LOCUS       CP057700                6663 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB17-C09 plasmid pRHB17-C09_5, complete
            sequence.
ACCESSION   CP057700
VERSION     CP057700.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148144
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6663)
  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 6663)
  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 T2-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.5809268322776x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 11:12:56
            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)                     :: 5,029
            CDSs (total)                      :: 4,911
            Genes (coding)                    :: 4,700
            CDSs (with protein)               :: 4,700
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 104 of 211
            Pseudo Genes (incomplete)         :: 105 of 211
            Pseudo Genes (internal stop)      :: 43 of 211
            Pseudo Genes (multiple problems)  :: 38 of 211
            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..6663
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB17-C09"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB17-C09_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5768..6663,1..85))
                     /locus_tag="HVX27_25050"
     CDS             complement(join(5768..6663,1..85))
                     /locus_tag="HVX27_25050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000019445.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element ISKpn26 family transposase"
                     /protein_id="QML80995.1"
                     /translation="MSHQLTFADSEFSTKRRQTRKEIFLSRMEQILPWQNMTAVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAMEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVKTLKQHPRKNKTAINIEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRVDQMIRQWERSQ"
                     /name="IS5-like element ISKpn26 family transposase"
     gene            complement(579..1703)
                     /locus_tag="HVX27_25055"
     CDS             complement(579..1703)
                     /locus_tag="HVX27_25055"
                     /inference="COORDINATES: protein motif:HMM:NF013211.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QML80990.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAV
                     NPIGILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="hypothetical protein"
     gene            complement(1924..2457)
                     /locus_tag="HVX27_25060"
     CDS             complement(1924..2457)
                     /locus_tag="HVX27_25060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QML80991.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLAEKPVTGKNRKN"
                     /name="hypothetical protein"
     gene            complement(2460..3386)
                     /locus_tag="HVX27_25065"
     CDS             complement(2460..3386)
                     /locus_tag="HVX27_25065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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="QML80992.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            3563..3961
                     /locus_tag="HVX27_25070"
     CDS             3563..3961
                     /locus_tag="HVX27_25070"
                     /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="QML80993.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(4222..5241)
                     /locus_tag="HVX27_25075"
     CDS             complement(4222..5241)
                     /locus_tag="HVX27_25075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QML80994.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     Typing          complement(4467..5241)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(2464..3386)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccatgcggga gaggaaaatc tcttttcggg tctgacggcg cttagtgctg aattcactat
       61 cggcgaaggt gagttgatgg ctcatgatgt ccctctggga tgcgctccgg atgaatatga
      121 tgatctcata tcaggaactt gttcgcacct tccctagatt tatggataaa gtaaggcaat
