D-I-TASSER Q8TEW0-D3

D-I-TASSER results for Q8TEW0-D3

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

Input Sequence in FASTA format

>Q8TEW0 (83 residues)
REFRERQARERDYAEIQDFHRTFGCDDELMYGGVSSYEGSMALNARPQSPREGHMMDALY
AQVKKPRNSKPSPVDSNRSTPSN

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| REFRERQARERDYAEIQDFHRTFGCDDELMYGGVSSYEGSMALNARPQSPREGHMMDALYAQVKKPRNSKPSPVDSNRSTPSN
Prediction	CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	24899888776678776321145777776768855457642147899999877630567776527888999998767778899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| REFRERQARERDYAEIQDFHRTFGCDDELMYGGVSSYEGSMALNARPQSPREGHMMDALYAQVKKPRNSKPSPVDSNRSTPSN
Prediction	86457554555424414523443436754334314324442415444744664543531243165445754444556544478
	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

CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC
REFRERQARERDYAEIQDFHRTFGCDDELMYGGVSSYEGSMALNARPQSPREGHMMDALYAQVKKPRNSKPSPVDSNRSTPSN

1l2fA1

0.04

1.78

0.61

CEthreader

KALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVETQISLEEAKKIDPLAEVGSIVKKELNVKN----------------

2k48A

0.04

1.93

0.52

EigenThreader

IDPFTMSTLQELQENITAHEQQLV----TARQKLKDAEKAVEVDPDDVNKSTLQNRRAAVSTLETKLGELKRQLADLVAAQKL

5x0mA2

0.09

0.08

3.23

0.31

FFAS-3D

----KGRGANKDRDGSAHPDQALEQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGEKSLWLDPFT

3bogA

0.12

0.11

3.84

1.17

SPARKS-K

KGADGAHGVGCPGTAGAAGSVGGPGCDGGHGGNGGNGCAGGVGGAGGASGGTGVGGRGG-----KGGSGTPKGADGAPGAP--

6ezvX

0.11

0.06

2.17

0.46

CNFpred

--GVLQNQIDDDYDSIAQEQKQ-KAEDQQQIIALQGLSNA---------------SSAVVSAI--------------------

1v34A

0.05

2.19

1.00

DEthreader

MLLCVCPICLNDAKEIVRDTVIILELIVSAFLGYFII-KLPLIIRKSIVSLAKLFLS-TFS-KSYFDTLP-AKFNPKH-----

1l2fA1

0.06

0.05

2.08

0.76

MapAlign

EKALVSAYRKNGNSKNVEVVIDRNTGNIKVYQLLEVVETQISLEEAKKIDPLAEVGSIVKKELNV------------------

5u0p2

0.11

0.10

3.48

0.59

MUSTER

MSLEEQRTRDELKHKLLDLNQLTICPSHPETGTVNSFYTHLKSSNDTENNETKS--------INGKSAKEPHHSEHDNDNF--

2pffB

0.12

4.23

0.50

HHsearch

PSILEDSLEEGVPSPMLSISNLTQEQ-VQDYVNTNSHLPAGQVEISLVNGAVSGPPQSLYGLLRKPSGLRIPFSE-RKLKFSN

5xxuG

0.08

3.28

0.57

CEthreader

VEVDDEKKLLPFFKRMGAEVAGDSKGYIFRISGGNDKQGPMMQGVLVNHRVRGPDLAVLNLVLVKKGPETIPGLTDAERPRRL

(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	0.4706

(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	5vy9A1	0.50	3.99	0.052	0.892	model1_5vy9A1.pdb.gz
2	2q1hA	0.47	4.45	0.072	0.928	model1_2q1hA.pdb.gz
3	3hq5B	0.47	4.34	0.075	0.904	model1_3hq5B.pdb.gz
4	4if8A	0.47	3.73	0.067	0.831	model1_4if8A.pdb.gz
5	1qvrA	0.47	4.37	0.038	0.916	model1_1qvrA.pdb.gz
6	1gwxB	0.46	4.46	0.049	0.892	model1_1gwxB.pdb.gz
7	1xvpD	0.46	4.42	0.024	0.892	model1_1xvpD.pdb.gz
8	2bj4B	0.44	4.69	0.038	0.892	model1_2bj4B.pdb.gz
9	1pduA	0.44	4.72	0.065	0.916	model1_1pduA.pdb.gz
10	1imvA	0.44	4.09	0.014	0.819	model1_1imvA.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:0032266	1.00	phosphatidylinositol-3-phosphate binding
GO:0005547	1.00	phosphatidylinositol-3,4,5-trisphosphate binding
GO:0005546	1.00	phosphatidylinositol-4,5-bisphosphate binding
GO:0019899	0.65	enzyme 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:0051960	1.00	regulation of nervous system development
GO:0051649	1.00	establishment of localization in cell
GO:0051641	1.00	cellular localization
GO:0048523	1.00	negative regulation of cellular process
GO:0022011	1.00	myelination in peripheral nervous system
GO:0016043	1.00	cellular component organization
GO:0007163	1.00	establishment or maintenance of cell polarity
GO:0032502	0.73	developmental process
GO:0044767	0.72	single-organism developmental process
GO:0048869	0.71	cellular developmental process
GO:0009653	0.71	anatomical structure morphogenesis
GO:0030030	0.70	cell projection organization
GO:0051128	0.69	regulation of cellular component organization
GO:0006996	0.69	organelle organization
GO:1902589	0.68	single-organism organelle organization
GO:0051642	0.68	centrosome localization
GO:0045197	0.68	establishment or maintenance of epithelial cell apical/basal polarity
GO:0016477	0.68	cell migration
GO:0048856	0.55	anatomical structure development
GO:0048518	0.54	positive regulation of biological process
GO:0030154	0.54	cell differentiation
GO:0060242	0.53	contact inhibition
GO:0051660	0.53	establishment of centrosome localization
GO:0048696	0.53	regulation of collateral sprouting in absence of injury
GO:0048048	0.53	embryonic eye morphogenesis
GO:0043010	0.53	camera-type eye development
GO:0036032	0.53	neural crest cell delamination
GO:0035845	0.53	photoreceptor cell outer segment organization
GO:0022010	0.53	central nervous system myelination
GO:0021535	0.53	cell migration in hindbrain
GO:0014033	0.53	neural crest cell differentiation
GO:0007405	0.53	neuroblast proliferation
GO:0001755	0.53	neural crest cell migration
GO:0080090	0.52	regulation of primary metabolic process
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0048522	0.52	positive regulation of cellular process
GO:0031323	0.52	regulation of cellular metabolic process
GO:0032268	0.50	regulation of cellular protein metabolic process
GO:0022607	0.50	cellular component assembly

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	0.96	cell part
GO:0044424	0.87	intracellular part
GO:0016020	0.67	membrane
GO:0030054	0.60	cell junction
GO:0005737	0.60	cytoplasm

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	1yrlA	0.430	4.72	0.038	0.892	1.1.1.86	NA
2	0.060	1bsgA	0.421	4.61	0.038	0.855	3.5.2.6	NA
3	0.060	3exeA	0.436	4.49	0.092	0.904	1.2.4.1	NA
4	0.060	1um9C	0.336	5.25	0.066	0.819	1.2.4.4	NA
5	0.060	1xmeA	0.431	4.17	0.096	0.855	1.9.3.1	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:

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	1e3kB	0.475	4.53	0.075	0.928	0.22	R18	complex1.pdb.gz	9,10,16,33,38
2	0.01	2w8yA	0.473	4.37	0.098	0.904	0.23	486	complex2.pdb.gz	7,10,11,14,15,31,32,39,46
3	0.01	1zucB	0.471	4.31	0.075	0.904	0.20	T98	complex3.pdb.gz	7,11,32,34,39,74
4	0.01	2q1hA	0.471	4.45	0.072	0.928	0.22	AS4	complex4.pdb.gz	10,11,14,32,39,47
5	0.01	2oaxC	0.337	4.55	0.028	0.735	0.12	SNL	complex5.pdb.gz	16,48,57

	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.