Detecting distant homology with Meta-BASIC.
Meta-BASIC (http://basic.bioinfo.pl) is a novel sensitive approach for recognition of distant similarity between proteins based on consensus alignments of meta profiles. Specifically, Meta-BASIC compares sequence profiles combined with predicted secondary structure by utilizing several scoring systems and alignment algorithms. In our benchmarking tests, Meta-BASIC outperforms many individual servers, including fold recognition servers, and it can compete with meta predictors that base their strength on the structural comparison of models. In addition, Meta-BASIC, which enables detection of very distant relationships even if the tertiary structure for the reference protein is not known, has a high-throughput capability. This new method is applied to 860 PfamA protein families with unknown function (DUF) and provides many novel structure-functional assignments available on-line at http://basic.bioinfo.pl/duf.pl. Detailed discussion is provided for two of the most interesting assignments. DUF271 and DUF431 are predicted to be a nucleotide-diphospho-sugar transferase and an alpha/beta-knot SAM-dependent RNA methyltransferase, respectively.
Ginalski
Krzysztof
K
Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA. kginal@bioinfo.pl
von Grotthuss
Marcin
M
Grishin
Nick V
NV
Rychlewski
Leszek
L
D000465:Algorithms; D016695:Glycosyltransferases / Q000737:chemistry / Q000145:classification; D020407:Internet; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000502:physiology; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software; D040681:Structural Homology, Protein; D012359:tRNA Methyltransferases / Q000737:chemistry / Q000145:classification
D011506:Proteins; D012359:tRNA Methyltransferases; D016695:Glycosyltransferases