Need help on protein alignment quick

In summary, the Blast program at www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html is used for protein alignment and can help answer questions about query and subject sequences, the significance of letters and symbols in the alignment, the concept of conservation in proteins, and the reason for actin's highly conserved sequence.
  • #1
megga124
3
0
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.
 
Last edited by a moderator:
Physics news on Phys.org
  • #2
Answer:
1. Query and Sbjct are short for 'query sequence' and 'subject sequence'. These terms represent the two sequences in the alignment being compared.
2. The letters of the middle row signify the similarity between the two sequences being compared. Identical residues are denoted with an '|', while conserved and semi-conserved residues are denoted with ':' and '.', respectively.
3. The '+' signs of the middle row signify the presence of an indel (insertion or deletion).
4. Conservation when referring to proteins means that the amino acid sequence of the protein is similar between different species, which is often due to the function of the protein.
5. Actin's ability to bind many other proteins causes its sequence to be highly conserved because it needs to maintain its functional structure in order to bind to other proteins. As a result, any mutations to its amino acid sequence may disrupt this functional structure, so the sequence remains largely unchanged over time.
 
  • #3


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!
 

What is protein alignment?

Protein alignment is the process of comparing and aligning the amino acid sequences of two or more proteins to identify similarities and differences. This can provide insights into their evolutionary relationships and functional similarities.

Why is protein alignment important?

Protein alignment is important because it can help researchers understand the structure, function, and evolution of proteins. It can also aid in the identification of new protein sequences and the design of experiments to study protein function.

What tools are available for protein alignment?

There are several tools available for protein alignment, including BLAST, Clustal Omega, and MUSCLE. These tools use different algorithms and methods to align protein sequences and each has its own strengths and limitations. It is important to choose the right tool for your specific needs.

How long does it take to perform protein alignment?

The time it takes to perform protein alignment depends on the size and complexity of the proteins being aligned, as well as the specific alignment tool being used. Some tools offer quick alignments, while others may take longer to provide more accurate results.

Can protein alignment be automated?

Yes, protein alignment can be automated using bioinformatics software and algorithms. This can save time and effort compared to manual alignment, especially for large datasets. However, it is important to carefully evaluate the results of automated alignments to ensure their accuracy.

Similar threads

  • Biology and Medical
Replies
3
Views
3K
  • Biology and Chemistry Homework Help
Replies
4
Views
1K
  • Biology and Medical
Replies
2
Views
2K
  • Introductory Physics Homework Help
Replies
1
Views
2K
  • Introductory Physics Homework Help
Replies
2
Views
2K
  • Introductory Physics Homework Help
Replies
2
Views
2K
  • Introductory Physics Homework Help
Replies
4
Views
1K
  • Introductory Physics Homework Help
Replies
8
Views
24K
  • Advanced Physics Homework Help
Replies
1
Views
3K
  • Introductory Physics Homework Help
Replies
4
Views
2K
Back
Top