LOCUS       CP058096                5682 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB01-C09 plasmid pRHB01-C09_4, complete
            sequence.
ACCESSION   CP058096
VERSION     CP058096.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147953
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5682)
  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 5682)
  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                     :: RH11 T1-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 90.9454302587345x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:43:09
            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)                     :: 4,860
            CDSs (total)                      :: 4,741
            Genes (coding)                    :: 4,643
            CDSs (with protein)               :: 4,643
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 48 of 98
            Pseudo Genes (incomplete)         :: 42 of 98
            Pseudo Genes (internal stop)      :: 23 of 98
            Pseudo Genes (multiple problems)  :: 15 of 98
            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..5682
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB01-C09"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB01-C09_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            1..900
                     /locus_tag="HVV36_24220"
     CDS             1..900
                     /locus_tag="HVV36_24220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMR28343.1"
                     /translation="MSAVLQRFREKLPHKPYCTNDFTYGVRILPKDIAILARFIQQNQP
                     HAQHWLVFDVDRTGAAIDWSDRNCPAPNITVKNPRNGHAHLLYALTLPVRTAPDASASA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHQEWQVVEWRLELYTLDELADYLDLSASA
                     RRRVDKDYGMGRNWYLFEKSRKWSYRAIRQGWPAFSQWLDAVIQRVEMYNASLLVPLSP
                     AECRAIGKSIAKYTYRKFSPEGFSAVQAARGRKGGKIGGAKSKRGAVATSARTLKPWET
                     LGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1104..1550)
                     /locus_tag="HVV36_24225"
     CDS             complement(1104..1550)
                     /locus_tag="HVV36_24225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="QMR28348.1"
                     /translation="MTNLEEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAILAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFNAAELVGALAGVAELPRNHPKWQEWEKRGKELLTKDGA"
                     /name="conjugal transfer protein TraD"
     gene            1721..2806
                     /locus_tag="HVV36_24230"
     CDS             1721..2806
                     /locus_tag="HVV36_24230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="QMR28344.1"
                     /translation="MASYHCTVKTGAKGVALKHADYISRSGEYKNYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKARF
                     GETPQERKSALVALRSHWADVQNEHLARHGHQSRVDHRSLKEQGIKRTPEVHLGPVRVA
                     VMNADQVCAILARRNAEREKLEAEQERDSIIDLKTTLKEALAERDNIPPSLDELGAELK
                     AFVESSFDELNEVMQLNSLINGALDSMMKQFQVEEERKLQQERLIEAEKQRDLERERER
                     VRQRAYSSPAPSRSRDYGMSR"
                     /name="MobA/MobL family protein"
     gene            2827..3543
