LOCUS       CP099000                3887 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB46-C05 plasmid unnamed4, complete
            sequence.
ACCESSION   CP099000
VERSION     CP099000.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488707
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3887)
  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  JOURNAL   Unpublished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 3887)
  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                     :: RHB46-C05
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 117x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:28:05
            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)                     :: 4,823
            CDSs (total)                      :: 4,706
            Genes (coding)                    :: 4,516
            CDSs (with protein)               :: 4,516
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 190
            CDSs (without protein)            :: 190
            Pseudo Genes (ambiguous residues) :: 0 of 190
            Pseudo Genes (frameshifted)       :: 59 of 190
            Pseudo Genes (incomplete)         :: 126 of 190
            Pseudo Genes (internal stop)      :: 39 of 190
            Pseudo Genes (multiple problems)  :: 31 of 190
            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..3887
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB46-C05"
                     /isolation_source="Pooled faeces sample collected from
                     floor of poultry farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3731..3887,1..956)
                     /locus_tag="NFL43_24090"
     CDS             join(3731..3887,1..956)
                     /locus_tag="NFL43_24090"
                     /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="DNA cytosine methyltransferase"
                     /protein_id="WGB63822.1"
                     /translation="MAKGLELAGFQHVGFVELNKHACDSLRLNFDEEKVFQGDIKNYDL
                     SSLDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPKAFIFENVKGLLR
                     KSFADYFEYIILRLTYPCLSLSNVSDWRIHLDVLRKARKDKHCGCTYDVSFKLINAADY
                     GVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRKHNIDAVIDKGIS
                     ERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARVYPGHTGSYIDLP
                     SKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAGAWGEAMRQIGNA
                     VPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     gene            complement(2005..2199)
                     /locus_tag="NFL43_24095"
     CDS             complement(2005..2199)
                     /locus_tag="NFL43_24095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="WGB63820.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3051..3695
                     /locus_tag="NFL43_24100"
     CDS             3051..3695
                     /locus_tag="NFL43_24100"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WGB63821.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHGRNIAKTSNLDLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     Typing          1848..1932
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          2236..2334
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          2459..2714
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1279..1828)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.224"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgttgctgg cgggcctcct tgccaaccat tttcattggg cggaaaacat aaagctcatg
       61 atgactctag ggatatgttt ccatttgcaa taaaagcaat tgaagtattg caaccaaaag
      121 cttttatttt tgaaaatgtt aaagggttgc ttagaaaatc atttgcggac tattttgaat
      181 acataattct tcgtttgact tatccttgtt tatcgttaag taatgtaagt gattggagaa
      241 tacatctaga tgtattaaga aaagctcgca aggataaaca ctgtgggtgt acatatgatg
      301 tcagttttaa attaatcaat gcagctgatt atggagttcc acaaattagg gaacgggtca
      361 taattgttgg tgttcgaagt gatttgaata aaaaatggtc ttttccaagt gtaacgcata
      421 ctcaagaaaa attgctgtgg gaacagcatg ttactggtga ctattggcga aagcataata
      481 ttgatgcggt tatagataaa ggtatttctg agcgtttaat gaaacgtttt ggtattttcc
