D-I-TASSER P10415

D-I-TASSER results for P10415

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

Summary of the Protein

Uniprot ID: P10415
Protein Name: Apoptosis regulator Bcl-2
Gene Name: BCL2

Input Sequence in FASTA format

>P10415 (239 residues)
MAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFSSQPGHTPHPA
ASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQAGDDFSRRYRRDFAEMSSQLH
LTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCVESVNREMSPLVDNIALWMTEY
LNRHLHTWIQDNGGWDAFVELYGPSMRPLFDFSWLSLKTLLSLALVGACITLGAYLGHK

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	P10415-D1	1-204	204		MAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFSSQPGHTPHPAASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQAGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCVESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGP
2	P10415-D2	205-239	35		SMRPLFDFSWLSLKTLLSLALVGACITLGAYLGHK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.66

(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	1lxlA	0.81	2.16	0.412	0.891	model1_1lxlA.pdb.gz
2	1g5mA	0.62	2.06	0.848	0.665	model1_1g5mA.pdb.gz
3	6wh0A	0.58	2.48	0.312	0.644	model1_6wh0A.pdb.gz
4	2a5yA	0.57	3.36	0.188	0.682	model1_2a5yA.pdb.gz
5	6yldA	0.56	1.88	0.280	0.607	model1_6yldA.pdb.gz
6	6v4mA	0.56	2.59	0.191	0.636	model1_6v4mA.pdb.gz
7	3qbrA	0.56	2.54	0.176	0.632	model1_3qbrA.pdb.gz
8	5wddA	0.55	2.01	0.186	0.607	model1_5wddA.pdb.gz
9	1wsxA	0.55	2.70	0.228	0.632	model1_1wsxA.pdb.gz
10	1o0lA	0.54	2.94	0.355	0.623	model1_1o0lA.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:0046983	0.96	protein dimerization activity
GO:0046982	0.95	protein heterodimerization activity
GO:0042803	0.93	protein homodimerization 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	0.99	regulation of cellular process
GO:0009987	0.98	cellular process
GO:0050896	0.92	response to stimulus
GO:0007165	0.91	signal transduction
GO:0035556	0.90	intracellular signal transduction
GO:0033554	0.90	cellular response to stress
GO:0097193	0.89	intrinsic apoptotic signaling pathway
GO:0097191	0.86	extrinsic apoptotic signaling pathway
GO:0008630	0.86	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0042981	0.85	regulation of apoptotic process
GO:0097192	0.83	extrinsic apoptotic signaling pathway in absence of ligand
GO:0048519	0.72	negative regulation of biological process
GO:0048523	0.71	negative regulation of cellular process
GO:0043066	0.69	negative regulation of apoptotic process
GO:0048583	0.67	regulation of response to stimulus
GO:0009966	0.65	regulation of signal transduction
GO:2001233	0.64	regulation of apoptotic signaling pathway
GO:1902531	0.64	regulation of intracellular signal transduction
GO:2001242	0.63	regulation of intrinsic apoptotic signaling pathway
GO:2001234	0.59	negative regulation of apoptotic signaling pathway
GO:0044699	0.59	single-organism process
GO:2001243	0.58	negative regulation of intrinsic apoptotic signaling pathway

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:0044444	1.00	cytoplasmic part
GO:0044446	0.98	intracellular organelle part
GO:0044429	0.97	mitochondrial part
GO:0016020	0.97	membrane
GO:0031090	0.94	organelle membrane
GO:0005741	0.93	mitochondrial outer membrane

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	3b9jI	0.202	5.74	0.042	0.331	1.17.1.4 1.17.3.2	121,153
2	0.060	2c4mC	0.389	5.99	0.047	0.665	2.4.1.1	NA
3	0.060	1ajbA	0.407	5.27	0.043	0.619	3.1.3.1	NA
4	0.060	3igyB	0.401	5.21	0.089	0.598	5.4.2.1	NA
5	0.060	1ahpA	0.374	6.29	0.059	0.674	2.4.1.1	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	0.89	2w3lA	0.558	1.57	0.929	0.590	1.81	DRO	complex1.pdb.gz	104,108,111,112,115,133,136,137,149,153
2	0.83	1yswA	0.605	2.72	0.841	0.678	1.96	43B	complex2.pdb.gz	100,103,104,108,112,115,133,136,137,144,145,146,148,149,152,153,198,202
3	0.78	3pl7A	0.566	1.28	0.610	0.590	1.64	III	complex3.pdb.gz	103,104,108,111,118,119,132,133,136,137,140,143,145,146,153,202
4	0.54	1ysiA	0.618	2.75	0.486	0.703	1.53	N3B	complex4.pdb.gz	104,108,111,112,137,144,145,146,148,202
5	0.32	3mk8A	0.528	2.05	0.252	0.582	1.19	III	complex5.pdb.gz	108,115,133,136,137,139,140,143,145,146,149,150,201,202
6	0.25	1ysgA	0.622	2.48	0.478	0.703	1.61	TN1	complex6.pdb.gz	100,103,104,148,198,202

	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.