In particular, when two proteins are distantly related, there is no good indicator to reliably assess whether they are homologous or not. Figure 1 shows the number of unique orthologous pairs between the yeast Saccharomyces cerevisiae and Arabidopsis thaliana acquired from the Website of Clusters of Orthologous Groups of proteins (COGs) [ 37].
As the molecular weight of the cleaved fragment was not the expected one, in silico analysis using the SitePrediction website of the beclin 1 protein sequence revealed several classical caspase recognition sites: of these, cleavage by caspase 3/7 after EASD105 would generate fragment of 40.3 kDa (Supplementary data 13).
On the website, proteins of interest can be searched by name, Uniprot, SwissProt or TrEMBL accession numbers.
The conserved domains of proteins were analysed at the website: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi.nih.gov/Structure/cdd/wrpsb.cgi
The list of KOGs (euKaryotic clusters of Orthologous Groups of proteins) with assigned genes was downloaded from the COG website [ 10].
This contains 528 proteins and consists largely of proteins with some relationship to the ribosome (based on short protein descriptions found on the SGD website).
Wheat contains several different classes of proteins.
Identification of proteins.
To address these limitations, HIVprotI has been developed employing more and varied inhibitors besides providing an open source integrated website for prediction and screening of protein specific anti-HIV compounds.
The GeneMANIA website provides a large number of protein-protein interaction and association networks generated using several types of evidence: co-expression, co-localization, genetic interactions, physical interactions and predicted interactions.
First, we illustrate the usage of the http://SignaLink.org website with a protein, AXIN1.
