Version 1 (modified by akinjo, 16 years ago) |
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A DDBJ-KEGG-PDBj workflow: from pathways to protein-protein interactions
- For the details of the project, see DDBJ-KEGG-PDBj.
Members
- Yasumasa Shigemoto (WABI/SABI; DDBJ, Japan)
- Akira Kinjo (PDBj, Japan)
- Soichi Ogishima (Tokyo Medical and Dental Univ, Japan)
- Masumi Itoh (Hokkaido Univ)
The objective
Given a KEGG pathway ID of a specific species,
- Identify homologous proteins of the pathway.
- Infer possible protein-protein interactions between components of the homologous pathways.
How?
- Input: KEGG pathway ID
- Get amino acid sequences of all the proteins involved in the given pathway. (KEGG API)
- For each protein sequence, run BLAST against the UniProt (SwissProt / !TrEMBL) database to identify its homologs. (WABI)
- Sort the BLAST results according to species. (a local program)
- At this point, we will have a phylogenetic profile.
- For each BLAST hit (a UniProt entry), run BLAST against PDB. (PDBj SeqNavi API).
- Find physical interactions between different components. (a local program)
- That is, if two (UniProt) sequences are homologous to different chains of the same PDB entry, they are predicted to be in physical contact.
- Output the phylogenetic profile and the predicted species-wise PPI.
An example
- KEGG pathway: path:eco00020
- Phylogenetic profile:
Attachments
-
sp_kegggene_matrix.2.xls
(59.1 KB) - added by akinjo
16 years ago.
a phylogenetic profile
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Acinetobacter_sp._strain_ADP1_..gif
(55.8 KB) - added by akinjo
16 years ago.
pathway colored by phylogenetic profile
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Yersinia_pestis.gif
(25.1 KB) - added by akinjo
16 years ago.
PPI
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eco00020.gif
(15.9 KB) - added by akinjo
16 years ago.
eco00020
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ppi_by_species.txt
(80.3 KB) - added by akinjo
16 years ago.
ppi list