LOCUS       CP055629                3125 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB38-C13 plasmid pRHB38-C13_6, complete
            sequence.
ACCESSION   CP055629
VERSION     CP055629.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148388
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3125)
  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 3125)
  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                     :: RH04 T3-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 141.823032401795x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/18/2020 17:21:02
            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)                     :: 5,514
            CDSs (total)                      :: 5,380
            Genes (coding)                    :: 5,207
            CDSs (with protein)               :: 5,207
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 104
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 173
            CDSs (without protein)            :: 173
            Pseudo Genes (ambiguous residues) :: 0 of 173
            Pseudo Genes (frameshifted)       :: 54 of 173
            Pseudo Genes (incomplete)         :: 109 of 173
            Pseudo Genes (internal stop)      :: 37 of 173
            Pseudo Genes (multiple problems)  :: 21 of 173
            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..3125
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB38-C13"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB38-C13_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            339..1091
                     /locus_tag="HVZ71_27545"
     CDS             339..1091
                     /locus_tag="HVZ71_27545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QLN31214.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGARYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVAG"
                     /name="hypothetical protein"
     gene            complement(1116..1259)
                     /locus_tag="HVZ71_27550"
     CDS             complement(1116..1259)
                     /locus_tag="HVZ71_27550"
                     /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="QLN31215.1"
                     /translation="MNTKVLFVKKALKSITCATLSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     gene            complement(2204..2398)
                     /locus_tag="HVZ71_27555"
     CDS             complement(2204..2398)
                     /locus_tag="HVZ71_27555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="QLN31216.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2682..3005
                     /locus_tag="HVZ71_27560"
     CDS             2682..3005
                     /locus_tag="HVZ71_27560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QLN31217.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          2434..2673
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.17"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          complement(1663..2169)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.226"
                     /coverage="95.0"
                     /evalue="3.85e-154"
     Typing          2683..3002
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.61e-62"
ORIGIN
        1 cagttttcac tgggtaaaac atctcttttt gcggtgtttg cggctgaatc gcgttcagcg
       61 cgttttagcg gtgcgcgtaa ggggagttat ggtaaattgg cagcaaagta ttttctgatg
      121 ttatggattg tgaagagtat tcaatcctta ttatgaaaca ataactataa atggttgttt
      181 catatagata aatataacaa aaaagcccac tctgtagtgg gcttttttgt tatattttac
      241 gctctagagg tacacagaaa aacggtagtt cgcctgctcc tcgaatgttg taatggtagt