                     /locus_tag="HVV36_24235"
     CDS             2827..3543
                     /locus_tag="HVV36_24235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235968.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMR28345.1"
                     /translation="MQLDEHSRKIAALVAYNDKQIKEMNRLITLLNERVNDLNTFTSTL
                     EREGKVVSGISYSFRDSVSNVKFYINKGMDEASCKLQKSVSDTLTSLLREKLSFTLNDV
                     KKEWVDFEEQTSKEIKESLKQTTREAEVATGIIRKTMEKYTVTRIVEKVIVLIVLFLLL
                     MIAPVFYAEYLKMNISSLMEEQKKHESMLKEWKEKAPLAEFSKCGDYRKACVLVDDESG
                     YYFNEQSPNKKYAILK"
                     /name="hypothetical protein"
     gene            complement(3601..4173)
                     /locus_tag="HVV36_24240"
     CDS             complement(3601..4173)
                     /locus_tag="HVV36_24240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522465.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="QMR28346.1"
                     /translation="MEYSTLLSFAIVTLSQTISIGPGVALVINNAFSHGLKSSIKTSIY
                     IRIGETIVMAISLFALSSTSSTEQHFHIIKIFGGGYLIYIGLMGLINKKNKQRKEQKPF
                     LMPLLNPKAYLFFAALIPTFIDNNTNITLNFFILGVLFIFISFLTDLIYIAISLTIRDK
                     LTPSFSRYISICSSIFILGTGIYFIFT"
                     /name="LysE family translocator"
     gene            complement(4180..5130)
                     /locus_tag="HVV36_24245"
     CDS             complement(4180..5130)
                     /locus_tag="HVV36_24245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001058673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMR28347.1"
                     /translation="MNNFINECISAPRINGMAEFFSSTASGEKHKPFRLVEIDDRLFHS
                     YDYIKFAKHLTKNSGPFVNHYFCSIPYSKEEECRLGTTVIKYAITLNKKLNTWCLGMAE
                     GAMARTISELSKGNIQTLTTSPTKENEHAFFKYGSSENAYFICTPFFLLEERLKNSNLK
                     QFNQGFDIIIEDTTFQMYSPNRSGQINHVKRLLNNDGIFIFTEKHSSEHDEYQKREIQK
                     DYSFKQRYFSKDEINTKKEIVLNTMNLNEVSVDDMLSAIKQHFKYASIYWNSGNFYSIA
                     ASNSLKHISTFINLLPKAAIPMEYVYEKLPRNISW"
                     /name="hypothetical protein"
     Typing          2..840
                     /name="rep_cluster_2141"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.738"
                     /coverage="93.0"
                     /evalue="0.0"
     Typing          1722..2803
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg tacttcaacg cttcagggaa aaattaccgc acaaaccgta ctgtacgaac
       61 gatttcacgt acggcgttcg cattctgccg aaagatatcg ccatccttgc ccgtttcatc
      121 cagcagaacc agccacatgc gcagcactgg cttgtttttg acgtggaccg gacgggcgca
      181 gcgatagact ggagcgaccg gaactgtccg gccccgaata tcaccgtaaa aaatccccgt
      241 aacgggcacg cgcatctgct ttacgcactc actcttccgg tgagaaccgc gccggatgca
      301 tcggcttcgg cgctcaaata cgctgctgcg attgagcgtg cactgtgtga aaaattaggc
      361 gcggatgtga actacagcgg cctgatctgc aaaaatccgt tccatcagga atggcaggtt
      421 gtggaatggc gtctggaact ctataccctc gatgaactgg cggattatct cgatttgagc
      481 gcctcagcgc gccgtcgcgt cgataaagat tacgggatgg ggcgaaactg gtatctgttc
      541 gaaaagagcc gtaaatggtc ttacagggcg attcgtcagg gttggccagc attctcacag
      601 tggcttgatg ccgtgattca gcgtgtcgaa atgtacaacg catcgcttct cgttccgctt
