EFI - Chemically-Guided Functional Profiling

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).

The tools are available without charge or license to both academic and commercial users.

Important Notice

The UniProtKB database used by the EFI tools is undergoing major reorganization starting with the just-released version 2025_04 (https://www.uniprot.org/help/refprot_only_changes). When the reorganization is fully implemented (2026_02 release, Spring 2026), the number of proteins in UniProtKB will decrease from ~253M accessions in the previous 2025_03 release to ~141M accessions in the 2026_02 release.

In response to these changes, we will provide the previous 2025_03 release until the 2026_02 release is available.

The current 2025_04 release removed 82M UniProt IDs; the UniProt pages providing functional annotation for these IDs are no longer active. A new Metadata Tool provides access to the node attribute metadata for all UniProt IDs in the 2025_03 release that the tools continue to use during the UniProtKB reorganization. The Tool is available using the tab at the top of each page.

More information about the reorganization is located here.

This site uses the CGFP-ShortBRED programs (https://github.com/biobakery/shortbred and http://huttenhower.sph.harvard.edu/shortbred).

For more information on CGFP-ShortBRED, see

Levin, B. J., Huang, Y. Y., Peck, S. C., Wei, Y., Martínez-del Campo, A., Marks, J. A., Franzosa, E. A., Huttenhower, C., Balskus, E. P. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science 355, eaai8386 (2017). (DOI: 10.1126/science.aai8386)

For more information on ShortBRED, see

Kaminski J., Gibson M. K., Franzosa E. A., Segata N., Dantas G., Huttenhower C. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput Biol. 2015 Dec 18;11(12):e1004557. DOI: 10.1371/journal.pcbi.1004557

These programs use data computed by MicrobeCensus.

Nayfach, S. and Pollard, K.S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biology 2015;16(1):51.

Portions of the metagenome data used on this site come from the Human Microbiome Project.

The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (14 June 2012). DOI: 10.1038/nature11234

The Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (14 June 2012). DOI: 10.1038/nature11209

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