D-I-TASSER Q9Y2W1-D5

D-I-TASSER results for Q9Y2W1-D5

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

Input Sequence in FASTA format

>Q9Y2W1 (87 residues)
PPSTGSTYGSSQKEESAASGGAAYTKRYLEEQKTENGKDKEQKQTNTDKEKIKEKGSFSD
TGLGDGKMKSDSFAPKTDSEKPFRGSQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| PPSTGSTYGSSQKEESAASGGAAYTKRYLEEQKTENGKDKEQKQTNTDKEKIKEKGSFSDTGLGDGKMKSDSFAPKTDSEKPFRGSQ
Prediction	CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	997665557773211468886312232267775312630666641311888863177321367776656788888777667788889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| PPSTGSTYGSSQKEESAASGGAAYTKRYLEEQKTENGKDKEQKQTNTDKEKIKEKGSFSDTGLGDGKMKSDSFAPKTDSEKPFRGSQ
Prediction	856445434445566444643342354225655476455465644646464357545146343545534565244555465436568
	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

CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
PPSTGSTYGSSQKEESAASGGAAYTKRYLEEQKTENGKDKEQKQTNTDKEKIKEKGSFSDTGLGDGKMKSDSFAPKTDSEKPFRGSQ

4q8jL

0.03

0.02

1.47

1.00

DEthreader

----GDS-K-KSIDLSFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGR--IESRIDINW---DVTPDELNC--I

4oltA2

0.05

2.24

0.49

CEthreader

ALGQFAYYDTLHGPGSQRDAFGGIRAEALSAALPPSQGGDETEYLEAFFDARNVIMREEPAHADTSRIDTAQRVFLQNTWSVYGDQY

6xbwH

0.11

4.10

0.57

EigenThreader

REAAFSLAEAKFTATGGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDERERE

7abiK

0.13

0.11

3.98

0.40

FFAS-3D

----------NDEEEYEA-WKVRELKRIKRDREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGA

3hgfA

0.07

2.85

0.92

SPARKS-K

-PMVKEIEKKIENIVTKIDKKKYIYDNMKKLLNEIAEIEKDKTSLEEVKNINMSYGKNKLFLEKIKKKSENMIKSMEKYIKDLDEIK

5z96A

0.15

0.06

1.94

0.36

CNFpred

-------------HHQYQEVMRNLVKRYVAAMIREAKTEEGLTEENV----------------------------------------

6thkA

0.08

0.07

2.74

1.00

DEthreader

-------LIKN--IGELVDEIASLQARLVKLNAETTRRRTEAERKAAEEQALQDAIKFTADKETSEMRQLAEGARGKNIRSEAAG--

1w2wB

0.10

3.79

0.79

MapAlign

NQGSRLTAYELVYDKIPSTLITDSSIAYRIRTIVRNGDTANKIGTLQLAVICKQFGIKFFVVALIDGIITEEGVFTKNSSGEFQLES

6bzlA

0.13

0.11

3.99

0.72

MUSTER

----GSVEKLTADAELQRLKNERHEEAELERLKSERHDHDKKEAERKALEDKLADKQEHLNGALRYINEKEAERKEKEAEQ------

5fwiC1

0.17

0.09

3.03

0.49

HHsearch

EGTIPKLKLSELQAVTDHDIPQQLVERLQEEKRIEAQKRKERQEAHLY---------------------------------------

(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	0.48

(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	3x0uA1	0.61	3.35	0.025	0.897	model1_3x0uA1.pdb.gz
2	5ijpA	0.60	3.06	0.038	0.874	model1_5ijpA.pdb.gz
3	3feyA	0.60	3.47	0.037	0.908	model1_3feyA.pdb.gz
4	5iigA	0.59	3.30	0.038	0.885	model1_5iigA.pdb.gz
5	5ijhA	0.56	2.88	0.061	0.805	model1_5ijhA.pdb.gz
6	1dlcA1	0.55	3.85	0.098	0.908	model1_1dlcA1.pdb.gz
7	2v6eA1	0.41	3.22	0.130	0.621	model1_2v6eA1.pdb.gz
8	2wqzA1	0.40	3.51	0.050	0.678	model1_2wqzA1.pdb.gz
9	1eq7A	0.38	2.39	0.036	0.471	model1_1eq7A.pdb.gz
10	1v8pF	0.37	3.69	0.028	0.598	model1_1v8pF.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:0051219	1.00	phosphoprotein binding
GO:0003713	1.00	transcription coactivator activity
GO:0001046	1.00	core promoter sequence-specific DNA binding
GO:0003723	0.79	RNA binding
GO:0044822	0.76	poly(A) RNA binding
GO:0001104	0.71	RNA polymerase II transcription cofactor activity
GO:0005102	0.70	receptor binding
GO:0004872	0.70	receptor activity
GO:0035257	0.69	nuclear hormone receptor binding
GO:0008134	0.69	transcription factor binding
GO:0046966	0.68	thyroid hormone receptor 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:0048255	1.00	mRNA stabilization
GO:0048026	1.00	positive regulation of mRNA splicing, via spliceosome
GO:0042753	1.00	positive regulation of circadian rhythm
GO:0000956	1.00	nuclear-transcribed mRNA catabolic process
GO:0000381	1.00	regulation of alternative mRNA splicing, via spliceosome
GO:1901576	0.74	organic substance biosynthetic process
GO:0044249	0.74	cellular biosynthetic process
GO:0032774	0.73	RNA biosynthetic process
GO:0031326	0.73	regulation of cellular biosynthetic process
GO:0006355	0.72	regulation of transcription, DNA-templated
GO:0045893	0.71	positive regulation of transcription, DNA-templated
GO:0007165	0.71	signal transduction
GO:0006367	0.70	transcription initiation from RNA polymerase II promoter
GO:0006357	0.69	regulation of transcription from RNA polymerase II promoter
GO:0045944	0.68	positive regulation of transcription from RNA polymerase II promoter
GO:0030521	0.68	androgen receptor signaling pathway

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:0035145	1.00	exon-exon junction complex
GO:0016607	1.00	nuclear speck
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	nucleus
GO:0016592	0.73	mediator complex
GO:0070062	0.69	extracellular exosome

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	1ukwA	0.567	3.72	0.075	0.897	1.3.99.3	NA
2	0.060	1qhaA	0.531	3.42	0.066	0.816	2.7.1.1	NA
3	0.060	3g4dA	0.528	4.01	0.110	0.874	4.2.3.13	NA
4	0.060	3a1cB	0.325	4.63	0.026	0.632	3.6.3.-	16
5	0.060	2pfmA	0.528	3.89	0.072	0.828	4.3.2.2	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	1h2u0	0.502	3.49	0.043	0.770	0.44	III	complex1.pdb.gz	51,55,56,64,65
2	0.01	3ag4C	0.577	3.37	0.026	0.862	0.48	CDL	complex2.pdb.gz	4,29,33,36
3	0.01	3asnP	0.577	3.37	0.026	0.862	0.42	CDL	complex3.pdb.gz	59,63,65

	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.