There are so many sequences in GenBank today, including many whole-genome sequen
ID: 162177 • Letter: T
Question
There are so many sequences in GenBank today, including many whole-genome sequences, that BLAST often fills up its list of top matching sequences without ever getting down to less related but potentially more interesting matches. In your initial BLAST results, for example, it's likely that most if not all of the sequences come from Gram-positive organisms, one major division of the bacteria. Horizontal gene transfer to the more distantly related Gram-negative organisms would be very interesting but is hard to assess from this list. Construct a BLAST search that requires matches to specific groups of Gram-negative organisms that you know live in the human gut, such as Bacteroides (the most common genus among human gut bacteria) or Escherichia. Be careful to ignore / exclude from consideration sequences that come from cloning vectors in this case—you only want sequences naturally found in these bacteria. Describe how you searched, the similarity of your results to the query and whether the percent identity suggests that your results represent horizontally transferred genes or genes arising by mutation.
Explanation / Answer
BLAST- Basic local alignment search tool
1) Take the nucleotide sequence of E.coli K12 gene, you can dowload FASTA format sequence and copy paste in BLAST tool.
2) Run a default Nucleotide nucleotide BLAST
3) In the exclude of the BLAST software give cloning vectors
4) In CDS gene of the E. coli mutation genes were found "acyl-CoA synthetase with NAD(P)-binding Rossmann-fold domain"
5) 4639675 base pairs found in E.coli full genome
6) Check for Distribution of BLAST protein homologs by Taxa - this protein shows all horizontal gene exchange of the bacteria with other microbs. HGT - horizontal gene transfer finding tool helps to find these genes.