So far I know it contains a large coiled-coil region. I found the potential homologue base sequence on the coiled-coil distribution within the protein, what else I could test to determine if this protein is the homologue of my protein?
Are there homologs in other, more closely related species? If yes you may be able to build a profile or a HMM from a multiple sequence alignment and use it to search for more distant homologues
If it has similar fold, you should be able to perform DALI search.
How do you know they are homologous? (weird wording if they have no sequence similarity) Did you look for conserved residues/pattern?
Thanks Tomáš,
So far no any experimental (or alignment based computative) folding models for either proteins.
the evidence for being homologues are still weak. When I first study the protein, the only known thing is that it is a coiled-coil protein. Later its turn out to be a centrosomal protein. However, by NCBI blast and HMM search, I can't get any significant hits in well studied organisms (Yeast, plant, human, etc).
In order to find any other structure similar protein in human database, I compared the coiled coil structure profile of my protein with all over 200 coiled-coil domain containing proteins in human by COILS server. The best fit protein in human is indeed known as a centrosomal protein. It encourages me to figure out whether it is true or just coincident.
One more thing, both proteins might contain SMC (structure maintance of chromosome) domain, although the e-value are not good about 1e-5.
Your question is a little vague, it doesn't tell what you want exactly. How do you know the protein is has a coiled - coil structure? is it based on previous crystallographic structures? COIL runs on sequence to structure matching, then my question is hw do u say that they don't have sequence similarity?
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