D-I-TASSER Q6UXC1-D4

D-I-TASSER results for Q6UXC1-D4

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

Input Sequence in FASTA format

>Q6UXC1 (99 residues)
VVDTSPDALPRGQTASLTSKEHRPLAQPACLTFWYHGSLRSPGTLRVYLEERGRHQVLSL
SAHGGLAWRLGSMDVQAERAWRVVFEAVAAGVAHSYVAL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| VVDTSPDALPRGQTASLTSKEHRPLAQPACLTFWYHGSLRSPGTLRVYLEERGRHQVLSLSAHGGLAWRLGSMDVQAERAWRVVFEAVAAGVAHSYVAL
Prediction	CSSCCCCCCCCCCSSSSSCCCCCCCCCCSSSSSSSSCCCCCCCSSSSSSSSCCCCSSSSSSCCCCCCSSSSSSSSCCCCCSSSSSSSSSCCCCCSSSSC
Confidence	922889999998299999564169999838999999248998579999994999247999847898428999997589987999999987987416659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| VVDTSPDALPRGQTASLTSKEHRPLAQPACLTFWYHGSLRSPGTLRVYLEERGRHQVLSLSAHGGLAWRLGSMDVQAERAWRVVFEAVAAGVAHSYVAL
Prediction	744033763554430202033143674520031213031643330201035786441143326446533414040437551200010233554412006
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80

                   |                   |                   |                   |

SS
Seq

CSSCCCCCCCCCCSSSSSCCCCCCCCCCSSSSSSSSCCCCCCCSSSSSSSSCCCCSSSSSSCCCCCCSSSSSSSSCCCCCSSSSSSSSSCCCCCSSSSC
VVDTSPDALPRGQTASLTSKEHRPLAQPACLTFWYHGSLRSPGTLRVYLEERGRHQVLSLSAHGGLAWRLGSMDVQAERAWRVVFEAVAAGVAHSYVAL

