LOCUS       CP057291                5128 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C16 plasmid pRHB30-C16_5, complete
            sequence.
ACCESSION   CP057291
VERSION     CP057291.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148295
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  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 5128)
  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 T3-C16
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 133.162200925436x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:08:53
            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)                     :: 5,197
            CDSs (total)                      :: 5,073
            Genes (coding)                    :: 4,833
            CDSs (with protein)               :: 4,833
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 71 of 240
            Pseudo Genes (incomplete)         :: 154 of 240
            Pseudo Genes (internal stop)      :: 35 of 240
            Pseudo Genes (multiple problems)  :: 19 of 240
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB30-C16"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C16_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5027..5128,1..222)
                     /locus_tag="HVY78_25925"
     CDS             join(5027..5128,1..222)
                     /locus_tag="HVY78_25925"
                     /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="QMF65527.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            380..922
                     /locus_tag="HVY78_25930"
                     /pseudo=""
     CDS             380..922
                     /locus_tag="HVY78_25930"
                     /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            900..1418
                     /locus_tag="HVY78_25935"
     CDS             900..1418
                     /locus_tag="HVY78_25935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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="QMF65528.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            1425..1658
                     /gene="mbeD"
                     /locus_tag="HVY78_25940"
     CDS             1425..1658
                     /gene="mbeD"
                     /locus_tag="HVY78_25940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="QMF65529.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(2251..2436)
                     /locus_tag="HVY78_25945"
     CDS             complement(2251..2436)
                     /locus_tag="HVY78_25945"
                     /inference="COORDINATES: protein motif:HMM:NF021447.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2158 domain-containing protein"
                     /protein_id="QMF65530.1"
                     /translation="MPFNIGDIVYLKSESKAMTVIGYGSSQNNGYIDLANCAWLDKDNR
                     YCQILFLFQTIEKRIS"
                     /name="DUF2158 domain-containing protein"
     gene            complement(2478..2879)
                     /locus_tag="HVY78_25950"
     CDS             complement(2478..2879)
                     /locus_tag="HVY78_25950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMF65531.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(2876..3760)
                     /locus_tag="HVY78_25955"
     CDS             complement(2876..3760)
                     /locus_tag="HVY78_25955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="QMF65532.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     gene            complement(4009..4140)
                     /locus_tag="HVY78_25960"
     CDS             complement(4009..4140)
