D-I-TASSER Q9UL15

D-I-TASSER results for Q9UL15

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

Summary of the Protein

Uniprot ID: Q9UL15
Protein Name: BAG family molecular chaperone regulator 5
Gene Name: BAG5

Input Sequence in FASTA format

>Q9UL15 (447 residues)
MDMGNQHPSISRLQEIQKEVKSVEQQVIGFSGLSDDKNYKKLERILTKQLFEIDSVDTEG
KGDIQQARKRAAQETERLLKELEQNANHPHRIEIQNIFEEAQSLVREKIVPFYNGGNCVT
DEFEEGIQDIILRLTHVKTGGKISLRKARYHTLTKICAVQEIIEDCMKKQPSLPLSEDAH
PSVAKINFVMCEVNKARGVLIALLMGVNNNETCRHLSCVLSGLIADLDALDVCGRTEIRN
YRREVVEDINKLLKYLDLEEEADTTKAFDLRQNHSILKIEKVLKRMREIKNELLQAQNPS
ELYLSSKTELQGLIGQLDEVSLEKNPCIREARRRAVIEVQTLITYIDLKEALEKRKLFAC
EEHPSHKAVWNVLGNLSEIQGEVLSFDGNRTDKNYIRLEELLTKQLLALDAVDPQGEEKC
KAARKQAVRLAQNILSYLDLKSDEWEY

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	Q9UL15-D1	1-169	169		MDMGNQHPSISRLQEIQKEVKSVEQQVIGFSGLSDDKNYKKLERILTKQLFEIDSVDTEGKGDIQQARKRAAQETERLLKELEQNANHPHRIEIQNIFEEAQSLVREKIVPFYNGGNCVTDEFEEGIQDIILRLTHVKTGGKISLRKARYHTLTKICAVQEIIEDCMKK
2	Q9UL15-D2	170-268	99		QPSLPLSEDAHPSVAKINFVMCEVNKARGVLIALLMGVNNNETCRHLSCVLSGLIADLDALDVCGRTEIRNYRREVVEDINKLLKYLDLEEEADTTKAF
3	Q9UL15-D3	269-354	86		DLRQNHSILKIEKVLKRMREIKNELLQAQNPSELYLSSKTELQGLIGQLDEVSLEKNPCIREARRRAVIEVQTLITYIDLKEALEK
4	Q9UL15-D4	355-447	93		RKLFACEEHPSHKAVWNVLGNLSEIQGEVLSFDGNRTDKNYIRLEELLTKQLLALDAVDPQGEEKCKAARKQAVRLAQNILSYLDLKSDEWEY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.58

