D-I-TASSER Q9NNX6-D2

D-I-TASSER results for Q9NNX6-D2

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

Input Sequence in FASTA format

>Q9NNX6 (94 residues)
ELPEKSKMQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQE
LTRLKAAVGELPEKSKQQEIYQELTQLKAAVERL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| ELPEKSKMQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTQLKAAVERL
Prediction	CCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCC
Confidence	9863110678887554310113568641137999998765333313687421027888887655676446986421489999998667775269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| ELPEKSKMQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTQLKAAVERL
Prediction	8357657355125514414332571476454561354245243434614675445613541452444346146756356125413524453677
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCC
ELPEKSKMQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTQLKAAVERL

4iggA

0.09

3.29

1.17

DEthreader

SQFLKEELVAAVEDVRKQGDLMKAAKNMVRAARALLSAVTRLLILADMADVYKLLVLKVVEDGILKLRNAL-ASYKNDLIYKQLQQAVTGISNA

1sl6A

0.40

0.31

9.11

1.30

HHsearch

--PEKSKLQEIYQELTQLKQQ-----------QIYQELTDLKTAFERLC----RHCPK----DWTFFQGNCYFMSNSQRNWHDSVTACQEVRAQ

4xngA

0.08

0.07

2.99

0.52

CEthreader

KRGFLLLERCSLVGLQQLELEYVNLLKTELLNNLKELVDEHFSDTEKIIN--TLEKIFDVIGGSEYTPVLNSFFNKLLSREIGLRQFIITLRQR

2ficB

0.07

3.01

0.53

EigenThreader

LTEGTRLQKDLRTYLASVKAMHANKIAENNDLLWMDYHQKLVDQALLFPDIKSRIAKRGRKLVDYDSARHHYESLQAEEELIKAQKVFEEMNVD

1sl6A

0.41

0.30

8.77

0.63

FFAS-3D

--PEKSKLQEIYQELTQLKQ-----------QQIYQELTDLKTAFERLCRHCPKD-----WTFFQGNCYFMSNSQRNWHDSVTACQ--------

2ip6A

0.15

0.14

4.63

0.73

SPARKS-K

----EHIKQQALDLFTRLQFLLQKHDTIEPYQYVLDILETGISKTKH-----NQQTPERQARVVYNKIASQALVDKLHFT-AEENKVLAAINEL

3kqgA

0.11

0.09

3.05

0.60

CNFpred

------------SDLEKASALNTKIRALQGSLENMSKLLKRQNDILQVVSQ-----------GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSH

3i9yA

0.10

3.56

1.17

DEthreader

REAGRVLFEQLESLLTHIKELGGESFDSKLLDALESNVQNVINNLAELGVTVERKLLAKEIDTRVEEMLLSLLLTELG-KRQ-VVFTILLQQEN

5hvdA

0.07

0.06

2.68

0.76

MapAlign

-KRFQNVITAIIVLNGAVLGLLTDTTLASSQNLLERVDQLCLTIFGVGSVAALLTVVFYIAA-VMATNLYGATFPEWFGDLSKSLYTLFQVM--

6gmmA2

0.14

4.72

0.73

MUSTER

DLDSYERLNNLLTNYSVLNALIRQSAFSSQYQKLGEHYDSITAAISSLPDAQSLQNVVSKKTNPNSPQGIQDNYYIDSNIHSQVQSRSQELKG-

(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	0.5741

(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	7jh5A	0.68	3.09	0.086	0.957	model1_7jh5A.pdb.gz
2	4q25A	0.67	2.81	0.085	0.883	model1_4q25A.pdb.gz
3	5azsA	0.66	3.06	0.090	0.936	model1_5azsA.pdb.gz
4	1sumB	0.66	2.88	0.064	0.894	model1_1sumB.pdb.gz
5	3i9yA	0.66	3.07	0.097	0.936	model1_3i9yA.pdb.gz
6	4mt4A	0.66	3.22	0.085	1.000	model1_4mt4A.pdb.gz
7	4mt0A	0.66	3.21	0.075	0.989	model1_4mt0A.pdb.gz
8	1xwmA	0.65	3.15	0.065	0.894	model1_1xwmA.pdb.gz
9	2i0mA	0.64	2.65	0.044	0.830	model1_2i0mA.pdb.gz
10	1tqqA	0.64	3.21	0.066	0.968	model1_1tqqA.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:0046790	1.00	virion binding
GO:0042605	1.00	peptide antigen binding
GO:0030246	1.00	carbohydrate binding
GO:0004872	0.57	receptor activity
GO:0036094	0.56	small molecule binding
GO:0004871	0.54	signal transducer activity