                     /locus_tag="HVY78_25960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMF65533.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="replication initiation protein"
     gene            complement(4771..4962)
                     /locus_tag="HVY78_25965"
     CDS             complement(4771..4962)
                     /locus_tag="HVY78_25965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="QMF65534.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4503..4676
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          complement(3993..4579)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.723"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          213..1762
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4998..5128
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="1.02e-20"
ORIGIN
        1 ccggttgccc gttccgggaa gctgccgaca ctggcaccgc cgttactgcg ccagctggct
       61 gccatcggga ataatctgaa tcagacggcg aggaaggtga acagcgggca gtggtcttcc
      121 ggtgaccggg ttcaggtggt ggccgcactg atggccatcg agagagagtt gcgcagctta
      181 cggcaggtcg tcagggaaca tggagcgcgg gatgatagtt aagtttcatg ccaggggaaa
      241 aggcggtggc agtggtccgg ttgattacct gctgggaagg gagcgtaacc gggaaggggc
      301 aacggtgctt cagggtaatc cggaagaagt ccgggaactc atcgatgcca cgccatttgc
      361 gaagaaatac acgtcaggtg ttctgtcgtt cgcggagaag gagctgccgc cgggaggacg
      421 tgaaaaggtg atggcgagct ttgagcgtgt actgatgccc ggtctcgaaa aaaatcagta
      481 cagcatcctg tgggtggagc accaggacaa gggacggctt gagctgaatt ttgtcattcc
      541 gaacatggag ctacagagcg gaaaacgcct ccagccgtac tacgaccggg cagacaggcc
      601 gagaattgat gcctggcaga cgctggttaa tcaccattac gggctgcatg accccaacgc
      661 cccggagaac cgccggatac tgactctccc tgataacctg ccggaaacga aacaggcgct
      721 tgcagagagc gtcacacgcg ggatagacgc tctttatcat gtcggggaga taaaaggccg
      781 tcaggatgtg attcaggcgc tcacagaggc agggcttgaa gtggtcaggg tgacgcgaag
      841 cagtatcagc attgcagacc cgaacggcgg gaagaatatc agactgaaag gagcattcta
      901 tgagcaatct tttacagacg ggcgcggagt tcgagaaaaa gctgaaagag agagccgaat
      961 ctacagagac aatgctgaac gacgagttca gcaagctcga aaaatctgta agcaaggctg
     1021 tgacatcaaa cgagacgaaa atcaaagacg ctatagccct gttcacagct tcgacagagg
     1081 aatcactgaa aaaacaccgg gaaggggtga aagaggcgat gatgcagcac aggaaggacg
     1141 tgttaaagct ggcagggaat acgggcatga tgttactggg gatggtcctt ttcctgttta
     1201 ccgtgagtgg cgggacgctc tggtatcttg gcgggcggat acaggcgaac ctggaagaaa
     1261 tcaggataca ggaagaaaca ttgcagaaac tgaacgcgaa gacatggggc gtggagtttg
     1321 tgcaggacgg gagaaggaaa tttctggtcc ttccgtacgg gaaatcggca acggtgattc
     1381 cctatcagga gaaggactgg gtacaactga cggagtgaca cagagtgacg gagctggaaa
     1441 gacatttgct gaacgcctta gagcaactgc aacaggacta tatgcagcgg ctgagcgaat
     1501 gggagagcgc cttcgtggaa ttgcagaaaa tgttttcgct tacgcaacgg gacaacgcga
     1561 tgctgaacga gcaggtcatg cagttgagtc agcaggtgca gcacttgagc gagcggacag
     1621 aacgcttgag ccagttatac agcgagaaca ggagataagg gacgaacggc tgatacagga
     1681 gcgcgaacat gagttatccc tggagcgtga gcgccagccg gaaatacagg aatggacaca
     1741 ggatggccct tcgcttggat ggtaatcaga gacaggctaa aatgttgtca gcgcgtttcc
     1801 ggtgcatttt ttgggataat ggttggttcg ggggcaccgg gaacgcgctt cagtcagacc
     1861 ttgctgaaaa cacaggaacg cgttaaaacg catacgggcg cgattctggt gtgtcttttg
     1921 ttgctgtgtt ttgcctctat tgccagatcg cgctcattcc cctgaacttc tgttttcccg
     1981 ctccggtccc cgtcttcttc gcttccgaaa gcatgaaaaa aatccgtttc agctgtctct
     2041 ggctggcaat tcctgcgtga ttcacatggc tgcatagcta tgcatgtggt taaaatttac
     2101 cgggtgcgat cgcggcagtt tttcgggtgg tttgttgcca tttttacctg tctgctgccg
     2161 tgatcgcacc gaacgcgttt ctgcggtgcg ggcaacggat gttatggtaa ataggttcgt
