Nucleic Acids Research, 2006, Vol. 34, Database issue D513 Table 1. List of species that have five or more experimentally elucidated pathways represented in MetaCyc No. of pathways Eukarya No. of pathways Archaea No. of pathways Sulfolobus solfataricus Methanocaldococcus jannaschii 15 5 Bacteria Escherichia coli Pseudomonas putida Bacillus subtilis Pseudomonas aeruginosa Mycobacterium tuberculosis Salmonella typhimurium Haemophilus influenzae Deinococcus radiodurans Mycoplasma pneuomiae Mycobacterium smegmatis Sinorhizobium meliloti Thauera aromatica Klebsiella pneumoniae Lactococcus lactis Corynebacterium glutamicum Methylobacterium extorquens AM1 Pseudomonas fluorescens Thermotoga maritima Paracoccus denitrificans Arthrobacter globiformis Mycoplasma capricolum Bradyrhizobium japonicum Bacillus cereus 179 35 24 19 17 14 13 12 8 8 8 7 7 6 6 6 6 6 5 5 5 5 5 Bacteria Proteobacteria Firmicutes Actinobacteria Deinococcus- Thermus Cyanobacteria Thermotogae Planctomycetes Bacteroidetes/ Chlorobi Nitrospirae Aquificae Chloroflexi Spirochaetes Chlamydiae Chrysiogenetes No. of pathways 598 169 94 18 13 8 6 6 5 2 2 1 1 1 Arabidopsis thaliana Homo sapiens Glycine max Saccharomyces cerevisiae Pisum sativum Zea mays Solanum tuberosum Cicer arietinum Oryza sativa Spinacia oleraca Rattus norvegicus Hordeum vulgare Nicotiana tabacum Lycopersicon esculentum Medicago sativa Brassica napus Glycyrrhiza echinata Triticum aestivum Cucumis sativus Ricinus communis Pueraria montana 116 42 36 31 20 19 12 12 12 11 10 8 8 7 7 6 6 6 5 5 5 The species are grouped by taxonomic domain and are ordered within each domain based on the number of pathways to which the given species was assigned. Some pathways may be labeled with a higher-level taxon, such as genus, if all the species within that genus are thought to have the given pathway. However, such higher-level taxa are not included in this table. Table 2. The distribution of pathways in MetaCyc based on the taxonomic classification of associated species Eukarya Viridiplantae Metazoa Fungi Euglenozoa No. of pathways 396 61 58 4 Archaea Euryarchaeota Crenarchaeota No. of pathways 47 26 The taxonomic groups (phyla for Bacteria and Archaea, kingdoms for Eukarya) are grouped by domain and are ordered within each domain based on the number of pathways associated with the taxon. Euglenozoa are listed separately as this group does not belong to any of the other eukaryotic kingdoms. A pathway may be associated with multiple organisms. detailed guidelines for deﬁning pathway boundaries (the com- pounds with which a pathway should begin and end) and for deﬁning links between pathways. To ensure the accuracy and coverage of new and existing 5 pathways, we are currently in the process of inviting outside experts to support the database as editors and/or curators in their ﬁelds of expertise. Pathways, enzymes, reactions and compounds Most of the pathways in MetaCyc occur in the microorganism 10 and plant kingdoms, a manifestation of their metabolic divers- ity. Nevertheless, animal pathways are also represented. Since November 2003 we added >140 new pathways in the areas of small molecule intermediary metabolism, and the biosynthesis and degradation of natural environmental compounds, envir- onmental pollutants, xenob15iotics and compounds involved in general cellular processes and secondary metabolism. Of these 63 are plant pathways, many of which concern the produc- tion of compounds involved in cellular regulation processes (phytohormones) and defense mechanisms (phytoalexins and phytoanticipins), and plant20 secondary (or specialized) meta- bolites. To accommodate these new types of pathways, we expanded the pathway ontology to include categories for plant secondary metabolism, comprising 8 main classes and 26 subclasses (see http://biocyc.org/META/class-tree?