D-I-TASSER Q96HY6

D-I-TASSER results for Q96HY6

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

Summary of the Protein

Uniprot ID: Q96HY6
Protein Name: DDRGK domain-containing protein 1
Gene Name: DDRGK1

Input Sequence in FASTA format

>Q96HY6 (314 residues)
MVAPVWYLVAAALLVGFILFLTRSRGRAASAGQEPLHNEELAGAGRVAQPGPLEPEEPRA
GGRPRRRRDLGSRLQAQRRAQRVAWAEADENEEEAVILAQEEEGVEKPAETHLSGKIGAK
KLRKLEEKQARKAQREAEEAEREERKRLESQREAEWKKEEERLRLEEEQKEEEERKAREE
QAQREHEEYLKLKEAFVVEEEGVGETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGL
RTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNS
LIAWGRESPAQAPA

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

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q96HY6-D1	1-314	314		MVAPVWYLVAAALLVGFILFLTRSRGRAASAGQEPLHNEELAGAGRVAQPGPLEPEEPRAGGRPRRRRDLGSRLQAQRRAQRVAWAEADENEEEAVILAQEEEGVEKPAETHLSGKIGAKKLRKLEEKQARKAQREAEEAEREERKRLESQREAEWKKEEERLRLEEEQKEEEERKAREEQAQREHEEYLKLKEAFVVEEEGVGETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGRESPAQAPA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5993

(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	5yfpE	0.42	6.13	0.056	0.685	model1_5yfpE.pdb.gz
2	6sl2A	0.41	6.12	0.038	0.656	model1_6sl2A.pdb.gz
3	1ciiA	0.40	5.59	0.049	0.586	model1_1ciiA.pdb.gz
4	2uvcG	0.40	6.76	0.039	0.704	model1_2uvcG.pdb.gz
5	4bujB	0.40	6.42	0.040	0.669	model1_4bujB.pdb.gz
6	5owvA	0.40	5.74	0.036	0.608	model1_5owvA.pdb.gz
7	6rwbA	0.39	4.86	0.032	0.522	model1_6rwbA.pdb.gz
8	5yfpC	0.38	6.41	0.051	0.627	model1_5yfpC.pdb.gz
9	7luvC	0.37	6.09	0.038	0.608	model1_7luvC.pdb.gz
10	6rw9A	0.37	5.42	0.071	0.513	model1_6rw9A.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:0019899	0.85	enzyme binding
GO:0044389	0.84	ubiquitin-like protein ligase 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:0009987	0.96	cellular process
GO:0008152	0.92	metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0044238	0.91	primary metabolic process
GO:0044237	0.90	cellular metabolic process
GO:0043170	0.90	macromolecule metabolic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0044267	0.84	cellular protein metabolic process
GO:0043412	0.84	macromolecule modification
GO:0006464	0.83	cellular protein modification process
GO:0071569	0.82	protein ufmylation
GO:1990592	0.81	protein K69-linked ufmylation
GO:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0048518	0.67	positive regulation of biological process
GO:0050896	0.66	response to stimulus
GO:0010468	0.66	regulation of gene expression
GO:0006950	0.65	response to stress
GO:0006355	0.65	regulation of transcription, DNA-templated
GO:0051092	0.63	positive regulation of NF-kappaB transcription factor activity
GO:0034976	0.62	response to endoplasmic reticulum stress
GO:0048584	0.60	positive regulation of response to stimulus
GO:0009967	0.59	positive regulation of signal transduction
GO:1903721	0.56	positive regulation of I-kappaB phosphorylation
GO:1901800	0.56	positive regulation of proteasomal protein catabolic process
GO:0033146	0.56	regulation of intracellular estrogen receptor signaling pathway

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:0044424	1.00	intracellular part
GO:0044444	0.99	cytoplasmic part
GO:0043231	0.99	intracellular membrane-bounded organelle
GO:0005783	0.97	endoplasmic reticulum

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	2vz8B	0.298	6.39	0.027	0.478	2.3.1.85	NA
2	0.060	3iydD	0.277	6.48	0.035	0.471	2.7.7.6	NA
3	0.060	1bucA	0.286	4.65	0.034	0.385	1.3.99.2	NA
4	0.060	2r0nA	0.273	5.13	0.032	0.379	1.3.99.7	74,78
5	0.060	2uv8G	0.358	7.05	0.013	0.653	2.3.1.86	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	0.02	1g8xA	0.355	6.69	0.035	0.621	0.17	ADP	complex1.pdb.gz	119,121,122,123,124
2	0.01	1w9kA	0.198	6.39	0.031	0.319	0.13	UUU	complex2.pdb.gz	117,118,121,122,123,124
3	0.01	2p3kA	0.145	5.15	0.047	0.207	0.19	MNA	complex3.pdb.gz	114,122,123,124
4	0.01	1ncg0	0.110	4.21	0.039	0.146	0.22	III	complex4.pdb.gz	79,82,118,119
5	0.01	2x9hA	0.234	6.05	0.032	0.382	0.21	KI9	complex5.pdb.gz	109,112,115,117,126
6	0.01	3q2vA	0.333	6.10	0.020	0.538	0.26	MAN	complex6.pdb.gz	116,118,119,124
7	0.01	3mylX	0.239	6.33	0.036	0.401	0.37	POP	complex7.pdb.gz	115,116,117,118
8	0.01	2xo8A	0.254	5.50	0.023	0.379	0.17	H70	complex8.pdb.gz	115,118,122
9	0.01	3mjxA	0.221	5.57	0.017	0.344	0.20	BIT	complex9.pdb.gz	114,118,121
10	0.01	1mmnA	0.202	5.46	0.016	0.290	0.14	ANP	complex10.pdb.gz	117,118,119,120,121,122,123

	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.