About this database (Updated on December 4, 2024)
This database provides plausible functional annotations of the genes in biosynthetic gene clusters based on the sequence similarity with functionally annotated proteins. The amino acid sequence of each gene product registered in the MIBiG (Minimum Information about Biosynthetic Gene) database was subjected to BLAST searches against the PDB and SwissProt sequence database. The results are stored in a relational database together with the functional annotation data provided by UniProt and the reaction data provided by Rhea. The user can search the database by MIBiG accession, protein ID, reaction participant name, or reaction participant substructre. This database helps the user to infer bound ligands and catalyzing reactions of a gene product and to find a gene product that is inferred to catalyze a reaction involving a given compound.
Search and browse database
- Browse clusters and genes
- BLAST search against MIBiG, PDB, or SwissProt sequences
- Find a gene cluster by MIBiG accession
- Find a gene by protein ID
- Find a gene by reaction participant name
- Find a gene by reaction participant substructure
Data sources
- Gene cluster information and sequences: MIBiG version 4.0 (November 15th, 2024)
- SwissProt BLAST data: Data of November 30, 2024 downloaded from NCBI
- PDB BLAST data: Data of November 30, 2024 downloaded from NCBI
- SwissProt: Release 2024_06 (November 27, 2024) downloaded on December 1, 2024 in XML format from UniProt
- UniProt: Release 2024_06 (November 27, 2024) downloaded on December 1, 2024 in FASTA format from UniProt
- Structral models: v4 models downloaded on December 2, 2024 from AlphaFold DB
- PDB and chemical component identifier correspondences: downloaded from Ligand Expo on December 1, 2024
- PDB chemical component dictionaries: downloaded in PDBML format from Ligand Expo on December l, 2024
- PubChem CIDs: Converted from InChI using PubChem Identifier Exchange Service on December 1, 2024
- Reaction data: Release 136 (November 27, 2024) downloaded on December 1, 2024 in RDF format from Rhea
- Reaction participant data: Release 136 (November 27, 2024) downloaded on December 1, 2024 in MDL Molfile format from Rhea
- Conserved domain data: version 3.21 downloaded on November 30, 2024 from the CDD FTP-archive.
Download
BLAST search results stored in this database can be downloaded in a tab-separated-values (tsv) format.- Against PDB sequences (113 MB)
File format: MIBiG_accession, Protein_ID, Descriptions, PDB_IDs, Chains, Identity, Cover, E-value, Hit_num, HSP_num - Against SwissProt sequences (231 MB)
File format: MIBiG_accession, Protein_ID, SwissProt_accession, Recname, Identity, Cover, E-value, Hit_num, HSP_num
Developed by Tohru Terada, Ryota Kobayashi,and Suguru Fujita
Computational Biology Laboratory, Department of Biotechnology, Graduate School of Agricultural and Life Sciences
The University of Tokyo, JAPAN