D-I-TASSER Q6ZR37

D-I-TASSER results for Q6ZR37

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

Summary of the Protein

Uniprot ID: Q6ZR37
Protein Name: Pleckstrin homology domain-containing family G member 7
Gene Name: PLEKHG7

Input Sequence in FASTA format

>Q6ZR37 (379 residues)
MIFMNTLRYLQTHEYLLDVDLWRLFANLEELTQTSLGFVNSLFGIIKDYVDASEISSSLD
FISVLTKYFRGSLCQSHQTYCLNYSAAIFYLESLRQRDDFGIYLKWCEQNEQCRRLHVPE
LLVAPLQRLTRYPLLLKNIWKRSMDSAEKIMIYSIKEKVEKSIRDLEGKVKWLDNFQKFR
YLQEIIVWPPLWDRDKRFFIPECLKHIFKEHMAENILSPTSRHLLYEGKLTLAESTRFLD
VYLFLFNDFLLVTKTKCNKKKLGGSDPGLMCPSLTPELQAVIKEGGSCTVLDQPIPLDRL
VVKSIEPLHVSVFGLRNAFLIQHENRYRQCIAAFLLQAQTENIKKTWMAQITTAISCFTK
SQETKKISLFTLPAESSEI

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	Q6ZR37-D1	1-168	168		MIFMNTLRYLQTHEYLLDVDLWRLFANLEELTQTSLGFVNSLFGIIKDYVDASEISSSLDFISVLTKYFRGSLCQSHQTYCLNYSAAIFYLESLRQRDDFGIYLKWCEQNEQCRRLHVPELLVAPLQRLTRYPLLLKNIWKRSMDSAEKIMIYSIKEKVEKSIRDLEG
2	Q6ZR37-D2	169-379	211		KVKWLDNFQKFRYLQEIIVWPPLWDRDKRFFIPECLKHIFKEHMAENILSPTSRHLLYEGKLTLAESTRFLDVYLFLFNDFLLVTKTKCNKKKLGGSDPGLMCPSLTPELQAVIKEGGSCTVLDQPIPLDRLVVKSIEPLHVSVFGLRNAFLIQHENRYRQCIAAFLLQAQTENIKKTWMAQITTAISCFTKSQETKKISLFTLPAESSEI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.77

(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	1ki1D	0.74	2.12	0.216	0.794	model1_1ki1D.pdb.gz
2	3odoA	0.71	3.13	0.152	0.818	model1_3odoA.pdb.gz
3	4d0nB	0.71	2.86	0.160	0.807	model1_4d0nB.pdb.gz
4	3ky9B	0.66	3.63	0.189	0.789	model1_3ky9B.pdb.gz
5	1x86A	0.65	3.94	0.172	0.799	model1_1x86A.pdb.gz
6	1xcgE	0.65	3.70	0.158	0.792	model1_1xcgE.pdb.gz
7	4yonA	0.61	3.97	0.177	0.773	model1_4yonA.pdb.gz
8	7csoA	0.60	4.22	0.179	0.762	model1_7csoA.pdb.gz
9	4xh9A	0.58	4.38	0.173	0.752	model1_4xh9A.pdb.gz
10	2pz1A	0.52	5.46	0.117	0.757	model1_2pz1A.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:0098772	0.93	molecular function regulator
GO:0005085	0.84	guanyl-nucleotide exchange factor activity
GO:0005089	0.78	Rho guanyl-nucleotide exchange factor activity
GO:0030695	0.64	GTPase regulator activity
GO:0008047	0.64	enzyme activator activity
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0043169	0.54	cation 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:0065007	0.94	biological regulation
GO:0050794	0.91	regulation of cellular process
GO:0044699	0.76	single-organism process
GO:0048583	0.71	regulation of response to stimulus
GO:0023051	0.70	regulation of signaling
GO:0010646	0.70	regulation of cell communication
GO:0009966	0.69	regulation of signal transduction
GO:1902531	0.68	regulation of intracellular signal transduction
GO:0048522	0.68	positive regulation of cellular process
GO:0009987	0.68	cellular process
GO:0051056	0.65	regulation of small GTPase mediated signal transduction
GO:0051128	0.61	regulation of cellular component organization
GO:0044763	0.61	single-organism cellular process
GO:0065009	0.60	regulation of molecular function
GO:0050790	0.59	regulation of catalytic activity
GO:0050793	0.57	regulation of developmental process
GO:0046578	0.57	regulation of Ras protein signal transduction
GO:0035023	0.55	regulation of Rho protein signal transduction
GO:0043087	0.54	regulation of GTPase activity
GO:0044093	0.53	positive regulation of molecular function
GO:0043085	0.52	positive regulation of catalytic activity
GO:0022603	0.52	regulation of anatomical structure morphogenesis
GO:0051239	0.50	regulation of multicellular organismal process
GO:0022604	0.50	regulation of cell morphogenesis

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:0044424	1.00	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0016020	0.92	membrane
GO:0005829	0.89	cytosol
GO:0005737	0.84	cytoplasm
GO:0043226	0.75	organelle
GO:0005886	0.69	plasma membrane
GO:0043229	0.62	intracellular organelle
GO:0043227	0.62	membrane-bounded organelle

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	2cseW	0.358	7.06	0.045	0.617	3.6.4.13	NA
2	0.060	3c46B	0.369	7.65	0.049	0.675	2.7.7.6	NA
3	0.060	2zuwC	0.375	7.23	0.039	0.665	2.4.1.211	NA
4	0.060	2np0A	0.350	7.08	0.041	0.602	3.4.24.69	NA
5	0.060	1rw9A	0.367	6.95	0.061	0.628	4.2.2.5	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:

No Binding sites was predicted

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

	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.