1. Overview of Microbial Pathway and Genome Databases

2. Overview
Survey of other databases / web sites that integrate hundreds of microbial genomes and pathway information
Most of these resources are described in publications that can be found via PubMed
Differences among each resource include:
Genomes included
What other information is integrated with the genome data
Value-added computational processing applied to each genome
Query, visualization, and analysis tools available at each site

3. Overall Comparison to BioCyc
Many of the other databases contain more genomes than BioCyc
This will change in 2011 as BioCyc transitions to RefSeq as its genome source
BioCyc Tier 1 and Tier 2 databases more highly curated than other databases
BioCyc has more extensive query, visualization, and analysis tools than other sites
BioCyc desktop version can be installed locally, and allows editing of PGDBs
Some other sites re-annotate the genomes, which may or may not improve data quality

4. Microbial Genome Resources
CMR – Comprehensive Microbial Resource
Entrez
IMG – Integrated Microbial Genomes
KEGG – Kyoto Encyclopedia of Genes and Genomes
PATRIC
SEED/NMPDR
UMBBD – Univ of Minnesota Biocatalysis Biodegradation Database

5. CMR – Comprehensive Microbial Resource J. Craig Venter Institute
~700 genomes
Genome data only, no pathways
Genome browser, gene pages
Many comparative operations
Will be discontinued later in 2010

6. Entrez Genomes National Center for Biotechnology Information
Web portal to Genbank genomes
Genome browser, gene pages

7. IMG – Integrated Microbial Genomes Joint Genome Institute
1,911 microbial genomes (approx half are draft quality)
Genome browser, gene pages
Many comparative operations
Genome context analyses available

8. PATRIC Virginia Bioinformatics Institute
Genome browser, gene pages
KEGG pathways

9. SEED / NMPDR Argonne National Laboratory
782 microbial genomes
Funding ended in 2009
Unique features:
Systems
Essential genes
Comparative genomics tools
Community annotation

10. UMBBD University of Minnesota
Database of ~150 microbial biodegradation pathways
Does not include full microbial genomes

11. KEGG – Kyoto Encyclopedia of Genes and Genomes Kyoto University
1,382 organisms
KEGG reannotates each genome
Static reference pathway maps are colored with the genes present in each organism

12. Comparison with KEGG KEGG vs MetaCyc: Reference pathway collections
KEGG maps are not pathways Nuc Acids Res 34:
KEGG maps contain multiple biological pathways
Two genes chosen at random from a BioCyc pathway are more likely to be related according to genome context methods than from a KEGG pathway
KEGG maps are composites of pathways in many organisms -- do not identify what specific pathways elucidated in what organisms
KEGG has no literature citations, no comments, less enzyme detail
KEGG assigns half as many reactions to pathways as MetaCyc
KEGG vs organism-specific PGDBs
KEGG does not curate or customize pathway networks for each organism
Highly curated PGDBs now exist for important organisms such as E. coli, yeast, mouse, Arabidopsis

13. Comparison of Pathway Tools to KEGG
Inference tools
KEGG does not predict presence or absence of pathways
KEGG lacks pathway hole filler, operon predictor
Curation tools
KEGG does not distribute curation tools
No ability to customize pathways to the organism
Pathway Tools schema much more comprehensive
Visualization and analysis
KEGG does not perform automatic pathway layout
KEGG metabolic-map diagram extremely limited
No comparative pathway analysis