Table 1
General-Purpose Metabolic Databases

Database Name Contents Support of Comments and References

Comparative Analysis of Metabolic Pathways Automated Metabolic Reconstruction Library of "Signature Enzymes"

The Boehringer Mannheim Biochemical Pathways (SwissProt) A collection of metabolic pathways integrated into the Swiss Protein Data Bank connected to data about enzymes, and sequence data.   No No No [3], [4], [5]

KEGG
(Kyoto University, Japan)

A collection of overview pathway diagrams, representing some alternative pathways. Connected to the sequence data and ligand database of enzymes.
Concentrates on representation of metabolic network rather then the processes. No Yes No [6], [7]

EcoCyc A detailed encoding of the metabolism of Escherichia coli and Haemophilus influenzae. Includes, besides the metabolic network, some of the kinetic and thermodynamic parameters when they are known. No No No [8], [9]

MetaCyc Contains pathway diagrams connected to sequence data. Linked to WIT system [17]. Represents initial stages of its development. No No No [10]

The Biocatalysis Biodegradation Database Covers a small, but significant, set of pathways that are of special interest in the area of xenobiotic degradation. No No No [11]

SoyBase A collection of the metabolic pathways relevant to legumes. Connected to the enzymatic and sequence data information No No No [12]

The Maize DB Maintains a comprehensive collection of what is known of the maize genetic and biochemistry. [13]

Proposed PUMA2 Based on collection of metabolic modules, derived from the EMP/MPW collection of metabolic pathways, other metabolic databases, and literature information. Yes Yes Yes

Database Name	Contents	Support of			Comments and References
Database Name	Contents	Comparative Analysis of Metabolic Pathways	Automated Metabolic Reconstruction	Library of "Signature Enzymes"	Comments and References
The Boehringer Mannheim Biochemical Pathways (SwissProt)	A collection of metabolic pathways integrated into the Swiss Protein Data Bank connected to data about enzymes, and sequence data.	No	No	No	[3], [4], [5]
KEGG (Kyoto University, Japan)	A collection of overview pathway diagrams, representing some alternative pathways. Connected to the sequence data and ligand database of enzymes. Concentrates on representation of metabolic network rather then the processes.	No	Yes	No	[6], [7]
EcoCyc	A detailed encoding of the metabolism of Escherichia coli and Haemophilus influenzae. Includes, besides the metabolic network, some of the kinetic and thermodynamic parameters when they are known.	No	No	No	[8], [9]
MetaCyc	Contains pathway diagrams connected to sequence data. Linked to WIT system [17]. Represents initial stages of its development.	No	No	No	[10]
The Biocatalysis Biodegradation Database	Covers a small, but significant, set of pathways that are of special interest in the area of xenobiotic degradation.	No	No	No	[11]
SoyBase	A collection of the metabolic pathways relevant to legumes. Connected to the enzymatic and sequence data information	No	No	No	[12]
The Maize DB	Maintains a comprehensive collection of what is known of the maize genetic and biochemistry.				[13]
Proposed PUMA2	Based on collection of metabolic modules, derived from the EMP/MPW collection of metabolic pathways, other metabolic databases, and literature information.	Yes	Yes	Yes