(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	6pzkA	0.43	7.48	0.051	0.732	model1_6pzkA.pdb.gz
2	5a22A	0.42	7.71	0.041	0.743	model1_5a22A.pdb.gz
3	2r7oA	0.42	7.23	0.066	0.694	model1_2r7oA.pdb.gz
4	6pnsA	0.41	7.53	0.027	0.709	model1_6pnsA.pdb.gz
5	6uebA	0.41	7.67	0.055	0.727	model1_6uebA.pdb.gz
6	7lhtA	0.41	7.41	0.057	0.700	model1_7lhtA.pdb.gz
7	5n0bA	0.41	6.52	0.055	0.633	model1_5n0bA.pdb.gz
8	5zvs2	0.41	7.59	0.041	0.707	model1_5zvs2.pdb.gz
9	7enjW	0.41	6.76	0.053	0.644	model1_7enjW.pdb.gz
10	2cse1	0.40	7.91	0.032	0.738	model1_2cse1.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:0031625	0.91	ubiquitin protein ligase binding
GO:0051087	0.86	chaperone binding
GO:0097159	0.59	organic cyclic compound binding
GO:0019901	0.59	protein kinase binding
GO:1901363	0.58	heterocyclic compound binding
GO:0036094	0.51	small molecule binding
GO:0017076	0.50	purine nucleotide 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:0009987	0.97	cellular process
GO:0065007	0.91	biological regulation
GO:0050794	0.90	regulation of cellular process
GO:0044699	0.90	single-organism process
GO:0048523	0.87	negative regulation of cellular process
GO:0044763	0.87	single-organism cellular process
GO:0080090	0.82	regulation of primary metabolic process
GO:0060255	0.82	regulation of macromolecule metabolic process
GO:0031323	0.82	regulation of cellular metabolic process
GO:0031324	0.80	negative regulation of cellular metabolic process
GO:0051128	0.78	regulation of cellular component organization
GO:0010605	0.78	negative regulation of macromolecule metabolic process
GO:0050790	0.77	regulation of catalytic activity
GO:0031399	0.77	regulation of protein modification process
GO:0008219	0.77	cell death
GO:0044087	0.76	regulation of cellular component biogenesis
GO:0043086	0.76	negative regulation of catalytic activity
GO:0031400	0.75	negative regulation of protein modification process
GO:0090083	0.74	regulation of inclusion body assembly
GO:0070997	0.74	neuron death
GO:0061084	0.74	negative regulation of protein refolding
GO:0051444	0.74	negative regulation of ubiquitin-protein transferase activity
GO:0042981	0.60	regulation of apoptotic process
GO:0016043	0.59	cellular component organization
GO:0048583	0.58	regulation of response to stimulus
GO:0043069	0.58	negative regulation of programmed cell death
GO:0043066	0.57	negative regulation of apoptotic process
GO:0080135	0.55	regulation of cellular response to stress
GO:0051129	0.54	negative regulation of cellular component organization
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:1902531	0.53	regulation of intracellular signal transduction
GO:0051239	0.52	regulation of multicellular organismal process
GO:0006996	0.52	organelle organization
GO:1903202	0.51	negative regulation of oxidative stress-induced cell death
GO:0051241	0.51	negative regulation of multicellular organismal process
GO:0050767	0.51	regulation of neurogenesis
GO:0045596	0.51	negative regulation of cell differentiation
GO:0030162	0.51	regulation of proteolysis
GO:0009968	0.51	negative regulation of signal transduction
GO:1902176	0.50	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:0032435	0.50	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0010977	0.50	negative regulation of neuron projection development
GO:0007030	0.50	Golgi organization

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0048471	0.74	perinuclear region of cytoplasm
GO:0016234	0.74	inclusion body
GO:0043229	0.71	intracellular organelle
GO:0005829	0.71	cytosol
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0016020	0.65	membrane
GO:0005634	0.64	nucleus
GO:0005739	0.52	mitochondrion

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	2ipyA	0.277	7.34	0.050	0.470	4.2.1.3	NA
2	0.060	3c46B	0.367	7.17	0.054	0.617	2.7.7.6	NA
3	0.060	3bq5A	0.274	8.22	0.042	0.517	2.1.1.14	NA
4	0.060	1j38A	0.351	6.57	0.065	0.530	3.4.15.1	NA
5	0.060	1fgjA	0.362	6.62	0.041	0.548	1.7.3.4	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	0.01	1mwhA	0.399	7.79	0.027	0.709	0.16	GTG	complex1.pdb.gz	387,388,438
2	0.01	2p5oA	0.301	7.73	0.041	0.532	0.16	QNA	complex2.pdb.gz	345,384,437
3	0.01	3tagD	0.313	7.79	0.042	0.553	0.27	QNA	complex3.pdb.gz	378,381,393
4	0.01	1n1hA	0.383	7.19	0.043	0.631	0.18	UUU	complex4.pdb.gz	381,382,439
5	0.01	2dtuA	0.320	6.75	0.045	0.494	0.17	UUU	complex5.pdb.gz	343,381,384,438
6	0.01	1q9xA	0.324	6.14	0.039	0.474	0.17	QNA	complex6.pdb.gz	345,384,437

	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.