What Does Each Element in a BLAST Protein Alignment Mean?

[megga124]

I am trying to do this protein alignment assignment for my Biotech class and I'm having trouble interpreting the results. I used the Blast program at www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html[/URL] and have to answer the following questions: What are "Query" and "Sbjct"?, What do the letters of the middle row signify?, What do the "+" signs of the middle row signify?, What does "conservation" mean when referring to proteins?, and Why does actin's ability to bind many other proteins cause its sequence to be highly conserved?

I don't really have a clue as to the answers to these questions, so any help at all would be grately appreciated! The project is due tomorrow (Thursday) at 1pm.

Thanks.

 

[M98Ranger]

Hi there,

First of all, don't panic! Protein alignment can be a bit tricky to understand at first, but with some guidance, you'll be able to interpret the results in no time.

To start, "Query" and "Sbjct" stand for "Query Sequence" and "Subject Sequence," respectively. The "Query Sequence" is the protein sequence that you entered into the Blast program, while the "Subject Sequence" is the protein sequence that the Blast program found to be the most similar to your query sequence.

The letters in the middle row signify the amino acid residues in the alignment. Each letter represents a specific amino acid, and the order of the letters shows the alignment of the amino acids between the query and subject sequences. For example, if the letter "G" appears in the middle row, it means that the amino acid glycine is present at that position in both the query and subject sequences.

The "+" signs in the middle row represent gaps in the alignment. These gaps occur when there is a mismatch between the amino acids in the query and subject sequences. The "+" sign helps to indicate where these gaps are located in the alignment.

"Conservation" in terms of proteins refers to the degree of similarity between two or more protein sequences. When a protein is highly conserved, it means that its sequence has remained relatively unchanged over time, indicating that it is important for the structure or function of the protein.

Actin is a highly conserved protein because it plays a crucial role in the structure and movement of cells. Its ability to bind to many other proteins is essential for its function, and any changes in its sequence could disrupt this binding ability and affect the overall function of the protein. Therefore, natural selection favors the conservation of actin's sequence to maintain its important role in cellular processes.

I hope this helps to clarify some of your questions. If you need more assistance, don't hesitate to reach out to your professor or classmates for help. Good luck with your assignment!