LOCUS       CP098960                3758 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB47-C04 plasmid unnamed5, complete
            sequence.
ACCESSION   CP098960
VERSION     CP098960.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488719
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3758)
  AUTHORS   Matlock,W.
  TITLE     Plasmid overlap and evolution between Enterobacterales isolates from
            bloodstream infections and non-human compartments
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3758)
  AUTHORS   Matlock,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2022) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Assembly Name                     :: RHB47-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 135x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:05:17
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.1
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,847
            CDSs (total)                      :: 4,733
            Genes (coding)                    :: 4,500
            CDSs (with protein)               :: 4,500
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 69 of 233
            Pseudo Genes (incomplete)         :: 158 of 233
            Pseudo Genes (internal stop)      :: 50 of 233
            Pseudo Genes (multiple problems)  :: 39 of 233
            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..3758
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB47-C04"
                     /isolation_source="Pooled faeces sample collected from
                     floor of poultry farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3634..3758,1..340))
                     /locus_tag="NFL55_24195"
     CDS             complement(join(3634..3758,1..340))
                     /locus_tag="NFL55_24195"
                     /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="WGC04375.1"
                     /translation="MSSALRIIPDQVDCVDVELKTYLVWRYVKEDHRENDNAVSAVCFC
                     LTERDGGHVSFSHSNKDNVNEMVAEIHRNIHVAKKTKPALYLSIDIKEAYEEINNPDEL
                     ITFKGCGYPHIGMYYHDYSDVAKRNLIIASLVELSDLYFRAEGGGVSKVE"
                     /name="hypothetical protein"
     gene            complement(349..1044)
                     /locus_tag="NFL55_24200"
     CDS             complement(349..1044)
                     /locus_tag="NFL55_24200"
                     /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="WGC04376.1"
                     /translation="MSICYNIEDVKIIDDDLEYSEPLFCSSLGIEGESACVEAYVELGK
                     GIDYSCNSYNNDVNVENYTILLYSKTESRLDLWNDILREINRKTSLRDVDYLYEILSVV
                     DKKGLAEYKSIISKICKVIDEYKGHLNDGVDLSSGAIFQLVRYIPFFFCKKNIDFYLEK
                     DTGFIGVIIPMRKNKKGTLNLTIMNTAEIYYSYVRKKTGLVKFSGKGFLGDDLKNSDAI
                     MSILRMSDW"
                     /name="hypothetical protein"
     gene            complement(1049..1294)
                     /locus_tag="NFL55_24205"
     CDS             complement(1049..1294)
                     /locus_tag="NFL55_24205"
                     /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="WGC04377.1"
                     /translation="MSADKPNKDSQDYIDSFDAMGRELPPAFPLSIRFGVVEDICIIDF
                     IDLPSKNTKKVFYSVAITKDHAKKMMSALKKFVDSE"
                     /name="hypothetical protein"
     gene            2518..2721
                     /locus_tag="NFL55_24210"
     CDS             2518..2721
                     /locus_tag="NFL55_24210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041634.1"
                     /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="WGC04374.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQATMCERLHELA
                     EELQNSIQTHFEAQYGIGVEQP"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2318..2396)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.25"
                     /coverage="83.0"
                     /evalue="3.6300000000000003e-22"
     Typing          2854..3341
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.278"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 gaggataacc acacccctta aatgtaatta gttcatctgg gttatttatt tcctcatacg
       61 cttctttaat atcaattgat aaatataaag caggcttagt tttttttgcc acatgaatat
      121 tacgatggat ctccgctacc atttcattaa cattatcctt gtttgaatga gaaaatgaca
      181 catgcccacc gtctctctct gttaagcaga agcaaacagc agaaactgca ttatcattct
      241 ctctatgatc ttccttaaca tacctccata ccaagtatgt ttttaattca acatctacgc
