LOCUS       CP057558                4721 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB23-C04 plasmid pRHB23-C04_4, complete
            sequence.
ACCESSION   CP057558
VERSION     CP057558.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148211
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4721)
  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 4721)
  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 T2-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 127.582362447169x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 09:42:14
            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)                     :: 4,811
            CDSs (total)                      :: 4,691
            Genes (coding)                    :: 4,575
            CDSs (with protein)               :: 4,575
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 52 of 116
            Pseudo Genes (incomplete)         :: 46 of 116
            Pseudo Genes (internal stop)      :: 37 of 116
            Pseudo Genes (multiple problems)  :: 19 of 116
            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..4721
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB23-C04"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB23-C04_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4128..4721,1..60))
                     /locus_tag="HVX94_24040"
     CDS             complement(join(4128..4721,1..60))
                     /locus_tag="HVX94_24040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016249761.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein phosphatase 2C family protein"
                     /protein_id="QMJ63579.1"
                     /translation="MIAFSFSDIGNRCENLDLLSTINCQNDVFGMVIMDGYSCSEWNMK
                     ILSGRLDKCVFSGDLNKDIIEPCKSVPVKAAVCFLFKNNTHLHIYNAGDCRVYNKSGVL
                     LTEDNSVAWKRLKENGIDNKKIPHLVCYCPDRNYLTSFVDFCSDEIIFNHSVFDLNDEN
                     KEVILCTDGFWEHFNDGTVIDLMKDNPESNLAKFTKNIPGNAENHTVCYVRFPS"
                     /name="protein phosphatase 2C family protein"
     gene            complement(57..923)
                     /locus_tag="HVX94_24045"
     CDS             complement(57..923)
                     /locus_tag="HVX94_24045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000409995.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="QMJ63576.1"
                     /translation="MEKEINNWIEESGGKYRLMRQAVHIILKSISIEESLNEMMVMKGG
                     TLLGVKHGSDRYTKDIDFSTEKKLSEIDLGDFFNRFNDSMDVAEAELGYGIKCKVQSHK
                     IQPNAQGTFPTVQINIAFCDRSNASAMKRLESNQSPSVINIDFSFNEKTYDFDFLSLDG
                     DDDNDSVKTYSLTDLMAEKYRSVLQQKVRERNREQDIYDINYLLGKYEFSRQDKYKILE
                     SLLKKSEGKQLDNLLNVKGIRDVEIIERSSQRYQDLSSTVKSLPLFEDAYEKVACFYES
                     LPWDIFK"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            complement(907..1863)
                     /locus_tag="HVX94_24050"
     CDS             complement(907..1863)
                     /locus_tag="HVX94_24050"
                     /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="QMJ63577.1"
                     /translation="MYLIEEALTSWLLNEYKKPVITKEEISLQIYLFYLKKEYNGERIY
                     QIRKNKAGPNEFEKNILKLLKSGVLSRVESNDKHHAYPHLIGGFYEVFFVKGNDGSPEN
                     DIVCSTYPYGYLSYLSAMDWHNITDKIPKIIHFTTCRSEQWKNKFYHDFQKDNPDIDEA
                     KQFMPRFPRNSEVNGIKIIVTQETNYVEPMKARNSPVRVSSIGKTFMDMTRRPDYCGGE
