D-I-TASSER Q9NX09

D-I-TASSER results for Q9NX09

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Summary of the Protein

Uniprot ID: Q9NX09
Protein Name: DNA damage-inducible transcript 4 protein
Gene Name: DDIT4

Input Sequence in FASTA format

>Q9NX09 (232 residues)
MPSLWDRFSSSSTSSSPSSLPRTPTPDRPPRSAWGSATREEGFDRSTSLESSDCESLDSS
NSGFGPEEDTAYLDGVSLPDFELLSDPEDEHLCANLMQLLQESLAQARLGSRRPARLLMP
SQLVSQVGKELLRLAYSEPCGLRGALLDVCVEQGKSCHSVGQLALDPSLVPTFQLTLVLR
LDSRLWPKIQGLFSSANSPFLPGFSQSLTLSTGFRVIKKKLYSSEQLLIEEC

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	Q9NX09-D1	1-232	232		MPSLWDRFSSSSTSSSPSSLPRTPTPDRPPRSAWGSATREEGFDRSTSLESSDCESLDSSNSGFGPEEDTAYLDGVSLPDFELLSDPEDEHLCANLMQLLQESLAQARLGSRRPARLLMPSQLVSQVGKELLRLAYSEPCGLRGALLDVCVEQGKSCHSVGQLALDPSLVPTFQLTLVLRLDSRLWPKIQGLFSSANSPFLPGFSQSLTLSTGFRVIKKKLYSSEQLLIEEC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5993

(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	3lq9A	0.50	1.70	0.905	0.530	model1_3lq9A.pdb.gz
2	6cptA	0.46	5.69	0.084	0.776	model1_6cptA.pdb.gz
3	5mz9A	0.45	5.52	0.052	0.737	model1_5mz9A.pdb.gz
4	6rj1A	0.44	5.64	0.041	0.737	model1_6rj1A.pdb.gz
5	1peuA	0.43	5.88	0.072	0.750	model1_1peuA.pdb.gz
6	5kzwA	0.42	5.73	0.088	0.733	model1_5kzwA.pdb.gz
7	5wtjA1	0.42	5.42	0.061	0.668	model1_5wtjA1.pdb.gz
8	7lo5A	0.41	5.85	0.065	0.716	model1_7lo5A.pdb.gz
9	4i0oA	0.41	5.17	0.051	0.642	model1_4i0oA.pdb.gz
10	7d3uA	0.41	5.66	0.080	0.685	model1_7d3uA.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:0071889	0.79	14-3-3 protein 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:0044699	1.00	single-organism process
GO:0065007	0.96	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0009987	0.95	cellular process
GO:0050896	0.93	response to stimulus
GO:0044763	0.93	single-organism cellular process
GO:0009966	0.93	regulation of signal transduction
GO:0044767	0.92	single-organism developmental process
GO:0032006	0.92	regulation of TOR signaling
GO:0006950	0.92	response to stress
GO:0048519	0.90	negative regulation of biological process
GO:0048518	0.85	positive regulation of biological process
GO:0033554	0.85	cellular response to stress
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0048522	0.84	positive regulation of cellular process
GO:0031323	0.84	regulation of cellular metabolic process
GO:0006974	0.84	cellular response to DNA damage stimulus
GO:0048523	0.83	negative regulation of cellular process
GO:0032268	0.83	regulation of cellular protein metabolic process
GO:0048856	0.82	anatomical structure development
GO:0035556	0.82	intracellular signal transduction
GO:0032269	0.82	negative regulation of cellular protein metabolic process
GO:0010941	0.82	regulation of cell death
GO:0001932	0.82	regulation of protein phosphorylation
GO:1901216	0.81	positive regulation of neuron death
GO:0048011	0.81	neurotrophin TRK receptor signaling pathway
GO:0042771	0.81	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0033137	0.81	negative regulation of peptidyl-serine phosphorylation
GO:0032007	0.81	negative regulation of TOR signaling
GO:0030182	0.81	neuron differentiation
GO:0010801	0.81	negative regulation of peptidyl-threonine phosphorylation
GO:0008283	0.81	cell proliferation
GO:0007420	0.81	brain development
GO:0001764	0.81	neuron migration
GO:0001666	0.81	response to hypoxia

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:0005737	1.00	cytoplasm
GO:0044444	0.51	cytoplasmic part

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	1vlbA	0.383	5.65	0.063	0.659	1.2.99.7	140,225
2	0.060	1gz3A	0.394	5.60	0.037	0.659	1.1.1.38	NA
3	0.060	1a5kC	0.363	6.23	0.047	0.677	3.5.1.5	NA
4	0.060	2uv8G	0.391	5.97	0.046	0.690	2.3.1.86	NA
5	0.060	2boaA	0.385	5.95	0.031	0.668	3.4.17.-	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	1peqA	0.391	5.83	0.036	0.672	0.45	TTP	complex1.pdb.gz	99,119,127,128
2	0.01	1z2bC	0.391	6.23	0.048	0.703	0.56	VLB	complex2.pdb.gz	127,128,145,147,149
3	0.01	2bq1E	0.358	6.08	0.059	0.638	0.48	DGT	complex3.pdb.gz	132,143,147,148
4	0.01	1peoA	0.373	6.27	0.045	0.690	0.57	DCP	complex4.pdb.gz	95,129,142,143
5	0.01	1ggyB	0.402	5.28	0.029	0.642	0.45	YB	complex5.pdb.gz	143,145,164

	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.