Difference between revisions of "Fabry:Homology based structure predictions"
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We performed a [http://toolkit.tuebingen.mpg.de/hhpred HHpred] as well as a [http://bioinformatics.ibt.lt:8085/coma/ COMA] search, to generate three distinct datasets. Since COMA did not find any homologue structures with a similarity above 41% (see <xr id="tab:datasetCOMA"/>), we used the dataset created with the HHpred search and the script described in the [[Fabry:Homology_based_structure_predictions/Journal|journal]]. Hereby we found one structure with a similarity above 80%, one with a similarity between 40 and 80% and 15 with sequence similarity below 30%, of which 14 had a similarity of under 20% (see <xr id="tab:datasetHHpred" />). All HHpred matches had an E-value below 1e-15, for the COMA homologues we tried a less strict threshold of 0.002.<br> |
We performed a [http://toolkit.tuebingen.mpg.de/hhpred HHpred] as well as a [http://bioinformatics.ibt.lt:8085/coma/ COMA] search, to generate three distinct datasets. Since COMA did not find any homologue structures with a similarity above 41% (see <xr id="tab:datasetCOMA"/>), we used the dataset created with the HHpred search and the script described in the [[Fabry:Homology_based_structure_predictions/Journal|journal]]. Hereby we found one structure with a similarity above 80%, one with a similarity between 40 and 80% and 15 with sequence similarity below 30%, of which 14 had a similarity of under 20% (see <xr id="tab:datasetHHpred" />). All HHpred matches had an E-value below 1e-15, for the COMA homologues we tried a less strict threshold of 0.002.<br> |
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In this case it is important to mention, that although the identity of 3hg3 is 100%, this structure is not derived from the α-Galactosidase A sequence, but the AGAL sequence is contained in the 3hg3 sequence 100%. |
In this case it is important to mention, that although the identity of 3hg3 is 100%, this structure is not derived from the α-Galactosidase A sequence, but the AGAL sequence is contained in the 3hg3 sequence 100%. |
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== Calculation of models == |
== Calculation of models == |
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Revision as of 20:20, 22 May 2012
Fabry Disease » Homology based structure predictions
The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.
Contents
Dataset preparation
<figtable id="tab:datasetHHpred"> Dataset HHpred
| pdb ID | E-value | Identity in % |
|---|---|---|
| > 80% sequence identity | ||
| 3hg3 | 8.6e-90 | 100 |
| 40% - 80% sequence identity | ||
| 1ktb | 4.2e-85 | 53 |
| < 30% sequence identity | ||
| 3cc1 | 5.5e-74 | 25 |
| 1zy9 | 3.1e-48 | 13 |
| 3a24 | 7.8e-40 | 17 |
| 2xn2 | 5.3e-37 | 15 |
| 2d73 | 5.7e-36 | 14 |
| 3mi6 | 1.4e-31 | 15 |
| 2yfo | 9.1e-30 | 13 |
| 2f2h | 2.7e-20 | 17 |
| 2g3m | 2.2e-20 | 16 |
| 3nsx | 6e-20 | 13 |
| 3lpp | 2.2e-18 | 15 |
| 3l4y | 1.9e-18 | 15 |
| 3top | 3.6e-18 | 12 |
| 2xvl | 3.2e-18 | 16 |
| 2x2h | 4.9e-16 | 13 |
</figtable>
<figtable id="tab:datasetCOMA"> Dataset COMA
| pdb ID | E-value | Identity in % |
|---|---|---|
| > 80% sequence identity | ||
| - | - | - |
| 40% - 80% sequence identity | ||
| 1ktb | 1.7e-61 | 52 |
| < 30% sequence identity | ||
| 3lrk | 1.2e-66 | 23 |
| 3a21 | 2.7e-65 | 26 |
| 1szn | 3.7e-59 | 22 |
| 3cc1 | 5.2e-58 | 19 |
| 1zy9 | 1.7e-39 | 9 |
| 3mi6 | 4.3e-38 | 11 |
| 2yfn | 4.4e-35 | 10 |
| 2d73 | 1.9e-32 | 9 |
| 3a24 | 5.6e-30 | 10 |
| 1xsi | 1.9e-12 | 10 |
| 2g3m | 2.4e-11 | 10 |
| 3pha | 2.9e-10 | 6 |
| 3lpo | 4.7e-09 | 8 |
| 2x2h | 8.2e-09 | 8 |
| 3mo4 | 1.2e-08 | 7 |
| 2xvg | 2.4e-08 | 8 |
| 3ton | 4.3e-08 | 8 |
| 2xib | 1e-07 | 7 |
| 3eyp | 1.6e-06 | 8 |
| 3k1d | 3.5e-06 | 9 |
| 2zwy | 8.8e-06 | 9 |
| 3gza | 1.8e-05 | 8 |
| 3m07 | 2.3e-05 | 7 |
| 1eh9 | 0.00013 | 6 |
| 1gvi | 0.00035 | 8 |
| 1aqh | 0.00039 | 5 |
| 1mwo | 0.00058 | 7 |
| 3vmn | 0.0018 | 9 |
| 1bf2 | 0.0019 | 6 |
| 3aml | 0.0019 | 8 |
</figtable>
We performed a HHpred as well as a COMA search, to generate three distinct datasets. Since COMA did not find any homologue structures with a similarity above 41% (see <xr id="tab:datasetCOMA"/>), we used the dataset created with the HHpred search and the script described in the journal. Hereby we found one structure with a similarity above 80%, one with a similarity between 40 and 80% and 15 with sequence similarity below 30%, of which 14 had a similarity of under 20% (see <xr id="tab:datasetHHpred" />). All HHpred matches had an E-value below 1e-15, for the COMA homologues we tried a less strict threshold of 0.002.
In this case it is important to mention, that although the identity of 3hg3 is 100%, this structure is not derived from the α-Galactosidase A sequence, but the AGAL sequence is contained in the 3hg3 sequence 100%.
