LOCUS       CP055729                4973 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB13-C14 plasmid pRHB13-C14_6, complete
            sequence.
ACCESSION   CP055729
VERSION     CP055729.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148098
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4973)
  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 4973)
  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..4973
                     /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_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4409..4973,1..152))
                     /locus_tag="HVW81_25690"
     CDS             complement(join(4409..4973,1..152))
                     /locus_tag="HVW81_25690"
                     /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="QLM74960.1"
                     /translation="MQLDEHSRKIAALVAYNEKQIKEINRIITLLNERVNDLNTFTDTL
                     EREGKVVSGISYSLRDSVSHVDFYLNKGMEEVSCKLQKSVSDTLTSLLREKLSFTLNDV
                     RQEWTDFEEQTSKEIKESLKQTTRDAEVATGIIRKTMEKYTVTRIVEKVLVLLVLFLLL
                     MIAPSFYAEYLKMNIGSLMEEQKKHESMLKEWKEKAPLAEFSKCGEYRDVCVLVDDKSG
                     YYSNEQTPNKKYAILK"
                     /name="hypothetical protein"
     gene            complement(174..1268)
                     /locus_tag="HVW81_25695"
     CDS             complement(174..1268)
                     /locus_tag="HVW81_25695"
                     /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="QLM74961.1"
                     /translation="MASYHCTVKTGAKGVALKHADYISRSGEYKNYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKARF
                     GETQQERKSALVALRSHWADVQNEHLARHGHQSRVDHRSLKEQGIKRTPEVHLGPVRVA
                     VMNADQVCAILAWRNAEREKLEAEKERDSIIDLKTTLKEALAERDNMPPTLDELGAELK
                     AFVESSFDELNEVMQLNSLIDGALDTMMKQFQVEEERKLQQERLIQAARDEAEKQRELE
                     RERVRRRAYSSPAPSRSRDYGMSR"
                     /name="MobA/MobL family protein"
     gene            1440..1886
                     /locus_tag="HVW81_25700"
     CDS             1440..1886
                     /locus_tag="HVW81_25700"
                     /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="QLM74962.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLAKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(2148..3179)
                     /locus_tag="HVW81_25705"
     CDS             complement(2148..3179)
                     /locus_tag="HVW81_25705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QLM74963.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSKNQADKGKVG
                     GKNSGVVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDSSGEWLAKKQI
                     IKY"
                     /name="replication initiation protein"
     gene            3779..4351
                     /locus_tag="HVW81_25710"
     CDS             3779..4351
                     /locus_tag="HVW81_25710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001681717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="QLM74964.1"
                     /translation="MEYSTLFSFAIVTLSQTISIGPGVALVINNAFLQGLKSSIKTSIY
                     IRAGEAIVMVISLFTLSSTSSIEQHFYIIKILGGSYLIYIGVMGLINKKNKKSKVQKPL
                     LIPLLNPKAYLFFAALIPAFIDDNTNIALNFFILGVLFIFISFLTDIIYIAISLTIRDK
