Homology Modeling of ARS A

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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.