LOCUS       CP057394                3374 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB28-C04 plasmid pRHB28-C04_5, complete
            sequence.
ACCESSION   CP057394
VERSION     CP057394.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148266
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3374)
  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 3374)
  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 T2-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 157.864143540528x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:46:57
            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)                     :: 4,445
            CDSs (total)                      :: 4,326
            Genes (coding)                    :: 4,062
            CDSs (with protein)               :: 4,062
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 264
            CDSs (without protein)            :: 264
            Pseudo Genes (ambiguous residues) :: 0 of 264
            Pseudo Genes (frameshifted)       :: 120 of 264
            Pseudo Genes (incomplete)         :: 122 of 264
            Pseudo Genes (internal stop)      :: 46 of 264
            Pseudo Genes (multiple problems)  :: 22 of 264
            CRISPR Arrays                     :: 3
            ##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..3374
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB28-C04"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB28-C04_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(30..389)
                     /locus_tag="HVY49_22190"
                     /pseudo=""
     CDS             complement(30..389)
                     /locus_tag="HVY49_22190"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and 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(547..870)
                     /locus_tag="HVY49_22195"
     CDS             complement(547..870)
                     /locus_tag="HVY49_22195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="QMG82581.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            934..1125
                     /locus_tag="HVY49_22200"
     CDS             934..1125
                     /locus_tag="HVY49_22200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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="QMG82578.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2443..2676)
                     /gene="mbeD"
                     /locus_tag="HVY49_22205"
     CDS             complement(2443..2676)
                     /gene="mbeD"
                     /locus_tag="HVY49_22205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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="QMG82579.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="mbeD"
     gene            complement(2683..3243)
                     /locus_tag="HVY49_22210"
     CDS             complement(2683..3243)
                     /locus_tag="HVY49_22210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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="QMG82580.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISGHTTSVKQQLDTLSATVSTQFSTTEAELSRQQKKLLWQVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     Typing          complement(1207..1290)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="95.0"
                     /evalue="4.11e-16"
     Typing          complement(4..557)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.378"
                     /coverage="99.0"
                     /evalue="4.06e-119"
     Typing          complement(2361..3373)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.087"
                     /coverage="99.0"
                     /evalue="2.14e-179"
ORIGIN
        1 gctccggcat ggtaaagcgc ctcaagaccc cgtgtaatcg cttctgcggc ctcctgtttc
       61 gcttttggca gattatttgg cgtgacaagc gtccgtctgt tctccggtgc gttcgggtca
      121 cgcagcccgt aatgatgatt aaccagcgtc tgccaggcat ttatcctcgg cctgtccgca
      181 cggtcgtagt acggctggag gcgcttaccg ctctgtagct ccatgttcgg gatgacaaaa
