MutS protein binds to DNA and specifically recognizes mismatched or small looped out heteroduplex DNA. In order to elucidate its structure-function relationships, the domain structure of Thermus thermophilus MutS protein was studied by performing denaturation experiments and limited proteolysis. The former suggested that T. thermophilus MutS consists of at least three domains with estimated sta...

Degenerate primers-based polymerase chain reaction (PCR) are commonly used for isolation of unidentified gene sequences in related organisms. For designing the degenerate primers, we propose the use of local alignment search method for searching the conserved regions long enough to design an acceptable primer pair. To test this method, a WD40 repeat-containing domain protein from Beauveria bass...

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming as a unified platform to analyze, compare and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provide...

A comparative analysis of protein kinases encoded in the human genome and those of the closest evolutionary relatives such as chimpanzee, gorilla and orangutan is made in the present study. Sequence comparisons of humans with their closest lineages are of considerable interest in order to understand the ambulatory mechanism behind the evolutionary relationship of apes. A total of 499, 478, 468 ...

Motivation: With rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics. Results: The ultrafast protein classification (UProC) toolbox implements a novel algorithm (‘Mosaic Matching’) for large-scale sequence analysis. UProC is by three orders of magnitude faster than ...

Domains present one of the most useful levels at which to understand protein function, and domain family-based analysis has had a profound impact on the study of individual proteins. Protein domain discovery has been progressing steadily over the past 30 years. What are the realistically achievable goals of sequence-based domain analysis, and how far off are they for the sequences encoded in eu...

The Caenorhabditis elegans genome sequencing project has completed over half of this nematode's 100-Mb genome. Proteins predicted in the finished sequence have been compiled and released in the data-base Wormpep. Presented here is a comprehensive analysis of protein domain families in Wormpep 11, which comprises 7299 proteins. The relative abundance of common protein domain families was counted...

The type IV pili (T4P) is a major virulence factor of Pseudomonas aeruginosa (P. aeruginosa) that is associated with primary adhesion, biofilm formation and twitching motility. This study focuses on the introduction of a novel biologically active subunit vaccine derived from the disulfide loop (DSL) of P. aeruginosa pilin. We investigated the expression of the novel PilA in-frame with pET26a ve...

The domains are the structural and functional units of proteins. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop effective methods for predicting the protein domains according to the sequences information alone, so as to facilitate the structure prediction of proteins and speed up their functional annotation. However, although many effor...