                     EHVLESFIEHGKKYAPLIIKEVDKLGRHIDKVRVGFILDRIIGVNNKKISEWKQEAGKY
                     RGSSKVLSPKSPFSPYFDEEWFISINVDMVKSYGKRN"
                     /name="hypothetical protein"
     gene            2944..3138
                     /locus_tag="HVX94_24055"
     CDS             2944..3138
                     /locus_tag="HVX94_24055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="QMJ63578.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2425..2680)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(2805..2908)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.286"
                     /coverage="100.0"
                     /evalue="4.87e-36"
     Typing          complement(3212..3294)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          3307..3865
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.484"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agataataag tctaagtttt cacatctgtt accaatatca ctaaaactga acgctatcat
       61 ttgaatatat cccacggaag actttcatag aaacaggcaa ctttttcata agcatcttca
      121 aaaagaggta atgatttaac ggtggatgat aaatcctgat atcgctgact ggaacgctcg
      181 ataatttcta catcccttat acctttaacg tttaagagat tatccaattg tttaccttca
      241 ctctttttta aaagagactc cagtatttta tacttatctt gccgagaaaa ctcatattta
      301 cctaaaagat aattgatatc atatatatct tgctctcgat ttctctctct aactttttgt
      361 tgcaaaacgg atcgatattt ttcagccatc aaatcagtta agctgtaggt ctttacgcta
      421 tcattgtcat catcaccatc taatgataaa aagtcaaaat catacgtttt ttcgttaaag
      481 ctaaaatcga tatttatcac tgaaggtgat tgattagatt caagcctttt cattgcagac
      541 gcattagaac gatcgcaaaa ggctatattt atctgtacag ttggaaatgt tccttgtgca
      601 ttaggttgaa ttttatgaga ttgaacttta catttaatac catatcccaa ttcagcctca
      661 gcaacatcca ttgagtcatt aaacctattg aaaaaatccc ccaagtcaat ttcagaaagt
      721 tttttttcgg tagaaaaatc aatatccttt gtgtatctat cactaccatg cttaacacca
      781 agaagagtcc ctcccttcat aaccatcatt tcattcaaac tctcctctat agaaatagat
      841 ttaagtatta tatgtacagc ctgccgcatc aacctgtact tcccaccaga ctcttcgatc
      901 caattattaa tttctttttc cataagactt aaccatatca acattaatag aaataaacca
      961 ttcttcatca aagtaaggtg agaatggact ctttggagat agcactttcg aactacctct
     1021 gtatttaccc gcctcttgtt tccattcgct tattttttta ttattaaccc caataattct
     1081 atccaaaatg aatccaaccc ttaccttgtc aatatgacgg ccaagcttat cgacttcctt
     1141 tataatcaga ggtgcatatt ttttaccgtg ctcaataaat gattccaata catgctcctc
     1201 accaccacag taatcaggcc gcctggtcat atccataaag gtcttaccga tagatgatac
     1261 cctgacaggg gaattacgag ccttcattgg ctcaacataa tttgtttctt gtgtaacgat
     1321 aatttttatt ccattgacct cagaatttct tggaaatcta ggcatgaatt gtttggcttc
     1381 gtctatatca ggattatcct tttgaaaatc atgatagaac ttattcttcc actgttcgga
     1441 acgacatgtc gtaaagtgga ttatcttggg tattttatct gtgatgttat gccaatccat
     1501 agcggataaa taggataagt atccatatgg atacgtagag cacactatat cattttccgg
     1561 agaaccatcg ttacctttaa caaaaaagac ctcatagaaa ccgccaatta aatgggggta
     1621 agcatgatgc ttatcgttac tttcaactct tgataaaacc cctgacttta ataattttaa
     1681 tatatttttt tcaaattcat taggtcctgc tttgttcttt ctaatttgat atatcctctc
     1741 accattatat tcttttttta aataaaaaag gtaaatctgc aaagagattt cttctttggt
     1801 tatgactggt tttttatatt cattcaacaa ccaagacgtt agcgcttctt cgataagata
     1861 catattcaac cttttcggtt tagtctctaa tagaatatac gtcctaagga cgtatattct
     1921 attagagatt gattgtcaag aaaaaaataa taacaaacaa gcatttgcca tttttatatt
