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.

Reorganization of UniProtKB

With the current 2026_02 release, the UniProtKB database is reorganized to include an expanded number of Reference Proteomes to better capture biodiversity. This includes the removal of proteins from taxonomically unclassified organisms, i.e., those without a binomial species name (genus and species). The total number of accessions in UniProtKB has been reduced from 253,635,358 in the “legacy” 2025_03 release to 149,810,139 in the current 2026_02 release.

We are providing the option to select either the “legacy” 2025_03 database or the current UniProtKB database (now 2026_02) when generating SSNs. You can select the database in the “Database” accordion on the pages for the EFI-EST options, the EFI-GNT tool, and the Taxonomy Tool. We suggest that you compare the SSNs, GNNs, and GNDs generated from both databases as you explore the information you are seeking.

Update of EFI Tools

The EFI Tools are being upgraded on 10/21/26. While the updated site is functionally identical to the old site, jobs run prior to that date will only be available through the results link in the finalization email (not the Previous Jobs tab). User accounts created on the old site will no longer be available, and users are encouraged to create new accounts when the upgraded site becomes available.

Quantify Results

Submitted SSN: 27076_26152_IP91_IPR004184_NoFragments_Archaea_UniRef90_NoFragments_IPR004184_Archaea_Minlen650_AS240_full_ssn_coloredssn

Job Name: 26152_IP91_IPR004184_NoFragments_Archaea_UniRef90_NoFragments_IPR004184_Archaea_Minlen650_AS240

Please cite your use of the EFI tools:

Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023. https://doi.org/10.1016/j.jmb.2023.168018

Submission Summary
Quantify Results
Heatmaps and Boxplots

Submission Summary Table

Input filename	27076_26152_IP91_IPR004184_NoFragments_Archaea_UniRef90_NoFragments_IPR004184_Archaea_Minlen650_AS240_full_ssn_coloredssn.zip
Identify/Quantify ID	840/780
Minimum sequence length	650
Identify search type	DIAMOND
Reference database	UNIREF90
CD-HIT identity for ShortBRED family definition	85
Quantify search type	USEARCH

