D-I-TASSER Q96D03

D-I-TASSER results for Q96D03

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Summary of the Protein

Uniprot ID: Q96D03
Protein Name: DNA damage-inducible transcript 4-like protein
Gene Name: DDIT4L

Input Sequence in FASTA format

>Q96D03 (193 residues)
MVATGSLSSKNPASISELLDCGYHPESLLSDFDYWDYVVPEPNLNEVIFEESTCQNLVKM
LENCLSKSKQTKLGCSKVLVPEKLTQRIAQDVLRLSSTEPCGLRGCVMHVNLEIENVCKK
LDRIVCDSSVVPTFELTLVFKQENCSWTSFRDFFFSRGRFSSGFRRTLILSSGFRLVKKK
LYSLIGTTVIEGS

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	Q96D03-D1	1-193	193		MVATGSLSSKNPASISELLDCGYHPESLLSDFDYWDYVVPEPNLNEVIFEESTCQNLVKMLENCLSKSKQTKLGCSKVLVPEKLTQRIAQDVLRLSSTEPCGLRGCVMHVNLEIENVCKKLDRIVCDSSVVPTFELTLVFKQENCSWTSFRDFFFSRGRFSSGFRRTLILSSGFRLVKKKLYSLIGTTVIEGS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.68

(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	0.59	2.09	0.349	0.648	model1_3lq9A.pdb.gz
2	3kdpA	0.47	5.32	0.076	0.793	model1_3kdpA.pdb.gz
3	2veoA	0.46	5.20	0.077	0.772	model1_2veoA.pdb.gz
4	1tubA	0.45	5.78	0.059	0.829	model1_1tubA.pdb.gz
5	3ixzA	0.45	5.58	0.055	0.808	model1_3ixzA.pdb.gz
6	2nuuD	0.44	4.89	0.042	0.689	model1_2nuuD.pdb.gz
7	3b8cA2	0.44	5.20	0.079	0.710	model1_3b8cA2.pdb.gz
8	3b9zA	0.43	4.92	0.052	0.663	model1_3b9zA.pdb.gz
9	1mhsA3	0.40	5.54	0.032	0.668	model1_1mhsA3.pdb.gz
10	4hxeB2	0.37	5.48	0.025	0.653	model1_4hxeB2.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:1901363	0.34	heterocyclic compound binding
GO:0097159	0.34	organic cyclic compound 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:0050794	0.95	regulation of cellular process
GO:0009987	0.95	cellular process
GO:0044763	0.93	single-organism cellular process
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	0.85	negative regulation of biological process
GO:0006974	0.77	cellular response to DNA damage stimulus
GO:0048522	0.75	positive regulation of cellular process
GO:0080090	0.73	regulation of primary metabolic process
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0031323	0.73	regulation of cellular metabolic process
GO:0007165	0.73	signal transduction
GO:0048856	0.72	anatomical structure development
GO:0048523	0.72	negative regulation of cellular process
GO:0032268	0.72	regulation of cellular protein metabolic process
GO:1902532	0.71	negative regulation of intracellular signal transduction
GO:0048869	0.71	cellular developmental process
GO:0048513	0.71	animal organ development
GO:0035556	0.71	intracellular signal transduction
GO:0010942	0.71	positive regulation of cell death
GO:0007166	0.71	cell surface receptor signaling pathway
GO:0001932	0.71	regulation of protein phosphorylation
GO:1901214	0.70	regulation of neuron death
GO:0072332	0.70	intrinsic apoptotic signaling pathway by p53 class mediator
GO:0038179	0.70	neurotrophin signaling pathway
GO:0036293	0.70	response to decreased oxygen levels
GO:0033135	0.70	regulation of peptidyl-serine phosphorylation
GO:0030154	0.70	cell differentiation
GO:0016477	0.70	cell migration
GO:0010799	0.70	regulation of peptidyl-threonine phosphorylation
GO:0008630	0.70	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0007169	0.70	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0001933	0.70	negative regulation of protein phosphorylation
GO:0032007	0.55	negative regulation of TOR signaling
GO:0007420	0.55	brain development
GO:1901216	0.54	positive regulation of neuron death
GO:0048011	0.54	neurotrophin TRK receptor signaling pathway
GO:0042771	0.54	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0033137	0.54	negative regulation of peptidyl-serine phosphorylation
GO:0030182	0.54	neuron differentiation
GO:0010801	0.54	negative regulation of peptidyl-threonine phosphorylation
GO:0008283	0.54	cell proliferation
GO:0001764	0.54	neuron migration
GO:0001666	0.54	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

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	1cg2A	0.410	5.26	0.052	0.689	3.4.17.11	NA
2	0.060	2et6A	0.404	5.18	0.047	0.684	1.1.1.-	NA
3	0.060	3b8eA	0.457	5.46	0.070	0.803	3.6.3.9	NA
4	0.060	3b8cB	0.438	5.16	0.080	0.705	3.6.3.6	88
5	0.060	3ce6A	0.414	4.88	0.068	0.648	3.3.1.1	92,105

	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	2agvA	0.440	5.43	0.055	0.782	0.25	BHQ	complex1.pdb.gz	99,101,105
2	0.01	1ia0A	0.452	5.78	0.053	0.829	0.15	GTP	complex2.pdb.gz	35,92,102,105,106
3	0.01	3fpbA	0.438	5.34	0.061	0.767	0.21	CZA	complex3.pdb.gz	92,103,106
4	0.01	2c88A	0.433	5.38	0.056	0.741	0.18	ACP	complex4.pdb.gz	132,133,134,181
5	0.01	2by4A	0.436	5.44	0.049	0.772	0.12	AD4	complex5.pdb.gz	35,37,38,41,42,93,97
6	0.01	3b8eC	0.459	5.42	0.058	0.803	0.11	III	complex6.pdb.gz	82,85,89,105
7	0.01	1ffxC	0.449	5.52	0.042	0.793	0.14	GTP	complex7.pdb.gz	92,96,102,104
8	0.01	2agvB	0.440	5.43	0.055	0.782	0.16	BHQ	complex8.pdb.gz	36,38,42,103,106
9	0.01	3hkbA	0.447	5.76	0.036	0.819	0.13	GTP	complex9.pdb.gz	25,26,27,28,105
10	0.01	2yfyA	0.433	5.58	0.041	0.772	0.26	9TN	complex10.pdb.gz	53,56,57,60,105

	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.