How to extract "High mobility group" sequence in multiple species ?

Question

[Farbod]

Dear Biostars, Hi

I want to extract the sequence (nucleotide or amino acid) of High mobility group (HMG) box domains in several species and compare their sequence.

Also, the HMG is present in some different genes (e.g SRY and SOX genes); by knowing its sequence, I can compare the situation that HMG is located in those genes in several species, I guess.

Q: In other word, I need the sequence of about 78 amino acids in the black box in Fig.1 of this paper , so then I can search for it's pattern in my sequence of interest.

~ Best

[Sej Modha]

I am not sure if this would help but you can download these sequences from InterPro.

[Farbod]

Dear Sej Modha, Hi and thank you.

Why there are 296 protein for HMG in human? have you any idea that which is the conserved core of it?

[Sej Modha]

Tbh I don't have any idea but I suppose you could run a multiple sequence alignment on these protein sequences to find out conserved region(s) if there are any.

[Farbod]

Thanks,

I have a nucleotide sequence for my species of interest gene and I want to compare it's HMG with the proteins you have kindly suggested.

Do you know any online tools that I can compare/align a nuclotide sequence with amino acid sequence ?

[Sej Modha]

I am not aware of any tools that might do that but you can always 6 frame translate the nucleotide sequences to protein and then run the MSA.

[Farbod]

Thanks but I think always the problem is this that which one of those 6 frames is better ?

[Sej Modha]

Hi I agree, that could be a problem. Another work around would be to download the coding sequences for these protein sequences from NCBI and then perform a Muscle codon alignment in MEGA or independently.