D-I-TASSER Q08881-D3

D-I-TASSER results for Q08881-D3

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>Q08881 (87 residues)
GLRYGKWVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEV
MMKLSHPKLVQLYGVCLEQAPICLVFE

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| GLRYGKWVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFE
Prediction	CCCCCCCSCCHHHCSSSSSSSCCCCCSSSSSSSCCCCSSSSSSCCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSSSSCCCCSSSSSC
Confidence	998110235745546978873168937999998399579999816999989999999999997799876469999926991599959
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| GLRYGKWVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFE
Prediction	846466230447505035304554344112030677440000103776444630352052045143520020100025653100028
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80

                   |                   |                   |                   |

SS
Seq

CCCCCCCSCCHHHCSSSSSSSCCCCCSSSSSSSCCCCSSSSSSCCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSSSSCCCCSSSSSC
GLRYGKWVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFE

1cdkA

0.18

0.17

5.63

1.33

DEthreader

--KPAQNTAHLDQFERIKTLGTGSFGRVMLVKHETGNHFAMKILDKQKVVQIETLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVME

7ax4A1

0.25

0.24

7.48

2.01

SPARKS-K

---LSFHRVDQKEITQLSHLGQGTRTNVYEGRLRVELRVVLKVLDSHHDIALAFYETASLMSQVSHTHLAFVHGVCVRGPENIMVTE

5ek7A

0.34

0.33

9.98

0.37

MapAlign

-VLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTEVPVAIKTLKAGYQ-RVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITE

5ek7A1

0.33

10.00

0.23

CEthreader

AVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTEVPVAIKTLKAGYTQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITE

4y93A

0.62

17.76

1.47

MUSTER

GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITE

2ozoA

0.34

0.33

9.99

0.86

HHsearch

ELKDKKLFLKRDNLLIDIELGCGNFGSVRQGVYRMQIDVAIKVLKQGTEDTEEMMREAQIMHQLDNPYIVRLIGVCQ-AEALMLVME

2fo0A2

0.40

0.37

10.86

1.57

FFAS-3D

------WEMERTDITMKHKLGGGQYGEVYEGVWKKSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITE

2biyA1

0.24

0.23

7.17

0.57

EigenThreader

PQPR---KKRPEDFKFGKILGEGSFSTVVLARELASREYAIKILEKRHIKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLS

3t9tA

0.99

0.92

25.76

1.73

CNFpred

------WVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVTE

1k9aB

0.40

0.39

11.52

1.33

DEthreader

ECRESGWALNMKELKLLQTIGKGEFGDVMLGDYR-GNKVAVKCIK--NDTAQAFLAEASVMTQLRHSNLVQLLGVIVEEGGLYIVTE

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7901

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4f0iB	0.87	1.33	0.349	0.954	model1_4f0iB.pdb.gz
2	4c8bA1	0.85	1.47	0.214	0.966	model1_4c8bA1.pdb.gz
3	7jy4A1	0.85	1.76	0.291	0.977	model1_7jy4A1.pdb.gz
4	4cdsA1	0.85	1.40	0.512	0.954	model1_4cdsA1.pdb.gz
5	4l00A	0.85	1.95	0.264	0.989	model1_4l00A.pdb.gz
6	7bttA	0.84	1.93	0.287	0.989	model1_7bttA.pdb.gz
7	3sxrA	0.84	1.16	0.506	0.908	model1_3sxrA.pdb.gz
8	2j0kB2	0.84	2.07	0.337	0.977	model1_2j0kB2.pdb.gz
9	1k9aB	0.84	1.74	0.393	0.966	model1_1k9aB.pdb.gz
10	4oliA	0.83	1.77	0.262	0.966	model1_4oliA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0016740	0.96	transferase activity
GO:0004672	0.95	protein kinase activity
GO:0004674	0.60	protein serine/threonine kinase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.89	cellular process
GO:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044238	0.82	primary metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0043170	0.81	macromolecule metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0065007	0.76	biological regulation
GO:0050789	0.76	regulation of biological process
GO:0019538	0.75	protein metabolic process
GO:0006796	0.75	phosphate-containing compound metabolic process
GO:0050794	0.74	regulation of cellular process
GO:0016310	0.74	phosphorylation
GO:0006464	0.74	cellular protein modification process
GO:0006468	0.73	protein phosphorylation
GO:0007165	0.60	signal transduction
GO:0050896	0.58	response to stimulus
GO:0044699	0.57	single-organism process
GO:0006950	0.53	response to stress
GO:0006952	0.50	defense response

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0044424	0.82	intracellular part
GO:0016020	0.67	membrane
GO:0005886	0.62	plasma membrane

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2j0lA	0.814	1.83	0.345	0.954	2.7.10.2	NA
2	0.060	3eqrB	0.800	1.85	0.341	0.943	2.7.10.2	NA
3	0.060	1sm2A	0.850	1.15	0.938	0.919	2.7.10.2	NA
4	0.060	1uwhA	0.803	1.51	0.287	0.919	2.7.11.1	NA
5	0.060	2j0kB	0.837	2.07	0.337	0.977	2.7.10.2	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.93	1sm2A	0.850	1.15	0.938	0.919	0.97	STU	complex1.pdb.gz	20,21,28,40,42,86,87
2	0.84	3mj1A	0.697	1.47	0.957	0.793	0.95	614	complex2.pdb.gz	20,21,22,28,40
3	0.50	1mp8A	0.809	1.66	0.358	0.931	0.85	ADP	complex3.pdb.gz	20,22,23,28,40,42,57,70
4	0.46	3f5pG	0.812	1.91	0.314	0.977	0.85	741	complex4.pdb.gz	20,28,40,41,42,54,57,61,70,84,86,87

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.