LOCUS       CP056925                3258 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB42-C22 plasmid pRHB42-C22_5, complete
            sequence.
ACCESSION   CP056925
VERSION     CP056925.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148440
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3258)
  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 3258)
  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-C22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 144.484403346878x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 04:59:14
            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)                     :: 4,864
            CDSs (total)                      :: 4,750
            Genes (coding)                    :: 4,646
            CDSs (with protein)               :: 4,646
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 45 of 104
            Pseudo Genes (incomplete)         :: 58 of 104
            Pseudo Genes (internal stop)      :: 21 of 104
            Pseudo Genes (multiple problems)  :: 17 of 104
            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..3258
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB42-C22"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB42-C22_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3174..3258,1..197))
                     /locus_tag="HV023_24290"
     CDS             complement(join(3174..3258,1..197))
                     /locus_tag="HV023_24290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="QMA68001.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            542..838
                     /locus_tag="HV023_24295"
     CDS             542..838
                     /locus_tag="HV023_24295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antidote protein"
                     /protein_id="QMA67999.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antidote protein"
     gene            complement(1836..2030)
                     /locus_tag="HV023_24300"
     CDS             complement(1836..2030)
                     /locus_tag="HV023_24300"
                     /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="QMA68000.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1681..1763
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          2067..2165
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2290..2545
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1110..1668)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.128"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaatactctc cttgacggtc tcccttcaat ggatggcagc gcaatgcctt taaatccatc
       61 atatcctgca agttcgtcgc tgtgcttaag gctgttagga tcagcttcag acgttgagta
      121 aactgttgcg gaattcctgc gttgttacct gtttcggcaa acttacgcaa acctttatgc
      181 ttgatattta tgatcattaa tcaccatccc atatttgttt agatagaaac atcgcagttt
      241 atttttccgg ttcatccgta tttccattgc aaaccccttg ctctatttga ataaatgacg
      301 taggttttac ttaaccaagt cgcattttaa tctgttgaca ttggtttgat gcgctgtaca
      361 atgccggggc cttgaatttc acatcaagta cccacatcat aaggaatgat tagacgcacc
      421 aatgtgcatc ataatgtcat tctttttttt agtcaacaat gagttgcgtt atgcgcaatg
      481 cgcaatctga aaacgcaata ggcctatctt tttaaaacta atataggctt cagaggaagg
      541 tatgattaat cttgtcgatc cagtacatcc aggggttttt atccgtgaga tgtttatgga
      601 accgtttgaa atatcagccg cggacctgtc tgaaaaactg catgtatcac cttccactct
      661 aagtagagtg ctgaatggaa aagctgattt aagtgttgag atggcattaa ggctttctcg
      721 agttcttggt cgcagtgccg agtcgtggat aaacatgcag actcaataca gtcttaacgc
      781 gagcaggaag tcacctaatg tcattaagga attagatgaa ttggttccta tattttgaga
      841 aaagaaaagg ccgctatatg cggccttttt ctgtcttgac tctcaggcaa ctggatcgta
      901 tcgtttctcg taaacgaaaa aaccacccgg caaggtggtt ttttcgaagg ttcagtaacc
      961 ggcaagtttc tgaaccaggg taactggctt ggaggagcgc agtcaccaaa acttgttctt
     1021 tcagtttagc cttaactggc gcataacttc aagactaact cctctaaatc agttaccagt
     1081 ggctgctgcc aatggtgttt tgcatgtctt tccgggttgg actcaagatg atagttaccg
     1141 gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga
     1201 acgacctaca ctgaaccgag atacctacag cgtgagctat gagaaagcgc cacgcttccc
     1261 gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg
     1321 agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc
     1381 tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
     1441 agcggcgcgg ccttttgttg ttctttgcct ttttgctcac atgttctttc cggccttatc
     1501 ccctgattct gtggataacc gtgctgccgt ttttgtgtaa gtcagtaccg ctcgccgcag
     1561 ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaaaagcgcc tggacgcgca
     1621 ttttctcctt acgcatctgt gcggaatttc acacccggca tggggcactt ttcatacaat
     1681 ctgcactgat gccgcatagt taagccagta tacactccgc tatcgctacg tgactgggtc
     1741 agggcttcgc cccgacaccc gctgacgcgc cctggcgggc ttgtctgctg ccgaaaacgc
     1801 tcgcggacaa gccgtgagcg cctccgtcag cttcgttatg ttcctgtttc actttcggtc
     1861 tcaaagcgaa cctggatgct gttctggagt tcttccgcga gttcgtgcag tcgttcgcac
     1921 atggccgcct gttcgtcggc atccagagca tccagttttt caagcagtgt caggctctgg
     1981 cttttgataa atcgcgccat attcagcgca gtttgttgct gtttgttcac cttccgttgt
     2041 tctccgtcag taccgggtgt cgggtggacc ctgaccaggt ggtaattgta agacgttgcg
     2101 ggcgacggta ttacaattac acatcctgtc ctgtttcttt aggacgtatc atggcacagc
     2161 atatcaactg ataaataatc cctgtgcagt gcagccgctg ttgcataaaa tttcgctctg
     2221 cgtcgagtgt ttcttaatca ataattccgc tgatactccg gaaaaacgcg agtctgttct
     2281 catgcctgaa atgcccacac cccacgcaaa aacaattttt tgctgatttt tctttataaa
     2341 tagagagtta tgacaaatta gttcttcttg ctctctttgt gatatttaaa aaagcggtgt
     2401 cggcgcggtg ttgtagctgc gccaacaccg ctttttaggg gtggtactga ctattttcat
     2461 aaaaaacatc attttatatt aggggtgctg ctagcggcgc ggtgtgtttt tttacaggac
     2521 gcccctgggg gcgctgctag gggtgtctgt tcagatatgt agcaatgagt cagggattca
     2581 cgaactgaaa atgtccgaaa atgtgtctca tgggcaccgt atgcgcccaa accgatcgcc
     2641 attcactttc atgcatagct atgcagtgag ctgaaagcga tcctgacgca tttttccggt
     2701 tttcgcttgg taaaacatct ctttttgcgg tgttcgcggc agaatcgcgt tcagcgcgtt
     2761 ttagcggtgc gcgtaatgcg acgttatggt aaatgctgtg atttacggga tggttttatc
     2821 tatgttgata tcaataccac ctcttatgga ggtggcttac accgattttt ccttgttgtc
     2881 tgtttcagaa cagatagagg cttttttggc aattatccaa ccactattga tagtgtttat
     2941 tactacttag ataactgagc ctttactgta tctgcccctg caagcaggaa cccaacagtt
     3001 aagaaccacc cccagccatt gatacctttt agcgctagaa ttgctgcgca aatgatggct
     3061 gctataggga ctatctggta cagaaaatac ttcatataac ttaccccgag gttttgcttt
     3121 tttatgagac cctaaagcat cgatactgtc actttgatgc tttaaggacc ttcttagtga
     3181 taatcctcga gatccacgtc aaagacgtta ggttcttcga gcttaaacac tacgcgccag
     3241 tttccattga cctctaac
//
