LOCUS       CP057081                5552 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB38-C24 plasmid pRHB38-C24_7, complete
            sequence.
ACCESSION   CP057081
VERSION     CP057081.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148394
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5552)
  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 5552)
  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                     :: RH04 T3-C24
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140.926036525725x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 05:31:07
            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)                     :: 5,830
            CDSs (total)                      :: 5,691
            Genes (coding)                    :: 5,293
            CDSs (with protein)               :: 5,293
            Genes (RNA)                       :: 139
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 398
            CDSs (without protein)            :: 398
            Pseudo Genes (ambiguous residues) :: 0 of 398
            Pseudo Genes (frameshifted)       :: 138 of 398
            Pseudo Genes (incomplete)         :: 233 of 398
            Pseudo Genes (internal stop)      :: 59 of 398
            Pseudo Genes (multiple problems)  :: 32 of 398
            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..5552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB38-C24"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB38-C24_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5434..5552,1..73))
                     /locus_tag="HVZ77_29065"
     CDS             complement(join(5434..5552,1..73))
                     /locus_tag="HVZ77_29065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017694268.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMC48072.1"
                     /translation="MKKLKELGFISCREGSTGEFHYVLIVHPLVAVKKLLDEGIIPKGK
                     TYNILSERVIEVGASWEG"
                     /name="hypothetical protein"
     gene            complement(766..930)
                     /locus_tag="HVZ77_29070"
     CDS             complement(766..930)
                     /locus_tag="HVZ77_29070"
                     /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="QMC48065.1"
                     /translation="MMDKDTTTLKRTLAHNRAFIDSINRSGIAWCYNTEIVLAACEAIE
                     AELQRRGCL"
                     /name="hypothetical protein"
     gene            complement(1365..1598)
                     /gene="mbeD"
                     /locus_tag="HVZ77_29075"
     CDS             complement(1365..1598)
                     /gene="mbeD"
                     /locus_tag="HVZ77_29075"
                     /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="QMC48066.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTEHLSQLYSENWR"
                     /name="mbeD"
     gene            complement(1605..2123)
                     /locus_tag="HVZ77_29080"
     CDS             complement(1605..2123)
                     /locus_tag="HVZ77_29080"
                     /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="QMC48067.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTTSTEESLKKHREGVKEAMMQHRKDVLKLAGNTGVMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGNRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(2101..2859)
                     /locus_tag="HVZ77_29085"
                     /pseudo=""
     CDS             complement(2101..2859)
                     /locus_tag="HVZ77_29085"
                     /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(2801..3124)
                     /locus_tag="HVZ77_29090"
     CDS             complement(2801..3124)
                     /locus_tag="HVZ77_29090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /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="QMC48068.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3190..3381
                     /locus_tag="HVZ77_29095"
     CDS             3190..3381
                     /locus_tag="HVZ77_29095"
                     /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="QMC48069.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4340..4906)
                     /locus_tag="HVZ77_29100"
     CDS             complement(4340..4906)
