LOCUS       CP055730                4286 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB13-C14 plasmid pRHB13-C14_7, complete
            sequence.
ACCESSION   CP055730
VERSION     CP055730.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148098
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4286)
  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 4286)
  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..4286
                     /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_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(40..1287)
                     /locus_tag="HVW81_25715"
     CDS             complement(40..1287)
                     /locus_tag="HVW81_25715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522448.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="QLM74965.1"
                     /translation="MIKFVDLFSGTGGIRLGFEQAMKEIGLSTKCVKSSEIDKKACETY
                     KLNFDEESYCDIHDVDIDESFDVLLAGFPCQAFSYAGKQLGFADTRGTLFFEVERIIKK
                     NKPKLCLLENVRGLTSHDKGRTFSTILKSLHDLGYHVEYRLLNTSNFGVPQNRVRIYII
                     ASLKKEVTLTIPNDLGAKDTHNYKPSKGGHDFYTESKVSDILEDSPDKSYDCSDWFKQR
                     LEDIFKGDLNKVHGIRLIDTRNGNSLHSWDLGLKGECSNDEIAFMNSLIANRRKHIFGT
                     HQDGKALSKAQIETFFKHSETTNIIKNLIKKGYLKEKNGLYNPVCGNMSFEVFKFLDPN
                     KVSITLTASDANRLGVYHNNRLRRLTPRECARLQGYPDSYILHPKDSMAYKQLGNAVSV
                     PVIKNIFLDIMKNNFI"
                     /name="DNA cytosine methyltransferase"
     gene            complement(1284..2294)
                     /locus_tag="HVW81_25720"
     CDS             complement(1284..2294)
                     /locus_tag="HVW81_25720"
                     /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="QLM74966.1"
                     /translation="MEFQELENSACLYWPKELAERAASISAISPLIETQDEFLSILTIS
                     TNKPTSCFDAVRLCNKISPNLFVKHLMVLSDIGGERLHRFFKDLDKIYPDRIMEFNIGN
                     NSYSYQFNSNRAWTTKNLNVEKSRLLQPVSDFTREMLDVCMLILWGGNTINNTNLPTEI
                     ENNCILGNLIGNKEAIEQFVKERYIMVSRQTGGATANDLGHICEIFIKEKLYKLIDDNI
                     SLDGHHIDGVTHNDKDLTTFDIVAKNTITKKCVGIEISFQVTTNSTIERKAGLAKSRRD
                     LLNSIGHKIAYVIDGSGNFQRSNAIKTIINHSDMTVNFSDNGINSLATFICETLK"
                     /name="hypothetical protein"
     gene            complement(3317..3511)
                     /locus_tag="HVW81_25725"
     CDS             complement(3317..3511)
                     /locus_tag="HVW81_25725"
                     /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="QLM74967.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3152..3237
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          3548..3646
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3771..4026
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(2582..3130)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.414"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aattaaataa ccatagagca gttttgctag taatatagtt tatatgaagt tattcttcat
       61 tatatcaaga aaaatatttt taatgactgg aacgcttaca gcattcccca attgtttata
      121 tgccatgcta tcttttgggt gtaagatata tgagtctggg taaccttgta gccttgcaca
      181 ttctcttggt gtaaggcgtc gcagtctatt gttgtgatag actccaagtc tattggcatc
      241 agatgcagta agtgtaattg acactttatt tgggtcaagg aatttgaata cttcaaaaga
      301 catatttccg caaactgggt tgtatagtcc gtttttttct ttaaggtaac cctttttaat
      361 tagatttttt attatgttgg tggtttcgct atgtttgaaa aatgtttcaa tttgtgcttt
      421 tgacaaagcc ttgccgtctt ggtgtgtgcc aaaaatatgc tttctacgat ttgcaattaa
      481 tgaattcatg aaagctattt catcatttga gcactcgcct tttagcccaa gatcccaaga
      541 gtgcaaggag ttgccgttcc ttgtgtcaat tagcctgatt ccatgaactt tattcaggtc
      601 acctttaaaa atatcttcaa ggcgttgctt gaaccaatcg ctgcaatcat atgacttgtc
      661 tggactatcc tctagtatgt cagaaacttt tgattctgta taaaaatcat gaccaccttt
      721 ggatggtttg taattgtgcg tatctttggc tccaagatca ttaggaatag taagcgttac
      781 ctcttttttt aatgaggcta ttatatatat tctaacccta ttttgaggga cgccaaaatt
      841 acttgtattt aatagtctgt attcaacatg ataccctaaa tcgtgaaggg attttaatat
      901 tgttgaaaat gtccttcctt tatcatgtga agttaatcca cgtacattct ccaaaagaca
