Homology Modelling GLA

^{by Benjamin Drexler and Fabian Grandke}

Calculation of Models

Available Homologous Structures

The HHpred search from Task1 output the following sequences(Top 10):

PDB-ID	Name	Probability	E-value	P-value	Identity
> 60% sequence identity
3hg3_A	Alpha-galactosidase A	1.0	0	0	97%
> 40% sequence identity
1ktb_A	Alpha-N-acetylgalactosaminidase	1.0	0	0	53%
< 40% sequence identity
1uas_A	Alpha-galactosidase	1.0	0	0	39%
3lrk_A	Alpha-galactosidase 1	1.0	0	0	32%
3a5v_A	Alpha-galactosidase	1.0	0	0	35%
1szn_A	Alpha-galactosidase	1.0	0	0	34%
3a21_A	Putative secreted alpha-galactosidase	1.0	0	0	34%
3cc1_A	BH1870 protein	1.0	0	0	26%
3a24_A	Alpha-galactosidase	1.0	0	0	14%
1zy9_A	Alpha-galactosidase	1.0	2.2E-37	8.8E-42	14%

iTasser

As the iTasser-server has very low capacities, only one job commitment at the same time was possible and one job took about 36 hours to run, we obtained a license for academic or non-profit use(takes another 36h). It empowered us to download the standalone package of iTasser. Unfortunately, it is about 8gb big and does not work properly! Thus we still used the server with different IP- and e-mail addresses.

SWISS-MODEL

Following sequences have been selected:

3hg3_A					1ktb_A					3cc1_A
	Automated Mode		Aligned Mode			Automated Mode		Aligned Mode			Automated Mode		Aligned Mode
Identity	Z-score	Model	Z-score	Model	Identity	Z-score	Model	Z-score	Model	Identity	Z-score	Model	Z-score	Model
97%	0		-0.415		53%	0		-2.261		26%	0		Error¹	NA

¹The sequences are to different to create a useful model from the alignment. In the automated mode the template itself has been used as model, what is useless, because the sequences have only 26% identity.

Aborting: too many unfruitful attempts to rebuild a loop. This is likely to indicate a misalignment in this region Use Swiss-PdbViewer to adjust your alignment in this region and resubmit an optimise mode modelling request.

References

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