LOCUS       CP057310                5775 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C09 plasmid pRHB30-C09_9, complete
            sequence.
ACCESSION   CP057310
VERSION     CP057310.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148293
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5775)
  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 5775)
  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-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132.647008810688x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:59:30
            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)                     :: 5,680
            CDSs (total)                      :: 5,553
            Genes (coding)                    :: 5,179
            CDSs (with protein)               :: 5,179
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 374
            CDSs (without protein)            :: 374
            Pseudo Genes (ambiguous residues) :: 0 of 374
            Pseudo Genes (frameshifted)       :: 134 of 374
            Pseudo Genes (incomplete)         :: 213 of 374
            Pseudo Genes (internal stop)      :: 59 of 374
            Pseudo Genes (multiple problems)  :: 31 of 374
            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..5775
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB30-C09"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C09_9"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(141..443)
                     /locus_tag="HVY76_28360"
     CDS             complement(141..443)
                     /locus_tag="HVY76_28360"
                     /inference="COORDINATES: protein motif:HMM:NF024139.1"
                     /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="QMF75903.1"
                     /translation="MKLLDSNEVCELLGISKSTLYRWCGVSEDFSGLGLSSGLPQANAT
                     QNSLGRENRLVRRELQQNALGVEETPSDFPRPFKIGRSFKWKDAEIMAWLETRRV"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(716..1210)
                     /locus_tag="HVY76_28365"
     CDS             complement(716..1210)
                     /locus_tag="HVY76_28365"
                     /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="QMF75904.1"
                     /translation="MAGTVWRDIRTGETVFPMGHLHPQRCCVDVNGTSVDIEISFGFHV
                     FTDEKQTGMLMKFKEEQRFFCRERYEGSKTIVHRILTAIENGEYITAFISKGQGQRYYH
                     LSHHDDFILMEIRKPQDRNNSLRIHVVTAYTLDEWGTVNKGRNLRFRYVLEQRLQGKKI
                     V"
                     /name="hypothetical protein"
     gene            complement(1211..1636)
                     /locus_tag="HVY76_28370"
     CDS             complement(1211..1636)
                     /locus_tag="HVY76_28370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640499.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMF75909.1"
                     /translation="MDTWHRLENDGYSTVPRYLPLIGDLMDGLSKGSPLSTTYLALWFR
                     VSDEGLIEIRDKAALAFESGFASERGVTTWAGRMKKLKELGFISCREGSTGEFHYVLIV
                     HPLVAVKKLLDEGIIPKGKTYNILSERVIEVGASWEG"
                     /name="hypothetical protein"
     gene            complement(2094..2258)
                     /locus_tag="HVY76_28375"
     CDS             complement(2094..2258)
                     /locus_tag="HVY76_28375"
                     /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="QMF75902.1"
                     /translation="MMDKDTTTLKRTLAHNRAFSDNINRSGIAWCYNTEIVLAACEAIE
                     AELQRRGCL"
                     /name="hypothetical protein"
     gene            complement(2929..3162)
                     /gene="mbeD"
                     /locus_tag="HVY76_28380"
     CDS             complement(2929..3162)
                     /gene="mbeD"
                     /locus_tag="HVY76_28380"
                     /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="QMF75905.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(3169..3687)
                     /locus_tag="HVY76_28385"
     CDS             complement(3169..3687)
                     /locus_tag="HVY76_28385"
                     /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="QMF75906.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(3665..4387)
