D-I-TASSER Q14164-D3

D-I-TASSER results for Q14164-D3

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

Input Sequence in FASTA format

>Q14164 (101 residues)
IGVTLYHAATGSLPFIPFGGPRRNKEIMYRITTEKPAGAIAGAQRRENGPLEWSYTLPIT
CQLSLGLQSQLVPILANILEVEQAKCWGFDQFFAETSDILQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| IGVTLYHAATGSLPFIPFGGPRRNKEIMYRITTEKPAGAIAGAQRRENGPLEWSYTLPITCQLSLGLQSQLVPILANILEVEQAKCWGFDQFFAETSDILQ
Prediction	CCSSSSSCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCSSSSSSCCCCCSSSSCCCCCCCCCCHCHHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHC
Confidence	93456741108888644899877857765543148998167788549973897215999643583189999999998865161212669999999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| IGVTLYHAATGSLPFIPFGGPRRNKEIMYRITTEKPAGAIAGAQRRENGPLEWSYTLPITCQLSLGLQSQLVPILANILEVEQAKCWGFDQFFAETSDILQ
Prediction	63011112223312132373455345202402454353102014547714141256126404136404520141033115346743131440163046328
	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

CCSSSSSCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCSSSSSSCCCCCSSSSCCCCCCCCCCHCHHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHC
IGVTLYHAATGSLPFIPFGGPRRNKEIMYRITTEKPAGAIAGAQRRENGPLEWSYTLPITCQLSLGLQSQLVPILANILEVEQAKCWGFDQFFAETSDILQ

4eutA

0.57

0.53

15.38

1.00

DEthreader

IGVTFYHAATGSLPFRPFEGRNK-EVMYKIITG-KPSGAISGVQAE---NGP-IDWSGDMPVCLRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

6cq0A1

0.71

20.25

1.35

SPARKS-K

IGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

4eutA

0.71

0.70

19.97

0.87

MapAlign

LGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDIL-

4eutA

0.71

20.25

0.57

CEthreader

IGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

6cq0A1

0.71

20.25

1.26

MUSTER

IGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

4iw0A

0.71

20.25

0.93

HHsearch

IGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

6cq0A1

0.71

20.25

1.11

FFAS-3D

IGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

6gu2A2

0.15

0.13

4.35

0.97

EigenThreader

IGTIFAELATKKPLFHGD----SEIDQLFRIF-----RALGTPNNEVWPEVFPKWGSLASHVKN--LDENGLDLLSKMLIYDPAKRISGKMALNHP--YFN

4eutA

0.71

20.25

1.36

CNFpred

IGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

6cq0A

0.55

0.52

15.12

1.00

DEthreader

IGVTFYHAATGSLPFRPFEGRNK-EVMYKIITGKP-SGAISGVQKAE--NGP-IDWSGDMPVCLRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILH

(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	0.66

(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	4iw0A	0.98	0.49	0.713	1.000	model1_4iw0A.pdb.gz
2	4eutA	0.98	0.52	0.713	1.000	model1_4eutA.pdb.gz
3	5ebzA	0.80	2.09	0.177	0.951	model1_5ebzA.pdb.gz
4	3qa8A	0.65	3.01	0.193	0.861	model1_3qa8A.pdb.gz
5	2vx3A2	0.65	2.79	0.095	0.852	model1_2vx3A2.pdb.gz
6	5l2qC	0.64	1.63	0.162	0.733	model1_5l2qC.pdb.gz
7	1z57A2	0.64	2.97	0.128	0.861	model1_1z57A2.pdb.gz
8	3zutA1	0.64	1.90	0.171	0.752	model1_3zutA1.pdb.gz
9	2ac3A2	0.64	2.32	0.152	0.772	model1_2ac3A2.pdb.gz
10	5ig1A	0.63	2.04	0.160	0.743	model1_5ig1A.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	0.67	catalytic activity
GO:0016740	0.65	transferase activity
GO:0004674	0.63	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:0048522	1.00	positive regulation of cellular process
GO:0009987	0.92	cellular process
GO:0044260	0.90	cellular macromolecule metabolic process
GO:0044238	0.90	primary metabolic process
GO:0006796	0.88	phosphate-containing compound metabolic process
GO:0006464	0.88	cellular protein modification process
GO:0006468	0.87	protein phosphorylation
GO:0048583	0.73	regulation of response to stimulus
GO:0080090	0.72	regulation of primary metabolic process
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0050896	0.72	response to stimulus
GO:0048584	0.72	positive regulation of response to stimulus
GO:0031323	0.72	regulation of cellular metabolic process
GO:0006950	0.71	response to stress
GO:0051246	0.69	regulation of protein metabolic process
GO:0031325	0.69	positive regulation of cellular metabolic process
GO:0010604	0.69	positive regulation of macromolecule metabolic process
GO:0051247	0.68	positive regulation of protein metabolic process
GO:0044699	0.64	single-organism process
GO:0016043	0.64	cellular component organization
GO:0051239	0.60	regulation of multicellular organismal process
GO:0048519	0.59	negative regulation of biological process
GO:0001817	0.59	regulation of cytokine production
GO:0002376	0.58	immune system process
GO:0045088	0.56	regulation of innate immune response
GO:0002684	0.56	positive regulation of immune system process
GO:0032479	0.55	regulation of type I interferon production
GO:0002218	0.55	activation of innate immune response
GO:0051707	0.54	response to other organism
GO:0018105	0.54	peptidyl-serine phosphorylation
GO:0007165	0.53	signal transduction

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	0.69	cytoplasmic part
GO:0005829	0.51	cytosol

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	2pk9A	0.614	3.01	0.138	0.812	2.7.11.22	24,32
2	0.060	1z57A	0.641	2.97	0.128	0.861	2.7.12.1	NA
3	0.060	2acxA	0.613	2.39	0.187	0.743	2.7.11.16	35
4	0.060	2welA	0.628	2.00	0.147	0.743	2.7.11.17	NA
5	0.060	2v7oA	0.635	2.08	0.171	0.752	2.7.11.17	56

	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	2a2aB	0.625	2.28	0.158	0.752	0.59	NA	complex1.pdb.gz	2,3,7,10
2	0.12	3bhhB	0.632	2.10	0.145	0.752	0.43	5CP	complex2.pdb.gz	1,7,11,12,13,14,38,41,56
3	0.10	2vn9A	0.631	2.09	0.171	0.752	0.41	GVD	complex3.pdb.gz	39,41,55,73

	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.