D-I-TASSER Q9UBN1

D-I-TASSER results for Q9UBN1

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

Summary of the Protein

Uniprot ID: Q9UBN1
Protein Name: Voltage-dependent calcium channel gamma-4 subunit
Gene Name: CACNG4

Input Sequence in FASTA format

>Q9UBN1 (327 residues)
MVRCDRGLQMLLTTAGAFAAFSLMAIAIGTDYWLYSSAHICNGTNLTMDDGPPPRRARGD
LTHSGLWRVCCIEGIYKGHCFRINHFPEDNDYDHDSSEYLLRIVRASSVFPILSTILLLL
GGLCIGAGRIYSRKNNIVLSAGILFVAAGLSNIIGIIVYISSNTGDPSDKRDEDKKNHYN
YGWSFYFGALSFIVAETVGVLAVNIYIEKNKELRFKTKREFLKASSSSPYARMPSYRYRR
RRSRSSSRSTEASPSRDVSPMGLKITGAIPMGELSMYTLSREPLKVTTAASYSPDQEASF
LQVHDFFQQDLKEGFHVSMLNRRTTPV

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	Q9UBN1-D1	1-233	233		MVRCDRGLQMLLTTAGAFAAFSLMAIAIGTDYWLYSSAHICNGTNLTMDDGPPPRRARGDLTHSGLWRVCCIEGIYKGHCFRINHFPEDNDYDHDSSEYLLRIVRASSVFPILSTILLLLGGLCIGAGRIYSRKNNIVLSAGILFVAAGLSNIIGIIVYISSNTGDPSDKRDEDKKNHYNYGWSFYFGALSFIVAETVGVLAVNIYIEKNKELRFKTKREFLKASSSSPYARM
2	Q9UBN1-D2	234-327	94		PSYRYRRRRSRSSSRSTEASPSRDVSPMGLKITGAIPMGELSMYTLSREPLKVTTAASYSPDQEASFLQVHDFFQQDLKEGFHVSMLNRRTTPV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.658

(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	7ocaI	0.52	2.12	0.632	0.557	model1_7ocaI.pdb.gz
2	8ss3A2	0.52	2.44	0.308	0.560	model1_8ss3A2.pdb.gz
3	7ryyA	0.51	2.60	0.320	0.563	model1_7ryyA.pdb.gz
4	7tnjA	0.51	2.63	0.636	0.557	model1_7tnjA.pdb.gz
5	6akfA	0.47	2.81	0.170	0.532	model1_6akfA.pdb.gz
6	6ov2A	0.47	2.74	0.177	0.523	model1_6ov2A.pdb.gz
7	6r9tA	0.47	5.56	0.059	0.691	model1_6r9tA.pdb.gz
8	5b2gA	0.47	3.30	0.184	0.541	model1_5b2gA.pdb.gz
9	6qkcI	0.46	2.07	0.679	0.492	model1_6qkcI.pdb.gz
10	6wxrB	0.46	3.97	0.062	0.584	model1_6wxrB.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:0016247	1.00	channel regulator activity
GO:0005245	1.00	voltage-gated calcium channel 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:2000311	1.00	regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity
GO:0044699	0.99	single-organism process
GO:0050877	0.98	neurological system process
GO:0044707	0.98	single-multicellular organism process
GO:0044700	0.98	single organism signaling
GO:0019226	0.97	transmission of nerve impulse
GO:0006810	0.96	transport
GO:0006811	0.93	ion transport
GO:0070588	0.92	calcium ion transmembrane transport

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:0044459	1.00	plasma membrane part
GO:0032281	0.99	AMPA 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	0.060	1rsrB	0.360	6.06	0.042	0.544	1.17.4.1	139
2	0.060	2p0mB	0.408	5.42	0.044	0.584	1.13.11.33	105
3	0.060	1biqB	0.359	6.03	0.037	0.544	1.17.4.1	NA
4	0.060	1ygeA	0.408	5.58	0.049	0.593	1.13.11.12	NA
5	0.060	3dy5A	0.398	5.34	0.049	0.557	1.13.11.40 4.2.1.92	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	0.01	3r6nB	0.373	5.17	0.030	0.520	0.79	D1D	complex1.pdb.gz	150,151,153,193,196
2	0.01	1cc1L	0.368	4.55	0.054	0.480	0.54	FCO	complex2.pdb.gz	13,122,141,142,199,202
3	0.01	3rrpA	0.329	5.03	0.062	0.468	0.74	LMR	complex3.pdb.gz	114,115,117,118,152
4	0.01	1frvD	0.365	4.20	0.058	0.465	0.51	FEL	complex4.pdb.gz	17,147,149,193,198
5	0.01	3rrpA	0.329	5.03	0.062	0.468	0.59	LMR	complex5.pdb.gz	151,153,188,189
6	0.01	3fg4C	0.392	5.35	0.040	0.560	0.83	ACD	complex6.pdb.gz	120,125,140,141,144
7	0.01	1h2aL	0.362	4.19	0.047	0.471	0.53	NFE	complex7.pdb.gz	17,21,148,149,192,195

	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.