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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, 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
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