D-I-TASSER P08151-D3

D-I-TASSER results for P08151-D3

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

Input Sequence in FASTA format

>P08151 (70 residues)
VGTSMVGSGLNPYMDNYGPNPCPQQASYPDPTQETWGEFPSHSGLYPGPKALGGTYSQCP
RLEHYGQVQV

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| VGTSMVGSGLNPYMDNYGPNPCPQQASYPDPTQETWGEFPSHSGLYPGPKALGGTYSQCPRLEHYGQVQV
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCC
Confidence	9743215777733334799999555678999987644487767777799899852124964222153249
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| VGTSMVGSGLNPYMDNYGPNPCPQQASYPDPTQETWGEFPSHSGLYPGPKALGGTYSQCPRLEHYGQVQV
Prediction	7544343431433156334441464263463446424514534332434544443344044254345358
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCC
VGTSMVGSGLNPYMDNYGPNPCPQQASYPDPTQETWGEFPSHSGLYPGPKALGGTYSQCPRLEHYGQVQV

7ct5A4

0.01

1.36

0.62

CEthreader

PLSETKCTLKSFTVEKGIYQT--SNFFGGVSVITPGTNTSNQVAVLYQDVNCTEVPSNVFQTRAGCLIGA

1nt0A

0.04

2.16

0.55

EigenThreader

LSYRCLCGQESTERAPGNDPFTDECRPCDYLGGYYGRSGPEYPQPYPKLSDVECDFCGKTLFTTNHTGWK

3jctw

0.20

6.40

0.31

FFAS-3D

VGGTGGQSSVMTLLQLPDPTDLPREKPLPKAKAMTWEKFAAKKGIKPKERAGKMIYDEASGVPKWGYKGA

3bogA

0.09

3.31

1.19

SPARKS-K

GAHGVGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTVGGRGGKGGSGTPKGADGA

4aroA

0.17

0.04

1.41

0.64

CNFpred

---------ADPLFHPVKAGICSMDKS-------------------------------------------

6ybjA

0.08

0.07

2.81

0.83

DEthreader

-------ATVDALKDAQTGSLYRLIISRYREQADQR-EFQGMKLDIKNEDVSRVMILFGAFVAKHLQECL

4nzrM2

0.06

2.53

0.82

MapAlign

-TLQNSDNSAIDANKLKQAVGDIYNYRRFERQFQGYFAGGYIDKYLVKNKELNLHLEEAYREGDNTYYRV

5w3nA

0.25

0.21

6.63

0.75

MUSTER

---SYSGYS-QS-TDTSGYGQ-SSYSSYGQSQNTGYGTQSTPQG-YGSTGGYGSSQSSQSS---YGQ-QS

7cn3A1

0.21

0.10

3.19

0.55

HHsearch

TGTRLLAVE-PPEVLARMLP-----YGYA-DEPGRWDHWPS-----------------------------

6jjaA

0.07

2.93

0.51

CEthreader

IGNPRKTTWIDIDLSSYTLTVGSYRNRITKLGPSKPNFIIEKVAAYAAPGDYKVVLVDEGSYAHRAAAGI

(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	0.5501

(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	6aqkA2	0.42	4.67	0.045	0.929	model1_6aqkA2.pdb.gz
2	2xivA	0.42	4.24	0.061	0.786	model1_2xivA.pdb.gz
3	2bi0A	0.42	4.01	0.046	0.843	model1_2bi0A.pdb.gz
4	6vcdA1	0.42	4.09	0.077	0.829	model1_6vcdA1.pdb.gz
5	1j33A	0.41	3.94	0.045	0.814	model1_1j33A.pdb.gz
6	5ksqA	0.41	4.10	0.059	0.814	model1_5ksqA.pdb.gz
7	5l4sA	0.40	3.56	0.044	0.743	model1_5l4sA.pdb.gz
8	4hdkB	0.40	4.09	0.015	0.857	model1_4hdkB.pdb.gz
9	1yu2A	0.40	4.37	0.060	0.871	model1_1yu2A.pdb.gz
10	5gjqV1	0.40	4.39	0.031	0.829	model1_5gjqV1.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:0003682	1.00	chromatin binding
GO:0000977	1.00	RNA polymerase II regulatory region sequence-specific DNA 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:0090090	1.00	negative regulation of canonical Wnt signaling pathway
GO:0045944	1.00	positive regulation of transcription from RNA polymerase II promoter
GO:0045880	1.00	positive regulation of smoothened signaling pathway
GO:0045740	1.00	positive regulation of DNA replication
GO:0044767	1.00	single-organism developmental process
GO:0009913	1.00	epidermal cell differentiation
GO:0009653	1.00	anatomical structure morphogenesis
GO:0008284	1.00	positive regulation of cell proliferation
GO:0007224	1.00	smoothened signaling pathway
GO:0001649	1.00	osteoblast differentiation
GO:0048546	0.57	digestive tract morphogenesis
GO:0030334	0.57	regulation of cell migration
GO:0030335	0.56	positive regulation of cell migration

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:0097542	1.00	ciliary tip
GO:0005829	1.00	cytosol
GO:0005737	1.00	cytoplasm
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	nucleus
GO:0097546	0.56	ciliary base

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	2zzgA	0.378	3.90	0.063	0.729	6.1.1.7	NA
2	0.060	1nwaA	0.378	4.29	0.032	0.829	1.8.4.11	32
3	0.060	3epsA	0.389	3.32	0.086	0.657	2.7.11.5	NA
4	0.060	3iv8D	0.360	4.15	0.034	0.714	3.5.1.25	NA
5	0.060	2ikoA	0.275	4.68	0.043	0.657	3.4.23.15	15

	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	0.01	1hbnA	0.365	4.62	0.031	0.857	0.42	UUU	complex1.pdb.gz	25,46,52
2	0.01	1m1kC	0.393	4.45	0.033	0.829	0.70	NA	complex2.pdb.gz	16,47,48,66
3	0.01	2h2sB	0.346	4.40	0.068	0.714	0.53	SEK	complex3.pdb.gz	44,45,46
4	0.01	1ogyA	0.394	4.41	0.049	0.800	0.50	SF4	complex4.pdb.gz	2,3,6,7,8,43,44
5	0.01	1jlrC	0.334	3.96	0.051	0.657	0.41	GTP	complex5.pdb.gz	1,4,43,45,52
6	0.01	3ml1A	0.369	4.32	0.071	0.771	0.48	SF4	complex6.pdb.gz	3,6,8,12,44

	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.