D-I-TASSER O95999

D-I-TASSER results for O95999

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

Summary of the Protein

Uniprot ID: O95999
Protein Name: B-cell lymphoma/leukemia 10
Gene Name: BCL10

Input Sequence in FASTA format

>O95999 (233 residues)
MEPTAPSLTEEDLTEVKKDALENLRVYLCEKIIAERHFDHLRAKKILSREDTEEISCRTS
SRKRAGKLLDYLQENPKGLDTLVESIRREKTQNFLIQKITDEVLKLRNIKLEHLKGLKCS
SCEPFPDGATNNLSRSNSDESNFSEKLRASTVMYHPEGESSTTPFFSTNSSLNLPVLEVG
RTENTIFSSTTLPRPGDPGAPPLPPDLQLEEEGTCANSSEMFLPLRSRTVSRQ

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	O95999-D1	1-233	233		MEPTAPSLTEEDLTEVKKDALENLRVYLCEKIIAERHFDHLRAKKILSREDTEEISCRTSSRKRAGKLLDYLQENPKGLDTLVESIRREKTQNFLIQKITDEVLKLRNIKLEHLKGLKCSSCEPFPDGATNNLSRSNSDESNFSEKLRASTVMYHPEGESSTTPFFSTNSSLNLPVLEVGRTENTIFSSTTLPRPGDPGAPPLPPDLQLEEEGTCANSSEMFLPLRSRTVSRQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5735

(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	6sdrA	0.45	5.96	0.057	0.768	model1_6sdrA.pdb.gz
2	1kqgA	0.45	6.02	0.076	0.790	model1_1kqgA.pdb.gz
3	5xb7A	0.45	5.57	0.045	0.743	model1_5xb7A.pdb.gz
4	7kiyA	0.45	6.02	0.036	0.768	model1_7kiyA.pdb.gz
5	1kwgA	0.44	5.44	0.054	0.721	model1_1kwgA.pdb.gz
6	6cinA2	0.44	6.08	0.044	0.790	model1_6cinA2.pdb.gz
7	2v45A	0.44	5.97	0.066	0.777	model1_2v45A.pdb.gz
8	1h0hA	0.44	6.02	0.028	0.772	model1_1h0hA.pdb.gz
9	1ogyA	0.44	5.74	0.056	0.760	model1_1ogyA.pdb.gz
10	4w8yA1	0.44	5.50	0.058	0.717	model1_4w8yA1.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:0019207	0.79	kinase regulator activity
GO:0008047	0.79	enzyme activator activity
GO:0043621	0.78	protein self-association
GO:0019209	0.78	kinase activator activity
GO:0008022	0.78	protein C-terminus binding
GO:0019899	0.77	enzyme binding
GO:0051059	0.75	NF-kappaB binding
GO:0043422	0.75	protein kinase B binding
GO:0043130	0.75	ubiquitin binding
GO:0031625	0.75	ubiquitin protein ligase binding
GO:0003713	0.75	transcription coactivator activity
GO:0042802	0.53	identical protein 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	1.00	regulation of cellular process
GO:0048518	1.00	positive regulation of biological process
GO:0048522	0.94	positive regulation of cellular process
GO:1902533	0.93	positive regulation of intracellular signal transduction
GO:0080090	0.83	regulation of primary metabolic process
GO:0060255	0.83	regulation of macromolecule metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0019219	0.82	regulation of nucleobase-containing compound metabolic process
GO:0065009	0.81	regulation of molecular function
GO:0009987	0.81	cellular process
GO:0006355	0.81	regulation of transcription, DNA-templated
GO:0051092	0.80	positive regulation of NF-kappaB transcription factor activity
GO:0044699	0.79	single-organism process
GO:0044763	0.77	single-organism cellular process
GO:0031325	0.75	positive regulation of cellular metabolic process
GO:0016043	0.75	cellular component organization
GO:0010604	0.75	positive regulation of macromolecule metabolic process
GO:0032270	0.74	positive regulation of cellular protein metabolic process
GO:0031399	0.74	regulation of protein modification process
GO:0019220	0.74	regulation of phosphate metabolic process
GO:0065008	0.73	regulation of biological quality
GO:0050896	0.73	response to stimulus
GO:0043123	0.73	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0042327	0.73	positive regulation of phosphorylation
GO:0031401	0.73	positive regulation of protein modification process
GO:0008219	0.73	cell death
GO:0007165	0.73	signal transduction
GO:0006461	0.73	protein complex assembly
GO:0051259	0.72	protein oligomerization
GO:0051239	0.72	regulation of multicellular organismal process
GO:0048519	0.72	negative regulation of biological process
GO:0002376	0.72	immune system process
GO:0048523	0.71	negative regulation of cellular process
GO:0045935	0.71	positive regulation of nucleobase-containing compound metabolic process
GO:0044767	0.71	single-organism developmental process
GO:0010557	0.71	positive regulation of macromolecule biosynthetic process
GO:0010033	0.71	response to organic substance
GO:0006950	0.71	response to stress
GO:0002757	0.71	immune response-activating signal transduction
GO:0001819	0.71	positive regulation of cytokine production
GO:0048646	0.70	anatomical structure formation involved in morphogenesis
GO:0045893	0.70	positive regulation of transcription, DNA-templated
GO:0045087	0.70	innate immune response
GO:0043065	0.70	positive regulation of apoptotic process
GO:0031396	0.70	regulation of protein ubiquitination
GO:0002768	0.70	immune response-regulating cell surface receptor signaling pathway
GO:0002683	0.70	negative regulation of immune system process
GO:0002237	0.70	response to molecule of bacterial origin
GO:2001238	0.69	positive regulation of extrinsic apoptotic signaling pathway
GO:0051260	0.69	protein homooligomerization
GO:0050852	0.69	T cell receptor signaling pathway
GO:0045416	0.69	positive regulation of interleukin-8 biosynthetic process
GO:0032094	0.69	response to food
GO:0031398	0.69	positive regulation of protein ubiquitination
GO:0002906	0.69	negative regulation of mature B cell apoptotic process
GO:0001843	0.69	neural tube closure

