Homology based structure predictions BCKDHA
Contents
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: -XP_971663.1 -> D6X542
< 40% sequence identity (ideally go towards 20%) : -2r8o_A -> P27302
Modeller
SWISS-MODEL
To find protein structure homology models SWISS-MODEL can be used. As input it needs a protein sequence or a UniProt AC Code. Optional the template PDB-Id and the chain or a template file can be assigned.
SWISS-MODEL is a fully automated protein structure homology-modeling server. It is accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
[SWISS-MODEL]
SWISS-MODEL server:
| ID | link |
|---|---|
| 1w85_A | [1w85_A] |
| 2r8o_A | [|2r8o_A] |
iTasser
2.Evaluation of models
Numeric evaluation
QMEAN4 global scores
QMEANscore4
| 1w85_A |
|---|
| 0.596 |
QMEAN Z-Score
| 1w85_A |
|---|
| -2.872 |
Score components
| 1w85_A |
|---|
Local scores
| 1w85_A |
|---|
Global scores: QMEAN4:
| 1w85_A | ||
|---|---|---|
| Scoring function term | Raw score | Z-score |
| C_beta interaction energy | -152.10 | 0.11 |
| All-atom pairwise energy | -9145.04 | -0.55 |
| Solvation energy | -14.56 | -2.14 |
| Torsion angle energy | -57.90 | -2.03 |
| QMEAN4 score | 0.596 | -2.87 |
Local Model Quality Estimation
| 1w85_A |
|---|
