D-I-TASSER Q9NZW5-D3

D-I-TASSER results for Q9NZW5-D3

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

Input Sequence in FASTA format

>Q9NZW5 (149 residues)
EEVAKMPPFQRKTLVLIGAQGVGRRSLKNRFIVLNPTRFTCILDVNPQALKVLRTSEFMP
YVVFIAAPELETLRAMHKAVVDAGITTKLLTDSDLKKTVDESARIQRAYNHYFDLIIIND
NLDKAFEKLQTAIEKLRMEPQWVPISWVY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EEVAKMPPFQRKTLVLIGAQGVGRRSLKNRFIVLNPTRFTCILDVNPQALKVLRTSEFMPYVVFIAAPELETLRAMHKAVVDAGITTKLLTDSDLKKTVDESARIQRAYNHYFDLIIINDNLDKAFEKLQTAIEKLRMEPQWVPISWVY
Prediction	CCCCCCCCCCSSSSSSSCCCCCCHHHHHHHHHHHCCCCCSSSSCCCHHHHHHHHHCCCCCSSSSSSCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCSSSSCCCHHHHHHHHHHHHHHHCCCCCSSSCSCCC
Confidence	95212489620037886799865799999999865689769960898999999970889689997099979999998601343434444529999999999999999824778899988879999999999999941898156132259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EEVAKMPPFQRKTLVLIGAQGVGRRSLKNRFIVLNPTRFTCILDVNPQALKVLRTSEFMPYVVFIAAPELETLRAMHKAVVDAGITTKLLTDSDLKKTVDESARIQRAYNHYFDLIIINDNLDKAFEKLQTAIEKLRMEPQWVPISWVY
Prediction	84247347443200000114423253045213433664320003143400420363433110000214337434534552456544455444530450254045125514531200000330350053035005616754101122247
	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

CCCCCCCCCCSSSSSSSCCCCCCHHHHHHHHHHHCCCCCSSSSCCCHHHHHHHHHCCCCCSSSSSSCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCSSSSCCCHHHHHHHHHHHHHHHCCCCCSSSCSCCC
EEVAKMPPFQRKTLVLIGAQGVGRRSLKNRFIVLNPTRFTCILDVNPQALKVLRTSEFMPYVVFIAAPELETLRAMHKAVVDAGITTKLLTDSDLKKTVDESARIQRAYNHYFDLIIINDNLDKAFEKLQTAIEKLRMEPQWVPISWVY

4wsiA

0.36

0.32

9.40

1.17

DEthreader

EEMSLYHQPRKRPIILIGPQNCGQNELRQRLMNKEKDRFICLLSLRTQSLKTLRNSDLKPYIIFIAPPSQELRALL-E------------LR-EIIEKTREMEQN-NGH--YFDTAIVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

1kjwA3

0.23

0.21

6.52

1.29

SPARKS-K

-TVTQMEVHYARPIIILGPT---KDRANDDLLSEFPDKFHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEIN----------KRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

3tvtA

0.23

0.21

6.50

0.66

MapAlign

EAVQRLSINYTRPVIILGP---LKDRINDDLISEYPDKFHCILDVSGNAIKRLQVAQLYPVAVFIKPKSVDSVMEMN----------RRMTEEQAKKTYERAIKMEQEFGEYFTGVVQGDTIEEIYSKVKSMIWSQSGPTIWVPS----

1kjwA3

0.23

0.21

6.52

0.72

CEthreader

-TVTQMEVHYARPIIILGP---TKDRANDDLLSEFPDKFHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEIN----------KRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA3

0.22

0.20

6.34

1.35

MUSTER

-TVTQMEVHYARPIIILGPT---KDRANDDLLSEFPDGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKR----------ITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

7m4rA

0.39

0.35

10.32

1.23

HHsearch

EEMSLYPANRKRPIILIGPQNCGQNELRQRLMNKEKDRFICLLSLRTQSLKTLRNSDLKPYIIFIAPPSQERLRALL----------------ELREIIEKTREMEQNNGHYFDTAIVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

4wsiA2

0.37

0.33

9.77

1.68

FFAS-3D

EEMSHQPANRKRPIILIGPQNCGQNELRQRVRQVINSGKICLLSLRTQSLKTLRNSDLKPYIIFIAPPSQERLRALLEL----------------REIIEKTREMEQNNGHYFDTAIVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

4wsiA2

0.39

0.34

10.13

0.63

EigenThreader

EMSLYQPANRKRPIILIGPQNCGQNELRQRLMNKEKDRKICLLSLRTQSLKTLRNSDLKPYIIFIAPPSQERLRALL-----------------ELREIIEKTREMEQNNGYFDTAIVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

