LOCUS       CP057285                5128 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB30-C17 plasmid pRHB30-C17_5, complete
            sequence.
ACCESSION   CP057285
VERSION     CP057285.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148296
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-C17
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 142.37324793805x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 07:16:45
            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)                     :: 5,196
            CDSs (total)                      :: 5,072
            Genes (coding)                    :: 4,832
            CDSs (with protein)               :: 4,832
            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-C17"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB30-C17_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4765..5128,1..521)
                     /locus_tag="HVY79_25920"
     CDS             join(4765..5128,1..521)
                     /locus_tag="HVY79_25920"
                     /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="QMF60694.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     gene            518..919
                     /locus_tag="HVY79_25925"
     CDS             518..919
                     /locus_tag="HVY79_25925"
                     /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="QMF60695.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            961..1146
                     /locus_tag="HVY79_25930"
     CDS             961..1146
                     /locus_tag="HVY79_25930"
                     /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="QMF60696.1"
                     /translation="MPFNIGDIVYLKSESKAMTVIGYGSSQNNGYIDLANCAWLDKDNR
                     YCQILFLFQTIEKRIS"
                     /name="DUF2158 domain-containing protein"
     gene            complement(1739..1972)
                     /gene="mbeD"
                     /locus_tag="HVY79_25935"
     CDS             complement(1739..1972)
                     /gene="mbeD"
                     /locus_tag="HVY79_25935"
                     /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="QMF60697.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(1979..2497)
                     /locus_tag="HVY79_25940"
     CDS             complement(1979..2497)
                     /locus_tag="HVY79_25940"
                     /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="QMF60698.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(2475..3197)
                     /locus_tag="HVY79_25945"
                     /pseudo=""
     CDS             complement(2475..3197)
                     /locus_tag="HVY79_25945"
                     /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(3175..3498)
                     /locus_tag="HVY79_25950"
     CDS             complement(3175..3498)
                     /locus_tag="HVY79_25950"
                     /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="QMF60701.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3563..3754
                     /locus_tag="HVY79_25955"
     CDS             3563..3754
                     /locus_tag="HVY79_25955"
                     /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="QMF60699.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4385..4516
                     /locus_tag="HVY79_25960"
     CDS             4385..4516
