D-I-TASSER Q9BRX2-D3

D-I-TASSER results for Q9BRX2-D3

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

Input Sequence in FASTA format

>Q9BRX2 (116 residues)
KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRY
VRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED
Prediction	CHHHHHHHHHHHHHHHHHCCCSSSSCHHHHHHHHHHCCCSSSSSSCHHHCCCCHHHHHHHHHHHHHHHHHCCSSSSSCCCCCHHHHHHCCCCSSSSSSCCCCCCCCCCCCCCCCCC
Confidence	75899999999999997299929977999999999199809998210322787688999999999999819989998899931689861698899992667532212345665689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED
Prediction	73352251044016204747310000261035016330021000113114475474254024005304746040200046353253046212000003140652455676667778
	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

CHHHHHHHHHHHHHHHHHCCCSSSSCHHHHHHHHHHCCCSSSSSSCHHHCCCCHHHHHHHHHHHHHHHHHCCSSSSSCCCCCHHHHHHCCCCSSSSSSCCCCCCCCCCCCCCCCCC
KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED

1x52A

0.98

0.88

24.64

1.33

DEthreader

KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPSG------------

3agjB3

0.27

0.25

7.67

2.28

SPARKS-K

SIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVDTLLHSPDDAVREAVDEALRLVESMGGRVIIIPGDSPAGERLVSFGGVIALLRYPVPQEARR---------

3agjB

0.27

0.24

7.41

1.08

MapAlign

SIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVDTLLHSPDDAVREAVDEALRLVESMGGRVIIIPGDSPAGERLVSFGGVIALLRYPVARR------------

1x52A

0.94

0.88

24.67

0.75

CEthreader

KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPSGPSSG--------

3mcaB

0.48

0.46

13.28

1.49

MUSTER

KYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSLFRSSDIATRKKWVSLVEGVKEINCPVYIFSSLHESGKQLDLLSGIAAILTYPVDEEDISEDE------

3mcaB

0.48

0.46

13.28

2.11

HHsearch

KYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSLFRSSDIATRKKWVSLVEGVKEINCPVYIFSSLHESGKQLDLLSGIAAILTYPVDEEDISEDE------

3agjB3

0.28

0.25

7.66

1.75

FFAS-3D

SIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVDTLLHSPDDAVREAVDEALRLVESMGGRVIIIPGDSPAGERLVSFGGVIALLRYPVPQEA-----------

3e20C2

0.18

0.17

5.62

1.03

EigenThreader

KYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFADLDMIITYMTKEQSEWLAEHYKDYGANLEFVSDRSQEGMQFVKGFGIGAVMRYQLDL----SMLDPESDE

1x52A

0.94

0.88

24.67

1.49

CNFpred

KAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPSGPSSG--------

3obwA

0.29

0.25

7.62

1.33

DEthreader

YIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVIEDLLS-SDEQERLTIERMLEDIENKRGEVILVPKESPIYFELKNLTGILAILRFRIN--------------

(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	0.8219

(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	1x52A	0.87	1.64	0.954	0.922	model1_1x52A.pdb.gz
2	3mcaB3	0.83	1.68	0.431	0.940	model1_3mcaB3.pdb.gz
3	2vgnA	0.83	1.22	0.433	0.897	model1_2vgnA.pdb.gz
4	3agjB	0.83	1.55	0.271	0.922	model1_3agjB.pdb.gz
5	5m1jA12	0.82	1.40	0.415	0.914	model1_5m1jA12.pdb.gz
6	3obwA	0.82	1.02	0.287	0.871	model1_3obwA.pdb.gz
7	5lzwii	0.81	1.34	1.000	0.888	model1_5lzwii.pdb.gz
8	3j15A2	0.78	1.19	0.357	0.845	model1_3j15A2.pdb.gz
9	3obyA	0.77	1.62	0.320	0.862	model1_3obyA.pdb.gz
10	3ir9A	0.77	1.71	0.280	0.862	model1_3ir9A.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	0.82	catalytic activity
GO:0016788	0.80	hydrolase activity, acting on ester bonds
GO:0004519	0.79	endonuclease activity
GO:0046872	0.75	metal ion binding
GO:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0044877	0.60	macromolecular complex binding
GO:0043021	0.59	ribonucleoprotein complex binding
GO:0003676	0.54	nucleic acid binding
GO:0003723	0.52	RNA 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:0009987	0.93	cellular process
GO:0071840	0.73	cellular component organization or biogenesis
GO:0016043	0.72	cellular component organization
GO:0006996	0.71	organelle organization
GO:0044699	0.70	single-organism process
GO:0008152	0.54	metabolic process
GO:0071704	0.52	organic substance metabolic process
GO:0044238	0.51	primary metabolic process
GO:0044237	0.51	cellular metabolic 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:0044424	1.00	intracellular part
GO:0005737	0.82	cytoplasm
GO:0044444	0.70	cytoplasmic part
GO:0043226	0.66	organelle
GO:0043229	0.64	intracellular organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0005829	0.59	cytosol
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0005634	0.54	nucleus

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	2uz1B	0.454	4.06	0.066	0.750	4.1.2.38	NA
2	0.060	5acnA	0.444	4.64	0.045	0.784	4.2.1.3	47
3	0.060	2hs4A	0.518	4.51	0.062	0.879	6.3.5.3	4
4	0.060	2cfbA	0.438	3.83	0.053	0.655	5.4.3.8	31,38
5	0.060	1dxeA	0.393	4.89	0.094	0.724	4.1.2.20	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	0.12	1rlgB	0.634	2.23	0.144	0.759	0.99	UUU	complex1.pdb.gz	25,26,27,28,29,32,36,48,91,92
2	0.04	3siuD	0.653	2.00	0.087	0.759	0.74	RQA	complex2.pdb.gz	24,25,26,27,28,29,32,35,47,48,91,92
3	0.03	3nviB	0.638	2.32	0.135	0.759	0.78	RQA	complex3.pdb.gz	25,26,27,28,29,32,48,91,92
4	0.02	3siuA	0.649	2.00	0.087	0.759	0.77	RQA	complex4.pdb.gz	24,25,26,27,28,29,32,48,91,92

	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.