D-I-TASSER Q9UBD3

D-I-TASSER results for Q9UBD3

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

Summary of the Protein

Uniprot ID: Q9UBD3
Protein Name: Cytokine SCM-1 beta
Gene Name: XCL2

Input Sequence in FASTA format

>Q9UBD3 (114 residues)
MRLLILALLGICSLTAYIVEGVGSEVSHRRTCVSLTTQRLPVSRIKTYTITEGSLRAVIF
ITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

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	Q9UBD3-D1	1-114	114		MRLLILALLGICSLTAYIVEGVGSEVSHRRTCVSLTTQRLPVSRIKTYTITEGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5926

(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	1esrA	0.53	1.50	0.306	0.579	model1_1esrA.pdb.gz
2	2mp1A	0.52	2.26	0.247	0.640	model1_2mp1A.pdb.gz
3	1b2tA	0.51	2.21	0.284	0.614	model1_1b2tA.pdb.gz
4	1eotA	0.51	2.42	0.310	0.605	model1_1eotA.pdb.gz
5	1nr4E	0.50	1.89	0.224	0.570	model1_1nr4E.pdb.gz
6	1j9oA	0.50	2.78	0.747	0.632	model1_1j9oA.pdb.gz
7	1g91A	0.49	2.92	0.264	0.614	model1_1g91A.pdb.gz
8	1eihA	0.49	2.08	0.271	0.570	model1_1eihA.pdb.gz
9	1donA	0.49	1.75	0.260	0.561	model1_1donA.pdb.gz
10	5ltlA	0.49	1.62	0.242	0.553	model1_5ltlA.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:0008009	1.00	chemokine activity
GO:0048020	0.96	CCR chemokine receptor 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	1.00	biological regulation
GO:0050794	0.99	regulation of cellular process
GO:0048584	0.98	positive regulation of response to stimulus
GO:0044699	0.98	single-organism process
GO:0007165	0.98	signal transduction
GO:0002376	0.98	immune system process
GO:0048522	0.97	positive regulation of cellular process
GO:0030595	0.97	leukocyte chemotaxis
GO:0023051	0.97	regulation of signaling
GO:0010646	0.97	regulation of cell communication
GO:0010033	0.97	response to organic substance
GO:0007166	0.97	cell surface receptor signaling pathway
GO:0097529	0.96	myeloid leukocyte migration
GO:0071310	0.96	cellular response to organic substance
GO:0070374	0.96	positive regulation of ERK1 and ERK2 cascade
GO:0007186	0.96	G-protein coupled receptor signaling pathway
GO:0072676	0.95	lymphocyte migration
GO:0070098	0.95	chemokine-mediated signaling pathway
GO:0006950	0.95	response to stress
GO:0002548	0.95	monocyte chemotaxis
GO:0048247	0.94	lymphocyte chemotaxis
GO:0030593	0.94	neutrophil chemotaxis
GO:0006954	0.94	inflammatory response
GO:0071356	0.93	cellular response to tumor necrosis factor
GO:0071347	0.93	cellular response to interleukin-1
GO:0071346	0.93	cellular response to interferon-gamma
GO:0043547	0.93	positive regulation of GTPase activity
GO:0032103	0.80	positive regulation of response to external stimulus
GO:0080134	0.78	regulation of response to stress
GO:0050729	0.77	positive regulation of inflammatory response

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:0005615	0.99	extracellular space
GO:0044464	0.71	cell 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	0.060	3c6gB	0.444	3.81	0.070	0.702	1.14.13.15	NA
2	0.060	1is9A	0.395	4.46	0.012	0.693	3.2.1.4	NA
3	0.060	3e6iA	0.442	3.89	0.095	0.693	1.14.13.-	NA
4	0.060	1gq6B	0.432	4.87	0.038	0.816	3.5.3.22	NA
5	0.060	2pywA	0.436	5.04	0.056	0.798	2.7.1.100	79

	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	0.15	1b3aB	0.486	1.64	0.323	0.535	1.43	SO4	complex1.pdb.gz	44,62,64,65,67
2	0.07	1eqt0	0.484	1.68	0.308	0.535	0.98	III	complex2.pdb.gz	30,31,32,33,34,36,59,69
3	0.07	1ilpA	0.472	2.01	0.194	0.561	0.77	III	complex3.pdb.gz	35,36,38,39,40,41,43,44,58,61,66,68,69
4	0.07	1ilqA	0.471	2.02	0.194	0.561	0.75	III	complex4.pdb.gz	33,35,40,44,59,62,63,64,66,67,68
5	0.04	1nr40	0.479	1.92	0.231	0.544	1.05	III	complex5.pdb.gz	30,31,32,33,34,35,36,46,48,61,65,67,69

	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.