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TCDB

http://www.tcdb.org/

Description :
The Transporter Classification Database (TCDB) is a curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a repository for information compiled from more than 10,000 references, encompassing approximately 3,000 representative transporters and putative transporters, classified into over 400 families. The Transporter Classification (TC) system is an International Union of Biochemistry and Molecular Biology (IUBMB) approved system of nomenclature for transport protein classification. The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins.

Aknowledgement :
Work in Saier laboratory is supported by NIH grants 2R01 AI14176 from The National Institute of Allergy and Infectious Diseases and 9RO1 GM55434 from the National Institute of General Medical Sciences, as well as by the M. H. Saier, Sr., Memorial Research Fund.

References :
1. Saier, M.H., Jr. (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev., 64, 354-411.
2. Busch, W. and M.H. Saier, Jr. (2002) The Transporter Classification (TC) System, 2002. CRC Crit. Rev. Biochem. Mol. Biol. 37, 287-337.

ARAMEMNON

http://aramemnon.botanik.uni-koeln.de/

Description :
ARAMEMNON is a curated database for Arabidopsis thaliana transmembrane (TM) proteins and transporters. The database compiles topology and signal sequence predictions and displays the results in a directly comparable graphical output format for presently 7139 genes/proteins. The reliability of TM prediction is improved by calculating a consensus TM prediction. ARAMEMNON also contains experimental intracellular localization data from the literature, a comprehensive bibliography and many other features for data mining and sequence interpretation of Arabidopsis membrane proteins. ARAMEMNON is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

The database query options are:

  • text strings in gene annotations, locus names, GenBank accession numbers or BAC names,
  • signal sequence/subcellular targeting predictions (plastids, mitochondria or the secretory pathway),
  • proteins with a user-defined range of TM spans,
  • predicted N-terminus orientation towards the cytoplasma or the extra-cytoplasmic space,
  • protein or nucleic acid BLAST searches against all Arabidopsis sequences in the database.

The ARAMEMNON output options are:

  • protein, ORF, cDNA (if available) and genomic DNA sequences with links to the respective NCBI, TAIR, TIGR and MIPS entries,
  • transmembrane topology prediction results by eleven programs (http://aramemnon.botanik.uni-koeln.de/links.ep):
  • the consensus TM topology calculated from these programs,
  • hydropathy profile graphical display,
  • sequence alignment (CLUSTAL W) of custom selected proteins,
  • TM span alignment of selected proteins,
  • subcellular localization predictions by eight programs (see http://aramemnon.botanik.uni-koeln.de/links.ep),
  • published experimental subcellular localization data
  • similar 'isospecic' proteins (i.e. paralogs) in Arabidopsis,
  • similar 'heterospecic' proteins (i.e. orthologs) in Synechocystis sp., Thermosynechococcus and Anabaena,
  • gene/protein family structure display (similar to phylogenetic tree)
  • neighboring genes on the same BAC (list and graphical representation),
  • improved gene annotation based on published data
  • bibliography with direct links to PubMed

The ARAMEMNON database is regularly updated with the latest Arabidopsis sequences and gene models from TIGR/TAIR, new bibliographic entries and published gene/protein nomenclatures. New signal sequence and topology predictions will be incorporated when they are made publicly available. The database will be further extended by incorporating the membrane proteins from other eukaryotes.

Aknowledgement :
We thank John Ward (University of Minnesota, St. Paul) who kindly provided the algorithm for the hydropathy profile display, and William Martin (Heinrich-Heine-Universität Düsseldorf) for helpful discussions on the gene family structure analysis. This work is funded in the frame of the GABI program by the German Federal Ministry of Education and Research (BMBF).

References :
Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flügge U-I, Kunze R (2003) ARAMEMNON: a novel database for Arabidopsis integral membrane proteins. Plant Physiology 131, 16-26. http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=12529511 [PubMed]

PlantsP/PlantsT

http://plantsp.sdsc.edu/

Description :
As one database with two functionally different web interfaces, PlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data. PlantsP focuses on proteins involved in the phosphorylation process (i.e. kinases and phosphatases), whereas PlantsT focuses on membrane transport proteins. Experimentally, PlantsP provides a resource for information on a collection of T-DNA insertion mutants (knockouts) in each kinase and phosphatase, primarily in Arabidopsis thaliana, and PlantsT uniquely combines experimental data regarding mineral composition (derived from inductively coupled plasma atomic emission spectroscopy) of mutant and wild-type strains. Both databases provide extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. PlantsP is available at http://plantsp.sdsc.edu and PlantsT is available at http://plantst.sdsc.edu.

Recent develoments :
The original PlantsP database has been extended to include PlantsT as a second view based on a common data and software model. A proteotyp system for acquiring and peer-reviewing user annotation has been implemented and is in use with over 200 registered users.

Aknowledgement :
This work is supported by the funding from National Science Foundation Plant Genome Program, DBI-9975808 (PlantsP) and DBI- 0077378 (PlantsT). This work is also assisted by the facilities of the National Biomedical Computation Resource at SDSC (NIH P41-RR08605).

References :
1. Gribskov M, Fana F, Harper J, Hope DA, Harmon AC, Smith DW, Tax FE, Zhang G. (2001) PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Res. Jan 1;29(1):111-3.
2. Van Belle D, Andre B. (2001) A genomic view of yeast membrane transporters. Curr Opin Cell Biol. Aug;13(4):389-98. Review.
3. Ward JM. (2001) Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics. Jun;17(6):560-3.
4. Krysan,P.J., Young,J.K. and Sussman,M.R. (1999). T-DNA as an Insertional Mutagen in Arabidopsis. Plant Cell, 2, 2283?2290.
5. Saier, M.H. (1999) A functional-phylogenetic system for the classification of transport proteins. J Cell Biochem.;Suppl 32-33:84-94. Review.
6. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. Sep 1;25(17):3389-402. Review.
7. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. Dec 15;25(24):4876-82.

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