D-I-TASSER Q9UIR0

D-I-TASSER results for Q9UIR0

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

Summary of the Protein

Uniprot ID: Q9UIR0
Protein Name: Butyrophilin-like protein 2
Gene Name: BTNL2

Input Sequence in FASTA format

>Q9UIR0 (455 residues)
MVDFPGYNLSGAVASFLFILLTMKQSEDFRVIGPAHPILAGVGEDALLTCQLLPKRTTMH
VEVRWYRSEPSTPVFVHRDGVEVTEMQMEEYRGWVEWIENGIAKGNVALKIHNIQPSDNG
QYWCHFQDGNYCGETSLLLKVAGLGSAPSIHMEGPGESGVQLVCTARGWFPEPQVYWEDI
RGEKLLAVSEHRIQDKDGLFYAEATLVVRNASAESVSCLVHNPVLTEEKGSVISLPEKLQ
TELASLKVNGPSQPILVRVGEDIQLTCYLSPKANAQSMEVRWDRSHRYPAVHVYMDGDHV
AGEQMAEYRGRTVLVSDAIDEGRLTLQILSARPSDDGQYRCLFEKDDVYQEASLDLKVVS
LGSSPLITVEGQEDGEMQPMCSSDGWFPQPHVPWRDMEGKTIPSSSQALTQGSHGLFHVQ
TLLRVTNISAVDVTCSISIPFLGEEKIATFSLSGW

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	Q9UIR0-D1	1-142	142		MVDFPGYNLSGAVASFLFILLTMKQSEDFRVIGPAHPILAGVGEDALLTCQLLPKRTTMHVEVRWYRSEPSTPVFVHRDGVEVTEMQMEEYRGWVEWIENGIAKGNVALKIHNIQPSDNGQYWCHFQDGNYCGETSLLLKVA
2	Q9UIR0-D2	143-239	97		GLGSAPSIHMEGPGESGVQLVCTARGWFPEPQVYWEDIRGEKLLAVSEHRIQDKDGLFYAEATLVVRNASAESVSCLVHNPVLTEEKGSVISLPEKL
3	Q9UIR0-D3	240-360	121		QTELASLKVNGPSQPILVRVGEDIQLTCYLSPKANAQSMEVRWDRSHRYPAVHVYMDGDHVAGEQMAEYRGRTVLVSDAIDEGRLTLQILSARPSDDGQYRCLFEKDDVYQEASLDLKVVS
4	Q9UIR0-D4	361-455	95		LGSSPLITVEGQEDGEMQPMCSSDGWFPQPHVPWRDMEGKTIPSSSQALTQGSHGLFHVQTLLRVTNISAVDVTCSISIPFLGEEKIATFSLSGW

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.66

(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	5oj2A	0.59	4.75	0.135	0.771	model1_5oj2A.pdb.gz
2	7khfH	0.51	6.20	0.083	0.752	model1_7khfH.pdb.gz
3	5xeqB	0.44	4.68	0.172	0.571	model1_5xeqB.pdb.gz
4	1ulvA	0.43	6.73	0.052	0.668	model1_1ulvA.pdb.gz
5	3k71G	0.43	7.30	0.055	0.730	model1_3k71G.pdb.gz
6	3fcsA	0.42	7.13	0.056	0.677	model1_3fcsA.pdb.gz
7	4g1eA	0.41	7.64	0.051	0.721	model1_4g1eA.pdb.gz
8	2dtgE	0.41	6.16	0.039	0.600	model1_2dtgE.pdb.gz
9	6iaaA	0.41	6.20	0.043	0.598	model1_6iaaA.pdb.gz
10	4frwA	0.41	2.76	0.172	0.448	model1_4frwA.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:0060089	0.67	molecular transducer activity
GO:0004872	0.61	receptor activity
GO:0042802	0.55	identical protein binding
GO:0046983	0.53	protein dimerization activity
GO:0042803	0.51	protein homodimerization activity

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	0.88	single-organism process
GO:0009987	0.85	cellular process
GO:0065007	0.81	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0044763	0.78	single-organism cellular process
GO:0050794	0.72	regulation of cellular process
GO:0032502	0.59	developmental process
GO:0048856	0.57	anatomical structure development
GO:0044767	0.52	single-organism developmental process
GO:0006928	0.52	movement of cell or subcellular component
GO:0050896	0.50	response to stimulus

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	0.99	cell part
GO:0044425	0.85	membrane part
GO:0044459	0.82	plasma membrane part
GO:0016020	0.80	membrane
GO:0005886	0.78	plasma membrane
GO:0043226	0.76	organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0031224	0.75	intrinsic component of membrane
GO:0016021	0.74	integral component of membrane
GO:0044424	0.68	intracellular part
GO:0043234	0.66	protein complex
GO:0044421	0.64	extracellular region part
GO:0031982	0.63	vesicle
GO:0031988	0.58	membrane-bounded vesicle
GO:0098797	0.57	plasma membrane protein complex
GO:0070062	0.55	extracellular exosome
GO:0009986	0.55	cell surface
GO:0030054	0.51	cell junction

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	1l9mB	0.351	6.82	0.046	0.534	2.3.2.13	NA
2	0.060	1ea0A	0.326	7.81	0.046	0.565	1.4.1.13	NA
3	0.060	2fhbA	0.399	6.92	0.050	0.631	3.2.1.41	NA
4	0.060	3iydC	0.336	7.39	0.070	0.571	2.7.7.6	NA
5	0.060	2o26U	0.343	4.15	0.110	0.424	2.7.10.1	45,47,140

	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	3cmvC	0.367	7.14	0.064	0.587	0.12	ANP	complex1.pdb.gz	117,119,168
2	0.01	3cmvF	0.366	7.10	0.064	0.582	0.13	ANP	complex2.pdb.gz	118,119,145,168
3	0.01	2vdqA	0.207	7.42	0.051	0.343	0.23	III	complex3.pdb.gz	114,142,144
4	0.01	3cmvE	0.366	7.23	0.064	0.589	0.11	ANP	complex4.pdb.gz	118,145,168
5	0.01	3cmvA	0.293	7.72	0.051	0.512	0.12	ANP	complex5.pdb.gz	41,42,120
6	0.01	3cmvE	0.366	7.23	0.064	0.589	0.21	ANP	complex6.pdb.gz	118,120,144,169
7	0.01	2fhcA	0.392	6.72	0.057	0.611	0.11	GLC	complex7.pdb.gz	44,171,221,222
8	0.01	3cmvB	0.366	7.18	0.064	0.587	0.19	ANP	complex8.pdb.gz	119,140,141,142

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.