                     DKNILKIIYNNKIAEYSCTFDYFRSVYLSSSGFLSLEKQKAKYFLAEGLDSLLNDYVGK
                     RLVRLSIKGDDGKVSIVEIYDENGKFLFKTKPLNKT"
                     /name="hypothetical protein"
     gene            complement(1350..1778)
                     /locus_tag="HVW81_25755"
     CDS             complement(1350..1778)
                     /locus_tag="HVW81_25755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001107325.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QLM74973.1"
                     /translation="MTKNKRSGSEVRQRTKVITLRVNNRIANEIRRRAKLEGLTISEYI
                     RTASLNNEIKQRVPSRYLDELIKLGRMQKNLFDKGKRPKDKEYLDVMHKIISLCGEMKT
                     VTQRISDIYNEMDLIKQEIKIIKRDHKNKYPGSNLFNR"
                     /name="mobilization protein"
     gene            complement(2422..2665)
                     /locus_tag="HVW81_25760"
                     /pseudo=""
     CDS             complement(2422..2665)
                     /locus_tag="HVW81_25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001482226.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="rep protein"
                     /name="rep protein"
ORIGIN
        1 ttttttagag ggtatgatag tgcccgtcaa gggtaaacaa gtcagacttt cccgtctagg
       61 tcgagatgaa aacatactgg ttaatcagaa cacgggagag gttcaaggta cccatgtaac
      121 aacatataaa cgggttgatg gtgagcagtt tgtaaaacta ttcactgcaa atatcgcgtt
      181 aacctttgat ttgtcagctc aaggaataaa agcatttaac gttttgatgt gggcaatgca
      241 aaagcagtca gtatcaaaag acgaagtttt tttagatact cacataagag aggagtttct
      301 tgctgtttat aatgataaag ataaaccaat taaattaagt cagccaacat ttgctagagg
      361 attagctgaa cttaccaaag ctcaaattat agcgaaaacc atacgtcaag gagtgtattg
      421 gataaatcca aattttgcat tcaacggtga tagaatagcg tttacaactc ttattgaaag
      481 gcaaagcaat aatgaaaaat aacagggtaa aaataatgag aaagaaaaat atgttcccgc
      541 caggttcttt gagtataaaa ttaaacaatc ctttaactaa atatgaaata attgagatat
      601 tatcagaata tctatctatg ttagaaataa cttttgggat aaaggaattt aggctttttt
      661 cttatttgga atgcgtgctc aatggagaaa aacaggctat ataccataaa ggtaataacg
      721 caatcgtgtc tggattttca cttgattcaa tggaggatat aaacaatagg aaaatcaata
      781 agataatgct tagttgcgat gattttgatg ccatgcaaaa aatcgataat atgttaaata
      841 tgaaagctga accaaatccg tatgaacatt ttaagagttt tttatcacta gttcctgcta
      901 atcttgcata tgatctcatc aggaaaaccg acgagttagt cgaacttgag agaatggaaa
      961 aaataaaaga aaaaaacgaa ttacgtgaaa agaaacgaga aaaagataaa aacatattaa
     1021 agattattta taacaataag atagctgagt attcatgtac ttttgattat tttagatctg
     1081 tatatttatc tagctctggt tttttatctt tagaaaaaca aaaggctaaa tattttcttg
     1141 cggaagggtt agattcactc ctaaatgatt atgttggtaa aaggttggta agattatcaa
     1201 ttaaaggcga tgatggtaaa gtttccatag tcgaaatata tgatgaaaat ggtaaatttt
     1261 tatttaagac aaaacctcta aataaaacat agagtaatct ttaatatgtt tagccgatat
     1321 atcaaataag atgatatatc ggctaatatt tatctattaa ataaattaga gcctgggtat
     1381 ttatttttgt gatctctttt tattattttt atttcctgtt ttattaaatc catttcatta
     1441 tatatatcag aaattcgctg cgttactgtt ttcatctcac cgcaaagtga aattatttta
     1501 tgcatcacat caagatactc tttgtccttc ggcctcttcc ctttatcaaa taaattcttc
     1561 tgcatccgac caagtttaat taattcatcc agatatctgg aaggcacgcg ctgttttatt
     1621 tcattattta aacttgccgt ccttatatat tctgaaatag tcagcccttc gagcttcgct
     1681 cgccgcctga tttcgtttgc gattctgtta tttactctaa gggtgataac cttagtcctc
     1741 tgccgtactt ctgaaccact acgcttattt ttagtcatcg taatgactct ccattttgca
     1801 cgtttggggt gtcggggctt gccctgacag gaggtattct catgcaagcg aatgtattcg
     1861 cggtatgacg aatacacatc ctgtcccgtt ttccgctaca acttttcgac gaaaataaaa
     1921 taccgcgtcg taacctggta tttctgatac aaaaaaatga tgcttcattc aatattattt
     1981 acacagattt taaaagttat catttgttat ttgataaata acgccttatt aattgattcc
     2041 tttgtccatt ttcgtttgtg tcttatttat gaaataaaga ttatgacttc ctaaatatat
     2101 gattacttgc ctgttagtga tgcggtaggt atccagagaa caggaagcag aagaacaaga
     2161 taattgcata tgtataaaat ataacactgt gagttattga tatggcgttt atatattaaa
     2221 aatataactt aacatcccgc ttaatattta ttttctccta gcaatgggag cattaatccc
     2281 cgtgtagtgc tctgccagct gctgacaacc tcgacataca accatcgatg cgatagaaca
     2341 tcagggcgcg tttccggcaa aaactaacca tggggatggt ttgcgtgcca acgaacgccg
     2401 gaaacgcgcc tcaaacccac cgagccgcca cggttccggc agcgccttga gcgcaaccgg
     2461 aaaccgtctg gggagacccc cagccccccc tcgctgtaac accgacggtc tacgaccacc
     2521 taccaaccga gtggctgtct gttccgtgca aatgggcttt gcaggggggc tggcgcggtt
     2581 cctggcgacc tgaaagcccc tggttagggg tatcggcgcg cctgacctcc tgagagccac
     2641 tgtaagcgtt tttcgcgcct tccatgccct gacgggcatc tgttggcatt tgatcgcgtc
     2701 tgggagcttc tgagcgcgtt taagggccaa agacgaccaa accccctacc aaaccctcaa
     2761 aaacgcgttt tggaatgtct gagagcttgc aaacggcgcg atcgtcacgg atcaaaaacg
     2821 ggatcgacgg caatgcgcga gtgttggtac cgctcgccgc aagtcgatga ccgaacgtag
     2881 tgagcgaatc gacgaggaag cggaagagaa ccgacagcta aattgagcac ttacgcactg
     2941 ccgttaagaa ctaagaaggg agtattgcgg aagccgcgaa aaatggggat cgaattttca
     3001 gatcatgtga gacggtctat cagacgtcct cagacggtct atcaaaaata tcgttgattt
     3061 tgatagaccg ggattctaag attgaatccc gtctatcaaa aaaaggatta attgtgataa
     3121 acagtcgata caaaactaac cc
//
