LOCUS       CP057950                4612 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB09-C13 plasmid pRHB09-C13_5, complete
            sequence.
ACCESSION   CP057950
VERSION     CP057950.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148045
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-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 86.802886913202x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 12:26:05
            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)                     :: 4,943
            CDSs (total)                      :: 4,824
            Genes (coding)                    :: 4,680
            CDSs (with protein)               :: 4,680
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 144
            CDSs (without protein)            :: 144
            Pseudo Genes (ambiguous residues) :: 0 of 144
            Pseudo Genes (frameshifted)       :: 47 of 144
            Pseudo Genes (incomplete)         :: 81 of 144
            Pseudo Genes (internal stop)      :: 46 of 144
            Pseudo Genes (multiple problems)  :: 27 of 144
            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-C13"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB09-C13_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(113..436)
                     /locus_tag="HVW28_24685"
     CDS             complement(113..436)
                     /locus_tag="HVW28_24685"
                     /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="QMO99675.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            501..692
                     /locus_tag="HVW28_24690"
     CDS             501..692
                     /locus_tag="HVW28_24690"
                     /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="QMO99676.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1906..2568
                     /locus_tag="HVW28_24695"
     CDS             1906..2568
                     /locus_tag="HVW28_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="QMO99680.1"
                     /translation="MELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEI
                     IGINYYTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKH
                     HLKNPNQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVK
                     SELSLYIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(2689..2925)
                     /locus_tag="HVW28_24700"
     CDS             complement(2689..2925)
                     /locus_tag="HVW28_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="QMO99677.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(3289..3522)
                     /gene="mbeD"
                     /locus_tag="HVW28_24705"
     CDS             complement(3289..3522)
                     /gene="mbeD"
                     /locus_tag="HVW28_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="QMO99678.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     gene            complement(3529..4047)
                     /locus_tag="HVW28_24710"
     CDS             complement(3529..4047)
                     /locus_tag="HVW28_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="QMO99679.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            complement(4025..4606)
                     /locus_tag="HVW28_24715"
                     /pseudo=""
     CDS             complement(4025..4606)
                     /locus_tag="HVW28_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"
     Typing          complement(778..863)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          885..1414
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.533"
                     /coverage="99.0"
                     /evalue="2.98e-155"
     Typing          complement(117..469)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.305"
                     /coverage="100.0"
                     /evalue="6.050000000000001e-70"
     Typing          complement(3186..4612)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.238"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccggacttct tccgggttac cctgaagcac ctttgcgccc tcccggttac gctccctccc
       61 cagcaggtaa tcaaccggac cactgccacc gccttttccc ctggcatgaa acttaactat
      121 catcccgcgt cccctgttcc ctgacggcca gacgcagccg gcgcagctca tccccgatgg
      181 ccatcagtgc ggccaccacc tgaacccggt caccggaaga ccactgcccg ctgttcacct
      241 tcctcgctgt ctgattcagg ttattcccga tggcggccag ctgacgcagt aacggcggtg
      301 ccagtgtcgg cagtttcccg gaacgggcaa ccggctcccc caggcagacc cgccgcatcc
      361 ataccgccag ttgtttaccc tcacagcgtt caagtaacct ggcatgttca tcatcagtaa
      421 cccgtatcgt gagcatcctc tcgcgtttca tcggtatcat tacccccatg aacagaaatc
      481 ccccttacac ggaggcatca gtgaccaaac aggaaaaaac cgcccttaac atggcccgct
      541 ttataagaag ccagacatta acgctgctgg agaagctcaa cgaactggac gcagatgaac
      601 aggccgatat ttgtgaatca cttcacgacc acgccgacga gctttaccgc agctgcctcg
      661 cacgcttcgg ggatgacggt gaaaacctct gacacataca gctcccggag acggtcacag
