D-I-TASSER Q9P2M1

D-I-TASSER results for Q9P2M1

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

Summary of the Protein

Uniprot ID: Q9P2M1
Protein Name: LRP2-binding protein
Gene Name: LRP2BP

Input Sequence in FASTA format

>Q9P2M1 (347 residues)
MKLTSEKLPKNPFYASVSQYAAKNQKFFQWKKEKTDYTHANLVDKALQLLKERILKGDTL
AYFLRGQLYFEEGWYEEALEQFEEIKEKDHQATYQLGVMYYDGLGTTLDAEKGVDYMKKI
LDSPCPKARHLKFAAAYNLGRAYYEGKGVKRSNEEAERLWLIAADNGNPKASVKAQSMLG
LYYSTKEPKELEKAFYWHSEACGNGNLESQGALGLMYLYGQGIRQDTEAALQCLREAAER
GNVYAQGNLVEYYYKMKFFTKCVAFSKRIADYDEVHDIPMIAQVTDCLPEFIGRGMAMAS
FYHARCLQLGLGITRDETTAKHYYSKACRLNPALADELHSLLIRQRI

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	Q9P2M1-D1	1-108	108		MKLTSEKLPKNPFYASVSQYAAKNQKFFQWKKEKTDYTHANLVDKALQLLKERILKGDTLAYFLRGQLYFEEGWYEEALEQFEEIKEKDHQATYQLGVMYYDGLGTTL
2	Q9P2M1-D2	109-225	117		DAEKGVDYMKKILDSPCPKARHLKFAAAYNLGRAYYEGKGVKRSNEEAERLWLIAADNGNPKASVKAQSMLGLYYSTKEPKELEKAFYWHSEACGNGNLESQGALGLMYLYGQGIRQ
3	Q9P2M1-D3	226-347	122		DTEAALQCLREAAERGNVYAQGNLVEYYYKMKFFTKCVAFSKRIADYDEVHDIPMIAQVTDCLPEFIGRGMAMASFYHARCLQLGLGITRDETTAKHYYSKACRLNPALADELHSLLIRQRI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.76

(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	2xm6A	0.68	3.76	0.220	0.824	model1_2xm6A.pdb.gz
2	7nscE	0.67	5.04	0.090	0.954	model1_7nscE.pdb.gz
3	6vbu4	0.67	3.60	0.147	0.816	model1_6vbu4.pdb.gz
4	6af0A	0.65	4.57	0.072	0.870	model1_6af0A.pdb.gz
5	6gmhQ	0.64	4.25	0.103	0.833	model1_6gmhQ.pdb.gz
6	4bujB	0.64	4.76	0.108	0.870	model1_4bujB.pdb.gz
7	6vbu8	0.64	4.70	0.120	0.859	model1_6vbu8.pdb.gz
8	6dehA	0.64	3.42	0.219	0.755	model1_6dehA.pdb.gz
9	1w3bA	0.63	4.47	0.140	0.836	model1_1w3bA.pdb.gz
10	6swy5	0.63	5.31	0.083	0.919	model1_6swy5.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	0.66	catalytic activity
GO:0036094	0.59	small molecule binding
GO:0016787	0.55	hydrolase activity
GO:0016740	0.53	transferase activity
GO:0016812	0.52	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides

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	0.90	cellular process
GO:0065007	0.83	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0044699	0.78	single-organism process
GO:0050794	0.77	regulation of cellular process
GO:0008152	0.76	metabolic process
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.75	primary metabolic process
GO:0044237	0.74	cellular metabolic process
GO:0044763	0.73	single-organism cellular process
GO:0043170	0.73	macromolecule metabolic process
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0019538	0.70	protein metabolic process
GO:0051179	0.64	localization
GO:0019222	0.62	regulation of metabolic process
GO:0080090	0.61	regulation of primary metabolic process
GO:0050896	0.61	response to stimulus
GO:0044267	0.60	cellular protein metabolic process
GO:0043412	0.60	macromolecule modification
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0006464	0.59	cellular protein modification process
GO:0044710	0.58	single-organism metabolic process
GO:0051641	0.57	cellular localization
GO:0051246	0.56	regulation of protein metabolic process
GO:0048583	0.55	regulation of response to stimulus
GO:0048519	0.55	negative regulation of biological process
GO:0016043	0.55	cellular component organization
GO:0009889	0.55	regulation of biosynthetic process
GO:0051716	0.54	cellular response to stimulus
GO:0048523	0.54	negative regulation of cellular process
GO:0048518	0.54	positive regulation of biological process
GO:0032502	0.54	developmental process
GO:0009056	0.54	catabolic process
GO:0051128	0.53	regulation of cellular component organization
GO:0044767	0.53	single-organism developmental process
GO:0032268	0.53	regulation of cellular protein metabolic process
GO:0009057	0.53	macromolecule catabolic process
GO:0048522	0.52	positive regulation of cellular process
GO:0031399	0.52	regulation of protein modification process
GO:0010468	0.52	regulation of gene expression
GO:0006950	0.52	response to stress
GO:2000112	0.51	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.51	regulation of nitrogen compound metabolic process
GO:0042221	0.51	response to chemical
GO:0033043	0.51	regulation of organelle organization
GO:0007165	0.51	signal transduction
GO:0050790	0.50	regulation of catalytic activity
GO:0033044	0.50	regulation of chromosome organization
GO:0010033	0.50	response to organic substance
GO:0009966	0.50	regulation of signal transduction
GO:0006996	0.50	organelle organization
GO:0006355	0.50	regulation of transcription, DNA-templated

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	0.98	intracellular part
GO:0044444	0.77	cytoplasmic part
GO:0043226	0.74	organelle
GO:0043229	0.72	intracellular organelle
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0044446	0.55	intracellular organelle part

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	0.209	1ouvA	0.582	3.63	0.212	0.715	3.5.2.6	89,100,122
2	0.060	2ri9B	0.408	5.03	0.058	0.579	3.2.1.113	66
3	0.060	1w3bA	0.631	4.47	0.140	0.836	2.4.1.-	83
4	0.060	1fp3A	0.422	4.49	0.067	0.565	5.1.3.8	173
5	0.060	1j0mA	0.422	5.45	0.067	0.637	4.2.2.12	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	3fp4A	0.567	4.53	0.070	0.752	0.79	III	complex1.pdb.gz	63,67,70,82,94
2	0.03	3fp2A	0.569	4.47	0.067	0.752	0.72	III	complex2.pdb.gz	97,101,114,137,141,182
3	0.02	1f59A	0.527	6.05	0.054	0.833	0.68	III	complex3.pdb.gz	94,97,98,101,102,142,146
4	0.01	2vglA	0.544	5.93	0.080	0.847	0.66	IHP	complex4.pdb.gz	93,111,115,116,119
5	0.01	2bptA	0.546	5.47	0.063	0.810	0.65	III	complex5.pdb.gz	137,140,141,147,157

	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.