Task 4: Homology-based structure prediction
More detailed information about the generation of the results can be found in the Task 4 Protocol.
Datasets
In order to generate a model for our protein we first need to find homologous structures on which we base our model on. For this task we use HHpred and COMA.
HHpred
Unfortunately the HHpred search did not produce any hits with a sequence identity between 40% and 80%. For testing purposes we assume 1qs0_A to fit in that category. The 2BFD hit with 99% sequence identity is a 3d structure of the actual human branched-chain alpha-ketoacid dehydrogenase that is only slightly modified. Therefore the hit is not really a homologous protein but the protein itself and is not viable to defer a model from, as we assume for this exercise that there is no actual 3d structure of our protein. The 1qs0_A protein is actually the BCAKD complex in Pseudomonas Putida. While the relationship between human and bacteria is quite distant, this structure is the only one available in the 40%-80% sequence identity range and might still produce a viable model. For sequences with sequence identitiy below 30% percent I currently have no idea thich one to choose as a model.
PDB ID | e-Value | Identity |
---|---|---|
>80% Sequence Identity | ||
2BFD | 1.2e-84 | 99% |
80-40% Sequence Identity | ||
1qs0_A | 1.1e-79 | 39% |
<30% Sequence Identity | ||
2ozl_A | 3.6e-71 | 27% |
2yic_A | 1.2e-55 | 14% |
2xt6_A | 2.9e-55 | 14% |
2jgd_A | 4e-55 | 14% |
2o1s_A | 2.1e-27 | 20% |
3kom_A | 2.4e-26 | 18% |
3m49_A | 2.4e-26 | 18% |
1gpu_A | 2.3e-26 | 18% |
2e6k_A | 1.1e-26 | 20% |
3l84_A | 6.4e-26 | 17% |
2r8o_A | 1.9e-25 | 20% |
3uk1_A | 2.6e-25 | 19% |
3rim_A | 1.2e-24 | 18% |
1r9j_A | 5.7e-24 | 17% |
2o1x_A | 1e-25 | 15% |
1itz_A | 7.4e-23 | 20% |
3mos_A | 2.3e-22 | 19% |
2qtc_A | 1.5e-21 | 16% |
3ahc_A | 7.2e-16 | 16% |
COMA
COMA didn't find any hits with sequence similarity between 40% and 80% either, this time however there weren't any hits in close proximity either. The hit above 80% is again the protein itself and can therefore not be used for structure modeling.
PDB ID | e-Value | Identity |
---|---|---|
>80% Sequence Identity | ||
1dtw_A | 8e-59 | 100% |
80-40% Sequence Identity | ||
- | - | - |
<30% Sequence Identity | ||
2xt6_A | 8.1e-56 | 12% |
3duf_A | 2.1e-53 | 28% |
3exe_A | 3.6e-50 | 25% |
3mos_A | 1e-45 | 15% |
1l8a_A | 7.5e-40 | 9% |
3m34_A | 1.2e-38 | 14% |
2o1x_A | 2.6e-37 | 12% |
3uk1_A | 2.4e-33 | 15% |
3ahc_A | 1.1e-25 | 8% |