3bsqA Methods & Materials

Multiple sequence alugnment was made using clustalX from the DVD. The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the PyMol (Downloaded version in 'colaborative learning center' (CLC)). The structural alignment was done using the DALI server using PDB identifiers. Protein interaction of ASK were searched with the programme STRING which is available online. The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used. Functions of selected proteins were searched using ProFunc, which is freely available online. 'Two sequence alignment' of ASK and STS was done with the programme SIM. The methode used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'. The pylogenic tree was made using the 'clusalX' alignment and viewed with Treeview from the DVD.