We are looking for an enzyme that appears in C. elegans but isn't common for: human, Drosophila or mouse. We need it for a little research project, thanks for your help!
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You might explore Li et al (2004) "Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene" Cell 117: 541-552. (Pubmed Abstract).
Largely the authors focused on comparisons of Arabidopsis, Chlamydomonas and Human genomes, but they did also include C. elegans for comparisons with at least Chlamydomonas (Summarized in Table 1). Even if they do not give you exactly what you need, you could apply their methods for your particular project.
One way to approach this is to use one of the protein database clusterings available.
Researchers have taken huge protein databases, like UniProt, which basically catalog all known protein sequences regardless of species and clustered the proteins by sequence. The results provide many interesting insights about protein families, but more importantly they are well-fitted for your problem. A cluster would be a set of sequences that are similar to each other but are relatively different from all other known proteins. So, essentially you would be interested in a cluster that is only has c elegans proteins.
I went ahead and used ProtoNet, which is one such tool, and searched for such a c elegans cluster. I found two potential clusters: 4375747 and 4430980, which have mainly c elegans proteins.
Disclaimer: I have been involved in the past in the development of ProtoNet.