LOCUS       CP057949                4924 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB09-C13 plasmid pRHB09-C13_4, complete
            sequence.
ACCESSION   CP057949
VERSION     CP057949.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148045
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4924)
  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 4924)
  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                     :: RH08 T1-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 86.802886913202x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 12:26:05
            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)                     :: 4,943
            CDSs (total)                      :: 4,824
            Genes (coding)                    :: 4,680
            CDSs (with protein)               :: 4,680
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 144
            CDSs (without protein)            :: 144
            Pseudo Genes (ambiguous residues) :: 0 of 144
            Pseudo Genes (frameshifted)       :: 47 of 144
            Pseudo Genes (incomplete)         :: 81 of 144
            Pseudo Genes (internal stop)      :: 46 of 144
            Pseudo Genes (multiple problems)  :: 27 of 144
            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..4924
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB09-C13"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB09-C13_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4869..4924,1..244)
                     /locus_tag="HVW28_24660"
     CDS             join(4869..4924,1..244)
                     /locus_tag="HVW28_24660"
                     /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="QMO99674.1"
                     /translation="MMMRLDVASTGATTTASYEPIAQIWDIINHPIPEMVNIMCKHQRK
                     HTKQAISRDYRNRMGKPITVSWKRSVTPLRVLLVDDMEQRWDEIRLVHELRKFI"
                     /name="hypothetical protein"
     gene            complement(330..962)
                     /locus_tag="HVW28_24665"
     CDS             complement(330..962)
                     /locus_tag="HVW28_24665"
                     /inference="COORDINATES: protein motif:HMM:NF012464.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="QMO99670.1"
                     /translation="MAVYGYIRVSTAKQVAEDTPDTQRDTIERLATEHNLLVDRIFEDD
                     AYTGNTDKPEQRPGFGALLSKIKPGDTIIMSQLNRIVRHGMVLMKFVSQWQYDKIKIIV
                     DNEFDQQACDRPVYLGMVCELAEMKLKEVSTATKAGMRRVMAETDEQRRKNDKKRVGRP
                     AKNQWYNKQDIIDALTAGERPDVIAKRFNVGVATVYRIRKAAATAIA"
                     /name="recombinase family protein"
     gene            complement(1489..2871)
                     /locus_tag="HVW28_24670"
     CDS             complement(1489..2871)
                     /locus_tag="HVW28_24670"
                     /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="QMO99671.1"
                     /translation="MSQQNNQPVIPFEIGMQQVVNKWKQMGWVWVYLQNSYALYDKNLQ
                     RICDQKTVRALVYRYIASDVAVPIREDKFQAVVLNSLNQLPLVEDVYGTYRPDIRERLI
                     PNENGRTFTVNTCHVYEEKTSPAQTDIGLIQPWLTIMAGLFPDTHERKRVIQYFAHALQ
                     KPMDKPSFALLITGAQGNGKSSMLINVFDIVFGETYITTFHNVSQLSTSIGAQRYGNRL
                     FAFVDDFADQTEKTSEKLKPVITSHTAVAKKLYCDEKEIHVITRFIFISNEHQPIPFYD
                     GHDRRYYAPAYAPAQDVSQTVDRFLAQLRDDSRTRDALYRYLMAYDISDFNPHVPEETR
                     NHARMVGGSTSTVIQQFTTIMNVERPEYITRNWYEHMMMDYFNTPLTPSQLDKQWRQVV
                     AYMKSKTDWVSKKIHTKIDDTDVWLVGWAIPDFDVRYWTKNVFTPLPEHQRGKWLFPVK
                     TY"
                     /name="hypothetical protein"
     gene            complement(2934..3971)
                     /locus_tag="HVW28_24675"
     CDS             complement(2934..3971)