      181 attataaaca tttaactaac gaggatttta taaatgaaaa aaatagatat ggaattctat
      241 ttaaggaatt ttatccttgc cttatccttt tacattttat cttttatcat cgcaagtttg
      301 aatctaagcc caacaagtat agaattattt atatttatac ttatatctct ttttggatcg
      361 tccacatacc ctttttgtct attactaata aataagcaag cacccttact aacaaaaaca
      421 acttttaact tcgttaactg gggttttata atatgcatta tattatcact acctccattt
      481 ggattgattt ttacagtcta ttactttata accaacaaaa agcgatagaa aaacaaaata
      541 aaggtcatac catatcaaac ggtacgacct tttgtttatt aaatgccgtt aataaagctg
      601 tttagttgtt tcagcctttc atctgtaatt aaggcactag tcactgccat aattactgca
      661 aaccctaaaa taccaatagg atttactgcc atagcactaa atgccactgt aaccataaca
      721 gatgctacct tgccgactgc gattttttcc ccgcttataa aagcctcatt ccagtcacca
      781 gttctgaatc ctttaactaa gccactgata aatccccccc actgaatagc ctcacctacg
      841 acaccaaagg ccttaccaaa aatttttaac tgtttagcca tttgatcttt attaagagac
      901 tccagtgctt ttgcaatcgc ttctcggtcg gatacgctga atttcttatt aagcacatcc
      961 ttgtacctat caaaggcttt aatcgcctca ttagcattgc gaattttttt ccctttagct
     1021 tcatcggcta gtgccttggc ttctttctcc aacttatcgc cgtattttga tgctaactct
     1081 ttataaaagt cattaacttt gcttattgca tcatttacag cattagcttc attttctgcc
     1141 ttgaattcta aaaagctttt tatagtatca cgagtcagtt tattacctga tgacggccca
     1201 ctaccgatat tatagtgaac attcatttta ttcacatcac cgtttggtac agttactgta
     1261 gctactgcac caccagtata atggatagtg tacgttccag aatggtcatc tattgactga
     1321 ataagtccct taattaactt atctttattt gtcggtaaat atctgccagg tttcccagag
     1381 tcagggctcc atccaggaat agacgttgtt tttccattgc cgcctgaatt gctgttatga
     1441 tttccagcac cgtgaccatt acctgagcca ccattaccgt gatgttttcc tggaggatct
     1501 ttttccatac caccggtaat gttgatatgc acctccccgt caggacctac agtgcttgca
     1561 ggaccttttc ccggattgta atgataccca ccgccagatg atggtcctcc atgtccagat
     1621 gagccattca cgtttccact gggtttacca ccgttatgtc caagccctgt attaccaggg
     1681 ccacgaccat ctccaccact cataaaaatt ccctctttta atcgttaaaa caattaatta
     1741 catagttaat actgtacata aaaccactgg ttttatgtac agatcaaaaa gtactcgcca
     1801 ttattttttc tgtcaagtca gggagggata ttttttggca gttcggagga atcactcatg
     1861 aaaacggtga acggaacgcg aaatcctttc gctgtccgtg aggcgttgga caagcgaagc
     1921 gcgtcagttt ttccggttct tacccgtgac aggtttttcc gccagtttat cttccagtat
     1981 cacaactttc tgatacaccg ccgctgtggc gttgtagttc ctgtcgagca ttgttttcat
     2041 tccccatccg agcacacaga acataactag aaaagccact gacaccccac ccagccattt
     2101 ccagctatac cctttaaggg tgttgtattc ctgcacgata ttgctgtgaa ttgtcgcaat
     2161 atccctgttc agggcatccg cgtttgcctt catgtttgcg actgactctt ccagccgctg
     2221 aaaatcctgg ctgatgcgct cacctatcag ccctgctacg tccagattct gcacctcatt
     2281 tctgacttca tccctgacct gttttgccac accgtcagaa atatcccgat atccgcgaag
     2341 tgtttccctt gccacagcca gagaatcagc aacagctttc tgttgctcca ttgcggtatg
     2401 ttgcaaatgc tccaccgata acaggagcgt gagtaatttt tcttctgtgc tggccatgtt
     2461 cagaatccca tagaaaatcc acgtgacggt gatttaaccc gttcaggttc agttcggtcc
     2521 tgtctgctca ctctgtctct catgtcaaag ccatgctccc gcgcaacatc atgttgcagc
     2581 cttctgacca gttcatgttg cttaaccgga gtgtccagcc attccatgat gtcatgcccg
     2641 accgttcgcg cctgttcaag atggcgggaa tagtccggtt cagaccgttt ttgcatgatg
     2701 tcatgacgct gggcatcatc aagccgtccg gcagcttcaa aacccagatg cacttcggga
     2761 cgtcgttcaa tgccctgttc tttcagcgtc cgacagtcaa tgaagcccct ttcaaagcca
     2821 ttttttctca tatgttcgtt gtgcttcacc tcccagcgtt ttcgcaattc ccgcaactgc
     2881 tctttttgct gagtgggagt caggcttcct gaatcctttt tcgcacctcc ccgctcggga
     2941 tacctggcgt tatagcgccg gaaatactgt tccggtgtac gttcaatgcc atcattcaca
     3001 cgctgactca tcatgatatg cgcatgaggc tgttcgcctc cctcaatgct cgctttcgga
     3061 ttgtgaatgg caaaactcca tgcatgccgt tcgccagctt cctgacgtac aaaatcctgc
     3121 accagttcaa ggcgctgttc cggtgtcagt tcacggggca gcgctatctc cagttcccga
     3181 taagtcgaac cgtttgcacg ttcaaactgg tcagccgcct gccagaaatg ggagggatta
     3241 tctcgcgccc attccggcat gtttccgtgt gcggaatatt ccaaatcttg acggtcgcgg
     3301 tatttctctt tgcgctcgat gtaatcggca tggtttgcag cctgtccctt gccaccaaac
     3361 ttaacgctga ggtgataggt cgccacggtt tcagccctcc gcaggagcgc actgtttctc
