Final answer:
BLOSUM 45 should be used for aligning more distantly related proteins, while BLOSUM 90 is better for sequences with high similarity. The matrix selection impacts the alignment scoring, considering matches, mismatches, and gaps. The E-value further assists in gauging the statistical significance of the alignment.
Step-by-step explanation:
The choice between BLOSUM 45 and BLOSUM 90 depends on the degree of similarity between the sequences being compared. The BLOSUM 45 matrix is used for aligning more distantly related proteins, that is when sequences share a lower percentage (<20%) of identity. BLOSUM 90, on the other hand, is more suitable for the comparison of sequences that are very similar to each other, typically with a high percentage (>50%) of identity.
The selection of the matrix affects alignment score calculation where matches, mismatches, and gaps are scored. Introducing and extending gaps come with penalties, and the objective is to achieve the highest overall score, which represents the best possible alignment. The E-value is also critical in assessing the significance of the alignment, with lower E-values indicating more statistically significant alignments that are less likely to be due to random chance.