Fabry:Homology based structure predictions

Fabry Disease » Homology based structure predictions

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The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.

Dataset preparation

<figtable id="tab:datasetHHpred"> Dataset HHpred

pdb ID	E-value	Identity in %
> 80% sequence identity
3hg3	8.6e-90	100
40% - 80% sequence identity
1ktb	4.2e-85	53
< 30% sequence identity
3cc1	5.5e-74	25
1zy9	3.1e-48	13
3a24	7.8e-40	17
2xn2	5.3e-37	15
2d73	5.7e-36	14
3mi6	1.4e-31	15
2yfo	9.1e-30	13
2f2h	2.7e-20	17
2g3m	2.2e-20	16
3nsx	6e-20	13
3lpp	2.2e-18	15
3l4y	1.9e-18	15
3top	3.6e-18	12
2xvl	3.2e-18	16
2x2h	4.9e-16	13

</figtable>

<figtable id="tab:datasetCOMA"> Dataset COMA

pdb ID	E-value	Identity in %
> 80% sequence identity
-	-	-
40% - 80% sequence identity
1ktb	1.7e-61	52
< 30% sequence identity
3lrk	1.2e-66	23
3a21	2.7e-65	26
1szn	3.7e-59	22
3cc1	5.2e-58	19
1zy9	1.7e-39	9
3mi6	4.3e-38	11
2yfn	4.4e-35	10
2d73	1.9e-32	9
3a24	5.6e-30	10
1xsi	1.9e-12	10
2g3m	2.4e-11	10
3pha	2.9e-10	6
3lpo	4.7e-09	8
2x2h	8.2e-09	8
3mo4	1.2e-08	7
2xvg	2.4e-08	8
3ton	4.3e-08	8
2xib	1e-07	7
3eyp	1.6e-06	8
3k1d	3.5e-06	9
2zwy	8.8e-06	9
3gza	1.8e-05	8
3m07	2.3e-05	7
1eh9	0.00013	6
1gvi	0.00035	8
1aqh	0.00039	5
1mwo	0.00058	7
3vmn	0.0018	9
1bf2	0.0019	6
3aml	0.0019	8

</figtable>

We performed a HHpred as well as a COMA search, to generate three distinct datasets. Since COMA did not find any homologue structures with a similarity above 41% (see <xr id="tab:datasetCOMA"/>), we used the dataset created with the HHpred search and the script described in the journal. Hereby we found one structure with a similarity above 80%, one with a similarity between 40 and 80% and 15 with sequence similarity below 30%, of which 14 had a similarity of under 20% (see <xr id="tab:datasetHHpred" />). All HHpred matches had an E-value below 1e-15, for the COMA homologues we tried a less strict threshold of 0.002.
In this case it is important to mention, that although the identity of 3hg3 is 100%, this structure is not derived from the α-Galactosidase A sequence, but the AGAL sequence is contained in the 3hg3 sequence 100%.