D-I-TASSER Q9BQA5-D6

D-I-TASSER results for Q9BQA5-D6

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

Input Sequence in FASTA format

>Q9BQA5 (123 residues)
RYESVELTQQLLRQPQEGSGLGTSLNESSLQGIILETVPGEPGRKEEEEEGKGSEGTALS
ASQDNPSSVIHVVNQTNAQGQQEIVYYVLSEAPGEPPPAPEPPSGGIMEKLQGIAEEPEI
QMV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| RYESVELTQQLLRQPQEGSGLGTSLNESSLQGIILETVPGEPGRKEEEEEGKGSEGTALSASQDNPSSVIHVVNQTNAQGQQEIVYYVLSEAPGEPPPAPEPPSGGIMEKLQGIAEEPEIQMV
Prediction	CCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCSSSSSCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCHHHHHHCHHHCCCCSCC
Confidence	941478999999632348997643364443345751589999752224466775542013368999861787514677786157999852699999999999973179997501213475119
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| RYESVELTQQLLRQPQEGSGLGTSLNESSLQGIILETVPGEPGRKEEEEEGKGSEGTALSASQDNPSSVIHVVNQTNAQGQQEIVYYVLSEAPGEPPPAPEPPSGGIMEKLQGIAEEPEIQMV
Prediction	846526224511643672654443245442420213244667564655666543544444456744341131244345644431011003434555453763455511541472375271547
	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                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCSSSSSCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCHHHHHHCHHHCCCCSCC
RYESVELTQQLLRQPQEGSGLGTSLNESSLQGIILETVPGEPGRKEEEEEGKGSEGTALSASQDNPSSVIHVVNQTNAQGQQEIVYYVLSEAPGEPPPAPEPPSGGIMEKLQGIAEEPEIQMV

3hxxA

0.07

2.76

0.69

CEthreader

VGIPRERIIRIGDNKGAPYASDNFWQMGDTGPCGPCTEIFYDHGDHIWGGPPGSPEEDGDRYIEIWNIVFMQFNRQADGTMEPLPKPSVDTGMGLERIAAVLQHVNSNYDIDLFRTLIQAVAK

5a96A

0.07

2.95

0.57

EigenThreader

ENSARQVAQDTRELHLLQHIKSDQSY--IYVFVFLYYNNVNRCYYREGITGNDAGDSIIDKAYCEPVSFMIVACGDITATKFIFYTYCGLFGHGDRGHPRNFWAKTEGQMVEQFIK-QQSIPY

4gwpG

0.15

4.90

0.40

FFAS-3D

-FDKTSNNQVIKMQRQFSQLNDPNAFADPARRQILFKYPMYMQLEEELMKLDGTEYVLSSV----REPDFWVIRKQRRTNNSGVDYYIIGANIYQSPTIFKIVQSRLMSHLNSTLESLY-DLI

6mccC

0.05

2.27

0.76

SPARKS-K

MTTARKKFYQAISEFEAMTGKDVERTPQIADAEYIAFTKTEKYALYLCTSNVEGLEDRYDEECLDSTFLETE------DNETYYIHFLQETEFSEDDNEDETEEQIEAYDKQEELKAVILKKE

5m41A

0.13

0.07

2.25

0.63

CNFpred

--GAAGLTADAIEGKEIDP---------DVISLSLAAIP--------------------------GGKIVAKLSKVSK-NLGQVVRGGISIAE------------------------TGVDIV

4f4cA4

0.05

0.04

1.96

0.83

DEthreader

----------VE-YEGDIDSNGIRETYAAGVGSLGMATIGFIYPTYSVFFSFMN-W---FLAAQGCSLMFFIASRDRLFRLAVPRIDFSTTTVSMGAITTSLGFATSYFPEYAKATFAGGF--

3hxxA

0.07

2.96

0.95

MapAlign

YESDDEAYEIWEKGDNKGAPYASDNFGDTGPCGPCTEIFYDHGDHIW--GGPPGSPEEDGDRYIEIWNIVFMQFNRQADGTMEPLSVDTGMGAVLQHVNSNYDIDLFRTLIQAVAKVTGATDL

6mccC

0.07

2.97

0.58

MUSTER

MTTARKKFYQAISEFEAMTGKDVE-RTPQIADEVLNDAEYIAFTKTEKYALYLCTSNVEGLEDRYDEECLDSTFLETEDNETYYIHFLQETEFSEDDNEDELPLATEEQIEAYDKQEELKAVI

