Difference between revisions of "Homology-modelling HEXA"
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(→Homology structure groups) |
(→Homology structure groups) |
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|Oligo-1,6-glucosidase |
|Oligo-1,6-glucosidase |
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|90% |
|90% |
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| − | | |
+ | | |
|- |
|- |
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|1h4p_A |
|1h4p_A |
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|AMYB, alpha amylase, ca |
|AMYB, alpha amylase, ca |
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|80.8% |
|80.8% |
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| − | | |
+ | |X |
|- |
|- |
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|2zum_A |
|2zum_A |
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|Xylanase, endo-1,4-beta |
|Xylanase, endo-1,4-beta |
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|61% |
|61% |
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| − | | |
+ | | |
|- |
|- |
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|colspan="4" | > 40% |
|colspan="4" | > 40% |
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|Xylanase B, thermostabl |
|Xylanase B, thermostabl |
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|54.9% |
|54.9% |
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| − | | |
+ | | |
|- |
|- |
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|3cui_A |
|3cui_A |
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|EXO-beta-1,4-glucanase; |
|EXO-beta-1,4-glucanase; |
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|49.5% |
|49.5% |
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| − | | |
+ | |X |
|- |
|- |
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|1vhc_A |
|1vhc_A |
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|D-psicose 3-epimerase |
|D-psicose 3-epimerase |
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|40.8% |
|40.8% |
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| − | | |
+ | | |
|- |
|- |
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|colspan="4" | < 40% |
|colspan="4" | < 40% |
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|LMO2234 protein; putati |
|LMO2234 protein; putati |
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|35.5% |
|35.5% |
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| − | | |
+ | | |
|- |
|- |
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|3q94_A |
|3q94_A |
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Revision as of 10:12, 9 June 2011
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% | |
| 3aj7_A | Oligo-1,6-glucosidase | 90% | |
| 1h4p_A | Glucan 1,3-beta-glucosidase | 85.2% | |
| 3bc9_A | AMYB, alpha amylase, ca | 80.8% | X |
| 2zum_A | 458AA long hypothetical | 75% | |
| 3bmv_A | Cyclomaltodextrin gluca | 70.3% | |
| 2f2h_A | Putative family 31 gluc | 64.8% | |
| 3emz_A | Xylanase, endo-1,4-beta | 61% | |
| > 40% | |||
| 2dep_A | Xylanase B, thermostabl | 54.9% | |
| 3cui_A | EXO-beta-1,4-glucanase; | 49.5% | X |
| 1vhc_A | Putative KHG/KDPG aldol | 45.1% | |
| 2hk0_A | D-psicose 3-epimerase | 40.8% | |
| < 40% | |||
| 2g0w_A | LMO2234 protein; putati | 35.5% | |
| 3q94_A | Fructose-bisphosphate a | 30.0% | |
| 3hn3_A | Beta-G1, beta-glucuroni | 25.1% | |
| 3lut_A | Voltage-gated potassium | 20.1% | X |
Methods
Swissmodel
Modeller
First of all we need a pairwise alignment. Therefore, we used the Needleman-Wunsch Algorithm implemented by EMBOSS http://www.ebi.ac.uk/Tools/psa/emboss_needle/. We used the standard parameter.
3AJ7_A:
