The ConSurf web‐sever for the analysis of proteins, RNA, and DNA provides a quick and accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals functionally important regions, such as catalytic and ligand‐binding sites, which often evolve slowly. Since the last report in 2016, ConSurf has been improved in multiple ways. It now has a user‐friendly interface that makes it easier to perform the analysis and to visualize the results. Evolutionary rates are calculated based on a set of homologous sequences, collected using hidden Markov model‐based search tools, recently embedded in the pipeline. Using these, and following the removal of redundancy, ConSurf assembles a representative set of effective homologues for protein and nucleic acid queries to enable informative analysis of the evolutionary patterns. The analysis is particularly insightful when the evolutionary rates are mapped on the macromolecule structure. In this respect, the availability of AlphaFold model structures of essentially all UniProt proteins makes ConSurf particularly relevant to the research community. The UniProt ID of a query protein with an available AlphaFold model can now be used to start a calculation. Another important improvement is the Python re‐implementation of the entire computational pipeline, making it easier to maintain. This Python pipeline is now available for download as a standalone version. We demonstrate some of ConSurf's key capabilities by the analysis of caveolin‐1, the main protein of membrane invaginations called caveolae.

Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e., their positions evolve at a slower rate than other positions) are particularly likely to be of biological importance, for example, for ligand binding. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each position in a protein family. Here we introduce a new release of ConSurf‐DB, a database of precalculated ConSurf evolutionary conservation profiles for proteins of known structure. ConSurf‐DB provides high‐accuracy estimates of the evolutionary rates of the amino acids in each protein. A reliable estimate of a query protein's evolutionary rates depends on having a sufficiently large number of effective homologues (i.e., nonredundant yet sufficiently similar). With current sequence data, ConSurf‐DB covers 82% of the PDB proteins. It will be updated on a regular basis to ensure that coverage remains high—and that it might even increase. Much effort was dedicated to improving the user experience. The repository is available at https://consurfdb.tau.ac.il/.Broader audience: By comparing a protein to other proteins of similar origin, it is possible to determine the extent to which each amino acid position in the protein evolved slowly or rapidly. A protein's evolutionary profile can provide valuable insights: For example, amino acid positions that are highly conserved (i.e., evolved slowly) are particularly likely to be of structural and/or functional importance, for example, for ligand binding and catalysis. We introduce here a new and improved version of ConSurf‐DB, a continually updated database that provides precalculated evolutionary profiles of proteins with known structure.

Cation/proton antiporters (CPAs) play a major role in maintaining living cells’ homeostasis. CPAs are commonly divided into two main groups, CPA1 and CPA2, and are further characterized by two main phenotypes: ion selectivity and electrogenicity. However, tracing the evolutionary relationships of these transporters is challenging because of the high diversity within CPAs. Here, we conduct comprehensive evolutionary analysis of 6537 representative CPAs, describing the full complexity of their phylogeny, and revealing a sequence motif that appears to determine central phenotypic characteristics. In contrast to previous suggestions, we show that the CPA1/CPA2 division only partially correlates with electrogenicity. Our analysis further indicates two acidic residues in the binding site that carry the protons in electrogenic CPAs, and a polar residue in the unwound transmembrane helix 4 that determines ion selectivity. A rationally designed triple mutant successfully converted the electrogenic CPA, EcNhaA, to be electroneutral.