2pffB

0.22

0.16

5.14

0.39

HHsearch

SIES--LVEVVFYMQVAVPRDE--LGRSNYGMIAINPG-----------------RVAASFSQEALQYVERVGKRTGW--LVEIVNYNVENQQYVA---A-----GDLRALDTVTNFIKLQKI

1xq4A

0.09

0.07

2.47

0.57

CEthreader

--------------------------PVKPYDLTVSVTPRYVPEQSDPSQQ---------QYVFAYTVRITNTGSHPQQPLLAPGETFEYTSGCPLPTPIGTRGTYHCVGENGIPFEVPIAEF

(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	0.4879

(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	3mk7A	0.55	3.76	0.058	0.846	model1_3mk7A.pdb.gz
2	1xmeA	0.53	4.12	0.041	0.854	model1_1xmeA.pdb.gz
3	6kobA	0.52	4.32	0.033	0.870	model1_6kobA.pdb.gz
4	1ukcA	0.51	4.58	0.043	0.878	model1_1ukcA.pdb.gz
5	6xkwn	0.50	4.31	0.025	0.878	model1_6xkwn.pdb.gz
6	1uwkA	0.50	4.48	0.033	0.854	model1_1uwkA.pdb.gz
7	1aknA	0.50	4.69	0.076	0.886	model1_1aknA.pdb.gz
8	1qe3A	0.50	4.80	0.061	0.870	model1_1qe3A.pdb.gz
9	4be4A	0.49	4.68	0.094	0.854	model1_4be4A.pdb.gz
10	6qq5A	0.49	4.65	0.008	0.846	model1_6qq5A.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:0044212	1.00	transcription regulatory region DNA binding
GO:0042393	1.00	histone binding
GO:0019899	1.00	enzyme binding
GO:0003713	1.00	transcription coactivator activity
GO:0003700	1.00	transcription factor activity, 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:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0045892	1.00	negative regulation of transcription, DNA-templated
GO:0045445	1.00	myoblast differentiation
GO:0045184	1.00	establishment of protein localization
GO:0006281	1.00	DNA repair
GO:0001701	1.00	in utero embryonic development
GO:0000083	1.00	regulation of transcription involved in G1/S transition of mitotic cell cycle
GO:0000082	1.00	G1/S transition of mitotic cell cycle
GO:0000077	1.00	DNA damage checkpoint
GO:0016070	0.53	RNA 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:0015030	1.00	Cajal body
GO:0005730	1.00	nucleolus
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	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	2fknB	0.467	4.21	0.068	0.772	4.2.1.49	NA
2	0.060	1occA	0.437	4.69	0.041	0.789	1.9.3.1	NA
3	0.060	1maaD	0.481	4.82	0.095	0.870	3.1.1.7	NA
4	0.060	3dwsB	0.450	4.40	0.063	0.780	1.3.3.3	107
5	0.060	1lpsA	0.489	4.43	0.053	0.837	3.1.1.3	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	2y2vB	0.380	4.68	0.034	0.699	0.37	P15	complex1.pdb.gz	10,14,18
2	0.01	2c0qB	0.460	4.46	0.036	0.789	0.13	NTJ	complex2.pdb.gz	5,109,111
3	0.01	1ukcA	0.505	4.58	0.043	0.878	0.23	UUU	complex3.pdb.gz	11,19,28,30
4	0.01	1aqlB	0.503	4.67	0.076	0.886	0.13	TCH	complex4.pdb.gz	4,107,108,109,110,111
5	0.01	2whqB	0.450	4.57	0.044	0.813	0.17	HI6	complex5.pdb.gz	12,18,21
6	0.01	2h9yA	0.352	5.20	0.061	0.683	0.13	NAF	complex6.pdb.gz	3,4,5,32
7	0.01	1lpmA	0.490	4.43	0.061	0.837	0.12	MPA	complex7.pdb.gz	5,108,110
8	0.01	2ha0A	0.459	4.69	0.114	0.813	0.16	NWA	complex8.pdb.gz	12,18,19,20
9	0.01	1ku60	0.414	5.47	0.084	0.862	0.13	III	complex9.pdb.gz	2,6,9,10,12,17,22
10	0.01	1aqlA	0.503	4.49	0.068	0.870	0.14	TCH	complex10.pdb.gz	7,107,111,114

	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.