Material and Method of SNAPG

Identifying Protein Structure

Structural comparison of 2ifu PDB entry was done against Dali and CE database. The results of closely related protein structure was used to analysed the unknown function of 2ifu query. The analysis of query protein secondary structure, structural classification, protein domains and binding site prediction were acquired from ProFunc. MacPymol, STRAP and Protein Workshop were used for physical properties and surface visualization. The electrostatic potential was calculated and mapped by SwissProt PDB viewer.

Identifying Protein Function

The Fasta format file of N-ethylmaleide-sensitive factor attachment protein, gamma (SNAPG) was first obtained from BLAST. Several internet databases and software were used to obtain all important data and information of SNAPG including ProFunc, ProKnow, GO, STRING, LOCATE, PDB, Scorecons and Pymol. The PDB file code of SNAPG is 2ifuA which was derived from Danio rerio. All of the data and useful information were accumulated and compared each other to give the function prediction of SNAPG. Comparisons of structure similarity and conserved residue domain sequence alignments were obtained by submitting the Fasta format into ProFunc and ProKnow; which are the primary approaches for SNAPG analysis. Protein-protein interaction data from STRING, genomic context and cellular context were collected to give additional approaches on predicting function. Further information and deeper understanding of SNAPG function were put into this report from pubmed literatures. The final datas and results were then recorded and presented into mediawiki.

Identifying Evolutionary Protein

In detecting evolunationary tree, BLAST was used to searching homologous sequence and to obtain the IDs of the homologous gene. The Protein IDs with suitable E value was chosen as Batch Entrez input. Approximately 20 IDs was used as Batch Entrez input. Batch Entrez is important resources to obtain full sequence of the correlated protein - SNAP gamma protein. The data obtained from Batch entrez was saved in fasta format. In addition, Clustal X was used to align the sequence specifically by using multiple alignment method. The input of Clustal X program is the fasta format data obtained from Bathc Entrez. Phylogenetic analysis was conducted using treeview program follows with editing the tree to adding the boostrap value.

Back to Scientific Report of N-ethylmaleide-sensitive factor attachment protein, gamma