GO:0048029	0.53	monosaccharide binding
GO:0038023	0.53	signaling receptor activity
GO:0005537	0.52	mannose binding
GO:0004888	0.52	transmembrane signaling receptor 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:0080134	1.00	regulation of response to stress
GO:0075733	1.00	intracellular transport of virus
GO:0046968	1.00	peptide antigen transport
GO:0035556	1.00	intracellular signal transduction
GO:0019882	1.00	antigen processing and presentation
GO:0019079	1.00	viral genome replication
GO:0019062	1.00	virion attachment to host cell
GO:0019048	1.00	modulation by virus of host morphology or physiology
GO:0009988	1.00	cell-cell recognition
GO:0007159	1.00	leukocyte cell-cell adhesion
GO:0048518	0.61	positive regulation of biological process
GO:0048584	0.55	positive regulation of response to stimulus
GO:0051239	0.54	regulation of multicellular organismal process
GO:0007166	0.54	cell surface receptor signaling pathway
GO:0002682	0.54	regulation of immune system process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0050865	0.53	regulation of cell activation
GO:0030155	0.53	regulation of cell adhesion
GO:0002253	0.53	activation of immune response
GO:0042129	0.52	regulation of T cell proliferation
GO:0007157	0.52	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0002223	0.52	stimulatory C-type lectin receptor signaling pathway
GO:0010468	0.50	regulation of gene expression

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:0016020	1.00	membrane
GO:0005737	1.00	cytoplasm
GO:0043226	0.61	organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0005886	0.58	plasma membrane
GO:0044421	0.57	extracellular region part
GO:0044425	0.56	membrane part
GO:0070062	0.54	extracellular exosome
GO:0031224	0.54	intrinsic component of membrane
GO:0016021	0.52	integral component of membrane
GO:0009986	0.52	cell surface
GO:0044459	0.51	plasma membrane part
GO:0005887	0.50	integral component of plasma 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	1ynnJ	0.364	3.87	0.100	0.585	2.7.7.6	NA
2	0.060	3fofA	0.554	3.52	0.115	0.862	5.99.1.-	NA
3	0.060	1bucB	0.593	3.36	0.048	0.894	1.3.99.2	17,37,41
4	0.060	2ix6A	0.594	3.30	0.093	0.904	1.3.3.6	NA
5	0.060	1jqkF	0.561	3.55	0.043	0.862	1.2.99.2	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	0.03	1zw2A	0.605	3.57	0.078	0.947	0.40	III	complex1.pdb.gz	7,8,11,14,15,18,21,37,44
2	0.02	3s90B	0.602	3.62	0.087	0.947	0.26	III	complex2.pdb.gz	18,19,24,30,44
3	0.02	1rw60	0.615	3.10	0.121	0.925	0.30	III	complex3.pdb.gz	8,12,16,22,49,53
4	0.01	2gdcA	0.569	3.76	0.087	0.936	0.23	III	complex4.pdb.gz	23,37,40,41,44,45,48,51
5	0.01	1rkcA	0.604	3.57	0.078	0.936	0.18	III	complex5.pdb.gz	30,31,34,35,38,41,44,45
6	0.01	1zvzA	0.607	3.13	0.065	0.915	0.28	III	complex6.pdb.gz	24,39,46
7	0.01	3s90A	0.577	3.75	0.078	0.957	0.26	III	complex7.pdb.gz	25,34,38,41,42,45
8	0.01	3tj5A	0.569	3.47	0.075	0.872	0.22	III	complex8.pdb.gz	28,30,31,34,37,38,40,41,44,45
9	0.01	1rke0	0.592	3.69	0.064	0.979	0.19	III	complex9.pdb.gz	23,31,35,38,41,42,45,46,49,50
10	0.01	1ydiA	0.588	3.47	0.054	0.925	0.22	III	complex10.pdb.gz	46,49,50,53,56,59,60,63,76

	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.