LOCUS       CP057701                4018 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB17-C09 plasmid pRHB17-C09_6, complete
            sequence.
ACCESSION   CP057701
VERSION     CP057701.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148144
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4018)
  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 4018)
  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                     :: RH03 T2-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.5809268322776x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 11:12:56
            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)                     :: 5,029
            CDSs (total)                      :: 4,911
            Genes (coding)                    :: 4,700
            CDSs (with protein)               :: 4,700
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 104 of 211
            Pseudo Genes (incomplete)         :: 105 of 211
            Pseudo Genes (internal stop)      :: 43 of 211
            Pseudo Genes (multiple problems)  :: 38 of 211
            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..4018
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB17-C09"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB17-C09_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3789..4018,1..94)
                     /locus_tag="HVX27_25080"
     CDS             join(3789..4018,1..94)
                     /locus_tag="HVX27_25080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QML80996.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            join(3997..4018,1..797)
                     /locus_tag="HVX27_25085"
                     /pseudo=""
     CDS             join(3997..4018,1..797)
                     /locus_tag="HVX27_25085"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="internal stop; incomplete; partial on complete
                     genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            772..1257
                     /locus_tag="HVX27_25090"
     CDS             772..1257
                     /locus_tag="HVX27_25090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="QML80997.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1261..1476
                     /gene="mbeD"
                     /locus_tag="HVX27_25095"
     CDS             1261..1476
                     /gene="mbeD"
                     /locus_tag="HVX27_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QML80998.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="mbeD"
     gene            1605..2132
                     /locus_tag="HVX27_25100"
     CDS             1605..2132
                     /locus_tag="HVX27_25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QML80999.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            2387..2599
                     /locus_tag="HVX27_25105"
     CDS             2387..2599
                     /locus_tag="HVX27_25105"
                     /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="QML81000.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKNFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(3028..3141)
                     /locus_tag="HVX27_25110"
     CDS             complement(3028..3141)
                     /locus_tag="HVX27_25110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QML81001.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     Typing          3499..3676
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          complement(3029..3549)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.753"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          85..1568
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3790..4016
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="99.0"
                     /evalue="3.17e-42"
ORIGIN
        1 cgtgcaggtt gtcgccgtgc tgatggccat tgatgccgga ctcgagcggc tgcggcacgc
       61 cgtgctggaa aagggggcag acgatgatcg ttaagtttca tcccagaggc cgcggcggtg
      121 gcggcggtcc ggtggattat ctgctgggga aagaccggca gcgcgacggc gccagcgttc
      181 tgcagggtaa gccggaggaa gtgcgggagc ttattgacgc ctcgccttac gccaagaaat
      241 acacctccgg cgtgctgtct tttgccgaac aggatttgcc gcccggccag cgtgaaaagc
      301 tgatggcgag ctttgagcgg gttctgatgc ccggactcga taaagaccag tacagcgtac
      361 tgtgggttga gcaccgggac aaagggcggc tggagctgaa cttcctgatc ccgaacacgg
      421 agctgctgac cggcagacgt ctccagccgt attacgaccg cgccgaccgt ccgcgcattg
