LOCUS       CP055673                5128 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C19 plasmid pRHB30-C19_5, complete
            sequence.
ACCESSION   CP055673
VERSION     CP055673.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148297
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-C19
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 168.684881854874x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/18/2020 16:37:18
            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)                     :: 5,187
            CDSs (total)                      :: 5,063
            Genes (coding)                    :: 4,824
            CDSs (with protein)               :: 4,824
            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)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 71 of 239
            Pseudo Genes (incomplete)         :: 153 of 239
            Pseudo Genes (internal stop)      :: 35 of 239
            Pseudo Genes (multiple problems)  :: 19 of 239
            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-C19"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C19_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4997..5128,1..753))
                     /locus_tag="HVY80_25875"
     CDS             complement(join(4997..5128,1..753))
                     /locus_tag="HVY80_25875"
                     /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="QLN07919.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     gene            complement(1002..1133)
                     /locus_tag="HVY80_25880"
     CDS             complement(1002..1133)
                     /locus_tag="HVY80_25880"
                     /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="QLN07913.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="replication initiation protein"
     gene            complement(1764..1955)
                     /locus_tag="HVY80_25885"
     CDS             complement(1764..1955)
                     /locus_tag="HVY80_25885"
                     /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="QLN07914.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2020..2343
                     /locus_tag="HVY80_25890"
     CDS             2020..2343
                     /locus_tag="HVY80_25890"
                     /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="QLN07920.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2321..3043
                     /locus_tag="HVY80_25895"
                     /pseudo=""
     CDS             2321..3043
                     /locus_tag="HVY80_25895"
                     /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            3021..3539
                     /locus_tag="HVY80_25900"
     CDS             3021..3539
                     /locus_tag="HVY80_25900"
                     /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="QLN07915.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            3546..3779
                     /gene="mbeD"
                     /locus_tag="HVY80_25905"
     CDS             3546..3779
                     /gene="mbeD"
                     /locus_tag="HVY80_25905"
                     /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="QLN07916.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(4372..4557)
                     /locus_tag="HVY80_25910"
     CDS             complement(4372..4557)
                     /locus_tag="HVY80_25910"
                     /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="QLN07917.1"
                     /translation="MPFNIGDIVYLKSESKAMTVIGYGSSQNNGYIDLANCAWLDKDNR
