D-I-TASSER Q9UHD2-D3

D-I-TASSER results for Q9UHD2-D3

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

Input Sequence in FASTA format

>Q9UHD2 (104 residues)
DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGD
MPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL
Prediction	CCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCSSSSSCCCCCCSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHC
Confidence	90347699999996799977788862019999999861886632323316788356403589878679889999999999997169888168999999997509
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL
Prediction	84101001301111232113346465424410340256445420332454762414235602662513640363025003300544364313154015205737
	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                 100

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCSSSSSCCCCCCSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHC
DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

6cq0A

0.79

0.75

21.20

1.17

DEthreader

DLWSIGVTFYHAATGSLPFRPFEGRRNKEVM-YKIITGKPSGAIS-GVQGPID--WSGDMPVS-CSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

3gc0A2

0.15

0.14

4.86

1.44

SPARKS-K

DIWSIACIWAEMLMKTPLFPG----DSEIDQLFKIFEVLGLPDDTTWPGTALPDWKQSFPKFRGKTLGALLDDEGLDLLTAMLEMDPVKRISAKNALEHPYFSH

4eutA

1.00

0.98

27.46

0.87

MapAlign

-LWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDI-

4eutA

1.00

28.00

0.54

CEthreader

DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

6cq0A1

1.00

28.00

1.31

MUSTER

DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

4iw0A

1.00

28.00

0.80

HHsearch

DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

4eutA

1.00

28.00

1.40

FFAS-3D

DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

4iw0A

1.00

28.00

0.88

EigenThreader

DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

4eutA

1.00

28.00

1.33

CNFpred

DLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

6cq0A1

0.79

0.75

21.20

1.17

DEthreader

DLWSIGVTFYHAATGSLPFRPFEGRRNKEVM-YKIITGKPSGAIS-GVQGPID--WSGDMPVS-CSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL

(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	0.7418

(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	4eutA	0.98	0.49	1.000	1.000	model1_4eutA.pdb.gz
2	4iw0A	0.98	0.53	1.000	1.000	model1_4iw0A.pdb.gz
3	5ebzA	0.80	2.10	0.222	0.952	model1_5ebzA.pdb.gz
4	3qa8A	0.66	2.95	0.231	0.865	model1_3qa8A.pdb.gz
5	2vx3A	0.66	2.79	0.111	0.865	model1_2vx3A.pdb.gz
6	1z57A	0.65	2.91	0.144	0.865	model1_1z57A.pdb.gz
7	3zutA	0.65	1.84	0.228	0.760	model1_3zutA.pdb.gz
8	4ianA2	0.65	3.16	0.196	0.846	model1_4ianA2.pdb.gz
9	5l2qC	0.65	1.63	0.169	0.740	model1_5l2qC.pdb.gz
10	2ac3A2	0.65	2.27	0.183	0.779	model1_2ac3A2.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	0.66	catalytic activity
GO:0016740	0.63	transferase activity
GO:0016301	0.61	kinase activity
GO:0004674	0.60	protein serine/threonine kinase 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:0050794	0.99	regulation of cellular process
GO:0048522	0.96	positive regulation of cellular process
GO:0009987	0.91	cellular process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0044238	0.88	primary metabolic process
GO:0006468	0.86	protein phosphorylation
GO:0080090	0.75	regulation of primary metabolic process
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0031323	0.75	regulation of cellular metabolic process
GO:0051246	0.74	regulation of protein metabolic process
GO:0031325	0.74	positive regulation of cellular metabolic process
GO:0010604	0.74	positive regulation of macromolecule metabolic process
GO:0051247	0.73	positive regulation of protein metabolic process
GO:0050896	0.71	response to stimulus
GO:0048583	0.70	regulation of response to stimulus
GO:0048584	0.69	positive regulation of response to stimulus
GO:0006950	0.69	response to stress
GO:0044699	0.66	single-organism process
GO:0051239	0.61	regulation of multicellular organismal process
GO:0048519	0.60	negative regulation of biological process
GO:0002376	0.60	immune system process
GO:0001817	0.60	regulation of cytokine production
GO:0080134	0.58	regulation of response to stress
GO:0051704	0.58	multi-organism process
GO:0043207	0.58	response to external biotic stimulus
GO:0018105	0.58	peptidyl-serine phosphorylation
GO:0002684	0.58	positive regulation of immune system process
GO:0051707	0.57	response to other organism
GO:0032479	0.57	regulation of type I interferon production
GO:0002218	0.57	activation of innate immune response
GO:0016043	0.53	cellular component organization
GO:0044763	0.50	single-organism cellular 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:0005737	1.00	cytoplasm
GO:0044444	0.67	cytoplasmic 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	2wu6A	0.647	2.85	0.135	0.856	2.7.12.1	NA
2	0.060	1tkiA	0.632	2.14	0.139	0.760	2.7.11.1	NA
3	0.060	2x4fA	0.625	2.12	0.165	0.760	2.7.11.1	42,45
4	0.060	3e3pA	0.633	2.73	0.155	0.817	2.7.1.37	64
5	0.060	3fbvD	0.621	2.22	0.190	0.760	2.7.11.1	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.03	3kl8C	0.628	2.22	0.190	0.760	0.40	III	complex1.pdb.gz	15,16,17,18,20,33

	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.