LOCUS       CP057158                4617 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB35-C09 plasmid pRHB35-C09_5, complete
            sequence.
ACCESSION   CP057158
VERSION     CP057158.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148350
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4617)
  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 4617)
  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                     :: RH06 T3-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 130.632759251172x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 06:06:10
            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)                     :: 5,293
            CDSs (total)                      :: 5,165
            Genes (coding)                    :: 4,923
            CDSs (with protein)               :: 4,923
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 119 of 242
            Pseudo Genes (incomplete)         :: 123 of 242
            Pseudo Genes (internal stop)      :: 53 of 242
            Pseudo Genes (multiple problems)  :: 47 of 242
            CRISPR Arrays                     :: 3
            ##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..4617
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB35-C09"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB35-C09_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4042..4617,1..87)
                     /locus_tag="HVZ33_26415"
     CDS             join(4042..4617,1..87)
                     /locus_tag="HVZ33_26415"
                     /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="QMD75011.1"
                     /translation="MELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEI
                     IGINYYTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKH
                     HLKNPNQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVK
                     SELSLYIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(208..444)
                     /locus_tag="HVZ33_26420"
     CDS             complement(208..444)
                     /locus_tag="HVZ33_26420"
                     /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="QMD75007.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(808..1041)
                     /gene="mbeD"
                     /locus_tag="HVZ33_26425"
     CDS             complement(808..1041)
                     /gene="mbeD"
                     /locus_tag="HVZ33_26425"
                     /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="QMD75008.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     gene            complement(1048..1566)
                     /locus_tag="HVZ33_26430"
     CDS             complement(1048..1566)
                     /locus_tag="HVZ33_26430"
                     /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="QMD75009.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            complement(1544..2302)
                     /locus_tag="HVZ33_26435"
                     /pseudo=""
     CDS             complement(1544..2302)
                     /locus_tag="HVZ33_26435"
                     /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(2244..2567)
                     /locus_tag="HVZ33_26440"
     CDS             complement(2244..2567)
                     /locus_tag="HVZ33_26440"
                     /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="QMD75012.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2632..2823
                     /locus_tag="HVZ33_26445"
     CDS             2632..2823
                     /locus_tag="HVZ33_26445"
                     /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="QMD75010.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2909..3001)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.617"
                     /coverage="100.0"
                     /evalue="5.38e-30"
     Typing          3021..3550
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.533"
                     /coverage="99.0"
                     /evalue="2.98e-155"
     Typing          complement(705..2254)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.42"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataagcgacc aatcaatagc tgatagccag tttgaagacg ttattgtagt tggtgagaaa
       61 accgtgacaa aaccagcaca gtggtagtgg ctacatactc gttctgttga aaaaaagccc
      121 gtcccccggg ctttttatgt tttgcattat accttcaggc aaatataaag agtatgaaat
      181 ctatagctat gtgcagaaaa taaaaaatta gctaatagca cttaaaatag caaagtgagt
      241 tgcaggatct gtactttcat tttcaaaatg aacagataag ttactatttc tagtatttct
      301 agagatacaa catgcaaaac cagtgtcgaa agaacacttc aatgtatatc catttggttg
      361 tacttttgag ccaacatatc cttgagatgt ctggatcaac gtcatcaaag cagtatattt
      421 ttcacgatca ataataatac tcatcacatc cccattagta ttactctgca ggcattaaac
      481 ctcagcaata aatctattta ccataactcc cgttgcccgc accgcctcag acgctctcag
      541 cgcgtttctg acgggaaacc ggaaaaacag gcaacaaacc tcccgaaaaa ctgccgcgat
      601 cgcgcctgat aaattttaac cgcatgaata cctatgcaac aagatggtgc agactacatt
