D-I-TASSER Q6PIZ9

D-I-TASSER results for Q6PIZ9

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

Summary of the Protein

Uniprot ID: Q6PIZ9
Protein Name: T-cell receptor-associated transmembrane adapter 1
Gene Name: TRAT1

Input Sequence in FASTA format

>Q6PIZ9 (186 residues)
MSGISGCPFFLWGLLALLGLALVISLIFNISHYVEKQRQDKMYSYSSDHTRVDEYYIEDT
PIYGNLDDMISEPMDENCYEQMKARPEKSVNKMQEATPSAQATNETQMCYASLDHSVKGK
RRKPRKQNTHFSDKDGDEQLHAIDASVSKTTLVDSFSPESQAVEENIHDDPIRLFGLIRA
KREPIN

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	Q6PIZ9-D1	1-186	186		MSGISGCPFFLWGLLALLGLALVISLIFNISHYVEKQRQDKMYSYSSDHTRVDEYYIEDTPIYGNLDDMISEPMDENCYEQMKARPEKSVNKMQEATPSAQATNETQMCYASLDHSVKGKRRKPRKQNTHFSDKDGDEQLHAIDASVSKTTLVDSFSPESQAVEENIHDDPIRLFGLIRAKREPIN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4053

(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	1jqkA	0.49	4.89	0.042	0.801	model1_1jqkA.pdb.gz
2	6t7jB	0.49	4.90	0.056	0.774	model1_6t7jB.pdb.gz
3	6yttB	0.49	5.02	0.043	0.780	model1_6yttB.pdb.gz
4	3i04A2	0.48	4.79	0.032	0.774	model1_3i04A2.pdb.gz
5	7by5A	0.47	5.12	0.077	0.780	model1_7by5A.pdb.gz
6	1st6A	0.47	5.30	0.044	0.801	model1_1st6A.pdb.gz
7	3qdeA	0.46	5.28	0.070	0.796	model1_3qdeA.pdb.gz
8	1f31A	0.46	4.96	0.059	0.769	model1_1f31A.pdb.gz
9	5n0bA1	0.46	4.82	0.066	0.747	model1_5n0bA1.pdb.gz
10	6ar6A	0.46	5.41	0.036	0.796	model1_6ar6A.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:0019900	1.00	kinase binding
GO:0003824	0.88	catalytic activity
GO:0016740	0.86	transferase activity
GO:0035004	0.85	phosphatidylinositol 3-kinase activity
GO:0016773	0.85	phosphotransferase activity, alcohol group as acceptor
GO:0005068	0.85	transmembrane receptor protein tyrosine kinase adaptor activity
GO:0046934	0.84	phosphatidylinositol-4,5-bisphosphate 3-kinase 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:0050794	1.00	regulation of cellular process
GO:0002682	1.00	regulation of immune system process
GO:0060255	0.92	regulation of macromolecule metabolic process
GO:0048518	0.92	positive regulation of biological process
GO:0031323	0.92	regulation of cellular metabolic process
GO:1902533	0.91	positive regulation of intracellular signal transduction
GO:0050776	0.91	regulation of immune response
GO:0031324	0.91	negative regulation of cellular metabolic process
GO:0010605	0.91	negative regulation of macromolecule metabolic process
GO:0002684	0.91	positive regulation of immune system process
GO:0051051	0.90	negative regulation of transport
GO:0050862	0.90	positive regulation of T cell receptor signaling pathway
GO:0050850	0.90	positive regulation of calcium-mediated signaling
GO:0001920	0.90	negative regulation of receptor recycling
GO:0007165	0.68	signal transduction
GO:0002376	0.58	immune system process
GO:0050896	0.57	response to stimulus
GO:0007166	0.56	cell surface receptor signaling pathway
GO:0006950	0.55	response to stress
GO:0035556	0.54	intracellular signal transduction
GO:0006952	0.54	defense response
GO:0002768	0.54	immune response-regulating cell surface receptor signaling pathway
GO:0002757	0.54	immune response-activating signal transduction
GO:0050852	0.53	T cell receptor signaling pathway
GO:0048015	0.53	phosphatidylinositol-mediated signaling
GO:0014066	0.53	regulation of phosphatidylinositol 3-kinase signaling
GO:0006968	0.53	cellular defense response

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:0005886	1.00	plasma membrane
GO:0032991	0.92	macromolecular complex
GO:0044459	0.91	plasma membrane part
GO:0043234	0.91	protein complex
GO:0042101	0.90	T cell receptor complex
GO:0044424	0.69	intracellular part
GO:0016021	0.55	integral component of membrane
GO:0005887	0.54	integral component of plasma 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	2vycA	0.415	4.53	0.045	0.634	4.1.1.19	NA
2	0.060	1z7hA	0.445	5.15	0.053	0.753	3.4.24.68	NA
3	0.060	3debA	0.444	5.00	0.033	0.742	3.4.24.69	NA
4	0.060	3n2oA	0.420	5.61	0.049	0.737	4.1.1.19	116,159,164
5	0.060	1g6tA	0.429	5.84	0.028	0.801	2.5.1.19	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	1i1eA	0.468	4.91	0.066	0.763	0.45	DM2	complex1.pdb.gz	65,119,124,125

	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.