      301 ctgaaaaata ttcatagtaa agagataagt gagttttcat ggatacaaca agtttaatta
      361 gctcaatttc tgtaccaaga ttatctttct atgaaacatt tcttgggtgc gctactgatc
      421 aagaaaaggt tggggcatac gttgcctacc aagatctgtc tggcgatttt ttttgtcttg
      481 tccagatgat tgaggttgct ctgcgtaatg cgataaacaa tacaatcaaa gctaatcatg
      541 ggcctgcttg gtacgactct atacctcaaa caaagaaatc tcaggatctt gttttaaatg
      601 cgaaacaaaa agcactagat gagtgtggcg caaggtatac ggatgatgat gttatttgcc
      661 gtctaacctt tggcttttgg gtttatatgt tagatgcccc atatagggat acgcaaaggc
      721 cgtgctacat ctggactcca gagaacaagg caaaaacatt tcctcatgcg aagaatcctt
      781 tgggtggggg ggatatgaag gttaaagcgc tgtttgacga gtttcataaa gttcttttgt
      841 ttaggaatcg actttttcac catgagccta tttggaaaaa acaccactgc aagtcgcata
      901 gtcaagccat aaataatatg ttgaaagagt tcaatttttt aatgaatgcc ttgagtatcg
      961 tctctaacga gaaaaaggaa cttattgagt ttattgggca cgataggcgc ttttatgaac
     1021 gctgcacgat agagtatgtt atggggatta tagggaggat taagtgcagg gagcttaagg
     1081 tagccggttg acttttaagg aaaaatgtga tacaatcaaa agctcttacc ggctttaagt
     1141 cgcgcagccg aaaggctacg taactctgtt actgcgcgac ttaaagccgg taagagcgaa
     1201 agagttgcgc aagtaattga tttcaaagct tttttcacaa aaagaacttt agtattcatt
     1261 ttcataatcc tctatttctt atgccgttct aatggcagcg ttgacttttt attccatcta
     1321 tttgaatggt taattatacc atatctaaca tcaaatctta aggataaata gctgattcac
     1381 atcagttttt ccattaattc acgaagtttt ataatttaat tacggatttc cttgagttca
     1441 tatcgcgccc atcgtaatct taaaaacgaa aaaaccaccc ggcaaggtgg tttttcgaag
     1501 gttcagcaac cggcaagttt ctgaaccgcg gtaactggct taagaggagc gcagtcacca
     1561 aaacttgtta ttccagttta gccttaactg gcacgtaact tcaagactaa ctcctctaaa
     1621 tcagttacca gtggctgctg ccaatggcga taagtcgtgc ctttccgggt tggactcaag
     1681 acgatagtta ccggataagg cgcagtagtc ggactgaacg gggggttcgt gcatacagtc
     1741 cagcttggag cgaactgcct acccggaact gagtgtcagg cgtggaatga gacaaacgcg
     1801 gccataacag cggaatgaca ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg
     1861 agccaccagg gggaaacgcc tggtatcttt aagtcctgtc gggtttcgcc acctctgact
     1921 tgagcgtcga tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgcctgcgg
     1981 cgctggcttc ttccggtgct ttgctttttg ctcacatgtt ctttccggct ttatcccctg
     2041 attctgtgga taaccgtatt accgcttttg agtgagctga caccgctcgc cgcagtcgaa
     2101 cgaccgagcg tagcgagtca gtgagcgagg aagcggaaga gcgccttatg tgacattttc
     2161 tccttacgct cctctatgcc gttctgcatc ctgtccggat gcgttatatc ccggtgcgat
     2221 tttccgcttc aaagcgtgtc tgtatgctgt tctgaagttc ttccgcgagt tcgtgcagct
     2281 tctcacacat ggcggcctgt tcgtcagcat tgagtgcgtc cagtttttcg agcagcgtca
     2341 ggctctggct ttttatgaat cctgccatgt tgagtacggc ttgctgctgc ttgttcatct
     2401 tttcgttttc tccgttctgt ctgtcatctg cgttgtgtga ttatatcgcg taccactttt
     2461 cgactgtttt accgccggta ttctgccgtc tgacgctttg acgggtattt ctgcctgaca
     2521 atactgtcac tgccaaaaaa ctgccgtgtc tttgtcggta attcgaactt gctgacagga
     2581 caggatgtgt aattgttata ccgcgcatgc atgcacgcta ttacaattac cctggtcagg
     2641 gctttgaccc gacacccatg tcagatacgg agccatgttt tatgacaaaa cgaagtggaa
     2701 gtaatacgcg caggcgggct atcagtcgcc ctgttcgtct gacggcagaa gaagaccagg
     2761 aaatcagaaa aagggctgct gaatgcggca agaccgtttc cggtttttta cgggcggcag
     2821 ctctcggtaa gaaagttaac tcactgactg atgatcgggt actgaaagaa gttatgagac
     2881 tgggggcgtt acagaaaaaa ctctttatcg acggcaagcg tgtcggggac agggagtatg
     2941 cggaggtgct gatcgctatt acggagtatc accgtgccct gttatccagg cttatggcag
     3001 attagcttcc cggagagaaa ctgtcgaaaa cagacggtat gaacgccgta agcccccaaa
     3061 ccgatcgcca ttcactttta tgcatagcta tgcagtgagc tgaaaacgat cctgacgcat
     3121 ttttc
//
