Question

Gaps within the BLASTN alignments suggest that two DNA sequences are not coding for the same protein, and therefore decrease the quality of the match. Gaps within a BLASTX alignment:

a) Are not significant for protein comparisons
b) Suggest conserved functional regions
c) Indicate sequence divergence
d) Are less informative than in BLASTN alignments

Answer 1

Gaps in BLASTX alignments can indicate sequence divergence and suggest conserved functional regions within proteins, reflecting evolutionary conservation of structure and function over sequence identity.

Step-by-step explanation:

Gaps within BLASTN and BLASTX alignments have different implications due to the nature of the sequences they compare. In BLASTN, which aligns nucleotide sequences, gaps often signify a lesser quality match since they disrupt the continuous coding sequence, potentially indicating that the DNA does not code for the same protein. On the other hand, gaps in BLASTX, which compares a nucleotide sequence to a protein sequence database, can indicate sequence divergence because proteins can tolerate certain insertions or deletions without loss of function. Therefore, gaps in BLASTX may suggest conserved functional regions where the overall structure and function of a protein are maintained despite sequence differences.

Moreover, when considering BLASTX, these gaps are particularly informative as they reflect evolutionary conservation of protein structure and function over sequence identity. This understanding is underscored by the fact that protein folding is more evolutionarily conserved than the sequences of DNA that encode for them, with 3D structures providing greater insight into phylogenetic relationships than the DNA sequences themselves.