NAR Molecular Biology Database Collection entry number 219

http://supfam.mbu.iisc.ernet.in/

Mudgal, R., Krishnadev, O., Mukherjee, S., and Srinivasan, N.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India

Contact ns@mbu.iisc.ernet.in

.Members of a superfamily of proteins could result from divergent evolution of homologues with very low similarity in the amino acid sequences. A superfamily relationship is often detected after the three-dimensional (3-D) structures of the proteins concerned are determined. The present SUPFAM update (Release 4) has been derived using Pfam [5] (version 25.0), and SCOP [6] database (version 1.75). In the first phase of SUPFAM generation, each of the Pfam family profiles in the form of an rHMM is searched against the SCOP family profiles to identify possible evolutionary relationships. In the next phase of mapping, the remaining Pfam families are searched against the Pfam rHMM database, to find Pfam families indirectly related to a SCOP family. In the present database, the first phase enabled association of 3,539 Pfam families (out of 12,273 ~ 29%) with a SCOP family. We could then associate 518 Pfam families with no structure annotation, indirectly to a SCOP family. SUPFAM database also consists of clusters wherein Pfam families which could not be mapped to any structural superfamilies, but are found to be related to one another are clustered together and called as "Potentially New Superfamilies (PNSFs)". These PNSF (284 in number) could provide an important resource for structural genomics initiative targets.

The Pfam and PALI releases used in the current update of SUPFAM correspond to much larger databases compared to the last update. The present updated revision of SUPFAM also resulted in grouping of 306 Pfam families into 122 new potential superfamilies. A new profile-profile based comparison method has been used for the generation of the database which has resulted in more Pfam families being related SCOP families than in the earlier release. DUF/UPF connections to other Pfam/SCOP families have been highlighted on the website.

O.K. is supported by fellowship from CSIR, New Delhi. This work is supported by the Department of Biotechnology, New Delhi

1.Krupa, A., Abhinandan, K.R., Srinivasan N. (2004) KinG: a database of protein kinases in genomes. Nucleic Acids Res. 32: D153-D155 2. Gowri VS,Tina KG,Krishnadev O,Srinivasan N. Strategies for the effective identification of remotely related sequences in multiple PSSM search approach. Proteins 2007; 67: 789–794. 3.Tyagi N, Anamika K, Srinivasan N, 2010 A Framework for Classification of Prokaryotic Protein Kinases. PLoS ONE 5(5): e10608. doi:10.1371/journal.pone.0010608 4.Hanks SK, Hunter T: Protein kinases 3. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. Faseb J 1995, 9(8):576-596.

Go to the abstract in the NAR 2003 Database Issue.

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