LOCUS       CP056980                4018 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C14 plasmid pRHB41-C14_7, complete
            sequence.
ACCESSION   CP056980
VERSION     CP056980.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148426
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                     :: RH01 T3-C14
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 173.996160485263x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 03:28:15
            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)                     :: 5,152
            CDSs (total)                      :: 5,031
            Genes (coding)                    :: 4,749
            CDSs (with protein)               :: 4,749
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 282
            CDSs (without protein)            :: 282
            Pseudo Genes (ambiguous residues) :: 0 of 282
            Pseudo Genes (frameshifted)       :: 99 of 282
            Pseudo Genes (incomplete)         :: 175 of 282
            Pseudo Genes (internal stop)      :: 42 of 282
            Pseudo Genes (multiple problems)  :: 32 of 282
            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..4018
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C14"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C14_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(240..767)
                     /locus_tag="HV009_25690"
     CDS             complement(240..767)
                     /locus_tag="HV009_25690"
                     /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="QMB17733.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            complement(896..1111)
                     /gene="mbeD"
                     /locus_tag="HV009_25695"
     CDS             complement(896..1111)
                     /gene="mbeD"
                     /locus_tag="HV009_25695"
                     /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="QMB17734.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="mbeD"
     gene            complement(1115..1600)
                     /locus_tag="HV009_25700"
     CDS             complement(1115..1600)
                     /locus_tag="HV009_25700"
                     /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="QMB17735.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(1575..2339)
                     /locus_tag="HV009_25705"
                     /pseudo=""
     CDS             complement(1575..2339)
                     /locus_tag="HV009_25705"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="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            complement(2278..2601)
                     /locus_tag="HV009_25710"
     CDS             complement(2278..2601)
                     /locus_tag="HV009_25710"
                     /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="QMB17737.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(3791..4003)
                     /locus_tag="HV009_25715"
     CDS             complement(3791..4003)
                     /locus_tag="HV009_25715"
                     /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="QMB17736.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     Typing          complement(2715..2892)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          2839..3362
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.434"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(805..2288)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aatttaataa aaaaacagat ttaaaatatc caaaagacac tcttatttac cataacatcc
       61 cttgttcgca ccgccgcaga cagcctcagc accgttctgc gccatgaacc gcaaaagagc
      121 acctcttacc acgtaaaaac gccgataaat gccccccgta agttcttacg gtatgcatag
      181 ttatgcacgg aaatgaactg acactctgtt caatggattt tcatgctgta agcagtattt
      241 tagtcttcta tgccccctcg aaacacacct gttcttgtgt agatcttttc gacccaagat
      301 ggtcttttat ccgagttcat gcagccgtac aggaacacac ctgttttggg tttatagctc
      361 cccccctcct gtggctggtt atctacaaat gaataatcaa tcttttcacc tttgactgaa
      421 gcacgccccc caacatgaac taaagaccag tgctcatgca tcacatggct ttcaatcaat
      481 ccaaatgaag aaaaacccca tgaatcaaaa aagaccttga gtccgtcaga cgcaccaaca
      541 ggagtaatga ttgcaaattc aacctgctca ccagtacctt caaggtaaga aggtttctcg
