LOCUS       CP057929                4612 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB09-C23 plasmid pRHB09-C23_3, complete
            sequence.
ACCESSION   CP057929
VERSION     CP057929.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148053
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-C23
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 95.6200003260411x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 12:11:00
            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)                    :: 4,598
            CDSs (with protein)               :: 4,598
            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)              :: 143
            CDSs (without protein)            :: 143
            Pseudo Genes (ambiguous residues) :: 0 of 143
            Pseudo Genes (frameshifted)       :: 46 of 143
            Pseudo Genes (incomplete)         :: 81 of 143
            Pseudo Genes (internal stop)      :: 46 of 143
            Pseudo Genes (multiple problems)  :: 27 of 143
            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-C23"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB09-C23_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(855..1046)
                     /locus_tag="HVW36_24270"
     CDS             complement(855..1046)
                     /locus_tag="HVW36_24270"
                     /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="QMO72116.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1111..1434
                     /locus_tag="HVW36_24275"
     CDS             1111..1434
                     /locus_tag="HVW36_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="QMO72117.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1592..2134
                     /locus_tag="HVW36_24280"
                     /pseudo=""
     CDS             1592..2134
                     /locus_tag="HVW36_24280"
                     /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            2112..2630
                     /locus_tag="HVW36_24285"
     CDS             2112..2630
                     /locus_tag="HVW36_24285"
                     /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="QMO72118.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            2637..2870
                     /gene="mbeD"
                     /locus_tag="HVW36_24290"
     CDS             2637..2870
                     /gene="mbeD"
                     /locus_tag="HVW36_24290"
                     /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="QMO72119.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     gene            3234..3470
                     /locus_tag="HVW36_24295"
     CDS             3234..3470
                     /locus_tag="HVW36_24295"
                     /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="QMO72120.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(3591..4253)
                     /locus_tag="HVW36_24300"
     CDS             complement(3591..4253)
                     /locus_tag="HVW36_24300"
                     /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="QMO72121.1"
                     /translation="MELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEI
                     IGINYYTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKH
                     HLKNPNQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVK
                     SELSLYIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     Typing          685..770
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          complement(131..659)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.636"
                     /coverage="98.0"
                     /evalue="3.01e-155"
     Typing          1425..2974
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.42"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgcgagaca tgtcaccaaa tctgtccttt cagtgtagcc gtagtcaggc cgccacttca
       61 agaactctcg atacatctct cgcacatcct gtttaccagt ggccgttgcc aatggcgatt
      121 agtcgtgtct ttccgggttg gactcaagtt gatagttacc ggataagacg cagcggtcgg
      181 actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc ccggagccga
      241 gtgtcaggcg tggaatgaga aaccgcggcc ataacagcgg aatgacaccg gtacaccgaa
      301 aggcaggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata
      361 gtcctgtcgg gtttcgccac ctctgacttg agcgtcaatt tttgtgatgc tcgtcagggg
      421 ggcggagcct atggaaaaac gcctgcggcg cggccttttt ccctggtttt gcctttttgt
      481 tcacatgttc tttccggcct tatcccctga ttctgtggat aaccgcatta ccgtctttgc
      541 gtgagctgat accgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga
      601 agcggaagag cgcctgatgc ggtattttct ccttacgcat ctgtgcggta tttcacaccg
      661 catatggtgc tcttttctta taatctgcac tgatgccaca tagttaagcc agtatacact
      721 ccgctatcgc tacgtgactg ggtcatggct gcgccccgac acccgctaaa accccctgac
