D-I-TASSER P49795

D-I-TASSER results for P49795

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Summary of the Protein

Uniprot ID: P49795
Protein Name: Regulator of G-protein signaling 19
Gene Name: RGS19

Input Sequence in FASTA format

>P49795 (217 residues)
MPTPHEAEKQITGPEEADRPPSMSSHDTASPAAPSRNPCCLCWCCCCSCSWNQERRRAWQ
ASRESKLQPLPSCEVCATPSPEEVQSWAQSFDKLMHSPAGRSVFRAFLRTEYSEENMLFW
LACEELKAEANQHVVDEKARLIYEDYVSILSPKEVSLDSRVREGINKKMQEPSAHTFDDA
QLQIYTLMHRDSYPRFLSSPTYRALLLQGPSQSSSEA

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 DeepPotential. 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	P49795-D1	1-217	217		MPTPHEAEKQITGPEEADRPPSMSSHDTASPAAPSRNPCCLCWCCCCSCSWNQERRRAWQASRESKLQPLPSCEVCATPSPEEVQSWAQSFDKLMHSPAGRSVFRAFLRTEYSEENMLFWLACEELKAEANQHVVDEKARLIYEDYVSILSPKEVSLDSRVREGINKKMQEPSAHTFDDAQLQIYTLMHRDSYPRFLSSPTYRALLLQGPSQSSSEA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5148

(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 DeepPotential, 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	2kzzA	0.45	5.48	0.047	0.765	model1_2kzzA.pdb.gz
2	4xviA	0.44	5.52	0.030	0.765	model1_4xviA.pdb.gz
3	5nz7A	0.44	5.43	0.071	0.728	model1_5nz7A.pdb.gz
4	2hhtA	0.44	5.39	0.061	0.733	model1_2hhtA.pdb.gz
5	1bgxT	0.44	5.60	0.054	0.760	model1_1bgxT.pdb.gz
6	5mpbN	0.44	5.62	0.025	0.751	model1_5mpbN.pdb.gz
7	5dktA	0.44	5.40	0.024	0.737	model1_5dktA.pdb.gz
8	2cqtA	0.43	5.41	0.043	0.724	model1_2cqtA.pdb.gz
9	2ajqA	0.43	5.30	0.051	0.724	model1_2ajqA.pdb.gz
10	3ikmD1	0.42	5.99	0.020	0.747	model1_3ikmD1.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:0005096	0.99	GTPase activator 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:0065007	0.98	biological regulation
GO:0050794	0.97	regulation of cellular process
GO:0007165	0.89	signal transduction
GO:0009966	0.84	regulation of signal transduction
GO:0044699	0.77	single-organism process
GO:0009987	0.74	cellular process
GO:0048519	0.72	negative regulation of biological process
GO:0048523	0.71	negative regulation of cellular process
GO:0044763	0.71	single-organism cellular process
GO:0032501	0.71	multicellular organismal process
GO:0080090	0.69	regulation of primary metabolic process
GO:0050896	0.69	response to stimulus
GO:0031323	0.69	regulation of cellular metabolic process
GO:0009968	0.69	negative regulation of signal transduction
GO:0060255	0.68	regulation of macromolecule metabolic process
GO:0044707	0.67	single-multicellular organism process
GO:0048869	0.65	cellular developmental process
GO:0031326	0.65	regulation of cellular biosynthetic process
GO:0019219	0.65	regulation of nucleobase-containing compound metabolic process
GO:0042221	0.64	response to chemical
GO:0007166	0.64	cell surface receptor signaling pathway
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0051716	0.63	cellular response to stimulus
GO:0032879	0.63	regulation of localization
GO:0030111	0.63	regulation of Wnt signaling pathway
GO:0010033	0.63	response to organic substance
GO:0007389	0.63	pattern specification process
GO:0071310	0.62	cellular response to organic substance
GO:0035412	0.62	regulation of catenin import into nucleus
GO:0030178	0.62	negative regulation of Wnt signaling pathway
GO:0016055	0.62	Wnt signaling pathway
GO:0014070	0.62	response to organic cyclic compound
GO:0009950	0.62	dorsal/ventral axis specification
GO:0090244	0.61	Wnt signaling pathway involved in somitogenesis
GO:0090090	0.61	negative regulation of canonical Wnt signaling pathway
GO:0071407	0.61	cellular response to organic cyclic compound
GO:0008219	0.61	cell death
GO:0030154	0.55	cell differentiation

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:0005886	0.98	plasma membrane
GO:0005737	0.98	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	1d8yA	0.369	6.47	0.030	0.737	2.7.7.7	NA
2	0.060	3eqvA	0.399	5.70	0.071	0.682	3.4.16.4	91
3	0.060	3g1uC	0.401	6.24	0.048	0.747	3.3.1.1	NA
4	0.060	1aroP	0.343	6.12	0.046	0.622	2.7.7.6	NA
5	0.060	2hpiA	0.383	6.03	0.087	0.687	2.7.7.7	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	3ti0A	0.371	6.32	0.042	0.710	0.11	DG3	complex1.pdb.gz	81,82,83,101,105

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.