Final answer:
The number at the start of the Query line in a BLASTP alignment refers to the identity count. The E-value indicates the number of expected hits by chance, with lower numbers signifying high significance. Differences in word length parameters in BLAST algorithms affect the number of matches found.
Step-by-step explanation:
The number at the start of the Query line of a BLASTP alignment refers to the identity count between the query sequence and the matched database sequences. When you find the E value for an alignment, such as between a query sequence and the subject Bacillus subtilis subsp. spizizenii str. W23, you are looking at a key parameter that indicates the number of alignments with a similar score that could be found by chance in a database of a given size. Specifically, an E-value offers an estimation of the number of hits one can expect to see by random chance when searching a database with a particular query sequence. Therefore, the lower the E value, the more significant the alignment is considered, with values closer to zero indicating a high level of significance.
The concept of an E value is also relevant when comparing sequences with gaps or using various BLAST algorithms like megablast or blastn. Differences in the word length parameter between these algorithms can lead to different numbers of matches due to the way BLAST handles sequence similarity and randomness.