D-I-TASSER O75899-D3

D-I-TASSER results for O75899-D3

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

Input Sequence in FASTA format

>O75899 (191 residues)
PDAATQNRRFQFTQNQKKEDSKTSTSVTSVNQASTSRLEGLQSENHRLRMKITELDKDLE
EVTMQLQDTPEKTTYIKQNHYQELNDILNLGNFTESTDGGKAILKNHLDQNPQLQWNTTE
PSRTCKDPIEDINSPEHIQRRLSLQLPILHHAYLPSIGGVDASCVSPCVSPTASPRHRHV
PPSFRVMVSGL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| PDAATQNRRFQFTQNQKKEDSKTSTSVTSVNQASTSRLEGLQSENHRLRMKITELDKDLEEVTMQLQDTPEKTTYIKQNHYQELNDILNLGNFTESTDGGKAILKNHLDQNPQLQWNTTEPSRTCKDPIEDINSPEHIQRRLSLQLPILHHAYLPSIGGVDASCVSPCVSPTASPRHRHVPPSFRVMVSGL
Prediction	CCCCCCCCCSSSSCCCCCCCCCCCCCSSSSCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCC
Confidence	95201133213320111112233321333211102555544212223444578888789999998505766431334546889987765402356875226788865402731024777865455771332479799988875311233332156557735433477779998976566898615653159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| PDAATQNRRFQFTQNQKKEDSKTSTSVTSVNQASTSRLEGLQSENHRLRMKITELDKDLEEVTMQLQDTPEKTTYIKQNHYQELNDILNLGNFTESTDGGKAILKNHLDQNPQLQWNTTEPSRTCKDPIEDINSPEHIQRRLSLQLPILHHAYLPSIGGVDASCVSPCVSPTASPRHRHVPPSFRVMVSGL
Prediction	87444674425134545565554444334245344540541457634132304513541551234145346434314553154143014034135656344321453256525451543445543542165164363044305041211220312313424241343334454445354134404121557
	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                  80                 100                 120                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSCCCCCCCCCCCCCSSSSCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCC
PDAATQNRRFQFTQNQKKEDSKTSTSVTSVNQASTSRLEGLQSENHRLRMKITELDKDLEEVTMQLQDTPEKTTYIKQNHYQELNDILNLGNFTESTDGGKAILKNHLDQNPQLQWNTTEPSRTCKDPIEDINSPEHIQRRLSLQLPILHHAYLPSIGGVDASCVSPCVSPTASPRHRHVPPSFRVMVSGL

1n73C

0.11

0.10

3.79

0.57

CEthreader

-------KTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTCSRSCQDTTANKISPITGKDCQQVVDNGGKDSGLYYIKPLKAKQPFLVFCEIENGNGWGSVNFTRDYLAPTLTTEFNEKIHLLTGQQAYRLRIDLTDWENTHRYADYGHFKLTPESDEYRLFYSMYLDGDAGN

5yfpC

0.07

2.98

0.57

EigenThreader

MSSDPLQQVCDLIKGDLSLERVRDIKEQLLKEKSVVEYQLNKESDKYYGEVEESLKLLNLSKNSVTSTKLYETVNTTNFVALMEHIERLLVAETGCPHLLEIHFLLTSARDFQEQVVVMAKEATEDAQRTVMKLFSRLSREDLRIEAIRNIIKKKEIEIEKSSIKKLPNSKNTARLQDETPKVIEYPTNKG

5tzs9

0.13

0.09

3.28

0.47

FFAS-3D

---------------RTYSKTYSTPKRPYESSRLDAELKLAGEFNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKK--------------------------LDYVLALKVEDFLERRLQTQVYLITQRHI-AVGKQIVNIPSFMVRLDSEKHIDFAPTS--------

3dl8A

0.06

2.68

0.77

SPARKS-K

FGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERIAAYTPRELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEP----DEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQG

4pasB

0.97

0.20

5.58

0.50

CNFpred

----------------------------SVNQASTSRLEGLQSENHHLRMKITELDKDLEEVTMQLQ----------------------------------------------------------------------------------------------------------------------------