     1981 tttgatgtcc tataaaataa atcctaagga tttattttat aggataataa gtaggaagtc
     2041 aagaaaaagt ttacttatat caccgttttc ataacacctc atgcgatcaa ttcagcggcg
     2101 gttatagttc aaatccatga ttaggacatc tgttgctcat aaacgatgag cgtaaaagat
     2161 catttttcag cgtcatttac cataacgtcg cattacgcgc accgctaaaa cgcgctgaac
     2221 gcgattctgc cgcgaacacc gcaaaaagag atgttttacc aagcgaaaac cggaaaaatg
     2281 cgtcaggatc gctttcagct cactgcatag ctatgcatga aagtgaatgg cgatcggttt
     2341 gggcgcatac ggtgcccatg agacacattt tcggacattt tcagttcgtg aatccctgac
     2401 tcattgctac atatctgaac agacacccct agcagcgccc ccaggggcgt cctgtaaaaa
     2461 aacacaccgc gccgctagca gcacccctaa tataaaatga tgttttttat gaaaatagtc
     2521 agtaccaccc ctaaaaagcg gtgttggcgc agctacaaca ccgcgccgac accgcttttt
     2581 taaatatcac aaagagagca agaagaacta atttgtcata actctctatt tataaagaaa
     2641 aatcagcaaa aaattgtttt tgcgtggggt gtgggcattt caggcatgag aacagactcg
     2701 cgtttttccg gagtatcagc ggaattattg attaagaaac actcgacgca gagcgaaatt
     2761 ttatgcaaca gcggctgcac tgcacaggga ttatttatca gttgatatgc ggtgccatga
     2821 tacgtcctaa aaaaacagga caggacagga tgtgcaattg taataccgtc gcccgcaacg
     2881 tcttacaatt accacctggt cagggtccac ccgacacccg gtactgacgg agaacaacgg
     2941 aaggtgaaca aacagcaaca aactgcgctg aatatggcgc gatttatcaa aagccagagc
     3001 ctgacactgc ttgaaaaact ggatgctctg gatgccgacg aacaggcggc catgtgcgaa
     3061 cgactgcacg aactcgcgga agaactccag aacagcatcc aggttcgctt tgagaccgaa
     3121 agtgaaacag gaacataacg aagctgacgg aggcgctcac ggcttgtccg cgagcgtttt
     3181 cggcagcaga caagcccgcc agggcgcgtc agcgggtgtc ggggcgaagc cctgacccag
     3241 tcacgtagcg atagcggagt gtatactggc ttaactatgc ggcatcagtg cagattgtat
     3301 gaaaagtgcc ccatgccggg tgtgaaattc cgcacagatg cgtaaggaga aaatgcgcgt
     3361 ccaggcgctt ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt cggctgcggc
     3421 gagcggtact gacttacaca aaaacggcag cacggttatc cacagaatca ggggataagg
     3481 ccggaaagaa catgtgagca aaaaggcaaa gaacaacaaa aggccgcgcc gctggcgttt
     3541 ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg
     3601 cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc
     3661 tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc
     3721 gtggcgcttt ctcatagctc acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc
     3781 aagctgggct gtgtgcacga accccccgtt cagcccgact gctgcgcctt atccggtaac
     3841 tatcgtcttg agtccaaccc ggtaagacac gccttaacgc cactggcagc agccactggt
     3901 aactgattta gaggagttag tcttgaagtc atgcgccagt taaggctaaa ctgaaagaac
     3961 aggttttggt gactgcgctc ctccaagcca gttaccttgg ttcttcgagc cgcaaactct
     4021 ttgaacctaa gagaaaaccg ccccgcaaag gcggtttttt tcttttacag aaaagagatt
     4081 atctatatga cacgaagatc tcaatagctt cttcaaaaaa cacgaaatca agaagggaat
     4141 ctaacgtagc aaaccgtatg attctctgcg ttacccggga tatttttagt aaatttagcc
     4201 aagttagatt ctgggttatc tttcatgagg tcaataacag taccatcatt aaaatgctcc
     4261 caaaacccat cagtacataa aataacctct ttgttttcat catttaaatc aaaaactgaa
     4321 tgattgaaaa ttatctcatc agagcagaaa tcaacaaatg atgttagata atttctgtct
     4381 gggcaataac aaacgaggtg aggtattttt ttattatcga ttccattttc ctttaatctt
     4441 ttccaggcaa ccgagttatc ctctgttaga aggactccac ttttgttata tacacggcaa
     4501 tctcctgcgt tatatatatg gaggtgcgta ttatttttaa aaaggaaaca tactgcagcc
     4561 ttaacaggaa ctgacttgca tggttcaata atatctttat tcagatcacc agaaaacacg
     4621 cacttatcta acctaccaga gagaattttc atattccact cagagcagga atacccatcc
     4681 ataataacca ttccaaacac atcattttga caatttatcg t
//
