Overview of Microbial Pathway and Genome Databases

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Overview

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Survey of other databases / web sites that integrate hundreds of microbial genomes and pathway information

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Most of these resources are described in publications that can be found via PubMed

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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

Overall Comparison to BioCyc

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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

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BioCyc has more extensive query, visualization, and analysis tools than other sites

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BioCyc desktop version can be installed locally, and allows editing of PGDBs

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Some other sites re-annotate the genomes, which may or may not improve data quality

Microbial Genome Resources

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CMR – Comprehensive Microbial Resource

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Entrez

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IMG – Integrated Microbial Genomes

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KEGG – Kyoto Encyclopedia of Genes and Genomes

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PATRIC

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SEED/NMPDR

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UMBBD – Univ of Minnesota Biocatalysis Biodegradation Database

CMR – Comprehensive Microbial

Bioinformatics

Resource J. Craig Venter Institute

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http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

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~700 genomes

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Genome data only, no pathways

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Genome browser, gene pages

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Many comparative operations

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Will be discontinued later in 2010

Entrez Genomes National Center for Biotechnology Information

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http://www.ncbi.nlm.nih.gov/sites/genome

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Web portal to Genbank genomes

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Genome browser, gene pages

IMG – Integrated Microbial Genomes Joint Genome Institute

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http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

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1,911 microbial genomes (approx half are draft quality)

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Genome browser, gene pages

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Many comparative operations

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Genome context analyses available

PATRIC Virginia Bioinformatics Institute

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http://patric.vbi.vt.edu/

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Genome browser, gene pages

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KEGG pathways

SEED / NMPDR Argonne National Laboratory

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http://www.nmpdr.org/FIG/wiki/view.cgi

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782 microbial genomes

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Funding ended in 2009

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Unique features:

 Systems  Essential genes  Comparative genomics tools  Community annotation

UMBBD University of Minnesota

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http://umbbd.msi.umn.edu/

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Database of ~150 microbial biodegradation pathways

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Does not include full microbial genomes

KEGG – Kyoto Encyclopedia of Genes and

Bioinformatics

Genomes Kyoto University

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http://www.genome.ad.jp/kegg/

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1,382 organisms

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KEGG reannotates each genome

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Static reference pathway maps are colored with the genes present in each organism

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Comparison with KEGG

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KEGG vs MetaCyc: Reference pathway collections

  KEGG maps are not pathways Nuc Acids Res 34:3687 2006    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

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Comparison of Pathway Tools to KEGG

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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