Quick search (query the database for individual Arabidopsis gene locus):

Home
Introduction
Main Conclusions
HOW-TO
FAQS
Implementation
Data description

Advanced Search

Locus Search

Search by Gene Family

 

 Welcome to the Plant Specific Database.




Click for the list of 3848 Arabidopsis Plant-Specific Proteins.


All other organisms (2436).
Eukaryota only (1152).
Bacteria but not in Archea or Eukaryota (576).
Bacteria and Eukaryota (249).
Cyanobacteria (316).
Multicellular eukaryotes only (163).
Archea and Eukaryota (141).
Bacteria and Archea but not Eukaryota (89).
Archea only (10).




National Science Foundation U.S. Department of Energy

What makes a plant different from other organisms?

To answer this question it is important to understand both what is similar between plants and other organisms and also what are the differences. Although many studies are based upon sequence similarities between genes in different species, suprisingly few studies have been reported that focus on the genome-wide differences between plants and organisms that belong to other phylogenetic lineages.

In an effort to shed light into this important question in plant biology, we have classified Arabidopsis protein-coding genes based on their pattern of sequence similarity to protein sequences of organisms that belong to the three domains of life (Eukaryota, Bacteria and Archea). This classification allowed the identification of 3848 Arabidopsis genes that encode putative plant-specific proteins, as similar protein sequences were only found in other plant species. Plant-specific proteins are likely to play important roles in processes that are unique and of significance to plants. Hence the study of their functions should greatly contribute to plant biology and to the understanding of how plants differ from other organisms. However, we found that many plant-specific proteins have unknown functions.

To facilitate the functional characterization of plant-specific proteins, we have compiled and integrated information from multiple public databases (e.g. TIGR, MIPS, TAIR, SIGNAL), as well as provide results obtained with predictive algorithms (e.g. TargetP, TMHMM, BLASTCLUST). We also provide flexible search capabilities that should allow the analysis of single as well as lists of proteins of interest to individual researchers.

A previous version of this work is available from:
http://www.bch.msu.edu/pamgreen/PS_project/front.html.

In addition to plant-specific proteins, we have also identified 5132 other Arabidopsis proteins that exhibit specific patterns of conservation across the three domains of life. We have classified these proteins in nine groups (below) according to the organisms in which we found similar protein sequences.

For a description of the database and its functionality see Gutierrez et al., 2004. Plant Physiol. 135, 1888-1892
The complete analysis of the plant specific proteins is described in Gutierrez et al., 2004. Genome Biol.. 5(8), R53
Follow this link for an introduction to this work and brief explanation of how it was done.
Follow this link for the main conclusions obtained in in this work.
Follow this link for a list of common questions about our work.

Use the links below to explore the list of plant-specific and other classifications of Arabidopsis proteins:

Click here to see a list of 3848 Arabidopsis proteins classified as plant-specific.

Click to see a list of Arabidopsis proteins found in:

All other organisms (2436).
Eukaryota only (1152).
Bacteria but not in Archea or Eukaryota (576).
Bacteria and Eukaryota (249).
Cyanobacteria (316).
Multicellular eukaryotes only (163).
Archea and Eukaryota (141).
Bacteria and Archea but not Eukaryota (89).
Archea only (10).

A total of 8980 Arabidopsis protein sequences are presented in this database, as plant-specific or in some of the other groups described above (click for a chart of the classification). More than half of the Arabidopsis proteins were not classified in this study. This number is largely explained by the stringent and conservative criteria we favored to define each of the categories.