D-I-TASSER Q9H606

D-I-TASSER results for Q9H606

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

Summary of the Protein

Uniprot ID: Q9H606
Protein Name: Proline-rich protein, Y-linked
Gene Name: PRORY

Input Sequence in FASTA format

>Q9H606 (182 residues)
MMRRSPSGLKSPRVSQGRKPRDPESLLFLRCCLGSEPHNLSSLLSPEAGQEPLPKLLPQP
LAGHAAWGIHGVPTSLLLAGECWGQGMAVPADPPPASPYRTSPRPPPGPLPRYRPQQHLL
LPLGRLHALCPGCPLQQSLQFERGTLSAPRLWSWMKLETIILSKLSQGQKTKHRMFSLIS
ES

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	Q9H606-D1	1-182	182		MMRRSPSGLKSPRVSQGRKPRDPESLLFLRCCLGSEPHNLSSLLSPEAGQEPLPKLLPQPLAGHAAWGIHGVPTSLLLAGECWGQGMAVPADPPPASPYRTSPRPPPGPLPRYRPQQHLLLPLGRLHALCPGCPLQQSLQFERGTLSAPRLWSWMKLETIILSKLSQGQKTKHRMFSLISES

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.487

(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	6eu6A	0.45	5.57	0.060	0.791	model1_6eu6A.pdb.gz
2	1ui7A	0.45	5.34	0.042	0.758	model1_1ui7A.pdb.gz
3	5aexA	0.45	5.76	0.058	0.802	model1_5aexA.pdb.gz
4	1ksiA	0.45	5.20	0.030	0.742	model1_1ksiA.pdb.gz
5	2wgqB	0.44	5.38	0.042	0.753	model1_2wgqB.pdb.gz
6	5cd6A1	0.44	5.57	0.060	0.775	model1_5cd6A1.pdb.gz
7	3b9zA	0.44	5.68	0.052	0.780	model1_3b9zA.pdb.gz
8	5aezA	0.43	5.72	0.109	0.780	model1_5aezA.pdb.gz
9	2nuuD	0.43	5.69	0.054	0.769	model1_2nuuD.pdb.gz
10	1ekmA3	0.42	5.66	0.060	0.736	model1_1ekmA3.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:0046914	0.55	transition metal ion binding
GO:0003824	0.55	catalytic 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:0044763	1.00	single-organism cellular process
GO:0006259	1.00	DNA metabolic process
GO:0097252	0.50	oligodendrocyte apoptotic process
GO:0090305	0.50	nucleic acid phosphodiester bond hydrolysis
GO:0090200	0.50	positive regulation of release of cytochrome c from mitochondria
GO:0032199	0.50	reverse transcription involved in RNA-mediated transposition
GO:0032197	0.50	transposition, RNA-mediated
GO:0030308	0.50	negative regulation of cell growth
GO:0007569	0.50	cell aging
GO:0007275	0.50	multicellular organism development
GO:0006289	0.50	nucleotide-excision repair
GO:0000733	0.50	DNA strand renaturation

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:0005739	1.00	mitochondrion
GO:0005737	1.00	cytoplasm
GO:0005730	1.00	nucleolus
GO:0005634	1.00	nucleus
GO:0016020	0.55	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	5r1rA	0.410	5.49	0.053	0.731	1.17.4.1	NA
2	0.060	3eifA	0.405	5.64	0.035	0.725	3.4.21.110	NA
3	0.060	3gpbA	0.402	5.44	0.057	0.692	2.4.1.1	NA
4	0.060	1l8aA	0.346	6.37	0.057	0.692	1.2.4.1	NA
5	0.060	2qllA	0.297	5.69	0.008	0.555	2.4.1.1	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:

Click to view	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	1peqA	0.401	5.80	0.054	0.753	0.26	TTP	complex1.pdb.gz	156,167,172,173

	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.