Metagenomes Submitted to Quantification Step

SRS017451: anterior nares
SRS015051: anterior nares
SRS016553: anterior nares
SRS016188: anterior nares
SRS019215: anterior nares
SRS019339: anterior nares
SRS016581: anterior nares
SRS019597: anterior nares
SRS019986: anterior nares
SRS017697: anterior nares
SRS020386: anterior nares
SRS018671: anterior nares
SRS016513: anterior nares
SRS014464: anterior nares
SRS052590: anterior nares
SRS053437: anterior nares
SRS054061: anterior nares
SRS058213: anterior nares
SRS011263: anterior nares
SRS012291: anterior nares
SRS011397: anterior nares
SRS018312: anterior nares
SRS018463: anterior nares
SRS017820: anterior nares
SRS018369: anterior nares
SRS011132: anterior nares
SRS018784: anterior nares
SRS019386: anterior nares
SRS020868: anterior nares
SRS046344: anterior nares
SRS050025: anterior nares
SRS051613: anterior nares
SRS020232: anterior nares
SRS018585: anterior nares
SRS017244: anterior nares
SRS015430: anterior nares
SRS012663: anterior nares
SRS017156: anterior nares
SRS013269: anterior nares
SRS013637: anterior nares
SRS013876: anterior nares
SRS013956: anterior nares
SRS014682: anterior nares
SRS014901: anterior nares
SRS015269: anterior nares
SRS013155: anterior nares
SRS015450: anterior nares
SRS016292: anterior nares
SRS015640: anterior nares
SRS017044: anterior nares
SRS016434: anterior nares
SRS016752: anterior nares
SRS016033: anterior nares
SRS015996: anterior nares
SRS015937: anterior nares
SRS015752: anterior nares
SRS016503: buccal mucosa
SRS019587: buccal mucosa
SRS016533: buccal mucosa
SRS017441: buccal mucosa
SRS017537: buccal mucosa
SRS017687: buccal mucosa
SRS018661: buccal mucosa
SRS019221: buccal mucosa
SRS019329: buccal mucosa
SRS023354: buccal mucosa
SRS019976: buccal mucosa
SRS020336: buccal mucosa
SRS022145: buccal mucosa
SRS022532: buccal mucosa
SRS022721: buccal mucosa
SRS045262: buccal mucosa
SRS050007: buccal mucosa
SRS050029: buccal mucosa
SRS055118: buccal mucosa
SRS016088: buccal mucosa
SRS016196: buccal mucosa
SRS016600: buccal mucosa
SRS014472: buccal mucosa
SRS015040: buccal mucosa
SRS014575: buccal mucosa
SRS011247: buccal mucosa
SRS011310: buccal mucosa
SRS015374: buccal mucosa
SRS012281: buccal mucosa
SRS011090: buccal mucosa
SRS014126: buccal mucosa
SRS015154: buccal mucosa
SRS013945: buccal mucosa
SRS013881: buccal mucosa
SRS013825: buccal mucosa
SRS013711: buccal mucosa
SRS013506: buccal mucosa
SRS013239: buccal mucosa
SRS015745: buccal mucosa
SRS042457: buccal mucosa
SRS043646: buccal mucosa
SRS045254: buccal mucosa
SRS048719: buccal mucosa
SRS050628: buccal mucosa
SRS011144: buccal mucosa
SRS015895: buccal mucosa
SRS045049: buccal mucosa
SRS020858: buccal mucosa
SRS019391: buccal mucosa
SRS017013: buccal mucosa
SRS015921: buccal mucosa
SRS016039: buccal mucosa
SRS014686: buccal mucosa
SRS015436: buccal mucosa
SRS016297: buccal mucosa
SRS016349: buccal mucosa
SRS015274: buccal mucosa
SRS015646: buccal mucosa
SRS017080: buccal mucosa
SRS017215: buccal mucosa
SRS014890: buccal mucosa
SRS017810: buccal mucosa
SRS018149: buccal mucosa
SRS018329: buccal mucosa
SRS017127: buccal mucosa
SRS018359: buccal mucosa
SRS022158: posterior fornix
SRS018769: posterior fornix
SRS019379: posterior fornix
SRS019600: posterior fornix
SRS019989: posterior fornix
SRS020349: posterior fornix
SRS051505: posterior fornix
SRS022734: posterior fornix
SRS042428: posterior fornix
SRS050184: posterior fornix
SRS052330: posterior fornix
SRS056695: posterior fornix
SRS057807: posterior fornix
SRS017520: posterior fornix
SRS017700: posterior fornix
SRS014494: posterior fornix
SRS017497: posterior fornix
SRS014629: posterior fornix
SRS016559: posterior fornix
SRS011269: posterior fornix
SRS011584: posterior fornix
SRS012294: posterior fornix
SRS013542: posterior fornix
SRS011355: posterior fornix
SRS015054: posterior fornix
SRS016516: posterior fornix
SRS015225: posterior fornix
SRS015425: posterior fornix
SRS016111: posterior fornix
SRS016191: posterior fornix
SRS015168: posterior fornix
SRS017701: stool
SRS017521: stool
SRS017433: stool
SRS016585: stool
SRS015133: stool
SRS016495: stool
SRS016203: stool
SRS015369: stool
SRS015217: stool
SRS019267: stool
SRS018656: stool
SRS052697: stool
SRS019601: stool
SRS019968: stool
SRS020328: stool
SRS022137: stool
SRS023346: stool
SRS043001: stool
SRS050752: stool
SRS053335: stool
SRS053398: stool
SRS054590: stool
SRS054956: stool
SRS015190: stool
SRS016095: stool
SRS014979: stool
SRS011302: stool
SRS012273: stool
SRS012902: stool
SRS014313: stool
SRS011586: stool
SRS011405: stool
SRS013521: stool
SRS011239: stool
SRS014459: stool
SRS014613: stool
SRS011061: stool
SRS013215: stool
SRS019397: stool
SRS018817: stool
SRS013158: stool
SRS020233: stool
SRS020869: stool
SRS045713: stool