      241 ttcagttcga gccgcccctt atcctggtgt tccacccaga gaatgctgta ctggtctttt
      301 tcgagaccgg gcataagaac acgctcaaag ctcgtcatca ctctttcgcg ttcacccggc
      361 ggtaactcct tctccgcgaa cgacagaacg cctgacgtgt atttcttcga aaatggcgtg
      421 gaatcaatga gttcccgcac ttcttccggg ttaccccgga gcaccgttgc gccttcgcgg
      481 ttacgctccc gccccagcag gtaatcgacc gggccacttc caccgccttt ccccctggca
      541 tgaaatttaa ctatcatccc gtaccccctg ttccctgaca gcctgccgca actggcgcaa
      601 ttcaccctcg atggccatca gtgcggccac cacatgaacc cggtcaatcg aagaccactg
      661 accgctgttc accttccggg ctgtctggtt caggttgttc ccgatggcag ccagatgccg
      721 cagcaatggc ggtgatagtg tcggcagttt tcctgtgcgt gcaaccggct cccccagaca
      781 gacccgccgc atccattctg ccagtcgttt accctcgcag cgttccagta accgggcgtg
      841 ctcctcatcg ctaacccgta tcgtgagcat cttctcgcgt ttcatcggta tcattccccc
      901 taacaaatcc ccaatacaag gagccttaag accatgacca aacaggaaaa aacagccctt
      961 aacatggccc gttttatcag aagccagacg ctgaccctgc tggaaaaact caacgagctg
     1021 gacgcggacg aacaggcaga catctgcgaa tcacttcacg accacgccga cgaactctac
     1081 cgcagttgcc tcgcacgctt cggcgatgac ggtgaaagca actgaaacat gcagctcccg
     1141 gagacgttca cagcttgcct gtgagcggat gccgggagca gacaagccca tgagggcgcg
     1201 tcagtgcggg tgtcggggcg cagccctgac ccagttcaca gagcgatagc gatgtgtata
     1261 ctggcttatc tcattttgca tcggagcaga gtggatggaa agtactccat gtcaggagta
     1321 aaaagccgca cagatgcgta aaaacagcgc acccgataaa cagcacacat gcggacacgg
     1381 gcacaggcgc gtaagtgcac aatgcttgcc tcggtgacac ttccgcttcc tcgcccactc
     1441 gctcactacg ttcggtcgct ggggctgcgg cgagcggtgt gatcactctc gttgtgatgc
     1501 agatccgttt tttttttttg cacaggagtt atcaggagtt gcggtgcaca tgggatcgtg
     1561 cgatatgccg gatggtgaaa ggttggaggg aacggcaaca actcacccct cccagtgaag
     1621 ggacgggtag tttgccgctc tcgatatgcc ggacggagcc aaggccatcg atcacggggc
     1681 gcgtcagtgg aagaacccgc gcctgcgtga cgtatgcgtc ttcgccgcac catctcaccc
     1741 gtcacgccac cacataccgg gaactgccgc caaggtctaa ctcaaccaat ctagccgcgc
     1801 tacatacggt ttttgtggca actcatcagg tgtccgctgt cgatgaaact ctctgcgccg
     1861 gtagcggaac tctcacgcgt gcggtcgccg tcgtcacagc tcccccaacc gcaaacggtc
     1921 tttgcaaaca cgcaagcatc tgcaaaaaaa ggtttttttt cgggtatctg ggaggctgtg
     1981 cagcggaaaa attcttgaag aatacagaag gttcatgcaa actgaatgaa ctggtttctg
     2041 tcgctgcgaa caacagactc cacaggaaca ttgaggaggt cgaaaacctc aatgaacccg
     2101 aagaagctcg cctaatggcg ggcttttttc gttctacgct ctccgacgaa agatcgcaag
     2161 tgaaataacg agatttttca cgtctttacg ctcaaaaagc aaaaaaacca tgttttcccc
     2221 tggctgaatc cccaaaaacg cgtgaaatgc gttttcagga tattgcatag ctatgcacaa
     2281 atacggcaca cgatttgttt cgctcgcccc cagccgtcga atgggtcaaa atggcaaggt
     2341 ttcgtcactt ccccggtcac atctccattg atggcccact ccgaacccgc gccgcgcgtt
     2401 cctgtacctc atgtctgtac cgggcacgct cctgttcatc ccttagctgt tgttcgcgat
     2461 aaataaccga ctcaagcgat ccacttgccc ggctaatctc tgcacctgct gactcaatat
     2521 cacgacgcgc tcgttcagta tcgcgttgtt ccgttgcgta acctcgtgca tcttctgcaa
     2581 ttccgcgaag gcgctctccc actcgttcag ccgccgcata tagtcctgtt gcaaatgctc
     2641 taaggcgttc agcaaatgcc cttccagttc cgtcatactc gtttactccc tgaccagcct
     2701 cacggcgttc ttgtcgccca ccgtccaggt gttttcccct ttcaccccgt ccggcagcac
     2761 cagaaatttc ccgttctcgc cattgacgaa cgtcaccccc caggtttttg cctcgagttt
     2821 cgccagcgtg ttttcctgct ctctgatagt caggatattt ttcgcaatct tgctttcttg
     2881 ccactccatc agcccccagc accccaggaa aatgccgccc gtgacgctga gcgcggtcag
     2941 cgccggaaac agtatccgcc ctttgatcac ctgccagagc agttttttct gctgccggga
     3001 cagttcggcc tctgtggtgc tgaactgcgt gctcacggtg gcgctcagtg tatccagttg
     3061 ctgtttcacg gatgttgtat gtccgctgat agcgtctctg attttctgcc tgtttaagct
     3121 cagtgccttg tctacagact cttcgagctt cctgaactcg ctgttcagca tgttctcggt
     3181 agaagcggct cgctctttca gtttcttctc gaagtctgtt cccatttgta aaagattgct
     3241 catacagcgc cccctttagc ctgagattcc gcccaccctc cgggtcggca atactgatac
     3301 tgcttctggt tgtcctcacc acctcaaaac ctgccgctgt gagcgcctca gtgacatcct
     3361 gacgcgtttt tatt
//
