D-I-TASSER Q9NUY8-D2

D-I-TASSER results for Q9NUY8-D2

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

Input Sequence in FASTA format

>Q9NUY8 (158 residues)
DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWD
GYLQQADPFFIYFLMLIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLA
QYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQALC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFLMLIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQALC
Prediction	CCCCCHHHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHCC
Confidence	97411128999999999979899999999299889999999999981569999999999999983995578999999999979999974645499999999854445786669999999999998097367888998744331233322246766409
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFLMLIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQALC
Prediction	84464332020043005411340051057370513300330020001430416101100100023434301110000001323530242436414300420342255143730440052044027421541355245124543454644565336437
	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                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHCC
DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFLMLIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQALC

6jl7A

1.00

0.89

24.81

1.33

DEthreader

DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFL-LIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGS-----------------

3qyeA2

0.20

0.17

5.48

1.62

SPARKS-K

DMIILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTE-VIFKVALSLLGSHKPLILQH--ENLETIVDFIKSTLPNLGLVQMEKTINQVFEMIAKQLQAYEVEYHVLQE------------------

6jl7A

0.85

0.84

23.54

1.26

MapAlign

DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFL-LIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRILQANQLEGVRFFVVDCRPAEQYNA-

6jl7A

1.00

0.99

27.82

1.00

CEthreader

DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFL-LIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQALC

3qyeA2

0.20

0.17

5.48

1.55

MUSTER

DMIILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTE-VIFKVALSLLGSHKPLILQH--ENLETIVDFIKSTLPNLGLVQMEKTINQVFEMIAKQLQAYEVEYHVLQE------------------

6jl7A1

0.97

0.96

26.79

2.64

HHsearch

DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADP-FFIYFLLIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQAL-

6jl7A1

0.98

0.96

26.78

2.04

FFAS-3D

--SQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFI-YFLLIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADLSQAL-

6jl7A1

1.00

0.96

26.94

1.85

EigenThreader

DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFL-LIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGSTLLGIKDDDADL-----

3qyeA

0.21

0.18

5.64

1.05

CNFpred

DMIILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGT-EVIFKVALSLLGSHKPLILQHE--NLETIVDFIKSTLPNLGLVQMEKTINQVFEMIAKQLQAYEVEYHVL--------------------

6jl7A1

1.00

0.89

24.81

1.33

DEthreader

DCSQKGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFL-LIILVNAKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGS-----------------

(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	0.8267

(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	6jl7A	0.98	0.51	0.987	0.994	model1_6jl7A.pdb.gz
2	2g77A1	0.73	1.89	0.219	0.810	model1_2g77A1.pdb.gz
3	3qyeA	0.72	2.64	0.174	0.867	model1_3qyeA.pdb.gz
4	2qfzA2	0.72	1.70	0.224	0.791	model1_2qfzA2.pdb.gz
5	2qq8A2	0.71	2.53	0.179	0.848	model1_2qq8A2.pdb.gz
6	4p17A	0.65	2.29	0.161	0.747	model1_4p17A.pdb.gz
7	3qwlA	0.62	3.02	0.181	0.772	model1_3qwlA.pdb.gz
8	3l2nA2	0.38	4.58	0.115	0.601	model1_3l2nA2.pdb.gz
9	1hg4A	0.36	5.12	0.041	0.639	model1_1hg4A.pdb.gz
10	3hzjC1	0.34	3.96	0.025	0.500	model1_3hzjC1.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:0030234	0.90	enzyme regulator activity
GO:0005096	0.89	GTPase activator activity
GO:0017137	0.80	Rab GTPase 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:0065007	1.00	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0006810	0.90	transport
GO:0043087	0.87	regulation of GTPase activity
GO:0050794	0.85	regulation of cellular process
GO:0032879	0.78	regulation of localization
GO:0046907	0.77	intracellular transport
GO:0033043	0.77	regulation of organelle organization
GO:0015031	0.77	protein transport
GO:0031338	0.76	regulation of vesicle fusion
GO:0043085	0.75	positive regulation of catalytic activity
GO:0006886	0.75	intracellular protein transport
GO:0090630	0.74	activation of GTPase 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 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:0044464	1.00	cell part
GO:0044424	0.91	intracellular part
GO:0012505	0.89	endomembrane system
GO:0005622	0.86	intracellular
GO:0043226	0.84	organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0044444	0.78	cytoplasmic part
GO:0043229	0.77	intracellular organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0044446	0.61	intracellular organelle part
GO:0016020	0.51	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

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	2vkzG	0.440	4.87	0.041	0.722	2.3.1.38 3.1.2.14	84
2	0.060	2b83C	0.440	4.81	0.081	0.728	1.1.1.2	NA
3	0.060	2ouiD	0.443	4.76	0.115	0.722	1.1.1.2	NA
4	0.060	2ckjA	0.430	5.06	0.056	0.722	1.17.1.4 1.17.3.2	NA
5	0.060	3fpcA	0.447	5.23	0.063	0.772	1.1.1.2	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	0.07	3ryhB	0.458	4.48	0.055	0.683	0.23	G2P	complex1.pdb.gz	11,12,15,35,72,76
2	0.01	1z2bB	0.393	5.00	0.043	0.696	0.24	CN2	complex2.pdb.gz	74,75,78,79,105,106
3	0.01	3n2kD	0.404	5.17	0.048	0.728	0.20	K2N	complex3.pdb.gz	43,61,62,74,78
4	0.01	1jffA	0.449	4.44	0.021	0.683	0.20	GTP	complex4.pdb.gz	6,42,68,72
5	0.01	3hkdD	0.389	5.16	0.041	0.715	0.11	GDP	complex5.pdb.gz	41,42,43,98,102
6	0.01	1jbwA	0.449	4.63	0.078	0.734	0.13	ACQ	complex6.pdb.gz	5,6,7,8,9
7	0.01	3du7B	0.410	5.36	0.055	0.741	0.35	CN2	complex7.pdb.gz	44,61,62,65,66,68,69
8	0.01	1ffxD	0.435	4.70	0.027	0.671	0.24	GDP	complex8.pdb.gz	10,11,74,75,78
9	0.01	3hkbB	0.335	5.47	0.054	0.639	0.12	GDP	complex9.pdb.gz	39,40,43,81
10	0.01	3hkeB	0.451	4.52	0.054	0.677	0.13	GDP	complex10.pdb.gz	38,39,43,46

	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.