D-I-TASSER Q9ULZ2

D-I-TASSER results for Q9ULZ2

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

Summary of the Protein

Uniprot ID: Q9ULZ2
Protein Name: Signal-transducing adaptor protein 1
Gene Name: STAP1

Input Sequence in FASTA format

>Q9ULZ2 (295 residues)
MMAKKPPKPAPRRIFQERLKITALPLYFEGFLLIKRSGYREYEHYWTELRGTTLFFYTDK
KSIIYVDKLDIVDLTCLTEQNSTEKNCAKFTLVLPKEEVQLKTENTESGEEWRGFILTVT
ELSVPQNVSLLPGQVIKLHEVLEREKKRRIETEQSTSVEKEKEPTEDYVDVLNPMPACFY
TVSRKEATEMLQKNPSLGNMILRPGSDSRNYSITIRQEIDIPRIKHYKVMSVGQNYTIEL
EKPVTLPNLFSVIDYFVKETRGNLRPFICSTDENTGQEPSMEGRSEKLKKNPHIA

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	Q9ULZ2-D1	1-295	295		MMAKKPPKPAPRRIFQERLKITALPLYFEGFLLIKRSGYREYEHYWTELRGTTLFFYTDKKSIIYVDKLDIVDLTCLTEQNSTEKNCAKFTLVLPKEEVQLKTENTESGEEWRGFILTVTELSVPQNVSLLPGQVIKLHEVLEREKKRRIETEQSTSVEKEKEPTEDYVDVLNPMPACFYTVSRKEATEMLQKNPSLGNMILRPGSDSRNYSITIRQEIDIPRIKHYKVMSVGQNYTIELEKPVTLPNLFSVIDYFVKETRGNLRPFICSTDENTGQEPSMEGRSEKLKKNPHIA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5036

(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	4po6A	0.59	3.72	0.073	0.705	model1_4po6A.pdb.gz
2	4z32A	0.57	3.13	0.117	0.675	model1_4z32A.pdb.gz
3	5ixdA	0.53	3.24	0.083	0.624	model1_5ixdA.pdb.gz
4	5u1sA	0.45	6.03	0.047	0.746	model1_5u1sA.pdb.gz
5	7ctpA	0.43	5.27	0.063	0.597	model1_7ctpA.pdb.gz
6	5jp0A	0.43	6.18	0.052	0.702	model1_5jp0A.pdb.gz
7	3iujA	0.43	5.61	0.025	0.647	model1_3iujA.pdb.gz
8	1h2xA	0.43	5.51	0.079	0.641	model1_1h2xA.pdb.gz
9	6vr4A	0.42	6.15	0.041	0.698	model1_6vr4A.pdb.gz
10	1yr2A	0.42	6.01	0.041	0.678	model1_1yr2A.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:0005102	0.69	receptor binding
GO:0004871	0.69	signal transducer activity
GO:0005068	0.64	transmembrane receptor protein tyrosine kinase adaptor activity
GO:0005070	0.63	SH3/SH2 adaptor activity
GO:0001784	0.63	phosphotyrosine 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:0050794	0.98	regulation of cellular process
GO:0009987	0.91	cellular process
GO:0007165	0.88	signal transduction
GO:0048522	0.85	positive regulation of cellular process
GO:0080090	0.84	regulation of primary metabolic process
GO:0031325	0.84	positive regulation of cellular metabolic process
GO:0010604	0.84	positive regulation of macromolecule metabolic process
GO:0050731	0.83	positive regulation of peptidyl-tyrosine phosphorylation
GO:0009967	0.83	positive regulation of signal transduction
GO:0050896	0.82	response to stimulus
GO:0007166	0.79	cell surface receptor signaling pathway
GO:0010033	0.78	response to organic substance
GO:0007169	0.77	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0048519	0.73	negative regulation of biological process
GO:0051128	0.72	regulation of cellular component organization
GO:0051049	0.72	regulation of transport
GO:0048585	0.72	negative regulation of response to stimulus
GO:0048523	0.72	negative regulation of cellular process
GO:0010468	0.72	regulation of gene expression
GO:0060627	0.71	regulation of vesicle-mediated transport
GO:0051130	0.71	positive regulation of cellular component organization
GO:0050776	0.71	regulation of immune response
GO:0031344	0.71	regulation of cell projection organization
GO:0031324	0.71	negative regulation of cellular metabolic process
GO:0010628	0.71	positive regulation of gene expression
GO:0009968	0.71	negative regulation of signal transduction
GO:0002694	0.71	regulation of leukocyte activation
GO:0002684	0.71	positive regulation of immune system process
GO:0002683	0.71	negative regulation of immune system process
GO:2000251	0.70	positive regulation of actin cytoskeleton reorganization
GO:1904151	0.70	positive regulation of microglial cell mediated cytotoxicity
GO:1903997	0.70	positive regulation of non-membrane spanning protein tyrosine kinase activity
GO:1903980	0.70	positive regulation of microglial cell activation
GO:1902227	0.70	negative regulation of macrophage colony-stimulating factor signaling pathway
GO:1900028	0.70	negative regulation of ruffle assembly
GO:0071222	0.70	cellular response to lipopolysaccharide
GO:0060100	0.70	positive regulation of phagocytosis, engulfment
GO:0050861	0.70	positive regulation of B cell receptor signaling pathway
GO:0042326	0.70	negative regulation of phosphorylation
GO:0010760	0.70	negative regulation of macrophage chemotaxis
GO:0044699	0.56	single-organism process
GO:0044763	0.54	single-organism cellular process

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	1.00	cell part
GO:0044424	0.94	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005737	0.75	cytoplasm
GO:0005634	0.73	nucleus
GO:0043234	0.66	protein complex
GO:0005739	0.63	mitochondrion
GO:0016020	0.51	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	1yr2A	0.424	6.01	0.041	0.678	3.4.21.26	NA
2	0.060	1qo9A	0.380	6.25	0.056	0.634	3.1.1.7	NA
3	0.060	2agsA	0.384	6.23	0.062	0.647	3.2.1.18	230
4	0.060	2b4kA	0.364	6.55	0.032	0.641	3.1.1.43	NA
5	0.060	3cf4A	0.382	6.17	0.033	0.634	1.2.99.2	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	3ai7E	0.408	6.38	0.031	0.692	0.16	TPP	complex1.pdb.gz	191,198,258
2	0.01	3ai7A	0.402	6.30	0.028	0.678	0.14	TPP	complex2.pdb.gz	195,196,215
3	0.01	2hu5A	0.329	6.22	0.054	0.546	0.17	UUU	complex3.pdb.gz	196,257,260
4	0.01	3aheA	0.406	6.39	0.049	0.692	0.16	THD	complex4.pdb.gz	196,197,198
5	0.01	2x2iA	0.403	6.23	0.043	0.678	0.23	QPS	complex5.pdb.gz	190,203,212
6	0.01	2w76B	0.322	6.37	0.045	0.542	0.27	PVE	complex6.pdb.gz	28,47,52
7	0.01	2iahA	0.302	6.64	0.059	0.539	0.39	PVE	complex7.pdb.gz	205,209,212,226

	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.