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Both genes encoding proteins with recognizable functions as well as genes without known functions (HYP genes) were included.
In the absence of any other information proteins are tagged with GO terms based on protein domains with recognizable functions such as kinase domains.
We resolved differences in gene structure predictions for the MFS5 gene, which encodes a predicted major facilitator superfamily membrane transporter and two hypothetical genes (i.e., genes without recognizable functions), HYP12 and HYP13.
Applied to a model of adipocyte metabolism, ShReD-based modules obtained using flux weights more consistently reflected recognizable functions of established pathways compared to the modules obtained without the weights.
There is no known function, and no recognizable functional domains could be identified in any of the homologues.
The molecular function of LISP1, annotated as a hypothetical protein with a predicted signal peptide but no recognizable functional domain, remains unknown.
The benefit of a modular approach is that one can be exhaustive in searching for all cyclical EFMs in a given module at a particular hierarchical resolution, which can then facilitate the association of a cyclical EFM with a recognizable metabolic function.
Collectively, the nemS-cIntFams identify a restricted set of recognizable, basic functions that have acquired molecular characteristics that distinguish nematodes from other outgroup species.
In this regard, genome-scale metabolic models representing the metabolic networks of multiple interacting cell types [ 29] or organisms [ 30] offer exciting possibilities to identify novel, inter-organ or inter-species substrate cycles in the context of recognizable biochemical functions as defined by the corresponding module.
Consequently, we performed ad hoc ascertainment of candidates based on recognizable predicted gene function and other evidence.
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