                     /locus_tag="HVY76_28390"
                     /pseudo=""
     CDS             complement(3665..4387)
                     /locus_tag="HVY76_28390"
                     /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(4365..4688)
                     /locus_tag="HVY76_28395"
     CDS             complement(4365..4688)
                     /locus_tag="HVY76_28395"
                     /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="QMF75907.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4753..4944
                     /locus_tag="HVY76_28400"
     CDS             4753..4944
                     /locus_tag="HVY76_28400"
                     /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="QMF75908.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(5037..5120)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
     Typing          complement(5553..5773)
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.892"
                     /coverage="87.0"
                     /evalue="1.1e-81"
     Typing          complement(2826..4375)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctcgcacaa ggctgttacc acggttattc aatctgccag gattaaataa ccttcgaaaa
       61 accacctgcc atggtggttt tttcgtttac aggacaaaag actacgacga gatccaaatg
      121 atctcaagaa gatctatcaa tcaaacgcgt cgcgtttcaa gccaagccat aatttcggcg
      181 tctttccatt taaacgaacg accgatcttg aaaggacgag ggaagtcgct tggcgtctct
      241 tcgacaccga gagcgttttg ctgtaattcc ctcctaacga gcctattttc cctgcctaaa
      301 gagttctgag tagcgttagc ctgaggaaga ccgctactta gacccaagcc agaaaaatcc
      361 tcagacaccc cgcaccaacg atacaaagtg gacttactga tgcctaagag ctcacacact
      421 tcattactat caagcaactt catatgaaca cctataaaaa acaatgaaaa cctataaaca
      481 cttataacca caaagagggt aaatgacaac ctataaacac caatgaacac caaaaagtac
      541 gctagtttga caacgaacat gtggaatagg atactaatgt tgtcagcaca aaccggaacc
      601 tcgagagagg ggtgctgatg ccgggggtca caccctccca gcctgtgagc gggataacga
      661 aaggccagac cgaaattctg caaaaaacaa aggcgcctta ggcgcttttt gttttttaca
      721 caatcttctt tccctgcagt cgctgttcca gcacatatct aaaccgcagg ttacgtcctt
      781 tatttacagt cccccattca tcaagcgtgt aagctgtaac aacatgaata cgcaaagaat
      841 tatttctatc ttgaggcttt cttatttcca tcaaaatgaa gtcatcatga tggctaagat
      901 ggtaataccg ctgcccctgc ccctttgaaa taaatgctgt aatgtattca ccgttttcta
      961 tcgctgtaag tattctgtga acgatagttt tgctgccctc atagcgttcc ctacaaaaaa
     1021 acctctgttc ctccttaaat ttcatcagca ttccggtttg tttttcatca gtaaaaacat
     1081 gaaaaccaaa actaatttct atatctacag aagtaccgtt tacatcaaca cagcacctct
     1141 gagggtgcag gtgccccata ggaaaaacag tctctcccgt tcttatgtca cgccatactg
     1201 tgcccgccat ttacccctcc caagaggctc ccacctcaat tacacgctcc gacaaaatgt
     1261 tataagtctt tcctttaggg ataatccctt catcaagcag ctttttgact gcaactaatg
     1321 ggtgaacaat taacacgtaa tgaaattcac cggtgctgcc ttcacgacag gatatgaacc
     1381 ccagttcttt tagctttttc attctccctg cccatgtagt tacgcctctt tcactagcga
     1441 accctgattc aaaagccagt gctgctttat ctcttatttc aatcaacccc tcatcagaaa
     1501 ccctgaacca taaagccaag taggttgttg ataatggtga tccttttgac agaccatcca
     1561 tgagatcgcc tatcaaaggc aaataacgtg gaactgttga gtacccatca ttttcaagtc
     1621 gatgccaagt atcgatttcg tcgtcttccc acaatttttc aatcaaatcc tgacgtcgtt
     1681 ctgactgatt tctcttacct gcttttcttg ctcttgcgga catagtcgtc tcccgtttgt
     1741 ctatggacac taatttattg aaaaaaccaa taaaatcaaa tagttattca ttgctggcag
     1801 cttgttctca tctgaaaaaa tagagttaaa aacaagctaa atcgcaataa acattacatt
     1861 taaaaacata aaaagtaata tatattacaa tgaagttgtt taattatatg attaataatg
     1921 atttataaga ggaaggcggt gctcattgtg ctcgttgtgc tcgatggttc tccctgtgct
     1981 ccttgtgctc catggggttg tagggggcaa gccagggcgg atagagagaa aaataattta
     2041 gcggtagcgc gtctcagaga ctaaaaaacc cgctgatgcg ggttttctta ttgttacaaa
     2101 catcctcgcc gttgtagttc ggcttcaatc gcctcacaag cagcgagtac aatctcagtg
     2161 ttatagcacc aggctatgcc actgcggtta atattatcgc taaaggctcg attatgagcc
     2221 aaagtgcgtt ttagggtggt ggtatctttg tccatcatca ggatctccat tcaggttaac
     2281 gagcttcatg ctcccagata tttactcttg ccgttcctga acaggctaaa atagcgaaaa
     2341 aaagcctatt ttcgcttcat cccagagcac caatatttac cataacatcc gttgcccgca
     2401 ccgcagaaac gcgttcggtg cgatcacggc agcagacagg taaaaatggc aacaaaccac
