To examine this possibility, we identified gene paralogs based on protein sequence homology (Table S3).
The entire interface between 14-3-3β 14-3-3β 14-3-3βand is similar in ExoS and ExotheSupplementART Fig. 5) andomained on proteis similare comparinon, appExoS to be well conserved in other 14-3-3-dependent toxins (Supplementand Fig. 6).
Functional description of protein domains was annotated by InterProScan based on protein sequence alignment method, and the InterPro domain database was used (Hunter et al. 2009).
As a result, developing a robust and effective computational approach based on protein sequence to detect SIPs has become more and more important.
To determine the regions required for mSYCP2 NTR binding, we co-expressed several truncations of the above candidates based on protein sequence analysis in a yeast two-hybrid assay.
Yang et al. [10] presented a new method based on protein sequence, which used local protein sequence descriptors as a novel representation and employed the k-nearest neighbors classifier to execute classification.
In the work, we presented a novel computational approach named WELM LAG, which combined the Weighed-Extreme Learning MaclassifierM) classifier with Local Average Group LAGG) to predict SIPs based on protein sequence.
We then predicted both potential N-glycosylation sites and the masses of potential deglycosylated peptides based on protein sequence.
These residues were predicted based on protein sequence analysis and are supported by experimental results (see methods).
However, helical cytokines are notoriously hard to detect based on protein sequence alone because their three-dimensional fold is particularly permissive to sequence perturbation [2].
Many groups have pursued the identification and functional annotation of novel mammalian helical cytokines (interleukins and interferons) based on protein sequence similarity.
