LOCUS       CP057030                4612 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB40-C03 plasmid pRHB40-C03_3, complete
            sequence.
ACCESSION   CP057030
VERSION     CP057030.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148409
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4612)
  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 4612)
  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                     :: RH08 T3-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132.657912608121x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 04:23:44
            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)                     :: 4,945
            CDSs (total)                      :: 4,825
            Genes (coding)                    :: 4,688
            CDSs (with protein)               :: 4,688
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 45 of 137
            Pseudo Genes (incomplete)         :: 76 of 137
            Pseudo Genes (internal stop)      :: 46 of 137
            Pseudo Genes (multiple problems)  :: 27 of 137
            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..4612
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB40-C03"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB40-C03_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            727..1389
                     /locus_tag="HVZ92_24695"
     CDS             727..1389
                     /locus_tag="HVZ92_24695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001423320.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="QMB85284.1"
                     /translation="MELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEI
                     IGINYYTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKH
                     HLKNPNQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVK
                     SELSLYIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(1510..1746)
                     /locus_tag="HVZ92_24700"
     CDS             complement(1510..1746)
                     /locus_tag="HVZ92_24700"
                     /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="QMB85279.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(2110..2343)
                     /gene="mbeD"
                     /locus_tag="HVZ92_24705"
     CDS             complement(2110..2343)
                     /gene="mbeD"
                     /locus_tag="HVZ92_24705"
                     /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="QMB85280.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     gene            complement(2350..2868)
                     /locus_tag="HVZ92_24710"
     CDS             complement(2350..2868)
                     /locus_tag="HVZ92_24710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001525988.1"
                     /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="QMB85281.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            complement(2846..3604)
                     /locus_tag="HVZ92_24715"
                     /pseudo=""
     CDS             complement(2846..3604)
                     /locus_tag="HVZ92_24715"
                     /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(3546..3869)
                     /locus_tag="HVZ92_24720"
     CDS             complement(3546..3869)
                     /locus_tag="HVZ92_24720"
                     /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="QMB85282.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3934..4125
                     /locus_tag="HVZ92_24725"
     CDS             3934..4125
                     /locus_tag="HVZ92_24725"
                     /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="QMB85283.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4211..4296)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          2..495
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.3"
                     /coverage="97.0"
                     /evalue="8.08e-141"
     Typing          complement(2007..3556)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.42"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt
       61 cctgcctttc ggtgtaccgg tgtcattccg ctgttatggc cgcggtttct cattccacgc
      121 ctgacactcg gctccgggaa ggcagttcgc tccaagctgg actgtatgca cgaacccccc
      181 gttcagtccg accgctgcgt cttatccggt aactatcaac ttgagtccaa cccggaaaga
      241 cacgactaat cgccattggc aacggccact ggtaaacagg atgtgcgaga gatgtatcga
      301 gagttcttga agtggcggcc tgactacggc tacactgaaa ggacagattt ggtgacatgt
      361 ctcgcacaag accgttaccg cggttagaga atctgccagg attaactaac cttcgaaaaa
      421 ccacctgcca gggtggtttt ttcgttttca aagcaggaga ttacgcgcag aaaaaaagga
      481 tctcaagaag atcttttctc ctttaggtag ggcttacttc gtcaccatat aaaacatttg
      541 cactagacaa aaaaaatgca ataatgttgg tacagacctg tggcgtgccg caggcgaaga
      601 aacaaccccc ctgtggcgtg ccgcaggcga agaaacaacc ctcctgtggc gagccgcagg
