C.L.asiaticus



Brief Description of the Webpage

In this website, each protein is represented by one webpage, and sorted by the position in the genome sequence. For each protein, information and analysis from the following perspectives are provided. Each webpage consists of the following parts:

Part I. Function prediction and Basic Information:

Each webpage is entitled by the gi (NCBI's protein identification) and the predicted function of the protein. In addition, as references, we provided its basic background and links to other useful resources.

Part II. Prediction of Local Features:

Several essential sequence features, including secondary structure, disordered region, signal peptide and transmembrane helices are predicted based on the consensus between multiple programs and the result is represented in one line. These features will help us to understand more about the structure, subcellular localization and function of the protein. Especially proteins with signal peptides, as they are likely to be secretted to the outside of the bacteria and are likely to be our target to control the bacteria. In addition, we provided the conservation map of the protein based on the multiple sequence alignment of the evolutionary related proteins, and the conserved residues in this map would highlight the important residues for the protein the maintain its structure and function.

Components:

2.1   Sequence (highlighted according to the property of amino acid) from NCBI database
2.2   Secondary structure prediction
2.3   Disordered region (highlighted in red) prediction
2.4   Transmembrane helix (highlighted in blue) prediction
2.5   Signal Peptide (highlighted in green) prediction
2.6   Conserved pattern (highlighted from white, through yellow to dark red as the level of conservation increases)

Part III. Domain achietecture:

Domains are the unit of protein evolution, structure and function. As the accumulation of known protein sequences and structures, such units have been analyzed and made into databases. The presence of certain structure domain usually implies certain structure, function and evolutionary history. Indentifying of such structure units in the protein will not only reveal the architecture of target protein, but provide hints about how the protein fold and function. In the webpage, the domain(s) are shown as colored boxes. The relative information will appear as the mouse cursor is hovered on top of the domain and more information about the doamin and the its family in the Structure Classificatio of Protein (SCOP) database will be available by clicking it.

Part IV. Structure models:

So far, homolog modeling is still the most reliable and effective way of structure prediction. In this part we presented homology based structure models for the protein. These models show the 3D view of each protein and can be downloaded for in-depth study of the domain.

Part V. Area for you to post your comments:

We appreciate your suggestions and comments, and please provide your email address for further contact :)