D-I-TASSER Q9Y5K8

D-I-TASSER results for Q9Y5K8

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

Summary of the Protein

Uniprot ID: Q9Y5K8
Protein Name: V-type proton ATPase subunit D
Gene Name: ATP6V1D

Input Sequence in FASTA format

>Q9Y5K8 (247 residues)
MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGE
VMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYE
LTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRI
ERTLAYIITELDEREREEFYRLKKIQEKKKILKEKSEKDLEQRRAAGEVLEPANLLAEEK
DEDLLFE

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	Q9Y5K8-D1	1-247	247		MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKSEKDLEQRRAAGEVLEPANLLAEEKDEDLLFE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8393

(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	6vq6H	0.84	0.97	0.995	0.866	model1_6vq6H.pdb.gz
2	5voxM	0.75	2.24	0.553	0.842	model1_5voxM.pdb.gz
3	6ly8G	0.72	2.84	0.273	0.846	model1_6ly8G.pdb.gz
4	7ogtB2	0.66	3.00	0.096	0.761	model1_7ogtB2.pdb.gz
5	6yvuB	0.61	2.64	0.069	0.700	model1_6yvuB.pdb.gz
6	7nnaA	0.60	2.34	0.105	0.672	model1_7nnaA.pdb.gz
7	3aonA	0.60	2.65	0.249	0.700	model1_3aonA.pdb.gz
8	7nyxA	0.59	3.28	0.042	0.705	model1_7nyxA.pdb.gz
9	6fkfg	0.59	3.71	0.037	0.725	model1_6fkfg.pdb.gz
10	6z9lA	0.59	3.34	0.045	0.705	model1_6z9lA.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:0005215	0.74	transporter activity
GO:0015075	0.73	ion transmembrane transporter activity
GO:0008324	0.72	cation transmembrane transporter activity
GO:0003824	0.69	catalytic activity
GO:0022890	0.66	inorganic cation transmembrane transporter activity
GO:0016787	0.66	hydrolase activity
GO:0016817	0.65	hydrolase activity, acting on acid anhydrides
GO:0015078	0.65	hydrogen ion transmembrane transporter activity
GO:0019829	0.64	cation-transporting ATPase activity
GO:0036442	0.63	hydrogen-exporting ATPase activity
GO:0046961	0.51	proton-transporting ATPase activity, rotational mechanism

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	1.00	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.91	single-organism cellular process
GO:0051179	0.83	localization
GO:0008104	0.60	protein localization
GO:0051641	0.58	cellular localization
GO:0034613	0.57	cellular protein localization
GO:0016043	0.57	cellular component organization
GO:0061512	0.56	protein localization to cilium
GO:0042384	0.56	cilium assembly
GO:0006810	0.53	transport
GO:0065007	0.51	biological regulation

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	0.97	cell part
GO:0044424	0.96	intracellular part
GO:0044446	0.91	intracellular organelle part
GO:0044444	0.84	cytoplasmic part
GO:0044437	0.69	vacuolar part
GO:0016020	0.66	membrane
GO:0032991	0.62	macromolecular complex
GO:0044425	0.60	membrane part
GO:0043234	0.60	protein complex
GO:0098796	0.58	membrane protein complex
GO:0043226	0.58	organelle
GO:0031090	0.56	organelle membrane
GO:0043229	0.55	intracellular organelle
GO:0098588	0.53	bounding membrane of organelle
GO:0005774	0.52	vacuolar 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	2iukB	0.322	5.17	0.046	0.474	1.13.11.12	NA
2	0.060	3ixzA	0.346	5.70	0.038	0.575	3.6.3.10	NA
3	0.060	1y2mB	0.367	5.01	0.053	0.530	4.3.1.24	NA
4	0.060	2b5uA	0.516	2.34	0.057	0.571	3.1.-.-	NA
5	0.060	1z0hB	0.256	5.71	0.044	0.425	3.4.24.69	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	0.01	1i490	0.426	3.46	0.095	0.530	0.63	III	complex1.pdb.gz	15,19,22,26,29,32,33,36,39,40,44,46,50,151,154,155,157,158,161,165,179
2	0.01	1zww0	0.407	3.44	0.029	0.506	0.50	III	complex2.pdb.gz	17,18,20,21,24,25,29,32,35,42,43,46,49,50,53,155
3	0.01	1wdz0	0.423	4.43	0.045	0.607	0.49	III	complex3.pdb.gz	15,18,22,25,26,29,32,33,35,36,39,151,154,157,158,161,165,179
4	0.01	2w6dB	0.439	5.13	0.042	0.648	0.55	CPL	complex4.pdb.gz	122,123,130,131,133
5	0.01	1i4d1	0.395	3.78	0.094	0.502	0.40	III	complex5.pdb.gz	63,66,69,77,78,135,138,139
6	0.01	1jch0	0.514	2.37	0.057	0.571	0.41	III	complex6.pdb.gz	28,35,38,39,139,143,150,154,158

	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.