Methods for Function Analysis

Structural-based methods was used to look for matching folds by sequence comparison (SSM) and the programme used to identify our protein, ATP binding domain 4, was ProFunc. The query protein was then analysed for nest and surface clefts. Subsequently, Sanger from Pfam and SCOP were studied to seek potential family members for structural and hence functional modelling, which was found to be another family member from N-type ATP pyrophosphatases, argininosuccinate synthetase (AS). This result confirms with those from Dali search, and therefore pdb file was aligned to look for conserved motifs our protein and AS using PyMOL. String 8.0 database was used to hunt for functional partners such as gene neighbourhood and co-occurrence patterns for functional prediction. All results were then compared against useful literatures from PubMed and collaborate with findings from structural and evolutionary analysis to draw functional hypothesis conclusions.