Difference between revisions of "Glucocerebrosidase homology modelling"
From Bioinformatikpedia
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| 2nt0 || Glucosylceramidase || Homo Sapiens || 99% || |
| 2nt0 || Glucosylceramidase || Homo Sapiens || 99% || |
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|colspan="5" |''' > 40% sequence identity ''' |
|colspan="5" |''' > 40% sequence identity ''' |
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| '''PDB-ID''' || '''name''' || '''identity''' || '''organism '''|| '''template ''' |
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|colspan="5" |''' > 0% sequence identity''' |
|colspan="5" |''' > 0% sequence identity''' |
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| 2c7f ||alpha-L-Arabinofuranosidase || Clostridium thermocellum || 16% || |
| 2c7f ||alpha-L-Arabinofuranosidase || Clostridium thermocellum || 16% || |
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Revision as of 18:17, 7 June 2011
Contents
Homologous Structures
The 10 best results of the sequence search with HHSearch (as retrieved in Task 1) are listed in the table below.
| > 60% sequence identity | ||||
| PDB-ID | name | identity | organism | template |
| 2nt0 | Glucosylceramidase | Homo Sapiens | 99% | |
| > 40% sequence identity | ||||
| PDB-ID | name | identity | organism | template |
| > 0% sequence identity | ||||
| PDB-ID | name | identity | organism | template |
| 2wnw | SrfJ | Salmonella enterica subsp. enterica | 29% | x |
| 3clw | conserved exported protein | Bacteroides fragilis | 13% | |
| 3kl0 | Glucuronoxylan Xylanohydrolase | Bacillus subtilis | 18% | x |
| 1nof | xylanase | Erwinia chrysanthemi | 18% | |
| 2e4t | Endoglucanase | Clostridium thermocellum | 11% | x |
| 3ii1 | Cellulase | Uncultured bacterium | 15% | |
| 1qw9 | Arabinosidase | Geobacillus stearothermophilus | 13% | |
| 1ik2 | Endoglucanase | Clostridium acetobutylicum | 12 % | |
| 2c7f | alpha-L-Arabinofuranosidase | Clostridium thermocellum | 16% | |
Calculation of Models
MODELLER
iTasser
SWISS-MODEL
SWISS-MODEL workspace was published by Arnold et al. in 2005. <ref> Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.</ref>
Usage - Automated Mode
- Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1
- Input: Sequence in fasta format
Usage - Alignment Mode
- Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_align1
- Input: Target-Template Alignment in different formats (FASTA, CLUSTALW, ...)
References
<references />
