D-I-TASSER O95789-D2

D-I-TASSER results for O95789-D2

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

Input Sequence in FASTA format

>O95789 (92 residues)
GPSVLLPSVPAVAIKVFCSGCKKMLYKGQTAYHKTGSTQLFCSTRCITRHSSPACLPPPP
KKTCTNCSKDILNPKDVITTRFENSYPSKDFC

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| GPSVLLPSVPAVAIKVFCSGCKKMLYKGQTAYHKTGSTQLFCSTRCITRHSSPACLPPPPKKTCTNCSKDILNPKDVITTRFENSYPSKDFC
Prediction	CCCCCCCCCCCCCCSSSSCCCCCHHHCCCSSSSSCCCHHHSSCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCC
Confidence	98766898998751677155541012474222326872304552666433565566899874124342115886533887427897421149
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| GPSVLLPSVPAVAIKVFCSGCKKMLYKGQTAYHKTGSTQLFCSTRCITRHSSPACLPPPPKKTCTNCSKDILNPKDVITTRFENSYPSKDFC
Prediction	86644344344542413033045214544412445433522023410442446444544454414404442444453132425567435736
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCSSSSCCCCCHHHCCCSSSSSCCCHHHSSCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCC
GPSVLLPSVPAVAIKVFCSGCKKMLYKGQTAYHKTGSTQLFCSTRCITRHSSPACLPPPPKKTCTNCSKDILNPKDVITTRFENSYPSKDFC

2dasA

0.39

0.24

7.08

1.32

SPARKS-K

SGQPTAQQQLTKPAKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSSGPSSG-----------------------------------

2dasA

0.39

0.24

7.08

1.23

CNFpred

SGQPTAQQQLTKPAKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSSGPSSG-----------------------------------

1x4uA

0.18

0.15

4.96

1.16

MUSTER

GSSGSSGRYPTNNFG-NCTGCSATFSVLKKRRSCSNCGNSFCSRCCSFKVPKSSMGATAPEAQCASCNQTLSKSG-------PSSG------

2dasA

0.39

0.24

7.08

2.45

HHsearch

SGQPTAQQQLTKPAKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSSGPS----SG-------------------------------

5v3gD

0.13

0.12

4.13

0.39

CEthreader

---------PGSEKPYVCRECGRGFSNGEKPYVCRECGRGFRDKSHLLSLSHQRTHTGEKPYVCRECGRGFSWQGEKPYVCRECGRGFRDKS

6wcwA

0.08

3.05

0.68

EigenThreader

AGCGIRTDPDYIKRLRYCEYLGKYFCQCCHEQMAIFSKYYVSNFSKDLLIKIWNDPLTCRLALTRAGATHVLCQAKGCRTCEECKACYHCFK

2dasA

0.44

0.26

7.64

0.70

FFAS-3D

GSSGSSQQQLTKPAKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSSGPS-------------------------------------

1x4jA

0.16

0.12

3.96

1.05

SPARKS-K

LPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHA-KCVDKWLKANR-------TCPICRADSGPSSG----------------

2dfyC

0.23

0.14

4.42

1.21

CNFpred

---------------LKCSSCQAQLGIGTSSYTKS--GMILCRNDYIRLFG--------NSGACSACGQSIPASELVMRAQ-----------

4jrfA

0.05

0.04

2.00

0.83

DEthreader

QTTSAVASA-V--YTPG------SFTVGESWFRL-LG-VTYKTLADLQVVYAAQVITDQYARKAAQLKG-YSKPVGVEYFQKG--VCPTP--

(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	0.4973

(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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6l8nA	0.50	3.89	0.106	0.880	model1_6l8nA.pdb.gz
2	1umgA	0.50	3.85	0.026	0.804	model1_1umgA.pdb.gz
3	3n6xA	0.48	4.25	0.070	0.848	model1_3n6xA.pdb.gz
4	5c17A	0.48	3.28	0.130	0.696	model1_5c17A.pdb.gz
5	6w2df	0.47	4.08	0.061	0.837	model1_6w2df.pdb.gz
6	1o57A	0.47	3.89	0.011	0.793	model1_1o57A.pdb.gz
7	3iibA2	0.47	4.09	0.075	0.848	model1_3iibA2.pdb.gz
8	6tbmQ1	0.47	2.84	0.125	0.663	model1_6tbmQ1.pdb.gz
9	1lf9A1	0.47	3.84	0.066	0.772	model1_1lf9A1.pdb.gz
10	1suvA	0.43	4.71	0.056	0.859	model1_1suvA.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:0003676	1.00	nucleic acid binding
GO:0000981	1.00	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677	0.99	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:0009987	0.99	cellular process
GO:0044699	0.96	single-organism process
GO:0050794	0.95	regulation of cellular process
GO:0048856	0.95	anatomical structure development
GO:0044767	0.95	single-organism developmental process
GO:0006996	0.95	organelle organization
GO:0022604	0.94	regulation of cell morphogenesis
GO:0007275	0.94	multicellular organism development
GO:0007010	0.94	cytoskeleton organization
GO:0008152	0.51	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:0044428	1.00	nuclear part
GO:0005737	1.00	cytoplasm
GO:0005654	0.99	nucleoplasm

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	2jkpB	0.441	3.02	0.014	0.663	3.2.1.20	NA
2	0.060	2hb6A	0.444	4.78	0.067	0.891	3.4.11.1	NA
3	0.060	1gu6A	0.396	4.32	0.027	0.739	1.7.2.2	NA
4	0.060	1t3qB	0.432	4.24	0.057	0.793	1.3.99.17	NA
5	0.060	3n2oA	0.440	3.85	0.037	0.783	4.1.1.19	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	3kalA	0.464	4.39	0.089	0.891	0.16	HGS	complex1.pdb.gz	20,32,33,35,36
2	0.01	2dtuA	0.436	4.37	0.033	0.837	0.13	UUU	complex2.pdb.gz	33,34,78
3	0.01	2p5oB	0.453	3.99	0.034	0.793	0.10	QNA	complex3.pdb.gz	6,68,79
4	0.01	1p4aA	0.463	3.85	0.023	0.783	0.31	PCP	complex4.pdb.gz	19,35,49,50,63,64
5	0.01	1p4aB	0.474	3.88	0.011	0.793	0.26	PCP	complex5.pdb.gz	18,19,20,36,48,64,65,66
6	0.01	3kalA	0.464	4.39	0.089	0.891	0.14	ADP	complex6.pdb.gz	21,23,27,28,29,66,77
7	0.01	3taeD	0.424	4.45	0.044	0.837	0.32	QNA	complex7.pdb.gz	21,29,33
8	0.01	2hc9A	0.462	4.37	0.033	0.913	0.22	BCT	complex8.pdb.gz	79,80,81
9	0.01	1clqA	0.437	4.42	0.066	0.848	0.14	GDP	complex9.pdb.gz	14,20,25,29,45,46
10	0.01	1clqA	0.437	4.42	0.066	0.848	0.12	QNA	complex10.pdb.gz	33,34,35,38,40

	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.