Hi,
I have some protein alignments and want to find their similarities. I tried using Uniprot, but it only provides identity information. I also tried using MEGA, but couldn't find a way to access similarities there.
Can someone help me find the similarities, please? Preferably in MEGA, but I would be grateful for any online tool as well.
Thank you.
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andre.arrudalima •
Thank you. Doing this, the blast only give me indentities. Is the "Positive" the similarity?
Yes. That is correct.
From: https://www.ncbi.nlm.nih.gov/books/NBK62051/
substitution : The presence of a non-identical amino acid at a given position in an alignment. If the aligned residues have similar physico-chemical properties or have a positive score in the governing scoring matrix the substitution is said to be conservative.
Hi again I just realize that blasp only gives me the similarity of a specific part o the protein that it align, overestimating the global similary. For example, I have a 100 aa protein that align just 70aa to another protein, but with 100% similarity. Blastp will give me 100% similarity but in reality the real complete aligment should give me 70%. How can I solve this?
Thank you for the answer and sorry for the multiple post. I though you wouldn see here.
I have two questions: 1) Is it possible to loose blast algorithms in a way that it will align the whole protein? 2) Is there a online tool with Needleman-Wunsch algorithms? I not willing to do a data base search, just a small aligment with less than 15 proteins.
No for the first question. For second you can use emboss needle: https://www.ebi.ac.uk/Tools/psa/emboss_needle/
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Can you provide a specific example of what you are looking to get? Are you looking for residues that are able to replace amino acids without changing function/structure of a protein?
I'm not trying to get in this level of detail. I only want to compare aminoacid for their chemical characteristics, which I think is the default for a similarity comparison.
Anyway, here are my sequences, the kinase domain of some plant receptors
I see. Have you tried a multiple sequence alignment in MEGA? I don't have MEGA available immediately but the color coding options should allow you to look at chemical similarity, if I recall.
Yes, I did. The point is there I want to see a number cause I want to make a similarity table. I cant find similarity or identity percentages on MEGA.