W130 Nucleic Acids Research, 2009, Vol. 37, Web Server issue based on available metabolic maps, it is still inconvenient to reconstruct metabolic pathways from two interesting metabolites. For instance, determining the metabolic path- way from glucose to pyruvate from those databases is arduous unless the two metabolites are already known to be involved in the glycolysis pathway. Moreover, only one metabolite can be input to any of those servers, and users need considerable time to ﬁnd a speciﬁc pathway in which they are interested. In addition, comparative ana- lysis of metabolic networks in various species yields important information for many topics in biology and life sciences, such as evolution and speciation, metabolic engineering, and drug design. Li et al. (19) adopted Metabolic Pathway Alignment and Scoring (M-PAS) for identifying and ranking conserved metabolic pathways based on a comprehen- sive and ﬂexible similarity measuring method. The Comparative Pathway Analyzer (CPA) calculates and displays the diﬀerences between the metabolic reaction contents of several organisms (20). The Roseobacter sys- tems biology database (ROSY) represents an integrated platform for studying the comparative genomics and sys- tems biology of Roseobacter-related species (21). However, even some of the resources for comparative ana- lysis of metabolic pathways of various species focus on a few species only or do not provide a convenient interface for analysis. The above considerations motivated the development of a novel and easy resource for use in synthetic biology, which is proposed herein. In this work, a new web server, FMM (From Metabolite to Metabolite), was designed to reconstruct metabolic pathways form one metabolite to another among diﬀerent species, based mainly on the KEGG database (12–15) and other inte- grated biological databases. Even though KEGG maps utilized in many metabolic tools, none of them can con- nect metabolites from diﬀerent KEGG maps. FMM sup- ports the connection of diﬀerent KEGG maps. Figure 1 depicts the basic concept of FMM which demonstrates that FMM has numerous applications in synthetic biology and metabolic engineering. For instance, the reconstruc- tion of metabolic pathways to produce valuable metabo- lites or secondary metabolites in bacteria or yeast is a promising strategy for producing drugs. FMM provides a very convenient way to elucidate which genes from which species should be cloned into those microor- ganisms based on FMM pathway comparative analysis. Accordingly, FMM is an eﬀective tool in synthetic biology and metabolic engineering, such as applications in drug production and biofuel production. METHODS Figure 1 displays metabolic pathways that can be easily reconstructed from two interesting metabolites among various species using the FMM system. Figure 2 presents the system ﬂow of FMM. A reaction matrix was devel- oped to identify numerous reaction processes from one metabolite to another. Enzyme annotations from UniProtKB/Swiss-Prot (22) were employed to identify enzymes from diﬀerent species in comparative analysis. Data collection and integration FMM reaction deﬁnitions, species-speciﬁc reactions, reac- tion maps and enzyme lists were obtained from KEGG/ LIGAND and KEGG/PATHWAY database Release Figure 1. A conceptual diagram of FMM.