D-I-TASSER Q9P2X3

D-I-TASSER results for Q9P2X3

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

Summary of the Protein

Uniprot ID: Q9P2X3
Protein Name: Protein IMPACT
Gene Name: IMPACT

Input Sequence in FASTA format

>Q9P2X3 (320 residues)
MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPN
EYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMT
EPGPDVKKKTEEEDVECEDDLILACQPESSLKALDFDISETRTEVEVEELPPIDHGIPIT
DRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCEDDG
ETAAGGRLLHLMEILNVKNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKNYTNSPEE
SSKALGKNKKVRKDKKRNEH

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 AttentionPotential. 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	Q9P2X3-D1	1-127	127		MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPNEYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMTEPGPDVK
2	Q9P2X3-D2	128-320	193		KKTEEEDVECEDDLILACQPESSLKALDFDISETRTEVEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKNYTNSPEESSKALGKNKKVRKDKKRNEH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.57

(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 AttentionPotential, 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	3zyvA	0.43	6.24	0.040	0.703	model1_3zyvA.pdb.gz
2	5nz7A	0.42	6.69	0.047	0.734	model1_5nz7A.pdb.gz
3	2cqtA	0.42	6.72	0.047	0.725	model1_2cqtA.pdb.gz
4	3qdeA	0.41	6.95	0.024	0.722	model1_3qdeA.pdb.gz
5	5w21A	0.41	6.62	0.030	0.694	model1_5w21A.pdb.gz
6	6z2wE	0.41	6.38	0.046	0.684	model1_6z2wE.pdb.gz
7	3s9vA	0.40	5.91	0.061	0.619	model1_3s9vA.pdb.gz
8	1kc7A	0.40	6.70	0.048	0.691	model1_1kc7A.pdb.gz
9	3p5pA	0.40	6.06	0.064	0.644	model1_3p5pA.pdb.gz
10	4mz0A	0.40	6.57	0.055	0.678	model1_4mz0A.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:0003824	0.81	catalytic activity
GO:0016740	0.73	transferase activity
GO:0061630	0.69	ubiquitin protein ligase activity
GO:0019899	0.64	enzyme binding
GO:0031624	0.63	ubiquitin conjugating enzyme 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	0.98	cellular process
GO:0080090	0.91	regulation of primary metabolic process
GO:0060255	0.91	regulation of macromolecule metabolic process
GO:0031323	0.91	regulation of cellular metabolic process
GO:0032268	0.90	regulation of cellular protein metabolic process
GO:0048518	0.88	positive regulation of biological process
GO:0031325	0.87	positive regulation of cellular metabolic process
GO:0010604	0.87	positive regulation of macromolecule metabolic process
GO:0032270	0.86	positive regulation of cellular protein metabolic process
GO:0044699	0.85	single-organism process
GO:0044763	0.80	single-organism cellular process
GO:0048523	0.77	negative regulation of cellular process
GO:0006950	0.76	response to stress
GO:0042221	0.75	response to chemical
GO:0034198	0.75	cellular response to amino acid starvation
GO:0010941	0.75	regulation of cell death
GO:0072755	0.74	cellular response to benomyl
GO:0071468	0.74	cellular response to acidic pH
GO:0070301	0.74	cellular response to hydrogen peroxide
GO:0060548	0.74	negative regulation of cell death
GO:2000112	0.72	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.72	regulation of nitrogen compound metabolic process
GO:0010468	0.72	regulation of gene expression
GO:0048583	0.71	regulation of response to stimulus
GO:0006417	0.71	regulation of translation
GO:0044767	0.70	single-organism developmental process
GO:0080134	0.68	regulation of response to stress
GO:0051128	0.68	regulation of cellular component organization
GO:0043555	0.68	regulation of translation in response to stress
GO:0031399	0.68	regulation of protein modification process
GO:0031324	0.68	negative regulation of cellular metabolic process
GO:0019220	0.68	regulation of phosphate metabolic process
GO:0010605	0.68	negative regulation of macromolecule metabolic process
GO:0060733	0.67	regulation of eIF2 alpha phosphorylation by amino acid starvation
GO:0051239	0.67	regulation of multicellular organismal process
GO:0031333	0.67	negative regulation of protein complex assembly
GO:0001933	0.67	negative regulation of protein phosphorylation
GO:2000026	0.66	regulation of multicellular organismal development
GO:0051240	0.66	positive regulation of multicellular organismal process
GO:0051173	0.66	positive regulation of nitrogen compound metabolic process
GO:0031328	0.66	positive regulation of cellular biosynthetic process
GO:0010628	0.66	positive regulation of gene expression
GO:0010557	0.66	positive regulation of macromolecule biosynthetic process
GO:0006355	0.66	regulation of transcription, DNA-templated
GO:1990253	0.65	cellular response to leucine starvation
GO:1990138	0.65	neuron projection extension
GO:0097201	0.65	negative regulation of transcription from RNA polymerase II promoter in response to stress
GO:0071494	0.65	cellular response to UV-C
GO:0071264	0.65	positive regulation of translational initiation in response to starvation
GO:0045666	0.65	positive regulation of neuron differentiation
GO:0042149	0.65	cellular response to glucose starvation
GO:0031953	0.65	negative regulation of protein autophosphorylation

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:0044424	1.00	intracellular part
GO:0032991	0.99	macromolecular complex
GO:0030529	0.76	intracellular ribonucleoprotein complex
GO:0005844	0.75	polysome

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	2vdcF	0.329	6.79	0.028	0.581	1.4.1.13	NA
2	0.060	2eabA	0.360	6.15	0.034	0.569	3.2.1.63	NA
3	0.060	1h54B	0.377	6.95	0.034	0.666	2.4.1.8	NA
4	0.060	2vdcA	0.384	6.29	0.076	0.634	1.4.1.13	NA
5	0.060	2x58A	0.354	6.54	0.037	0.597	5.3.3.8 4.2.1.17 1.1.1.35	281

	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	3fahA	0.381	6.46	0.030	0.622	0.52	GOL	complex1.pdb.gz	270,271,272,274
2	0.01	1dgjA	0.386	6.61	0.034	0.634	0.40	FES	complex2.pdb.gz	239,240,241,244,265,266
3	0.01	2vdcA	0.384	6.29	0.076	0.634	0.63	F3S	complex3.pdb.gz	236,237,239,240,243

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.