D-I-TASSER P50749

D-I-TASSER results for P50749

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

Summary of the Protein

Uniprot ID: P50749
Protein Name: Ras association domain-containing protein 2
Gene Name: RASSF2

Input Sequence in FASTA format

>P50749 (326 residues)
MDYSHQTSLVPCGQDKYISKNELLLHLKTYNLYYEGQNLQLRHREEEDEFIVEGLLNISW
GLRRPIRLQMQDDNERIRPPPSSSSWHSGCNLGAQGTTLKPLTVPKVQISEVDAPPEGDQ
MPSSTDSRGLKPLQEDTPQLMRTRSDVGVRRRGNVRTPSDQRRIRRHRFSINGHFYNHKT
SVFTPAYGSVTNVRINSTMTTPQVLKLLLNKFKIENSAEEFALYVVHTSGEKQKLKATDY
PLIARILQGPCEQISKVFLMEKDQVEEVTYDVAQYIKFEMPVLKSFIQKLQEEEDREVKK
LMRKYTVLRLMIRQRLEEIAETPATI

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	P50749-D1	1-326	326		MDYSHQTSLVPCGQDKYISKNELLLHLKTYNLYYEGQNLQLRHREEEDEFIVEGLLNISWGLRRPIRLQMQDDNERIRPPPSSSSWHSGCNLGAQGTTLKPLTVPKVQISEVDAPPEGDQMPSSTDSRGLKPLQEDTPQLMRTRSDVGVRRRGNVRTPSDQRRIRRHRFSINGHFYNHKTSVFTPAYGSVTNVRINSTMTTPQVLKLLLNKFKIENSAEEFALYVVHTSGEKQKLKATDYPLIARILQGPCEQISKVFLMEKDQVEEVTYDVAQYIKFEMPVLKSFIQKLQEEEDREVKKLMRKYTVLRLMIRQRLEEIAETPATI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5675

(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	6eojA	0.42	6.82	0.029	0.724	model1_6eojA.pdb.gz
2	7abhE	0.42	6.89	0.051	0.730	model1_7abhE.pdb.gz
3	5lqwX	0.41	6.75	0.058	0.730	model1_5lqwX.pdb.gz
4	5hy7A	0.41	6.63	0.036	0.696	model1_5hy7A.pdb.gz
5	5a22A	0.40	6.34	0.067	0.666	model1_5a22A.pdb.gz
6	6bllA	0.39	6.99	0.048	0.703	model1_6bllA.pdb.gz
7	4xc6A	0.39	6.24	0.077	0.632	model1_4xc6A.pdb.gz
8	5ganC	0.39	6.74	0.050	0.666	model1_5ganC.pdb.gz
9	6w1sR	0.38	6.22	0.050	0.632	model1_6w1sR.pdb.gz
10	3jb9B	0.38	6.72	0.038	0.672	model1_3jb9B.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	0.49	catalytic activity
GO:0016740	0.46	transferase activity
GO:0004672	0.43	protein kinase 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:0050794	1.00	regulation of cellular process
GO:0048522	0.93	positive regulation of cellular process
GO:0048523	0.88	negative regulation of cellular process
GO:0080090	0.81	regulation of primary metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0032268	0.80	regulation of cellular protein metabolic process
GO:0031325	0.80	positive regulation of cellular metabolic process
GO:0010604	0.80	positive regulation of macromolecule metabolic process
GO:0043065	0.79	positive regulation of apoptotic process
GO:0031401	0.79	positive regulation of protein modification process
GO:0065008	0.74	regulation of biological quality
GO:0009966	0.74	regulation of signal transduction
GO:0050821	0.73	protein stabilization
GO:0019220	0.67	regulation of phosphate metabolic process
GO:0050790	0.66	regulation of catalytic activity
GO:0048584	0.66	positive regulation of response to stimulus
GO:0031400	0.66	negative regulation of protein modification process
GO:0001934	0.66	positive regulation of protein phosphorylation
GO:0046330	0.65	positive regulation of JNK cascade
GO:0045860	0.65	positive regulation of protein kinase activity
GO:0033137	0.65	negative regulation of peptidyl-serine phosphorylation
GO:0031954	0.65	positive regulation of protein autophosphorylation
GO:0007165	0.55	signal transduction

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043229	0.93	intracellular organelle
GO:0043232	0.87	intracellular non-membrane-bounded organelle
GO:0044446	0.83	intracellular organelle part
GO:0032991	0.81	macromolecular complex
GO:0043234	0.80	protein complex
GO:0000776	0.79	kinetochore
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0005634	0.70	nucleus
GO:0005737	0.68	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	3ciaA	0.347	6.43	0.050	0.583	3.4.11.-	NA
2	0.060	1t7nA	0.340	6.43	0.033	0.568	2.3.1.7	NA
3	0.060	1ea0A	0.339	6.39	0.059	0.574	1.4.1.13	NA
4	0.060	2fy3A	0.339	6.77	0.037	0.592	2.3.1.6	NA
5	0.060	1gw6A	0.360	6.51	0.066	0.598	3.3.2.6	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	0.01	2chwA	0.360	6.34	0.052	0.595	0.11	039	complex1.pdb.gz	224,225,226
2	0.01	1e8wA	0.366	6.22	0.052	0.595	0.12	QUE	complex2.pdb.gz	231,251,256
3	0.01	1ofdB	0.324	6.56	0.042	0.549	0.36	F3S	complex3.pdb.gz	246,247,248,249,250,251
4	0.01	1ofdA	0.356	6.36	0.038	0.589	0.37	F3S	complex4.pdb.gz	228,229,230,231,232,233,255,257,258
5	0.01	3ibeA	0.349	6.82	0.075	0.610	0.13	L64	complex5.pdb.gz	257,259,268,271
6	0.01	1q16A	0.327	6.73	0.024	0.574	0.14	SF4	complex6.pdb.gz	224,258,260
7	0.01	1e7uA	0.371	6.33	0.049	0.610	0.12	KWT	complex7.pdb.gz	226,255,256,257
8	0.01	1siwA	0.360	6.59	0.031	0.604	0.32	SF4	complex8.pdb.gz	230,231,232,234,257

	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.