D-I-TASSER Q9HD47

D-I-TASSER results for Q9HD47

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

Summary of the Protein

Uniprot ID: Q9HD47
Protein Name: Ran guanine nucleotide release factor
Gene Name: RANGRF

Input Sequence in FASTA format

>Q9HD47 (186 residues)
MEPTRDCPLFGGAFSAILPMGAIDVSDLRPVPDNQEVFCHPVTDQSLIVELLELQAHVRG
EAAARYHFEDVGGVQGARAVHVESVQPLSLENLALRGRCQEAWVLSGKQQIAKENQQVAK
DVTLHQALLRLPQYQTDLLLTFNQPPPDNRSSLGPENLSPAPWSLGDFEQLVTSLTLHDP
NIFGPQ

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	Q9HD47-D1	1-186	186		MEPTRDCPLFGGAFSAILPMGAIDVSDLRPVPDNQEVFCHPVTDQSLIVELLELQAHVRGEAAARYHFEDVGGVQGARAVHVESVQPLSLENLALRGRCQEAWVLSGKQQIAKENQQVAKDVTLHQALLRLPQYQTDLLLTFNQPPPDNRSSLGPENLSPAPWSLGDFEQLVTSLTLHDPNIFGPQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8653

(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	5yfgA	0.86	2.54	0.956	0.979	model1_5yfgA.pdb.gz
2	1jhsA	0.79	3.04	0.253	0.935	model1_1jhsA.pdb.gz
3	5zx9A	0.65	2.91	0.107	0.801	model1_5zx9A.pdb.gz
4	2xb3A	0.65	2.66	0.102	0.790	model1_2xb3A.pdb.gz
5	4rthA	0.63	3.17	0.060	0.806	model1_4rthA.pdb.gz
6	3jcuP	0.63	3.07	0.081	0.801	model1_3jcuP.pdb.gz
7	6kacP	0.63	3.18	0.060	0.812	model1_6kacP.pdb.gz
8	1v2bB	0.62	2.86	0.070	0.763	model1_1v2bB.pdb.gz
9	2lnjA	0.62	3.10	0.101	0.790	model1_2lnjA.pdb.gz
10	6e5dA	0.60	2.86	0.125	0.731	model1_6e5dA.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:0008536	1.00	Ran GTPase binding
GO:0005215	0.80	transporter activity
GO:0098772	0.79	molecular function regulator
GO:0022892	0.79	substrate-specific transporter activity
GO:0005087	0.78	Ran guanyl-nucleotide exchange factor activity
GO:0044325	0.77	ion channel binding
GO:0017080	0.77	sodium channel regulator activity
GO:0008565	0.77	protein transporter 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:0071702	1.00	organic substance transport
GO:0046907	1.00	intracellular transport
GO:0015031	0.89	protein transport
GO:0006886	0.88	intracellular protein transport
GO:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0065008	0.78	regulation of biological quality
GO:0048522	0.78	positive regulation of cellular process
GO:0048193	0.78	Golgi vesicle transport
GO:2000649	0.77	regulation of sodium ion transmembrane transporter activity
GO:0060341	0.77	regulation of cellular localization
GO:0003254	0.77	regulation of membrane depolarization
GO:2000010	0.76	positive regulation of protein localization to cell surface
GO:0090004	0.76	positive regulation of establishment of protein localization to plasma membrane
GO:0032527	0.76	protein exit from endoplasmic reticulum
GO:0006888	0.76	ER to Golgi vesicle-mediated transport
GO:0006913	0.62	nucleocytoplasmic transport

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:0005634	1.00	nucleus
GO:0044444	0.93	cytoplasmic part
GO:0005737	0.80	cytoplasm
GO:0044446	0.78	intracellular organelle part
GO:0016020	0.74	membrane
GO:0044428	0.73	nuclear part
GO:0044425	0.72	membrane part
GO:0044459	0.70	plasma membrane part
GO:0014704	0.68	intercalated disc
GO:0005901	0.68	caveola
GO:0005791	0.68	rough endoplasmic reticulum
GO:0005654	0.68	nucleoplasm

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	0.429	5.84	0.052	0.790	1.2.99.7	NA
2	0.060	1eqrA	0.447	4.35	0.039	0.650	6.1.1.12	NA
3	0.060	12asA	0.451	4.59	0.039	0.672	6.3.1.1	45
4	0.060	3b9jC	0.442	5.44	0.057	0.769	1.17.3.2 1.17.1.4	NA
5	0.060	1rp5A	0.443	5.13	0.037	0.737	3.4.-.-	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	0.02	1tu10	0.540	3.09	0.109	0.661	0.53	III	complex1.pdb.gz	34,35,36,37,38,39,40,49,129,140,164,167,173,174
2	0.01	3eubS	0.274	5.45	0.034	0.462	0.58	FES	complex2.pdb.gz	10,11,12,14
3	0.01	2ckjD	0.451	5.38	0.034	0.785	0.45	FES	complex3.pdb.gz	72,73,74,76
4	0.01	2ckjC	0.450	5.31	0.040	0.780	0.54	FES	complex4.pdb.gz	69,73,75,76,78,80

	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.