Functional Annotation of Conserved Hypothetical Proteins from Haemophilus influenzae Rd KW20

Abstract

Haemophilus influenzae is a Gram negative bacterium that belongs to the family Pasteurellaceae, causes bacteremia, pneumonia and acute bacterial meningitis in infants. The emergence of multi-drug resistance H. influenzae strain in clinical isolates demands the development of better/new drugs against this pathogen. Our study combines a number of bioinformatics tools for function predictions of previously not assigned proteins in the genome of H. influenzae. This genome was extensively analyzed and found 1,657 functional proteins in which function of 429 proteins are unknown, termed as hypothetical proteins (HPs). Amino acid sequences of all 429 HPs were extensively annotated and we successfully assigned the function to 296 HPs with high confidence. We also characterized the function of 124 HPs precisely, but with less confidence. We believed that sequence of a protein can be used as a framework to explain known functional properties. Here we have combined the latest versions of protein family databases, protein motifs, intrinsic features from the amino acid sequence, pathway and genome context methods to assign a precise function to hypothetical proteins for which no experimental information is available. We found these HPs belong to various classes of proteins such as enzymes, transporters, carriers, receptors, signal transducers, binding proteins, virulence and other proteins. The outcome of this work will be helpful for a better understanding of the mechanism of pathogenesis and in finding novel therapeutic targets for H. influenzae.

Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

“…Although, many studies have analysed hypothetical proteins in different microorganisms such as Candida dubliniensis [10], Haemophilus influenza [16], Clostridium tetani [17], and Treponema pallidum ssp. Pallidum [15], there is no similar study on M. tuberculosis.…”

“…The already sequenced genome of the M. tuberculosis was taken in our study to explore the function of these HPs with high precision using well optimized bioinformatics tools described elsewhere [16]. To predict function of HPs with high confidence, their sequences are retrieved from the NCBI and analyzed by using various bioinformatics tools for the prediction of physicochemical properties, sub-cellular localization, sequence similarity search, virulence factor prediction, etc.…”

In silicofunctional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway

“…2 The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play central roles in signal transduction; however, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs. antagonism).…”

In silico characterization of hypothetical proteins from Paracoccidioides lutzii

“…HPs are proteins predicted from nucleic acid sequences, based on computational identification of gene structure, but for which no evidence of in vivo expression exists. These proteins may represent up to half of the proteome for several organisms (Loewenstein et al, 2009;Shahbaaz et al, 2013;Ijaq et al, 2015).…”