48.0, updated on 1 October 2008 (12–15). Some informa- tion (including gene names, Enzyme Commission (EC) numbers, and species-speciﬁc enzymes) was supplied from UniProtKB/Swiss-Prot Release 14.0 (22) and NCBI Taxonomy database (23,24). The data in the pro- posed FMM will be updated regularly. The current meta- bolites (including ATP, NADH, H2O and CO2) are generally used as carriers for transferring electrons or cer- tain functional groups (including phosphate group, amino group, one carbon unit, and methyl group); they are like the external metabolites that participate in many reactions and are not in pseudo steady state in a sub-network. The connections through current metabolites should be avoided in calculating the path length from one metabolite to another. Hence, the connections through current meta- bolites and cofactors were deleted manually to make the path length analysis physiologically more meaningful. The current metabolites are displayed in Table S1 (See Supplementary Data). However, some current metabolites are primary metabolites. For example, asparate is not only a current metabolite involved in transamination mech- anism (oxaloacetate + NH3 + NADPH = asparate + NADP + H2O), but also a primary metabolite in biosyn- thesis of amino acids. When the current metabolites are Nucleic Acids Research, 2009, Vol. 37, Web Server issue W131 involved in the primary pathway as primary metabolites, such reactions and metabolites are collected in FMM. Therefore, biosynthesis of amino acids can be conducted in FMM. Posttranslational modiﬁcation (PTM) is the chemical modiﬁcation of a protein after its translation. In eukar- yote, the PTM of amino acids extends numerous functions of the protein involving protein structure change, such as formation of disulﬁde bridges and regulation of transcrip- tion. However, there is no PTM mechanism after protein translation in prokaryote. Therefore, a functional enzyme that needed PTM in eukaryote was no function when cloning into prokaryote. It is important to know the PTM information before cloning one gene from eukaryote to prokaryote. dbPTM (25) is a database that compiles information on protein post-translational modiﬁcations (PTMs), such as the catalytic sites, solvent accessibility of amino-acid residues, protein secondary and tertiary structures, protein domains and protein variations. Protein post-translational modiﬁcation (PTM) informa- tion was extracted from dbPTM (25). The numbers of collected metabolites, enzymes, reactions, species and KEGG maps are 16 832, 2336, 4288, 1491 and 149 in FMM, respectively. Figure 2. System ﬂow of FMM.