      301 aatcaacttg atctggtatt attcttaaag cagaactcat ccctatccct accaatcaga
      361 cattctcaat attgacataa ttgcatctga attttttaag tcatccccca aaaaaccttt
      421 tccagagaat ttaacaagac ctgttttttt tctaacatag gagtaataaa tctctgcagt
      481 attcattatt gtcaaattca aagttccctt tttatttttt ctcattggta ttatcacccc
      541 aataaaaccg gtgtctttct ccaaataaaa atctatattc ttcttacaaa agaagaatgg
      601 aatatatcta accaattgaa aaatcgcacc actagacaaa tcaacaccat cattaagatg
      661 acctttatat tcgtctatta ccttgcatat tttagatatt attgatttat attcagcaag
      721 tcctttctta tctaccacac taagtatttc ataaagataa tcaacatctc ttaaagatgt
      781 ttttctattt atctccctta atatatcatt ccaaagatca aggcgacttt ctgttttaga
      841 gtaaagaagt attgtataat tttctacatt tacatcattg ttatatgaat tacaggaata
      901 atcaataccc ttgccaagtt ccacataagc ttcaacacaa gcagattcgc cctcaatacc
      961 aagagaacta cagaacaaag gctcggaata ttctaaatca tcatcgatga tttttacatc
     1021 ctcaatgtta tagcatatag acattttact attccgaatc cacaaacttt ttaagtgcag
     1081 acatcatttt ctttgcatgg tctttcgtta tagccaccga gtagaaaact tttttcgtat
     1141 ttttagatgg taaatctata aaatctataa tgcatatatc ttcaacaacc ccaaacctta
     1201 ttgataaagg aaatgctggc ggcaattccc gtcccatagc atcaaaagaa tcaatataat
     1261 cctgactatc tttatttggc ttatctgccg acatatcaac cgtccataac aaaatagaca
     1321 catttaaagt ttaacattca acctaaaaaa ctactactca aacaccacga acatccataa
     1381 tgtaacatgc aacatcatac catttaccat aacgtcgcat tacgcgcacc gccaaaacgc
     1441 actcagcgcg attctggcgc aaaaaccgta aaaagggatg ctttccccgg ggtaaaccgg
     1501 aaaaatgcgt caggattgtt ttcagcgcgt tgcatgacta tgcatgaaac tgaatggcaa
     1561 tcggtctggg cgcgtccgtt gtccctgagg cttatttttg gcagttttct ttctgtctgc
     1621 gtcacattcc atgccagaac acatccgtca gcaacgacat tcaacagccc accattagcc
     1681 cacacacaaa ataccgatgg gcacaccgat gtatcataaa aatttatccg ttatatttca
     1741 tacaaataag aggccaccat cagcccactc tattagccca caaaacgccc acacttttgc
     1801 tatcactatg attatcaata taaaacccac aaaagtgggc tgatgatggg ctaactgtgg
     1861 gcgtagaagc ccatcatcag cccaccacat ccgacaaaat agaatttttt gccagataaa
     1921 cgccactata acgcactgaa tttaaagtaa aatcacgcaa aacgcagttt tgcgacaggt
     1981 gtggtaaatg caggtcagag gagaggggaa tttcaggcgc ggagccggtc ctggttcggg
     2041 ctacaggact ctcagaaaaa gcgaataaat ttgcgctggc cgtcagagca ttacgccggg
     2101 gtatcggggt gaaaccctga gcaggaggta attgtaatag cgtcacgggt gacggtatta
     2161 caattacaca tcctgtcctg tgtcaggcag ccggatacgg tcgccctggt ggcaacagtc
     2221 cggcaggggg tacaactgta ccccgtcaca tccgcaaaag atttacggca cgaaacagga
     2281 gcgacgcaac aactgccggt aacacgaccc catgaacggg acaggatgtg taatcgtata
     2341 accgcgcacg cacgttcatc cgattacaac ctggtcagag ctttaccccg acacccacga
     2401 tgtgatgaac ggatgaacat caaacaaccg gaaaaacgct cactgtccag gcaaagaacg
     2461 gaacacggca taatcacatg atgctgaata cagagacaga acggagaacg acagaaggtg
     2521 aacaaacagc agcaaaccgc acttaacatg gcgcgattca tcaaaagcca gagtctgaca
     2581 ctgcttgaaa agctggatgc cctcgatgcc gacgaacagg caaccatgtg tgaacggctg
     2641 cacgaactgg cggaagaact gcagaacagc atacagacgc attttgaagc gcagtacggc
     2701 attggagtgg aacaaccata aagacgctgg cgaaagcggt cgcggcttgt ccgtgagcgt
     2761 tttcgccagc agacaagccc gcagggcgcg tcaggacagt gacctgagaa agacactggc
     2821 gcgtaagtgc tcaaagcaaa cgggcggaga aattccgctt cctcgcccac tcgctcacta
     2881 cgttcggtcg ctggggctgc ggcgagcggt ggcggctctc taataacggc aggcagttta
     2941 tccacagaat cgggggataa ccaggacaga acatgtgggc aaaagagcac gaccgtaaaa
     3001 ggctgcgacg atgccgtttt tccataggct ccgcccccct gacgagcatc acaaaaatcg
     3061 acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg cgtttccccc
     3121 tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg tttaccggat acctgtccgc
     3181 ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgtaggt atctcggccc
     3241 ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg
     3301 ctgcgcctta tccggtaact atcgtcttga gtccaacccg gaaagacacg acttaacgcc
     3361 actggcagca gccattggta aacagaatgt gcgagagatg catcgagagt tcttgaagtg
     3421 atggccttac tccggctaca ctgaaaggac agatttggtg gcatgtctcg cacaagactg
     3481 ttaccacggt tagaaaatct gccaggatta actaaccttc gaaaaaccac cttgccgggt
     3541 ggttttttcg ttttcagagc aagagattac gctcaccaaa aaaggatctc aagaagatcc
     3601 tgttcaaaga gtgccgcaaa tgttaatttt atctcactca accttactaa ccccaccccc
     3661 ctcagctcga aagtaaaggt ctgataactc aacaagagag gctattatca agttgcgctt
     3721 agccacatca gaataatcat gataatacat ccctatat
//
