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For example, we can have an instance of each of the modules belonging to the Analysis domain, the Orchestrator, the Classifier, and the Matcher, in the same box.
It should also be noted that target 35 is not a biological complex, but the assembly of two different modules belonging to the same protein chain.
We calculated the proportion of modules belonging to each functional class in the four genomes studied.
We then performed this same test for each of 1709 modules belonging to the 100 random networks.
We calculate the frequency of the corresponding annotation terms of all the modules belonging to this pattern as Table 2 shows.
In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre.
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Furthermore, the module selections formed by these modules belong to superior solutions in the enumerated set (top 15%).
As shown in Additional file 1: Table S1, these 55 modules belong to 35 GO_BP terms.
We evaluated the predicted node assignments obtained by the methods against the known assignments, in which most nodes are assigned to exactly one module with probability 1, and those shared by two modules belong to each with probability 0.5.
With a 37,000 Da molecular mass, this enzyme is composed of a signal peptide for secretion, of 37 aminoacids, a catalytic module belonging to the GH 12 family, of 222 aminoacids, bound through a small linker region to a carbohydrate binding module (CBM) belonging to the family CMB2 (Henrissat and Bairoch 1996) of 107 aminoacids.
This is because each module is compatible and can be ligated only to a module belonging to the next consecutive set of homologous modules, or to the acceptor vector for the first and last modules, and because each module from a set of homologous modules can be ligated with equal probability to each module of a contiguous set.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com