      661 tcaccggctg aatgtcgggc tattggcaag agtattgcta aatacaccta ccgaaaattc
      721 tctcctgaag gtttttctgc ggtacaggct gcgcgtggtc gcaagggcgg gaaaattgga
      781 ggtgctaagt ctaagcgtgg tgctgttgcc acatctgcgc gaacgttgaa accgtgggag
      841 actcttggaa ttagccgcgc ctggtattac caactgaaaa aacgaggtct tgtagagtag
      901 accagataaa gccttatcag ataacagcgc tccgttggcg tttttttgag ctgttggttt
      961 tgctgtgtat ttctctgctc acccccgcaa tggtgcggct ttccgcatga ttgcgggggt
     1021 agtgctcgcc gcagtctcat gaccgagcgt agcgagcgaa tgagcgagga agcaccaggg
     1081 taccagaacg cgaacggaga ctcttacgca ccgtctttgg tgagtagctc tttcccgcgt
     1141 ttttcccatt cctgccattt tggatggttg cgtggtagct ctgctactcc tgctagtgcg
     1201 cctaccagtt cggcagcatt aaattttggt tttccggttt tgctgtccac tagtccagca
     1261 acaatcatga ggcctgcggc tttgtagagt tcgtgatccc gcgcctttcg ttctgccctt
     1321 gcggcagcct tccgttctgc cgcaaggatt gctgttaccc tagcttttgc agcggcggct
     1381 ttctccgcgg ttttttctgc tcgtattagt gcggataacg ttttttcatc cgtcgttgtt
     1441 cggttttttt tctctgccag taatacaagt aatcgctgct gctcagatgg tgatttcaga
     1501 ccgttgatgt aggcaatttt tgcacttaac cactcttcaa gatttgtcat tcttatctcc
     1561 gcacttttgc cgtttattgt tttggtattg cgcataatat caccttgtat gcccgagtac
     1621 gtgaccgtaa aatcatccct gataaactca gggatgcgca cttagacgtt tctctccttc
     1681 gtcgagaaac agtgcgctcc tgcggagggc ttaacggcag atggcaagct accattgtac
     1741 agttaaaact ggagcaaaag gcgtagcctt aaaacatgct gattatattt ctagatccgg
     1801 cgaatataag aactacaaat cgcgggagga tctggaattt tcgtcatccg gtaacatgcc
     1861 atcatgggcg aagaaaaatc ccgcagagct atggaaagca gcagatgaat ttgaacgaaa
     1921 aaacgggacg gcataccgtg aaattgagat cgcattaccg cgagaactga cacgcgaaca
     1981 acggatagaa cttgttgaag atttcgtgca aaaggagctt ggtgatcgcc atgcctatca
     2041 gtacgcgatc cacaatccgc caggtgcaat cgacggaaag gaacaaccac acgcacatat
     2101 catgttttgc gagcggatta atgatggtat tgaacgcgat ccgcagcagt tttttaaacg
     2161 tgccaacagc aaatcaccgg agcggggagg tgcaaaaaag gcacgctttg gtgagacacc
     2221 acaagagcga aaatcagcct tggttgcgct acgttctcac tgggctgatg tgcagaatga
     2281 acaccttgcg cggcacggcc atcagtcgcg cgttgatcat cgttcactga aagaacaggg
     2341 tatcaagcgc acaccggaag ttcatcttgg tcccgttcgt gttgctgtta tgaatgctga
     2401 tcaggtttgt gcaattctgg cacggagaaa cgcggaacgg gagaagctag aagcagagca
     2461 ggaacgggac agcatcattg accttaaaac gaccttgaag gaagcgttag ctgaacggga
     2521 taacatacca ccaagcctgg atgagcttgg ggcagaattg aaggcgtttg ttgaaagctc
     2581 gtttgatgaa ctcaatgagg taatgcagct taattcattg attaacggtg cgctggactc
     2641 aatgatgaag caattccagg tggaagagga gcggaagttg caacaggaac gactaattga
     2701 agccgaaaag caaagagacc tggagaggga aagagaaaga gtgcgccagc gtgcgtattc
     2761 ctcaccagca ccatcacgtt cacgtgatta tggtatgagc cgttaagcac tggaggtttt
     2821 tattttatgc aattggatga acattcaaga aaaattgctg ctcttgttgc gtataatgat
     2881 aaacaaataa aagaaatgaa caggctaatt actctgctta atgaaagagt gaatgactta
     2941 aataccttta caagtactct tgaacgtgaa ggtaaagttg tttctggaat ttcttattcc
     3001 tttagggata gtgtgtctaa tgttaaattt tatattaata aaggaatgga tgaggcatct
     3061 tgtaaattac agaaatcagt ctcagataca ctaacgtcat tactccgcga aaaattatct
     3121 ttcactctca atgatgtaaa gaaagagtgg gttgatttcg aggagcaaac aagtaaagag
