LOCUS       CP058097                5569 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB01-C09 plasmid pRHB01-C09_5, complete
            sequence.
ACCESSION   CP058097
VERSION     CP058097.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147953
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5569)
  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 5569)
  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                     :: RH11 T1-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 90.9454302587345x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:43:09
            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)                     :: 4,860
            CDSs (total)                      :: 4,741
            Genes (coding)                    :: 4,643
            CDSs (with protein)               :: 4,643
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 48 of 98
            Pseudo Genes (incomplete)         :: 42 of 98
            Pseudo Genes (internal stop)      :: 23 of 98
            Pseudo Genes (multiple problems)  :: 15 of 98
            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..5569
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB01-C09"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB01-C09_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(587..1504)
                     /locus_tag="HVV36_24250"
     CDS             complement(587..1504)
                     /locus_tag="HVV36_24250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001189381.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="restriction endonuclease"
                     /protein_id="QMR28354.1"
                     /translation="MQRLSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYF
                     LNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTH
                     IYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVM
                     PGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILY
                     EANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILK
                     QIEKYSDFPYVVNYYRNRLSALFD"
                     /name="restriction endonuclease"
     gene            1614..2753
                     /locus_tag="HVV36_24255"
     CDS             1614..2753
                     /locus_tag="HVV36_24255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="QMR28349.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKKKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="DNA (cytosine-5-)-methyltransferase"
     gene            complement(3119..3352)
                     /gene="mbeD"
                     /locus_tag="HVV36_24260"
     CDS             complement(3119..3352)
                     /gene="mbeD"
                     /locus_tag="HVV36_24260"
                     /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="QMR28350.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(3359..3877)
                     /locus_tag="HVV36_24265"
     CDS             complement(3359..3877)
                     /locus_tag="HVV36_24265"
                     /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="QMR28351.1"
                     /translation="MSNLLQTGVEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(3855..4613)
                     /locus_tag="HVV36_24270"
                     /pseudo=""
     CDS             complement(3855..4613)
                     /locus_tag="HVV36_24270"
                     /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(4555..4878)
                     /locus_tag="HVV36_24275"
     CDS             complement(4555..4878)
                     /locus_tag="HVV36_24275"
                     /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="QMR28352.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4942..5133
                     /locus_tag="HVV36_24280"