                     /locus_tag="HVZ77_29100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001178816.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="QMC48070.1"
                     /translation="MQNFGLAFRYPAHRLGGCDPRHQHPSLEVPVCADNISILFHMFVV
                     KLAYFLVFAGVYRLSFTLFVVISVYRFSLFFIGVHMKLLDSNEVCELLGISKSTLYRWC
                     GVSEDFSGLGLSSGLPQANALNSRLAKATQNSLGWENRLVRRELQQKALGVEETPSDFP
                     RPFKIGRSFKWKDAEIMAWLETRRV"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4939..5433)
                     /locus_tag="HVZ77_29105"
     CDS             complement(4939..5433)
                     /locus_tag="HVZ77_29105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000929317.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMC48071.1"
                     /translation="MAGTVWRDIRTGETVFPMGHLHPQRCCVDVNGTSVDIEISFGFHV
                     FTDEKQTGMLMKFKEEQRFFCRERYEGSKTIVHRILTAIENGEYITAFISKGQGQRYYH
                     LSHHDDFILMEIRKPQDRNNSLRIHVVTAYTLDEWGSINKGRNLRFRYVLEQRLQGKKI
                     V"
                     /name="hypothetical protein"
     Typing          complement(3460..3544)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          complement(3977..4207)
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.241"
                     /coverage="91.0"
                     /evalue="3.05e-87"
     Typing          complement(1268..2811)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2808..3157)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.436"
                     /coverage="99.0"
                     /evalue="1.4499999999999998e-68"
ORIGIN
        1 ttaacacgta atgaaattca ccggtgctgc cttcacgaca ggatatgaac cccagttctt
       61 ttaacttttt cattctccct gcccatgtag ttacgcctct ttcactagcg aaccctgatt
      121 caaaagccag tgctgcttta tctcttattt caaccaaacc ctcatcagaa accctgaacc
      181 ataaagccaa gtaggttgtt gataatggtg atccttttga cagaccatcc atgagatcgc
      241 ctatcaaagg caaataacgt ggaactgttg agtacccatc attttcaagt cgatgccaag
      301 tatcgatttc gtcgtcttcc cacaattttt caatcaaatc ctgacgtcgt tctgactgat
      361 ttctcttacc tgcttttctt gctcttgcgg acatagtcgt ctcccgtttg tctatggaca
      421 ctaatttatt aaaaaaaatc aataaaatca aagagttatt cattactggc agcttgttct
      481 catctgaaaa aatagagtta aaaacaagct aaatcgcaat aaacattaca tttaaaaata
      541 taaaaagtaa tatatattac aatgaagttg tttaattata tgattaataa tgatttataa
      601 gaggaaggcg gtgctcattg tgctcgttgt cctcgatggt tctccctgtg ctccttgtgc
      661 tccatggggt tgtagggggc aagccagggc ggatagagag aaaaataatt tagcggtagc
      721 gcgtctcaga gactaaaaaa cccgctgatg cgggttttct tattgttaca aacatcctcg
      781 ccgttgtagt tcggcttcaa tcgcctcaca agcagcgagt acaatctcag tgttatagca
      841 ccaggctatg ccactgcggt taatactatc gataaaggct cgattatgag ccaaagtgcg
      901 ttttagggtg gtggtatctt tgtccatcat caggatctcc attcaggtta acgagcttca
      961 tgctcccaga tatttactct tgccgttcct gaacaggcta aaatagcgaa aaaaagccta
     1021 ttttcgcttc atcccagagc accaatattt accataactc ccgttgcccg caccgccccg
     1081 gacagcttcg ccgcgaacgg ggcggcagtc agccaaaacc aacaacaaat cacccgaaaa
     1141 gctaccgcga tcgcgcctga taaattttaa ccgcatgaat acctatgcaa ccagatggtg
     1201 cagactacat tagcccgtca aaatccactg aatctgccat tttttatagt ttcgccatca
     1261 cagcgacaac gaaggaccat ccagtgtgcg ttcctgtatt tccagctggc gttcccgttc
     1321 cagggataac gcatgttcgc gctcctgtat cagccgttcc tctcttatct ccagttctcg
     1381 ctgtataact ggctcaagtg ttctgtccgc tcgctcaagt gctgtacctg ctgactcaac
     1441 tgcatgaccc gctcgttcag catcgcgttg tcccgttgcg taagcgaaaa catcttctgc
     1501 aattccacga aggcgctctc ccattcgttc agccgctgca tatagtcctg ttgcagttgc
     1561 tctaatgcgt tcagcaaatg tctttccagc tccgtcactc tgtgtcactc cgtcagttgt
     1621 acccagtcct tcccctgata gggaatcacc gttgccgatt tcccctgcgg gatgaccaga
     1681 aatttcctgt tcccgtcctg cacaaactcc acgccccatg tcttcgcgtt cagtttctgc
     1741 aatgtctctt cctgtatcct gatttcttcc aggttcgcct gtatccgccc gccaagatac
     1801 cagagcgtcc cgccactcgc ggtaaacagg agaaagacta tccccagtaa catcacgccc
     1861 gtattccctg ccagctttaa cacgtccttc cggtgctgca tcatcgcctc tttcacccct
     1921 tcccggtgtt ttttcagcga ttcctctgtc gacgttgtga acagggctat agcgtctctg
     1981 attttcgtct cgtttgatgt cacagcctcg cttacagatt cgccgagcct cctgaactcg
     2041 ttgttcagca ttttctctgt agattcggct ctctctttca gctttttctc gaactccgcg
     2101 cccgtctgta aaagattgct cataaaatgc tcctttcagc ctgatattcc tcccgccgtt