                     /locus_tag="HVY79_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="QMF60700.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="replication initiation protein"
     Typing          complement(3850..4023)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          3947..4533
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.723"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(1636..3185)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgccattct tttacagcat ttaaaaacca taagcgctgt attatcacct attgcagata
       61 attatgacta catattgatt gattcacacc ccgaagtttc tgatgtcatg cgctctataa
      121 tctacgcatc agattattgt gtatcaccgg taaaactaga caggcaatca tctattggtg
      181 tggccacggt cataggtgag ataaataatg taaatgaaga tattgaaatg ctaagaaagg
      241 cactgcaagt cggcgattca tataaggaca cagttttcgc cggagcaatg ggaatgatgg
      301 ccagagaata tgcagaagaa ctgaagcaaa cagagcaata tgaatacaac aggcttcggc
      361 aagcaggtga catcttcaag cactacataa cggaaggtga tgggctaaga gtagctgcag
      421 cagagcgcgt ttcagtgtat gatgtacaga taagtaacgc ttacaaacaa gcgtcacagt
      481 ttaagaactt gacgattgag tttatgagga cttgtcgatg atagatatcc aaaaactgat
      541 atcttggctt ggcgttgagg gagctaaagc tggcttggat aaaagtgaaa tgactaatgc
      601 cgagctaatt gaatcctttg gtaatttact tccaaagaac ccaagcaaat taaaacgctc
      661 cgatctcgtt gaggagatta ttttagcaac aaggagaatg acacataaat cagttgaaga
      721 actgatggaa atgtcaaaag aagatctgta ttcatatttc cacgatcaga aatatagcag
      781 aaaagaactt cttgatttgt tatatactct tgaaatcaga cctgggagct cagcaaagaa
      841 aaatctaacc gagttcacaa taagtgagat aagtgatatt ggcatgtatc gtcgcgtagc
      901 gaaagggaat catgcataaa taaaagccac ctgtgaggtg gctttttata ggataaaaaa
      961 atgccattta atataggcga tatagtttac ttaaagtcag aatcaaaagc gatgacggtc
     1021 atcggatatg gatcgtctca aaataacggt tacatagatc tagctaattg tgcttggcta
     1081 gataaagaca accgctattg ccaaatacta ttcttgtttc aaacgatcga aaaaagaatc
     1141 agttaaaaac tggcttatct tcattgagca taccggacga acctatttac cataacatcc
     1201 gttgcccgca ccgcagaaac gcgttcggtg cgatcacggc agcagacagg taaaaatggc
     1261 aacaaaccac ccgaaaaact gccgcgatcg cacccggtaa attttaacca catgcatagc
     1321 tatgcagcca tgtgaatcac gcaggaattg ccagccagag acagctgaaa cggatttttt
     1381 tcatgctttc ggaagcgaag aagacgggga ccggagcggg aaaacagaag ttcaggggaa
     1441 tgagcgcgat ctggcaatag aggcaaaaca cagcaacaaa agacacacca gaatcgcgcc
     1501 cgtatgcgtt ttaacgcgtt cctgtgtttt cagcaaggtc tgactgaagc gcgttcccgg
     1561 tgcccccgaa ccaaccatta tcccaaaaaa tgcaccggaa acgcgctgac aacattttag
     1621 cctgtctctg attaccatcc aagcgaaggg ccatcctgtg tccattcctg tatttccggc
     1681 tggcgctcac gctccaggga taactcatgt tcgcgctcct gtatcagccg ttcgtccctt
     1741 atctcctgtt ctcgctgtat aactggctca agcgttctgt ccgctcgctc aagtgctgca
     1801 cctgctgact caactgcatg acctgctcgt tcagcatcgc gttgtcccgt tgcgtaagcg
     1861 aaaacatttt ctgcaattcc acgaaggcgc tctcccattc gctcagccgc tgcatatagt
     1921 cctgttgcag ttgctctaag gcgttcagca aatgtctttc cagctccgtc actctgtgtc
     1981 actccgtcag ttgtacccag tccttctcct gatagggaat caccgttgcc gatttcccgt
     2041 acggaaggac cagaaatttc cttctcccgt cctgcacaaa ctccacgccc catgtcttcg
     2101 cgttcagttt ctgcaatgtt tcttcctgta tcctgatttc ttccaggttc gcctgtatcc
     2161 gcccgccaag ataccagagc gtcccgccac tcacggtaaa caggaaaagg accatcccca
     2221 gtaacatcat gcccgtattc cctgccagct ttaacacgtc cttcctgtgc tgcatcatcg
     2281 cctctttcac cccttcccgg tgttttttca gtgattcctc tgtcgaagct gtgaacaggg
     2341 ctatagcgtc tttgattttc gtctcgtttg atgtcacagc cttgcttaca gatttttcga