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:0043234	1.00	protein complex
GO:0044464	0.98	cell part
GO:0044424	0.97	intracellular part
GO:0044444	0.94	cytoplasmic part
GO:0005829	0.74	cytosol
GO:0005737	0.74	cytoplasm
GO:0043229	0.73	intracellular organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0044425	0.70	membrane part
GO:0005634	0.70	nucleus
GO:0044459	0.68	plasma membrane part
GO:0048471	0.67	perinuclear region of cytoplasm
GO:0046696	0.67	lipopolysaccharide receptor complex
GO:0044446	0.67	intracellular organelle part
GO:0042101	0.67	T cell receptor complex
GO:0005764	0.67	lysosome
GO:0044430	0.63	cytoskeletal part
GO:0099513	0.62	polymeric cytoskeletal fiber

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	3d2rB	0.430	5.58	0.053	0.700	2.7.11.2	NA
2	0.060	1dkpA	0.429	5.99	0.050	0.738	3.1.3.2 3.1.3.26	NA
3	0.060	1dkmA	0.430	5.91	0.050	0.734	3.1.3.26 3.1.3.2	NA
4	0.060	1yqwR	0.418	5.49	0.029	0.661	1.12.2.1	NA
5	0.060	1y791	0.414	5.98	0.065	0.717	3.4.15.5	54,71

	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	1jm6B	0.423	5.62	0.060	0.704	0.24	ADP	complex1.pdb.gz	19,23,24,100
2	0.01	2zxgA	0.426	6.15	0.033	0.760	0.15	S23	complex2.pdb.gz	65,68,69,80,81
3	0.01	2q8iA	0.429	5.63	0.059	0.708	0.33	RDC	complex3.pdb.gz	16,19,20,23
4	0.01	2zdxB	0.425	5.46	0.049	0.691	0.29	P4A	complex4.pdb.gz	68,69,77
5	0.01	2dqmA	0.428	6.11	0.038	0.764	0.29	BES	complex5.pdb.gz	22,65,68,69,72,77,84
6	0.01	3kedA	0.425	6.16	0.033	0.760	0.21	DAB	complex6.pdb.gz	22,69,70,73
7	0.01	3b34A	0.425	6.15	0.033	0.760	0.16	PHE	complex7.pdb.gz	20,71,80
8	0.01	2e0aB	0.429	5.45	0.070	0.695	0.32	ANP	complex8.pdb.gz	32,33,34,79,84,85,86,93,96
9	0.01	3b2pA	0.426	6.15	0.033	0.760	0.13	ARG	complex9.pdb.gz	24,27,28,29,79,82

	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.