merged multiple sequence alignments

Question

[olle.nordesjo]

I'm looking for a certain database that definitely should exist, but I can't seem to find it by just googling, interestingly.

Ultimately, I need the following data for a certain number of proteins:

• Evidence of interaction between pairs of proteins (say protein 1 and protein 2)
• Sequences of homologs among at least 20 species (species should have both protein 1 and protein 2 in their genomes)
• Structures of the two interacting proteins (I can easily cross-check on pdb to see if these exist)
• Experimental information of mutational effects of the binding affinity between protein 1 and protein 2

The difficulty lies in finding sequences for both proteins for the same N>20 species so that the proteins can said to definitely co-exist in the same species.

Maybe I'm missing something obvious here, but I'd be happy to get any help with this.

[GenoMax]

Have you looked at Homologene: http://www.ncbi.nlm.nih.gov/homologene

Similar resource from Ensembl: http://www.ensembl.org/info/website/tutorials/compara.html

[olle.nordesjo]

That's really nice! Thanks. I've taken a look at it

It seems the homologene is limited to eukaryotic proteins though? I'm afraid that might be limiting as there will be a greater requirement for longer protein sequences. It would be great if they extended the service to other proteins as well. I guess it presents considerable obstacles though.

[h.mon]

Do you have some taxon in mind?

[olle.nordesjo]

Bacterial sequences would be optimal, given the availability of >20 species with a conserved PPI

Answer 1

[Antonio R. Franco]

Have you gave a look to the NCBI Conserved Domain Database ?

It contains many sequences already aligned, and cross references to many of the material you are asking