LOCUS       CP056989                3173 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C11 plasmid pRHB41-C11_5, complete
            sequence.
ACCESSION   CP056989
VERSION     CP056989.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148424
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                     :: RH01 T3-C11
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 134.704823216905x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 04:10:52
            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)                     :: 5,228
            CDSs (total)                      :: 5,103
            Genes (coding)                    :: 4,846
            CDSs (with protein)               :: 4,846
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 95 of 257
            Pseudo Genes (incomplete)         :: 143 of 257
            Pseudo Genes (internal stop)      :: 48 of 257
            Pseudo Genes (multiple problems)  :: 24 of 257
            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="RHB41-C11"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C11_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(933..1127)
                     /locus_tag="HV007_26120"
     CDS             complement(933..1127)
                     /locus_tag="HV007_26120"
                     /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="QMB22604.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1972..3081
                     /gene="fepE"
                     /locus_tag="HV007_26125"
     CDS             1972..3081
                     /gene="fepE"
                     /locus_tag="HV007_26125"
                     /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="QMB22605.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEGIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDNAFDLF
                     IKKFQSVNSLNEYMRSSPYVMEMIKKNNISALELHRAIVELSKNMKSVDDNTSKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="fepE"
     Typing          767..853
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.455"
                     /coverage="100.0"
                     /evalue="1.14e-31"
     Typing          1164..1262
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          1394..1641
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="86.0"
                     /evalue="1.58e-110"
     Typing          complement(216..742)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 tctagaaaac gaaaaaacca cctggggagg tggtttttcg aaggttcagt aagttgggga
       61 acttctgaac cgtggtaaca gtcttgtgcg agacatgtca ccaaatctgt ccttctagtg
      121 tagcctcagt aaggctgcca cttcaagaac tctcaataca tctctcgcac atcctgttta
      181 ccagtggccg ctgccaatgg cgttaagtcg tgtcttaccg ggttggactc aagacgatag
      241 ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg
      301 gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagacgaac gcggccataa
      361 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagccacc
      421 agggggaaac gcctggtatc tttaagtcct gtcgggtttc gccacctctg acttgagcgt
      481 cgatttttgt gatgcttgtc aggggggcgg agcctatgga aaaacgccac cggcgcggcc
      541 ttttttcggg gcctcttttt tgctcacatg ttttttccgg tgttatcccc tgattctgtg
      601 gataaccgta tatccgtctt tgcgtgagca gacaccgctc gccgcagccg aacgaccgag
      661 cgcagcgagt cagtgagcga ggaagcggaa gagcgccgga agctgcattt tctccttacg
      721 tatctgtgca gcatttcaca cctcatatgt cgctgttctc tcaccatctg ctctggcgcc
      781 gcataattaa gctagtatac actccgctat cgctacgtga ctgggtcatg gctgcgcccc
      841 gacacccgct aaaaccccct gacgcgccct gacgggcttg tctgctgacg aaaacgccca
      901 cgggaaagcc gtgaccgcct ccgtcagctt cgttatgttc ctgtttcatt ttcggcctca
      961 aagcgaatct ggatgctgtt ctggagttct tctgcgagtt cgtgcagtcg ttcgcacatg
     1021 gccgcctgtt cgtcggcatc cagagcatcc agtttttcaa gcagtgtcag gctctggctt
     1081 ttgataaatc gcgccatatt cagcgcagtt tgttgttgtt tgttcacctt ccgttgttct
     1141 ccgtcagttc cgggtgtcgg ggggaccctg agcaggtggt aattgtaaga cgttgcgggc
     1201 gacggtatta caattgcaca tcctgtcctg tttctttagg acgtatcatg gcacagcata
     1261 tcaactgata aataatccct gtgcagtgca gccgctgttg cataaaattt cgctctgcgt
     1321 cgagtgtttc ttaatcaata attccgctga tactccggaa aaacgcgagt ctgttctcat
     1381 gcctgaaatg ctcacacccc acgcaaaaca attttttgct gatttttctt tataaataga
     1441 gagttatgac aaattagttc ttcttgctct ctttgtgata tttaaaaaag cggtgtcggc
     1501 gcggtgttgt agctgcgcca acaccgcttt ttaggggtgg tactgactat tttcataaaa
     1561 aacatcatct tatattagga gtgctgctag cggcgcggtg tgttttttta caggacgccc
     1621 ctgggggcgc tgctaggggt gtctgttcag atatgtagca atgagtcagg gattcacgaa
     1681 ctgaaaatgt ccgaaaatgt gtctcatggg cactgtatgc gccaaaaccg atcgtcattc
     1741 actttcatgc atagctatgc agtgagctga aagcgatcct gacgcatttt tccggtttac
     1801 cccggggaaa acatatcttt ttgcggtgtt tgcggctgaa tcgcgttcag cgcgttttag
     1861 cggtgcgcgt aataaaatgt tatgttaaat gtctgctgaa tggtttttag gttttttcct
     1921 aacatatgat agaataaaaa accatatgtt aatatattgt gttttttttc aatgaaaatc
     1981 tcaaaggtat ctgacgaaca tttttctaat tacaacatgt tgccgaatgg taatgaagga
     2041 attgatcttt ttggcttgat tagcgtttta tgggcagcaa aaataaaaat tgttggggtg
     2101 attctatttt ttgcttgtat tggctttctt gtttcttttg ttttgccaca aaaatggact
     2161 agttctgctg tggttactcc tgctgagtct gttcaatgga gtgaattaaa taaggagctt
     2221 tctaagcttc atgttctggg agtggatttt gatatcaatc gtgataacgc atttgatctg
     2281 tttattaaga aattccagtc cgttaattcg ttgaatgagt atatgagatc atctccttat
     2341 gttatggaga tgattaaaaa gaataacatt agcgctctcg aactgcatcg tgcaattgtt
     2401 gagttgagta aaaatatgaa gtcggttgat gataatacca gtaagaaaaa cgacaagtca
     2461 tcattgtatg tatcatggac tctgagtttt actgctccaa caagtaaaga agctcacgat
     2521 gtgttgtctg ggtatattaa ttatgtttct tcccttgttg taagggattt gatggaagat
     2581 ataagaaata aactagaagt taaaactaat gttgaaaaag aaattcttgc actggatgag
     2641 ataaaaatta gaaaccagct gaatgcagat attcgacgcc tcaattattc actggaggtt
     2701 gctaatgcgg ctggaataaa aaaacctgta tacagcaatg gtcagattat gaaggatgac
     2761 ccagattttc ctgtggctct cggttctgat ggtatagcaa ctaaattgaa catcaaaaaa
     2821 tcaatcaagg atgtttcgga attgagtggg gagttgcgaa atcgtcaata tgttgtgaat
     2881 caattggttg tggcgaaagt gggggatgtt gattttatgc cgtttcagta tcaattgagc
     2941 ccaacgttac cggtcagaaa ggatgggcca agtaatgcca taattgtaat tctttcttct
     3001 gtcattggag ggatgcttgc atgtggctat atacttttac gtcatgccat ggaggccaga
     3061 aagatgagtg tgattgagta aaagttgtgc tgatgcatca ttttataagc aacttttata
     3121 aaaagttcaa aggatcttct tgagatcatt cccttacagc cgtagtcttc tac
//
