Based on sequence analytic considerations, we generated the two constructs yGPAA170 247 and yGPAA170 339 of the luminal domain of S. cerevisiae GPAA1.
Splitting domains based on sequence, structure and evolutionary considerations may not be necessary for evaluation of all targets.
Based on sequence comparisons, homology searches and considerations concerning the protein domain structure, there might be an explanation why the Val109Asp SNP does not associate with the clinical parameters investigated in our cohort of patients and why allelic frequencies are very similar between subgroups.
The values between brackets indicate a more precise estimate as taking into consideration the functional assignments based on sequence similarities to biochemically characterized enzymes.
Both SIFT and PolyPhen-2 are based on sequence information and do not take account of structure-function data pertaining specifically to the protein under consideration.
Another consideration is that enzymes of the GH9 family are often assumed to be endo- 1,4 -β-glucanases, but thendo- 1,4 -β-glucanasesally basendo- 1,4 -β-glucanases rathendo- 1,4 -β-glucanasesstrate specificity studies.
In particular, we will show that there is a growing evidence suggesting that the compact structures of folded proteins are selected in their gross topological features based on geometry and symmetry rather than on sequence consideration.
Putative L. major and Trypanosoma brucei ARF/ARL family members have been classified based on structural considerations, amino acid sequence conservation combined with functional data on Kinetoplastid and human orthologues.
Based on these considerations, we analyzed the sequence of the msp gene in 17 clinical samples from acute periodontitis patients who were positive for T. denticola by real-time PCR [ 8].
We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case.
