LOCUS       CP057675                5686 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB18-C12 plasmid pRHB18-C12_3, complete
            sequence.
ACCESSION   CP057675
VERSION     CP057675.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148156
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5686)
  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 5686)
  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                     :: RH13 T2-C12
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 87.576727862526x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 11:13:33
            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)                     :: 5,060
            CDSs (total)                      :: 4,944
            Genes (coding)                    :: 4,861
            CDSs (with protein)               :: 4,861
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 83
            CDSs (without protein)            :: 83
            Pseudo Genes (ambiguous residues) :: 0 of 83
            Pseudo Genes (frameshifted)       :: 30 of 83
            Pseudo Genes (incomplete)         :: 43 of 83
            Pseudo Genes (internal stop)      :: 25 of 83
            Pseudo Genes (multiple problems)  :: 12 of 83
            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..5686
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB18-C12"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB18-C12_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5500..5686,1..944))
                     /locus_tag="HVX39_25255"
     CDS             complement(join(5500..5686,1..944))
                     /locus_tag="HVX39_25255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="QML41155.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVIHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            1021..2088
                     /locus_tag="HVX39_25260"
     CDS             1021..2088
                     /locus_tag="HVX39_25260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="QML41151.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPVLE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKYIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            complement(3101..3292)
                     /locus_tag="HVX39_25265"
     CDS             complement(3101..3292)
                     /locus_tag="HVX39_25265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="QML41152.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3357..3680
                     /locus_tag="HVX39_25270"
     CDS             3357..3680
                     /locus_tag="HVX39_25270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QML41156.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTSRKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3622..4380
                     /locus_tag="HVX39_25275"
                     /pseudo=""
     CDS             3622..4380
                     /locus_tag="HVX39_25275"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4358..4876
                     /locus_tag="HVX39_25280"
     CDS             4358..4876
                     /locus_tag="HVX39_25280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="QML41153.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMLQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            4883..5116
                     /gene="mbeD"
                     /locus_tag="HVX39_25285"
     CDS             4883..5116
                     /gene="mbeD"
                     /locus_tag="HVX39_25285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QML41154.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSRTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     Typing          2929..3013
