Final answer:
A BLASTN search alignment with a gap suggests that introducing gaps can improve the match between two sequences. An E-value nearing zero implies a significant alignment, while a higher E-value may indicate less biological relevance. BLASTN scores alignments by rewarding matches and penalizing mismatches and gaps to determine the best match.
Step-by-step explanation:
When a student obtains an alignment in their BLASTN search with a gap that results in a better match between two sequences, it suggests that sometimes introducing gaps (insertions or deletions) can improve the overall alignment score. BLASTN, the Basic Local Sequence Alignment Tool for nucleotides, compares nucleotide sequences by breaking down the query sequence into shorter segments or 'words' and finding the highest scoring matches within a database, like GenBank.
The E-value is a critical metric in assessing the significance of the BLASTN result. It represents the number of random hits one can expect to see by chance with a particular word size in a database search. An E-value close to zero indicates a more significant alignment, meaning that it is less likely to have occurred by chance and is more likely to be biologically relevant. Conversely, a higher E-value suggests that the alignment might not be biologically meaningful.
BLASTN employs a scoring system where matches add points, mismatches deduct points, and gaps incur a penalty to ensure the best possible alignment is reported. A -3 penalty is applied for introducing a gap, and a -1 penalty for extending a gap. The alignment with the highest score, weighted by these factors, is considered the best. These features make BLASTN a powerful tool for comparing sequences and predicting evolutionary relationships and functional conservation between organisms.