LOCUS       CP056959                4593 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C22 plasmid pRHB41-C22_5, complete
            sequence.
ACCESSION   CP056959
VERSION     CP056959.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148430
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4593)
  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 4593)
  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                     :: RH01 T3-C22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 147.446626226081x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 03:49:53
            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)                     :: 4,816
            CDSs (total)                      :: 4,694
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 52 of 136
            Pseudo Genes (incomplete)         :: 82 of 136
            Pseudo Genes (internal stop)      :: 22 of 136
            Pseudo Genes (multiple problems)  :: 20 of 136
            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..4593
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C22"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C22_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3861..4593,1..107)
                     /locus_tag="HV013_24040"
     CDS             join(3861..4593,1..107)
                     /locus_tag="HV013_24040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMA99499.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(795..1028)
                     /gene="mbeD"
                     /locus_tag="HV013_24045"
     CDS             complement(795..1028)
                     /gene="mbeD"
                     /locus_tag="HV013_24045"
                     /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="QMA99500.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="mbeD"
     gene            complement(1035..1595)
                     /locus_tag="HV013_24050"
     CDS             complement(1035..1595)
                     /locus_tag="HV013_24050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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="QMA99501.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(1570..2283)
                     /locus_tag="HV013_24055"
                     /pseudo=""
     CDS             complement(1570..2283)
                     /locus_tag="HV013_24055"
                     /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(2273..2596)
                     /locus_tag="HV013_24060"
     CDS             complement(2273..2596)
                     /locus_tag="HV013_24060"
                     /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="QMA99503.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2659..2850
                     /locus_tag="HV013_24065"
     CDS             2659..2850
                     /locus_tag="HV013_24065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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="QMA99502.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2939..3023)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(3411..3862)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(698..2283)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgacagagtc attagaaatg gagttactag aatacttaga gttaagaaat gaattattca
       61 atgacataga agaagtaatg ggtagctatg ctcagagggc accatagttc atgatagtcc
      121 tcgatagtac ttacttatat ttttagagag gtttaagtgt aagtagaggg agtaacacct
      181 ggtttttcag catccactcc aatgaatgct gacaccgata cgcgataatt ctctttatcg
      241 tagcaaaatc atcctccaga ttgcggttga gaataggttc atggtgcgca atacgattgc
      301 gcagttttct cacgggactt gttagcagta atgcttcccc ccggggacaa acgacagaga
      361 tatacaacaa aggcccgcaa ttaaaatact ccgtatttac cataacgtcg cattgcgcgt
      421 accgcttaaa cgcgttcagc gcgatcacgg cagcagacag gtaaaaacag caacaaacca
      481 cccgaaaaac tgccgcgatc gcgcctggta aattttaacc tcatgcatag ttatgcgcga
      541 aactgaatga cgatcagttt cgcacgttcc agccgtcgaa cggggcaaaa tggggaggtt
      601 tggatattgt taatgctaat gtacgtacat taacattggc gccatccggg tagggcgtgc
      661 cacaaactgg ctcgatttca gggggtaccc cggtcacatc cccattgacg ggccacgcca
      721 gatccgcgct tcgggttcct gctcttcatg ccagcgccgg gcaagctcct gcgcctgacg
      781 ctcctgttca tcccttatct gttgttcgtg ataaataacc gactcaagcg gtcgacttgc
      841 ccggctaata gctgcacctg ctgactcaag ttcacgacac gctcgttcag tatcgcgttg
      901 ttctgttgcg taaccgcgtg catcttctgc aattctgcga aggcgctctc ccactcgttc
      961 agccgccgca tatagtcctg ttgcaaatgc tctaaggcgt tcagcaaatg cccttccagt
