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%

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 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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