Related Experiment Video
Updated: Jun 26, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function
Sarah Addou1, Robert Rentzsch, David Lee
1Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
Abstract:
Divergence in function of homologous proteins is based on both sequence and structural changes. Overall enzyme function has been reported to diverge earlier (50% sequence identity) than overall structure (35%). We herein study the functional conservation of enzymes and non-enzyme sequences using the protein domain families in CATH-Gene3D. Despite the rapid increase in sequence data since the last comprehensive study by Tian and Skolnick, our findings suggest that generic thresholds of 40% and 60% aligned sequence identity are still sufficient to safely inherit third-level and full Enzyme Commission numbers, respectively. This increases to 50% and 70% on the domain level, unless the multi-domain architecture matches. Assignments from the Kyoto Encyclopedia of Genes and Genomes and the Munich Information Center for Protein Sequences Functional Catalogue seem to be less conserved with sequence, probably due to a more pathway-centric view: 80% domain sequence identity is required for safe function transfer. Comparing domains (more pairwise relationships) and the use of family-specific thresholds (varying evolutionary speeds) yields the highest coverage rates when transferring functions to model proteomes. An average twofold increase in enzyme annotations is seen for 523 proteomes in Gene3D. As simple 'rules of thumb', sequence identity thresholds do not require a bioinformatics background. We will provide and update this information with future releases of CATH-Gene3D.
Related Concept Videos
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Families
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Complexes with Interchangeable Parts
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

