Final answer:
E-values between BLASTx and BLASTp can be significantly different because BLASTx translates nucleotide sequences for protein comparison, while BLASTp directly compares protein sequences.
Step-by-step explanation:
The E-values generated from a BLASTx and a BLASTp search for the same protein can show significant variation. BLASTx compares nucleotide sequences translated into protein sequences against a protein database, whereas BLASTp compares protein sequences against a protein database. An E-value represents the number of random hits one can expect to see by chance when searching a database with a particular query sequence.
The lower the E-value, the more significant the alignment and the less likely it is to occur by chance, indicating a strong similarity between the sequences. When assessing the alignment of two sequences, the introduction of gaps might be penalized, but can lead to a better overall match. The difference in E-values between BLASTx and BLASTp reflects the nuances in comparing nucleotide to protein sequences versus protein to protein sequences, providing useful complementary information about the similarity and potential homology of the sequences in question.