D-I-TASSER Q9H2L5

D-I-TASSER results for Q9H2L5

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Summary of the Protein

Uniprot ID: Q9H2L5
Protein Name: Ras association domain-containing protein 4
Gene Name: RASSF4

Input Sequence in FASTA format

>Q9H2L5 (321 residues)
MKEDCLPSSHVPISDSKSIQKSELLGLLKTYNCYHEGKSFQLRHREEEGTLIIEGLLNIA
WGLRRPIRLQMQDDREQVHLPSTSWMPRRPSCPLKEPSPQNGNITAQGPSIQPVHKAESS
TDSSGPLEEAEEAPQLMRTKSDASCMSQRRPKCRAPGEAQRIRRHRFSINGHFYNHKTSV
FTPAYGSVTNVRVNSTMTTLQVLTLLLNKFRVEDGPSEFALYIVHESGERTKLKDCEYPL
ISRILHGPCEKIARIFLMEADLGVEVPHEVAQYIKFEMPVLDSFVEKLKEEEEREIIKLT
MKFQALRLTMLQRLEQLVEAK

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	Q9H2L5-D1	1-321	321		MKEDCLPSSHVPISDSKSIQKSELLGLLKTYNCYHEGKSFQLRHREEEGTLIIEGLLNIAWGLRRPIRLQMQDDREQVHLPSTSWMPRRPSCPLKEPSPQNGNITAQGPSIQPVHKAESSTDSSGPLEEAEEAPQLMRTKSDASCMSQRRPKCRAPGEAQRIRRHRFSINGHFYNHKTSVFTPAYGSVTNVRVNSTMTTLQVLTLLLNKFRVEDGPSEFALYIVHESGERTKLKDCEYPLISRILHGPCEKIARIFLMEADLGVEVPHEVAQYIKFEMPVLDSFVEKLKEEEEREIIKLTMKFQALRLTMLQRLEQLVEAK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5915

(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	3ixzA	0.41	6.34	0.040	0.667	model1_3ixzA.pdb.gz
2	3kdpA	0.41	6.13	0.050	0.654	model1_3kdpA.pdb.gz
3	5m59A	0.39	6.75	0.046	0.673	model1_5m59A.pdb.gz
4	6eojA	0.39	6.05	0.032	0.617	model1_6eojA.pdb.gz
5	7abhE	0.38	6.86	0.039	0.679	model1_7abhE.pdb.gz
6	6bllA	0.38	6.44	0.051	0.651	model1_6bllA.pdb.gz
7	5kf6A	0.38	6.33	0.063	0.639	model1_5kf6A.pdb.gz
8	5cskA	0.38	6.44	0.050	0.664	model1_5cskA.pdb.gz
9	6wmpC	0.38	6.44	0.034	0.639	model1_6wmpC.pdb.gz
10	5u71A	0.38	6.37	0.035	0.623	model1_5u71A.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:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound 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:0050794	0.97	regulation of cellular process
GO:0048522	0.75	positive regulation of cellular process
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0048523	0.70	negative regulation of cellular process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0051246	0.69	regulation of protein metabolic process
GO:0031399	0.68	regulation of protein modification process
GO:0010604	0.63	positive regulation of macromolecule metabolic process
GO:0051247	0.62	positive regulation of protein metabolic process
GO:0031325	0.62	positive regulation of cellular metabolic process
GO:0007165	0.62	signal transduction
GO:0065008	0.61	regulation of biological quality
GO:0048583	0.61	regulation of response to stimulus
GO:0031401	0.60	positive regulation of protein modification process
GO:0009966	0.60	regulation of signal transduction
GO:0042981	0.56	regulation of apoptotic process
GO:0009987	0.56	cellular process
GO:0043065	0.55	positive regulation of apoptotic process
GO:0044699	0.54	single-organism process
GO:0050821	0.53	protein stabilization
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0001932	0.50	regulation of protein phosphorylation

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:0043229	0.87	intracellular organelle
GO:0005737	0.76	cytoplasm
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0044446	0.71	intracellular organelle part
GO:0043232	0.68	intracellular non-membrane-bounded organelle
GO:0043234	0.63	protein complex
GO:0016020	0.63	membrane
GO:0005634	0.62	nucleus
GO:0000776	0.55	kinetochore

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	3b8eA	0.406	6.41	0.028	0.673	3.6.3.9	NA
2	0.060	1q6xA	0.319	6.58	0.031	0.545	2.3.1.6	NA
3	0.060	1wz2A	0.345	6.42	0.040	0.579	6.1.1.4	NA
4	0.060	1mo7A	0.204	5.17	0.030	0.296	3.6.3.9	NA
5	0.060	1eloA	0.324	6.60	0.052	0.554	3.6.5.3	142,172

	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	3pgqB	0.312	6.94	0.046	0.554	0.28	GY3	complex1.pdb.gz	245,248,255
2	0.01	1t36A	0.327	6.29	0.037	0.542	0.23	U	complex2.pdb.gz	224,227,229,246,247,250
3	0.01	3kdpC	0.405	6.29	0.047	0.664	0.10	III	complex3.pdb.gz	215,216,219
4	0.01	1uyrA	0.376	6.73	0.039	0.670	0.21	D1L	complex4.pdb.gz	246,247,250,251
5	0.01	1a9xA	0.319	6.42	0.035	0.536	0.13	ADP	complex5.pdb.gz	230,246,254,255,256
6	0.01	1m6vC	0.315	6.05	0.042	0.505	0.16	ADP	complex6.pdb.gz	185,186,214,215,219,220,256,257,264
7	0.01	1bxrA	0.368	6.29	0.043	0.601	0.13	ANP	complex7.pdb.gz	186,187,213,214,215,216,272
8	0.01	1od2A	0.372	6.65	0.035	0.654	0.21	ACO	complex8.pdb.gz	215,217,260,261

	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.