Homology based structure predictions BCKDHA

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Revision as of 10:14, 5 June 2011 by Reisinger (talk | contribs) (1.Calculation of models)

1.Calculation of models

To find similar structures to BCKDHA we ran HHsearch:
hhsearch -i query -d database -o output

It found the following 10 hits in the pdb70 database.

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM Identity
1 2bfd_A 2-oxoisovalerate dehydr 1.0 1 1 791.3 0.0 400 1-400 1-400 (400) 99%
2 1qs0_A 2-oxoisovalerate dehydr 1.0 1 1 571.5 0.0 349 32-382 52-407 (407) 39%
3 1w85_A Pyruvate dehydrogenase 1.0 1 1 530.8 0.0 356 8-382 6-362 (368) 34%
4 1umd_A E1-alpha, 2-OXO acid de 1.0 1 1 521.8 0.0 351 34-386 16-367 (367) 37%
5 2ozl_A PDHE1-A type I, pyruvat 1.0 1 1 482.7 0.0 331 46-380 25-356 (365) 27%
6 3l84_A Transketolase; TKT, str 1.0 1 1 85.4 0.0 133 161-297 113-252 (632) 21%
7 2r8o_A Transketolase 1, TK 1; 1.0 1 1 74.5 0.0 121 161-285 113-245 (669) 33%
8 2o1x_A 1-deoxy-D-xylulose-5-ph 1.0 1 1 74.2 0.0 127 161-287 122-254 (629) 18%
9 1gpu_A Transketolase; transfer 1.0 1 1 74.2 0.0 140 161-302 115-265 (680) 22%
10 3m49_A Transketolase; alpha-be 1.0 1 1 68.8 0.0 121 161-285 139-271 (690) 31%
> 60% sequence identity:
  -1w85_A
> 40% sequence identity:

< 40% sequence identity (ideally go towards 20%) : -1qs0_A, 1umd_A, 1w85_A, 2r8o_A, 3m49_A, 2ozl_A, 1gpu_A, 3l84_A, 2o1x_A


HHSearch has only hits with an identity higher than 60% or lower than 40%. This is why we had to take one hit of our BLAST run.

>gi|91094507|ref|XP_971663.1|  Score=507 bits (1306), E-value=e-142, Identities=228/397 (57%), Positives=296/397 (74%), Gaps=2/397 (0%)


These are the templates we will work with:

> 60% sequence identity:
  -1w85_A  -> P21873
> 40% sequence identity:
< 40% sequence identity (ideally go towards 20%) : -2r8o_A -> P27302

2.Evaluate your models