ARAMEMNON, a novel database for Arabidopsis integral membrane proteins.
A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.
Schwacke
Rainer
R
Universität zu Köln, Botanisches Institut, Gyrhofstrasse 15, 50931 Köln, Germany. rainer.schwacke@uni-koeln.de
Schneider
Anja
A
van der Graaff
Eric
E
Fischer
Karsten
K
Catoni
Elisabetta
E
Desimone
Marcelo
M
Frommer
Wolf B
WB
Flügge
Ulf-Ingo
UI
Kunze
Reinhard
R
D026905:Amino Acid Transport Systems / Q000235:genetics; D020346:Aquaporins / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D016000:Cluster Analysis; D000458:Cyanobacteria / Q000235:genetics; D030562:Databases, Protein; D020407:Internet; D008565:Membrane Proteins / Q000235:genetics*; D010802:Phylogeny; D021382:Protein Sorting Signals / Q000235:genetics
D026905:Amino Acid Transport Systems; D020346:Aquaporins; D008565:Membrane Proteins; D021382:Protein Sorting Signals