                     LTPSFSRYISICSSIFILGTGIYFILT"
                     /name="LysE family translocator"
     Typing          complement(2404..3179)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.169"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(178..1268)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.055"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actttacctt cacgttcaag agtatctgta aaggtattta agtcattcac tctttcatta
       61 agcagagtaa ttatcctgtt tatttctttt atttgctttt cattatacgc aacaagggca
      121 gcaatttttc ttgaatgttc atccaattgc ataaaataaa aaacctccag tgcttaacgg
      181 ctcataccat aatcgcgtga acgtgatggt gctggtgaag aatacgcacg ccggcgcact
      241 ctttccctct ccagctctct ttgcttttcg gcttcatctc gcgcagcctg aattagtcgt
      301 tcctgttgca acttccgctc ctcttccacc tggaattgct tcatcattgt gtccagcgca
      361 ccgtcaatca atgaattaag ctgcattacc tcattgagtt catcaaacga gctttcaaca
      421 aacgctttca attctgcccc aagctcatcc agggttggtg gcatgttatc ccgttcagct
      481 aacgcttcct tcaaggtcgt tttaaggtca atgatgctgt cccgttcctt ctcggcctcc
      541 agcttctccc gttccgcatt tctccatgcc agaattgcac aaacctgatc agcgttcata
      601 acagcaacac gaacgggacc aagatgcacc tccggcgtac gcttgatacc ctgttctttc
      661 agcgaacgat gatcaacgcg cgactggtgg ccgtgtcgcg caaggtgttc attctgcaca
      721 tcagcccagt gagagcgtag cgcaaccagg gctgattttc gctcttgttg tgtctcgcca
      781 aagcgtgctt tttttgcgcc cccccgctct ggtgatttgc tgttggcacg tttaaaaaac
      841 tgctgcggat cgcgttcaat accatcatta atccgttcgc aaaacatgat atgcgcgtgt
      901 ggctgttcct tcccgtcaat tgcacctggt ggattgtgga tcgcgtactg ataggcatgg
      961 cgatcaccaa gttccttttg cacgaaatct tcaacaagct ctatccgttg ttcacgtgtc
     1021 agttctcgcg gtaatgcgat ctcaatttca cggtatgccg tcccgttttt tcgttcaaat
     1081 tcatcagcag ctttccacag ttctgcggga tttttcttcg cccatgatgg catgttaccg
     1141 gatgaagaaa attccagatc ctcccgcgat ttatagtttt tatattcgcc ggatctggaa
     1201 atgtaatcag catgttttaa ggctacgcct tttgctccag ttttaactgt gcaatggtag
     1261 cttgccatct gccgttaagc cctccgcagg agcgcactgt ttctcgacaa aggagagaaa
     1321 cgtctaagtg cgcatccctg aattaatcag ggatgatttt acggtatcac acgcaggcag
     1381 acaaggtgat attatgcaca ataacaactc acattaacgg caaaagtgca gaggtaagaa
     1441 tgacaaatcg tgaagagtgg ttaagtgcaa aaattgccta catcaacgga ctgaaatcac
     1501 cgtcagagca gcagagatta cttgtgttac tggcagagaa aaaaaaccga acaacgacgg
     1561 atgaaaaaac gttgtccgca ctgatacggg cagaaaaaac cgcagagaaa gcagccgcag
     1621 caaaagccag ggtaacggca atcatagcgg cagaacggaa ggcagccgca agggcagaac
     1681 gaaaggcgcg ggatcatgaa ctctacaagg ccgcaggcct catgattgtg gcaggactgg
     1741 tggacagcaa aaccggaaaa ccaaagttta gtgctgccga actggtaggc gcactcgcag
     1801 gaatcgcaga gctaccgcgc aaccatccca aatggcagga atgggaaaaa cgcgggaaag
     1861 agctactcgc caaagacagt gcgtaagagc ctccgttcac gttccggttc cctggtgctt
     1921 cctcgctcat tcgctcgcta cgctcggtca tgagactgcg gcgagcacaa ccacctcaat
     1981 catgcggtaa gccgcaccat tgctgggctg aaaggagaaa accgccggaa agcccgctgc
     2041 tcaaaaagac gccgaaaggc gctgttatct gatataggct tgcttcgtgt ccgcaaattt
     2101 aacaacccat taacaaaaac cagggggttt gttgcttttt ttgtaaacta atatttaatt
     2161 atttgtttct ttgctagcca ttctccagag ctatccatcc agcgtcgaat agtccgactg
     2221 ctaacaccaa ccgccactgc aatatcttct gttgacgctc ccaagatgta catatcaagc
     2281 gccctacgac gtttatcatc gttagccgtc caccggacaa caccgctgtt tttcccgcca
