D-I-TASSER Q15846

D-I-TASSER results for Q15846

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

Summary of the Protein

Uniprot ID: Q15846
Protein Name: Clusterin-like protein 1
Gene Name: CLUL1

Input Sequence in FASTA format

>Q15846 (466 residues)
MKPPLLVFIVCLLWLKDSHCAPTWKDKTAISENLKSFSEVGEIDADEEVKKALTGIKQMK
IMMERKEKEHTNLMSTLKKCREEKQEALKLLNEVQEHLEEEERLCRESLADSWGECRSCL
ENNCMRIYTTCQPSWSSVKNKIERFFRKIYQFLFPFHEDNEKDLPISEKLIEEDAQLTQM
EDVFSQLTVDVNSLFNRSFNVFRQMQQEFDQTFQSHFISDTDLTEPYFFPAFSKEPMTKA
DLEQCWDIPNFFQLFCNFSVSIYESVSETITKMLKAIEDLPKQDKAPDHGGLISKMLPGQ
DRGLCGELDQNLSRCFKFHEKCQKCQAHLSEDCPDVPALHTELDEAIRLVNVSNQQYGQI
LQMTRKHLEDTAYLVEKMRGQFGWVSELANQAPETEIIFNSIQVVPRIHEGNISKQDETM
MTDLSILPSSNFTLKIPLEESAESSNFIGYVVAKALQHFKEHFKTW

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	Q15846-D1	1-383	383		MKPPLLVFIVCLLWLKDSHCAPTWKDKTAISENLKSFSEVGEIDADEEVKKALTGIKQMKIMMERKEKEHTNLMSTLKKCREEKQEALKLLNEVQEHLEEEERLCRESLADSWGECRSCLENNCMRIYTTCQPSWSSVKNKIERFFRKIYQFLFPFHEDNEKDLPISEKLIEEDAQLTQMEDVFSQLTVDVNSLFNRSFNVFRQMQQEFDQTFQSHFISDTDLTEPYFFPAFSKEPMTKADLEQCWDIPNFFQLFCNFSVSIYESVSETITKMLKAIEDLPKQDKAPDHGGLISKMLPGQDRGLCGELDQNLSRCFKFHEKCQKCQAHLSEDCPDVPALHTELDEAIRLVNVSNQQYGQILQMTRKHLEDTAYLVEKMRGQFG
2	Q15846-D2	384-466	83		WVSELANQAPETEIIFNSIQVVPRIHEGNISKQDETMMTDLSILPSSNFTLKIPLEESAESSNFIGYVVAKALQHFKEHFKTW

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.64

(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	1ciiA	0.41	4.45	0.078	0.509	model1_1ciiA.pdb.gz
2	6yvuB	0.37	5.63	0.042	0.506	model1_6yvuB.pdb.gz
3	6gy6B	0.34	5.07	0.037	0.457	model1_6gy6B.pdb.gz
4	6el1O	0.34	5.23	0.057	0.459	model1_6el1O.pdb.gz
5	6ek4A	0.34	5.02	0.077	0.449	model1_6ek4A.pdb.gz
6	6l7eA	0.33	6.78	0.027	0.504	model1_6l7eA.pdb.gz
7	6r3qA	0.33	6.16	0.045	0.485	model1_6r3qA.pdb.gz
8	6rw9A	0.33	6.89	0.026	0.506	model1_6rw9A.pdb.gz
9	6rw8A	0.33	6.62	0.029	0.487	model1_6rw8A.pdb.gz
10	6z6fC	0.33	5.19	0.064	0.433	model1_6z6fC.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	0.89	catalytic activity
GO:0016787	0.88	hydrolase activity
GO:0051787	0.87	misfolded protein binding
GO:0031625	0.87	ubiquitin protein ligase binding
GO:0016887	0.87	ATPase activity
GO:0043169	0.51	cation 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:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0010941	0.91	regulation of cell death
GO:0009987	0.78	cellular process
GO:0050896	0.62	response to stimulus
GO:0065008	0.61	regulation of biological quality
GO:0051128	0.61	regulation of cellular component organization
GO:0048519	0.61	negative regulation of biological process
GO:0080090	0.60	regulation of primary metabolic process
GO:0048523	0.60	negative regulation of cellular process
GO:0048518	0.60	positive regulation of biological process
GO:0031326	0.60	regulation of cellular biosynthetic process
GO:0006950	0.60	response to stress
GO:0051246	0.59	regulation of protein metabolic process
GO:0051129	0.59	negative regulation of cellular component organization
GO:0044093	0.59	positive regulation of molecular function
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0023051	0.59	regulation of signaling
GO:0019219	0.59	regulation of nucleobase-containing compound metabolic process
GO:0010646	0.59	regulation of cell communication
GO:0010556	0.59	regulation of macromolecule biosynthetic process
GO:0010033	0.59	response to organic substance
GO:2001244	0.58	positive regulation of intrinsic apoptotic signaling pathway
GO:2000060	0.58	positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:1902230	0.58	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:0097193	0.58	intrinsic apoptotic signaling pathway
GO:0061077	0.58	chaperone-mediated protein folding
GO:0051788	0.58	response to misfolded protein
GO:0051092	0.58	positive regulation of NF-kappaB transcription factor activity
GO:0050821	0.58	protein stabilization
GO:0032463	0.58	negative regulation of protein homooligomerization
GO:0032436	0.58	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:1901214	0.55	regulation of neuron death
GO:0044699	0.53	single-organism process
GO:0008152	0.50	metabolic process

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:0032991	0.89	macromolecular complex
GO:0044421	0.88	extracellular region part
GO:0048471	0.87	perinuclear region of cytoplasm
GO:0034366	0.87	spherical high-density lipoprotein particle
GO:0031012	0.87	extracellular matrix
GO:0005615	0.87	extracellular space
GO:0043231	0.65	intracellular membrane-bounded organelle
GO:0044422	0.54	organelle part
GO:0016020	0.50	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	1wleB	0.260	5.87	0.064	0.360	6.1.1.11	NA
2	0.060	2hc8A	0.086	4.80	0.027	0.112	3.6.3.-	46
3	0.060	2ckjA	0.255	7.22	0.071	0.414	1.17.1.4 1.17.3.2	NA
4	0.060	2b5uA	0.250	5.03	0.065	0.318	3.1.-.-	NA
5	0.060	2vz8B	0.248	6.80	0.049	0.380	2.3.1.85	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:

Click to view	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	2w6dB	0.310	6.10	0.039	0.442	0.44	CPL	complex1.pdb.gz	42,51,53

	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.