LOCUS       CP058108                5569 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB01-C04 plasmid pRHB01-C04_5, complete
            sequence.
ACCESSION   CP058108
VERSION     CP058108.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15147948
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-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 115.102049370518x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 14:38:15
            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)                     :: 4,859
            CDSs (total)                      :: 4,740
            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)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 47 of 97
            Pseudo Genes (incomplete)         :: 42 of 97
            Pseudo Genes (internal stop)      :: 23 of 97
            Pseudo Genes (multiple problems)  :: 15 of 97
            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-C04"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB01-C04_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5250..5569,1..4))
                     /locus_tag="HVV31_24245"
     CDS             complement(join(5250..5569,1..4))
                     /locus_tag="HVV31_24245"
                     /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="QMR37930.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            68..259
                     /locus_tag="HVV31_24250"
     CDS             68..259
                     /locus_tag="HVV31_24250"
                     /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="QMR37926.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1282..2199)
                     /locus_tag="HVV31_24255"
     CDS             complement(1282..2199)
                     /locus_tag="HVV31_24255"
                     /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="QMR37931.1"
                     /translation="MQRLSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYF
                     LNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTH
                     IYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVM
                     PGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILY
                     EANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILK
                     QIEKYSDFPYVVNYYRNRLSALFD"
                     /name="restriction endonuclease"
     gene            2309..3448
                     /locus_tag="HVV31_24260"
     CDS             2309..3448
                     /locus_tag="HVV31_24260"
                     /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="QMR37927.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKKKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="DNA (cytosine-5-)-methyltransferase"
     gene            complement(3814..4047)
                     /gene="mbeD"
                     /locus_tag="HVV31_24265"
     CDS             complement(3814..4047)
                     /gene="mbeD"
                     /locus_tag="HVV31_24265"
                     /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="QMR37928.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(4054..4572)
                     /locus_tag="HVV31_24270"
     CDS             complement(4054..4572)
                     /locus_tag="HVV31_24270"
                     /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="QMR37929.1"
                     /translation="MSNLLQTGVEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(4550..5308)
                     /locus_tag="HVV31_24275"
                     /pseudo=""
     CDS             complement(4550..5308)
                     /locus_tag="HVV31_24275"