     3421 gacgaaggag agaaacatat aagtgcgctt ccttctaatt ttacgaatta gcacggaaga
     3481 taccccctgc acccgccgac cgcaagcgat atactgcacg accacaacac accgcaaaaa
     3541 aacaccaggg agcaccacga acatgcgcat cagcaacatc gaatggctga agaaacggat
     3601 cggattcatc aggaagctcg gagaacagac cgcacgacag agacagatta ttgacctgct
     3661 cgacaacgaa gcaggactca cagaacagga acgcaaactc ctccacgtac tggcaacagc
     3721 ggaaaaaaac gacttacagg cacaggagag cgaacgaaaa caggcggtcc aaaaacgaat
     3781 cgagggaaaa aaacaacgac gagaacgcaa tcaccgactc tttctcgcgg ctgggctact
     3841 gatcgaagca ggactggtag acacaaaaac aggcgagcta tgctataaaa aagacaggat
     3901 attacaggca cttaaggaaa ttaagtacga tctggagaca tccccaaacc cagacgcgta
     3961 agtgcctcca tccgtgttcc ggttccctgg tgcttcctcg ctcattcgct cgctacgctc
     4021 ggtcatgaga ctgcggcgag cacgaccacc tcaatcatgc ggtaagccgc accattgctg
     4081 ggctgagagg agaaaaccgc cggaaagccc gctgctcaaa aagacgccga aaggcgctgt
     4141 tatctgatat aggcttgttc atgtccgcga atttaacatc ccattaacaa aaaacagggg
     4201 gtagtgttgc ttctttgtta actaacattt aattatttgt ttcttggtta gccattctcc
     4261 agaattatcc atccagcgtc gaatagtccg gctgctaaca ccaaccgcca ctgcaatatc
     4321 ttccgttgac gctcccaaga tatacatatc aagcgcccta cgacgtttgt cgtcgttagc
     4381 agtccaccga acagcggcgc tttttttccc tttgtccgac tgattttctg acgaattggc
     4441 cttcccgccc ttgcgaccgc gtgctgcctg aatttctggc gtgtgcgtat cagccacata
     4501 ctgtgcgaaa gtttccggcg tgaagttcct gtgcgtgtat ttcgcaatgc tcttgccaat
     4561 agcccgacat tcagccagtg aaagcggaac gggaagcgat gcattgtaca tttcgacacg
     4621 ctggatcacc gcttcaagcc actgtgagaa cgctggccag ccctgacgaa tcgccctgta
     4681 agcccatttg cgcgtcattt cgaacaggtg gcagtttcgc cccatcccgt aatgtttatc
     4741 gatgctacga cgctctgagg cgctcaaatc gagataatct gccagttcat cgagggtata
     4801 ggcgtcctcg cgccactcca tcacctgcca ttccaggtgg aacggatttt tgcaaatcag
     4861 gccgctgtag ttcacatcag cacaaagttt ctcacacagc gaacgttcaa ccgctgcggc
     4921 atatttcagc gccttaaccg aggcatcagg cgcggttctc acggcgatgt tgagtgcgta
     4981 gagcaggtga gcgtgtccgt tcacaggatt tttaacggtg atgttcggcg cgggggcgtt
     5041 ccggtcgctc cagtcaatcg cagccccctc gcggtcaacg tcaaaaacca gccagaactg
     5101 cgcatgaggc tggttctgct ggatgtaccg cgcaagaagc gcacgccctt tgccggagat
     5161 gcgaaggccg aaagcgagat catccgtgtg ataggggcgg tggggtaaat tttcttcgaa
     5221 gtattgaagc gcggcgctca tgtgttacga ttccttccag gttatcgacc gacctcgccc
     5281 ctgtattctc gtgacaatct tggcggagag acacgaattt caggggcgtt tgtttttcag
     5341 tcgcttacac tacccccaac aacaaaacct gtcgagcctt cccgcaaaac cgatccattt
     5401 accataactc ccgttgtacg taccccttaa aacgccctca gtcgctttct ggcgcaaaaa
     5461 acgcaaaaag acaaggaaac accaggccaa accagaaaaa tgcgtcagaa tcactttcag
     5521 ggcgttgcat aactatgcac gaaagcgatt cgcaaacagt ttcgaccgtt caaaagggcg
     5581 aacgagtcaa aaaagtaact tttgtgataa ctacttctag ggaaggtgcg aataagcagg
     5641 tcatttcttc ccaagctgac tcgttgatta aaatttcgcg gatctgggcc gatttttttc
     5701 ccgcaaacac atcgaatcag cctatttagg ctattttttc caccatttct ggcgttattt
     5761 ccggttttta ctgagatctc tcccactgac gtatcatttg gtccacccga aacaggttgg
     5821 ccagggtgaa taacatcgcc agttggttat cgtttttcag cagccccttg tatctggctt
     5881 tcacgaagcc gaactgccgc ttgatgatgc gaaacgggtg ctccaccttg gcacggatgc
     5941 tggctttcat gtattcgatg ttgatggccg ttttgttctt gcgcggatgc tgcttcaagg
     6001 tttttacctt gccgggacgc tcggcgatca gccagtccac atccacctcg gccagctcct
     6061 cgcgctgtgg cgctccttgg tagccggcat cggctgagac aaattgctcc tctccatgaa
     6121 gcagattacc cagctgattg aggtcatgct cgttggccgc ggtggtgact aggctgtggg
     6181 tcaggccact cttggcatcg acaccaatgt gggccttcat gccaaagtgc cactgattgc
     6241 ctttcttggt ctgatgcatc tccggatcgc gttgctgctc tttgttcttg gtagagctgg
     6301 gtgcctcaat gatggtggca tccaccaaag tgccttgggt catcatgacg cctgcttcgg
     6361 ccagccagcg attgatggtc ttgaacaatt gacgggccag ttgatgctgc tcgagcaggt
     6421 ggcggaaatt catgatggtg gtgcgatccg gcagggcgct atccagagat aatcgggcaa
     6481 acaggcgcat ggaggcgatt tcgtacaggg catcttccat ggcaccgtcg ctcaggttgt
     6541 accaatgctg catgcagtga atacgcagca tggtctccag cggatagggc cgtcggccat
     6601 tgcccgcctt gggataaaac ggctcgatga cagcggtcat attctgccat ggcagaatct
     6661 gct
//
