6 replies to this topic

[xiaoposhi]

I was trying to identify some proteins of my interest. So I did a organelle prep, run SDS-page gel, cut the band, send for MALDI-MS. (eg. 180kDa)
Now I got the sequence back. The result shows: first top one is a 130kDa unknow protein (score = 1554) and the rest of the sequencing result are all from a 50kDa known protein. So presumably, those two proteins were in complex when running the PAGE gel.
My question is now, when I try to figure out what this unknown protein is by blasting in ncbi, the only result returns is itself. No other homology occur at all. (Pfam does not identify any domain from the sequence.)
So something must be wrong, right?.. One particular protein cannot be from nowhere but itself, it has to have some relatives...

I'm lost. Any suggestion will be appreciated!

[mdfenko]

other sources or this protein from other sources are not yet in the database.

[HomeBrew]

How is the protein returned from BLAST annotated in the database?  Does using one of the more advanced BLAST algorithms (PSI-BLAST or PHI-BLAST) help?

[xiaoposhi]

mdfenko, on Feb 19 2010, 10:40 AM, said:

other sources or this protein from other sources are not yet in the database.

I'm working on a photosynthetic single cell Eukaryote. So other major model photosynthetic organism are supposed to have something similar to my protein...Is it?

[xiaoposhi]

HomeBrew, on Feb 19 2010, 11:53 AM, said:

How is the protein returned from BLAST annotated in the database?  Does using one of the more advanced BLAST algorithms (PSI-BLAST or PHI-BLAST) help?

yeah..three of the methods all yield the same result, the protein itself.  

But thank you for your suggestion~~

Edited by xiaoposhi, 19 February 2010 - 11:40 AM.

[mdfenko]

xiaoposhi, on Feb 19 2010, 02:35 PM, said:

I'm working on a photosynthetic single cell Eukaryote. So other major model photosynthetic organism are supposed to have something similar to my protein...Is it?

are you sure that the other major model photosynthetic organisms' complete genome are in the database?

[xiaoposhi]

mdfenko, on Feb 22 2010, 08:30 AM, said:

xiaoposhi, on Feb 19 2010, 02:35 PM, said:

I'm working on a photosynthetic single cell Eukaryote. So other major model photosynthetic organism are supposed to have something similar to my protein...Is it?

are you sure that the other major model photosynthetic organisms' complete genome are in the database?

No, I'm not sure. If it's the case, I'm glad to accept it:)