D-I-TASSER Q6UW10

D-I-TASSER results for Q6UW10

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

Summary of the Protein

Uniprot ID: Q6UW10
Protein Name: Surfactant-associated protein 2
Gene Name: SFTA2

Input Sequence in FASTA format

>Q6UW10 (78 residues)
MGSGLPLVLLLTLLGSSHGTGPGMTLQLKLKESFLTNSSYESSFLELLEKLCLLLHLPSG
TSVTLHHARSQHHVVCNT

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	Q6UW10-D1	1-78	78		MGSGLPLVLLLTLLGSSHGTGPGMTLQLKLKESFLTNSSYESSFLELLEKLCLLLHLPSGTSVTLHHARSQHHVVCNT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.526

(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	4jpjA	0.62	2.77	0.105	0.897	model1_4jpjA.pdb.gz
2	3jc5c2	0.61	2.67	0.113	0.910	model1_3jc5c2.pdb.gz
3	6i2vA	0.60	2.75	0.053	0.872	model1_6i2vA.pdb.gz
4	7vkaA2	0.59	3.20	0.065	0.936	model1_7vkaA2.pdb.gz
5	4eplA2	0.59	3.09	0.068	0.897	model1_4eplA2.pdb.gz
6	1ym5A	0.59	3.11	0.113	0.872	model1_1ym5A.pdb.gz
7	4b2gA	0.59	3.22	0.052	0.936	model1_4b2gA.pdb.gz
8	1u0kA1	0.57	2.93	0.134	0.833	model1_1u0kA1.pdb.gz
9	1qyaB1	0.57	3.21	0.106	0.833	model1_1qyaB1.pdb.gz
10	4ewvA2	0.57	3.47	0.082	0.897	model1_4ewvA2.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:0005198	0.15	structural molecule activity
GO:0043138	0.13	3'-5' DNA helicase activity
GO:0003697	0.13	single-stranded DNA binding
GO:0003688	0.13	DNA replication origin binding
GO:0003682	0.13	chromatin 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:1903911	0.15	positive regulation of receptor clustering
GO:1903908	0.15	positive regulation of plasma membrane raft polarization
GO:1903905	0.15	positive regulation of establishment of T cell polarity
GO:0090527	0.15	actin filament reorganization
GO:0075512	0.15	clathrin-mediated endocytosis of virus by host cell
GO:0039654	0.15	fusion of virus membrane with host endosome membrane
GO:0030683	0.15	evasion or tolerance by virus of host immune response
GO:0019082	0.15	viral protein processing
GO:0019068	0.15	virion assembly
GO:0019064	0.15	fusion of virus membrane with host plasma membrane
GO:0019062	0.15	virion attachment to host cell
GO:0002223	0.15	stimulatory C-type lectin receptor signaling pathway
GO:1902977	0.13	mitotic DNA replication preinitiation complex assembly
GO:1900087	0.13	positive regulation of G1/S transition of mitotic cell cycle
GO:0032508	0.13	DNA duplex unwinding
GO:0031938	0.13	regulation of chromatin silencing at telomere
GO:0006270	0.13	DNA replication initiation
GO:0006267	0.13	pre-replicative complex assembly involved in nuclear cell cycle DNA replication
GO:0000727	0.13	double-strand break repair via break-induced replication

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:0055036	0.88	virion membrane
GO:0019031	0.88	viral envelope
GO:0019012	0.88	virion
GO:0044175	0.81	host cell endosome membrane
GO:0044174	0.81	host cell endosome
GO:0016021	0.81	integral component of membrane
GO:0020002	0.75	host cell plasma 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	2hawB	0.568	2.77	0.056	0.821	3.6.1.1	NA
2	0.060	2ocgA	0.544	3.30	0.055	0.859	3.1.-.-	NA
3	0.060	3ejxD	0.535	3.18	0.092	0.821	5.1.1.7	NA
4	0.060	1wppA	0.563	3.02	0.055	0.846	3.6.1.1	27
5	0.060	1qtrA	0.536	3.51	0.086	0.859	3.4.11.5	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	0.02	1u1wA	0.561	2.88	0.108	0.808	0.18	3HA	complex1.pdb.gz	55,62,63,64
2	0.01	1bcsA	0.567	3.33	0.107	0.923	0.21	III	complex2.pdb.gz	20,21,24
3	0.01	2pw0B	0.549	3.13	0.059	0.846	0.17	TRC	complex3.pdb.gz	21,22,24

	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.