D-I-TASSER Q9NQE9

D-I-TASSER results for Q9NQE9

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

Summary of the Protein

Uniprot ID: Q9NQE9
Protein Name: Histidine triad nucleotide-binding protein 3
Gene Name: HINT3

Input Sequence in FASTA format

>Q9NQE9 (182 residues)
MAEEQVNRSAGLAPDCEASATAETTVSSVGTCEAAGKSPEPKDYDSTCVFCRIAGRQDPG
TELLHCENEDLICFKDIKPAATHHYLVVPKKHIGNCRTLRKDQVELVENMVTVGKTILER
NNFTDFTNVRMGFHMPPFCSISHLHLHVLAPVDQLGFLSKLVYRVNSYWFITADHLIEKL
RT

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	Q9NQE9-D1	1-182	182		MAEEQVNRSAGLAPDCEASATAETTVSSVGTCEAAGKSPEPKDYDSTCVFCRIAGRQDPGTELLHCENEDLICFKDIKPAATHHYLVVPKKHIGNCRTLRKDQVELVENMVTVGKTILERNNFTDFTNVRMGFHMPPFCSISHLHLHVLAPVDQLGFLSKLVYRVNSYWFITADHLIEKLRT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7295

(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	5bv3A	0.70	3.28	0.110	0.863	model1_5bv3A.pdb.gz
2	1st0A	0.69	3.23	0.120	0.841	model1_1st0A.pdb.gz
3	6gbsA	0.69	3.08	0.087	0.852	model1_6gbsA.pdb.gz
4	4ndfA	0.61	2.50	0.252	0.709	model1_4ndfA.pdb.gz
5	3l7xA	0.58	2.76	0.166	0.676	model1_3l7xA.pdb.gz
6	3sp4A	0.58	3.13	0.165	0.714	model1_3sp4A.pdb.gz
7	3imiA	0.57	2.51	0.173	0.659	model1_3imiA.pdb.gz
8	3n1sA	0.56	2.04	0.209	0.621	model1_3n1sA.pdb.gz
9	4eguA	0.56	2.02	0.259	0.621	model1_4eguA.pdb.gz
10	1y23B	0.56	2.44	0.194	0.637	model1_1y23B.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	0.95	catalytic activity
GO:0016787	0.86	hydrolase activity
GO:0097159	0.74	organic cyclic compound binding
GO:1901363	0.73	heterocyclic compound binding
GO:0036094	0.66	small molecule binding
GO:0000166	0.63	nucleotide binding
GO:0043169	0.53	cation binding
GO:0019899	0.53	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:0071704	0.99	organic substance metabolic process
GO:0044238	0.99	primary metabolic process
GO:0009987	0.97	cellular process
GO:0044237	0.96	cellular metabolic process
GO:1901360	0.95	organic cyclic compound metabolic process
GO:0006807	0.95	nitrogen compound metabolic process
GO:0006139	0.94	nucleobase-containing compound metabolic process
GO:0044699	0.92	single-organism process
GO:0044710	0.91	single-organism metabolic process
GO:0044281	0.89	small molecule metabolic process
GO:0044763	0.87	single-organism cellular process
GO:0055086	0.82	nucleobase-containing small molecule metabolic process
GO:0006796	0.82	phosphate-containing compound metabolic process
GO:0009117	0.81	nucleotide metabolic process
GO:0065007	0.80	biological regulation
GO:1901564	0.78	organonitrogen compound metabolic process
GO:0072521	0.76	purine-containing compound metabolic process
GO:0050794	0.76	regulation of cellular process
GO:1901135	0.75	carbohydrate derivative metabolic process
GO:0006163	0.75	purine nucleotide metabolic process
GO:0007165	0.74	signal transduction
GO:0009056	0.73	catabolic process
GO:0009150	0.72	purine ribonucleotide metabolic process
GO:1901575	0.71	organic substance catabolic process
GO:0044712	0.70	single-organism catabolic process
GO:0035556	0.69	intracellular signal transduction
GO:0044248	0.67	cellular catabolic process
GO:0097193	0.66	intrinsic apoptotic signaling pathway
GO:0080090	0.66	regulation of primary metabolic process
GO:0072331	0.66	signal transduction by p53 class mediator
GO:0031323	0.66	regulation of cellular metabolic process
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0034655	0.65	nucleobase-containing compound catabolic process
GO:1901565	0.64	organonitrogen compound catabolic process
GO:1901136	0.64	carbohydrate derivative catabolic process
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0009166	0.63	nucleotide catabolic process
GO:2000112	0.62	regulation of cellular macromolecule biosynthetic process
GO:1903506	0.62	regulation of nucleic acid-templated transcription
GO:0010468	0.62	regulation of gene expression
GO:0009261	0.62	ribonucleotide catabolic process
GO:0006195	0.62	purine nucleotide catabolic process
GO:0048584	0.55	positive regulation of response to stimulus
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:0050848	0.50	regulation of calcium-mediated signaling

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	0.97	cell part
GO:0043227	0.93	membrane-bounded organelle
GO:0044424	0.90	intracellular part
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0044444	0.54	cytoplasmic part
GO:0005634	0.50	nucleus

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	0.066	2fitA	0.483	2.55	0.156	0.566	3.6.1.29	NA
2	0.060	1gaiA	0.446	5.40	0.045	0.780	3.2.1.3	105
3	0.060	1lf6A	0.447	5.38	0.047	0.802	3.2.1.3	NA
4	0.060	2d0vA	0.460	5.70	0.047	0.852	1.1.99.8	NA
5	0.060	1lrwC	0.454	5.59	0.030	0.830	1.1.99.8	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	0.22	1av5B	0.555	1.83	0.270	0.604	0.87	AP2	complex1.pdb.gz	50,74,75,76,77,78,86,145,147
2	0.18	3lb5A	0.544	1.92	0.202	0.610	1.11	UNL	complex2.pdb.gz	50,53,60,74,77
3	0.07	1guqC	0.533	3.74	0.092	0.714	0.86	GUD	complex3.pdb.gz	49,50,58,74,76,77,132,134,138,139,140,147,149
4	0.04	3llj0	0.559	2.01	0.257	0.610	1.06	III	complex4.pdb.gz	80,96,97,99,100,101,104,105,108,109,112,115,128,129,130,131,132,133,134,135,137,147
5	0.03	2eo40	0.517	2.20	0.191	0.582	0.93	III	complex5.pdb.gz	96,97,99,104,105,108,109,112,115,129,130,131,132,133,135,137,138

	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.