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Metabolic Engineering Working Group

 
               
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MetaCyc: A multiorganism database of metabolic pathways and enzymes

Peter D. Karp

SRI International 

Objectives:

Develop a finely curated database of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants that contains a representative of every experimentally elucidated metabolic pathway.

Propose an initiative to determine sequences for the many biochemically characterized enzymes for which no sequence has ever been determined.  Such enzymes cannot at present be recognized in a sequenced genome, and are not accessible to genetic engineering techniques.  

Describe the BioPAX standard for exchange of metabolic data.

 Approach: 

Capture experimentally elucidated pathways, reactions, chemical compounds, and genes from the biomedical literature. 

Accomplishments:

MetaCyc describes 1543 enzymes in 491 metabolic pathways derived from more than 200 organisms.

Impact:

 MetaCyc provides a readily accessible comprehensive resource on microbial and plant enzymes that can be metabolically engineered into other species.

MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to predict the metabolic network of an organism from its annotated genome. Qualitative models of a metabolic network are an important step toward metabolic engineering.

Abstract:

The MetaCyc database (see URL http://MetaCyc.org/ ) is a collection of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants. The goal of MetaCyc is to contain a representative sample of each experimentally elucidated pathway, and thereby to catalog the universe of metabolism. MetaCyc also describes reactions, chemical compounds, and genes. Many of the pathways and enzymes in MetaCyc contain extensive information, including comments and literature citations. SRI's Pathway Tools software supports querying, visualization, and curation of MetaCyc.  MetaCyc serves two roles in metabolic engineering.  It is a readily accessible comprehensive resource on microbial and plant enzymes that can be inserted into other species.  In addition, MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to predict the metabolic network of an organism from its annotated genome.  Qualitative models of a metabolic network are an important step toward metabolic engineering. 

The talk will propose an initiative to determine sequences for the many biochemically characterized enzymes for which no sequence has ever been determined.  Such enzymes cannot at present be recognized in a sequenced genome, and are not accessible to genetic engineering techniques. 

The talk will present a status report on the BioPAX standard for exchange of metabolic information.

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