                     /locus_tag="HVW28_24675"
                     /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="QMO99672.1"
                     /translation="MNDVLIEQVPNIVKAIWDYYGKPCREHYLLNIPKTIEAKVAPGIT
                     CRMLTDAIDGYIDEYPQEAIKHGLLVWFGELLCYQKSGEMDIEHEIWVSCIGRAYQKQD
                     DGSFIELPRELICHGSNVYWRYAFPWAKEPLQEMSEYDVDMNSLAPHRIVCYFPGLPMP
                     KIWSKLFDARRNGIPPKMQKSGGKYYVIKYGKVSDIIDMEVIRKENGKVYPRPVGCRKP
                     LNHRADHVFNDTAQEPGVHLWFACRLVFEDINRLNNHSSTNNDRDCLSWPMPQPVGFAQ
                     QIQYDPWQYVEYTQYATHNPYQFDRVGDRAIRYYHQMIQQYFDAVNNGCSPVDIDEYDW
                     CEAMK"
                     /name="hypothetical protein"
     gene            complement(3964..4392)
                     /locus_tag="HVW28_24680"
     CDS             complement(3964..4392)
                     /locus_tag="HVW28_24680"
                     /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="QMO99673.1"
                     /translation="MKPTVNESVMETSLFENIINNNAYIKNTGHVSRVIMVDDELVAVP
                     ESYFTMFAYLLAKATADITYPVVTYISQEANNVLRPFVRSPQHTANAMLLGLIALGLVE
                     GDTKTQYKRSITVKLPPVVNTEEIAGQTMLVIKTREHE"
                     /name="hypothetical protein"
ORIGIN
        1 acctattgcc caaatttggg atatcattaa ccaccccatc cccgaaatgg tgaacatcat
       61 gtgcaaacat caacggaaac acaccaaaca agcaatatca cgcgattatc gtaaccggat
      121 gggcaaaccc attaccgttt cctggaaacg ttctgtaacg ccgctacgtg tgctgctggt
      181 ggatgatatg gaacaacgat gggatgaaat ccggttggtg catgaactgc ggaaatttat
      241 ttgacattca cgatgttcat ggggaccggc ggtatgtacg atgtgtcaaa cgcgtgcggg
      301 tacgtcgaaa taattaccgg tcgtgatttt caagcaatcg ctgtcgctgc tgctttgcgg
      361 atacggtaca cggttgccac accaacattg aaacgtttgg cgatgacgtc ggggcgttca
      421 ccggcggtta atgcatcaat gatatcttgc ttgttgtacc actggttttt tgctgggcgt
      481 ccaacacgtt ttttgtcatt tttacgacgt tgttcgtcgg tttctgccat aacacggcgc
      541 atgcctgctt tggtggcggt gctgacttcc ttcaatttca tttctgccaa ttcgcacacc
      601 atacccaaat ataccggcct atcgcatgcc tgttggtcga attcgttatc cacgataatt
      661 ttgattttgt cgtactgcca ttgactgaca aatttcatca acaccatacc gtgacgtacg
      721 atacggttta actgactcat gatgatggtg tcaccgggtt tgattttgct gagcaatgca
      781 ccaaaccccg gacgttgttc cggtttatcg gtattgccgg tgtatgcgtc atcttcaaat
      841 atccggtcca ccagcaaatt atgttccgtt gctaaccgtt cgatggtgtc gcgttgggta
      901 tccggtgtat cttctgccac ctgtttcgct gtagatacgc gaatgtaacc atataccgcc
      961 atgattgaat cccccgttcc gcttgatggg aacatcatac atcaaaccga cgtgtattat
     1021 caattggaac cgtttgataa tccgataacg tcatgtgatt gtcacgatgt attattatca
     1081 cggtattaac atacgaataa catcgaatgt cgggtatttg ttgggaatga ttcgcattac
     1141 atgattgacg atgtttaccg atgttcgaat ggttgttcgg gtaattcgtg tacaatcgac
     1201 gaatgttgtg tatgacaaat tatttttcca caaatttctg gattaatggc ggggagaaca
     1261 tcgtgtcagg cacatccggc ccgacaacga cgttgtgaat aatcacatcc ccagtaattt
     1321 atctgttgcc catacgggtc gggataaccc gaaacagatt tatataaagt aaattcgaaa
     1381 cctgcatcac acaatcacat tttgttgcgc aatcaactgt gacgcgggtt tgcgggggac
     1441 tgggtgacgt cacatttgtg tatcaaacac ctcccaacct gcatcacatt aatatgtttt
     1501 aacggggaac aaccatttac cgcgttgatg ttccggcaac ggtgtgaata cgttttttgt
     1561 ccaataccgt acgtcgaaat cggggattgc ccaaccaacc aaccacacat cggtatcatc
     1621 aatttttgtg tgaatcttct tgctgaccca atccgttttg cttttcatgt acgccacaac
     1681 ttgtcgccat tgcttgtcta actgggacgg tgttaacggg gtgttgaaat aatccatcat
     1741 catatgctcg taccaatttc tggtgatgta ttccggacgt tccacgttca tgatggttgt
     1801 gaactgctga atgacggtgc tggtggaacc gcctaccata cgtgcatgat tgcgggtttc
     1861 ttccggaaca tgcgggttga aatcactgat atcgtatgcc atcaaatacc gatacaatgc
     1921 gtcacgggtc cgtgagtcat cacgcaactg tgccaggaaa cggtcgacgg tttgggatac