     2461 ccgaaaaact gccgcgatcg cacccggtaa attttaacca catgcatagc tatgcagcca
     2521 tgtgaatcac gcaggaattg ccagccagag acagctgaaa cggatttttt tcatgctttc
     2581 ggaagcgaag aagacgggga ccggagcggg aaaacagaag ttcaggggaa tgagcgcgat
     2641 ctggcaatag aggcaaaaca cagcaacaaa agacacacca gaatcgcgcc cgtatgcgtt
     2701 ttaacgcgtt cctgtgtttt cagcaaggtc tgactgaagc gcgttcccgg tgcccccgaa
     2761 ccaaccatta tcccaaaaaa tgcaccggaa acgcgctgac aacattttag cctgtctctg
     2821 attaccatcc aagcgaaggg ccatcctgtg tccattcctg tatttccggc tggcgctcac
     2881 gctccaggga taacgcatgt tcgcgctcct gtatcagccg ttcgtccctt atctcctgtt
     2941 ctcgctgtat aactggctca agcgttctgt ccgctcgctc aagtgctgca cctgctgact
     3001 caactgcatg acctgctcgt tcagcatcgc gttgtcccgt tgcgtaagcg aaaacatttt
     3061 ctgcaattcc acgaaggcgc tctcccattc gctcagccgc tgcatatagt cctgttgcag
     3121 ttgctctaag gcgttcagca aatgtctttc cagctccgtc actctgtgtc actccgtcag
     3181 ttgtacccag tccttctcct gatagggaat caccgttgcc gatttcccgt acggaaggac
     3241 cagaaatttc cttctcccgt cctgcacaaa ctccacgccc catgtcttcg cgttcagttt
     3301 ctgcaatgtt tcttcctgta tcctgatttc ttccaggttc gcctgtatcc gcccgccaag
     3361 ataccagagc gtcccgccac tcacggtaaa caggaaaagg accatcccca gtaacatcat
     3421 gcccgtattc cctgccagct ttaacacgtc cttcctgtgc tgcatcatcg cctctttcac
     3481 cccttcccgg tgttttttca gtgattcctc tgtcgaagct gtgaacaggg ctatagcgtc
     3541 tttgattttc gtctcgtttg atgtcacagc cttgcttaca gatttttcga gcttgctgaa
     3601 ctcgtcgttc agcattgtct ctgtagattc ggctctctct ttcagctttt tctcgaactc
     3661 cgcgcccgtc tgtaaaagat tgctcataga atgctccttt cagtctgata ttcttcccgc
     3721 cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct gaccacttca agccctgcct
     3781 ctgtgagcgc ctgaatcaca tcctgacggc cttttatctc cccgacatga taaagagcgt
     3841 ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt ttccggcagg ttatcaggga
     3901 gagtcagtat ccggcggttc tccggggcgt tggggtcatg cagcccgtaa tggtgattaa
     3961 ccagcgtctg ccaggcatca attctcggcc tgtctgcccg gtcgtagtac ggctggaggc
     4021 gttttccgct ctgtagctcc atgttcggaa tgacaaaatt cagctcaagc cgtcccttgt
     4081 cctggtgctc cacccacagg atgctgtact gatttttttc gagaccgggc atcagtacac
     4141 gctcaaagct cgccatcacc ttttcacgtc ctcccggcgg cagctccttc tccgcgaacg
     4201 acagaacacc tgacgtgtat ttcttcgcaa atggcgtggc atcgatgagt tcccggactt
     4261 cttccggatt accctgaagc accgttgccc cttcccggtt acgctccctt cccagcaggt
     4321 aatcaaccgg accactgcca ccgccttttc ccctggcatg aaacttaact atcatcccgc
     4381 gctccatgtt ccctgacgac ctgccgtaag ctgcgcaact ctctctcgat ggccatcagt
     4441 gcggccacca cctgaacccg gtcaccggaa gaccactgcc cgctgttcac cttcctcgcc
     4501 gtctgattca gattattccc gatggcagcc agctggcgca gtaacggcgg tgccagtgtc
     4561 ggcagcttcc cggaacgggc aaccggctca cccagacaga cccgccgcat ccataccgcc
     4621 agctgtttac cctcacagcg ttccagtaac cgtgcatgtt catcatcagt aacccgtatc
     4681 gtgagcatcc tctcgcgttt catcggtatc attaccccat gaacagaaat ccccccttac
     4741 acggaggcat cagtgactaa acaggaaaaa accgccctta acatggcccg ctttatcaga
     4801 agccagacat taacgctgct ggaaaagctc aacgaactgg acgcggatga acaggcagac
     4861 atctgtgaat cgcttcacga ccacgccgat gagctttacc gcagctgcct cgcacgcttc
     4921 ggggatgacg gtgaaaacct ctgacacata cagctcccgg agacggtcac agcttgtctg
     4981 tgagcggatg ccgggagcag acaagcccgt cagggcgcgt caggccgttg accttgcggg
     5041 tgtcggggcg cagccatgac ccagtcacgt agcgatagcg gagtgtatac tggcttaacc
     5101 atgcggcatc agtgcggatt gtatgaaaag tgcgccatgc cgggtgtgaa atgccgcaca
     5161 gatgtgtaag gagaaaatgc aacttccgac gctcttccgc ttcctcgctc actgactcgc
     5221 tacgctcggt cgttcggctg cggcgagcgg tatcagctca ctcaaagacg gtaatgcggt
     5281 tatccacaga atcaggggat aacaccaaaa gaaacatgtg agcaaaaaac aagaacccag
     5341 agaaggccac gccgctggcg tttttccata ggctccgccc ccctgacgag catcacaaaa
     5401 atcgacgctc aagtcagagg tggcgaaacc cgacaggact taaagatacc aggcgtttcc
     5461 ccctggcggc tccctcttgc gctctcctgt tcccgtcctg cggcatccgt gttgtggtgg
     5521 aagctttacc taaatcacca cgtcccgttc cgtttagaca gttcgctcca agctgggctg
     5581 tatgcaagaa ccccccgttc agcccgacta ccacgttgtc ccggtaacta tcatcttgag
     5641 tccaacccgg aacagacacg aaaaatcgcc agtggcggta gccattggta aacaggatgt
     5701 gcgagagatg tattcaaagt tcttgaagtg gtggccttag tgaggctaca ctgaaaggac
     5761 agatttggtg acacg
//
