LOCUS       CP057945                4612 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB09-C15 plasmid pRHB09-C15_4, complete
            sequence.
ACCESSION   CP057945
VERSION     CP057945.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148047
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 T1-C15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 51.6152809990565x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 13:08:33
            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)                     :: 5,016
            CDSs (total)                      :: 4,896
            Genes (coding)                    :: 4,771
            CDSs (with protein)               :: 4,771
            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)              :: 125
            CDSs (without protein)            :: 125
            Pseudo Genes (ambiguous residues) :: 0 of 125
            Pseudo Genes (frameshifted)       :: 50 of 125
            Pseudo Genes (incomplete)         :: 68 of 125
            Pseudo Genes (internal stop)      :: 34 of 125
            Pseudo Genes (multiple problems)  :: 24 of 125
            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="RHB09-C15"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB09-C15_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4496..4612,1..117))
                     /gene="mbeD"
                     /locus_tag="HVW30_25050"
     CDS             complement(join(4496..4612,1..117))
                     /gene="mbeD"
                     /locus_tag="HVW30_25050"
                     /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="QMO94994.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     gene            complement(124..642)
                     /locus_tag="HVW30_25055"
     CDS             complement(124..642)
                     /locus_tag="HVW30_25055"
                     /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="QMO94995.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            complement(620..1162)
                     /locus_tag="HVW30_25060"
                     /pseudo=""
     CDS             complement(620..1162)
                     /locus_tag="HVW30_25060"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and 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(1320..1643)
                     /locus_tag="HVW30_25065"
     CDS             complement(1320..1643)
                     /locus_tag="HVW30_25065"
                     /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="QMO94996.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1708..1899
                     /locus_tag="HVW30_25070"
     CDS             1708..1899
                     /locus_tag="HVW30_25070"
                     /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="QMO94997.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3113..3775
                     /locus_tag="HVW30_25075"
     CDS             3113..3775
                     /locus_tag="HVW30_25075"
                     /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="QMO94999.1"
                     /translation="MELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEI
                     IGINYYTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKH
                     HLKNPNQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVK
                     SELSLYIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(3896..4132)
                     /locus_tag="HVW30_25080"
     CDS             complement(3896..4132)
                     /locus_tag="HVW30_25080"
                     /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="QMO94998.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     Typing          complement(1985..2070)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          2092..2621
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.533"
                     /coverage="99.0"
                     /evalue="2.98e-155"
     Typing          complement(3..1330)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.614"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aagcgaaaac atcttctgca attccacgaa ggcgctctcc cattcgctca gccgctgcat
       61 atagtcctgt tgcagctgct ctaaggcgtt cagcaaatgt gtttccagct ctgtcactct
      121 gtgtcacccc ttcagatgta cccattcctt cccctgaaag gaaatcacct ctgctgactt
      181 cccgtaagga aggaccagaa atttcctgtt cccgtcctgc acaaactcca cgccccatgt
      241 cttcgcgttc agtttctgca atgtctcttc ctgcttcctg atatcttcca ggttcgcctg
      301 tatcctcccg ccaagatacc agagcgtccc gccactcacg gtaaacagga gaaagactat
      361 ccccagcaac atcatgcccg tattccctgc cagctttaac acgtccctcc tgtgctgcat
      421 catcgcctct ttcacccctt cccggtgttt ttccagagat tcctctgtcg aggctgtgaa
      481 cagggctata gcgtctctga ttttcgtctc gtttgatgtc acagcctcgc ttacagattc
      541 gccgagcctc ctgaactcgt tgttcagcat tttctctgta gattcggctc tctctttcag
      601 ctttttctcg aactccgcgc ccgtctgcaa aagattgctc ataaaatgct cctttcagcc