     CDS             4942..5133
                     /locus_tag="HVV36_24280"
                     /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="QMR28353.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(5219..5306)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.753"
                     /coverage="100.0"
                     /evalue="1.48e-35"
     Typing          2..343
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.793"
                     /coverage="84.0"
                     /evalue="2.14e-160"
     Typing          5330..5569
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.712"
                     /coverage="99.0"
                     /evalue="9.2e-81"
     Typing          complement(3016..4565)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat
       61 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
      121 cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
      181 cacgctgttg gtatctcggc ccggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
      241 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
      301 cggtaagaca cgccttaacg ccactggcag cagccactgg taaccggatt agcagagcga
      361 gatttatcca gatgcttaca gagttcttga agtgatggcc taactacggc tacactggaa
      421 ggacagtatt tggtatctgt gctctgctga agccagatta cctcggttag ataatctgcc
      481 aggattagct aaccttcgaa aaaaccacct gccagggtgg ttttttcgtt tacaggtcca
      541 agattacgcg cagaaaaaaa ggatctcaag agatcctttt agttttttag tcaaaaagag
      601 cactaagcct atttctataa taattaacaa cataagggaa atcactatat ttttctattt
      661 gttttaatat tgactgttga atttcctctt tttcagagtc tgtgtaactt acattattcc
      721 actttcttga taattccatt gctgactgta gcatatcttc aaaggttagc accctattat
      781 tatttttata tttgaaattt ttattttcta tcgtcgttac aacgaccaca ttagcctcgt
      841 ataatatatt tattgtctcc tcgctaaaag aatcatctag tgtagctaga tacatttctc
      901 taatacctgt tctattaacc tcttcaggta cttcttgcca tcgctccctc agcgttgttt
      961 tagcggaaat caacattgta tttcttttgt tagatgtgta ctggactaca cctggcataa
     1021 caagatctac aagtttacct atttggtttt tttgaaaaaa tgacttccca atagccccct
     1081 gcacatcaac aggaattcct gcccccatca ttaatagctc aagaatagac tcaaactctt
     1141 ttcctgccct gctacgtctg gattgagtgt tagacagtgc caaatcatat atgtgtgtag
     1201 ggtattccat cgtaaaatca cgaatggcat cataaggact catatctttt attctttctt
     1261 catcaataag atatgataac attcttgttg tgaattcttt ttcaaatggt tcaaattctt
     1321 tccaacagtt ttttctcatt gcaattatat attcacttgg attattcaaa aaataatcac
     1381 tatttttttg atcataccct aaatcacaaa atgttttata aaccaaagca aatggcgtaa
     1441 taaaatgcga ctttctctct ttagaaatta gagttttaaa ttcaccagga ctcaatcttt
     1501 gcataaaaaa taacctttta tatctacttg aaagtttttt catgcacgtt cataattgga
     1561 atcaaaacag gacaaattgt cctaaaacca acacttaatt ctggtagaca tgcatgactg
     1621 ataatatcgc agcaacaatc aaaggaaaaa gagaaagact tcatatgact caaaaagagt
     1681 ttgcagacgc ccttggtctt tcaaaatatg gagacagaac cataagaaga tgggagcgcg
     1741 gggaaacaaa acctactggg gcggaactaa aagcagttat ggactttcca gacacaccac
     1801 cttacccaaa caacgagaat ggcagatatc gcatgatcga tttatttgct ggaatcggtg
     1861 gaaccagact tggatttcat caaactaacg ctgtaaatgt tgttttttcc agcgaatggg
     1921 ataagtttgc tcaaaagaca tatcatgcaa attatggtga tttccctgat ggggacataa
     1981 caaaaatcga tgaaaaagat attcctgatc atgaaattct tgtcggtggg tttccttgcg
     2041 tagcattctc tcaagcaggg ctcaaaaaag gatttaatga tacaagagga actttgtttt
     2101 ttgatatagc aaggataata aagaaaaaaa aacctcatgc ttttttactt gaaaatgtaa
     2161 aaaacttgct aggacatgat aaaggtagaa ctttttcaat aataaaaaac acacttgaag
     2221 aattgaatta cactgtgtat tacaatatct tcgctgcaaa agactttggt gttccacaaa
     2281 atagagaacg catatacatt gtaggcttta ataaagaaaa agtaagaaat catgaacatt
     2341 ttacttttcc aaccccatta aaaacaaaaa caagagttgg agatattctt gaaaagagcg
     2401 tagacaataa atatacgcta tcagatgcgc tctggaatgg acaccaacgc aggaaacttg
     2461 taaatgcagc agccggtaaa ggctttgggt atggtttatt taatgaaaat agcccatata