      541 ccccatcggg gaaaagctgg gttactgtta gggacgcatt aaagaatgtt cctcaaccgt
      601 atgagtcaca tggtattgga gatcatatct ttaaagatgg cgctcgagtt tatcctggtc
      661 atactggaag ttatatcgat ttgccttcaa aaacacttaa ggctggcgct catggcgtac
      721 ctggaggtga aaatatgatt aggtatgagg atgggactgt tcgttatttt acggtttatg
      781 aagggaagct tcttcagact tttcctcgag agtttctgat tgcaggagct tggggggagg
      841 ctatgaggca gattggtaat gcagttcctg tgttgctagc tcagaagata gggcagcaat
      901 tgtataactt attgaatgaa gaggttgagc cgttattgtg ctctaacttc aattaaaagt
      961 ttgtgtctct atggtggtga tacagccata gaggcaattt gcaaaaaaag atcaaaggat
     1021 cttcttgaga tccttttttt ctgcgcgtaa tctgctgcct gtaaacaaaa aaaccaccgc
     1081 taccaacggt ggttcgtttg ccggaatcaa gagctaccaa ctctttttcc cgaaggtaac
     1141 tggcttggtg gagcgcagat accaaatact gtccttctag tgtagcctca gttaggccac
     1201 cacttcaaga actcttaata tctcaatcca ccttgtccag ttaccaatgg ctgctgccag
     1261 tggcgttaag gcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca
     1321 gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac
     1381 cgaactgaga taccaacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa
     1441 ggcggagagg tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc
     1501 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg
     1561 tcgatttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcct gcgtcgctgg
     1621 cttcttccgg tgctttgctt tttgctcaca tgttctttcc ggctttatcc cttgattctg
     1681 tggataacag tatcactgct tttgagtgag cagacaccgc tcgccacagc cgaacgaccg
     1741 agcgtagcga gtcagtgagc gaggaagcgg aagagcgccg gaagctgcat tttctcctta
     1801 cgcatctgtg cagcatttca caccgcatat ggcgctgttt tcttacaatc cgcactgatg
     1861 ccgcatagtt aagccagtat acactccgct atcgctacgt gactgggtca gggcttcgcc
     1921 ccgacacccg ctgacgcgcc ctggcgggct tgtctgctgc cgaaaacgct cgcggacaag
     1981 ccgtgagcgc ctccgtcagc ttcgttatgt tcctgtttca ctttcggtct caaagcgaac
     2041 ctggatgctg ttctggagtt cttccgcgag ttcgtgcagt cgttcgcaca tggccgcctg
     2101 ttcgtcggca tccagagcat ccagtttttc aagcagtgtc aggctctggc ttttgataaa
     2161 tcgcgccata ttcagcgcag tttgttgctg tttgttcacc ttccgttgtt ctccgtcagt
     2221 accgggtgtc gggtggaccc tgaccaggtg gtaattgtaa gacgttgcgg gcgacggtat
     2281 tacaattgca catcctgtcc tgttttttta ggacgtatca tggcacagca tatcaactga
     2341 taaataatcc ctgtgcagtg cagccgctgt tgcataaaat ttcgctctgc gtcgagtgtt
     2401 tcttaatcaa taattccgct gatactccgg aaaaacgcga gtctgttctc atgcctgaaa
     2461 tgcccacacc ccacgcaaaa acaatttttt gctgattttt ctttataaat agagagttat
     2521 gacaaattag ttcttcttgc tctctttgtg atatttaaaa aagcggtgtc ggcgcggtgt
     2581 tgtagctgcg ccaacaccgc tttttagggg tggtactgac tattttcata aaaaacatca
     2641 ttttatatta ggggtgctgc tagcggcgcg gtgtgttttt ttacaggacg cccctggggg
     2701 cgctgctagg ggtgtctgtt cagatatgta gcaatgagtc agggattcac gaactgaaaa
     2761 tgtccgaaaa tgtgtctcat gggcaccgta tgcgcccaaa ccgatcgcca ttcactttca
     2821 tgcatagcta tgcagtgagc tgaaagcgat cctgacgcat ttttccggtt ttcgcttggt
     2881 aaaacatctc tttttgcggt gttcgcggca gaatcgcgtt cagcgcgttt tagcggtgcg
     2941 cgtaatgaga cgttatggta aatgcgtatg ggttggggta ttagctttat gatcgtatca
     3001 taggtgatgt tgagtaggag tgttaatata aagacctttc ggaaaacata atgcacaata
     3061 agaaatttga tagatctgag catgtttata gaaatgactc tttcctagag ttaataaaag
     3121 atgccgttcg tttttttagt ggtacgcctg ttcattcatt accaccaccg gaacggtttc
     3181 aaggtgctgg ggtgtatgct ctttactata caggacatta ttcattatat gatgaatatt
     3241 ctcgtataaa taggttggca tataaccttc ctatttatgt tggcaaggct gttcctgctg
     3301 gttggcgtca gtctagaatt agtgatcatg aaactagggc tggttctgaa ctatctaata
     3361 gaattagaga acatggccga aatatagcaa aaacatcgaa tctagatttg tgtgattttt
     3421 catgtcgctt tgttatcttt gaggctacgg ggtctgatat gattagtaca gttgaggccg
     3481 ctcttattaa aatttataag cctttgtgga ataccgttgt tgatggcttt ggaaatcata
     3541 cccctggtgc cgggcgattt gcgcaagcta aatctgattg ggatgtaata catcctggca
     3601 gggagtgggc tgagaaatgt acaggtgttc attctgagcc atactttatt gaggagagaa
     3661 ttaaacagta tttttctaag agtaatttta cataatgaga tcattagaga ttttttcagg
     3721 agccggcggc ttggctaaag gtctagagtt ggcaggattt cagcatgtag gatttgttga
     3781 gttaaacaag catgcatgtg attctttgcg acttaatttt gatgaggaga aggtatttca
     3841 gggagatatt aaaaattatg acctttcatc tctagataaa atagata
//