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          complement(2360..2906)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.364"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3671..5220
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.275"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctgccagac cgtatggaaa tgtagcagga tgttttctgt tacgagatgg atttattttc
       61 cataggtttg tcttttcgta atcgtcgccg atttttgagt caaaaacatc ctctttgcta
      121 tgatggtttc ttatgttcca atctattaat ttatcagttt tttttctgta aacaagaatg
      181 tactcagtta ctggtactgg tttatattgc aacggattgc ggtcagctgc gaatcgacgg
      241 cctctaccta aagcccagcc agctccttct ggtttaaccc aatgtatatc atctatgaat
      301 tcatagcctt cttctataaa taacctgtgc aagtcaaaag gaacagctat tctttttgat
      361 gcttcattcc gtgacgccct tcttattaaa acgggcgaga cattgatgac gaaaaaacga
      421 ccttcgctta aaactctatg gcactctttt attactgaac gtaatagaga gaggtattca
      481 tcatatgtat gatattcgga atactctggt ttggcattgt aatatggcgg tgatgtgaat
      541 actaagttca ctgattcatc aggtaatttt ttcaaggtct ccgcgcagtt gccttgtagt
      601 aacatgttat ttaatggtga ctttgatatg attttttttt ctttttttac cttttttggg
      661 gtatggataa cctccattgc tttcttaata agaaatggag acttcgaact tttcttataa
      721 tcaatagttg acgtttttga atttataact atttcaccaa tcctgtggcc tgtcgctact
      781 aatggtacac gccatacatg gtaccgatca tcgacttcag gtaacccaaa ggaaaattta
      841 tcagctaagt ctaatttctc taggtgcaac tttgctattt ttttcgcctg agtcgtagag
      901 gttaccaaat aacctctgtt taagtaattg tttttaactg tcatttttcc taactatcga
      961 tctgttacca tacaacctgc tatcttagca tctcattttt actatgtcca tggtgaggat
     1021 atgaatttca aggataaaaa ttgtttccct aacgaactca tagcgttggc gaaaatttca
     1081 aaaaatgatg ttttagataa gttcggaacg gatgttttta aaaaggttgt ttatgatgtt
     1141 ttaacaggta aaaatgttcg cgaattcact gaaatactaa ctcgtactag attgttagaa
     1201 agcaatctct ctttttttga cttttttgtg gataaaatga aagaggggat aacgccaaag
     1261 cagctttatc tctatgcaaa aaatgcatta tcgaacaagt cttatgttaa gtctaatcaa
     1321 cctgttctcg agtggatggt tatgatgaca aataaacaga cccaaaatgt tttaagagat
     1381 gagcatgggg atggttttga taggcttgct ttaaggacgc aagaagaaat acttaaaata
     1441 aaaaacgggt atgaagataa aattggagag atatctattg gtgggcaaaa ggtgtcttta
     1501 gaagattttt gctatattat tttatctctt ggttcgcaaa ctttaactat tagggggtct
     1561 gagaaatctc ttcatggtaa atattttgaa aagctaatac tcggttcttt atttacaata
     1621 atgggttttg aatataaaga aaaaattgaa gaagggttaa atgctaaatg ttttactctt
     1681 tcaacaagag ctgatgacag ggagtctgat gctactcttg tttttaatgg gaaggcgatt
     1741 agggttgata ttggttttat tggtaggggt aacacagaaa taagtttgga taaagtatct
     1801 agatttagac gaatggatga tattggcgga gtgatgcata atataagcac aatggttatt
     1861 gttgacgtta ttggtgatag aagtagaata gttaatatgg ctgaagagat tgatggtaaa
     1921 gttgttgcga tgagtgatcc gtattgggtt gcaaaggtat cttcctatat tagttcgaaa
     1981 ctgaatgtag atgatctttt agaggataaa cctcaactta aatacataca gtcttttata
     2041 tctgatgcat tagagaatgt agatctggaa aaatacatta aattataaga gattgtaatc
     2101 cttgactgcg tgcttattaa aagcataatc tctacataaa gaaaaaccac cctggcaggt
     2161 ggtttttcaa aggttagcta atcctggcag attatctaac caggtaatct ggcttaagca
     2221 gagcgcagac acctaaaact tgttcttcta gtgtagccag aatcaggctg atacttcaag
     2281 aactctgtta ccaacttata aatctcgctc tgctaatccg gttaccagtg gctgctgcca
     2341 gtggcgttaa ggcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc
     2401 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     2461 ccgggccgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     2521 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc
     2581 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc
     2641 gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcggcgcgg
     2701 ccttttgttg ccctttgcct ttttactcac atgttctttc cggccttatc ccctgattct
