title: Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria.
abstract: Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed analyses of sequence and structural features resulted in the recognition of potential cyclase function conferring residues and presence of signature topological motif (βααββαβ) in the uncharacterized set of bacterial proteins. Lack of transmembrane domains and signal peptide cleavage sites is suggestive of their cytosolic subcellular localization. Furthermore, analysis on evolutionarily conserved gene clusters of the predicted nucleotide cyclase-like proteins and their evolutionary relationship with nucleotide cyclases suggest their participation in cellular signalling events. Our analyses suggest expansion of class III nucleotide cyclases.
  
  
  
  This article was reviewed by Eugene Koonin and Michael Gromiha.
authors.affiliation: Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India.|Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Gayatri
authors.initials: G
authors.lastname: Ramakrishnan
authors.affiliation: Undergraduate studies, Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Abha
authors.initials: A
authors.lastname: Jain
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Nagasuma
authors.initials: N
authors.lastname: Chandra
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India. ns@mbu.iisc.ernet.in.
authors.forename: Narayanaswamy
authors.initials: N
authors.lastname: Srinivasan
mesh_terms: D039903:Actinobacteria / Q000201:enzymology / Q000235:genetics; D000262:Adenylyl Cyclases / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D041963:Bacteroidetes / Q000201:enzymology / Q000235:genetics; D019295:Computational Biology; D019143:Evolution, Molecular; D008958:Models, Molecular; D009711:Nucleotides / Q000235:genetics; D020560:Proteobacteria / Q000201:enzymology / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D009711:Nucleotides; D000262:Adenylyl Cyclases
keywords: Distant relationship; Domain of unknown function; Mycobacteria; Nucleotide cyclase; Protein evolution; Sequence analysis