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

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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