7auwA2

0.22

7.00

1.33

DEthreader

FMHFDSSSVNVGATAVLESRTLYPKRGFQCLQFYLYNSGSESDQLNIYIREGNLTLVEEIKEIPTGSWQLYHVTLKVTKKFRVVFEGRKGGSLGGLSID

5l73A

0.27

0.26

8.07

1.40

SPARKS-K

YSQADENQK--GKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYEYDQLVWMAIGHQGDHWKEGRVLLHSLKLYQVIFEGEIGKGNLGGIAV

5l73A

0.27

8.36

0.61

MapAlign

FIYSQADENQKGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRQEYDQLVWMAIGHQGDHWKEGRVLLHKSKLYQVIFEGEIGKGLGGAVDD

5l73A

0.27

8.36

0.61

CEthreader

FIYSQADENQKGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYEYDQLVWMAIGHQGDHWKEGRVLLHKSKLYQVIFEGEIGKGNLGGIAV

5l73A

0.27

0.26

8.07

1.33

MUSTER

YSQADENQ--KGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYQKPQLVWMAIGHQGDHWKEGRVLLHKLKLYQVIFEGEIGKGNLGGIAV

7auwA2

0.24

0.23

7.25

2.97

HHsearch

HFDSSSV--NVGATAVLESRTLYPKRGFQCLQFYLYNSGSESDQLNIYIRESALTLVEEIKEIPTGSWQLYHVTLKVTKKFRVVFEGRKGSGSLGGLSI

4gwmA3

0.21

6.72

1.22

FFAS-3D

-MHFDSSSVNVGATAVLESRTLYPKRGFQCLQFYLYNSGSESDQLNIYIREYSATLVEEIKEIPTGSWQLYHVTLKVTKKFRVVFEGRKGSGSLGGLSI

4gwmA3

0.22

7.00

0.67

EigenThreader

FMHFDSSSVNVGATAVLESRTLYPKRGFQCLQFYLYNSGSESDQLNIYIREYDLTLVEEIKEIPTGSWQLYHVTLKVTKKFRVVFEGRKGSGASGGLSI

5l73A

0.27

0.26

8.07

1.63

CNFpred

YSQADE--NQKGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYQYDQLVWMAIGHQGDHWKEGRVLLHKLKLYQVIFEGEIGKGNLGGIAV

7auwA

0.22

7.00

1.33

DEthreader

FMHFDSSSVNVGATAVLESRTLYPKRGFQCLQFYLYNSGSESDQLNIYIREGNLTLVEEIKEIPTGSWQLYHVTLKVTKKFRVVFEGRKGGSLGGLSID

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8727

(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	7auwA	0.91	1.26	0.222	1.000	model1_7auwA.pdb.gz
2	5l73A	0.81	2.10	0.276	0.990	model1_5l73A.pdb.gz
3	2v5yA1	0.80	1.99	0.204	0.990	model1_2v5yA1.pdb.gz
4	2wo2A	0.77	2.14	0.138	0.950	model1_2wo2A.pdb.gz
5	3fl7A	0.77	2.24	0.106	0.950	model1_3fl7A.pdb.gz
6	4bk4A	0.74	2.55	0.129	0.939	model1_4bk4A.pdb.gz
7	1lb4A	0.54	3.33	0.058	0.828	model1_1lb4A.pdb.gz
8	1x4xA	0.48	3.97	0.059	0.748	model1_1x4xA.pdb.gz
9	1cn4B2	0.45	4.13	0.067	0.737	model1_1cn4B2.pdb.gz
10	1i1rA3	0.45	3.92	0.060	0.727	model1_1i1rA3.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	0.81	catalytic activity
GO:0004872	0.71	receptor activity
GO:0004871	0.60	signal transducer activity
GO:0004888	0.59	transmembrane signaling receptor activity
GO:0016740	0.53	transferase activity
GO:0016787	0.51	hydrolase 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	0.96	single-organism process
GO:0009987	0.95	cellular process
GO:0044763	0.87	single-organism cellular process
GO:0006928	0.78	movement of cell or subcellular component
GO:0065007	0.77	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:0007411	0.68	axon guidance
GO:0050896	0.67	response to stimulus
GO:0032502	0.66	developmental process
GO:0051179	0.61	localization
GO:0044767	0.60	single-organism developmental process
GO:0071704	0.59	organic substance metabolic process
GO:0007165	0.58	signal transduction
GO:0048856	0.57	anatomical structure development
GO:0051239	0.55	regulation of multicellular organismal process
GO:0051270	0.54	regulation of cellular component movement
GO:0044238	0.54	primary metabolic process
GO:0044237	0.54	cellular metabolic process
GO:0043170	0.54	macromolecule metabolic process
GO:0040012	0.54	regulation of locomotion
GO:0006810	0.54	transport
GO:2000026	0.53	regulation of multicellular organismal development
GO:0022603	0.52	regulation of anatomical structure morphogenesis
GO:0044260	0.51	cellular macromolecule metabolic process
GO:0007166	0.51	cell surface receptor signaling pathway

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:0044424	0.86	intracellular part
GO:0044444	0.75	cytoplasmic part
GO:0043226	0.71	organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0044425	0.66	membrane part
GO:0043229	0.65	intracellular organelle
GO:0016020	0.65	membrane
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0031224	0.58	intrinsic component of membrane
GO:0044459	0.53	plasma membrane part
GO:0005886	0.53	plasma membrane
GO:0016021	0.50	integral component of 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	0.067	2bbaA	0.789	2.15	0.126	0.960	2.7.10.1	44,62
2	0.067	1pmjX	0.738	2.56	0.093	0.980	3.2.1.78	41
3	0.067	1gu3A	0.675	2.73	0.098	0.929	3.2.1.4	17,98
4	0.066	1cx1A	0.623	3.30	0.052	0.970	3.2.1.4	NA
5	0.066	2w1uB	0.640	3.16	0.043	0.939	3.2.1.35	17

	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	0.06	2gmmB	0.708	2.95	0.082	0.990	0.66	MAN	complex1.pdb.gz	11,43,90,91,92
2	0.03	2bbaA	0.789	2.15	0.126	0.960	0.47	III	complex2.pdb.gz	1,3,35,37,96,97
3	0.03	2qbxB	0.753	2.52	0.138	0.950	0.46	III	complex3.pdb.gz	2,3,4,5,7,35,36,37,38
4	0.03	2fmdA	0.724	2.74	0.122	0.990	0.46	MAN	complex4.pdb.gz	38,39,91,96

	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.