                     YCQILFLFQTIEKRIS"
                     /name="DUF2158 domain-containing protein"
     gene            complement(4599..5000)
                     /locus_tag="HVY80_25915"
     CDS             complement(4599..5000)
                     /locus_tag="HVY80_25915"
                     /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="QLN07918.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     Typing          1496..1669
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          complement(986..1572)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.723"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2334..3883
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatgtagtgc ttgaagatgt cacctgcttg ccgaagcctg ttgtattcat attgctctgt
       61 ttgcttcagt tcttctgcat attctctggc catcattccc attgctccgg cgaaaactgt
      121 gtccttatat gaatcgccga cttgcagtgc ctttcttagc atttcaatat cttcatttac
      181 attatttatc tcacctatga ccgtggccac accaatagat gattgcctgt ctagttttac
      241 cggtgataca caataatctg atgcgtagat tatagagcgc atgacatcag aaacttcggg
      301 gtgtgaatca atcaatatgt agtcataatt atctgcaata ggtgataata cagcgcttat
      361 ggtttttaaa tgctgtaaaa gaatggcatt gttcgatctt atattgtttg tactaggtag
      421 cttatcagtt gaaacggttg ataagcgagg gtcggctgga atgacatcga taccactatt
      481 aaatttaatt atgtctatgt cagtcgtttg ttgtgccgcg ctatataatt gctgatactt
      541 gttaaataac gttgttcctt gcggtgcttg atttccaaag ttttcgatca gtttagggaa
      601 aaatcttcca gttatacctc cgcgttgata atctgcatct ataactaaaa cacgtttttc
      661 atgaaaacga ctaagtcctt cggcaatgtg ataacaggac gttgttttac caaccccacc
      721 tttctcacta ataaacccaa ctgtcacagc catttttatt ccttacaaat ctcttttttt
      781 tggtagaggg aacagcgtca acgctttcct tgacgttcag tataacgtca gcgtactctt
      841 agccatcaaa cgaaaaaaac cgactgggga gtcggttttt tcgagggttc agtaagttgg
      901 ggaacttctg aaccgtggta acagggtgta caagaccgct gaaaccaaat tctgttattc
      961 cagtttagcc tctctaaggc tgatacttca agaactctca ctcagtaaat cttgtacacc
     1021 cctttactca tggctgctgc cagtggcgct ttgtcgtgtc tttccgggtt ggactcaagt
     1081 cgatagttac cggaacaggc gcagcagtcg gactgaacgg ggggttcgtg catacagtcc
     1141 agcttggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag ataaacgcgg
     1201 ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga
     1261 gccaccaggg ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc accactgatt
     1321 tgagcgtcag atttcgtgat gcttgtcagg ggggcggagc ctatggaaaa acggcttcgc
     1381 cgcgacccta tcgcttccct gttaagtatc ttcctggcat cttccaggaa atctccgccc
     1441 cgttcgtaag ccatttccgc tcgccgcagt cgaacgaccg agcgtagcga gtcagtgagc
     1501 gaggaagcgg aatatatcct gtatcacata ttctgctgac gctccggtgc cgcctttttt
     1561 ctcctgccac atgaagcact ttcctgatac ccgcactcat gccaacatag taagccagta
     1621 tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc gcaaggtcaa
     1681 cggcctgacg cgccctgacg ggcttgtctg ctcccggcat ccgctcacag acaagctgtg
     1741 accgtctccg ggagctgtat gtgtcagagg ttttcaccgt catccccgaa gcgtgcgagg
     1801 cagctgcggt aaagctcatc ggcgtggtcg tgaagcgatt cacagatgtc tgcctgttca
     1861 tccgcgtcca gttcgttgag cttttccagc agcgttaatg tctggcttct gataaagcgg
     1921 gccatgttaa gggcggtttt ttcctgttta gtcactgatg cctccgtgta aggggggatt
     1981 tctgttcatg gggtaatgat accgatgaaa cgcgagagga tgctcacgat acgggttact
     2041 gatgatgaac atgcacggtt actggaacgc tgtgagggta aacagctggc ggtatggatg
     2101 cggcgggtct gtctgggtga gccggttgcc cgttccggga agctgccgac actggcaccg
     2161 ccgttactgc gccagctggc tgccatcggg aataatctga atcagacggc gaggaaggtg
     2221 aacagcgggc agtggtcttc cggtgaccgg gttcaggtgg tggccgcact gatggccatc