     2221 ccggtatgct caatgaagat aagccagttt ttaactgatt cttttttcga tcgtttgaaa
     2281 caagaatagt atttggcaat agcggttgtc tttatctagc caagcacaat tagctagatc
     2341 tatgtaaccg ttattttgag acgatccata tccgatgacc gtcatcgctt ttgattctga
     2401 ctttaagtaa actatatcgc ctatattaaa tggcattttt ttatcctata aaaagccacc
     2461 tcacaggtgg cttttattta tgcatgattc cctttcgcta cgcgacgata catgccaata
     2521 tcacttatct cacttattgt gaactcggtt agatttttct ttgctgagct cccaggtctg
     2581 atttcaagag tatataacaa atcaagaagt tcttttctgc tatatttctg atcgtggaaa
     2641 tatgaataca gatcttcttt tgacatttcc atcagttctt caactgattt atgtgtcatt
     2701 ctccttgttg ctaaaataat ctcctcaacg agatcggagc gttttaattt gcttgggttc
     2761 tttggaagta aattaccaaa ggattcaatt agctcggcat tagtcatttc acttttatcc
     2821 aagccagctt tagctccctc aacgccaagc caagatatca gtttttggat atctatcatc
     2881 gacaagtcct cataaactca atcgtcaagt tcttaaactg tgacgcttgt ttgtaagcgt
     2941 tacttatctg tacatcatac actgaaacgc gctctgctgc agctactctt agcccatcac
     3001 cttccgttat gtagtgcttg aagatgtcac ctgcttgccg aagcctgttg tattcatatt
     3061 gctctgtttg cttcagttct tctgcatatt ctctggccat cattcccatt gctccggcga
     3121 aaactgtgtc cttatatgaa tcgccgactt gcagtgcctt tcttagcatt tcaatatctt
     3181 catttacatt atttatctca cctatgaccg tggccacacc aatagatgat tgcctgtcta
     3241 gttttaccgg tgatacacaa taatctgatg cgtagattat agagcgcatg acatcagaaa
     3301 cttcggggtg tgaatcaatc aatatgtagt cataattatc tgcaataggt gataatacag
     3361 cgcttatggt ttttaaatgc tgtaaaagaa tggcattgtt cgatcttata ttgtttgtac
     3421 taggtagctt atcagttgaa acggttgata agcgagggtc ggctggaatg acatcgatac
     3481 cactattaaa tttaattatg tctatgtcag tcgtttgttg tgccgcgcta tataattgct
     3541 gatacttgtt aaataacgtt gttccttgcg gtgcttgatt tccaaagttt tcgatcagtt
     3601 tagggaaaaa tcttccagtt atacctccgc gttgataatc tgcatctata actaaaacac
     3661 gtttttcatg aaaacgacta agtccttcgg caatgtgata acaggacgtt gttttaccaa
     3721 ccccaccttt ctcactaata aacccaactg tcacagccat ttttattcct tacaaatctc
     3781 ttttttttgg tagagggaac agcgtcaacg ctttccttga cgttcagtat aacgtcagcg
     3841 tactcttagc catcaaacga aaaaaaccga ctggggagtc ggttttttcg agggttcagt
     3901 aagttgggga acttctgaac cgtggtaaca gggtgtacaa gaccgctgaa accaaattct
     3961 gttattccag tttagcctct ctaaggctga tacttcaaga actctcactc agtaaatctt
     4021 gtacacccct ttactcatgg ctgctgccag tggcgctttg tcgtgtcttt ccgggttgga
     4081 ctcaagtcga tagttaccgg aacaggcgca gcagtcggac tgaacggggg gttcgtgcat
     4141 acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg gaatgagata
     4201 aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca
     4261 cgagggagcc accaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc
     4321 actgatttga gcgtcagatt tcgtgatgct tgtcaggggg gcggagccta tggaaaaacg
     4381 gcttcgccgc gaccctatcg cttccctgtt aagtatcttc ctggcatctt ccaggaaatc
     4441 tccgccccgt tcgtaagcca tttccgctcg ccgcagtcga acgaccgagc gtagcgagtc
     4501 agtgagcgag gaagcggaat atatcctgta tcacatattc tgctgacgct ccggtgccgc
     4561 cttttttctc ctgccacatg aagcactttc ctgatacccg cactcatgcc aacatagtaa
     4621 gccagtatac actccgctat cgctacgtga ctgggtcatg gctgcgcccc gacacccgca
     4681 aggtcaacgg cctgacgcgc cctgacgggc ttgtctgctc ccggcatccg ctcacagaca
     4741 agctgtgacc gtctccggga gctgtatgtg tcagaggttt tcaccgtcat ccccgaagcg
     4801 tgcgaggcag ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac agatgtctgc
     4861 ctgttcatcc gcgtccagtt cgttgagctt ttccagcagc gttaatgtct ggcttctgat
     4921 aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct ccgtgtaagg
     4981 ggggatttct gttcatgggg taatgatacc gatgaaacgc gagaggatgc tcacgatacg
     5041 ggttactgat gatgaacatg cacggttact ggaacgctgt gagggtaaac agctggcggt
     5101 atggatgcgg cgggtctgtc tgggtgag
//