3uatA

0.26

0.21

6.61

0.95

CNFpred

-----------KFIEAGQLYGTSVQSVRAVAEK----GKHCILDVSGNAIKRLQIAQLYPISIFIKPKSMENIMEMNK----------RLTDEQARKTFERAVRLEQEFTEHFTAIVQGDTLEDIYNQVKQIIEEQSGPYIWVPAK---

4wsiA2

0.36

0.32

9.40

1.17

DEthreader

EEMSLYHQPRKRPIILIGPQNCGQNELRQRLMNKEKDRFICLLSLRTQSLKTLRNSDLKPYIIFIAPPSQELRALL-E------------LR-EIIEKTREMEQN-NGH--YFDTAIVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

(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	0.8617

(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	4wsiA2	0.79	1.98	0.376	0.893	model1_4wsiA2.pdb.gz
2	7m4rA	0.76	2.16	0.376	0.893	model1_7m4rA.pdb.gz
3	3tvtA	0.74	2.25	0.227	0.886	model1_3tvtA.pdb.gz
4	3lh5A	0.73	2.73	0.199	0.906	model1_3lh5A.pdb.gz
5	1kjwA	0.73	2.60	0.221	0.893	model1_1kjwA.pdb.gz
6	2xkxA	0.73	2.60	0.221	0.893	model1_2xkxA.pdb.gz
7	3kfvA	0.70	2.88	0.158	0.886	model1_3kfvA.pdb.gz
8	1s96A2	0.69	2.41	0.188	0.805	model1_1s96A2.pdb.gz
9	1ex7A2	0.69	2.09	0.267	0.805	model1_1ex7A2.pdb.gz
10	1lvgA	0.69	2.54	0.246	0.819	model1_1lvgA.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:0016301	0.83	kinase activity
GO:0004385	0.82	guanylate kinase activity
GO:0005102	0.56	receptor binding
GO:0035254	0.51	glutamate receptor 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	0.92	cellular process
GO:0044699	0.90	single-organism process
GO:0044763	0.89	single-organism cellular process
GO:0016043	0.82	cellular component organization
GO:0032502	0.75	developmental process
GO:0051179	0.74	localization
GO:0048856	0.69	anatomical structure development
GO:0008104	0.68	protein localization
GO:0007163	0.64	establishment or maintenance of cell polarity
GO:0035088	0.61	establishment or maintenance of apical/basal cell polarity
GO:1902578	0.53	single-organism localization
GO:0065007	0.53	biological regulation
GO:0051641	0.53	cellular localization
GO:0045197	0.53	establishment or maintenance of epithelial cell apical/basal polarity
GO:0007267	0.53	cell-cell signaling
GO:0034613	0.52	cellular protein localization
GO:0044802	0.51	single-organism membrane organization
GO:0072657	0.50	protein localization to membrane
GO:0051668	0.50	localization within 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 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:0044425	0.83	membrane part
GO:0044424	0.82	intracellular part
GO:0044459	0.81	plasma membrane part
GO:0016020	0.80	membrane
GO:0043226	0.69	organelle
GO:0032991	0.64	macromolecular complex
GO:0098590	0.63	plasma membrane region
GO:0043229	0.62	intracellular organelle
GO:0097458	0.53	neuron part
GO:0043234	0.53	protein complex
GO:0044456	0.51	synapse part
GO:0098797	0.50	plasma membrane protein complex

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	0.165	2an9A	0.702	2.53	0.182	0.832	2.7.4.8	114
2	0.073	1gkyA	0.691	2.09	0.267	0.805	2.7.4.8	44,48
3	0.067	2bwjA	0.665	2.62	0.149	0.819	2.7.4.3	18,21,23,40,43
4	0.067	1tevA	0.678	2.66	0.136	0.839	2.7.4.14	NA
5	0.067	1ki9B	0.660	2.30	0.151	0.799	2.7.4.3	18,21,23,44

	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	0.19	2qorA	0.695	2.74	0.192	0.846	0.99	POP	complex1.pdb.gz	21,22,23,24,25
2	0.14	1kofA	0.668	2.36	0.133	0.792	0.88	ACP	complex2.pdb.gz	19,20,21,22,23,24,25,26,73,120,121,122,125
3	0.01	2i0iA	0.247	4.19	0.063	0.369	0.77	III	complex3.pdb.gz	18,19,23,24,27

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.