SRS011529: stool
SRS011452: stool
SRS045004: stool
SRS018575: stool
SRS048164: stool
SRS049712: stool
SRS049900: stool
SRS014923: stool
SRS011271: stool
SRS011134: stool
SRS013476: stool
SRS049959: stool
SRS018427: stool
SRS014235: stool
SRS018351: stool
SRS014683: stool
SRS015264: stool
SRS015578: stool
SRS015663: stool
SRS015960: stool
SRS016018: stool
SRS016056: stool
SRS014287: stool
SRS016267: stool
SRS016335: stool
SRS015782: stool
SRS013951: stool
SRS017307: stool
SRS016753: stool
SRS017821: stool
SRS013687: stool
SRS013800: stool
SRS017247: stool
SRS017191: stool
SRS017103: stool
SRS016989: stool
SRS016954: stool
SRS018133: stool
SRS022725: supragingival plaque
SRS016092: supragingival plaque
SRS022536: supragingival plaque
SRS022149: supragingival plaque
SRS020340: supragingival plaque
SRS019980: supragingival plaque
SRS019591: supragingival plaque
SRS017445: supragingival plaque
SRS016200: supragingival plaque
SRS019333: supragingival plaque
SRS016575: supragingival plaque
SRS019225: supragingival plaque
SRS018665: supragingival plaque
SRS017511: supragingival plaque
SRS017691: supragingival plaque
SRS015378: supragingival plaque
SRS023358: supragingival plaque
SRS052876: supragingival plaque
SRS015215: supragingival plaque
SRS051941: supragingival plaque
SRS011098: supragingival plaque
SRS011255: supragingival plaque
SRS011343: supragingival plaque
SRS012285: supragingival plaque
SRS055401: supragingival plaque
SRS013533: supragingival plaque
SRS052604: supragingival plaque
SRS054653: supragingival plaque
SRS014476: supragingival plaque
SRS014578: supragingival plaque
SRS015044: supragingival plaque
SRS015158: supragingival plaque
SRS020226: supragingival plaque
SRS020862: supragingival plaque
SRS043755: supragingival plaque
SRS019387: supragingival plaque
SRS051244: supragingival plaque
SRS045313: supragingival plaque
SRS018778: supragingival plaque
SRS018573: supragingival plaque
SRS018394: supragingival plaque
SRS058053: supragingival plaque
SRS058808: supragingival plaque
SRS018337: supragingival plaque
SRS018157: supragingival plaque
SRS017814: supragingival plaque
SRS015470: supragingival plaque
SRS017304: supragingival plaque
SRS011126: supragingival plaque
SRS011152: supragingival plaque
SRS013170: supragingival plaque
SRS013252: supragingival plaque
SRS013836: supragingival plaque
SRS013949: supragingival plaque
SRS014690: supragingival plaque
SRS014894: supragingival plaque
SRS015278: supragingival plaque
SRS015440: supragingival plaque
SRS013723: supragingival plaque
SRS015574: supragingival plaque
SRS016360: supragingival plaque
SRS015650: supragingival plaque
SRS017227: supragingival plaque
SRS017139: supragingival plaque
SRS017025: supragingival plaque
SRS016746: supragingival plaque
SRS016331: supragingival plaque
SRS016043: supragingival plaque
SRS015989: supragingival plaque
SRS015947: supragingival plaque
SRS015899: supragingival plaque
SRS015755: supragingival plaque
SRS022719: tongue dorsum
SRS019974: tongue dorsum
SRS022530: tongue dorsum
SRS022143: tongue dorsum
SRS020334: tongue dorsum
SRS016086: tongue dorsum
SRS016225: tongue dorsum
SRS017713: tongue dorsum
SRS016501: tongue dorsum
SRS016529: tongue dorsum
SRS016569: tongue dorsum
SRS019607: tongue dorsum
SRS017439: tongue dorsum
SRS017533: tongue dorsum
SRS019327: tongue dorsum
SRS019219: tongue dorsum
SRS015395: tongue dorsum
SRS023352: tongue dorsum
SRS052227: tongue dorsum
SRS018739: tongue dorsum
SRS014124: tongue dorsum
SRS011243: tongue dorsum
SRS011306: tongue dorsum
SRS012279: tongue dorsum
SRS056323: tongue dorsum
SRS054687: tongue dorsum
SRS053854: tongue dorsum
SRS050244: tongue dorsum
SRS014573: tongue dorsum
SRS014470: tongue dorsum
SRS047824: tongue dorsum
SRS044373: tongue dorsum
SRS015038: tongue dorsum
SRS015209: tongue dorsum
SRS049389: tongue dorsum
SRS020220: tongue dorsum
SRS042643: tongue dorsum
SRS018591: tongue dorsum
SRS020856: tongue dorsum
SRS055426: tongue dorsum
SRS019389: tongue dorsum
SRS057539: tongue dorsum
SRS018791: tongue dorsum
SRS043663: tongue dorsum
SRS015762: tongue dorsum
SRS018439: tongue dorsum
SRS015434: tongue dorsum
SRS011140: tongue dorsum
SRS013164: tongue dorsum
SRS013234: tongue dorsum
SRS013502: tongue dorsum
SRS013705: tongue dorsum
SRS013818: tongue dorsum
SRS013879: tongue dorsum
SRS014271: tongue dorsum
SRS014684: tongue dorsum
SRS014888: tongue dorsum
SRS015272: tongue dorsum
SRS015537: tongue dorsum
SRS018357: tongue dorsum
SRS015644: tongue dorsum
SRS015893: tongue dorsum
SRS015941: tongue dorsum
SRS016002: tongue dorsum
SRS016037: tongue dorsum
SRS016319: tongue dorsum
SRS016342: tongue dorsum
SRS017120: tongue dorsum
SRS017209: tongue dorsum
SRS017808: tongue dorsum
SRS018145: tongue dorsum
SRS018300: tongue dorsum
SRS057791: tongue dorsum

