Difference between revisions of "Homology Modelling GLA"
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− | ¹The sequences are to different to create a useful model from the alignment. In the automated the template itself has been used as model, what is useless, because the sequences have only 26% identity. |
+ | ¹The sequences are to different to create a useful model from the alignment. In the automated mode the template itself has been used as model, what is useless, because the sequences have only 26% identity. |
<code>Aborting: too many unfruitful attempts to rebuild a loop. |
<code>Aborting: too many unfruitful attempts to rebuild a loop. |
Revision as of 23:35, 11 June 2011
by Benjamin Drexler and Fabian Grandke
Calculation of Models
Available Homologous Structures
The HHpred search from Task1 output the following sequences(Top 10):
PDB-ID | Name | Probability | E-value | P-value | Identity |
---|---|---|---|---|---|
> 60% sequence identity | |||||
3hg3_A | Alpha-galactosidase A | 1.0 | 0 | 0 | 97% |
> 40% sequence identity | |||||
1ktb_A | Alpha-N-acetylgalactosaminidase | 1.0 | 0 | 0 | 53% |
< 40% sequence identity | |||||
1uas_A | Alpha-galactosidase | 1.0 | 0 | 0 | 39% |
3lrk_A | Alpha-galactosidase 1 | 1.0 | 0 | 0 | 32% |
3a5v_A | Alpha-galactosidase | 1.0 | 0 | 0 | 35% |
1szn_A | Alpha-galactosidase | 1.0 | 0 | 0 | 34% |
3a21_A | Putative secreted alpha-galactosidase | 1.0 | 0 | 0 | 34% |
3cc1_A | BH1870 protein | 1.0 | 0 | 0 | 26% |
3a24_A | Alpha-galactosidase | 1.0 | 0 | 0 | 14% |
1zy9_A | Alpha-galactosidase | 1.0 | 2.2E-37 | 8.8E-42 | 14% |
MODELLER
iTasser
SWISS-MODEL
Following sequences have been selected:
3hg3_A | 1ktb_A | 3cc1_A | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Automated Mode | Aligned Mode | Automated Mode | Aligned Mode | Automated Mode | Aligned Mode | |||||||||
Identity | Z-score | Model | Z-score | Model | Identity | Z-score | Model | Z-score | Model | Identity | Z-score | Model | Z-score | Model |
97% | 0 | -0.415 | 53% | 0 | -2.261 | 26% | 0 | Error¹ | NA |
¹The sequences are to different to create a useful model from the alignment. In the automated mode the template itself has been used as model, what is useless, because the sequences have only 26% identity.
Aborting: too many unfruitful attempts to rebuild a loop.
This is likely to indicate a misalignment in this region
Use Swiss-PdbViewer to adjust your alignment in this
region and resubmit an optimise mode modelling request.
Evaluation of Models
MODELLER
Numeric Evaluation
Comparison to Experimental Structure
iTasser
Numeric Evaluation
Comparison to Experimental Structure
SWISS-MODEL
Numeric Evaluation
Comparison to Experimental Structure
References
<references />