      661 tgatattctt cccaccgttc gggtctgcaa tgctgatact gcttcgcgtc accctgacca
      721 cttcaagccc tgcctctgtg agcgcctgaa tcacatcctg acggcctttt atctccccga
      781 catgataaag agcgtctatc ccgcgtgtga cgctctctgc aagcgcctgt ttcgtttccg
      841 gcaggttatc agggagagtc agtatccggc ggttctccgg ggcgttgggg tcatgcagcc
      901 cgtaatggtg attcaccagc gtctgccagg catcaattct cggcctgtct gcgcggtcgt
      961 agtacggctg gaggcgtttt ccgctctgta gctccatgtt cggaatgaca aaattaagct
     1021 caagccgccc cttgtcctgg tgctccaccc acagaatgct gtactgattt ttttcgagac
     1081 cgggcatcag tacacgctca aaactcgcca tcactttttc acgtcctccc ggcggcagtt
     1141 ccttctccgc gaacgacaga acaccggacg tgtatttctt cgcaaatggc gtggcatcga
     1201 tgagttcccg gacttcttcc gggttaccct gaagcacctt tgcgccctcc cggttacgct
     1261 ccctccccag caggtaatca accggaccac tgccaccgcc ttttcccctg gcatgaaact
     1321 taactatcat cccgcgtccc ctgttccctg acggccagac gcagccggcg cagctcatcc
     1381 ccgatggcca tcagtgcggc caccacctga acccggtcac cggaagacca ctgcccgctg
     1441 ttcaccttcc tcgctgtctg attcaggtta ttcccgatgg cggccagctg acgcagtaac
     1501 ggcggtgcca gtgtcggcag tttcccggaa cgggcaaccg gctcccccag gcagacccgc
     1561 cgcatccata ccgccagttg tttaccctca cagcgttcaa gtaacctggc atgttcatca
     1621 tcagtaaccc gtatcgtgag catcctctcg cgtttcatcg gtatcattac ccccatgaac
     1681 agaaatcccc cttacacgga ggcatcagtg accaaacagg aaaaaaccgc ccttaacatg
     1741 gcccgcttta taagaagcca gacattaacg ctgctggaga agctcaacga actggacgca
     1801 gatgaacagg ccgatatttg tgaatcactt cacgaccacg ccgacgagct ttaccgcagc
     1861 tgcctcgcac gcttcgggga tgacggtgaa aacctctgac acatacagct cccggagacg
     1921 gtcacagctt gtctgtgagc ggatgccggg agcagacaag cccgtcaggg cgcgtcaggg
     1981 ggttttagcg ggtgtcgggg cgcagccatg acccagtcac gtagcgatag cggagtgtat
     2041 actggcttaa ctatgtggca tcagtgcaga ttataagaaa agagcaccat atgcggtgtg
     2101 aaataccgca cagatgcgta aggagaaaat accgcatcag gcgctcttcc gcttcctcgc
     2161 tcactgactc gctacgctcg gtcgttcggc tgcggcgagc ggtatcagct cacgcaaaga
     2221 cggtaatgcg gttatccaca gaatcagggg ataaggccgg aaagaacatg tgaacaaaaa
     2281 ggcaaaacca gggaaaaagg ccgcgccgca ggcgtttttc cataggctcc gcccccctga
     2341 cgagcatcac aaaaattgac gctcaagtca gaggtggcga aacccgacag gactataaag
     2401 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttcctg cctttcggtg
     2461 taccggtgtc attccgctgt tatggccgcg gtttctcatt ccacgcctga cactcggctc
     2521 cgggaaggca gttcgctcca agctggactg tatgcacgaa ccccccgttc agtccgaccg
     2581 ctgcgtctta tccggtaact atcaacttga gtccaacccg gaaagacacg actaatcgcc
     2641 attggcaacg gccactggta aacaggatgt gcgagagatg tatcgagagt tcttgaagtg
     2701 gcggcctgac tacggctaca ctgaaaggac agatttggtg acatgtctcg cacaagaccg
     2761 ttaccgcggt tagagaatct gccaggatta actaaccttc gaaaaaccac ctgccagggt
     2821 ggttttttcg ttttcaaagc aggagattac gcgcagaaaa aaaggatctc aagaagatct
     2881 tttctccttt aggtagggct tacttcgtca ccatataaaa catttgcact agacaaaaaa
     2941 aatgcaataa tgttggtaca gacctgtggc gtgccgcagg cgaagaaaca acccccctgt
     3001 ggcgtgccgc aggcgaagaa acaaccctcc tgtggcgagc cgcaggcaaa cacccctcct
     3061 acggcgtgcc gtaggaaaaa aaaccgcaga tgcggttttt tttatatcta aaatggagct
     3121 aaccccattg aaaacaatag tttatgttga tggctttaac ttttattatc gtaagctgaa
     3181 agattccaac aaaaagtggc tgaacataaa agcaatggtc gaaaaattgc taccggatga
     3241 tgaaataata ggaattaact attacacggc taggatctca ggaaggattg attctgacgc
     3301 acctcgtagg caacaaatat atttcaatgc actgaaaagc atagataacc taagtatcca
     3361 ttatggtact ttttcggtga atgaaagcag aatgttttta gtgcagcctc ttgatttcaa
     3421 acatcactta aaaaacccga atcaaaaaat aaagtttgca aacgtcttaa agacagaaga
     3481 aaagggttct gacgttaatt taggttgcca cttggttaga gatggtttcc aagggaaata
     3541 cgagaaggct gtaataataa ctaatgatac agatttggct gaaccaatga gagtagtcaa
     3601 atcagagctc agcctttata ttgaactact ttctcctgta aacaaaccag caagaaccct
     3661 gagcgcaata tgcgataagg tcactcttat aagcgaccaa tcaatagctg atagccagtt
     3721 tgaagacgtt attgtagttg gtgagaaaac cgtgacaaaa ccagcacagt ggtagtggct
     3781 acatactcgt tctgttgaaa aaaagcccgt cccccgggct ttttatgttt tgcattatac
     3841 cttcaggcaa atataaagag tatgaaatct atagctatgt gcagaaaata aaaaattagc
     3901 taatagcact taaaatagca aagtgagttg caggatctgt actttcattt tcaaaatgaa
     3961 cagataagtt actatttcta gtatttctag agatacaaca tgcaaaacca gtgtcgaaag
     4021 aacacttcaa tgtatatcca tttggttgta cttttgagcc aacatatcct tgagatgtct
     4081 ggatcaacgt catcaaagca gtatattttt cacgatcaat aataatactc atcacatccc
     4141 cattagtatt actctgcagg cattaaacct cagcaataaa tctatttacc ataactcccg
     4201 ttgcccgcac cgcctcagac gctctcagcg cgtttctgac gggaaaccgg aaaaacaggc
     4261 aacaaacctc ccgaaaaact gccgcgatcg cgcctgataa attttaaccg catgaatacc
     4321 tatgcaacaa gatggtgcag actacattag tccgtcaaaa tccactgaac ctgccatttt
     4381 tcatagtttc accatcccag cgaagggcca tccagcgtgc gttcctgtat ttccggctga
     4441 cgctcccgtt ccagggataa cgcatattcg cgctcctgta tcaaccgttc ctctcttatc
     4501 tccagttctc gctgtataac tggctcaagc gttctgtctg ctcgctcaag tgctgcacct
     4561 gctgactcaa ctgcatgacc cgctcgttca gcatcgcgtt gtcccgttgc gt
//