      961 caatttaggc ttgtttttct ttataattct ttctacttca aaaaataatg tacctcgggt
     1021 gtctgcaaaa ccaagttgtt ttccagcata agagaatgct tggcaaggaa atcctgccaa
     1081 taaaacatcg aagctttcat ctatatcaac atcatgtata tcacaatatg attcttcgtc
     1141 gaagttaagt ttgtatgttt cgcatgcttt tttgtcaatt tctgagcttt ttacacattt
     1201 tgttgacaat ccaatttctt tcatggcttg ctcaaaacca agtctaatac cacctgtgcc
     1261 agaaaaaagg tcaacaaatt taatcatttc aatgtctcgc agatgaatgt tgctagtgaa
     1321 tttataccat tatctgaaaa gttaacagtc atgtcactat ggttaattat tgtttttatg
     1381 gcatttgagc gctgaaaatt accagaccca tcaatcacat atgctatttt atgccctatt
     1441 gaattgagta aatctcttct gcttttggct aatcctgctt ttctttctat tgttgagttt
     1501 gttgtaactt gaaaacttat ttcaatacca acacattttt ttgttatcgt gttttttgct
     1561 acaatatcaa aagtcgtaag gtctttatcg ttatgagtta caccatcgat atggtgtcca
     1621 tctagagata tattatcatc aataagttta taaagttttt cttttataaa gatctcgcat
     1681 atgtgtccaa gatcatttgc cgttgcacct cctgtttgtc tgctaaccat tatatatctt
     1741 tcttttacaa attgttctat tgcttctttg ttcccaatta aatttcccaa aatacagtta
     1801 ttttctattt cagttggaag gtttgtattg tttatagtgt tacctcccca caggatcagc
     1861 atgcaaacat caagcatttc tcgtgtaaaa tcacttacag gttgcaaaag tcgtgatttt
     1921 tccacgttta aattcttggt tgtccatgct ctattgctat tgaattggta agagtaagag
     1981 ttattcccta tattgaactc cattattctg tcaggataga ttttatctaa atctttaaaa
     2041 aagcgatgaa gtctttcgcc tccaatatct gacaaaacca ttaggtgctt gacaaatagg
     2101 ttgggtgata tcttattgca taaccgtaca gcatcaaaac aagatgtagg cttatttgtt
     2161 gatattgtta gtattgataa aaattcatct tgggtctcta taagagggct tatggcgcta
     2221 atagatgctg ctctttctgc aagttctttg ggccagtata agcatgcgct attttctaat
     2281 tcttggaact ccatgattat tccttggtaa aactatccaa atagaccttg agttacaccc
     2341 ctatgatggg taatctctac gggcgtaaac gaaaaaaccc acgttctcag gcgtgggttt
     2401 ttcgaaggtt agaagtttct caggctttct aacccaaggt aacagggcgt acaagaccgc
     2461 tgccaccaaa tctgtccttt cagtgtagcc gcagtcgggc cttcacttca agaactccgt
     2521 atcagcaatt tcttgtacac cctctaccaa tggctgctgc cagtggtgct tttgcatgtc
     2581 tttccgggtt ggactcaaga cgacagttac cggataaggc gcagcggtcg ggctgaacgg
     2641 ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg agataccaac
     2701 agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg
     2761 taagcggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt
     2821 atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcggttt ttgtgatgct
     2881 cgtcaggggg gcggagccta tggaaaaacg ccagcggcgt ggccttttcc gggttctcgt
     2941 tttttgctca catgtttctt ttggcgttat cccctgattc tgtggataac cgcatctccg
     3001 cttttgagtg agccgacacc gctcgccgca gccgaacgac cgagcgtagc gagtcagtga
     3061 gcgaggaagc ggaagagcgc cggaacgtgc attttctcct tacgcatctg tgcggcattt
     3121 cacaccgcat atggcgctct tttcttacaa tctgcactga tgccgcatgg ttaagccagt
     3181 atacactccg ctatcgctac gtgactgggt catggctgcg ccccgacacc cgctaaaacc
     3241 ccctgacgcg ccctgacggg cttgtctgct gacgaaaacg cccacgggaa agccgtgacc
     3301 gcctccgtca gcttcgttat gttcctgttt cactttcggc ctcaaagcga atctggatgc
     3361 tgttctggag ttcttctgcg agttcgtgca gtcgttcgca catggccgcc tgttcgtcgg
     3421 catccagagc atccagtttt tcaagcagtg tcaggctctg gcttttgata aatcgcgcca
     3481 tattcagcgc agtttgttgt tgtttgttca ccttccgttg ttctccgtca gttccgggtg
     3541 tcggggggac cctgagcagg tggtaattgt aagacgttgc gggcgacggt attacaattg
     3601 cacatcctgt cctgtttctt taggacgtat catggcacag catatcaact gataaataat
     3661 ccctgtgcag tgcagccgct gttgcataaa atttcgctct gcgtcgagtg tttcttaatc
     3721 aataattccg ctgatactcc ggaaaaacgc gagtctgttc tcatgcctga aatgcccaca
     3781 ccccacgcaa aaacaagttt ttgctgattt ttctttataa atagagagtt atgacaaatt
     3841 agttcttctt gctctctttg tgatatttaa aaaagcggtg tcggcgcggt gttgtagctg
     3901 cgccaacacc gctttttagg ggtggtactg actattttca taaaaaacat catcttatat
     3961 taggggtgct gctagcggcg cggtgtgttt ttttacagga cacccctggg ggcgctgcta
     4021 ggggtgtctg ttcagatatg tagcaatgag tcagggattc acgaactgaa aatgtccgaa
     4081 aatgtgtctc atgggcactg tatgcgccca aaccgatcgt cattcacttt catgcatagc
     4141 tatgcagtga gctgaaagcg atcctgacgc atttttccgg tttaccccgg ggagaacatc
     4201 tctttttgcg gtgttcgcgg cagaatcgct ttcagcgcgt tttagcggtg cgcgcaatgc
     4261 gacattatgg taaatctgtt aaattt
//