      481 atgcctggca gaccatagtg aacggcagac tggggctgca cgacccgaac gcgccggaaa
      541 accggcgggc gctggttaca ccgtccgcgc tgccggaagc gaagcaggaa gccgcccagg
      601 cgattacgcg cggcctactt tcccttgcct catccgggga gctgaaaacc cgtcaggacg
      661 tcactgaggc gctggaaagt gcgggttttg aggtggtgcg caccacgaaa agcagcatca
      721 gcattgccga ccctgacggg gggcgaaaca tccgactgaa gggagccatc tatgaacagt
      781 cttttaacgc tggcgaagga cttagagcag aaatcgaaag cgcagcagca gactaccggc
      841 gagatgctga aagccgcatt cagcgagcac gagaagtctg tcagagcgga actgagcgaa
      901 agcgagaaga gaatcagcgc cgccatcctc gaccacgacc ggaagctgtc ctcagccatg
      961 agccaacgca cgaaagggat gctgcgtatg atcagccaga cgtggctgac catagtcctg
     1021 gtctccgcgc tactgatcgc ctcgagcgcg ggcattctgt ggtggcaggg gcaacagata
     1081 ctcgacaact acacgaccat ccaggaacag aagagcacgc aggccatgct ttcagagaag
     1141 aacaacggcg tccagctcac gacctgcggg gaggagagac gccgctgcgt gagggtgaac
     1201 ccggaagcgg gaagattcgg agaggattcg agctggatga tactggcggg gaaatagcac
     1261 atgacggaac tggaaaaaca gttgctgagc gcattagagc agctacagca ggactactcg
     1321 aaaaggctgg acgagtggga gaacgccttc gcggaatggc ggacgatgtc tgggcttatg
     1381 caacgggaga acgcggcgct gagcgagcgc gtcacgggct tgagcaggca ggtgcagagt
     1441 ttgagcgatc agctgcgccg attgtcgcaa ggctgaatgg catcgaggcg caccgggagc
     1501 aggagcgcgc ggcgcagcac cagaaagcgc tggagctgga acgatcgcag cggcagaaag
     1561 gttttgagct tggaatgtag ttaatcaatg aaaagggatg cgttatgaaa tgtttctggg
     1621 cttgctcagt ctcggtggtt ttggctatgt catttacagt cgctgctgcg gagaataacg
     1681 acaacgttac atatacaaaa ccgtcagccg ggagggactt atatcttacc tgtaaaggtt
     1741 atcaggtgaa gggggcatct gtaattaacg tcgagaaacc ttcttacctt gaaggtactg
     1801 gtgagcaggt tgaatttgca atcattactc ctgttggtgc gtctgacgga ctcaaggtct
     1861 tttttgattc atggggtttt tcttcatttg gattgattga aagccatgtg atgcatgagc
     1921 actggtcttt agttcatgtt ggggggcgtg cttcagtcaa aggtgaaaag attgattatt
     1981 catttgtaga taaccagcca caggaggggg ggagctataa acccaaaaca ggtgtgttcc
     2041 tgtacggctg catgaactcg gataaaagac catcttgggt cgaaaagatc tacacaagaa
     2101 caggtgtgtt tcgagggggc atagaagact aaaatactgc ttacagcatg aaaatccatt
     2161 gaacagagtg tcagttcatt tccgtgcata actatgcata ccgtaagaac ttacgggggg
     2221 catttatcgg cgtttttacg tggtaagagg tgctcttttg cggttcatgg cgcagaacgg
     2281 tgctgaggct gtctgcggcg gtgcgaacaa gggatgttat ggtaaataag agtgtctttt
     2341 ggatatttta aatctgtttt tttattaaat ttaatggggg cagaaaatgg gggattttga
     2401 gcgtaccttt ggagctggtg ctgattttga tcggataatt gatgagaata acagcgaata
     2461 ttttcgagaa gatcgccgaa aaactaaaaa ttcaaaaaaa aatttctctt cttttcaaga
     2521 tgctttggtt tgggcgaaag ctaatcctgg caaaacgata ataagatctc cagacggtgt
     2581 ggggtttatt gaaaaatgaa agagtggatt cactgtaaaa caacagtcat tttttggaca
     2641 acactgtcta tatacgtact catatgtttc acagtgtcgt atgttggagt ctatgttacg
     2701 tacgttgcag ggcctatttt gttagttaca ggcattcttg catggcttac gaaacctagc
     2761 tgtaatccaa agtgactggg ctagacgaac tttatccccc cataaaaccc gcttttttaa
     2821 acggatcttc ttgagatcat tcatggagaa tcgtaatctc ttagcactgt aaacgaaaaa
     2881 accgcccagc aaggcggttt tttcgaaggt tctcagagca gcaactcttt gaaccgaggt
     2941 aactggcttg gaggagcaca gtcaccaaaa cttgtccttt cagtttagcc ttaaccggcg
     3001 cataacttca agactaactc ctctaaatca gttaccagtg gctgctgcca gtggcgtttt
     3061 gtcgtgtctt tccgggttgg actcaagtcg atagttaccg gataaggcgc agcggtcgga
     3121 ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag
     3181 tgtcaggcgt ggaatgagat aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa
     3241 aggcaggaac aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata
     3301 gtcctgtcgg gtttcgccac cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg
     3361 ggcggagcct atggaaaaac ggcaacgccg catccttttt ccgccctttc tgattgattt
     3421 ccgcttagtc tctttatcca gccattcgta agctggcaac gcccgccgca gtctcacggc
     3481 aggagcgcag cgaccgagtg agcgaggagg cgtcatttca ccgggatctg catttcgcac
     3541 ttacgcccca cagcagcatt ttctccctgc cacatgaagc actttcctga atccccactc
     3601 cgatttacca tgttaagcca gtatacactc cgctagcgct acgtgactgg ttcagggctg
     3661 cgccccgaaa cccgctgaaa agtactgccg cgccctgcgg gcttgcccaa caccgctccg
     3721 gacaggaaaa aatttcccgc ccgaaccggt gttatccgga ggatggtttg gcagaaaagc
     3781 gcaacaaaat gctcactatg tgggtgacag aagacgagca ccgccgactt ctggagcgct
     3841 gtgagggtaa acaactcgcg gcctggatgc gccagatatg cctggacgaa aagccctcgc
     3901 gtgctggcaa acttccatcc atctcgccgg cgctgcttcg tcagcttgcc ggcatgggta
     3961 acaacctcaa ccagattgcc cggcaggtta acgccggtgg cggtactggg cacgatcg
//
