D-I-TASSER Q96LC9

D-I-TASSER results for Q96LC9

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

Summary of the Protein

Uniprot ID: Q96LC9
Protein Name: Bcl-2-modifying factor
Gene Name: BMF

Input Sequence in FASTA format

>Q96LC9 (184 residues)
MEPSQCVEELEDDVFQPEDGEPVTQPGSLLSADLFAQSLLDCPLSRLQLFPLTHCCGPGL
RPTSQEDKATQTLSPASPSQGVMLPCGVTEEPQRLFYGNAGYRLPLPASFPAVLPIGEQP
PEGQWQHQAEVQIARKLQCIADQFHRLHVQQHQQNQNRVWWQILLFLHNLALNGEENRNG
AGPR

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	Q96LC9-D1	1-184	184		MEPSQCVEELEDDVFQPEDGEPVTQPGSLLSADLFAQSLLDCPLSRLQLFPLTHCCGPGLRPTSQEDKATQTLSPASPSQGVMLPCGVTEEPQRLFYGNAGYRLPLPASFPAVLPIGEQPPEGQWQHQAEVQIARKLQCIADQFHRLHVQQHQQNQNRVWWQILLFLHNLALNGEENRNGAGPR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4198

(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	6tjvP	0.48	5.29	0.045	0.793	model1_6tjvP.pdb.gz
2	4a5bA	0.46	5.13	0.064	0.755	model1_4a5bA.pdb.gz
3	6gypB	0.46	5.02	0.070	0.750	model1_6gypB.pdb.gz
4	1n5dA	0.46	5.01	0.052	0.745	model1_1n5dA.pdb.gz
5	3agrA	0.46	5.12	0.034	0.745	model1_3agrA.pdb.gz
6	5t8vA	0.46	5.42	0.062	0.783	model1_5t8vA.pdb.gz
7	1j33A	0.46	4.88	0.081	0.739	model1_1j33A.pdb.gz
8	1d0vA	0.44	5.03	0.054	0.723	model1_1d0vA.pdb.gz
9	1geeA	0.41	4.75	0.051	0.636	model1_1geeA.pdb.gz
10	1nfqA	0.40	4.83	0.052	0.630	model1_1nfqA.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:0016616	0.38	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

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:0043065	1.00	positive regulation of apoptotic process
GO:0009987	0.88	cellular process
GO:0044699	0.83	single-organism process
GO:0044763	0.82	single-organism cellular process
GO:0048583	0.80	regulation of response to stimulus
GO:2001233	0.79	regulation of apoptotic signaling pathway
GO:0032464	0.78	positive regulation of protein homooligomerization
GO:0006915	0.78	apoptotic process
GO:0090200	0.77	positive regulation of release of cytochrome c from mitochondria
GO:0043276	0.77	anoikis

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:0044444	0.87	cytoplasmic part
GO:0044422	0.82	organelle part
GO:0044446	0.81	intracellular organelle part
GO:0032991	0.72	macromolecular complex
GO:0043234	0.71	protein complex
GO:0044430	0.70	cytoskeletal part
GO:0016459	0.69	myosin complex
GO:0043229	0.67	intracellular organelle
GO:0044429	0.58	mitochondrial part
GO:0016020	0.56	membrane
GO:0031966	0.52	mitochondrial membrane
GO:0005741	0.50	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	1h19A	0.433	5.62	0.026	0.755	3.3.2.6	131
2	0.060	1itxA	0.424	4.82	0.072	0.690	3.2.1.14	NA
3	0.060	1dwaM	0.426	5.17	0.041	0.696	3.2.1.147	NA
4	0.060	2bfpD	0.418	4.92	0.021	0.663	1.5.1.33	NA
5	0.060	2pffA	0.433	5.05	0.034	0.712	2.3.1.41 2.3.1.86	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	0.03	3g4gD	0.430	5.47	0.082	0.745	0.21	D71	complex1.pdb.gz	7,10,11,101,135,136
2	0.03	1xomB	0.375	5.63	0.060	0.668	0.25	CIO	complex2.pdb.gz	98,101,138
3	0.02	3k4sA	0.374	5.94	0.059	0.690	0.22	0MO	complex3.pdb.gz	87,98,103
4	0.02	3g4iA	0.374	5.84	0.059	0.679	0.26	D71	complex4.pdb.gz	137,140,141,144
5	0.02	1tbbA	0.373	5.70	0.060	0.668	0.25	ROL	complex5.pdb.gz	140,141,144,161
6	0.01	3ly2G	0.385	5.47	0.056	0.690	0.16	Z72	complex6.pdb.gz	101,102,114
7	0.01	1xlzA	0.390	5.41	0.058	0.685	0.26	FIL	complex7.pdb.gz	70,97,102
8	0.01	1xn0A	0.405	5.45	0.040	0.679	0.29	ROL	complex8.pdb.gz	133,134,137,140,169
9	0.01	3g4gC	0.429	5.51	0.092	0.750	0.18	D71	complex9.pdb.gz	10,11,99,135
10	0.01	3d3pA	0.375	5.64	0.053	0.674	0.22	20A	complex10.pdb.gz	133,136,166

	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.