Figure 3. An example of web interface in FMM. (A) ‘Vertical graph’ and (B) ‘Global graph’ (KEGG map) of the metabolic pathway from tyrosine to resveratrol. or the species from which they can be cloned, are unknown, FMM identiﬁes them most easily. 4-Coumarate (C00811) and naringenin (C00509) were inputted into FMM; one E. coli was selected from ‘major species’ and ‘Arabidopsis thaliana’ and ‘Oryza sativa’ were selected from ‘comparative species’ in the ‘Comparative Analysis’ web page. Figure S6 (See Supplementary Data) indicates the eﬀortlessness of under- standing how the metabolic pathway from 4-coumarate to naringenin passes through three enzymes (4-coumarate- CoA ligase, chalcone synthase and chalcone isomerase), none of which are present in E. coli. Nevertheless, the results of FMM reveal that all of these genes can be cloned from A. thaliana, Oryza sativa, Populus tricho- carpa, Glycine max and Vitis vinifera. Watts et al. (28) cloned 4-coumarate-CoA ligase, chalcone synthase, and chalcone isomerase genes from Arabidopsis into E. coli; the results herein provide information that supports this cloning. FMM is thus a very useful tool in microbial engi- neering in synthetic biology. Case study II—application in pharmaceuticals. Plants are well known to generate large amounts of Nucleic Acids Research, 2009, Vol. 37, Web Server issue W133 phenylpropanoids which are important sources of phar- maceuticals due to their diverse chemical structures; for example, resveratrol is a chemopreventive anti-cancer agent (29). The inhibition of inﬂammation, tumor promo- tion, angiogenesis and metastasis and regulation of cell cycle progression are all pharmaceutical beneﬁts of resver- atrol (30). However, the mass-production of resveratrol is expensive because of the extraction processes are costly. However, the superb health eﬀects of resveratrol are moti- vating scientists to synthesize resveratrol using metabolic engineering methods in bacteria. When synthetic engineer- ing in bacteria, genes from which organisms are cloned into bacteria should be identiﬁed. FMM is an eﬀective tool for this purpose. For instance, if E. coli is to be used to produce resveratrol, resveratrol and tyrosine (which is a well known amino acid for the production of plant secondary metabolites) can be input into FMM. The synthesis pathway of resveratrol from tyrosine is easily determined (Figure 3A). Figure 3A reveals that E. coli and yeast cannot synthesize resveratrol unless several crit- ical genes are cloned into their cells from other species. For example, tyrosine-ammonia-lyase can be obtained from R. sphaeroides, 4-coumarate-CoA-lagase can be obtained from V. vinifera or A. thaliana, and trihydroxys- tilbene synthase can be obtained from A. hypogaea or V. vinifera. The results can be used as candidates for fur- ther experimental conﬁrmation. Accordingly, FMM has practical and eﬀective functions in synthetic biology. Certainly, FMM is also useful in the reconstruction of synthesis (metabolic) pathways. The metabolic pathways of interest can be signiﬁcantly identiﬁed in KEGG maps in FMM. Furthermore, FMM is particularly convenient when the metabolic pathway traverses more than one KEGG map. Figure S5 (See Supplementary Materials) indicates that the metabolic pathway from D-erythrose-4- -phosphate to chorismate passes through three KEGG maps. No other server has presented such a convenient interface for identifying metabolic pathway. SUMMARY The concept of FMM is illustrated in Figure 1, which demonstrates that metabolic pathways can be easily recon- structed among various species using the FMM system. The results suggest that FMM is helpful in metabolic engi- neering by reconstructing metabolic pathways for produ- cing some valuable metabolites or secondary metabolites in bacteria or yeast, which approach has potential in drug production. Moreover, FMM can be used to compare the metabolic pathways between numerous species and connect metabolic pathways of diﬀerent KEGG maps, suggesting that FMM is not only an eﬀective tool for syn- thetic biology, such as in the production of drugs and biofuels, but also a useful resource for investigation in metabolism. In order to connect metabolic pathways of diﬀerent KEGG maps in FMM, the compounds and reactions are restricted by the KEGG database. However, people may argue the incompleteness of FMM database for extract- ing metabolic pathway, due to several shortcomings of