D-I-TASSER Q9H2X6-D2

D-I-TASSER results for Q9H2X6-D2

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

Input Sequence in FASTA format

>Q9H2X6 (114 residues)
GPHNLMRRSTVSLLDTYQKCGLKRKSEEIENTSSVQIIEEHPPMIQNNASGATVATATTS
TATSKNSGSNSEGDYQLVQHEVLCSMTNTYEVLEFLGRGTFGQVVKCWKRGTNE

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GPHNLMRRSTVSLLDTYQKCGLKRKSEEIENTSSVQIIEEHPPMIQNNASGATVATATTSTATSKNSGSNSEGDYQLVQHEVLCSMTNTYEVLEFLGRGTFGQVVKCWKRGTNE
Prediction	CCHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCSSCCCCCCSSSSSSSCCCCCCCSSSSSSCCCCC
Confidence	961478876322555567635444311112766413203567533445566654334678787889987999757998062713688708999852687763079999646799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GPHNLMRRSTVSLLDTYQKCGLKRKSEEIENTSSVQIIEEHPPMIQNNASGATVATATTSTATSKNSGSNSEGDYQLVQHEVLCSMTNTYEVLEFLGRGTFGQVVKCWKRGTNE
Prediction	855522442444236235413462446547545434435634543444445555553446655555433365230201021203366431301431452211200302346488
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCSSCCCCCCSSSSSSSCCCCCCCSSSSSSCCCCC
GPHNLMRRSTVSLLDTYQKCGLKRKSEEIENTSSVQIIEEHPPMIQNNASGATVATATTSTATSKNSGSNSEGDYQLVQHEVLCSMTNTYEVLEFLGRGTFGQVVKCWKRGTNE

3kvwA1

0.17

0.15

4.89

1.14

SPARKS-K

-------------HHSGVDLGTENLYFQSMGKVKATPMTPKLTAFEFSYPEIYFLGLNAKKRQGMTGYDDDQGSYVQVPHDHVA---YRYEVLKVIGKGSFGQVVKAYDHKVHQ

5y86A

0.28

0.12

3.75

1.01

CNFpred

-------------------------------------------------------------GPNNGGYDDADGAYIHVPRDHLA---YRYEVLKIIGKGSFGQVARVYDHKLRQ

5fmwA4

0.03

1.53

1.13

MapAlign

----------EFYNGLCNRDRDGNTLTYYRRPWNVASLIYE-----------TKGEKNFRTEHYEEQEKMFLHVKGEIHLGRFVMRSSSGSLGGLYELIYVSLIRVLSQKLSPI

3kvwA1

0.17

5.46

1.35

MUSTER

GVDLGTENLYFQSMGKVKATPMTKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGM--TGGPNNGGYDDDQGSYVQVPHDHVA---YRYEVLKVIGKGSFGQVVKAYDHKVHQ

