LOCUS       CP056943                5301 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB42-C04 plasmid pRHB42-C04_4, complete
            sequence.
ACCESSION   CP056943
VERSION     CP056943.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148434
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5301)
  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 5301)
  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                     :: RH12 T3-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 151.53365995679x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 03:47:40
            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)                     :: 4,795
            CDSs (total)                      :: 4,673
            Genes (coding)                    :: 4,575
            CDSs (with protein)               :: 4,575
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 48 of 98
            Pseudo Genes (incomplete)         :: 46 of 98
            Pseudo Genes (internal stop)      :: 25 of 98
            Pseudo Genes (multiple problems)  :: 18 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..5301
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB42-C04"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB42-C04_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            1..915
                     /locus_tag="HV017_23935"
     CDS             1..915
                     /locus_tag="HV017_23935"
                     /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="QMA86053.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNVPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRGTVATSARTL
                     KPWEKLGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1119..1517)
                     /locus_tag="HV017_23940"
     CDS             complement(1119..1517)
                     /locus_tag="HV017_23940"
                     /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="QMA86054.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            1694..2620
                     /locus_tag="HV017_23945"
     CDS             1694..2620
                     /locus_tag="HV017_23945"
                     /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="QMA86055.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2623..3156
                     /locus_tag="HV017_23950"
     CDS             2623..3156
                     /locus_tag="HV017_23950"
                     /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="QMA86056.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLAEKPVTGKNRKN"
                     /name="hypothetical protein"
     gene            3377..4501
                     /locus_tag="HV017_23955"
     CDS             3377..4501
                     /locus_tag="HV017_23955"
                     /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="QMA86057.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAV
                     NPIGILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="hypothetical protein"
     Typing          2..915
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.586"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1695..2617
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg cgcttcaata cttcgaagaa aatttacccc accgtcccta tcacacggat
       61 gatctcgctt tcggccttcg tatctccggc aaagggcgcg cgcttcttgc acggtatatc
      121 cagcagaacc agcctcatgc acagttctgg ctggtttttg acgttgaccg cgagggggct
      181 gcgattgact ggagcgaccg gaacgttccc gcgccgaaca tcaccgttaa aaatcctgtg
      241 aacggacacg ctcacctgct ctacgcactc aacatcgccg tgagaaccgc gcctgatgcc
      301 tcggttaagg cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga gaaactttgt
      361 gcggatgtga actacagcgg cctgatttgc aaaaatccgt tccacctgga atggctggtg
      421 atggagtggc gcgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc
      481 gcctcagagc gtcgtagcat cgataaacat tacgggatgg ggcgaaactg ccacctgttc
      541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc gttctcacag
      601 tggcttgaag cggtgatcca gcgtgtcgaa atgtacaatg catcgcttcc cgttccgctt
      661 tcactggctg aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc
      721 acgccggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggcagca
      781 cgcggtcgca agggcggttc taagtctaag cgcggcacag tagctacatc agcacgcacg
      841 ctgaaacctt gggagaaatt agggatcagt cgcgcctggt attaccaact gaaaaaacga
      901 ggtctcgtag agtagaccaa ataagcctat atcagataac agcgcctttt tggcgttctt
      961 ttgagcagct tggtttgttg ctatttccct cgttgaatcc cgcaatggcg cggctttccg
     1021 catgattgag gcggtagtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc
     1081 gaggaagcac cagggaaccg gaacacggat ggaggcactt acgcgtctgg gtttggggat
     1141 gtctccagat cgtacttaat ttccttaagt gcctgtaata tcctgtcttt tttatagcat
     1201 agctcgcctg tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag
     1261 agtcggtgat tgcgttctcg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt
     1321 tttcgttcgc tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggagg
