D-I-TASSER Q8WVP7

D-I-TASSER results for Q8WVP7

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

Summary of the Protein

Uniprot ID: Q8WVP7
Protein Name: Limb region 1 protein homolog
Gene Name: LMBR1

Input Sequence in FASTA format

>Q8WVP7 (490 residues)
MEGQDEVSAREQHFHSQVRESTICFLLFAILYVVSYFIITRYKRKSDEQEDEDAIVNRIS
LFLSTFTLAVSAGAVLLLPFSIISNEILLSFPQNYYIQWLNGSLIHGLWNLASLFSNLCL
FVLMPFAFFFLESEGFAGLKKGIRARILETLVMLLLLALLILGIVWVASALIDNDAASME
SLYDLWEFYLPYLYSCISLMGCLLLLLCTPVGLSRMFTVMGQLLVKPTILEDLDEQIYII
TLEEEALQRRLNGLSSSVEYNIMELEQELENVKTLKTKLERRKKASAWERNLVYPAVMVL
LLIETSISVLLVACNILCLLVDETAMPKGTRGPGIGNASLSTFGFVGAALEIILIFYLMV
SSVVGFYSLRFFGNFTPKKDDTTMTKIIGNCVSILVLSSALPVMSRTLGITRFDLLGDFG
RFNWLGNFYIVLSYNLLFAIVTTLCLVRKFTSAVREELFKALGLHKLHLPNTSRDSETAK
PSVNGHQKAL

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	Q8WVP7-D1	1-490	490		MEGQDEVSAREQHFHSQVRESTICFLLFAILYVVSYFIITRYKRKSDEQEDEDAIVNRISLFLSTFTLAVSAGAVLLLPFSIISNEILLSFPQNYYIQWLNGSLIHGLWNLASLFSNLCLFVLMPFAFFFLESEGFAGLKKGIRARILETLVMLLLLALLILGIVWVASALIDNDAASMESLYDLWEFYLPYLYSCISLMGCLLLLLCTPVGLSRMFTVMGQLLVKPTILEDLDEQIYIITLEEEALQRRLNGLSSSVEYNIMELEQELENVKTLKTKLERRKKASAWERNLVYPAVMVLLLIETSISVLLVACNILCLLVDETAMPKGTRGPGIGNASLSTFGFVGAALEIILIFYLMVSSVVGFYSLRFFGNFTPKKDDTTMTKIIGNCVSILVLSSALPVMSRTLGITRFDLLGDFGRFNWLGNFYIVLSYNLLFAIVTTLCLVRKFTSAVREELFKALGLHKLHLPNTSRDSETAKPSVNGHQKAL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6054

(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	4a01A	0.46	6.26	0.067	0.655	model1_4a01A.pdb.gz
2	4av3A	0.44	6.40	0.068	0.633	model1_4av3A.pdb.gz
3	6kobA	0.43	6.87	0.057	0.655	model1_6kobA.pdb.gz
4	6t15a	0.43	6.66	0.049	0.643	model1_6t15a.pdb.gz
5	1m56A	0.42	6.33	0.055	0.620	model1_1m56A.pdb.gz
6	6hwhV	0.42	6.44	0.077	0.629	model1_6hwhV.pdb.gz
7	7jroa	0.42	6.57	0.070	0.626	model1_7jroa.pdb.gz
8	1ocrN	0.42	6.33	0.049	0.610	model1_1ocrN.pdb.gz
9	2yevA	0.41	6.58	0.071	0.622	model1_2yevA.pdb.gz
10	1fftA	0.41	6.52	0.054	0.604	model1_1fftA.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:0005215	0.70	transporter activity
GO:1901363	0.58	heterocyclic compound binding
GO:0097159	0.58	organic cyclic compound binding
GO:0043167	0.56	ion binding
GO:0046872	0.55	metal ion binding
GO:0003824	0.54	catalytic activity
GO:0046914	0.51	transition metal ion 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:0044699	0.81	single-organism process
GO:0032502	0.75	developmental process
GO:0044767	0.74	single-organism developmental process
GO:0009653	0.72	anatomical structure morphogenesis
GO:0048598	0.70	embryonic morphogenesis
GO:0035137	0.70	hindlimb morphogenesis
GO:0042733	0.69	embryonic digit morphogenesis
GO:0035116	0.69	embryonic hindlimb morphogenesis
GO:0065007	0.53	biological regulation
GO:0050789	0.52	regulation of biological 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:0044464	0.97	cell part
GO:0016020	0.97	membrane
GO:0044425	0.80	membrane part
GO:0044424	0.79	intracellular part
GO:0016021	0.79	integral component of membrane
GO:0005886	0.76	plasma membrane
GO:0044444	0.60	cytoplasmic part
GO:0043226	0.54	organelle
GO:0043229	0.51	intracellular organelle
GO:0043227	0.51	membrane-bounded organelle

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	3i39X	0.337	6.03	0.069	0.484	1.2.99.2	NA
2	0.060	2e1qA	0.313	7.61	0.048	0.531	1.17.3.2 1.17.1.4	NA
3	0.060	3dy5A	0.320	7.16	0.048	0.516	1.13.11.40 4.2.1.92	NA
4	0.060	2vumA	0.269	7.41	0.040	0.441	2.7.7.6	NA
5	0.060	2vuaA	0.207	7.09	0.051	0.327	3.4.24.69	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	2dysN	0.416	6.30	0.054	0.606	0.14	HEA	complex1.pdb.gz	67,74,197,198,200,201
2	0.01	1ocoA	0.411	6.44	0.056	0.614	0.13	UUU	complex2.pdb.gz	67,71,74
3	0.01	1qleA	0.423	6.61	0.083	0.643	0.11	HEA	complex3.pdb.gz	115,119,120,122,123,126
4	0.01	3dtuC	0.418	6.58	0.070	0.633	0.11	HEA	complex4.pdb.gz	131,135,136
5	0.01	1oczN	0.414	6.29	0.049	0.606	0.13	HEA	complex5.pdb.gz	64,71,198,199,201
6	0.01	2eijN	0.415	6.34	0.049	0.610	0.13	HEA	complex6.pdb.gz	67,74,75,78
7	0.01	2zxwA	0.418	6.37	0.057	0.616	0.15	UUU	complex7.pdb.gz	116,117,123,126,193,197,200,201,204,205
8	0.01	3omaA	0.411	6.70	0.062	0.633	0.14	HEA	complex8.pdb.gz	63,64,133,136,137
9	0.01	3ehbA	0.421	6.56	0.074	0.641	0.13	UUU	complex9.pdb.gz	63,132,135,136
10	0.01	3ag4A	0.414	6.42	0.056	0.610	0.10	HEA	complex10.pdb.gz	17,20,24,27

	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.