Methods for function analysis

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The amino acid sequence (2ph1) given is originated from Archaeoglobus fulgidus. The objective of this project is to analysis the novel protein, NUBP2 which is a homolog to E. coli MinD. Functional analysis on NUBP2 protein was conducted by submitting the PBD of 2ph1 to Profunc webserver. Profunc is a platform that integrates several databases together, for example UniProt and InterPro. Results returned included motif/domain analysis, sequence analysis, search against existing PDB entries, and fold analysis. All these search were based in prokaryotes. The use of UnitProtKB/Swiss-Prot database was to search the crosslink functions of 2ph1 protein and NUBP2 protein. This search enabled us to relate the possible function of the novel protein, NUBP2 from the known function of related sequence. Further confirmation was to be analysed by employing Dali database to study on the protein structure as structure denotes a protein’s functions. Moreover protein-protein interactions were examined individually by employing database String. This approach allowed us to select the conserved function that can be found in eukaryotes and prokaryotes. The subcellular location of the protein is critical for the deduction of protein function. We used GNF SymAtlas database to predict features relevant to the expression of NUBP2 protein in mouse and human. Several academic journals were used to support our hypothesed functions of NUBP2 protein. This is because analysis was done solely on 2ph1 protein. However, the potential functions of NUBP2 were counterchecked by generating amino acid sequence alignment and structural analysis between 2ph1 and NUBP2.