Homology based structure predictions

Homologous

Because we found no homologous structures in Task 2, we extended our list by using HHSearch.

We will use 13 proteins for creating a multiple alignment for homologous modeling. We choosen sequences to cover the whole protein and we payed specific attention on the transmembrane region.

PDB-ID	Identity	Description
1s79	37%	Kram
2yc6	32%	Kram
3p73	28%	Kram
1kcg	22%	Kram
1jfm	14%	Kram
1bii	22%	Kram
2p24	21%	Kram
1cd1	21%	Kram
2wy3	29%	Kram
1lqv	14%	Kram
3jts	25%	Kram
1ow0	22%	Kram
1hxm	18%	Kram
3lmy	19%	Kram

ITasser

Predicted Secondary Structure by I-Tasser

Sequence:   MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDF
Predicted:  CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCCCCCSSSSSSSCCCSSSSCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Conf-Score: 985028899999999899875122045421036641367999985269985643743686068998778788540145583478888887676654315558

Sequence:   WTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQ
Predicted:  HHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCSSSSCCCHHHCHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCHHHHHC
Conf-Score: 888755315777644463525565898763541000558873365263022202455666677878887004598888767064299999999747666642

Sequence:   QVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLV
Predicted:  CCCCCCCCCCCCCCCHHHHCHHHHCCCCCCSSSSSSSCCCCCCCCCCSSSSCCCCCCCCCCCSSSSSCCCCCCCCSSSSCCCCCCCCCSSSSCCCCCCCCCC
Conf-Score: 599877567699854442101541541332479864358754456553541024888652112699807986310267512589998726840688766531

Sequence:   IGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
Prediction: CCCCCCHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCHCCCC
Conf-Score: 010211112222100246665443013678898651020169

Secondary structure elements are shown as H for Alpha helix,S for Beta sheet & C for Coil

Predicted Solvent Accessibility by I-Tasser

Sequence:   MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDF
Prediction: 723312000000000101112222011200120120023333331200000102322003123724434241311436413610352044144313323230

Sequence:   WTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQ
Prediction: 220132133351310001010021136231211333023032003016303403102321432433044143404422010333005103400630351154

Sequence:   QVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLV
Prediction: 342353313321443300000100101014010203346564435434135233334221320000000347533120214264144202020214542200

Sequence:   IGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
Prediction: 000001100000011100000001334446443132333438

Values range from 0 (buried residue) to 9 (highly exposed residue)

I-Tasser predicted five Models with a C-Score from -0.557 to -3.298. They are ranked from one to five as seen below.

Model 1 with a C-Score of -0.557

Model 2 with a C-Score of -2.539

Model 3 with a C-Score of -2.266

Model 4 with a C-Score of -2.772

Model 5 with a C-Score of -3.298

Model1 has a TM-Score of about 0.64 and a RMSD of 7.7Å. For the prediction, I-Tasser used 10 Templates found on PDB which are:

SwissModel

SwissProt is a server based tool provided by the SIB. It combines tools like PSI-PRED and DISOPRED for secondary structure and disordered region prediction.

The model created by SwissModel is based on a self hit, but we had no chance to exclude the protein itself from the prediction. Therefore we also run SwissModel in Alignment-Mode.(TODO)

Automated Mode

predicted model

Model information: Modelled residue range: 26 to 297
Based on template: 1a6zC (2.60 Å)
Sequence Identity [%]: 100
Evalue: 7.66e-163

Quality information: QMEAN Z-Score: -1.035

Estimated absolute model quality

Estimated density of model quality

Z-Score by category

predicted error

Even though the model is based on a self hit, the Z-Score is about -1, which means that the model is one standard deviation from the mean. The model is not quite unlikely but also not the most probable one.