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.

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

Chemically guided functional profiling (CGFP) maps metagenome protein abundance to clusters in sequence similarity networks (SSNs) generated by the EFI-EST web tool.

EFI-CGFP uses the ShortBRED software package developed by Huttenhower and colleagues in two successive steps: 1) identify sequence markers that are unique to members of families in the input SSN that are identified by ShortBRED and share 85% sequence identity using the CD-HIT algorithm (CD-HIT 85 clusters) and 2) quantify the marker abundances in metagenome datasets and then map these to the SSN clusters.

Currently, a library of 380 metagenomes is available for analysis. The dataset originates from the Human Microbiome Project (HMP) and consists of metagenomes from healthy adult women and men from six body sites [stool, buccal mucosa (lining of cheek and mouth), supragingival plaque (tooth plaque), anterior nares (nasal cavity), tongue dorsum (surface), and posterior fornix (vagina)].

Previous Jobs
Run CGFP/ShortBRED

Previous Jobs

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Upload the SSN for which you want to run CGFP/ShortBRED. The initial identify step will be performed: unique markers in the input SSN will be identified.

SSN File:

Select a XGMML or zip file to upload

Cytoscape-edited SSN can serve as input. The accepted format is XGMML (or compressed XGMML as zip).

Sequence Length Restriction Options

If the submitted SSN was generated using the UniRef90 or 50 option, then it is recommended to specify a minimum sequence length, in order to eliminate fragments that may be included in UniRef clusters. A maximum length can also be specified.

Minimum Length:

Maximum Length:

Marker Identification Options

Several parameters are available for the identify step.

Reference database:

ShortBRED uses the UniProt, UniRef90 or UniRef50 databases to evaluate markers in order to eliminate those that could give false positives during the quantify step. The default database used in this process is UniRef90.

CD-HIT sequence identity (default 85%):

This is the sequence identity parameter that will be used for determining the ShortBRED consensus sequence families.

Job name:

Database Version:

E-mail:

You will be notified by e-mail when your submission has been processed.