     1021 tccgtcatac tcgtttactc cctgaccagc ctcacggcgt tcttgtcgcc caccgtccag
     1081 gtgttttccc ctttcacccc gtccggcagc accagaaatt tcccgttctc gccattgacg
     1141 aacgtcaccc cccaggtttt tgcctcgagt ttcgccagcg tgttttcctg ctctctgatg
     1201 gtcaagatat ttttcgcaat cctgctttcc tgccactgaa tcagccccca gcaccccagg
     1261 aaaatgccgc ccgtgacgct gagcgcggtc agcgccggaa acagtacccg ccctttgatc
     1321 acctgccaga gcaggttttt ctgctgccgg gacagttcgg cctctgtggt gctgagctgc
     1381 gtgctcacgg tggtgctcag cgtatccagt tgctgtttca cggatgttgt atgttcgctg
     1441 atagcgtctc tgattttctg cctgtttaag ctcagtgcct tgtctacaga ctcttctagc
     1501 ttcctgaact cgctgttcag catgttctcg gtagaagcgg ctcgctcttt cagtttcttc
     1561 tcgaagtccg ttcccatttg taaaagattg ctcatacagc gcccccttta gcctgagatt
     1621 ccgccccccc tccgggtcgg caatactgat actgcttctg gttgtcctca ccacctcaaa
     1681 acctgccgct gtgagcgcct cagtgacatc ctgacgcgtt tttattgctc cggcacggta
     1741 aagcgcctca agaccccgtg taatcgcttc tgcggcctcc tgtttcgctt ttggcagatt
     1801 attcggtgtg acaagcgtcc gtctgttctc cggtgcgttc gggtcacgca gcccgtaatg
     1861 atgattaacc agcgtctgcc aggcatttat cctcggcctg tccgcacggt cgtagtacgg
     1921 ctggaggcgc ttaccgctct gtagttccat gttcggaatg acaaaattca gttcgagccg
     1981 ccccttatcc tggtgttcca cccagagaat gctgtactgg tctttttcga gaccgggcat
     2041 aagaacacgc tcaaagctcg tcatcactct ttcgcgttca cccggcggta actccttctc
     2101 cgcgaacgac agaacgcctg acgtgtattt cttcgaaaat ggcgtggcat caatgagttc
     2161 ccggatttct tccgggttac cccggagcac cgttgcgcct tcgcggttac gctcccgccc
     2221 cagcaggtaa tcgaccgggc cacttccacc gcctttcccc ctggcatgaa atttaactat
     2281 catcccgtcc cccctgttcc ctgacagcct gccgcaactg gcgcaattca ccctcgatgg
     2341 ccatcagagc ggccaccaca tgaacccggt caatcgaaga ccagtggccg ctgttcacct
     2401 tccgggctgt ctggttcaga ttgttcccga tggcagccag atgccgcagc aatggcggcg
     2461 atagtgtcgg cagttttcct gtgcgcgcaa ccggctcccc cagacagacc cgccgcatcc
     2521 attctgccag tcgtttaccc tcgcagcgtt ccagtaaccg ggcgtgctcc tcatcgctaa
     2581 cccgtatcgt gagcatcttc tcgcgtttca tcggtatcat tccccctaaa aaatccccta
     2641 ttaaggagcc ttaagaccat gaccaaacag gaaaaaacag cccttaacat ggcccgcttt
     2701 atcagaagcc agacgctgac cctgctggaa aaactcaacg agctggacgc ggacgaacag
     2761 gcagacatct gcgaatcact tcacgaccac gccgacgaac tctaccgtag ttgcctcgca
     2821 cgcttcggcg atgacggtga aagcaactga aacatgcagc tcccggagac gttcacagct
     2881 tgcctgtgag cggatgccgg gagcagacaa gcccgtcagg gcgcgtcagc gggttttagc
     2941 gggtgtcggg gcgcagccct gacccagtca cgtagcgata gcggagtgta tactggctta
     3001 actatgtggc atcagtgcgg attataagaa aagtgcacca tatgcggtgt gaaataccgc
     3061 acagatgcgt aaggagaaaa tgccgcatca ggcgctcttc cgcttcctcg ctcactgact
     3121 cgctacgctc ggtcgttcgg ctgcggcgag cggtatcagc tcactcaaag acggtgatgc
     3181 ggttatccac agaatcaggg gataacgcca aaagaaacat gtgagcaaaa ggccaggaac
     3241 aggaagaagg ctgcgccgct ggcgtttttc cataggctcc gcccccctga cgagcatcac
     3301 aaaaacagat gctcaagtca gaggtggcga aacccgacag gactataaag ataccaggcg
     3361 tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac
     3421 ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgttggtat
     3481 ctcggcccgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag
     3541 cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccgga aagacacgta
     3601 aaaacgccac tggcagcagc cattggtaac cgtttagagg agttagtctt gaagttatgc
     3661 gccggttaag gctaaactga aaggacagat ttggtggctg tgctcctcca agccagttac
     3721 cttggttcaa agagttgctg ctctgagaac cttcgaaaag ccgccttgct gggcggtttt
     3781 ttcgtttacg gacaagacta ccttcaggat cgttagatct caagacaatc atgcatagtg
     3841 agcatacaca ggagccgaac ttgcttacac tgttcatctt ttttgtttta ttaatagctg
     3901 catgtttctt ttgttttgct ccaccacgaa gaggatatga cagaaatgag atcattccat
     3961 acaaaataaa actatcaata aataaatatc gcctttacat atactcatcg ggaaaggtaa
     4021 gacaatacct tttattttta gttattttat cactgtacta ctccatagcg gaaccattta
     4081 agtctgagtt aataaaaaac atatcatatt cactgatggc tgcatttatt tttgatacag
     4141 ggcttaattt tagcaaggag aatataacta aaggagtgat ttcaacaagg tggcataatg
     4201 acctatattc atcatttgag agaatgaaag caattaataa aatttactac ccatccaaca
     4261 aagagataaa cacagaaggt ctatccaaag ccatcacatc atctcttttc aatgatgacg
     4321 cgaactcgtt cgcaaagaga gattttcgct tgatgtggga cttatcttct gaaaaatatc
     4381 tttcctataa agaaataata ataagaaaag gcgataagct tgacgctgta tgcttgagat
     4441 ttataaatga tgactacaag tttttagtta atttcaacag agatgaagag gttttcaaat
     4501 actttccatc tataatgcaa ccttcactca aaacatatag agcgttatca agactagtaa
     4561 actcaatcaa agatccttct agatttaagt tca
//