     2761 gtgggtaacc gtattaccgc ctttgagtga gctggcaccg ctcgccgcag ccgaacgacc
     2821 gagcgtagcg agtccgtgag cgaggaagcg gaagagtgtc ggaagttgca ttttctcctt
     2881 acgcatctgt gcggcatttc acaccgtcca tggcgcactt ttcatacaat tcgcatcgat
     2941 gccgcatagt taagccagta tacactccgc tatcgctacg tgactgggtc agggctgcgc
     3001 cccgacaccc gctaaaacct gctgacgcgc cctgacgggc ttgtcagctc ccggcatccg
     3061 ctcacaggca agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat
     3121 ccccgaagcg tgcgagacag ctgcggtaaa gctcgtcggc gtggtcgtga agcgattcac
     3181 agatatctgc ctgttcatct gcgtccagtt cgttgagctt ctccagcagc gttaatgtct
     3241 ggcttctgat aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct
     3301 ccgtgtaagg gggatttctg ttcatggggg taatgatacc gatgaaacgc gagaggatgc
     3361 tcacgatacg ggttactgat gatgaacatg cccggttact ggaacgctgt gagggtaaac
     3421 aactggcggt atggatgcgg cgggtctgtc tgggtgagcc ggttgcccgt tccgggaggc
     3481 tgccgacact ggcaccaccg ttactgcgtc agctggccgc catcgggaat aatctgaatc
     3541 agacatcccg taaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg
     3601 ccgcactgat ggccatcggg gatgagctgc gccggctgcg tctggccgtc agggaacagg
     3661 ggacgcggga tgatagttaa gtttcatgcc aggggaaaag gcggtggcag tggtccggtt
     3721 gattacctgc tgggaaggga gcgtaaccgg gaaggggcaa cggtgcttca gggtaatccg
     3781 gaagaagtcc gggaactcat cgatgccacg ccatttgcga agaaatacac gtcaggtgtt
     3841 ctgtcgttcg cggagaagga gctgccgccg ggaggacgtg aaaaagtgat ggcgagcttt
     3901 gagcgtgtac tgatgcccgg tctcgaaaaa aatcagtaca gcattctgtg ggtggagcac
     3961 caggacaagg ggcggcttga gctgaatttt gtcattccga acatggagct acagaccgga
     4021 aaacgcctcc agccgtacta tgatcgcgca gacagaccga gaattgatgc ctggcagacg
     4081 ctggttaatc accattacgg gctgcatgac ccgaacgccc cggagaaccg ccggacgctg
     4141 actctccctg ataacctgcc ggaaacgaaa caggcgcttg ctgagagcgt tacacggggg
     4201 cttgatgtgc tttaccgtgc cggagagata aaagaccgtc aggatgtgat tcaggctctc
     4261 actgatgtgg gggttgaggt tgtcagggtg acgcgaagca gtatcagcat tgcagacccg
     4321 aacggcggga ggaatatcag actgaaagga gcgttttatg agcaatcttt tacagacggg
     4381 cgcggagttc gagaaaaagc tgaaagagag agccgaatct acagagaaaa tgctgaacaa
     4441 cgagttcagg aggctcggcg aatctgtaag cgaggctgtg acatcaaacg agacgaaaat
     4501 cagagacgct atagccctgt tcacagcctc gacagaggaa tcgctggaga aacaccggga
     4561 aggggtgaaa gaggcgatgt tgcagcaccg gaaggacgtg ttaaagctgg cagggaatac
     4621 gggcatgatg ttactgggga tagtctttct cctgtttacc gcgagtggcg ggacgctctg
     4681 gtatcttggc gggaggatac aggcgaacct ggaagatatc aggaagcagg aagagacatt
     4741 gcagaaactg aacgcgaaga catggggcgt ggagtttgtg caggacggga acaggaaatt
     4801 tctggtcctt ccgtacggga aatcagcaga ggtgattccc tttcagggga aagagtgggt
     4861 acatctgaag gagtgacaca gaatgacaga gctggaaaca catttgctga acgccttaga
     4921 gcagctgcaa caggactata tgcagcggct gagcgaatgg gagagcgcct tcgtggaatt
     4981 gcagaagatg ttttcgcgta cgcaacggga caacgcgatg ctgaacgagc gggtcatgca
     5041 gttgagtcag caggtgcagc acttgagcga gcagacagaa cgcttgagcc agttatacag
     5101 cgagaactgg agataagaga ggaacggctg atacaggagt gcgaacatgc gttatccctg
     5161 gagtgtgagc gccagctgga aatacaggaa cgcacactgg atggtccttc gctgggatgg
     5221 tgaaactatg aaaaatggca ggttaagtgg attaagacgg gctaatgtgg tctgtaccat
     5281 ctggttgcat aggtattcat gcggttaaaa tttatcaggc gcgatcgcgg cagtttttcg
     5341 ggggggttgt tgccattttt acctgtctgc tgccgtgttc gcgctgaacg cgttttggcg
     5401 gtgcgtacaa ttaagggatt atggtaaatt cgacaatgtg gctgatgttg acgcgtaaat
     5461 aagccgcctt aaggcggctt ttaccacagt aaagtttgat taatttatga tttttaaatc
     5521 accacctagc atggttcctt ctatgattag atcaatatac tgctttgata tctcacacat
     5581 cacaaatctt ctgcctaaat caattgctgc ttttgctgtt gttcccgaac cagcaaaagg
     5641 atctaaaatg acatcatttt tgaaagaata gtattttata actctt
//