                     /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(345..432)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.753"
                     /coverage="100.0"
                     /evalue="1.48e-35"
     Typing          456..1001
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.536"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3711..5260)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcatcctctc gcgtttcatc ggtatcatta ccccatgaac agaaatcccc cttacacgga
       61 ggcatcagtg actaaacagg aaaaaacagc ccttaacatg gcgcgcttta tcagaagcca
      121 gacattaacg ctgctggaaa agctcaacga actggacgcg gatgaacagg cagacatctg
      181 tgaatcgctt cacgaccacg ccgatgagct ttaccgcagc tgcctcgcac gtttcgggga
      241 tgacggtgaa aacctctgac acatgcagct cccggagacg gtcacagctt gtctgtgagc
      301 ggatgccggg agcagacaag cccgtcaggg cgcgtcagca ggttttaggg ggtgtcgggg
      361 cgcagccctg acccagtcac gtagcgatag cggagtgtat actggcttaa ctatgcggca
      421 tcagtgcgga ttgtatgaaa agcacgccat gccgggtgtg aaatgccgca cagatgcgta
      481 aggagaacat accgcatcag gcgctcttcc gcttcctcgc tcactgactc gctgcgctcg
      541 gtcgttcggc tgcggcaagc ggtgccggct cactcaaagg cggaaatacg gttatccaca
      601 gaatcagggg ataaggccgg aaagaacatg tgagtaaaaa ggcaaagggc aacaaaaggc
      661 cgcgccgctg gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg
      721 ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg
      781 aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt
      841 tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgttggtatc tcggcccggt
      901 gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg
      961 cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgcct taacgccact
     1021 ggcagcagcc actggtaacc ggattagcag agcgagattt atccagatgc ttacagagtt
     1081 cttgaagtga tggcctaact acggctacac tggaaggaca gtatttggta tctgtgctct
     1141 gctgaagcca gattacctcg gttagataat ctgccaggat tagctaacct tcgaaaaaac
     1201 cacctgccag ggtggttttt tcgtttacag gtccaagatt acgcgcagaa aaaaaggatc
     1261 tcaagagatc cttttagttt tttagtcaaa aagagcacta agcctatttc tataataatt
     1321 aacaacataa gggaaatcac tatatttttc tatttgtttt aatattgact gttgaatttc
     1381 ctctttttca gagtctgtgt aacttacatt attccacttt cttgataatt ccattgctga
     1441 ctgtagcata tcttcaaagg ttagcaccct attattattt ttatatttga aatttttatt
     1501 ttctatcgtc gttacaacga ccacattagc ctcgtataat atatttattg tctcctcgct
     1561 aaaagaatca tctagtgtag ctagatacat ttctctaata cctgttctat taacctcttc
     1621 aggtacttct tgccatcgct ccctcagcgt tgttttagcg gaaatcaaca ttgtatttct
     1681 tttgttagat gtgtactgga ctacacctgg cataacaaga tctacaagtt tacctatttg
     1741 gtttttttga aaaaatgact tcccaatagc cccctgcaca tcaacaggaa ttcctgcccc
     1801 catcattaat agctcaagaa tagactcaaa ctcttttcct gccctgctac gtctggattg
     1861 agtgttagac agtgccaaat catatatgtg tgtagggtat tccatcgtaa aatcacgaat
     1921 ggcatcataa ggactcatat cttttattct ttcttcatca ataagatatg ataacattct
     1981 tgttgtgaat tctttttcaa atggttcaaa ttctttccaa cagttttttc tcattgcaat
     2041 tatatattca cttggattat tcaaaaaata atcactattt ttttgatcat accctaaatc
     2101 acaaaatgtt ttataaacca aagcaaatgg cgtaataaaa tgcgactttc tctctttaga
     2161 aattagagtt ttaaattcac caggactcaa tctttgcata aaaaataacc ttttatatct
     2221 acttgaaagt tttttcatgc acgttcataa ttggaatcaa aacaggacaa attgtcctaa
     2281 aaccaacact taattctggt agacatgcat gactgataat atcgcagcaa caatcaaagg
     2341 aaaaagagaa agacttcata tgactcaaaa agagtttgca gacgcccttg gtctttcaaa
     2401 atatggagac agaaccataa gaagatggga gcgcggggaa acaaaaccta ctggggcgga
     2461 actaaaagca gttatggact ttccagacac accaccttac ccaaacaacg agaatggcag
     2521 atatcgcatg atcgatttat ttgctggaat cggtggaacc agacttggat ttcatcaaac
     2581 taacgctgta aatgttgttt tttccagcga atgggataag tttgctcaaa agacatatca