     1981 atcctgtgcc ggtgcgtatg ccggtgcgta ataccggcgg tcgtgcccat cgtaaaacgg
     2041 aatgggctga tgttcgttgc tgatgaatat gaaacgcgtg atgacgtgaa tttctttttc
     2101 gtcgcaatac aatttttttg ccactgccgt atgactggta atgaccggtt tcaatttctc
     2161 ggatgttttt tccgtttgat ctgcgaaatc gtccacgaat gcaaataaac gattcccgta
     2221 acgttgggca ccgatgctgg tggataactg ggacacatta tgaaatgtcg taatgtatgt
     2281 ttccccaaac acaatatcga atacatttat taacatcgac gacttgccgt tgccttgtgc
     2341 accggttatc aataatgcga atgatggttt atccattggt ttttgtaatg cgtgggcgaa
     2401 atattgaatg acacgtttgc gttcatgggt atccggaaat aaccccgcca taatcgtcaa
     2461 ccacggttgt attaatccaa tatcggtttg tgctggggat gttttctcct cgtaaacatg
     2521 gcatgtatta accgtgaatg tacgaccatt ttcgttgggg attaatcgtt cacgaatatc
     2581 ggggcggtat gtaccgtata cgtcctcgac caatggtaac tgatttaatg aattcaatac
     2641 cacggcctga aatttatcct cacggatggg aacggccacg tcgctggcaa tataccgata
     2701 aactaatgcc cgaacggttt tttggtcgca aatacgttgc aaatttttat catacaatgc
     2761 ataactgttt tgcaaataca cccaaaccca tcccatttgt ttccacttat tgacgacctg
     2821 ttgcatacct atttcaaacg ggatgacggg ttgattattt tgctgtgaca ttataaacta
     2881 ctcctatcga tgattgcttg gggtattacg aaattttcgt agtaccccta tttttatttc
     2941 attgcttcac accaatcata ttcatcgata tcaactgggg aacatccatt attaacggca
     3001 tcgaaatatt gctgaatcat ttgatggtaa taacggattg ccctgtcgcc tacacgatcg
     3061 aattgatatg gattatgtgt ggcatattgc gtgtattcga cgtattgcca cgggtcgtac
     3121 tgtatctgct gtgcgaaacc aactggttgt ggcatgggcc acgacaggca atccctgtcg
     3181 ttattggtgc tgctgtgatt gttcaaacgg ttaatgtcct caaacaccaa ccgacaagca
     3241 aaccacaaat gcacgccggg ttcttgtgct gtgtcgttga atacatggtc tgccctatgg
     3301 ttcaacggtt ttcgacaacc aaccggacgc gggtatacct tgccgttttc tttacggatg
     3361 acttccatat caataatgtc agatactttc ccgtatttga tgacataata tttgccgccc
     3421 gatttttgca tttttggcgg gatgccatta cgacgggcat cgaataattt gctccatatt
     3481 ttcggcatcg gtaaaccggg gaaataacac acaatccggt gtggtgccaa tgaattcata
     3541 tcaacgtcat attccgacat ttcctgcaat ggttcttttg cccacgggaa ggcataacgc
     3601 caatacacat tggaaccgtg acatattaat tcgcggggta actcaatgaa actgccgtca
     3661 tcctgttttt gatatgcacg accgatgcaa ctgacccata tttcatgttc gatatccatt
     3721 tcacctgatt tttggtaaca caataattca ccgaaccata ccaacaatcc atgtttaatt
     3781 gcttcctgcg gatattcatc aatgtatccg tcaatcgcat cggttaacat ccgacatgtt
     3841 attccggggg cgacttttgc ttcaatggtt ttcggaatgt tcaacaaata atgttcacga
     3901 catggtttgc cgtaataatc ccaaattgct ttaacgatgt tggggacttg ttcgattaat
     3961 acatcattca tgttccctcg ttttaattac taacattgtc tgacctgcta tttcttcggt
     4021 attcactacc ggcggtaatt tcactgtgat tgaacgtttg tattgggttt tggtatcgcc
     4081 ttcgaccaac cctaatgcaa ttaatcccaa caacattgca ttcgcggtgt gctgcggtga
     4141 ccttacaaat ggacgtaaca cgttatttgc ctcctgtgaa atatacgtaa caaccggata
     4201 cgttatatcg gcggttgcct ttgctaacaa atacgcgaac atcgtgaaat atgattccgg
     4261 cactgcaact aattcgtcat ccaccataat tacacgggat acgtgaccgg tatttttaat
     4321 gtacgcgtta ttattaataa tgttttcgaa caatgatgtt tccataactg actcgttaac
     4381 tgtcggtttc ataactcggg tgccttctca aattgttgtt aatggttggt taatgatttg
     4441 gatgttgact cacaactttg cgtcgttgtc aatatatata tcatggattt tttcaattta
     4501 caaccggacg gaaatggtgg atcatttttg ttgaacatga acaatggtga ccgcacacgc
     4561 ggtactgctt cacccagtat atcggcgacg ccacggactg ggttaccaaa caattacacg
     4621 gcggttctgt tccgtttgtt gtgtacgact tgatgcggtc gtcaatgtga tgcatacgga
     4681 tttgcggaca ttggataaac gcgcgattgt ggtggtttga cggatgtgta ccacaacact
     4741 ccgtccacgg gttctcgggg tgacctgcta cggacaatgt gactgcggaa atgatgcttt
     4801 ctctccacat tcatattggt gacacagcaa atacactcac acgataatta cacaacaact
     4861 gactactgat gatgatgcga ctggacgtcg cttccaccgg tgccaccaca acggcatcat
     4921 atga
//
