LOCUS       CP058069                3173 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB02-C19 plasmid pRHB02-C19_7, complete
            sequence.
ACCESSION   CP058069
VERSION     CP058069.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147970
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3173)
  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 3173)
  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                     :: RH02 T1-C19
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 87.6863361089072x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:54:22
            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)                     :: 5,577
            CDSs (total)                      :: 5,449
            Genes (coding)                    :: 5,191
            CDSs (with protein)               :: 5,191
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 258
            CDSs (without protein)            :: 258
            Pseudo Genes (ambiguous residues) :: 0 of 258
            Pseudo Genes (frameshifted)       :: 91 of 258
            Pseudo Genes (incomplete)         :: 157 of 258
            Pseudo Genes (internal stop)      :: 43 of 258
            Pseudo Genes (multiple problems)  :: 28 of 258
            CRISPR Arrays                     :: 1
            ##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..3173
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB02-C19"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB02-C19_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(2307..3173,1..243))
                     /gene="fepE"
                     /locus_tag="HVV53_27880"
     CDS             complement(join(2307..3173,1..243))
                     /gene="fepE"
                     /locus_tag="HVV53_27880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator"
                     /protein_id="QMQ78473.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEGIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDNAFDLF
                     IKKFQSVNSLNEYMRSSPYVMEMIKKNNISALELHRAIVELSKNMKSVDDNTSKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="fepE"
     gene            1088..1282
                     /locus_tag="HVV53_27885"
     CDS             1088..1282
                     /locus_tag="HVV53_27885"
                     /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="QMQ78474.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(575..822)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="86.0"
                     /evalue="1.58e-110"
     Typing          complement(954..1052)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1363..1449)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.455"
                     /coverage="100.0"
                     /evalue="1.14e-31"
     Typing          1474..2000
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 cttatttaat tcactccatt gaacagactc agcaggagta accacagcag aactagtcca
       61 tttttgtggc aaaacaaaag aaacaagaaa gccaatacaa gcaaaaaata gaatcacccc
      121 aacaattttt atttttgctg cccataaaac gctaatcaag ccaaaaagat caattccttc
      181 attaccattc ggcaacatgt tgtaattaga aaaatgttcg tcagatacct ttgagatttt
      241 cattgaaaaa aaacacaata tattaacata tggtttttta ttctatcata tgttaggaaa
      301 aaacctaaaa accattcagc agacatttaa cataacattt tattacgcgc accgctaaaa
      361 cgcgctgaac gcgattcagc cgcaaacacc gcaaaaagat atgttttccc cggggtaaac
      421 cggaaaaatg cgtcaggatc gctttcagct cactgcatag ctatgcatga aagtgaatga
      481 cgatcggttt tggcgcatac agtgcccatg agacacattt tcggacattt tcagttcgtg
      541 aatccctgac tcattgctac atatctgaac agacacccct agcagcgccc ccaggggcgt
      601 cctgtaaaaa aacacaccgc gccgctagca gcactcctaa tataagatga tgttttttat
      661 gaaaatagtc agtaccaccc ctaaaaagcg gtgttggcgc agctacaaca ccgcgccgac
      721 accgcttttt taaatatcac aaagagagca agaagaacta atttgtcata actctctatt
      781 tataaagaaa aatcagcaaa aaattgtttt gcgtggggtg tgagcatttc aggcatgaga
      841 acagactcgc gtttttccgg agtatcagcg gaattattga ttaagaaaca ctcgacgcag
      901 agcgaaattt tatgcaacag cggctgcact gcacagggat tatttatcag ttgatatgct
      961 gtgccatgat acgtcctaaa gaaacaggac aggatgtgca attgtaatac cgtcgcccgc
     1021 aacgtcttac aattaccacc tgctcagggt ccccccgaca cccggaactg acggagaaca
     1081 acggaaggtg aacaaacaac aacaaactgc gctgaatatg gcgcgattta tcaaaagcca
     1141 gagcctgaca ctgcttgaaa aactggatgc tctggatgcc gacgaacagg cggccatgtg
     1201 cgaacgactg cacgaactcg cagaagaact ccagaacagc atccagattc gctttgaggc
     1261 cgaaaatgaa acaggaacat aacgaagctg acggaggcgg tcacggcttt cccgtgggcg
     1321 ttttcgtcag cagacaagcc cgtcagggcg cgtcaggggg ttttagcggg tgtcggggcg
     1381 cagccatgac ccagtcacgt agcgatagcg gagtgtatac tagcttaatt atgcggcgcc
     1441 agagcagatg gtgagagaac agcgacatat gaggtgtgaa atgctgcaca gatacgtaag
     1501 gagaaaatgc agcttccggc gctcttccgc ttcctcgctc actgactcgc tgcgctcggt
     1561 cgttcggctg cggcgagcgg tgtctgctca cgcaaagacg gatatacggt tatccacaga
     1621 atcaggggat aacaccggaa aaaacatgtg agcaaaaaag aggccccgaa aaaaggccgc
     1681 gccggtggcg tttttccata ggctccgccc ccctgacaag catcacaaaa atcgacgctc
     1741 aagtcagagg tggcgaaacc cgacaggact taaagatacc aggcgtttcc ccctggtggc
     1801 tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg
     1861 ccgcgttcgt ctcattccac gcctgacact cagttccggg taggcagttc gctccaagct
     1921 gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg
     1981 tcttgagtcc aacccggtaa gacacgactt aacgccattg gcagcggcca ctggtaaaca
     2041 ggatgtgcga gagatgtatt gagagttctt gaagtggcag ccttactgag gctacactag
     2101 aaggacagat ttggtgacat gtctcgcaca agactgttac cacggttcag aagttcccca
     2161 acttactgaa ccttcgaaaa accacctccc caggtggttt tttcgttttc tagagtagaa
     2221 gactacggct gtaagggaat gatctcaaga agatcctttg aactttttat aaaagttgct
     2281 tataaaatga tgcatcagca caacttttac tcaatcacac tcatctttct ggcctccatg
     2341 gcatgacgta aaagtatata gccacatgca agcatccctc caatgacaga agaaagaatt
     2401 acaattatgg cattacttgg cccatccttt ctgaccggta acgttgggct caattgatac
     2461 tgaaacggca taaaatcaac atcccccact ttcgccacaa ccaattgatt cacaacatat
     2521 tgacgatttc gcaactcccc actcaattcc gaaacatcct tgattgattt tttgatgttc
     2581 aatttagttg ctataccatc agaaccgaga gccacaggaa aatctgggtc atccttcata
     2641 atctgaccat tgctgtatac aggttttttt attccagccg cattagcaac ctccagtgaa
     2701 taattgaggc gtcgaatatc tgcattcagc tggtttctaa tttttatctc atccagtgca
     2761 agaatttctt tttcaacatt agttttaact tctagtttat ttcttatatc ttccatcaaa
     2821 tcccttacaa caagggaaga aacataatta atatacccag acaacacatc gtgagcttct
     2881 ttacttgttg gagcagtaaa actcagagtc catgatacat acaatgatga cttgtcgttt
     2941 ttcttactgg tattatcatc aaccgacttc atatttttac tcaactcaac aattgcacga
     3001 tgcagttcga gagcgctaat gttattcttt ttaatcatct ccataacata aggagatgat
     3061 ctcatatact cattcaacga attaacggac tggaatttct taataaacag atcaaatgcg
     3121 ttatcacgat tgatatcaaa atccactccc agaacatgaa gcttagaaag ctc
//