     3181 ataaaggaat cattaaagca gacgaccaga gaggccgaag ttgcgacagg tataattaga
     3241 aaaacaatgg agaagtatac agtaacaagg attgtcgaaa aggtaattgt gttgattgta
     3301 ttatttttat tgctaatgat cgctcctgtt ttctatgctg aatatctcaa aatgaatatt
     3361 agttcgctaa tggaagaaca gaaaaaacat gaatccatgt taaaagaatg gaaagaaaaa
     3421 gctccattgg ccgagttctc gaagtgtgga gattatcgta aagcatgcgt gttagttgat
     3481 gacgaaagcg gatattattt taatgaacaa tcaccaaata aaaaatatgc catactgaaa
     3541 tagtgttaag taactcatgc cgtcttatga ctaaggctgc atgagtataa aaacggcgtt
     3601 tcacgtaaaa ataaaataaa tacctgtacc taatataaaa atggaactac atatgcttat
     3661 gtatcttgag aatgatggtg tcaatttatc ccttatcgtt aagctaatag ctatgtaaat
     3721 aagatctgtt aggaatgata taaatataaa taaaacaccc aatataaaaa agtttaatgt
     3781 gatatttgta ttattatcta taaaggttgg tattaacgca gcaaagaaaa gatacgcctt
     3841 ggggtttaat aatggcatca aaaaaggttt ttgctctttt ctttgtttgt tttttttatt
     3901 aattaaaccc attaatccta tgtatattaa atagcctcca ccgaatattt ttataatgtg
     3961 aaaatgttgt tctgtgctgg atgttgagga taacgcgaaa agagatattg ccatgacgat
     4021 agtctcgcca attcttatgt atatacttgt ttttattgat gactttaatc catgtgaaaa
     4081 ggcattgttt ataaccaatg caacgccagg ccctattgat atagtttgcg ataaggttac
     4141 gatagcaaat gataataatg ttgaatattc catgtttact taccatgata tatttcgtgg
     4201 gagcttttca tatacatatt ccataggaat tgcagctttc ggtaataaat ttataaatgt
     4261 tgatatgtgt tttagtgaat tgctggcggc gattgagtaa aaatttccgc tattccaata
     4321 tattgatgcg tatttaaaat gttgtttaat tgcggaaagc atatcgtcaa cactaacttc
     4381 attcaaattc attgtgttta gtacgatttc ctttttggtg ttaatctcat ctttcgagaa
     4441 atacctttgt ttgaatgaat aatctttttg gatttctctt ttttgatatt catcatgttc
     4501 tgaactatgt ttttctgtaa atatgaaaat accatcatta tttaatagcc tttttacgtg
     4561 gtttatttgc ccagatctgt taggtgagta catttgaaat gtggtgtctt ctattataat
     4621 atcgaatcct tgattaaatt gtttaagatt tgaatttttt agtctttcct ctaacaggaa
     4681 aaatggagtg caaataaaat aagcgttttc acttgagcca tacttaaaaa atgcatgttc
     4741 attttctttt gttggactgg ttgttaatgt ttgtatgttt ccttttgata attctgaaat
     4801 ggttcttgcc attgcgccct cagccatacc aagacaccat gtgtttaatt ttttgtttag
     4861 cgtgattgcg tattttatta ctgttgttcc taatctgcac tcttcttcct tgctgtatgg
     4921 tatactgcaa aaataatgat taacgaaagg gccgctgttt tttgtgaggt gtttggcaaa
     4981 cttaatgtaa tcataagaat gaaaaagccg atcatctatt tctactagtc taaaaggttt
     5041 gtgtttttcc cctgatgcag ttgatgagaa aaattctgcc atgccgttta ttctcggagc
     5101 ggaaatacat tcatttataa aattattcat tttcctatcc tctggtttga tttttggaat
     5161 ttgttgttat gactcttcaa tgctaattct cttgtaagct tttttacacg ccataaacac
     5221 gattatgatg ttttatattg tcgatatttc gttgtccaga ctggatatgt ttggaaattt
     5281 gttttcatgc gggttagttc agctggcttt ctggatgaga aagtttgctg ttttgaccag
     5341 ttcgcgcttc tgaaggggtg aaaccgatca ttaatcgctt ttgtgcatag ttatgcaggc
     5401 ccctaaaaac gattctgacg cgttttttgt gttttcccta ggtttatctt gtctttttga
     5461 gttttttgcg tcagaaagcg attgagagcg ttttagaggg tacgtacaag gggagttatg
     5521 gtaaatggat cgggttttcg tgatggatcg acagggtttg tcgttgggtg tagtgtaagc
     5581 agctgaaaaa caaacgcccc tgaaattcgt gccgatccgc caagactgtc acgaaaattc
     5641 aaggggcgtg tgggttgtaa cacacagagg aaatcctaac ac
//