      721 cttgtctgtg agcggatgcc gggagcagac aagcccgtca gggcgcgtca gggggtttta
      781 gcgggtgtcg gggcgcagcc atgacccagt cacgtagcga tagcggagtg tatactggct
      841 taactatgtg gcatcagtgc agattataag aaaagagcac catatgcggt gtgaaatacc
      901 gcacagatgc gtaaggagaa aataccgcat caggcgctct tccgcttcct cgctcactga
      961 ctcgctacgc tcggtcgttc ggctgcggcg agcggtatca gctcacgcaa agacggtaat
     1021 gcggttatcc acagaatcag gggataaggc cggaaagaac atgtgaacaa aaaggcaaaa
     1081 ccagggaaaa aggccgcgcc gcaggcgttt ttccataggc tccgcccccc tgacgagcat
     1141 cacaaaaatt gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag
     1201 gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc ctgcctttcg gtgtaccggt
     1261 gtcattccgc tgttatggcc gcggtttctc attccacgcc tgacactcgg ctccgggaag
     1321 gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccgctgcgtc
     1381 ttatccggta actatcaact tgagtccaac ccggaaagac acgactaatc gccattggca
     1441 acggccactg gtaaacagga tgtgcgagag atgtatcgag agttcttgaa gtggcggcct
     1501 gactacggct acactgaaag gacagatttg gtgacatgtc tcgcacaaga ccgttaccgc
     1561 ggttagagaa tctgccagga ttaactaacc ttcgaaaaac cacctgccag ggtggttttt
     1621 tcgttttcaa agcaggagat tacgcgcaga aaaaaaggat ctcaagaaga tcttttctcc
     1681 tttaggtagg gcttacttcg tcaccatata aaacatttgc actagacaaa aaaaatgcaa
     1741 taatgttggt acagacctgt ggcgtgccgc aggcgaagaa acaacccccc tgtggcgtgc
     1801 cgcaggcgaa gaaacaaccc tcctgtggcg agccgcaggc aaacacccct cctacggcgt
     1861 gccgtaggaa aaaaaaccgc agatgcggtt ttttttatat ctaaaatgga gctaacccca
     1921 ttgaaaacaa tagtttatgt tgatggcttt aacttttatt atcgtaagct gaaagattcc
     1981 aacaaaaagt ggctgaacat aaaagcaatg gtcgaaaaat tgctaccgga tgatgaaata
     2041 ataggaatta actattacac ggctaggatc tcaggaagga ttgattctga cgcacctcgt
     2101 aggcaacaaa tatatttcaa tgcactgaaa agcatagata acctaagtat ccattatggt
     2161 actttttcgg tgaatgaaag cagaatgttt ttagtgcagc ctcttgattt caaacatcac
     2221 ttaaaaaacc cgaatcaaaa aataaagttt gcaaacgtct taaagacaga agaaaagggt
     2281 tctgacgtta atttaggttg ccacttggtt agagatggtt tccaagggaa atacgagaag
     2341 gctgtaataa taactaatga tacagatttg gctgaaccaa tgagagtagt caaatcagag
     2401 ctcagccttt atattgaact actttctcct gtaaacaaac cagcaagaac cctgagcgca
     2461 atatgcgata aggtcactct tataagcgac caatcaatag ctgatagcca gtttgaagac
     2521 gttattgtag ttggtgagaa aaccgtgaca aaaccagcac agtggtagtg gctacatact
     2581 cgttctgttg aaaaaaagcc cgtcccccgg gctttttatg ttttgcatta taccttcagg
     2641 caaatataaa gagtatgaaa tctatagcta tgtgcagaaa ataaaaaatt agctaatagc
     2701 acttaaaata gcaaagtgag ttgcaggatc tgtactttca ttttcaaaat gaacagataa
     2761 gttactattt ctagtatttc tagagataca acatgcaaaa ccagtgtcga aagaacactt
     2821 caatgtatat ccatttggtt gtacttttga gccaacatat ccttgagatg tctggatcaa
     2881 cgtcatcaaa gcagtatatt tttcacgatc aataataata ctcatcacat ccccattagt
     2941 attactctgc aggcattaaa cctcagcaat aaatctattt accataactc ccgttgcccg
     3001 caccgcctca gacgctctca gcgcgtttct gacgggaaac cggaaaaaca ggcaacaaac
     3061 ctcccgaaaa actgccgcga tcgcgcctga taaattttaa ccgcatgaat acctatgcaa
     3121 caagatggtg cagactacat tagtccgtca aaatccactg aacctgccat ttttcatagt
     3181 ttcaccatcc cagcgaaggg ccatccagcg tgcgttcctg tatttccggc tgacgctccc
     3241 gttccaggga taacgcatat tcgcgctcct gtatcaaccg ttcctctctt atctccagtt
     3301 ctcgctgtat aactggctca agcgttctgt ctgctcgctc aagtgctgca cctgctgact
     3361 caactgcatg acccgctcgt tcagcatcgc gttgtcccgt tgcgtaagcg aaaacatctt
     3421 ctgcaattcc acgaaggcgc tctcccattc gctcagccgc tgcatatagt cctgttgcag
     3481 ctgctctaag gcgttcagca aatgtgtttc cagctctgtc actctgtgtc accccttcag
     3541 atgtacccat tccttcccct gaaaggaaat cacctctgct gacttcccgt aaggaaggac
     3601 cagaaatttc ctgttcccgt cctgcacaaa ctccacgccc catgtcttcg cgttcagttt
     3661 ctgcaatgtc tcttcctgct tcctgatatc ttccaggttc gcctgtatcc tcccgccaag
     3721 ataccagagc gtcccgccac tcacggtaaa caggagaaag actatcccca gcaacatcat
     3781 gcccgtattc cctgccagct ttaacacgtc cctcctgtgc tgcatcatcg cctctttcac
     3841 cccttcccgg tgtttttcca gagattcctc tgtcgaggct gtgaacaggg ctatagcgtc
     3901 tctgattttc gtctcgtttg atgtcacagc ctcgcttaca gattcgccga gcctcctgaa
     3961 ctcgttgttc agcattttct ctgtagattc ggctctctct ttcagctttt tctcgaactc
     4021 cgcgcccgtc tgcaaaagat tgctcataaa atgctccttt cagcctgata ttcttcccac
     4081 cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct gaccacttca agccctgcct
     4141 ctgtgagcgc ctgaatcaca tcctgacggc cttttatctc cccgacatga taaagagcgt
     4201 ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt ttccggcagg ttatcaggga
     4261 gagtcagtat ccggcggttc tccggggcgt tggggtcatg cagcccgtaa tggtgattca
     4321 ccagcgtctg ccaggcatca attctcggcc tgtctgcgcg gtcgtagtac ggctggaggc
     4381 gttttccgct ctgtagctcc atgttcggaa tgacaaaatt aagctcaagc cgccccttgt
     4441 cctggtgctc cacccacaga atgctgtact gatttttttc gagaccgggc atcagtacac
     4501 gctcaaaact cgccatcact ttttcacgtc ctcccggcgg cagttccttc tccgcgaacg
     4561 acagaacacc ggacgtgtat ttcttcgcaa atggcgtggc atcgatgagt tc
//