     2521 ctaataccat aagtgcgagg tactataaag atggtagcga aatattaata gagcaaaaag
     2581 gaagtaaccc aagaaaaata actccgcggg aagcgtcaag acttcaaggg tttcctagtg
     2641 attttattat ccctgtatcg gatacacagg cttataagca atttgggaat tcagtcgcag
     2701 tccctgttat caatgcaata gcagaaaaaa tcatatcgac cttagattca taaactaagt
     2761 cataaggaca caatgcggcc cagaatccaa ttccccctcc atatggattt accataacgt
     2821 cgcattacac gcaccgctaa aacgcgttca gcgcgatcac ggcagcagac aggtaaaaat
     2881 ggcaacaaac cacccgaaaa actgccgcga tcgcgcctga taaattttaa ccgcatgaat
     2941 acctatgcaa ccagatggta caggccacat taacccctct taatccactg aagctgccat
     3001 ttttcatggt ttcaccatcc cagcgaagga ccatccagcg tgcgttcctg tatttccggc
     3061 tgacgctccc gttccaggga taacgcatgt tcgcgttcct gtatcagccg ttcgtccctt
     3121 atctcctgtt ctcgctgtat aactggctca agcgttctgt ccgctcgctc aagtgctgca
     3181 cctgctgact caactgcatg acctgctcgt tcagcatcgc gttgtcccgt tgcgtaagcg
     3241 aaaacatttt ctgcaattcc acgaaggcgc tctcccattc gctcagccgc tgcatatagt
     3301 cctgttgcag ttgctctaat gcgttcagca aatgtctttc cagctccgtc actctgtgtc
     3361 actccgtcag ttgtacccag tccttcccct gatagggaat caccgttgcc gatttcccgt
     3421 acggaaggac cagaaatttc cttctcccgt cctgcacaaa ctccacgccc catgtcttcg
     3481 cgttcagttt ctgcaatgtc tcttcctgta tcctgatttc ttccaggttc gcctgtatcc
     3541 gcccgccaag ataccagagc gtcccgccac tcgcggtaaa caggagaaag actatcccca
     3601 gcaacctcat gcccgtattc cctgccagct ttaacatgtc cttccggtgc tgcatcatcg
     3661 cctctttcac cccttcccgg tgttttttca gcgattcctc cgtcgaggcc gtaaactggg
     3721 ctatagcgcc tttgattttc gtctcgtttg aggtcacagc ctcgcttaca gattcgccga
     3781 gcttcctgaa ttcgtcgttc agcattttct ctgtagattc ggctctctct ttcagctttt
     3841 tctcgaactc cacgcccgtc tgtaaaagat tgctcataaa atgctccttt cagcctgata
     3901 ttcttcccgc cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct gaccacttca
     3961 agccctgcct ctgtgagcgc ctgaatcaca tcctgacggc ctcttatctc cccgacatga
     4021 taaagagcgt ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt ttccggcagg
     4081 ttatcaggga gtgtcagtat ccggcggttc tccggggcgt tggggtcatg cagcccgtaa
     4141 tggtgattca ccagcgtctg ccaggcatca attctcggcc tgtctgcccg gtcgtagtac
     4201 ggctggaggc gttttccggt ctgtagctcc atgttcggaa tgacaaaatt cagctcaagc
     4261 cgtcccttgt cctggtgctc cacccacagg atgctgtact gattcttttc gagaccgggc
     4321 atcagtacgc gctcaaagct cgccatcact ttttcacgtc ctcccggcgg cagctccttc
     4381 tccgcgaacg acagaacacc ggacgtgtat ttcttcgcaa atggcgtggc atcgatgagt
     4441 tcccggactt cttccggatt accctgaagc accgttgcgc cttcgcggtt acgctccctc
     4501 cccagcaggt aatcaaccgg accactgcca ccaccttttc ccctggcatg aaatttaact
     4561 atcatcccgc gccccctgtt ccctgacggc cagacgcagc cggcgcagct catccccgat
     4621 ggccatcagt gcggccacta cctgaacccg gtcaccggaa gaccactgcc cgctgttcac
     4681 cttacgggct gtctgattca ggttatttcc gatggcggcc agctgacgca gtaacggcgg
     4741 tgccagtgtc ggcagtttcc cggaacgggc aaccggctca cccaggcaga cccgccgcat
     4801 ccataccgcc agttgtttac cctcacagcg ttcaagtaac ctggcatgtt catcatcagt
     4861 aacccgtatc gtgagcatcc tctcgcgttt catcggtatc attaccccat gaacagaaat
     4921 cccccttaca cggaggcatc agtgactaaa caggaaaaaa cagcccttaa catggcgcgc
     4981 tttatcagaa gccagacatt aacgctgctg gaaaagctca acgaactgga cgcggatgaa
     5041 caggcagaca tctgtgaatc gcttcacgac cacgccgatg agctttaccg cagctgcctc
     5101 gcacgtttcg gggatgacgg tgaaaacctc tgacacatgc agctcccgga gacggtcaca
     5161 gcttgtctgt gagcggatgc cgggagcaga caagcccgtc agggcgcgtc agcaggtttt
     5221 agggggtgtc ggggcgcagc cctgacccag tcacgtagcg atagcggagt gtatactggc
     5281 ttaactatgc ggcatcagtg cggattgtat gaaaagcacg ccatgccggg tgtgaaatgc
     5341 cgcacagatg cgtaaggaga acataccgca tcaggcgctc ttccgcttcc tcgctcactg
     5401 actcgctgcg ctcggtcgtt cggctgcggc aagcggtgcc ggctcactca aaggcggaaa
     5461 tacggttatc cacagaatca ggggataagg ccggaaagaa catgtgagta aaaaggcaaa
     5521 gggcaacaaa aggccgcgcc gctggcgttt ttccataggc tccgccccc
//
