EFI - Genome Neighborhood Tool

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

The EFI Tools were upgraded on 10/26/26. While the updated site is functionally identical to the old site, jobs run prior to 10/24/26 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.

If you encounter issues, please report it to us via the Feedback page and our team will address your specific problem.

EFI-GNT allows exploration of the genome neighborhoods for sequence similarity network (SSN) clusters in order to facilitate the assignment of function within protein families and superfamilies.

In GNT Submission, each sequence within a SSN is used as a query for interrogation of its genome neighborhood. A colored SSN identifying clusters, Genome Neighborhood Networks (GNNs) providing statistical analysis of neighboring Pfam families, Genome Neighborhood Diagrams (GNDs), sets of IDs and sequences per cluster and additional files are created. For the Retrieve Neighorhood Diagrams option, only GNDs will be created.

Create a user account or login to see job history.

In a submitted SSN, each sequence is considered as a query. Information associated with protein encoding genes that are neighbors of input queries (within a defined window on either side) are collected from sequence files for bacterial (prokaryotic and archaeal) and fungal genomes in the European Nucleotide Archive (ENA) database. The neighboring genes are sorted into neighbor Pfam families. For each cluster, the co-occurrence frequencies of the identified neighboring Pfam families with the input queries are calculated.

SSN File:

Select a XGMML or zip file to upload

SSNs generated by EFI-EST are compatible with GNT analysis (with the exception of SSNs from the FASTA sequences without the "Read FASTA header" option), even when they have been modified in Cytoscape. The accepted format is XGMML (or compressed XGMML as zip).

If a SSN that contains UniRef sequences is uploaded to the GNT, the resulting GNDs will also include GNDs for UniRef90 cluster IDs that group together UniProt sequences by 90% sequence identiy. For networks that also contain UniRef50 sequences, GNDs will also include UniProt sequences that are grouped by 50% sequence identity.

Neighborhood Size:

The Pfam families for N neighboring genes upstream and downstream will be collected and analyzed. The default value is 10 and the minimum and maximum are 3 and 20, respectively.

Minimal Co-occurrence Percentage Lower Limit:

Filters out the neighboring Pfams for which the co-occurrence percentage is lower than the set value (noise filter). The default value is 20 and valid values are 0-100.

Database Version:

E-mail:

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

Clicking on the headers below provides access to various ways of generating genomic neighborhood diagrams.

Single Sequence BLAST
Sequence ID Lookup
FASTA Sequence Lookup

The provided sequence is used as the query for a BLAST search of the UniProt database. The retrieved sequences are used to generate genomic neighborhood diagrams.

If the Sequence Database is set to UniRef90, the resulting GNDs will also include GNDs for UniRef90 cluster IDs that group together UniProt sequences by 90% sequence identiy. For UniRef50, the GNDs will also include UniProt sequences that are grouped by 50% sequence identity. Any of the "Exclude Fragments" options will exclude UniProt-defined sequence fragments.

Query Sequence:

UniProt BLAST query e-value:

Negative log of e-value for retrieving similar sequences (≥ 1; default: 5)

Input a larger e-value (smaller negative log) to retrieve homologues if the query sequence is short. Input a smaller e-value (larger negative log) to retrieve more similar homologues.

Maximum number of sequences retrieved:

(≤ 500, default 200)

Sequence database:

Exclude Fragments:

Check to exclude UniProt-defined fragments in the results. [default: off]

Neighborhood Size:

Number of neighbors to retrieve on either side of the query sequence for each BLAST result (default: 10)

Job name:

Database Version:

E-mail:

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

The genomic neighborhoods are retreived for the UniProt, NCBI, EMBL-EBI ENA, and PDB identifiers that are provided in the input box below. Not all identifiers may exist in the EFI-GNT database so the results will only include diagrams for sequences that were identified.

Sequence database:

Alternatively, a file containing a list of sequence IDs can be uploaded:

Select a text file containing IDs to upload

Exclude Fragments:

Check to exclude UniProt-defined fragments in the results. [default: off]

Neighborhood Size:

The Pfam families for N neighboring genes upstream and downstream will be collected and analyzed. The default value is 10 and the minimum and maximum are 3 and 20, respectively.

Job name:

Database Version:

E-mail:

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

The genomic neighborhoods are retreived for the UniProt, NCBI, EMBL-EBI ENA, and PDB identifiers that are identified in the FASTA headers. Not all identifiers may exist in the EFI-GNT database so the results will only include diagrams for sequences that were identified.

FASTA:

Alternatively, a file containing FASTA headers and sequences can be uploaded:

Select a FASTA file to upload

Neighborhood Size:

The Pfam families for N neighboring genes upstream and downstream will be collected and analyzed. The default value is 10 and the minimum and maximum are 3 and 20, respectively.

Job name:

Database Version:

E-mail:

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

Upload a saved diagram data file for visualization.

Select a file to upload:

Select a GND sqlite or zip file to upload

The acceptable format is a SQLite file downloaded from the Genome Neighborhood Diagram viewer (optionally zip-compressed).

Database Version:

E-mail:

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