     2161 cgggtctgca atgctgatac tgcttcgcgt caccctgacc acttcaatcc ctgcctccgt
     2221 gagcgcctga atcacatcct gacggccttt tatctccccg acatgataaa gagcgtctat
     2281 cccgcgtgtg acgctctcag caagcgcctg tttcgtttcc ggcaggttat cagagagagt
     2341 cagtatccgg cggttctccg gggcgttggg gtcatgcagc ccgtaatggt gattcaccag
     2401 tgtctgccag gcatcaattc tcggcctgtc tgcccggtcg tagtacggct ggaggcgttt
     2461 tccggtctgt agctccatat tcggaatgac aaaattcagc tcaagccgtc ccttgtcctg
     2521 gtgctccacc cacaggatgc tgtactgatt tttttcgaga ccgggcatca gtacacgctc
     2581 aaagctcgcc atcacttttt cacgccctcc cggcggcagc tccttctccg cgaacgacag
     2641 aacacctgac gtgtatttct tcgcaaatgg cgtggcatcg atgagttccc tgacttcttc
     2701 cggattaccc tgaagcaccg ttgcgccttc gcgattacgc tccctcccca gcaggtaatc
     2761 aaccggacca ctgccaccac cttttcccct ggcatgaaat ttaacaatca tcccgcgccc
     2821 cctgttccct gacggccaga cgcagccggc gcagctcatc cccgatggcc atcagtgcgg
     2881 ccaccacctg aacccggtcg ccggaagacc actgcccgct gttcaccttc ctcgccgtct
     2941 gattcaggtt attcccgatg gcggccaact gacgcagtaa cggcggagcc aaagttggca
     3001 gcttcccgga acgggcaacc ggctcaccca ggcagacccg ccgcatccat accgccagtt
     3061 gtttaccctc acagcgttcc agtaaccggg catgttcatc atcagtaacc cgtatcgtga
     3121 gcatcctctc gcgtttcatc ggtatcatta cccccatgaa cagaaatccc cccttacacg
     3181 gaggcatcag tgactaaaca ggaaaaaact gcccttaaca tggcccgctt tatcagaagc
     3241 cagacattaa cgctgctgga gaaactcaac gaactggacg cggatgaaca ggcagatatc
     3301 tgtgaatcgc ttcacgacca cgccgatgag ctttaccgca gctgcctcgc gcgcttcggg
     3361 gatgacggtg aaaacctctg acacatacag ctcccggaga cggtcacagc ttgcctgtga
     3421 gcggataccg ggagcagaca agcccgtcag ggcgcgtcag ggggtttcgg ggcgaagccc
     3481 tgaaccagtc acgtagcgat agcggagtgt atactggctt aaccatgcgg catcagtgca
     3541 gattgtaaga aaagagcacc atatgcggtg tgaaatgccg cacagatgcg taaggagaaa
     3601 atgcacgttc cggcgctctt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg
     3661 gctgcggcga gcggtgtcgg ctcactcaaa gacggtaatg cggttatcca cagaatcagg
     3721 ggataacgcc aaaagaaaca tgtgagcaaa aaacaagaac ccggaaaagg ccacgccgct
     3781 ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac gctcaagtca
     3841 gaggtggcga aacccgacag gacttaaaga taccaggcgt ttccccctgg cggctccctc
     3901 ttgcgctctc ctgttcccgt cctgcggcat ccgtgttgtg gtggaagctt tacctaaatc
     3961 accacgtccc gttccgttta gacagttcgc tccaagctgg gctgtgtgca agaacccccc
     4021 gttcagcccg actaccacgt tgtcccggta actatcatct tgagtccaac ccggaacaga
     4081 cacgaaaaat cgccagtggc ggtagccatt ggtaaacagg atgtgcgaga gatgtattca
     4141 aagttcttga agtggtggcc ttagtgaggc tacactgaaa ggacagattt ggtgacacgt
     4201 ctcgcacaag gctgttacca cggttattca atctgccagg attaaataac cttcgaaaaa
     4261 ccacctgcca tggtggtttt ttcgtttaca ggacaaaaga ctacgacgag atccaaatga
     4321 tctcaagaag atctatcaat caaacgcgtc gcgtttcaag ccaagccata atttcggcgt
     4381 ctttccattt aaacgaacga ccgatcttga aaggacgagg gaagtcgctt ggcgtctctt
     4441 cgacaccgag agctttttgc tgtaattccc tcctaacgag cctattttcc cagcctaaag
     4501 agttctgagt agccttagcc agccggctat tcaaagcgtt agcctgagga agaccgctac
     4561 ttagacccaa gccagaaaaa tcctcagaca ccccgcacca acgatacaaa gtggacttac
     4621 tgatgcctaa gagctcacac acttcattac tatcaagcaa cttcatatga acacctataa
     4681 aaaacaatga aaacctataa acacttataa ccacaaagag ggtaaatgac aacctataaa
     4741 caccagcgaa caccaaaaag tacgctagtt tgacaacgaa catgtggaat aggatactaa
     4801 tgttgtcagc acaaaccgga acctcgagag aggggtgctg atgccggggg tcacaccctc
     4861 ccagcctgtg agcgggataa cgaaaggcca gaccgaaatt ctgcaaaaaa caaaggcgcc
     4921 ttaggcgctt tttgtttttt acacaatctt ctttccctgc agtcgctgtt ccagcacata
     4981 tctaaaccgc aggttacgtc ctttatttat actcccccat tcatcaagcg tgtaagctgt
     5041 aacaacatga atacgcaaag aattatttct atcttgaggc tttcttattt ccatcaaaat
     5101 gaagtcatca tgatggctaa gatggtaata ccgctgcccc tgcccctttg aaataaatgc
     5161 tgtaatgtat tcaccgtttt ctatcgctgt aagtattctg tgaacgatag ttttgctgcc
     5221 ctcatagcgt tccctacaaa aaaacctctg ttcctcctta aatttcatca gcattccggt
     5281 ttgtttttca tcagtaaaaa catgaaaacc aaaactaatt tctatatcta cagaagtacc
     5341 gtttacatca acacagcacc tctgagggtg caggtgcccc ataggaaaaa cagtctctcc
     5401 cgttcttatg tcacgccata ctgtgcccgc catttaaccc tcccaagagg ctcccacctc
     5461 aattacacgc tccgacaaaa tgttataagt ctttccttta gggataatcc cttcatcaag
     5521 cagctttttg actgcaacta atgggtgaac aa
//
