Homology Modeling of ARS A

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 1p49.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 2vqr.needle 1AUK.fasta.txt 2VQR.fasta.txt
needle -gapopen 10 -gapextend 0.5 -outfile 3ed4.needle 1AUK.fasta.txt 3ED4.fasta.txt


A tutorial on the usage of needle can be found here.