Homology structure groups
We decided to choose every 5% one protein:
|> 60% sequence identity|
|PDB id||name||similarity||single template|
|1ht6_A||AMY1, alpha-amylase iso||95%|
|3bc9_A||AMYB, alpha amylase, ca||80.8%||X|
|2zum_A||458AA long hypothetical||75%|
|2f2h_A||Putative family 31 gluc||64.8%|
|2dep_A||Xylanase B, thermostabl||54.9%|
|1vhc_A||Putative KHG/KDPG aldol||45.1%|
|2g0w_A||LMO2234 protein; putati||35.5%|
Calculation of the models
To calculate the models with Swiss-Model we used the [Webserver]. For the template with high sequence identity, we used the automated and the alignment method, for the other two templates we only used the alignment method.
The used alignments can be found [here].
We used Modeller from the command line. Therefore we followed the instructions, described [here].
First of all, we created an alignment for each of our three selected sequences. In the next step we used Modeller to model the 3D structure of the protein.
For Modeller we used the Pir Alignment format, which can be found here: [3BC9], [3CUI], [3LUT]
To calculate our models with iTasser we used the [Webserver]. We defined the target and template sequence, but this time without an alignment. We used the same template sequences as before.
The detailed prediction can be found [here]
Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.
The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.
|Scoring function term||Raw score||Z score|
|C_beta interaction energy||202.24||-4.65|
|All-atom pairwise energy||9942.28||-6.16|
|Torsion angle energy||76.36||-7.72|
Swiss-Modeler also returns some pictures, which show the qualitity of the model.