D-I-TASSER Q92796-D6

D-I-TASSER results for Q92796-D6

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

Input Sequence in FASTA format

>Q92796 (136 residues)
PVTRQEIHYARPVIILGPMKDRVNDDLISEFPHKFGHCILDVSGNAIKRLQQAQLYPIAI
FIKPKSIEALMEMNRRQTYEQANKIYDKAMKLEQEFGEYFTAIVQGDSLEEIYNKIKQII
EDQSGHYIWVPSPEKL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PVTRQEIHYARPVIILGPMKDRVNDDLISEFPHKFGHCILDVSGNAIKRLQQAQLYPIAIFIKPKSIEALMEMNRRQTYEQANKIYDKAMKLEQEFGEYFTAIVQGDSLEEIYNKIKQIIEDQSGHYIWVPSPEKL
Prediction	CCSSSCCCCCCCSSSSCCHHHHHHHHHHHHHHHHCCCSSSSSCHHHHHHHHHCCCCCSSSSSCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCSSSCCCCCC
Confidence	9245037888877997236889999999999986891588717999999997199968999729999999999840564779999999999999963138399979889999999999999973897353488889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PVTRQEIHYARPVIILGPMKDRVNDDLISEFPHKFGHCILDVSGNAIKRLQQAQLYPIAIFIKPKSIEALMEMNRRQTYEQANKIYDKAMKLEQEFGEYFTAIVQGDSLEEIYNKIKQIIEDQSGHYIWVPSPEKL
Prediction	7454463724110000112343034400540274443010103240043046361300000020432730462265345641540253045026514620210031430450053035105615753211236668
	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                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCSSSCCCCCCCSSSSCCHHHHHHHHHHHHHHHHCCCSSSSSCHHHHHHHHHCCCCCSSSSSCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCSSSCCCCCC
PVTRQEIHYARPVIILGPMKDRVNDDLISEFPHKFGHCILDVSGNAIKRLQQAQLYPIAIFIKPKSIEALMEMNRRQTYEQANKIYDKAMKLEQEFGEYFTAIVQGDSLEEIYNKIKQIIEDQSGHYIWVPSPEKL

7luyA

0.16

0.15

4.87

1.33

DEthreader

----NQR-RGFLFILSSSGKSTLSRLLLK-DGKLERDMLFDIDYQGTKQLQKKMPDTVSVFILPPSMKELISRLRADSQDIINLRLKNARTEMQH-WRSYDYVIINENLNQSVSLIKSIYLAETVKRER-------

1kjwA3

0.67

19.07

1.85

SPARKS-K

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA

0.67

19.07

0.79

MapAlign

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA3

0.67

19.07

0.85

CEthreader

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA3

0.68

19.26

1.96

MUSTER

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA

0.68

19.26

2.01

HHsearch

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA3

0.64

0.63

18.07

1.93

FFAS-3D

-VTQMEVHYARPIIILGPTKDRANDDLVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA3

0.67

19.07

0.73

EigenThreader

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

3uatA

0.65

0.54

15.53

1.17

CNFpred

--------------LYGTSVQSVRAVAEK-----GKHCILDVSGNAIKRLQIAQLYPISIFIKPKSMENIMEMNKRLTDEQARKTFERAVRLEQEFTEHFTAIVQGDTLEDIYNQVKQIIEEQSGPYIWVPAK---

7luyA2

0.17

0.15

4.86

1.33

DEthreader

----NQR-RGFLFILSSSGKSTLSRLLLK-DGK-LEDMLFDIDYQGTKQLQKKMPDTVSVFILPPSMKELISRLRADSQDIINLRLKNARTEMQ-HWRSYDYVIINENLNQSVSLIKSIYLAETVKRER-------

(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	0.7956

(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	3tvtA	0.93	0.91	0.712	0.971	model1_3tvtA.pdb.gz
2	2xkxA	0.92	1.34	0.662	0.985	model1_2xkxA.pdb.gz
3	1kjwA3	0.92	1.34	0.662	0.985	model1_1kjwA3.pdb.gz
4	3lh5A	0.85	2.12	0.311	0.963	model1_3lh5A.pdb.gz
5	3kfvA	0.82	2.18	0.320	0.926	model1_3kfvA.pdb.gz
6	4wsiA	0.79	2.48	0.215	0.956	model1_4wsiA.pdb.gz
7	1kgdA	0.71	2.32	0.214	0.824	model1_1kgdA.pdb.gz
8	3neyA	0.69	2.77	0.184	0.838	model1_3neyA.pdb.gz
9	1s96A	0.68	2.62	0.177	0.846	model1_1s96A.pdb.gz
10	1lvgA	0.66	2.96	0.252	0.846	model1_1lvgA.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	0.89	transferase activity
GO:0004385	0.88	guanylate kinase activity
GO:0005102	0.82	receptor binding
GO:0035255	0.81	ionotropic glutamate receptor binding

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:0044699	0.98	single-organism process
GO:0009987	0.96	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0016043	0.90	cellular component organization
GO:0051179	0.89	localization
GO:0032502	0.88	developmental process
GO:0008104	0.88	protein localization
GO:0007163	0.87	establishment or maintenance of cell polarity
GO:0045197	0.84	establishment or maintenance of epithelial cell apical/basal polarity
GO:0097120	0.80	receptor localization to synapse
GO:0048856	0.80	anatomical structure development
GO:0051641	0.78	cellular localization
GO:0034613	0.76	cellular protein localization
GO:1902578	0.73	single-organism localization
GO:0007267	0.73	cell-cell signaling
GO:1902580	0.72	single-organism cellular localization
GO:0044802	0.71	single-organism membrane organization
GO:0043113	0.70	receptor clustering
GO:0048731	0.69	system development
GO:0007268	0.64	chemical synaptic transmission
GO:0007399	0.62	nervous system development

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	0.88	intracellular part
GO:0016020	0.87	membrane
GO:0044425	0.84	membrane part
GO:0044459	0.83	plasma membrane part
GO:0098590	0.78	plasma membrane region
GO:0043226	0.77	organelle
GO:0043229	0.75	intracellular organelle
GO:0016323	0.75	basolateral plasma membrane
GO:0097458	0.74	neuron part
GO:0032991	0.73	macromolecular complex
GO:0043234	0.72	protein complex
GO:0098797	0.70	plasma membrane protein complex
GO:0034702	0.70	ion channel complex
GO:0044456	0.68	synapse part
GO:0097060	0.67	synaptic membrane
GO:0043232	0.67	intracellular non-membrane-bounded organelle
GO:0045211	0.66	postsynaptic membrane
GO:0014069	0.66	postsynaptic density
GO:0008328	0.66	ionotropic glutamate receptor complex

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	0.067	1kofA	0.648	2.74	0.139	0.831	2.7.1.12	NA
2	0.066	1rkbA	0.645	2.57	0.130	0.824	2.7.4.3	NA
3	0.066	2o6hE	0.517	4.13	0.061	0.831	2.5.1.9	44
4	0.066	2f59D	0.519	4.18	0.061	0.831	2.5.1.9	NA
5	0.066	1iibA	0.490	2.81	0.011	0.640	2.7.1.69	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	0.04	1vytA	0.668	3.25	0.218	0.912	0.68	III	complex1.pdb.gz	21,23,62,63,64,65,77,106,107,108,109,112
2	0.04	1t3lA	0.675	3.18	0.219	0.912	0.55	III	complex2.pdb.gz	63,64,66,106,107,108,109,112
3	0.01	2i0iA	0.262	4.12	0.057	0.426	0.46	III	complex3.pdb.gz	17,18,42,43,44,47

	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.