     2281 gagagagagt tgcgcagctt acggcaggtc gtcagggaac atggagcgcg ggatgatagt
     2341 taagtttcat gccaggggaa aaggcggtgg cagtggtccg gttgattacc tgctgggaag
     2401 ggagcgtaac cgggaagggg caacggtgct tcagggtaat ccggaagaag tccgggaact
     2461 catcgatgcc acgccatttg cgaagaaata cacgtcaggt gttctgtcgt tcgcggagaa
     2521 ggagctgccg ccgggaggac gtgaaaaggt gatggcgagc tttgagcgtg tactgatgcc
     2581 cggtctcgaa aaaaatcagt acagcatcct gtgggtggag caccaggaca agggacggct
     2641 tgagctgaat tttgtcattc cgaacatgga gctacagagc ggaaaacgcc tccagccgta
     2701 ctacgaccgg gcagacaggc cgagaattga tgcctggcag acgctggtta atcaccatta
     2761 cgggctgcat gaccccaacg ccccggagaa ccgccggata ctgactctcc ctgataacct
     2821 gccggaaacg aaacaggcgc ttgcagagag cgtcacacgc gggatagacg ctctttatca
     2881 tgtcggggag ataaaaggcc gtcaggatgt gattcaggcg ctcacagagg cagggcttga
     2941 agtggtcagg gtgacgcgaa gcagtatcag cattgcagac ccgaacggcg ggaagaatat
     3001 cagactgaaa ggagcattct atgagcaatc ttttacagac gggcgcggag ttcgagaaaa
     3061 agctgaaaga gagagccgaa tctacagaga caatgctgaa cgacgagttc agcaagctcg
     3121 aaaaatctgt aagcaaggct gtgacatcaa acgagacgaa aatcaaagac gctatagccc
     3181 tgttcacagc ttcgacagag gaatcactga aaaaacaccg ggaaggggtg aaagaggcga
     3241 tgatgcagca caggaaggac gtgttaaagc tggcagggaa tacgggcatg atgttactgg
     3301 ggatggtcct tttcctgttt accgtgagtg gcgggacgct ctggtatctt ggcgggcgga
     3361 tacaggcgaa cctggaagaa atcaggatac aggaagaaac attgcagaaa ctgaacgcga
     3421 agacatgggg cgtggagttt gtgcaggacg ggagaaggaa atttctggtc cttccgtacg
     3481 ggaaatcggc aacggtgatt ccctatcagg agaaggactg ggtacaactg acggagtgac
     3541 acagagtgac ggagctggaa agacatttgc tgaacgcctt agagcaactg caacaggact
     3601 atatgcagcg gctgagcgaa tgggagagcg ccttcgtgga attgcagaaa atgttttcgc
     3661 ttacgcaacg ggacaacgcg atgctgaacg agcaggtcat gcagttgagt cagcaggtgc
     3721 agcacttgag cgagcggaca gaacgcttga gccagttata cagcgagaac aggagataag
     3781 ggacgaacgg ctgatacagg agcgcgaaca tgagttatcc ctggagcgtg agcgccagcc
     3841 ggaaatacag gaatggacac aggatggccc ttcgcttgga tggtaatcag agacaggcta
     3901 aaatgttgtc agcgcgtttc cggtgcattt tttgggataa tggttggttc gggggcaccg
     3961 ggaacgcgct tcagtcagac cttgctgaaa acacaggaac gcgttaaaac gcatacgggc
     4021 gcgattctgg tgtgtctttt gttgctgtgt tttgcctcta ttgccagatc gcgctcattc
     4081 ccctgaactt ctgttttccc gctccggtcc ccgtcttctt cgcttccgaa agcatgaaaa
     4141 aaatccgttt cagctgtctc tggctggcaa ttcctgcgtg attcacatgg ctgcatagct
     4201 atgcatgtgg ttaaaattta ccgggtgcga tcgcggcagt ttttcgggtg gtttgttgcc
     4261 atttttacct gtctgctgcc gtgatcgcac cgaacgcgtt tctgcggtgc gggcaacgga
     4321 tgttatggta aataggttcg tccggtatgc tcaatgaaga taagccagtt tttaactgat
     4381 tcttttttcg atcgtttgaa acaagaatag tatttggcaa tagcggttgt ctttatctag
     4441 ccaagcacaa ttagctagat ctatgtaacc gttattttga gacgatccat atccgatgac
     4501 cgtcatcgct tttgattctg actttaagta aactatatcg cctatattaa atggcatttt
     4561 tttatcctat aaaaagccac ctcacaggtg gcttttattt atgcatgatt ccctttcgct
     4621 acgcgacgat acatgccaat atcacttatc tcacttattg tgaactcggt tagatttttc
     4681 tttgctgagc tcccaggtct gatttcaaga gtatataaca aatcaagaag ttcttttctg
     4741 ctatatttct gatcgtggaa atatgaatac agatcttctt ttgacatttc catcagttct
     4801 tcaactgatt tatgtgtcat tctccttgtt gctaaaataa tctcctcaac gagatcggag
     4861 cgttttaatt tgcttgggtt ctttggaagt aaattaccaa aggattcaat tagctcggca
     4921 ttagtcattt cacttttatc caagccagct ttagctccct caacgccaag ccaagatatc
     4981 agtttttgga tatctatcat cgacaagtcc tcataaactc aatcgtcaag ttcttaaact
     5041 gtgacgcttg tttgtaagcg ttacttatct gtacatcata cactgaaacg cgctctgctg
     5101 cagctactct tagcccatca ccttccgt
//
