Hello, I am trying to search for the methyltransferase sequence in a set of complete prokaryotic genomes (ex: L. fermentum; L. plantarum ). However, I can't find any results. The question would be, how to change the code to find some nucleotide sequence similar to the methyltransferase?

    library(Biostrings)
    library(ape)

    genbank_ids <- c(
      "NZ_CP124737.1", "NZ_CP010413.1", "NZ_CP022988.1", "NC_021181.2",
      "NZ_CP014170.1", "NZ_CP021061.1", "NZ_CP026038.1", "NZ_CP040780.1",
      "NZ_CP028221.1", "NZ_CP038996.1", "NZ_AP012544.1", "NZ_CP059276.1"
    )

    seq_bche<-read.GenBank(genbank_ids)
    seq_bche

    metiltransferase <- DNAString("GATCCGTTCGCACAGCATCGCCCGCTTGATGATAAACGCTACGCGCTGGATCATTTCCAGACTAAGTTGCTGAAGCTACCGCAAACCATGCAAACCGCAAGAGGCAAGCAGCTGGCGCAGCACAACGCGCATTTTTTAGTCGAGTTTATGGCGAAGCTCAGTGCCGAACTGGCGGGGGAGAATGAAGGTGTTGATCACAAGGTGATAGATGCGTTTTCATCCGCTGGCTGAGCGCGTGGCCCTAAATGGCTGTAATTATGTTAACCTGTCGGCCATCTCAGATGGCCGGTGAAATCTATGCAGGAAAATATATCAGTAACCGATTCATACAGCACCGGGAATGCCGCACAGGCAATGCTGGAGAAACTGCTGCAAATTTATGATGTTAAAACGTTGGTGGCGCAGCTTAATGGTGTAGGTGAGAATCACTGGAGCGCGGCAATTTTAAAACGTGCGCTGGCGAATGACTCGGCATGGCACCGTTTAAGTGAGAAAGAGTTCGCCCATCTGCAAACGTTATTACCCAAACCACCGGCACATCATCCGCATTATGCGTTTCGCTTTATCGATCTATTCGCCGGAATTGGCGGCATCCGTCGCGGTTTTGAATCGATTGGCGGACAGTGCGTGTTTACCAGCGAATGGAACAAACATGCGGTACGCACTTATAAAGCCAACCATTATTGCGATCCGGCGACGCATCATTTTAATGAAGATATCCGCGACATCACCCTCAGCCATAAAGAAGGCGTGAGTGATGAGGCGGCGGCGGAACATATTCGTCAACACATTCCTGAACACGATGTTTTACTGGCCGGTTTCCCTTGTCAGCCATTTTCGCTGGCTGGCGTATCGAAAAAGAACTCGCTCGGGCGGGCGCACGGTTTTGCCTGCGATACCCAGGGCACGCTGTTTTTTGATGTGGTACGCATTATCGACGCGCGTCGTCCGGCGATGTTTGTGCTCGAAAACGTCAAAAACCTGAAAAGTCACGACCAGGGTAAAACGTTCCGCATCATCATGCAGACGCTGGACGAACTGGGCTATGACGTGGCTGATGCAGAAGATAATGGGCCAGACGATCCGAAAATCATCGACGGCAAACATTTTCTGCCGCAGCACCGTGAACGCATCGTGCTGGTGGGTTTTCGTCGCGATCTGAATCTGAAAGCCGATTTTACCCTGCGTGATATCAGCGAATGTTTCCCTGCGCAGCGAGTGACGCTGGCGCAGCTGTTGGACCCGATGGTCGAGGCGAAATATATCCTGACGCCGGTGCTGTGGAAGTACCTCTATCGATATGCGAAAAAACATCAGGCGCGCGGTAACGGCTTCGGTTATGGAATGGTTTATCCGAACAATCCGCAAAGCGTCACGCGTACGCTGTCTGCGCGTTATTACAAAGATGGCGCGGAAATTTTAATCGATCGCGGCTGGGATATGGCCACGGGTGAGAAAGACTTTGACGATCCGCTGAATCAGCAACATCGTCCACGTCGGTTAACGCCTCGGGAATGCGCGCGCTTAATGGGTTTTGAAGCGCCGGGAGAAGCGAAATTCCGTATTCCGGTTTCGGACACTCAGGCCTATCGCCAGTTCGGTAACTCGGTGGTCGTGCCGGTCTTTGCCGCGGTGGCAAAACTGCTTGAGCCAAAAATCAAACAGGCGGTGGCGTTGCGTCAGCAAGAGGCACAACATGGCCGACGTTCACGATAAGGCCACTCGCAGCAAAAATATGCGCGCGATTGCCACGCGTGATACGGCGATAGAGAAGCGCCTCGCCAGTCTGTTAACCGGGCAGGGCCTGGCATTTCGCGTTCAGGACGCCAGTCTGCCCGGACGTCCGGATTTTGTCGTTGATGAATATCGCTGCGTGATATTTACCCATGGCTGCTTCTGGCATCATCATCACTGCTATCTGTTTAAAGTGCCTGCGACTCGAACCGAGTTCTGGCTGGAGAAGATAGGTAAAAATGTTGAGCGCGATCGCCGCGATATCAGTCGCTTGCAGGAACTCGGCTGGCGCGTATTGATTGTCTGGGAGTGCGCGTTACGTGGGCGCGAGAAGCTGACGGATGAAGCGCTTACCGAGCGTCTGGAAGAGTGGATCTGCGGCGAAGGTGCCAGCGCGCAGATCGACACGCAGGGGATTCATTTACTCGCTTGATGCGTCCTGAATAACTGGCGCAACTACGGGTTTTGCCGGGAAGAGATATTTTCCCAACGTGACCAGTACCACCGCGAAGACAATTACGCCGAGCGCCAGCCATTCAATCTTCGACAGTGTTTCTCCACCCAGTCCCGTACCCAGCAAGACCGCGACCACCGGGTTAACGTAAGCGTAGCTGGTGGCGAGAGCCGGACTGACATTACGGATTAAATACATATAAGCGTTGATGGCGATAATCGAACCAAACAGCGCCAGATAGCCGACCGCAAGGAAGCCTGAAAGGGAAGGGAGCGCCGTCAGTTTTTCACCCGCAATCATCGACGCGATCATTAACACCACGCCTGCCGCCAGCATCTCAATCGCACCCGCCATCATCCCTACAGGTAAGGTAATGCGCGAGCCATAAACTGAGCCAAACGCCCAGCTAATCGAGCCGATTAAAATCAGAATCGCGCCCCACGGATTGCCGCTTAAATTTCCACCGCTATTGAGCATGATGATTCCGGCAAGCCCAATGGCAATACCCACCCATTCCAGTTTGCGCGTTTTAATGCCAAACAGGCGGCTGAAGCACAGGGTAAAGAGGGGCACGGTTGCAACCACTACGGCGGCGATGCCGGAAGGAACATTTTGATGTTCGGCAACCGTCACCATGCCATTACCGACAGCCAGCAATAACAGGCCAATCAGCGCGGCATTGAGCAGCGGACGTAGCGGGGGGAGTTTGTGTCCGCGCAGTAGCAAAAATGCCAGCAATAAAATACCGGCTGCCAGGAATCGAACGCCCGCCATCATTAACGGAGGCCAGCTTTCCACGCCAATCCGAATGACAAAATAGGTTGAGCCCCAAATGATATACAACGCAAACAGCGCGCCAAAAAGCGGTAACAACTGGCGGAAACGCATAATCCCTCACGGTGGAAATAAAAAGGTGGTTCATAGTAAACGTGAAAATCATTCTGCTGGCGAGAGATATAATTGCACTTGATTGTTAAAAAAATGTTGACCTGTGAAGCAAGTATCAGAGCTGCCGTTTTTGCTTCATACTTACACCCTTCAACAATAAAAATGAGAGGGAATGCTTTTGGCCGGGAGTAGTTTACTGACGTTGCTCGATGATATCGCCACACTACTGGACGATATCTCCGTGATGGGCAAACTGGCGGCGAAGAAAACCGCCGGTGTATTAGGGGATGACTTATCGCTCAATGCGCAACAAGTTTCAGGCGTGCGGGCCAACCGGGAACTTCCCGTGGTCTGGGGCGTGGCGAAAGGATCGCTGATTAATAAAGTGATTCTGGTGCCGCTGGCGCTGATCATCAGTGCGTTTATCCCGTGGGCGATTACGCCTCTGTTGATGATTGGTGGCGCGTTTCTCTGCTTTGAAGGAGTAGAGAAAGTGCTGCATATGCTGGAGGCGCGTAAACATAAAGAAGATCCGGCGCAGAGCCAGCAGCGTCTGGAGAAGCTGGCGGCGCAGGATCC")

    library(magrittr)

    seq_bche_dnastring <-seq_bche %>% 
      as.character %>% 
      lapply(., paste0, collapse="") %>% 
      unlist %>% 
      DNAStringSet

    matches <- vmatchPattern(metiltransferase, seq_bche_dnastring)
    elementNROWS(matches)
    matches

Here are the results

    > matches <- vmatchPattern(metiltransferase, seq_bche_dnastring)
    > elementNROWS(matches)
    [1] 0 0 0 0 0 0 0 0 0 0 0 0
    > matches
    MIndex object of length 12
    $NZ_CP124737.1
    IRanges object with 0 ranges and 0 metadata columns:
       start       end     width
    <integer> <integer> <integer>

     $NZ_CP010413.1
     IRanges object with 0 ranges and 0 metadata columns:
       start       end     width
     <integer> <integer> <integer>

      $NZ_CP022988.1
      IRanges object with 0 ranges and 0 metadata columns:
       start       end     width
      <integer> <integer> <integer>

       ...
       <9 more elements>