Homology based structure predictions
Contents
Homologous
Because we found no homologous structures in Task 2, we extended our list by using HHSearch.
We will use 13 proteins for creating a multiple alignment for homologous modeling. We choosen sequences to cover the whole protein and we payed specific attention on the transmembrane region.
| PDB-ID | Identity | Description |
| 1s79 | 37% | Kram |
| 2yc6 | 32% | Kram |
| 3p73 | 28% | Kram |
| 1kcg | 22% | Kram |
| 1jfm | 14% | Kram |
| 1bii | 22% | Kram |
| 2p24 | 21% | Kram |
| 1cd1 | 21% | Kram |
| 2wy3 | 29% | Kram |
| 1lqv | 14% | Kram |
| 3jts | 25% | Kram |
| 1ow0 | 22% | Kram |
| 1hxm | 18% | Kram |
| 3lmy | 19% | Kram |
ITasser
SwissModel
SwissProt is a server based tool provided by the SIB. It combines tools like PSI-PRED and DISOPRED for secondary structure and disordered region prediction.
The model created by SwissModel is based on a self hit, but we had no chance to exclude the protein itself from the prediction. Therefore we also run SwissModel in Alignment-Mode.(TODO)
Automated Mode
Model information:
Modelled residue range: 26 to 297
Based on template: 1a6zC (2.60 Å)
Sequence Identity [%]: 100
Evalue: 7.66e-163
Quality information:
QMEAN Z-Score: -1.035
Even though the model is based on a self hit, the Z-Score is about -1, which means that the model is one standard deviation from the mean. The model is not quite unlikely but also not the most probable one.
