D-I-TASSER Q9UKE5-D8

D-I-TASSER results for Q9UKE5-D8

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

Input Sequence in FASTA format

>Q9UKE5 (75 residues)
VAYIHSNQIMGWGEKAIEIRSVETGHLDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSS
QVFFMTLNRNSMMNW

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| VAYIHSNQIMGWGEKAIEIRSVETGHLDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSSQVFFMTLNRNSMMNW
Prediction	CCSSSCCCSSCCCCCSSSSSSCCCCCCHHHHHHHHHHHHHHHHHCCCSSSSSSCCCCCCSSSSSSSSCCCCCCCC
Confidence	925625815625640589885134754102133325563221001982787421489961799987056434579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| VAYIHSNQIMGWGEKAIEIRSVETGHLDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSSQVFFMTLNRNSMMNW
Prediction	644344730332354314243264441433144543540410054444320322456543301112134533465
	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

                   |                   |                   |

SS
Seq

CCSSSCCCSSCCCCCSSSSSSCCCCCCHHHHHHHHHHHHHHHHHCCCSSSSSSCCCCCCSSSSSSSSCCCCCCCC
VAYIHSNQIMGWGEKAIEIRSVETGHLDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSSQVFFMTLNRNSMMNW

4noxA2

0.07

2.79

1.17

DEthreader

MDFEWAQLFCFWTEARVGLMSIPSKQIVRTLNLFSVSDVKMH-WQEGYLCVKVDRHSQATTLEIFRVEVPVEVVD

5o51A

0.21

0.19

5.92

0.77

SPARKS-K

AFALSYPYILAFEPNFIEIRHIETSELIHIMTGK---NIRMLHSSTREILYAYEDEGGEDVVASLDFWN------

6xr4A

0.08

3.16

0.45

MapAlign

ITVVVDTALYIANSPVVEVWDKKTEKLCGLIDVTALWIGTGGGHIFCNSVRVMMTAQNVMLVLGYNREIQSCLTV

1sq9A

0.08

3.16

0.28

CEthreader

VDISERGLIATGFNGTVQISELSTLRPLYNFESQHNNSNSVKFSPQGSLLAIAHDSNSFGCITLYETEFGERIGS

5o51A

0.23

0.20

6.27

0.94

MUSTER

FALSY-PYILAFEPNFIEIRHIETSELIHIMTGK---NIRMLHSSTREILYAYEDEGGEDVVASLDFWN------

5o51A

0.23

0.20

6.27

0.82

HHsearch

FALS-YPYILAFEPNFIEIRHIETSELIHIMTGK---NIRMLHSSTREILYAYEDEG-GEDVVA-SLDFWN----

5o51A

0.21

0.17

5.52

0.48

FFAS-3D

-FALSYPYILAFEPNFIEIRHIETSELIHIM---TGKNIRMLHSSTREILYAYEDEGGEDVVASLDF--------

1flgA2

0.07

2.73

0.50

EigenThreader

GAAIYGDKVFFGLDASVVALNKNTGKVVWKKKFADTWAGVLAT--AGNLVFTGTG---DGYFKAFDAKSKELWGI

3vl1A

0.09

0.07

2.56

0.79

CNFpred

-------IYAGYENGMLAQWDLRSPCPVGEFLINEGTPINNVYFAAGALFVSSGF----DTSIKLDII-------

4noxA

0.04

2.07

1.17

DEthreader

MDFEWAQLFFWTPIARVGLMSIPSKQIVRTLNLFSVSDVKM-HWQEGYLCVKVDRHSQATTLEIFRVEVPVEVVT

(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	0.6043

(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	4i0oA	0.78	1.93	0.082	0.973	model1_4i0oA.pdb.gz
2	6ww7A	0.78	2.03	0.120	1.000	model1_6ww7A.pdb.gz
3	1sq9A2	0.77	1.91	0.081	0.987	model1_1sq9A2.pdb.gz
4	6wb913	0.77	2.11	0.107	1.000	model1_6wb913.pdb.gz
5	4noxA2	0.77	1.95	0.053	1.000	model1_4noxA2.pdb.gz
6	5a5uB2	0.76	1.94	0.122	0.987	model1_5a5uB2.pdb.gz
7	2ovqB	0.74	1.92	0.100	0.933	model1_2ovqB.pdb.gz
8	1erjC3	0.71	1.99	0.086	0.933	model1_1erjC3.pdb.gz
9	4ui9R	0.70	2.18	0.056	0.947	model1_4ui9R.pdb.gz
10	1p22A	0.70	2.07	0.114	0.933	model1_1p22A.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:0004702	1.00	receptor signaling protein serine/threonine kinase 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	1.00	regulation of cellular process
GO:0044699	0.85	single-organism process
GO:0023051	0.81	regulation of signaling
GO:0010646	0.81	regulation of cell communication
GO:0009987	0.79	cellular process
GO:0048583	0.77	regulation of response to stimulus
GO:0050793	0.70	regulation of developmental process
GO:0071704	0.69	organic substance metabolic process
GO:0044763	0.69	single-organism cellular process
GO:0044238	0.69	primary metabolic process
GO:0051128	0.68	regulation of cellular component organization
GO:0044260	0.68	cellular macromolecule metabolic process
GO:0009966	0.67	regulation of signal transduction
GO:0044767	0.66	single-organism developmental process
GO:0044267	0.65	cellular protein metabolic process
GO:0019222	0.65	regulation of metabolic process
GO:0016043	0.65	cellular component organization
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0016310	0.64	phosphorylation
GO:0009653	0.64	anatomical structure morphogenesis
GO:0007165	0.64	signal transduction
GO:0006464	0.64	cellular protein modification process
GO:0032268	0.63	regulation of cellular protein metabolic process
GO:0006468	0.63	protein phosphorylation
GO:0035556	0.62	intracellular signal transduction
GO:0001932	0.62	regulation of protein phosphorylation
GO:1902531	0.61	regulation of intracellular signal transduction
GO:0065008	0.60	regulation of biological quality
GO:0048518	0.60	positive regulation of biological process
GO:0043408	0.60	regulation of MAPK cascade
GO:0048522	0.58	positive regulation of cellular process
GO:0022604	0.58	regulation of cell morphogenesis
GO:0065009	0.57	regulation of molecular function
GO:0051239	0.55	regulation of multicellular organismal process
GO:2000026	0.54	regulation of multicellular organismal development
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:1902533	0.51	positive regulation of intracellular signal transduction
GO:0001934	0.51	positive regulation of protein phosphorylation
GO:0048523	0.50	negative regulation of cellular process
GO:0043410	0.50	positive regulation of MAPK cascade

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:0005737	0.98	cytoplasm

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	1yr2A	0.710	2.22	0.110	0.973	3.4.21.26	NA
2	0.060	3g0bB	0.699	2.46	0.068	0.987	3.4.14.5	NA
3	0.060	1w6sC	0.691	2.15	0.100	0.933	1.1.99.8	NA
4	0.060	1k32A	0.696	2.37	0.096	0.973	3.4.21.-	NA
5	0.060	2vskC	0.596	3.05	0.041	0.973	3.2.1.18	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:

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	0.02	3ijeA	0.745	2.10	0.093	1.000	0.41	UUU	complex1.pdb.gz	17,19,26,29
	2	0.02	3hx6A	0.731	2.34	0.027	1.000	0.77	CA	complex2.pdb.gz	18,20,28,30

	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.