Related Experiment Video
Updated: Jun 8, 2026
16:02
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison
Meric A Ovacik1, Ioannis P Androulakis
1Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854, USA.
Toxicology and Applied Pharmacology
|September 21, 2010
Summary
Comparing metabolic pathways across species is crucial for understanding evolution and drug development. Our improved reaction alignment method, incorporating enzyme sequence similarity, offers a more accurate way to analyze these cross-species pathway differences.
Area of Science:
- Bioinformatics
- Systems Biology
- Evolutionary Biology
Background:
- Pathway-based information is vital for evolutionary studies and understanding drug mechanisms across species.
- Cross-species pathway comparison aids in evolutionary relationship establishment and extrapolating species differences for applications like drug and toxicity testing.
- Comparing metabolic pathways across species is complex due to multiple modeling and comparison features.
Purpose of the Study:
- To improve existing reaction alignment methods for cross-species pathway comparison.
- To enhance the accuracy of predicting phylogenetic relationships and understanding species-specific pathway variations.
- To evaluate the efficacy of incorporating enzyme sequence similarity into reaction alignment.
Main Methods:
- Utilized reaction alignment, a successful method for predicting phylogenetic relationships.
- Developed an improved method by integrating enzyme sequence similarity with reaction alignment.
- Analyzed the conservation of glycolysis and citrate cycle pathways across nine species (including human, model, and test organisms).
- Extended the analysis to nine central metabolism pathways and a comprehensive set of 36 common pathways.
Main Results:
- The improved method, combining reaction alignment and enzyme sequence similarity, provides a more accurate representation of cross-species pathway similarities and differences.
- Evaluated standard and improved methods using glycolysis and citrate cycle pathways.
- Demonstrated organism comparison using cumulative data from multiple metabolic pathways.
Conclusions:
- Incorporating enzyme sequence similarity into reaction alignment significantly enhances the accuracy of cross-species pathway comparison.
- The enhanced method offers a more robust approach for evolutionary and toxicological applications.
- This approach refines our understanding of metabolic pathway conservation and divergence across species based on NCBI taxonomy.