     2641 tgcaaattat ggtgatttcc ctgatgggga cataacaaaa atcgatgaaa aagatattcc
     2701 tgatcatgaa attcttgtcg gtgggtttcc ttgcgtagca ttctctcaag cagggctcaa
     2761 aaaaggattt aatgatacaa gaggaacttt gttttttgat atagcaagga taataaagaa
     2821 aaaaaaacct catgcttttt tacttgaaaa tgtaaaaaac ttgctaggac atgataaagg
     2881 tagaactttt tcaataataa aaaacacact tgaagaattg aattacactg tgtattacaa
     2941 tatcttcgct gcaaaagact ttggtgttcc acaaaataga gaacgcatat acattgtagg
     3001 ctttaataaa gaaaaagtaa gaaatcatga acattttact tttccaaccc cattaaaaac
     3061 aaaaacaaga gttggagata ttcttgaaaa gagcgtagac aataaatata cgctatcaga
     3121 tgcgctctgg aatggacacc aacgcaggaa acttgtaaat gcagcagccg gtaaaggctt
     3181 tgggtatggt ttatttaatg aaaatagccc atatactaat accataagtg cgaggtacta
     3241 taaagatggt agcgaaatat taatagagca aaaaggaagt aacccaagaa aaataactcc
     3301 gcgggaagcg tcaagacttc aagggtttcc tagtgatttt attatccctg tatcggatac
     3361 acaggcttat aagcaatttg ggaattcagt cgcagtccct gttatcaatg caatagcaga
     3421 aaaaatcata tcgaccttag attcataaac taagtcataa ggacacaatg cggcccagaa
     3481 tccaattccc cctccatatg gatttaccat aacgtcgcat tacacgcacc gctaaaacgc
     3541 gttcagcgcg atcacggcag cagacaggta aaaatggcaa caaaccaccc gaaaaactgc
     3601 cgcgatcgcg cctgataaat tttaaccgca tgaataccta tgcaaccaga tggtacaggc
     3661 cacattaacc cctcttaatc cactgaagct gccatttttc atggtttcac catcccagcg
     3721 aaggaccatc cagcgtgcgt tcctgtattt ccggctgacg ctcccgttcc agggataacg
     3781 catgttcgcg ttcctgtatc agccgttcgt cccttatctc ctgttctcgc tgtataactg
     3841 gctcaagcgt tctgtccgct cgctcaagtg ctgcacctgc tgactcaact gcatgacctg
     3901 ctcgttcagc atcgcgttgt cccgttgcgt aagcgaaaac attttctgca attccacgaa
     3961 ggcgctctcc cattcgctca gccgctgcat atagtcctgt tgcagttgct ctaatgcgtt
     4021 cagcaaatgt ctttccagct ccgtcactct gtgtcactcc gtcagttgta cccagtcctt
     4081 cccctgatag ggaatcaccg ttgccgattt cccgtacgga aggaccagaa atttccttct
     4141 cccgtcctgc acaaactcca cgccccatgt cttcgcgttc agtttctgca atgtctcttc
     4201 ctgtatcctg atttcttcca ggttcgcctg tatccgcccg ccaagatacc agagcgtccc
     4261 gccactcgcg gtaaacagga gaaagactat ccccagcaac ctcatgcccg tattccctgc
     4321 cagctttaac atgtccttcc ggtgctgcat catcgcctct ttcacccctt cccggtgttt
     4381 tttcagcgat tcctccgtcg aggccgtaaa ctgggctata gcgcctttga ttttcgtctc
     4441 gtttgaggtc acagcctcgc ttacagattc gccgagcttc ctgaattcgt cgttcagcat
     4501 tttctctgta gattcggctc tctctttcag ctttttctcg aactccacgc ccgtctgtaa
     4561 aagattgctc ataaaatgct cctttcagcc tgatattctt cccgccgttc gggtctgcaa
     4621 tgctgatact gcttcgcgtc accctgacca cttcaagccc tgcctctgtg agcgcctgaa
     4681 tcacatcctg acggcctctt atctccccga catgataaag agcgtctatc ccgcgtgtga
     4741 cgctctctgc aagcgcctgt ttcgtttccg gcaggttatc agggagtgtc agtatccggc
     4801 ggttctccgg ggcgttgggg tcatgcagcc cgtaatggtg attcaccagc gtctgccagg
     4861 catcaattct cggcctgtct gcccggtcgt agtacggctg gaggcgtttt ccggtctgta
     4921 gctccatgtt cggaatgaca aaattcagct caagccgtcc cttgtcctgg tgctccaccc
     4981 acaggatgct gtactgattc ttttcgagac cgggcatcag tacgcgctca aagctcgcca
     5041 tcactttttc acgtcctccc ggcggcagct ccttctccgc gaacgacaga acaccggacg
     5101 tgtatttctt cgcaaatggc gtggcatcga tgagttcccg gacttcttcc ggattaccct
     5161 gaagcaccgt tgcgccttcg cggttacgct ccctccccag caggtaatca accggaccac
     5221 tgccaccacc ttttcccctg gcatgaaatt taactatcat cccgcgcccc ctgttccctg
     5281 acggccagac gcagccggcg cagctcatcc ccgatggcca tcagtgcggc cactacctga
     5341 acccggtcac cggaagacca ctgcccgctg ttcaccttac gggctgtctg attcaggtta
     5401 tttccgatgg cggccagctg acgcagtaac ggcggtgcca gtgtcggcag tttcccggaa
     5461 cgggcaaccg gctcacccag gcagacccgc cgcatccata ccgccagttg tttaccctca
     5521 cagcgttcaa gtaacctggc atgttcatca tcagtaaccc gtatcgtga
//
