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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.
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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