The markers that uniquely define clusters in the submitted SSN have been quantified in the metagenomes selected for analysis.

Files are provided that contain details about the markers that have been identified present in metagenomes and their abundances.

SSN and CD-HIT Files
CGFP Output (using median method)
CGFP Output (using mean method)

SSN With Quantify Results

The SSN submited has been edited so that the markers and their abundances in the selected metagenomes are included as node attributes.

	File	Size
	SSN with quantify results (ZIP)

CGFP Family and Marker Data

The CD-HIT ShortBRED families by cluster file contains mappings of ShortBRED families to SSN cluster number as well as a color that is assigned to each unique ShortBRED family. The ShortBRED marker data file lists the markers that were identified. Finally, the Description of selected metagenomes file provides available metadata associated with the selected metagenomes.

	File	Size
	CD-HIT ShortBRED families by cluster
	ShortBRED marker data
	Description of selected metagenomes	<1 MB

The default is for ShortBRED to report the abundance of metagenome hits for CD-HIT families using the "median method." The numbers of metagenome hits identified by all of the markers for a CD-HIT consensus sequence are arranged in increasing numerical order; the value for the median marker is used as the abundance. This method assumes that the distribution of hits across the markers for CD-HIT consensus sequence is uniform (expected if the metagenome sequencing is "deep," i.e., multiple coverage). For seed sequences with an even number of markers, the average of the two "middle" markers is used as the abundance.

Files detailing the abundance information are available for download.

Raw Abundance Data

Raw results for the individual proteins in the SSN (Protein abundance data (median)) as well as summarized by SSN cluster (Cluster abundance data (median)) are provided. Units are in reads per kilobase of sequence per million sample reads (RPKM).

	File	Size
	Protein abundance data (median)
	Cluster abundance data (median)

Average Genome Size-Normalized Abundance Data

Data are provided using Average Genome Size (AGS) normalization for individual proteins in the SSN as well as summarized by SSN cluster. Units are have been converted from RPKM to counts per microbial genome, using AGS estimated by MicrobeCensus.

	File	Size
	Average genome size (AGS) normalized protein abundance data (median)
	Average genome size (AGS) normalized cluster abundance data (median)

In the mean method for reporting abundances, the average value the abundances identified by the markers for each CD-HIT consensus sequence marker is used to report abundance. This method reports the presence of "any" hit for a marker for a seed sequence. An asymmetric distribution of hits a seed sequence with multiple markers is expected for "false positives," so the mean method should be used with caution.

Files detailing the abundance information are available for download.

Raw Abundance Data

Raw results for the individual proteins in the SSN (Protein abundance data (mean)) as well as summarized by SSN cluster (Cluster abundance data (mean)) are provided. Units are in reads per kilobase of sequence per million sample reads (RPKM).

	File	Size
	Protein abundance data (mean)
	Cluster abundance data (mean)

Average Genome Size-Normalized Abundance Data

	File	Size
	Average genome size (AGS) normalized protein abundance data (mean)
	Average genome size (AGS) normalized cluster abundance data (mean)

Heatmaps representing the quantification of sequences from SSN clusters per metagenome are available.

The y-axis lists the SSN cluster numbers for which metagenome hits were identified; the x-axis lists the metagenome datasets selected on the Identify Results page. A color scale is located on the right that displays the AGS normalized abundance of the number of gene copies for the "hit" per microbial genome in the metagenome sample.

The metagenomes are grouped according to body site so that trends/consensus across the six body sites can be easily discerned. The default heat map is calculated using the median method to report abundances.

Cluster Heatmap and Boxplots
Singleton Heatmap and Boxplots
Combined Heatmap and Boxplots

This heatmap presents information for SSN cluster/metagenome hit pairs.

This heatmap presents information for SSN singleton/metagenome hit pairs instead of SSN cluster/metagenome hit pairs.

This heatmap combines the information obtained for SSN cluster and singleton/metagenome hit pairs.

Tools for downloading and manipulating the heat map can be accessed by hovering and clicking above and to the right of the plot.

Several filters are available for manipulating the heatmap.

Show specific clusters: input individual cluster numbers separated by commas and/or a range of cluster numbers. Only these input clusters are displayed in the heatmap.
Abundance to display: hide any data values that are outside of the minimum and/or maximum. These hidden values appear as a zero value cell (i.e. the lowest color range).
Use mean: display the heatmap using the mean method for reporting abundances instead of the defaut median method.
Display hits only: show a black and white heatmap showing presence/absence of "hits" (which makes it easier to see low abundance hits).
Body Sites: checkboxes are provided for each body site in the heatmap; selecting one or more of these checkboxes will show data for those body sites only.

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