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 Online Journal of Bioinformatics  

 Volume 11 (1):125-133, 2009

Towards establishing the molecular function of Pfam Domain DUF294 by sequence analysis and homology modeling


Goonesekere NCW1*, Beaudry S1, Tasovski I2


1Department of chemistry and biochemistry, 2Department of Biology, University of Northern Iowa, Cedar Falls, USA




Goonesekere NCW, Beaudry S, Tasovski I., Towards Establishing the Molecular Function of Pfam Domain DUF294 by Sequence Analysis and Homology Modeling, Onl J Bioinform., 11 (1):125-133, 2009. The curated protein domains in Pfam have been used extensively in the annotation of new genomes. However, Pfam has many domains known as Domains of Unknown Function (DUFs), that have so far defied proper characterization. Here, we report the detection of an adenylyl transferase from E. coli as a remote homolog of a sequence from Pfam DUF294, using a recently-developed computer program, CSSM-BLAST.  The result is highly significant, with an E-value of 4.4 x 10-64.  A secondary structure analysis of the two sequences yields a high Sov value, which provides additional support for the implied homology.  A sequence analysis reveals that despite low overall sequence identity (12%), key residues in the active site are conserved between the two sequences.  Homology modeling of the DUF294 sequence reveals the presence of two ligand binding sites, which are important for the adenylate transferase activity in the remote homolog. Taken together, the bioinformatics investigations are consistent with the functional prediction for DUF294 as a putative adenylate transferase domain.


Keywords: sequence homology, Pfam, domains of unknown function, DUF294, homology modeling