     2401 gcttgctgaa ctcgtcgttc agcattgtct ctgtagattc ggctctctct ttcagctttt
     2461 tctcgaactc cgcgcccgtc tgtaaaagat tgctcataga atgctccttt cagtctgata
     2521 ttcttcccgc cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct gaccacttca
     2581 agccctgcct ctgtgagcgc ctgaatcaca tcctgacggc cttttatctc cccgacatga
     2641 taaagagcgt ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt ttccggcagg
     2701 ttatcaggga gagtcagtat ccggcggttc tccggggcgt tggggtcatg cagcccgtaa
     2761 tggtgattaa ccagcgtctg ccaggcatca attctcggcc tgtctgcccg gtcgtagtac
     2821 ggctggaggc gttttccgct ctgtagctcc atgttcggaa tgacaaaatt cagctcaagc
     2881 cgtcccttgt cctggtgctc cacccacagg atgctgtact gatttttttc gagaccgggc
     2941 atcagtacac gctcaaagct cgccatcacc ttttcacgtc ctcccggcgg cagctccttc
     3001 tccgcgaacg acagaacacc tgacgtgtat ttcttcgcaa atggcgtggc atcgatgagt
     3061 tcccggactt cttccggatt accctgaagc accgttgccc cttcccggtt acgctccctt
     3121 cccagcaggt aatcaaccgg accactgcca ccgccttttc ccctggcatg aaacttaact
     3181 atcatcccgc gctccatgtt ccctgacgac ctgccgtaag ctgcgcaact ctctctcgat
     3241 ggccatcagt gcggccacca cctgaacccg gtcaccggaa gaccactgcc cgctgttcac
     3301 cttcctcgcc gtctgattca gattattccc gatggcagcc agctggcgca gtaacggcgg
     3361 tgccagtgtc ggcagcttcc cggaacgggc aaccggctca cccagacaga cccgccgcat
     3421 ccataccgcc agctgtttac cctcacagcg ttccagtaac cgtgcatgtt catcatcagt
     3481 aacccgtatc gtgagcatcc tctcgcgttt catcggtatc attaccccat gaacagaaat
     3541 ccccccttac acggaggcat cagtgactaa acaggaaaaa accgccctta acatggcccg
     3601 ctttatcaga agccagacat taacgctgct ggaaaagctc aacgaactgg acgcggatga
     3661 acaggcagac atctgtgaat cgcttcacga ccacgccgat gagctttacc gcagctgcct
     3721 cgcacgcttc ggggatgacg gtgaaaacct ctgacacata cagctcccgg agacggtcac
     3781 agcttgtctg tgagcggatg ccgggagcag acaagcccgt cagggcgcgt caggccgttg
     3841 accttgcggg tgtcggggcg cagccatgac ccagtcacgt agcgatagcg gagtgtatac
     3901 tggcttacta tgttggcatg agtgcgggta tcaggaaagt gcttcatgtg gcaggagaaa
     3961 aaaggcggca ccggagcgtc agcagaatat gtgatacagg atatattccg cttcctcgct
     4021 cactgactcg ctacgctcgg tcgttcgact gcggcgagcg gaaatggctt acgaacgggg
     4081 cggagatttc ctggaagatg ccaggaagat acttaacagg gaagcgatag ggtcgcggcg
     4141 aagccgtttt tccataggct ccgcccccct gacaagcatc acgaaatctg acgctcaaat
     4201 cagtggtggc gaaacccgac aggactataa agataccagg cgtttccccc tggtggctcc
     4261 ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg tcattccgct gttatggccg
     4321 cgtttatctc attccacgcc tgacactcag ttccgggtag gcagttcgct ccaagctgga
     4381 ctgtatgcac gaaccccccg ttcagtccga ctgctgcgcc tgttccggta actatcgact
     4441 tgagtccaac ccggaaagac acgacaaagc gccactggca gcagccatga gtaaaggggt
     4501 gtacaagatt tactgagtga gagttcttga agtatcagcc ttagagaggc taaactggaa
     4561 taacagaatt tggtttcagc ggtcttgtac accctgttac cacggttcag aagttcccca
     4621 acttactgaa ccctcgaaaa aaccgactcc ccagtcggtt tttttcgttt gatggctaag
     4681 agtacgctga cgttatactg aacgtcaagg aaagcgttga cgctgttccc tctaccaaaa
     4741 aaaagagatt tgtaaggaat aaaaatggct gtgacagttg ggtttattag tgagaaaggt
     4801 ggggttggta aaacaacgtc ctgttatcac attgccgaag gacttagtcg ttttcatgaa
     4861 aaacgtgttt tagttataga tgcagattat caacgcggag gtataactgg aagatttttc
     4921 cctaaactga tcgaaaactt tggaaatcaa gcaccgcaag gaacaacgtt atttaacaag
     4981 tatcagcaat tatatagcgc ggcacaacaa acgactgaca tagacataat taaatttaat
     5041 agtggtatcg atgtcattcc agccgaccct cgcttatcaa ccgtttcaac tgataagcta
     5101 cctagtacaa acaatataag atcgaaca
//