5yfpB

0.04

1.81

0.83

DEthreader

NYQKILNYQATKKFELFYLLRRRQIILFSKLTSSSNPILRWMSIKMNGFQNELNELSGHMISKIIHSQRILQNNT-QDGCVE-SY-YL----------------KI-NQLFQSDTGYLNLNCQP-SSQGLDSPTEMWLLILKYINDLWKICDQFIE-F-WEHIEKFGTYQNSI-----------QLNIIIC

6tpiA2

0.11

0.08

3.03

0.97

MapAlign

-------------------------------QQGQQQLSELRANESRLRNSIARAEAAAKARAEREATRKGTTYKPTESEKSLMSRTGPTLHRYGEQLQGELRWKGMVI-------------GASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQPIALVGSSGGQGRPSLYFEIRRQG

5n5xA2

0.12

4.23

0.62

MUSTER

IIVDHPEWASLFNNADEREKESIGALVSQIKLKERERISRVQNLIHDEDKYLQDLSIATNELLESWQKTKDESILSGSLSHSKLKNLLENSDSFASIPEFSSLLDQFFQYYQDQDVTFIGFEKLLHLFLEDVPGLDIFYNKLL-QAELLTKEIVKDII---WSLARLEKPSLFEPIQNEISRSLSGPYQDI

5x9xB

0.20

0.05

1.51

1.45

HHsearch

------------------------GPLGSSVSELEQRLRDVKNTNSRFRKALMEKENELQALIRKLGPE--------------------------------------------------------------------------------------------------------------------------

4u8uM

0.09

0.07

2.80

0.54

CEthreader

----------------------------------TYKDRRFQYILTNQHLFIDKLERDLHEIDDEFKKLGSDVKDQTVRHLKARISNLEEHEAPCGGDVPQCISDLFFRDEDKEVCSEVPADIGSSFAGVVSWQACEEATPHHAVVTITANERKEFFKPRIWVRAILAFEEEEHEHHIKTFQLRGYYSFGD

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5113

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5v8kA	0.50	4.81	0.066	0.744	model1_5v8kA.pdb.gz
2	5owvC2	0.49	4.69	0.065	0.749	model1_5owvC2.pdb.gz
3	6m32A	0.49	4.60	0.068	0.712	model1_6m32A.pdb.gz
4	3vvnA	0.48	4.24	0.045	0.681	model1_3vvnA.pdb.gz
5	5u1sA	0.48	4.83	0.055	0.764	model1_5u1sA.pdb.gz
6	5y50A	0.48	4.66	0.034	0.738	model1_5y50A.pdb.gz
7	3mktA	0.48	4.44	0.056	0.712	model1_3mktA.pdb.gz
8	5twvB	0.48	5.15	0.032	0.764	model1_5twvB.pdb.gz
9	6ww2R	0.48	4.70	0.072	0.723	model1_6ww2R.pdb.gz
10	4aurA	0.48	5.02	0.058	0.733	model1_4aurA.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:0004965	1.00	G-protein coupled GABA receptor activity

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:0007214	1.00	gamma-aminobutyric acid signaling pathway
GO:0044699	0.62	single-organism process
GO:0009987	0.58	cellular process
GO:0044763	0.53	single-organism cellular 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:0038039	1.00	G-protein coupled receptor heterodimeric complex
GO:0005887	1.00	integral component of plasma membrane
GO:0016020	0.60	membrane
GO:0044424	0.56	intracellular part
GO:0005886	0.53	plasma membrane

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

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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	3h8eA	0.450	4.45	0.024	0.675	3.4.11.1	NA
2	0.060	2vycA	0.431	5.25	0.051	0.744	4.1.1.19	NA
3	0.060	3gehA	0.424	5.15	0.054	0.686	3.6.-.-	20
4	0.060	1peuA	0.410	5.63	0.056	0.733	1.17.4.1	44
5	0.060	1gytJ	0.467	4.47	0.047	0.691	3.4.11.1	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

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Template proteins with similar binding site:

Click to view	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	3kqzL	0.334	5.80	0.046	0.613	0.11	CO3	complex1.pdb.gz	33,35,36,37,39

	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.