     2341 actttccctt tgtccgcctg attttttgac gaattggcct taccgccctt gcgacctcgt
     2401 gcggcctgaa tttctggcgt gtgcgtatca gccacatact gtgcgaaagt ttccggcgtg
     2461 aagttcctgt gcgtgtattt cgcaatgctc ttgccaatag cccgacattc agccagtgaa
     2521 agcggaacgg gaagcgatgc attgtacatt tcgacacgct ggatcaccgc ttcaagccac
     2581 tgtgagaacg ctggccagcc ctgacgaatc gccctgtaag cccatttgcg cgtcatttcg
     2641 aacaggtggc agtttcgccc catcccgtaa tgtttatcga tgctacgacg ctctgaggcg
     2701 ctcaaatcga gataatctgc cagttcatcg agggtatagg cgtcctcgcg ccactccatc
     2761 acctgccatt ccaggtggaa cggatttttg caaatcaggc cgctgtagtt cacatcagca
     2821 caaagtttct cacacagcga acgttcaacc gctgcggcat atttcagcgc cttaaccgag
     2881 gcatcaggcg cggttctcac ggcgatgttg agtgcgtaga gcaggtgagc gtgtccgttc
     2941 acaggatttt taacggtgat gttcggcgcg ggggcgttcc ggtcgctcca gtcaatcgca
     3001 gccccctcgc ggtcaacgtc aaaaaccagc cagaactgcg catgaggctg gttctgctgg
     3061 atgtaccgcg caagaagcgc acgccctttg ccggagatgc gaagaccaaa agcgagatca
     3121 tccgtgtgat agggacggtg gggtaaattt tcttcgaagt attgaagtgc ggcgctcatg
     3181 tgttaggatt tcctccgtgt gttacgaccc acacgcccct tgaattttcg tgacaatctt
     3241 ggcggagagg cacgaatttc aggggcgttt gtttttcagt cgcttacact acccccaacg
     3301 acaaaacctg tcgagtcttc ccgcaaaccc gatccattta ccataactcc cgttgtacgt
     3361 accctctaaa acgctctcaa tcgctttctg acgcaaaaaa ctcaaaaaga caagaaaaca
     3421 ctagggtaaa ccataaaaac gcgtcagaat cgtttttatg ggcctgcata actatgcaca
     3481 aaagcgattc atgatcggtt tccccccttc agaagcgcga acgggtcaaa acagcaaact
     3541 ttctcatcca aaaagccagc taaacggaac gaacccgtat gcaaacaaat ttccaaacat
     3601 atacagtctg gacaacgaaa tatcgacaat atattggaat agcggaaatt tttactcaat
     3661 cgccgccagc aattcactaa agcacatatc cacatttata aatttattac cgaaagccgc
     3721 aattcctatg gaatatgtat atgaaaagct cccacgaaat atatcatggt aagtaaatat
     3781 ggaatattca acattatttt catttgctat cgtaacttta tctcaaacta tatcaatagg
     3841 acctggtgtt gcattggtta taaacaacgc ctttttacaa ggacttaaat catcaataaa
     3901 aacaagtata tacataagag ctggcgaagc aatcgtcatg gtaatatctc ttttcacgtt
     3961 atcttcaaca tccagcatag aacaacactt ttacattata aagatcttag gtggaagcta
     4021 tttaatatac ataggggtaa tgggtttaat taataaaaaa aacaaaaaaa gcaaagtaca
     4081 aaaaccttta cttataccat tattaaaccc aaaggcgtat ttattctttg cggcattaat
     4141 accagcattt atagatgata atacaaatat cgcattaaat ttctttatat tgggtgtttt
     4201 gtttatattt atatcattcc tgacagatat tatttacata gctattagct tgacgataag
     4261 ggataaatta actccgtcat tctcaaggta cataagtata tgtagctcca tttttatatt
     4321 aggtacaggt atttatttta tcttgacgtg aaacgccgtt tttatactca tgcagcctta
     4381 gtcataagac ggcatgagtt acttaacact atttcagtat ggcatatttt ttatttgggg
     4441 tttgttcatt ggaataatat ccgcttttat catcaactaa cacgcatacg tccctatact
     4501 ctccacactt agagaactct gccaatggtg ctttttcctt ccactctttt aacatagatt
     4561 catgtttttt ctgttcttcc attagagaac cgatattcat tttgagatat tcagcataaa
     4621 aactaggagc aatcattaac aataaaaata atacaagcaa cacaagtacc ttttcgacta
     4681 tccttgttac tgtatacttc tccattgttt ttctaattat acctgtcgca acttcagcat
     4741 ctctggtcgt ctgctttaat gattccttta tctctttact tgtttgctct tcaaaatcag
     4801 tccactcttg ccttacatca ttaagtgtga aagataattt ttcacggagt aatgatgtta
     4861 gtgtgtctga gacagatttc tgtaatttac aggatacttc ttccattcct ttattaagat
     4921 aaaaatcaac atgagacaca ctatccctca aggaataaga aattccagat aca
//
