D-I-TASSER Q8N907

D-I-TASSER results for Q8N907

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

Summary of the Protein

Uniprot ID: Q8N907
Protein Name: DAN domain family member 5
Gene Name: DAND5

Input Sequence in FASTA format

>Q8N907 (189 residues)
MLLGQLSTLLCLLSGALPTGSGRPEPQSPRPQSWAAANQTWALGPGALPPLVPASALGSW
KAFLGLQKARQLGMGRLQRGQDEVAAVTLPLNPQEVIQGMCKAVPFVQVFSRPGCSAIRL
RNHLCFGHCSSLYIPGSDPTPLVLCNSCMPARKRWAPVVLWCLTGSSASRRRVKISTMLI
EGCHCSPKA

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	Q8N907-D1	1-189	189		MLLGQLSTLLCLLSGALPTGSGRPEPQSPRPQSWAAANQTWALGPGALPPLVPASALGSWKAFLGLQKARQLGMGRLQRGQDEVAAVTLPLNPQEVIQGMCKAVPFVQVFSRPGCSAIRLRNHLCFGHCSSLYIPGSDPTPLVLCNSCMPARKRWAPVVLWCLTGSSASRRRVKISTMLIEGCHCSPKA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5843

(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	4hmcA	0.43	5.36	0.068	0.725	model1_4hmcA.pdb.gz
2	5m45A	0.43	5.38	0.043	0.730	model1_5m45A.pdb.gz
3	5l9wA	0.42	5.62	0.022	0.751	model1_5l9wA.pdb.gz
4	6q55A	0.42	5.48	0.082	0.720	model1_6q55A.pdb.gz
5	5nd1A	0.42	5.57	0.089	0.730	model1_5nd1A.pdb.gz
6	6yraB1	0.42	5.17	0.062	0.688	model1_6yraB1.pdb.gz
7	2zt6A	0.41	4.96	0.055	0.682	model1_2zt6A.pdb.gz
8	3ebvA	0.40	5.64	0.069	0.682	model1_3ebvA.pdb.gz
9	2i4nB	0.37	5.03	0.022	0.598	model1_2i4nB.pdb.gz
10	1nj1A1	0.36	5.42	0.045	0.619	model1_1nj1A1.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:0016015	0.93	morphogen 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:0044699	0.99	single-organism process
GO:0050794	0.98	regulation of cellular process
GO:0080090	0.96	regulation of primary metabolic process
GO:0060255	0.96	regulation of macromolecule metabolic process
GO:0031323	0.96	regulation of cellular metabolic process
GO:0006357	0.95	regulation of transcription from RNA polymerase II promoter
GO:0048523	0.94	negative regulation of cellular process
GO:0048583	0.93	regulation of response to stimulus
GO:0090101	0.92	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0050793	0.92	regulation of developmental process
GO:0032501	0.92	multicellular organismal process
GO:2000026	0.91	regulation of multicellular organismal development
GO:0007389	0.91	pattern specification process
GO:0007165	0.90	signal transduction
GO:0030514	0.89	negative regulation of BMP signaling pathway
GO:1900116	0.86	extracellular negative regulation of signal transduction
GO:0051093	0.86	negative regulation of developmental process
GO:0051241	0.85	negative regulation of multicellular organismal process
GO:1900107	0.84	regulation of nodal signaling pathway
GO:0035582	0.84	sequestering of BMP in extracellular matrix
GO:0032926	0.84	negative regulation of activin receptor signaling pathway
GO:1900145	0.83	regulation of nodal signaling pathway involved in determination of left/right asymmetry
GO:2000381	0.82	negative regulation of mesoderm development
GO:1900108	0.82	negative regulation of nodal signaling pathway
GO:0007368	0.82	determination of left/right symmetry
GO:1900146	0.81	negative regulation of nodal signaling pathway involved in determination of left/right asymmetry
GO:1900176	0.80	negative regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry
GO:0023019	0.80	signal transduction involved in regulation of gene expression
GO:0061371	0.79	determination of heart left/right asymmetry

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:0005615	0.99	extracellular space
GO:0044464	0.74	cell part
GO:0044424	0.57	intracellular 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	2ze9A	0.407	5.38	0.054	0.725	3.1.4.4	NA
2	0.060	1wcgA	0.399	5.55	0.025	0.698	3.2.1.147	NA
3	0.060	2pffD	0.386	6.02	0.033	0.746	2.3.1.86	NA
4	0.060	1hqfA	0.312	5.62	0.066	0.561	3.5.3.1	181
5	0.060	3gmzA	0.405	4.92	0.032	0.645	3.5.3.1	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	3gmzA	0.405	4.92	0.032	0.645	0.42	ORN	complex1.pdb.gz	98,100,127

	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.