      661 caaacacccc tcctacggcg tgccgtagga aaaaaaaccg cagatgcggt tttttttata
      721 tctaaaatgg agctaacccc attgaaaaca atagtttatg ttgatggctt taacttttat
      781 tatcgtaagc tgaaagattc caacaaaaag tggctgaaca taaaagcaat ggtcgaaaaa
      841 ttgctaccgg atgatgaaat aataggaatt aactattaca cggctaggat ctcaggaagg
      901 attgattctg acgcacctcg taggcaacaa atatatttca atgcactgaa aagcatagat
      961 aacctaagta tccattatgg tactttttcg gtgaatgaaa gcagaatgtt tttagtgcag
     1021 cctcttgatt tcaaacatca cttaaaaaac ccgaatcaaa aaataaagtt tgcaaacgtc
     1081 ttaaagacag aagaaaaggg ttctgacgtt aatttaggtt gccacttggt tagagatggt
     1141 ttccaaggga aatacgagaa ggctgtaata ataactaatg atacagattt ggctgaacca
     1201 atgagagtag tcaaatcaga gctcagcctt tatattgaac tactttctcc tgtaaacaaa
     1261 ccagcaagaa ccctgagcgc aatatgcgat aaggtcactc ttataagcga ccaatcaata
     1321 gctgatagcc agtttgaaga cgttattgta gttggtgaga aaaccgtgac aaaaccagca
     1381 cagtggtagt ggctacatac tcgttctgtt gaaaaaaagc ccgtcccccg ggctttttat
     1441 gttttgcatt ataccttcag gcaaatataa agagtatgaa atctatagct atgtgcagaa
     1501 aataaaaaat tagctaatag cacttaaaat agcaaagtga gttgcaggat ctgtactttc
     1561 attttcaaaa tgaacagata agttactatt tctagtattt ctagagatac aacatgcaaa
     1621 accagtgtcg aaagaacact tcaatgtata tccatttggt tgtacttttg agccaacata
     1681 tccttgagat gtctggatca acgtcatcaa agcagtatat ttttcacgat caataataat
     1741 actcatcaca tccccattag tattactctg caggcattaa acctcagcaa taaatctatt
     1801 taccataact cccgttgccc gcaccgcctc agacgctctc agcgcgtttc tgacgggaaa
     1861 ccggaaaaac aggcaacaaa cctcccgaaa aactgccgcg atcgcgcctg ataaatttta
     1921 accgcatgaa tacctatgca acaagatggt gcagactaca ttagtccgtc aaaatccact
     1981 gaacctgcca tttttcatag tttcaccatc ccagcgaagg gccatccagc gtgcgttcct
     2041 gtatttccgg ctgacgctcc cgttccaggg ataacgcata ttcgcgctcc tgtatcaacc
     2101 gttcctctct tatctccagt tctcgctgta taactggctc aagcgttctg tctgctcgct
     2161 caagtgctgc acctgctgac tcaactgcat gacccgctcg ttcagcatcg cgttgtcccg
     2221 ttgcgtaagc gaaaacatct tctgcaattc cacgaaggcg ctctcccatt cgctcagccg
     2281 ctgcatatag tcctgttgca gctgctctaa ggcgttcagc aaatgtgttt ccagctctgt
     2341 cactctgtgt caccccttca gatgtaccca ttccttcccc tgaaaggaaa tcacctctgc
     2401 tgacttcccg taaggaagga ccagaaattt cctgttcccg tcctgcacaa actccacgcc
     2461 ccatgtcttc gcgttcagtt tctgcaatgt ctcttcctgc ttcctgatat cttccaggtt
     2521 cgcctgtatc ctcccgccaa gataccagag cgtcccgcca ctcacggtaa acaggagaaa
     2581 gactatcccc agcaacatca tgcccgtatt ccctgccagc tttaacacgt ccctcctgtg
     2641 ctgcatcatc gcctctttca ccccttcccg gtgtttttcc agagattcct ctgtcgaggc
     2701 tgtgaacagg gctatagcgt ctctgatttt cgtctcgttt gatgtcacag cctcgcttac
     2761 agattcgccg agcctcctga actcgttgtt cagcattttc tctgtagatt cggctctctc
     2821 tttcagcttt ttctcgaact ccgcgcccgt ctgcaaaaga ttgctcataa aatgctcctt
     2881 tcagcctgat attcttccca ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc
     2941 tgaccacttc aagccctgcc tctgtgagcg cctgaatcac atcctgacgg ccttttatct
     3001 ccccgacatg ataaagagcg tctatcccgc gtgtgacgct ctctgcaagc gcctgtttcg
     3061 tttccggcag gttatcaggg agagtcagta tccggcggtt ctccggggcg ttggggtcat
     3121 gcagcccgta atggtgattc accagcgtct gccaggcatc aattctcggc ctgtctgcgc
     3181 ggtcgtagta cggctggagg cgttttccgc tctgtagctc catgttcgga atgacaaaat
     3241 taagctcaag ccgccccttg tcctggtgct ccacccacag aatgctgtac tgattttttt
     3301 cgagaccggg catcagtaca cgctcaaaac tcgccatcac tttttcacgt cctcccggcg
     3361 gcagttcctt ctccgcgaac gacagaacac cggacgtgta tttcttcgca aatggcgtgg
     3421 catcgatgag ttcccggact tcttccgggt taccctgaag cacctttgcg ccctcccggt
     3481 tacgctccct ccccagcagg taatcaaccg gaccactgcc accgcctttt cccctggcat
     3541 gaaacttaac tatcatcccg cgtcccctgt tccctgacgg ccagacgcag ccggcgcagc
     3601 tcatccccga tggccatcag tgcggccacc acctgaaccc ggtcaccgga agaccactgc
     3661 ccgctgttca ccttcctcgc tgtctgattc aggttattcc cgatggcggc cagctgacgc
     3721 agtaacggcg gtgccagtgt cggcagtttc ccggaacggg caaccggctc ccccaggcag
     3781 acccgccgca tccataccgc cagttgttta ccctcacagc gttcaagtaa cctggcatgt
     3841 tcatcatcag taacccgtat cgtgagcatc ctctcgcgtt tcatcggtat cattaccccc
     3901 atgaacagaa atccccctta cacggaggca tcagtgacca aacaggaaaa aaccgccctt
     3961 aacatggccc gctttataag aagccagaca ttaacgctgc tggagaagct caacgaactg
     4021 gacgcagatg aacaggccga tatttgtgaa tcacttcacg accacgccga cgagctttac
     4081 cgcagctgcc tcgcacgctt cggggatgac ggtgaaaacc tctgacacat acagctcccg
     4141 gagacggtca cagcttgtct gtgagcggat gccgggagca gacaagcccg tcagggcgcg
     4201 tcagggggtt ttagcgggtg tcggggcgca gccatgaccc agtcacgtag cgatagcgga
     4261 gtgtatactg gcttaactat gtggcatcag tgcagattat aagaaaagag caccatatgc
     4321 ggtgtgaaat accgcacaga tgcgtaagga gaaaataccg catcaggcgc tcttccgctt
     4381 cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggta tcagctcacg
     4441 caaagacggt aatgcggtta tccacagaat caggggataa ggccggaaag aacatgtgaa
     4501 caaaaaggca aaaccaggga aaaaggccgc gccgcaggcg tttttccata ggctccgccc
     4561 ccctgacgag catcacaaaa attgacgctc aagtcagagg tggcgaaacc cg
//
