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OJBTM
Online Journal of Bioinformatics ©
Volume 15 (3): 253-266, 2014.
Re-annotation of
hypothetical proteins of Geobacter sulfurreducens
PCA by integrated computation
Ashok Selvaraj
(M.Sc), Rajadurai Chinnasamy Perumal (Ph.D), Nupoor Chowdhary (M.Sc), Palani Kannan Kandavel (M.S),
Vijayaraghavan Radhakrishnan (Ph.D) and Ramesh Kumar Gopal (Ph.D)*
Bioinformatics Lab, AU-KBC Research Centre, M.I.T
Campus of Anna University, Chromepet, Chennai 600044,
India.
ABSTRACT
Selvaraj
A, Chinnasamy Perumal R, Chowdhary N, Kannan Kandavel P, Radhakrishnan V, Kumar Gopal R., Re-annotation of
hypothetical proteins of Geobacter sulfurreducens PCA by
integrated computation, Onl J Bioinform., 15 (3): 253-266, 2014. Functional re-annotation of the G. sulfurreducens
genome is necessary since only 78% of the G. sulfurreducens
protein coding genes have
well characterized functions. Therefore, we followed a robust and integrated bioinformatics
approach which uses different Primary, Secondary and Tertiary analysis
bioinformatics tools for functional re-annotation of hypothetical proteins of G.sulfurreducens PCA. Using four different primary analysis tools in addition to BLAST, we predicted new protein functions for
365 hypothetical proteins. Functions of
92 of the 365 proteins were re-annotated with high confidence since they were
identified by 3-5 tools for primary analysis. Using Swiss-Prot,
we could divide the 92 predicted proteins into 14 functional classes. We also analyzed 8 of 92 hypothetical
proteins associated with electricity production, organism growth and biofilm
formation, and obtained good BLAST scores or Pfam
scores for most of these proteins. Secondary analysis confirmed that 5 of these
8 proteins encode 3 AAA ATPase, a Cation efflux
protein and an ATP-dependent Lon protease. Tertiary analysis for these 5 proteins
provided strong structural evidence. A Tertiary model for a newly predicted ATP-dependent Lon protease (NP_953154.1) represents the first report for this hypothetical protein in G. sulfurreducens PCA.
Keywords:
Geobacter sulfurreducens, Hypothetical proteins, Protein annotation, Sequence similarity, Protein
motif, Protein Fold recognition.
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