      661 agtccgtcaa aatccactga acctgccatt tttcatagtt tcaccatccc agcgaagggc
      721 catccagcgt gcgttcctgt atttccggct gacgctcccg ttccagggat aacgcatatt
      781 cgcgctcctg tatcaaccgt tcctctctta tctccagttc tcgctgtata actggctcaa
      841 gcgttctgtc tgctcgctca agtgctgcac ctgctgactc aactgcatga cccgctcgtt
      901 cagcatcgcg ttgtcccgtt gcgtaagcga aaacatcttc tgcaattcca cgaaggcgct
      961 ctcccattcg ctcagccgct gcatatagtc ctgttgcagc tgctctaagg cgttcagcaa
     1021 atgtgtttcc agctctgtca ctctgtgtca ccccttcaga tgtacccatt ccttcccctg
     1081 aaaggaaatc acctctgctg acttcccgta aggaaggacc agaaatttcc tgttcccgtc
     1141 ctgcacaaac tccacgcccc atgtcttcgc gttcagtttc tgcaatgtct cttcctgctt
     1201 cctgatatct tccaggttcg cctgtatcct cccgccaaga taccagagcg tcccgccact
     1261 cacggtaaac aggagaaaga ctatccccag caacatcatg cccgtattcc ctgccagctt
     1321 taacacgtcc ctcctgtgct gcatcatcgc ctctttcacc ccttcccggt gtttttccag
     1381 agattcctct gtcgaggctg tgaacagggc tatagcgtct ctgattttcg tctcgtttga
     1441 tgtcacagcc tcgcttacag attcgccgag cctcctgaac tcgttgttca gcattttctc
     1501 tgtagattcg gctctctctt tcagcttttt ctcgaactcc gcgcccgtct gcaaaagatt
     1561 gctcataaaa tgctcctttc agcctgatat tcttcccacc gttcgggtct gcaatgctga
     1621 tactgcttcg cgtcaccctg accacttcaa gccctgcctc tgtgagcgcc tgaatcacat
     1681 cctgacggcc ttttatctcc ccgacatgat aaagagcgtc tatcccgcgt gtgacgctct
     1741 ctgcaagcgc ctgtttcgtt tccggcaggt tatcagggag agtcagtatc cggcggttct
     1801 ccggggcgtt ggggtcatgc agcccgtaat ggtgattcac cagcgtctgc caggcatcaa
     1861 ttctcggcct gtctgcgcgg tcgtagtacg gctggaggcg ttttccgctc tgtagctcca
     1921 tgttcggaat gacaaaatta agctcaagcc gccccttgtc ctggtgctcc acccacagaa
     1981 tgctgtactg atttttttcg agaccgggca tcagtacacg ctcaaaactc gccatcactt
     2041 tttcacgtcc tcccggcggc agttccttct ccgcgaacga cagaacaccg gacgtgtatt
     2101 tcttcgcaaa tggcgtggca tcgatgagtt cccggacttc ttccgggtta ccctgaagca
     2161 cctttgcgcc ctcccggtta cgctccctcc ccagcaggta atcaaccgga ccactgccac
     2221 cgccttttcc cctggcatga aacttaacta tcatcccgcg tcccctgttc cctgacggcc
     2281 agacgcagcc ggcgcagctc atccccgatg gccatcagtg cggccaccac ctgaacccgg
     2341 tcaccggaag accactgccc gctgttcacc ttcctcgctg tctgattcag gttattcccg
     2401 atggcggcca gctgacgcag taacggcggt gccagtgtcg gcagtttccc ggaacgggca
     2461 accggctccc ccaggcagac ccgccgcatc cataccgcca gttgtttacc ctcacagcgt
     2521 tcaagtaacc gggcatgttc atcatcagta acccgtatcg tgagcatcct ctcgcgtttc
     2581 atcggtatca ttacccccat gaacagaaat cccccttaca cggaggcatc agtgaccaaa
     2641 caggaaaaaa ccgcccttaa catggcccgc tttataagaa gccagacatt aacgctgctg
     2701 gagaagctca acgaactgga cgcagatgaa caggccgata tttgtgaatc acttcacgac
     2761 cacgccgacg agctttaccg cagctgcctc gcacgcttcg gggatgacgg tgaaaacctc
     2821 tgacacatac agctcccgga gacggtcaca gcttgtctgt gagcggatgc cgggagcaga
     2881 caagcccgtc agggcgcgtc agggggtttt agcgggtgtc ggggcgcagc catgacccag
     2941 tcacgtagcg atagcggagt gtatactggc ttaactatgt gatgtggcat cagtgcagat
     3001 tataagaaaa gagcaccata tgcggtgtga aataccgcac agatgcgtaa ggagaaaata
     3061 ccgcatcagg cgctcttccg cttcctcgct cactgactcg ctacgctcgg tcgttcggct
     3121 gcggcgagcg gtatcagctc acgcaaagac ggtaatgcgg ttatccacag aatcagggga
     3181 taaggccgga aagaacatgt gaacaaaaag gcaaaaccag ggaaaaaggc cgcgccgcag
     3241 gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaattgacg ctcaagtcag
     3301 aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg aagctccctc
     3361 gtgcgctctc ctgttcctgc ctttcggtgt accggtgtca ttccgctgtt atggccgcgg
     3421 tttctcattc cacgcctgac actcggctcc gggaaggcag ttcgctccaa gctggactgt
     3481 atgcacgaac cccccgttca gtccgaccgc tgcgtcttat ccggtaacta tcaacttgag
     3541 tccaacccgg aaagacacga ctaatcgcca ttggcaacgg ccactggtaa acaggatgtg
     3601 cgagagatgt atcgagagtt cttgaagtgg cggcctgact acggctacac tgaaaggaca
     3661 gatttggtga catgtctcgc acaagaccgt taccgcggtt agagaatctg ccaggattaa
     3721 ctaaccttcg aaaaaccacc tgccagggtg gttttttcgt tttcaaagca ggagattacg
     3781 cgcagaaaaa aaggatctca agaagatctt ttctccttta ggtagggctt acttcgtcac
     3841 catataaaac atttgcacta gacaaaaaaa atgcaataat gttggtacag acctgtggcg
     3901 tgccgcaggc gaagaaacaa cccccctgtg gcgtgccgca ggcgaagaaa caaccctcct
     3961 gtggcgagcc gcaggcaaac acccctccta cggcgtgccg taggaaaaaa aaccgcagat
     4021 gcggtttttt ttatatctaa aatggagcta accccattga aaacaatagt ttatgttgat
     4081 ggctttaact tttattatcg taagctgaaa gattccaaca aaaagtggct gaacataaaa
     4141 gcaatggtcg aaaaattgct accggatgat gaaataatag gaattaacta ttacacggct
     4201 aggatctcag gaaggattga ttctgacgca cctcgtaggc aacaaatata tttcaatgca
     4261 ctgaaaagca tagataacct aagtatccat tatggtactt tttcggtgaa tgaaagcaga
     4321 atgtttttag tgcagcctct tgatttcaaa catcacttaa aaaacccgaa tcaaaaaata
     4381 aagtttgcaa acgtcttaaa gacagaagaa aagggttctg acgttaattt aggttgccac
     4441 ttggttagag atggtttcca agggaaatac gagaaggctg taataataac taatgataca
     4501 gatttggctg aaccaatgag agtagtcaaa tcagagctca gcctttatat tgaactactt
     4561 tctcctgtaa acaaaccagc aagaaccctg agcgcaatat gcgataaggt cactctt
//
