Introduction of a database

In plants protein phosphorylation has been implicated in the control of most developmental events and environmental responses including governance of the cell cycle, transcriptional and translational regulation, control of carbon and nitrogen metabolism, regulation of growth and differentiation, and responses to abiotic and biotic environmental cues. Currently it is estimated that nearly 1000 genes encode proteins belonging to the eukaryotic protein kinase superfamily in Arabidopsis thaliana. An additional 300 genes encode protein phosphatases. Furthermore, at least 50 members of two-component systems are predicted to be present in Arabidopsis (e.g. histidine kinases and response regulators).

Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function

The search function is the entry point to information about specific genes, protein motif/domain diagrams, exon/intron digrams, and BLAST database searches of both PlantsP, Arabidopsis genome, and all plant sequences.

Introduction of a analysis tool

Jpred is a internet web server that takes either a protein sequence or a mulitple alignment of protein sequences, and predicts secondary structure. It works by combining a number of modern, high quality prediction methods to form a consensus.

The server runs in two modes, single sequence and multiple sequence.
1. Multiple sequence

If you already have a set of aligned sequences you may submit them as either MSF format or BLC format, and the predictions will run. Your alignment will be modified so that it does not contain gaps in the first sequence. The first sequence should therefore always be your target sequence.

2. Single sequence

For single sequences an automatic alignment method is used. This alignment method takes your sequence and scans against the non redundant sequence database. The hits are then post filtered with SCANPS, using length dependent cut-offs. The resulting sequences are aligned with CLUSTALW (v1.7). The resulting alignments are automatically modified to have no gaps in the target sequence. Then the prediction algorithms are run. More detail can be found in the technical detail section.