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One technology that has arisen to meet this challenge is activity-based protein profiling (ABPP) that uses activity-based chemical probes to broadly assess the functional states of both characterized and uncharacterized enzymes.
Many of the characterized and uncharacterized genes have orthologues in model organisms, which can be used to study biological function.
Based on the most recently available information of the zebrafish gene annotation, these gene sets were classified as characterized and uncharacterized genes (Table 1).
Not surprisingly, many poorly characterized and uncharacterized genes were found exclusively or predominantly in air data relative to sequence from previously examined outdoor environments.
Given that the computational screen identified the three known targets of SXL as well as a novel target of SXL, characterization of Rm62 using molecular genetics should provide important new insights into the function and regulation of both previously characterized and uncharacterized genes, the mechanisms of action of SXL, and the basis for sexual dimorphism.
Furthermore, precursor peptides from both characterized and uncharacterized families were analyzed to identify common motifs.
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As a first step in addressing these critical gaps in our knowledge, we have analyzed a systematic series of (smaller) structurally characterized and (larger) uncharacterized DEBS fragments using small-angle X-ray scattering (SAXS).
Of these 91 genes, only 27 genes were previously characterized and 64 were uncharacterized genes or ESTs (Table 1, Table S4, q = 0.0 and score(d)>4.0).
Versions of these methods should be applicable to any collection of sequence information where uncharacterized proteins or genes need to be distinguished from those that are characterized and should be especially applicable to enzymes that act on biological polymers.
In the accessory genomes of the reference P. aeruginosa strains, on the other hand, more than two-thirds of the accessory genes fell into the categories of poorly characterized or uncharacterized functions, and almost half had no identifiable ortholog in the COG database.
These combinations and a number of other factors, such as low water activity, hydrogen peroxide, low pH, and other partially characterized or uncharacterized compounds, produce a high antimicrobial action [ 5- 9].
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