      781 gcgccctgac gggcttgtct gctcccggca tccgctcaca gacaagctgt gaccgtctcc
      841 gggagctgta tgtgtcagag gttttcaccg tcatccccga agcgtgcgag gcagctgcgg
      901 taaagctcgt cggcgtggtc gtgaagtgat tcacaaatat cggcctgttc atctgcgtcc
      961 agttcgttga gcttctccag cagcgttaat gtctggcttc ttataaagcg ggccatgtta
     1021 agggcggttt tttcctgttt ggtcactgat gcctccgtgt aagggggatt tctgttcatg
     1081 ggggtaatga taccgatgaa acgcgagagg atgctcacga tacgggttac tgatgatgaa
     1141 catgccaggt tacttgaacg ctgtgagggt aaacaactgg cggtatggat gcggcgggtc
     1201 tgcctggggg agccggttgc ccgttccggg aaactgccga cactggcacc gccgttactg
     1261 cgtcagctgg ccgccatcgg gaataacctg aatcagacag cgaggaaggt gaacagcggg
     1321 cagtggtctt ccggtgaccg ggttcaggtg gtggccgcac tgatggccat cggggatgag
     1381 ctgcgccggc tgcgtctggc cgtcagggaa caggggacgc gggatgatag ttaagtttca
     1441 tgccagggga aaaggcggtg gcagtggtcc ggttgattac ctgctgggga gggagcgtaa
     1501 ccgggagggc gcaaaggtgc ttcagggtaa cccggaagaa gtccgggaac tcatcgatgc
     1561 cacgccattt gcgaagaaat acacgtccgg tgttctgtcg ttcgcggaga aggaactgcc
     1621 gccgggagga cgtgaaaaag tgatggcgag ttttgagcgt gtactgatgc ccggtctcga
     1681 aaaaaatcag tacagcattc tgtgggtgga gcaccaggac aaggggcggc ttgagcttaa
     1741 ttttgtcatt ccgaacatgg agctacagag cggaaaacgc ctccagccgt actacgaccg
     1801 cgcagacagg ccgagaattg atgcctggca gacgctggtg aatcaccatt acgggctgca
     1861 tgaccccaac gccccggaga accgccggat actgactctc cctgataacc tgccggaaac
     1921 gaaacaggcg cttgcagaga gcgtcacacg cgggatagac gctctttatc atgtcgggga
     1981 gataaaaggc cgtcaggatg tgattcaggc gctcacagag gcagggcttg aagtggtcag
     2041 ggtgacgcga agcagtatca gcattgcaga cccgaacggt gggaagaata tcaggctgaa
     2101 aggagcattt tatgagcaat cttttgcaga cgggcgcgga gttcgagaaa aagctgaaag
     2161 agagagccga atctacagag aaaatgctga acaacgagtt caggaggctc ggcgaatctg
     2221 taagcgaggc tgtgacatca aacgagacga aaatcagaga cgctatagcc ctgttcacag
     2281 cctcgacaga ggaatctctg gaaaaacacc gggaaggggt gaaagaggcg atgatgcagc
     2341 acaggaggga cgtgttaaag ctggcaggga atacgggcat gatgttgctg gggatagtct
     2401 ttctcctgtt taccgtgagt ggcgggacgc tctggtatct tggcgggagg atacaggcga
     2461 acctggaaga tatcaggaag caggaagaga cattgcagaa actgaacgcg aagacatggg
     2521 gcgtggagtt tgtgcaggac gggaacagga aatttctggt ccttccttac gggaagtcag
     2581 cagaggtgat ttcctttcag gggaaggaat gggtacatct gaaggggtga cacagagtga
     2641 cagagctgga aacacatttg ctgaacgcct tagagcagct gcaacaggac tatatgcagc
     2701 ggctgagcga atgggagagc gccttcgtgg aattgcagaa gatgttttcg cttacgcaac
     2761 gggacaacgc gatgctgaac gagcgggtca tgcagttgag tcagcaggtg cagcacttga
     2821 gcgagcagac agaacgcttg agccagttat acagcgagaa ctggagataa gagaggaacg
     2881 gttgatacag gagcgcgaat atgcgttatc cctggaacgg gagcgtcagc cggaaataca
     2941 ggaacgcacg ctggatggcc cttcgctggg atggtgaaac tatgaaaaat ggcaggttca
     3001 gtggattttg acggactaat gtagtctgca ccatcttgtt gcataggtat tcatgcggtt
     3061 aaaatttatc aggcgcgatc gcggcagttt ttcgggaggt ttgttgcctg tttttccggt
     3121 ttcccgtcag aaacgcgctg agagcgtctg aggcggtgcg ggcaacggga gttatggtaa
     3181 atagatttat tgctgaggtt taatgcctgc agagtaatac taatggggat gtgatgagta
     3241 ttattattga tcgtgaaaaa tatactgctt tgatgacgtt gatccagaca tctcaaggat
     3301 atgttggctc aaaagtacaa ccaaatggat atacattgaa gtgttctttc gacactggtt
     3361 ttgcatgttg tatctctaga aatactagaa atagtaactt atctgttcat tttgaaaatg
     3421 aaagtacaga tcctgcaact cactttgcta ttttaagtgc tattagctaa ttttttattt
     3481 tctgcacata gctatagatt tcatactctt tatatttgcc tgaaggtata atgcaaaaca
     3541 taaaaagccc gggggacggg ctttttttca acagaacgag tatgtagcca ctaccactgt
     3601 gctggttttg tcacggtttt ctcaccaact acaataacgt cttcaaactg gctatcagct
     3661 attgattggt cgcttataag agtgacctta tcgcatattg cgctcagggt tcttgctggt
     3721 ttgtttacag gagaaagtag ttcaatataa aggctgagct ctgatttgac tactctcatt
     3781 ggttcagcca aatctgtatc attagttatt attacagcct tctcgtattt cccttggaaa
     3841 ccatctctaa ccaagtggca acctaaatta acgtcagaac ccttttcttc tgtctttaag
     3901 acgtttgcaa actttatttt ttgattcggg ttttttaagt gatgtttgaa atcaagaggc
     3961 tgcactaaaa acattctgct ttcattcacc gaaaaagtac cataatggat acttaggtta
     4021 tctatgcttt tcagtgcatt gaaatatatt tgttgcctac gaggtgcgtc agaatcaatc
     4081 cttcctgaga tcctagccgt gtaatagtta attcctatta tttcatcatc cggtagcaat
     4141 ttttcgacca ttgcttttat gttcagccac tttttgttgg aatctttcag cttacgataa
     4201 taaaagttaa agccatcaac ataaactatt gttttcaatg gggttagctc cattttagat
     4261 ataaaaaaaa ccgcatctgc ggtttttttt cctacggcac gccgtaggag gggtgtttgc
     4321 ctgcggctcg ccacaggagg gttgtttctt cgcctgcggc acgccacagg ggggttgttt
     4381 cttcgcctgc ggcacgccac aggtctgtac caacattatt gcattttttt tgtctagtgc
     4441 aaatgtttta tatggtgacg aagtaagccc tacctaaagg agaaaagatc ttcttgagat
     4501 cctttttttc tgcgcgtaat ctcctgcttt gaaaacgaaa aaaccaccct ggcaggtggt
     4561 ttttcgaagg ttagttaatc ctggcagatt ctctaaccgc ggtaacggtc tt
//
