Task 4: Homology-based structure prediction
From Bioinformatikpedia
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
PDB ID | e-Value | Identity | Similarity |
---|---|---|---|
>80% Sequence Identity | |||
2BFD | 1.2e-84 | 99% | 1.508 |
80-40% Sequence Identity | |||
1qs0_A | 1.1e-79 | 39% | 0.580 |
<30% Sequence Identity | |||
2ozl_A | 3.6e-71 | 27% | 0.403 |
2yic_A | 1.2e-55 | 14% | 0.116 |
2xt6_A | 2.9e-55 | 14% | 0.121 |
2jgd_A | 4e-55 | 14% | 0.099 |
2o1s_A | 2.1e-27 | 20% | 0.200 |
3kom_A | 2.4e-26 | 18% | 0.148 |
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.
COMA
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% |
1y9d_A | 1e-12 | 10% |
3ey9_A | 1.8e-12 | 11% |
2c31_A | 1.7e-11 | 16% |
1zpd_A | 2.1e-11 | 12% |
3d7k_A | 2.7e-11 | 9% |
1upa_A | 3.7e-11 | 10% |
1ozf_A | 1.3e-10 | 9% |
1qpb_A | 2e-10 | 10% |
2pgn_A | 3e-10 | 11% |
2jlc_A | 3e-10 | 10% |
>2vbf_A mol:protein length:570 BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE
Query length = 445 Subject length = 570 Score = 267.30 (61.7 bits) Expect = 5.1e-10 P-value = 5.1e-10 Identities = 33/376 (8%) Positives = 146/376 (38%) Gaps = 112/376 (29%) |
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