Difference between revisions of "Homology Modeling of ARS A"
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| + | needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1P49.fasta.txt <br> |
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needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1FSU.fasta.txt <br> |
needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1FSU.fasta.txt <br> |
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| − | needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt |
+ | needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 2VQR.fasta.txt <br> |
| − | needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt |
+ | needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 3ED4.fasta.txt <br> |
| − | needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1FSU.fasta.txt <br> |
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Revision as of 12:54, 7 June 2011
HHpred
We used the webserver and
Modeller
Proteins used as templates
We identified the following proteins (see Alignment TASK) as potential targets for homology modeling:used the following
| SeqIdentifier | Seq Identity (from TASK 2) | source | Protein function | True homolog (HSSP) | Seq Identity (pairw. ali.) |
|---|---|---|---|---|---|
| 1P49 | 39.0% | Homo Sapiens | Steryl-Sulfatase | yes | ? |
| 1FSU | 28.0% | Homo Sapiens | Arylsulfatase B | yes | 26.5% |
| 2VQR | 20.0% | Rhizobium leguminosarum | Sulfatase | no | ? |
| 3ED4 | 32.0% | Escherichia coli | Arylsulfatase | yes | ? |
Our potential tmeplates, identified by the database searches contain all homologs with known structure, regarding to HSSP.
Pairwise alignments
The programs used for TASK 2 are heuristics, which produce local alignments. If we call modeller with only one template structure, we need to globally align the seqeunces. To create pairwise alignments with the Needleman-Wunsch algorithm, we installed the European Molecular Biology Open Software (EMBOSS).
sudo apt-get install emboss
Then, we executed the needle program with the following commands:
needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1P49.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 1FSU.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 2VQR.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 1fsu.needle 1AUK.fasta.txt 3ED4.fasta.txt
A tutorial on the usage of needle can be found here.