     1381 agtttgcgtt cctgttctgt gagtcctgct tcgttgtcga gcaggtcaat aatctgtctc
     1441 tgtcgtgcgg tctgttctcc gagcttcctg atgaatccga tccgtttctt cagccattcg
     1501 atgttgctga tgcgcatgtt cgtggtgctc cctggtgttt ttttgcggtg tgttgtggtc
     1561 gtgcagtata tcgcttgcgg tcggcgggtg cagggggtat cttccgtgct aattcgtaaa
     1621 attagaagga agcgcactta tatgtttctc tccttcgtcg agaaacagtg cgctcctgcg
     1681 gagggctgaa accgtggcga cctatcacct cagcgttaag tttggtggca agggacaggc
     1741 tgcaaaccat gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aagatttgga
     1801 atattccgca cacggaaaca tgccggaatg ggcgcgagat aatccctccc atttctggca
     1861 ggcggctgac cagtttgaac gtgcaaacgg ttcgacttat cgggaactgg agatagcgct
     1921 gccccgtgaa ctgacaccgg aacagcgcct tgaactggtg caggattttg tacgtcagga
     1981 agctggcgaa cggcatgcat ggagttttgc cattcacaat ccgaaagcga gcattgaggg
     2041 aggcgaacag cctcatgcgc atatcatgat gagtcagcgt gtgaatgatg gcattgaacg
     2101 tacaccggaa cagtatttcc ggcgctataa cgccaggtat cccgagcggg gaggtgcgaa
     2161 aaaggattca ggaagcctga ctcccactca gcaaaaagag cagttgcggg aattgcgaaa
     2221 acgctgggag gtgaagcaca acgaacatat gagaaaaaat ggctttgaaa ggggcttcat
     2281 tgactgtcgg acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt
     2341 tgaagctgcc ggacggcttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga
     2401 accggactat tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca tcatggaatg
     2461 gctggacact ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atgttgcgcg
     2521 ggagcatggc tttgacatga gagacagagt gagcagacag gaccgaactg aacctgaacg
     2581 ggttaaatca ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa
     2641 aaattactca cgctcctgtt atcggtggag catttgcaac ataccgcaat ggagcaacag
     2701 aaagctgttg ctgattctct ggctgtggca agggaaacac ttcgcggata tcgggatatt
     2761 tctgacggtg tggcaaaaca ggtcagggat gaagtcagaa atgaggtgca gaatctggac
     2821 gtagcagggc tgataggtga gcgcatcagc caggattttc agcggctgga agagtcagtc
     2881 gcaaacatga aggcaaacgc ggatgccctg aacagggata ttgcgacaat tcacagcaat
     2941 atcgtgcagg aatacaacac ccttaaaggg tatagctgga aatggctggg tggggtgtca
     3001 gtggcttttc tggttatgtt ctgtgtgctc ggatggggaa tgaaaacaat gctcgacagg
     3061 aactacaacg ccacagcggc ggtgtatcag aaagttgtga tactggaaga taaactggcg
     3121 gaaaaacctg tcacgggtaa gaaccggaaa aactgacgcg cttcgcttgt ccaacgcctc
     3181 acggacagcg aaaggatttc gcgttccgtt caccgttttc atgagtgatt cctccgaact
     3241 gccaaaaaat atccctccct gacttgacag aaaaaataat ggcgagtact ttttgatctg
     3301 tacataaaac cagtggtttt atgtacagta ttaactatgt aattaattgt tttaacgatt
     3361 aaaagaggga atttttatga gtggtggaga tggtcgtggc cctggtaata cagggcttgg
     3421 acataacggt ggtaaaccca gtggaaacgt gaatggctca tctggacatg gaggaccatc
     3481 atctggcggt gggtatcatt acaatccggg aaaaggtcct gcaagcactg taggtcctga
     3541 cggggaggtg catatcaaca ttaccggtgg tatggaaaaa gatcctccag gaaaacatca
     3601 cggtaatggt ggctcaggta atggtcacgg tgctggaaat cataacagca attcaggcgg
     3661 caatggaaaa acaacgtcta ttcctggatg gagccctgac tctgggaaac ctggcagata
     3721 tttaccgaca aataaagata agttaattaa gggacttatt cagtcaatag atgaccattc
     3781 tggaacgtac actatccatt atactggtgg tgcagtagct acagtaactg taccaaacgg
     3841 tgatgtgaat aaaatgaatg ttcactataa tatcggtagt gggccgtcat caggtaataa
     3901 actgactcgt gatactataa aaagcttttt agaattcaag gcagaaaatg aagctaatgc
     3961 tgtaaatgat gcaataagca aagttaatga cttttataaa gagttagcat caaaatacgg
     4021 cgataagttg gagaaagaag ccaaggcact agccgatgaa gctaaaggga aaaaaattcg
     4081 caatgctaat gaggcgatta aagcctttga taggtacaag gatgtgctta ataagaaatt
     4141 cagcgtatcc gaccgagaag cgattgcaaa agcactggag tctcttaata aagatcaaat
     4201 ggctaaacag ttaaaaattt ttggtaaggc ctttggtgtc gtaggtgagg ctattcagtg
     4261 ggggggattt atcagtggct tagttaaagg attcagaact ggtgactgga atgaggcttt
     4321 tataagcggg gaaaaaatcg cagtcggcaa ggtagcatct gttatggtta cagtggcatt
     4381 tagtgctatg gcagtaaatc ctattggtat tttagggttt gcagtaatta tggcagtgac
     4441 tagtgcctta attacagatg aaaggctgaa acaactaaac agctttatta acggcattta
     4501 ataaacaaaa ggtcgtaccg tttgatatgg tatgaccttt attttgtttt tctatcgctt
     4561 tttgttggtt ataaagtaat agactgtaaa aatcaatcca aatggaggta gtgataatat
     4621 aatgcatatt ataaaacccc agttaacgaa gttaaaagtt gtttttgtta gtaagggtgc
     4681 ttgcttattt attagtaata ggcaaaaagg gtatgtggac gatccaaaaa gagatataag
     4741 tataaatata aataattcta tacttgttgg gcttagattc aaacttgcga tgataaaaga
     4801 taaaatgtaa aaggataagg caaggataaa attccttaaa tagaattcca tatctatttt
     4861 tttcatttat aaaatcctcg ttagttaaat gtttataata ttgccttact ttatccataa
     4921 atctagaagt agttatcaca aaagttactt ttttgactcg ttcgcccttt tgaacggtcg
     4981 aaactgtttg cgaatcgctt tcgtgcatag ttatgcaacg ccctgaaagt gattctgacg
     5041 catttttctg gtttggcctg gtgtttcctt gtctttttgc gttttttgcg ccagaaagcg
     5101 actgagggcg ttttaagggg tacgtacaac gggagttatg gtaaatggat cggatttgcg
     5161 ggaaggctcg acaggttttg tcgttggggg tagtgtaagc gactgaaaaa caaacgcccc
     5221 tgaaattcgt gtctctccgc caagactttc acgaaaatac aggggcgatg tcggtcgata
     5281 acctggaagg aatcgtaaca c
//