      601 acgttaatta cagatgcccc cttcacctga taacctttac aggtaagata taagtccctc
      661 ccggctgacg gttttgtata tgtaacgttg tcgttattct ccgcagcagc gactgtaaat
      721 gacatagcca aaaccaccga gactgagcaa gcccagaaac atttcataac gcatcccttt
      781 tcattgatta actacattcc aagctcaaaa cctttctgcc gctgcgatcg ttccagctcc
      841 agcgctttct ggtgctgcgc cgcgcgctcc tgctcccggt gcgcctcgat gccattcagc
      901 cttgcgacaa tcggcgcagc tgatcgctca aactctgcac ctgcctgctc aagcccgtga
      961 cgcgctcgct cagcgccgcg ttctcccgtt gcataagccc agacatcgtc cgccattccg
     1021 cgaaggcgtt ctcccactcg tccagccttt tcgagtagtc ctgctgtagc tgctctaatg
     1081 cgctcagcaa ctgtttttcc agttccgtca tgtgctattt ccccgccagt atcatccagc
     1141 tcgaatcctc tccgaatctt cccgcttccg ggttcaccct cacgcagcgg cgtctctcct
     1201 ccccgcaggt cgtgagctgg acgccgttgt tcttctctga aagcatggcc tgcgtgctct
     1261 tctgttcctg gatggtcgtg tagttgtcga gtatctgttg cccctgccac cacagaatgc
     1321 ccgcgctcga ggcgatcagt agcgcggaga ccaggactat ggtcagccac gtctggctga
     1381 tcatacgcag catccctttc gtgcgttggc tcatggctga ggacagcttc cggtcgtggt
     1441 cgaggatggc ggcgctgatt ctcttctcgc tttcgctcag ttccgctctg acagacttct
     1501 cgtgctcgct gaatgcggct ttcagcatct cgccggtagt ctgctgctgc gctttcgatt
     1561 tctgctctaa gtccttcgcc agcgttaaaa gactgttcat agatggctcc cttcagtcgg
     1621 atgtttcgcc ccccgtcagg gtcggcaatg ctgatgctgc ttttcgtggt gcgcaccacc
     1681 tcaaaacccg cactttccag cgcctcagtg acgtcctgac gggttttcag ctccccggat
     1741 gaggcaaggg aaagtaggcc gcgcgtaatc gcctgggcgg cttcctgctt cgcttccggc
     1801 agcgcggacg gtgtaaccag cgcccgccgg ttttccggcg cgttcgggtc gtgcagcccc
     1861 agtctgccgt tcactatggt ctgccaggca tcaatgcgcg gacggtcggc gcggtcgtaa
     1921 tacggctgga gacgtctgcc ggtcagcagc tccgtgttcg ggatcaggaa gttcagctcc
     1981 agccgccctt tgtcccggtg ctcaacccac agtacgctgt actggtcttt atcgagtccg
     2041 ggcatcagaa cccgctcaaa gctcgccatc agcttttcac gctggccggg cggcaaatcc
     2101 tgttcggcaa aagacagcac gccggaggtg tatttcttgg cgtaaggcga ggcgtcaata
     2161 agctcccgca cttcctccgg cttaccctgc agaacgctgg cgccgtcgcg ctgccggtct
     2221 ttccccagca gataatccac cggaccgccg ccaccgccgc ggcctctggg atgaaactta
     2281 acgatcatcg tctgccccct tttccagcac ggcgtgccgc agccgctcga gtccggcatc
     2341 aatggccatc agcacggcga caacctgcac gcgatcgtgc ccagtaccgc caccggcgtt
     2401 aacctgccgg gcaatctggt tgaggttgtt acccatgccg gcaagctgac gaagcagcgc
     2461 cggcgagatg gatggaagtt tgccagcacg cgagggcttt tcgtccaggc atatctggcg
     2521 catccaggcc gcgagttgtt taccctcaca gcgctccaga agtcggcggt gctcgtcttc
     2581 tgtcacccac atagtgagca ttttgttgcg cttttctgcc aaaccatcct ccggataaca
     2641 ccggttcggg cgggaaattt tttcctgtcc ggagcggtgt tgggcaagcc cgcagggcgc
     2701 ggcagtactt ttcagcgggt ttcggggcgc agccctgaac cagtcacgta gcgctagcgg
     2761 agtgtatact ggcttaacat ggtaaatcgg agtggggatt caggaaagtg cttcatgtgg
     2821 cagggagaaa atgctgctgt ggggcgtaag tgcgaaatgc agatcccggt gaaatgacgc
     2881 ctcctcgctc actcggtcgc tgcgctcctg ccgtgagact gcggcgggcg ttgccagctt
     2941 acgaatggct ggataaagag actaagcgga aatcaatcag aaagggcgga aaaaggatgc
     3001 ggcgttgccg tttttccata ggctccgccc ccctgacaag catcacgaaa tctgacgctc
     3061 aaatcagtgg tggcgaaacc cgacaggact ataaagatcc caggcgtttc cccctggtag
     3121 ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg
     3181 gccgcgttta tctaattcca cgcctgacac tcagttccgg gtaggcagtt cgctccaagc
     3241 tggactgtat gcacgaaccc cccgttcagt ccgaccgctg cgccttatcc ggtaactatc
     3301 gacttgagtc caacccggaa agacacgaca aaacgccact ggcagcagcc actggtaact
     3361 gatttagagg agttagtctt gaagttatgc gccggttaag gctaaactga aaggacaagt
     3421 tttggtgact gtgctcctcc aagccagtta cctcggttca aagagttgct gctctgagaa
     3481 ccttcgaaaa aaccgccttg ctgggcggtt ttttcgttta cagtgctaag agattacgat
     3541 tctccatgaa tgatctcaag aagatccgtt taaaaaagcg ggttttatgg ggggataaag
     3601 ttcgtctagc ccagtcactt tggattacag ctaggtttcg taagccatgc aagaatgcct
     3661 gtaactaaca aaataggccc tgcaacgtac gtaacataga ctccaacata cgacactgtg
     3721 aaacatatga gtacgtatat agacagtgtt gtccaaaaaa tgactgttgt tttacagtga
     3781 atccactctt tcatttttca ataaacccca caccgtctgg agatcttatt atcgttttgc
     3841 caggattagc tttcgcccaa accaaagcat cttgaaaaga agagaatttt ttttttgaat
     3901 ttttagtttt tcggcgatct tctcgaaaat attcgctgtt attctcatca attatccgat
     3961 caaaatcagc accagctcca aaggtacgct caaaatcccc cattttctgc ccccatta
//
