Question: Database For Motifs Or Motif Scanning Tools Or Functional Prediction.
gravatar for Wayne
8.0 years ago by
United States
Wayne1.0k wrote:

Hello all, I have a short sequence with what looks like a motif, I want to get an idea what its doing.

I have a very short sequence segment (~20 amino acids) of interest that I know is definitely doing something. There is a well defined segment of this that looks like a motif and it is invariantly conserved when I check as far back as Xenopus also suggesting it is a motif with some sort of function. I have tried using Expasys prosite and the other tools listed there to find out what this motif might be doing, searched the literature, and also tried simple blasting to find it in other proteins. None of these strategies have panned out too well. Looking for other methods of figuring out what this motif is... can anyone suggest tools, reading, or ideas for learning something about this motif ?

motif protein sequencing • 2.0k views
ADD COMMENTlink modified 7.0 years ago by Biostar ♦♦ 20 • written 8.0 years ago by Wayne1.0k

If you could disclose the sequence I'd be pleased to take a look - otherwise the problem is just to wide to generalise. (I promise not to write a paper if you want to send it direct..). Two suggestions but not answers per se a) If the alligments are robust it should appear in Pfam as a "DUF" (Domain of unknown function) b) note all "doing something" annotation is anchored back to experimental data, so you need the requisite lab work to test any hypothesis as to what its doing.

ADD REPLYlink modified 8.0 years ago • written 8.0 years ago by cdsouthan1.8k

ask cdsouthan says, need more info to be able to give useful help - although it sounds like this is something that the ELM server might be able to help with, or some of the resources listed in the links pages on that site (I work in the group that develops ELM)

ADD REPLYlink written 8.0 years ago by aidan-budd1.9k

Is it naturally occurring portion of a known gene with an annotated genome? Is so, have you tried going to those coordinates in the various genome browsers (Entrez, Ensembl, UCSC) and just turning on any tracks that seem even remotely relevant? Maybe that will give you some clues?

ADD REPLYlink written 8.0 years ago by Obi Griffith19k
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