D-I-TASSER Q96L46

D-I-TASSER results for Q96L46

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

Summary of the Protein

Uniprot ID: Q96L46
Protein Name: Calpain small subunit 2
Gene Name: CAPNS2

Input Sequence in FASTA format

>Q96L46 (248 residues)
MFLAKALLEGADRGLGEALGGLFGGGGQRREGGGRNIGGIVGGIVNFISEAAAAQYTPEP
PPTQQHFTSVEASESEEVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKDLKTDGFS
LDTCRSIVSVMDSDTTGKLGFEEFKYLWNNIKKWQCVYKQYDRDHSGSLGSSQLRGALQA
AGFQLNEQLYQMIVRRYANEDGDMDFNNFISCLVRLDAMFRAFKSLDRDRDGLIQVSIKE
WLQLTMYS

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	Q96L46-D1	1-150	150		MFLAKALLEGADRGLGEALGGLFGGGGQRREGGGRNIGGIVGGIVNFISEAAAAQYTPEPPPTQQHFTSVEASESEEVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKDLKTDGFSLDTCRSIVSVMDSDTTGKLGFEEFKYLWNN
2	Q96L46-D2	151-248	98		IKKWQCVYKQYDRDHSGSLGSSQLRGALQAAGFQLNEQLYQMIVRRYANEDGDMDFNNFISCLVRLDAMFRAFKSLDRDRDGLIQVSIKEWLQLTMYS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	1kfuL	0.59	3.70	0.300	0.734	model1_1kfuL.pdb.gz
2	1aj5A	0.58	2.78	0.684	0.690	model1_1aj5A.pdb.gz
3	1juoA	0.58	2.80	0.285	0.677	model1_1juoA.pdb.gz
4	1k94A	0.56	2.87	0.303	0.665	model1_1k94A.pdb.gz
5	4okhA	0.56	3.16	0.386	0.669	model1_4okhA.pdb.gz
6	3siaA	0.54	3.45	0.157	0.673	model1_3siaA.pdb.gz
7	1qxpB3	0.52	2.88	0.351	0.613	model1_1qxpB3.pdb.gz
8	2i7aA	0.51	2.90	0.257	0.613	model1_2i7aA.pdb.gz
9	1hqvA	0.51	3.83	0.249	0.690	model1_1hqvA.pdb.gz
10	1ij5A	0.49	3.24	0.083	0.593	model1_1ij5A.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	0.93	catalytic activity
GO:0008233	0.87	peptidase activity
GO:0004198	0.83	calcium-dependent cysteine-type endopeptidase activity
GO:0043167	0.52	ion binding
GO:0046872	0.51	metal ion 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:0071704	0.98	organic substance metabolic process
GO:0044238	0.98	primary metabolic process
GO:0019538	0.97	protein metabolic process
GO:0006508	0.87	proteolysis
GO:0009987	0.53	cellular process
GO:0065007	0.50	biological regulation

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:0005737	0.97	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	0.415	3bowB	0.568	3.21	0.665	0.698	3.4.22.53	150,153,159,176,180,182,216
2	0.060	1dkmA	0.380	5.60	0.052	0.621	3.1.3.26 3.1.3.2	NA
3	0.060	2g8eA	0.291	5.64	0.044	0.472	3.4.22.52	NA
4	0.060	1fftA	0.380	5.65	0.068	0.613	1.10.3.-	NA
5	0.060	3g0iA	0.378	5.80	0.080	0.641	3.3.2.3	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	0.53	1alvA	0.560	3.13	0.696	0.690	1.37	CA	complex1.pdb.gz	162,164,166,168,173
2	0.36	1alwB	0.556	3.21	0.738	0.694	1.85	CA	complex2.pdb.gz	132,134,136,138,139,140,143
3	0.34	1alwB	0.556	3.21	0.738	0.694	1.46	CA	complex3.pdb.gz	89,92,94,95
4	0.10	1alv0	0.560	3.13	0.696	0.690	1.21	III	complex4.pdb.gz	122,123,125,129,135,137,186,188,189,192,195,196,208,212,215,216,219,220,223,232,233
5	0.09	1nx0A	0.551	3.38	0.661	0.690	1.12	III	complex5.pdb.gz	182,183,184,217,220,224
6	0.09	1nx0B	0.551	3.32	0.667	0.685	0.85	III	complex6.pdb.gz	88,103,107,148
7	0.09	1nx1A	0.556	3.33	0.667	0.690	0.81	III	complex7.pdb.gz	87,88,103,107,148
8	0.09	1nx0A	0.551	3.38	0.661	0.690	0.88	III	complex8.pdb.gz	88,103,106,107,110,148

	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.