Model Organism Mutagenesis Data Sources?

Question

[Nathan Nehrt]

Hello,

I am looking for results of site-directed mutagenesis experiments in model organisms. Specifically, I want to find non-synonymous mutations that are known to either alter protein function, or to cause no change in function - neutral mutations. The Protein Mutant Database seems to be a good source for this data, but hasn't been updated since 2007.

I've also been looking around the individual model organism databases like FlyBase, WormBase, etc., but it's been very difficult to find neutral mutations (given, it's hard to prove a mutation is truly completely neutral). Are there any other good databases with this sort of data? Thanks.

Answer 1

[Nathan Nehrt]

One good resource I found for mutagenesis data from all organisms is the UniProtKB sequence annotation table (the feature table). The protein position, amino acid change, and a description of the effect of each mutation is listed. See an example here. The B-SIFT paper methods section describes how each mutation can be classified as deleterious, neutral, or activating based on the text description of the effect of the mutation. A search for the term "mutagenesis" in the sequence annotation field in UniProt listed over 8,400 proteins, so this is a relatively large source of data.