3kvwA1

0.21

0.19

6.11

1.70

HHsearch

-----HHS-GVDLGTENLYQSVKATPMTPEQKQYMQKLTAYPEIYFLGLNAKKR-QG-MTGGPNNGGYDDDQGSYVQVPHDHV---AYRYEVLKVIGKGSFGQVVKAYDHKVHQ

2vx3A

0.31

0.13

3.98

1.04

HHsearch

--------------------------------------------------------------VYNDGYDDDNYDYIVKNGEKW---MDRYEIDSLIGKGSFGQVVKAYDRVEQE

5lalA

0.07

0.05

2.15

0.59

CEthreader

-------------------------DQKKPCKHFSFYFHDILYDGDNVANATSAAIVSPP------GLGNFKFGKFVIFDGPITMDKARAQGFYFYDMKMDFNSWFSYTLVFNS

2cp5A

0.10

0.08

2.96

0.75

EigenThreader

SMLK------PSGLKAPTKILKPGSTAL------KTPTAVVAPVEKTISSEK----ASSTPSSETQEEFV----DDFRVGERVWVGNKPGFIQFLGETFAPGQWAGIVLDEPIG

2vx3A1

0.31

0.13

3.98

0.73

FFAS-3D

--------------------------------------------------------------VYNDGYDDDNYDYIVKNGEKW---MDRYEIDSLIGKGSFGQVVKAYDRVEQE

6yrfA2

0.18

0.15

4.88

0.72

SPARKS-K

KPEDWIPSGNVQMKDGGRGDGYFKQFIKLENDSTYHLRTGRVSIIDESKYLLFVNVKDEDTRVIKNTSSKGECFIALEGT---YVENSSTIFSNV-------SIVKE-------

(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	0.5171

(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	4fsxA3	0.47	4.66	0.058	0.851	model1_4fsxA3.pdb.gz
2	3g7uA	0.46	4.68	0.057	0.833	model1_3g7uA.pdb.gz
3	4wxxA	0.46	4.64	0.029	0.825	model1_4wxxA.pdb.gz
4	3pt6A2	0.46	4.29	0.040	0.816	model1_3pt6A2.pdb.gz
5	5xrfA	0.45	4.26	0.102	0.728	model1_5xrfA.pdb.gz
6	1c5mD	0.45	4.52	0.071	0.754	model1_1c5mD.pdb.gz
7	3kvwA	0.45	3.41	0.195	0.632	model1_3kvwA.pdb.gz
8	3h09B	0.45	4.36	0.052	0.754	model1_3h09B.pdb.gz
9	2pffA	0.45	4.47	0.074	0.781	model1_2pffA.pdb.gz
10	4xzyA2	0.45	4.51	0.054	0.746	model1_4xzyA2.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	0.78	catalytic activity
GO:0016772	0.77	transferase activity, transferring phosphorus-containing groups
GO:0004672	0.76	protein kinase activity
GO:0004674	0.66	protein serine/threonine kinase activity
GO:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding
GO:0003714	0.52	transcription corepressor 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:0050794	0.90	regulation of cellular process
GO:0009987	0.86	cellular process
GO:0044699	0.78	single-organism process
GO:0008152	0.71	metabolic process
GO:0071704	0.70	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0032502	0.65	developmental process
GO:0044767	0.64	single-organism developmental process
GO:0019538	0.58	protein metabolic process
GO:0006796	0.57	phosphate-containing compound metabolic process
GO:0006464	0.57	cellular protein modification process
GO:0006468	0.56	protein phosphorylation
GO:0019222	0.55	regulation of metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0048583	0.52	regulation of response to stimulus
GO:0023051	0.52	regulation of signaling
GO:0010646	0.52	regulation of cell communication
GO:0048518	0.51	positive regulation of biological process
GO:0009966	0.51	regulation of signal transduction
GO:0050896	0.50	response to stimulus
GO:0031323	0.50	regulation of 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:0043229	0.90	intracellular organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005634	0.84	nucleus
GO:0005737	0.75	cytoplasm
GO:0044446	0.57	intracellular organelle part
GO:0044428	0.51	nuclear part

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	2eekA	0.413	4.66	0.071	0.728	3.4.21.4	NA
2	0.060	1tonA	0.439	4.52	0.070	0.754	3.4.21.35	NA
3	0.060	1zjkA	0.427	4.56	0.089	0.737	3.4.21.104	NA
4	0.060	1ao5A	0.431	4.36	0.041	0.728	3.4.21.119	NA
5	0.060	2pffA	0.446	4.47	0.074	0.781	2.3.1.41 2.3.1.86	75

	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	0.27	3kvwA	0.449	3.44	0.193	0.640	0.33	IRB	complex1.pdb.gz	93,95,96,97
2	0.26	1ioeA	0.434	4.40	0.101	0.737	0.23	XMA	complex2.pdb.gz	74,75,95,96,97,98,99,103,104,105
3	0.23	1faxA	0.441	4.32	0.101	0.737	0.23	DX9	complex3.pdb.gz	96,97,98,103,105
4	0.21	2cjiA	0.435	4.40	0.101	0.737	0.21	GSK	complex4.pdb.gz	1,75,97,103,104
5	0.19	1g2mA	0.439	4.37	0.101	0.737	0.23	R11	complex5.pdb.gz	75,79,95,96,97,103
6	0.01	2w3iA	0.436	4.31	0.101	0.737	0.29	L1C	complex6.pdb.gz	76,92,94,95,105,106,107
7	0.01	1iqfA	0.433	4.36	0.101	0.737	0.30	XMD	complex7.pdb.gz	75,77,79,92,94,95,96,97,98,105,106,107
8	0.01	2q1jA	0.437	4.29	0.101	0.737	0.20	FXI	complex8.pdb.gz	75,92,103,105
9	0.01	3kqbA	0.436	4.38	0.101	0.737	0.26	LGJ	complex9.pdb.gz	56,79,92,94,96,97,98,105
10	0.01	2p3uB	0.437	4.30	0.101	0.737	0.24	663	complex10.pdb.gz	74,75,92,93,94,95,104,105,106

	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.