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OJBTM
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,
Goonesekere NCW, Beaudry
S, Tasovski I., Towards Establishing the Molecular
Function of Pfam Domain DUF294 by Sequence Analysis
and Homology Modeling, Online J Bioinformatics, 11 (1):125-133, 2009. The curated
protein domains in Pfam has
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