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Model file(.xml)  

Metabolites dictionary(.txt)  

Reaction mapping(.txt)  

External reactions(.xml) optional  

Organism proteome sequence(.fsa) optional  


DEF - Dead End Filler is a webserver aimed at aiding the gap filling step by finding the most biological meaningful candidate reactions in the metabolic network reconstruction.

It constructs an endosymbiosis-resembling model to maximize the flux of certain dead-end metabolites deriving the wisdom from evolution of metabolic systems, thus to get the most probable candidate reactions.

Input your Job ID to retrieve results

Job ID:

Please remember you Job ID to retrieve the results any time within 30 days after your submission.

Model construction

The model consists of two parts, i.e. the endosymbiosis compartment(presented as square) and the original model(presented as circle). As the figure on the right shows, the dead-end metabolite is solved by addition of the reactions through the endosymbiosis compartment. The constructed endosymbiosis-resembling model maximizes the utilization of the dead-end metabolites deriving the wisdom from the evolution of metabolic systems, that the selection pressure upon certain metabolic enzymes would benefit the preservation of most efficiency for metabolite usage. Thus the reactions are most likely to be present in target organisms.

Upload file format

Suspend your mouse at question marks on the Job Submission page to view the help informations.

Results Retrival

Once your job is successfully submitted, a Job ID will be generated. Since it takes quite a long time to find & fill all dead end gaps in a model, the Job ID is the only key to access the results afterwards. The Job ID could be seen after submission, in the 'Results Retrieval' page. You could stay on that page to see the progress of computation, or access the results via Job ID any time with 30 days after your submission

Results interpretation

Results consist of metabolites flow into & out of the introduced compartment through exchange reactions, and reactions essential for maximum flux for the production/consumption of certain dead end metabolite.

Also, when KEGG database is used as reaction background and the organism proteome sequence is provided, the validation of the candidate enzymes will be performed shortly after the results are given. The validation thresholds are as follows: BLAST e-value<1e-5, identity>30%, coverage>90% and then the protein domain from Pfam are searched.

Output Format: Reactants Flux Reaction Products Boolean_in_Draft

How to cite

Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen* (2016) DEF: An automated dead-end filling approach based on quasi-endosymbiosis. Bioinformatics, DOI: 10.1093/bioinformatics/btw604.


©2014-2016 Developed and Maintained by Lili Liu (liu7923@gmail.com) and Zijun Zhang (zzj.zju@gmail.com)