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Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains
David R Fidler1, Sarah E Murphy1, Katherine Courtis1
1Department of Cell Biology, UCL Institute of Ophthalmology, London, UK.
Traffic (Copenhagen, Denmark)
|September 8, 2016
Summary
Structural bioinformatics tools like HHsearch can identify unknown protein functions. Applying HHsearch to yeast pleckstrin homology (PH)-like domains revealed 16 new domains, aiding cell biology research.
Area of Science:
- Structural bioinformatics
- Molecular biology
- Yeast genetics
Background:
- Many proteins lack functional annotations, hindering biological research.
- Existing domain annotation tools miss remote homologies.
Purpose of the Study:
- To demonstrate the utility of HHsearch for identifying novel protein domains.
- To improve functional annotation of yeast proteins.
Main Methods:
- Applied HHsearch to the pleckstrin homology (PH) domain clan in yeast.
- Systematically analyzed protein domains for remote homologies.
Main Results:
- Accurately identified known PH-like domains.
- Predicted 16 new PH-like domains in 13 yeast proteins.
- Confirmed the functional importance of a predicted PH-like domain in Vps13p.
Conclusions:
- HHsearch is effective for discovering novel protein domains.
- Predicted domains, like those in Vps13p, are valuable for understanding intracellular traffic.
- Wider application of HHsearch across proteomes can significantly enhance database annotations.
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